WO2015066432A1

WO2015066432A1 - Method of treating post-myeloproliferative neoplasms (mpns) and post-mpn acute myeloid leukemia

Info

Publication number: WO2015066432A1
Application number: PCT/US2014/063353
Authority: WO
Inventors: Matthew J. HAWRYLUK; Vincent A. MILLER; Philip James STEPHENS; Kai Wang; Omar Abdel-Wahab; Ross LEVINE; Raajit RAMPAL; Marcel Van Den Brink
Original assignee: Foundation Medicine, Inc.; Memorial Sloan-Kettering Cancer Center
Priority date: 2013-11-01
Filing date: 2014-10-31
Publication date: 2015-05-07
Also published as: WO2015066432A8

Abstract

Methods and compositions for treating post-myeloproliferative neoplasm acute myeloid leukemia are disclosed.

Description

METHODS OF TREATING POST-MYELOPROLIFERATIVE NEOPLASMS (MPNs) AND POST-MPN ACUTE MYELOID LEUKEMIA

FIELD OF THE INVENTION

The invention relates to methods and compositions for treating post-myeloproliferative neoplasm acute myeloid leukemia.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application claims the benefit of U.S. Provisional Application No.

61/898,807, filed November 1, 2013, the contents of which are hereby incorporated by reference in their entirety.

SEQUENCE LISTING

The present application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on October 27, 2014, is named "Sequence_Listing_ST25.txt" and is 8 KB in size.

BACKGROUND OF THE INVENTION

Myeloproliferative neoplasms (MPN) are clonal blood cancers initiated an abnormal mutation in a bone marrow stem cell. The mutation leads to an overproduction of any combination of white blood cells, red blod cells and platelets. MPNs are commonly divided into two major subtypes: Philadelphia-chromosome positive (e.g., chronic myelogenous leukemia (CML)) and Philadelphia-chromosome negative (e.g., polycythemia vera (PV), essential thrombocytosus (ET), and myelofibrosis (MF)). A subset of patients with

Philadelphia-chromosome negative MPNs develops acute myeloid leukemia (AML) (post- MPN AML) (Heaney et al. Curr Hematol Malig Rep (2013) 8: 116). Post-MPN AML usually occurs years after the initial MPN diagnosis with an average age of onset between 64 and 68 years. Chromosome abnormalities are common and many patients have cytogenetic changes that are associated with poor risk features. Post-MPN AML is characterized by acquired somatic gene mutations. Conventional AML- style treatment appears to have limited efficacy, although when coupled to allogeneic stem cell transplantation, some patients have long-term survival. Less-intensive therapies such as hypomethylating agents and the JAK inhibitor, ruxolitinib, may be effective in some patients.

The JAK2 mutation at position 617, JAK2V617F, is a unifying, although not universal, genetic abnormality found in MPNs (Heaney, supra). However, in approximately 50% of cases, patients with JAK2V617F mutant chronic-phase MPN transform to JAK2 wildtype AMLs, indicating that diverse genomic paths lead to development of post-MPN AML.

Current treatment regimens include an anthracycline (commonly idarubicin or daunorubicin) or an anthracenedione (commonly mitoxantrone); cytarabine combined with idarubicin, daunorubicin, or mitoxantrone; high-dose cytarabine; stem cell transplantation, and bone marrow transplantation. Despite treatment options, post-MPN AML is generally an aggressive form of leukemia that tends to be resistant to treatment, and carries a very poor prognosis. Therefore, the need exists for novel therapeutic approaches for treating post-MPN conditions, such as post-MPN AML.

SUMMARY OF THE INVENTION

The invention is based, at least in part, on the discovery of alterations in post- myeloproliferative neoplasms (MPNs), such as post-MPN acute myeloid leukemia (AML) (referred to herein as "post-MPN AML"). In certain embodiments, the post-MPN AML has a mutation in a Janus Kinase 2 (JAK2), e.g., a mutation at position 617 (e.g., JAK2V617F), referred to herein as "JAK2V617F positive post-MPN AML." In other embodiments, the post-MPN AML does not have a mutation in JAK2 at position 617, e.g., has a wild-type JAK2, referred to herein as "JAK2V617F negative post-MPN AML.

In certain embodiments, Applicants have identified, of 33 post-MPN AML cases analyzed (of which 17 were JAK2V617F positive and 16 were JAK2V617F negative), about 37.5% of the JAK2V617F negative cases had an alteration in NRAS. The NRAS and the JAK2 alterations were mutually exclusive in the entire cohort examined. Additional alterations identified in JAK2V617F negative post-MPN AML cases include alterations in ASXL1 (at a frequency of about 56.3%), alterations in SETBP1 (at a frequency of about 19%), as well as the alterations shown in FIG. 1. In other embodiments, about 41.2% of the JAK2V617F positive cases had an alteration in IDH2. Additional alterations in JAK2V617F positive cases identified include alterations in ASXL1, TP53, as well as the alterations shown in FIG. 1. Alterations in MLL were observed in both JAK2V617F negative and JAK2V617F positive cases.

Therefore, the invention provides, at least in part, methods for treating post- MPN related disorders, e.g., post- MPN AML. In one embodiment, a JAK2V617F negative post- MPN AML is treated with an agent that targets and/or inhibits a MAPK pathway gene or gene product. In other embodiments, a JAK2V617F positive post-MPN AML is treated with an agent that targets and/or inhibits an IDH2 gene or gene product. In yet other embodiments, a post-MPN AML (e.g., a JAK2V617F negative and/or JAK2V617F positive post-MPN AML) is treated with an agent that targets and/or inhibits an MLL gene or gene product. Methods and reagents for identifying, assessing or detecting an alteration as described herein, e.g., a NRAS, IDH2, MLL mutation, and/or the alterations described in FIG. 1 or Table 1, in post- MPN AML are also discosed.

JAK2 V617F Negative Post-MPN AML

Accordingly, in one aspect, the invention features a method of treating a subject having post-MPN AML, e.g., a JAK2V617F negative post-MPN AML. The method includes administering to the subject an effective amount of an agent (e.g., a therapeutic agent) that targets and/or inhibits a MAPK pathway gene or gene product (e.g., a MAPK pathway inhibitor), thereby treating the subject.

In one embodiment, the method further includes acquiring knowledge of the presence (or absence) of an alteration in NRAS. In one embodiment, the NRAS alteration is, or comprises, a mutation, e.g., a somatic mutation, (e.g., mutation chosen from a substitution (e.g., a base substitution), a deletion, an insertion, or a missense mutation). In one

embodiment, the NRAS alteration is a missense mutation or a point mutation. Exemplary NRAS mutations are described in, e.g., Bacher U. et al. (2006) Blood 107:3847-53; Banerji U. et al. (2008) Mol Cancer Ther. 7:737-9, and Table 1. In some embodiments, the NRAS mutation is a point mutation, (e.g., a point mutation in amino acid position 12 (e.g., G12S; G12D; G12A; G12V; G12S); a point mutation in amino acid position 61 (e.g., Q61R); a point mutation in amino acid position 13 (e.g., G13R; G13D). In another embodiment, the method further includes identifying the subject, or a cancer sample from the subject, as having or not having an alteration in NRAS, e.g., an NRAS alteration as described herein.

In certain embodiments, the presence of the NRAS alteration in the subject, or the cancer sample from the subject, is indicative that the subject is likely to respond to the agent, e.g., the MAPK pathway inhibitor.

In yet other embodiments, the agent is administered responsive to a determination of the presence of the NRAS alteration in the subject, or the cancer sample from the subject.

In one embodiment, the method further includes acquiring knowledge of one or both of:

(i) the presence (or absence) of an alteration in NRAS; or

(ii) the presence (or absence) of an alteration in JAK2, e.g., a JAK2V617F mutation.

In another embodiment, the method further includes identifying the subject, or a cancer sample from the subject, as having one or both of:

(i) the presence (or absence) of an alteration in NRAS; or

In certain embodiments, the presence of the NRAS alteration, the absence of the alteration in JAK2, e.g., JAK2V617F, or both, in the subject is indicative that the subject is likely to respond to the agent, e.g., the MAPK pathway inhibitor.

In yet other embodiments, the agent, e.g., the MAPK pathway inhibitor, is

administered responsive to a determination of the presence of the NRAS alteration, a determination of the absence of the JAK2 alteration, e.g., JAK2V617F, or both, in the subject, or the cancer sample from the subject.

In certain embodiments, the method further comprises acquiring knowledge that the cancer, e.g., post-MPN AML, does not have an alteration in JAK2, e.g., JAK2V617F, or a JAK2 gene product. Cancers

In certain embodiments, the cancer is a post-MPN AML. In certain embodiments the cancer is a refractory post-MPN AML. In other embodiments, the cancer is a relapsed post- MPN AML.

In other embodiments, the cancer, e.g., post-MPN AML, comprises, or is identified or determined as having, an alteration in NRAS, e.g., an alteration in NRAS as described herein.

In certain embodiments, the alteration in NRAS results in increased activity of a NRAS gene product (e.g., a NRAS protein), compared to a wild-type activity of NRAS. For example, the alteration can result in an alteration (e.g., an increase) in the GTPase activity of a NRAS protein, and/or increased activity or phosphorylation of a downstream component of the MAPK pathway, including, but not limited to, MEK (MAP/ERK kinase) (e.g., MEK1 and/or MEK2). In one embodiment, the NRAS alteration is, or comprises, a mutation (e.g., a somatic mutation), e.g., a substitution (e.g., a base substitution), a deletion or an insertion. In one embodiment, the NRAS alteration is a missense mutation or a point mutation.

In other embodiments, the cancer, e.g., post-MPN AML, comprises, or is identified or determined as not having, an alteration in JAK2, e.g., as not having an alteration in JAK2 as described herein, e.g., JAK2V617F, or having a wild-type JAK2 sequence.

In other embodiments, the cancer, e.g., post-MPN AML, comprises, or is identified or determined as not having, an alteration in JAK2, e.g., a JAK2V617F, or having a wild type JAK2; and having, an alteration in NRAS, e.g., an alteration in NRAS as described herein.

Subjects

In certain embodiments, the subject has an alteration in NRAS, e.g., the subject has a post-MPN AML comprising an NRAS alteration described herein. In other embodiments, the subject is identified, or has been previously identified, as having a cancer (e.g., a post-MPN AML) comprising an NRAS alteration.

In certain embodiments, the subject has an alteration in NRAS, e.g., the subject has post-MPN AML comprising an NRAS alteration described herein; and the subject does not have an alteration in JAK2, e.g., JAK2V617F (e.g., the subject has a wild type JAK2). In other embodiments, the subject is identified, or has been previously identified, as having a cancer (e.g., post-MPN AML) comprising a NRAS alteration and not having an alteration in JAK2, e.g., JAK2V617F (e.g., the cancer has a wild type JAK2).

In one embodiment, the subject is a human. In other embodiments, the subject is a cancer patient, e.g., a patient having a post-MPN AML as described herein.

In one embodiment, the subject is undergoing or has undergone treatment with a different (e.g., non-NRAS or non-MAPK pathway) therapeutic agent or therapeutic modality. In one embodiment, the different therapeutic agent or therapeutic modality is a chemotherapy, immunotherapy, or a surgical procedure. In one embodiment, the different therapeutic agent or therapeutic modality comprises one or more of: an anthracycline, idarubicin,

daunorubicin/daunomycin, anthracenedione, mitoxantrone, cytarabine (cytosine arabinose, ara-C), idarubicin, cladribine (Leustatin, 2-CdA), fludarabine (Fludara), topotecan, etoposide (VP- 16), 6-thioguanine (6-TG), hydroxyurea (Hydrea), corticosteroid drugs (e.g., prednisone or dexamethasone (Decadron)), methotrexate (MTX), 6-mercaptopurine (6-MP), azacitidine (Vidaza), clofarabine (Colar), decitabine (Dacogen), stem cell transplantation, gemtuzumab ozogamicin, or a bone marrow transplantation.

In one embodiment, responsive to the determination of the presence of the NRAS alteration described herein, the different therapeutic agent or therapeutic modality is discontinued. In yet other embodiments, the subject has been identified as being likely or unlikely to respond to the different therapeutic agent or therapeutic modality.

In certain embodiments, the subject has participated previously in a clinical trial, e.g., a clinical trial for a different (e.g., non-NRAS or non-MAPK pathway) therapeutic agent or therapeutic modality. In other embodiments, the subject is a cancer patient who has participated in a clinical trial, e.g., a clinical trial for a different (e.g., non-NRAS or non- MAPK pathway) therapeutic agent or therapeutic modality.

Agents

In certain embodiments, the agent (e.g., the therapeutic agent) used in the methods targets and/or inhibits a MAPK pathway gene or gene product. In one embodiment, the MAPK pathway gene or gene product is a RAS (e.g., an NRAS), and/or MEK (mitogen activated protein kinase kinase or MAP/ERK kinase), or results in increased activity, e.g., constitutive action of the MAPK pathway gene or gene product. In one embodiment, the agent binds and/or inhibits NRAS or MEK.

In yet other embodiments, the agent (e.g., the therapeutic agent) used in the methods targets, binds, and/or inhibits NRAS and/or MEK (e.g., a MEKl and/or a MEK2 gene or gene product). In one embodiment, the agent is a reversible or an irreversible inhibitor of the MAPK pathway gene or gene product, e.g., NRAS and/or MEK.

In one embodiment, the agent is chosen from: a multi- specific kinase inhibitor; a small molecule inhibitor that is selective for a MAPK pathway gene or gene product, e.g., NRAS and/or MEK; a MAPK inhibitor; a MEK inhibitor; an antibody molecule against a MAPK pathway gene or gene product, e.g., NRAS and/or MEK; or a nucleic acid inhibitor.

A MEK inhibitor can include an agent that inhibits the mitogen- activated protein kinase kinase enzymes MEKl and/or MEK2. In certain embodiments, the MEK inhibitor is chosen from: ARRY- 162 (MEK162), Trametinib (GSK1120212), Selumetinib (AZD6244, ARRY142886), XL518 (GDC-0973), CI-1040 (PD184352), PD035901, U0126-EtOH, PD198306, PD98059, BIX 02189, TAK-733, Honokiol, AZD8330 (ARRY-424704),

PD318088, BIX 02188, AS703026 (Pimasertib), ABT-348 and/or SL327.

In some embodiments, the MEK inhibitor is ARRY-162 (MEK 162). In one embodiment, ARRY-162 has the chemical name: 5-((4-bromo-2-fluorophenyl)amino)-4- fluoro-N-(2-hydroxyethoxy)-l-methyl-lH-benzo[d]imidazole-6-carboxamide; and has the following structure:

In some embodiments, the MEK inhibitor is Trametinib (GSK1120212). In one embodiment, Trametinib has the chemical name: N-(3-{ 3-Cyclopropyl-5-[(2-fluoro-4- iodophenyl)amino]-6,8-dimethyl-2,4,7-trioxo-3,4,6,7-tetrahydropyrido[4,3-d]pyrimidin- l(2H)-yl}phenyl)acetamide; and has the following structure:

In some embodiments, the MEK inhibitor is Selumetinib (also known as AZD6244, ARRY142886). In one embodiment, Selumetinib has the chemical name: 6-(4-bromo-2- chloroanilino)-7-fluoro-N-(2-hydroxyethoxy)-3-methylbenzimidazole-5-carboxamide; and has the following structure:

In some embodiments, the MEK inhibitor is XL518 (GDC-0973). In one embodiment, XL518 has the chemical name: [3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]phenyl][3- hydroxy-3-[(2S)-2-piperidinyl]-l-azetidinyl]methanone; and has the following structure:

In some embodiments, the MEK inhibitor is CI- 1040 (PD184352). In one

embodiment, CI- 1040 is an ATP non-competitive MEKl/2 inhibitor with IC50 of 17 nM, 100-fold more selective for MEKl/2 than MEK5. CI- 1040 has the chemical name: 2-(2- chloro-4-iodophenylamino)-N-(cyclopropylmethoxy)-3,4-difluorobenzamide; and has the following structure:

In some embodiments, the MEK inhibitor is PD035901. In one embodiment,

PD035901 has the chemical name: (R)-N-(2,3-dihydroxypropoxy)-3,4-difluoro-2-(2-fluoro-4- iodophenylamino)benzamide; and has the following structure:

In some embodiments, the MEK inhibitor is U0126-EtOH. In one embodiment, U0126-EtOH has the chemical name: (2Z,3Z)-2,3-bis(amino(2-aminophenylthio) methylene) succinonitrile, ethanol; and has the following structure:

EtON

In some embodiments, the MEK inhibitor is PD198306. In one embodiment,

PD198306 has the chemical name: Benzamide, N-(cyclopropylmethoxy)-3,4,5-trifluoro-2-[(4- iodo-2-methylphenyl)amino]-; and has the following structure:

In some embodiments, the MEK inhibitor is PD98059. In one embodiment, PD98059 has the chemical name: 2-(2-amino-3-methoxyphenyl)-4H-chromen-4-one; and has the following structure:

In some embodiments, the MEK inhibitor is BIX 02189. In one embodiment, BIX 02189 has the chemical name: (Z)-3-((3-((dimethylamino)methyl)phenylamino)

(phenyl)methylene)-N,N-dimethyl-2-oxoindoline-6-carboxamide; and has the following structure:

In some embodiments, the MEK inhibitor is TAK-733. In one embodiment, TAK-733 has the chemical name: (R)-3-(2,3-dihydroxypropyl)-6-fluoro-5-(2-fluoro-4- iodophenylamino)-8-methylpyrido[2,3-d]pyrimidine-4,7(3H,8H)-dione; and has the following structure:

In some embodiments, the MEK inhibitor is Honokiol. In one embodiment, Honokiol has the chemical name: 2-(4-hydroxy-3-prop-2-enyl-phenyl)- 4-prop-2-enyl-phenol; and has the following structure:

In some embodiments, the MEK inhibitor is AZD8330 (ARRY-424704). In one embodiment, AZD8330 has the chemical name: 2-(2-fluoro-4-iodophenylamino)-N-(2- hydroxyethoxy)-l,5-dimethyl-6-oxo-l,6-dihydropyridine-3-carboxamide; and has the following structure:

In some embodiments, the MEK inhibitor is PD318088. In one embodiment,

PD318088 has the chemical name: 5-bromo-N-(2,3-dihydroxypropoxy)-3,4-difluoro-2-(2- fluoro-4-iodophenylamino)benzamide; and has the following structure:

In some embodiments, the MEK inhibitor is BIX 02188. In one embodiment, BIX02188 has the chemical name: (Z)-3-((3-((dimethylamino)methyl)

phenylamino)(phenyl)methylene)-2-oxoindoline-6-carboxamide; and has the following structure:

In some embodiments, the MEK inhibitor is AS703026 (Pimasertib). In one embodiment, AS703026 has the chemical name: (S)-N-(2,3-dihydroxypropyl)-3-(2-fluoro-4- iodophenylamino)isonicotinamide; and has the following structure:

In some embodiments, the MEK inhibitor is SL327. In one embodiment, SL327 has the chemical name: (Z)-3-amino-3-(4-aminophenylthio)-2-(2- (trifluoromethyl)phenyl)acrylonitrile; and has the following structure:

In one embodiment, the agent is an antibody molecule, e.g., an anti-MEK or anti- NRAS antibody molecule (e.g., a monoclonal or a bispecific antibody), or a conjugate thereof (e.g., an antibody to MEK or NRAS conjugated to a cytotoxic agent (e.g., mertansine DM1)), and/or a MEK or NRAS cellular immunotherapy.

In other embodiments, the agent is chosen from a nucleic acid molecule (e.g., an antisense molecule, a ribozyme, a double stranded RNA, or a triple helix molecule) that hybridizes to and/or inhibits a MEK or NRAS nucleic acid, e.g., a MEK or NRAS nucleic acid encoding the alteration, or a transcription regulatory region that blocks or reduces mRNA expression of the alteration.

JAK2V617F Positive Post-MPN AML

In another aspect, the invention features a method of treating a subject having post- MPN AML, e.g., JAK2V617F positive -MPN AML. The method includes administering to the subject an effective amount of an agent (e.g., a therapeutic agent) that targets and/or inhibits isocitrate dehydrogenase isoform 2 (IDH2) (e.g., an IDH2 gene product, e.g., an IDH2 protein), thereby treating the subject.

In one embodiment, the method further includes acquiring knowledge of the presence (or absence) of an alteration in IDH2.

In another embodiment, the method further includes identifying the subject, or a cancer sample from the subject, as having the presence (or absence) of an alteration in IDH2.

In certain embodiments, the presence of the IDH2 alteration in the subject is indicative that the subject is likely to respond to the agent.

In yet other embodiments, the agent is administered responsive to a determination of the presence of the IDH2 alteration in the subject, or the cancer sample from the subject.

(i) the presence (or absence) of an alteration in IDH2; or (ii) the presence (or absence) of an alteration in JAK2, e.g., JAK2V617F.

(i) the presence of an alteration in IDH2; or

(ii) the presence of an alteration in JAK2, e.g., JAK2V617F.

(i) the presence of an alteration in IDH2; or

(ii) the presence of an alteration in JAK2, e.g., JAK2V617F.

In certain embodiments, the presence of the IDH2 alteration, the presence of the alteration in JAK2, e.g., JAK2V617F, or both, in the subject is indicative that the subject is likely to respond to the agent.

In yet other embodiments, the agent is administered responsive to a determination of the presence of the IDH2 alteration, a determination of the presence of the JAK2, e.g., JAK2V617F, or both, in the subject, or the cancer sample from the subject.

In certain embodiments, the method further comprises acquiring knowledge that the cancer, e.g., post-MPN AML has an alteration in JAK2, e.g., JAK2V617F, or a JAK2 gene product.

Cancers

In certain embodiments, the cancer is a post-MPN AML. In certain embodiments the cancer is refractory a post-MPN AML. In certain embodiments the cancer is a relapsed post- MPN AML.

In other embodiments, the cancer, e.g., post-MPN AML, comprises, or is identified or determined as having, an alteration in IDH2, e.g., an alteration in IDH2 as described herein.

In certain embodiments, the alteration in IDH2 results in increased activity of an IDH2 gene product (e.g., an IDH2 protein), compared to a wildtype activity of IDH2. For example, the alteration can result in an alteration (e.g., an increase) in one or more of: an increase in dehydrogenase activity of an IDH2 protein; an increase in DNA hypermethylation; or inhibition of TET2-induced cytosine 5-hydroxymethylation, DNA demethylation. In one embodiment, the IDH2 alteration is, or comprises, a mutation (e.g., a somatic mutation), e.g., a substitution (e.g., a base substitution), a deletion or an insertion. In one embodiment, the alteration is a missense mutation. In certain embodiments, the alteration in IDH2 is a point mutation, e.g., a mutation in codon 140 or 172 of IDH2 (e.g., a mutation of R140K or R172Q). In one embodiment, the alteration is a point mutation in codon 140 from an arginine to a lysine. In one embodiment, the alteration is a point mutation in codon 172 from an arginine to a glutamine. In other embodiment, the alteration in IDH2 is an alteration provided in FIG. 1 or Table 1.

In other embodiments, the cancer, e.g., post-MPN AML, comprises, or is identified or determined as having, an alteration in JAK2, e.g., an alteration in JAK2 as described herein, e.g., JAK2V617F.

In other embodiments, the cancer, e.g., post-MPN AML, comprises, or is identified or determined as having, an alteration in JAK2, e.g., an alteration in JAK2 as described herein, e.g., JAK2V617F; and having, an alteration in IDH2, e.g., an alteration in IDH2 as described herein.

Subjects

In certain embodiments, the subject has an alteration in IDH2, e.g., the subject has post-MPN AML comprising an IDH2 alteration described herein. In other embodiments, the subject is identified, or has been previously identified, as having a cancer (e.g., post-MPN AML) comprising an IDH2 alteration.

In certain embodiments, the subject has an alteration in IDH2, e.g., the subject has post-MPN AML comprising an IDH2 alteration described herein; and the subject has an alteration in JAK2, e.g., JAK2V617F. In other embodiments, the subject is identified, or has been previously identified, as having a cancer (e.g., post-MPN AML) comprising an IDH2 alteration and having an alteration in JAK2, e.g., JAK2V617F.

In one embodiment, the subject is a human. In other embodiments, the subject is a cancer patient, e.g., a patient having post-MPN AML as described herein. In one embodiment, the subject is undergoing or has undergone treatment with a different (e.g., non-IDH2) therapeutic agent or therapeutic modality. In one embodiment, the non-IDH2 therapeutic agent or therapeutic modality is a chemotherapy, immunotherapy, or a surgical procedure. In one embodiment, the non-IDH2 therapeutic agent or therapeutic modality comprises one or more of: an anthracycline, idarubicin, daunorubicin/daunomycin, anthracenedione, mitoxantrone, cytarabine (cytosine arabinose, ara-C), idarubicin, cladribine (Leustatin, 2-CdA), fludarabine (Fludara), topotecan, etoposide (VP-16), 6-thioguanine (6- TG), hydroxyurea (Hydrea), corticosteroid drugs (e.g., prednisone or dexamethasone

(Decadron)), methotrexate (MTX), 6-mercaptopurine (6-MP), azacitidine (Vidaza), clofarabine (Colar), decitabine (Dacogen), stem cell transplantation, gemtuzumab ozogamicin, and bone marrow transplantation.

In one embodiment, responsive to the determination of the presence of the IDH2 alteration described herein, the different therapeutic agent or therapeutic modality is discontinued. In yet other embodiments, the subject has been identified as being likely or unlikely to respond to the different therapeutic agent or therapeutic modality.

In certain embodiments, the subject has participated previously in a clinical trial, e.g., a clinical trial for a different (e.g., non-IDH2) therapeutic agent or therapeutic modality. In other embodiments, the subject is a cancer patient who has participated in a clinical trial, e.g., a clinical trial for a different (e.g., non-IDH2) therapeutic agent or therapeutic modality.

Agents

In certain embodiments, the agent (e.g., the therapeutic agent) used in the methods targets and/or inhibits IDH2 (e.g., an IDH2 gene or gene product as described herein). In one embodiment, the agent binds and inhibits IDH2. In one embodiment, the agent is a reversible or an irreversible IDH2 inhibitor.

In one embodiment, the agent is chosen from: a dehydrogenase inhibitor, a multi- specific dehydrogenase inhibitor; a small molecule inhibitor that is selective for IDH2; an antibody molecule against IDH2; or a nucleic acid inhibitor.

In one embodiment, the dehydrogenase inhibitor is AGI-6780 described by, e.g., Wang, F. et al. (2013) Science Vol. 340 no. 6132 pp. 622-626; In other embodiments, the agent is chosen from a nucleic acid molecule (e.g., an antisense molecule, a ribozyme, a double stranded RNA, or a triple helix molecule) that hybridizes to and/or inhibits an IDH2 nucleic acid, e.g., an IDH2 nucleic acid encoding the alteration, or a transcription regulatory region that blocks or reduces mRNA expression of the alteration.

Post-MPNAML

In other embodiments, several alterations not previously described in post-MPN AML were identified in both JAK2V617F positive AML and JAK2V617F negative AML, including a partial tandem duplication (PTD) of the mixed-lineage leukemia (MLL) gene (MLL-PTD). Other alterations identified in post-MPN AML included homozygous deletions of TET2 and ETV6, MYC amplifications, and other alterations identified in FIG. 1. TP53 mutations were associated with significantly impaired overall survival.

Accordingly, in one aspect, the invention features a method of treating a subject having post-MPN AML, e.g., JAK2V617F positive AML or JAK2V617F negative AML, or both. The method includes administering to the subject an effective amount of an agent (e.g., a therapeutic agent) that targets and/or inhibits MLL (e.g., an MLL gene product, e.g., an MLL protein), thereby treating the subject. In one embodiment, the MLL is a tandem duplication (e.g., a partial or full tandem duplication) of an MLL gene, or a gene fusion of an MLL sequence (full or partial) to another partner.

In one embodiment, the method further includes acquiring knowledge of the presence (or absence) of an alteration in MLL.

In another embodiment, the method further includes identifying the subject, or a cancer or tumor sample from the subject, as having the presence (or absence) of an alteration in MLL.

In certain embodiments, the presence of the MLL alteration in the subject is indicative that the subject is likely to respond to the agent.

In yet other embodiments, the agent is administered responsive to a determination of the presence of the MLL alteration in the subject, or the cancer sample from the subject. In one embodiment, the method further includes acquiring knowledge of one or both of:

(i) the presence (or absence) of an alteration in MLL; or

(ii) the presence (or absence) of an alteration in JAK2, e.g., JAK2V617F.

In another embodiment, the method further includes identifying the subject, or a cancer or tumor sample from the subject, as having one or both of:

(i) the presence (or absence) of an alteration in MLL; or

(ii) the presence (or absence) of an alteration in JAK2, e.g., JAK2V617F.

In certain embodiments, the presence of the MLL alteration, the presence of the alteration in JAK2, e.g., JAK2V617F, or both, in the subject is indicative that the subject is likely to respond to the agent.

In yet other embodiments, the agent is administered responsive to a determination of the presence of the MLL alteration, a determination of the presence of the JAK2, e.g., JAK2V617F, or both, in the subject, or the cancer or tumor sample from the subject.

In certain embodiments, the method further comprises acquiring knowledge that the cancer, e.g., post-MPN AML has an alteration in JAK2, e.g., JAK2V617F or a JAK2 gene product.

In certain embodiments, the presence of the MLL alteration, the absence of the alteration in JAK2, e.g., JAK2V617F, or both, in the subject is indicative that the subject is likely to respond to the agent.

In yet other embodiments, the agent is administered responsive to a determination of the presence of the MLL alteration, a determination of the absence of the JAK2, e.g., JAK2V617F, or both, in the subject, or the cancer or tumor sample from the subject.

In certain embodiments, the method further comprises acquiring knowledge that the cancer, e.g., post-MPN AML does not have an alteration in JAK2, e.g., JAK2V617F or a JAK2 gene product. Cancers

In certain embodiments, the cancer is post-MPN AML. In certain embodiments the cancer is refractory post-MPN AML. In certain embodiments the cancer is relapsed post-MPN AML.

In other embodiments, the cancer, e.g., post-MPN AML, comprises, or is identified or determined as having, an alteration in MLL, e.g., an alteration in MLL as described herein.

In certain embodiments, the alteration in MLL results in increased activity of a MLL gene product (e.g., a MLL protein), compared to a wild-type activity of MLL. For example, the alteration can result in an alteration (e.g., an increase) in methyltransferase activity of a MLL protein. In one embodiment, the MLL alteration is, or comprises, a tandem (e.g., partial or full tandem) of an MLL gene; a mutation (e.g., a somatic mutation), e.g., a substitution (e.g., a base substitution); a deletion; an insertion; or a gene fusion. In one embodiment, the alteration is a tandem duplication or a gene fusion, e.g., an alteration described in FIG. 1 or Table 1.

In other embodiments, the cancer, e.g., post-MPN AML, comprises, or is identified or determined as not having, an alteration in JAK2, e.g., an alteration in JAK2 as described herein, e.g., JAK2V617F.

In other embodiments, the cancer, e.g., post-MPN AML, comprises, or is identified or determined as not having, an alteration in JAK2, e.g., an alteration in JAK2 as described herein, e.g., JAK2V617F; and having, an alteration in MLL, e.g., an alteration in MLL as described herein.

Subjects

In certain embodiments, the subject has an alteration in MLL, e.g., the subject has post-MPN AML comprising a MLL alteration described herein. In other embodiments, the subject is identified, or has been previously identified, as having a cancer (e.g., post-MPN AML) comprising a MLL alteration.

In certain embodiments, the subject has an alteration in MLL, e.g., the subject has post-MPN AML comprising a MLL alteration described herein; and the subject does not have an alteration in JAK2, e.g., JAK2V617F. In other embodiments, the subject is identified, or has been previously identified, as having a post-MPN AML comprising an MLL alteration and not having an alteration in JAK2, e.g., JAK2V617F.

In certain embodiments, the subject has an alteration in MLL, e.g., the subject has post-MPN AML comprising a MLL alteration described herein; and the subject has an alteration in JAK2, e.g., JAK2V617F. In other embodiments, the subject is identified, or has been previously identified, as having a post-MPN AML comprising an MLL alteration and having an alteration in JAK2, e.g., JAK2V617F.

In one embodiment, the subject is a human. In other embodiments, the subject is a cancer patient, e.g., a patient having post-MPN AML as described herein.

In one embodiment, the subject is undergoing or has undergone treatment with a different (e.g., non-MLL) therapeutic agent or therapeutic modality. In one embodiment, the non-MLL therapeutic agent or therapeutic modality is a chemotherapy, immunotherapy, or a surgical procedure. In one embodiment, the non-MLL therapeutic agent or therapeutic modality comprises one or more of: an anthracycline, idarubicin, daunorubicin/daunomycin, anthracenedione, mitoxantrone, cytarabine (cytosine arabinose, ara-C), idarubicin, cladribine (Leustatin, 2-CdA), fludarabine (Fludara), topotecan, etoposide (VP-16), 6-thioguanine (6- TG), hydroxyurea (Hydrea), corticosteroid drugs (e.g., prednisone or dexamethasone

(Decadron)), methotrexate (MTX), 6-mercaptopurine (6-MP), azacitidine (Vidaza), clofarabine (Colar), decitabine (Dacogen), stem cell transplantation, gemtuzumab ozogamicin, and/or a bone marrow transplantation.

In one embodiment, responsive to the determination of the presence of the MLL alteration described herein, the different therapeutic agent or therapeutic modality is discontinued. In yet other embodiments, the subject has been identified as being likely or unlikely to respond to the different therapeutic agent or therapeutic modality.

In certain embodiments, the subject has participated previously in a clinical trial, e.g., a clinical trial for a different (e.g., non-MLL) therapeutic agent or therapeutic modality. In other embodiments, the subject is a cancer patient who has participated in a clinical trial, e.g., a clinical trial for a different (e.g., non-MLL) therapeutic agent or therapeutic modality. Agents

In certain embodiments, the agent (e.g., the therapeutic agent) used in the methods targets and/or inhibits an MLL (e.g., an alteration in an MLL gene or gene product as described herein), or an MLL- signalling component. In one embodiment, the agent binds and/or inhibits MLL. In one embodiment, the agent is a reversible or an irreversible MLL inhibitor.

In one embodiment, the agent is chosen from: a methyltransferase inhibitor, a multi- specific methyltransferase inhibitor; an inhibitor, e.g., a small molecule inhibitor that is selective for MLL or an MLL-signaling component; an antibody molecule against MLL; or a nucleic acid inhibitor.

In one embodiment, the MLL-signaling component is a histone methyltransferase, e.g., DOT 1 -like, histone H3 methyltransferase (DOTIL). In one embodiment, the agent is an inhibitor of DOTIL, e.g., an aminonucleoside inhibitor of histone methyltransferase activity. In certain embodiments, the MLL inhibitor is chosen from: Epizyme EPZ-5676, SGC0946 and combinations thereof. In one embodiment, the agent is Epizyme EPZ-5676 (Daigle, S.R. et al., (2013) Blood 122(6): 1017-25). In one embodiment, Epizyme EPZ-5676 has the chemical name: (2R,3R,4S,5R)-2-(6-Amino-9H-purin-9-yl)-5-((((lr,3S)-3-(2-(5-(tert-butyl)- lH-benzo[d] imidazol-2-yl)ethyl)cyclobutyl)(isopropyl)amino)methyl)tetrahydrofuran-3,4- diol; and has the following structure:

Epizyme EPZ-5676 Chemical Structure

Molecular Weight: 563 Da In one embodiment, the agent is SGC0946 (Wenyu, Y., et ah, (2012) Nature

Communications 3: 1288). In one embodiment, SGC0946 has the chemical name: 3-(((5-(5- amino-7-bromo-2,4,9-triaza-bicyclo[4.3.0]nona-l,3,5,7-tetraen-9-yl)-3,4-dihydroxy- tetrahydro-furan-2-yl)-methyl)-(l-methyl-ethyl)-amino)-propylamino)-(4-tert-butyl- phenylamino)-methanone; and has the following structure:

SGC0946 Chemical Structure

Molecular Weight: 653.02

In other embodiments, the agent is chosen from a nucleic acid molecule (e.g., an antisense molecule, a ribozyme, a double stranded RNA, or a triple helix molecule) that hybridizes to and/or inhibits a MLL nucleic acid, e.g., a MLL nucleic acid encoding the alteration, or a transcription regulatory region that blocks or reduces mRNA expression of the alteration.

In certain embodiments, the agents (e.g., therapeutic agents) described herein can be used in combination with a therapeutic agent or therapeutic modality chosen from one or more of: an anthracycline, idarubicin, daunorubicin/daunomycin, anthracenedione, mitoxantrone, cytarabine (cytosine arabinose, ara-C), idarubicin, cladribine (Leustatin, 2-CdA), fludarabine (Fludara), topotecan, etoposide (VP-16), 6-thioguanine (6-TG), hydroxyurea (Hydrea), corticosteroid drugs (e.g., prednisone or dexamethasone (Decadron)), methotrexate (MTX), 6- mercaptopurine (6-MP), azacitidine (Vidaza), clofarabine (Colar), decitabine (Dacogen), stem cell transplantation, gemtuzumab ozogamicin, and/or a bone marrow transplantation.

Additional aspects or embodiments of the invention include one or more of the following.

Compositions, e.g., pharmaceutical compositions, comprising one or more of the agents, e.g., the therapeutic agents described herein, for use, e.g., in treating post-MPN AML, e.g., JAK2V617F negative or positive post-MPN AML, as described herein are also disclosed.

Additionally, kits comprising the agents, e.g., the therapeutic agents (and compositions thereof), with instructions for use in treating post-MPN AML, e.g., JAK2V617F negative or positive post-MPN AML, and/or determining the presence of an alteration described herein are also provided.

In another aspect, the invention features a kit comprising one or more detection reagents (e.g., probes, primers, antibodies), capable, e.g., of specific detection of a nucleic acid or protein comprising an alteration described herein.

The invention also provides methods of: identifying, assessing or detecting an alteration described herein. In one embodiment, the alteration is in a JAK2V617F negative post-MPN AML e.g., an alteration in Table 1 (e.g., an NRAS mutation), or in a sample derived from a patient diagnosed with or suspected of having a JAK2V617F negative post-MPN AML. In another embodiment, the alteration is in a JAK2V617F positive post-MPN AML e.g., an alteration in Table 1 (e.g., an IDH2 mutation), or in a sample derived from a patient diagnosed with or suspected of having a JAK2V617F positive post-MPN AML. In one embodiment, the alteration is in a JAK2V617F negative and positive post-MPN AML e.g., an alteration in MLL, or in a sample derived from a patient diagnosed with or suspected of having a JAK2V617F negative and positive post-MPN AML.

Applicants have further identified that ASXLl mutations occur frequently in JAK2 wild- type Philadelphia-Chromosome negative MPNs, and are associated with impaired overall survival. Accordingly, another aspect of the invention features a method of assessing or evaluating survival of a sublect, e.g., a subject with a JAK2 wild-type Philadelphia-Chromosome negative MPN. The method comprises detecting an ASXLl alteration, e.g., an ASXLl mutation described herein, wherein the presence of the ASXLl mutation is indicative of impaired survival of the subject. Methods of detecting, or determining the presence of, the ASXLl alteration are described herein. Included are isolated nucleic acid molecules comprising the alterations, nucleic acid constructs, host cells containing the nucleic acid molecules; purified polypeptides comprising the alteration described herein and binding agents; detection reagents (e.g., probes, primers, antibodies, kits, capable, e.g., of specific detection of a nucleic acid or protein comprising an alteration described herein); screening assays for identifying molecules that interact with, e.g., inhibit the alterations, e.g., novel GTPase inhibitors or binders of NRAS. In one embodiment, the detection of the alteration comprises sequencing, e.g., nucleic acid sequencing or amino acid sequencing.

Alternatively, or in combination with the methods described herein, the invention features a method of determining the presence of an alteration described herein in a cancer, e.g., post-MPN AML, e.g., JAK2V617F negative and/or positive post-MPN AML. The method includes: acquiring knowledge (e.g., directly acquiring knowledge) that the alteration described herein is present in a subject, e.g., a sample (e.g., a cancer or tumor sample) from the subject. In one embodiment, the acquiring step comprises a determination of the presence of the alteration in a nucleic acid molecule from the subject, e.g., by performing a sequencing step. In other embodiments, the acquiring step comprises a determination of the presence of a polypeptide or a protein comprising the alteration described herein in the sample from the subject.

In one embodiment, the subject, or the sample, comprises one or more cells or tissue from post-MPN AML, e.g., JAK2V617F negative and/or positive post-MPN AML.

In one embodiment the method further comprises administering an agent, e.g., a therapeutic agent that targets and/or inhibits an alteration described herein, e.g., an inhibitor of MAPK signaling, MLL, or IDH2 as described herein, to the subject responsive to the

determination of the presence of the alteration in the sample from the subject.

In one embodiment, the mutation is detected in a nucleic acid molecule or a polypeptide. The method includes detecting whether a mutated nucleic acid molecule or polypeptide is present in a cell (e.g., a circulating cell), a tissue (e.g., a tumor), or a sample, e.g., a tumor sample, from a subject. In one embodiment, the sample is a nucleic acid sample. In one embodiment, the nucleic acid sample comprises DNA, e.g., genomic DNA or cDNA, or RNA, e.g., mRNA. In other embodiments, the sample is a protein sample. In one embodiment, the sample or tissue is, or has been, classified as non-malignant or malignant using other diagnostic techniques, e.g., immunohistochemistry.

In one embodiment, the sample is acquired from a subject (e.g., a subject having or at risk of having a cancer, e.g., a patient), or alternatively, the method further includes acquiring a sample from the subject. In certain embodiments, the sample is a blood sample. In certain embodiments, the sample is a blood sample, a whole blood sample, or a serum sample. The sample can be chosen from one or more of: tissue, e.g., cancerous tissue (e.g., a tissue biopsy), whole blood, serum, plasma, buccal scrape, sputum, saliva, cerebrospinal fluid, urine, stool, circulating tumor cells, circulating nucleic acids, or bone marrow. In certain embodiments, the sample is a tissue (e.g., a tumor biopsy), a circulating tumor cell or nucleic acid.

In embodiments, the sample is from a cancer described herein, e.g., post-MPN AML, e.g., JAK2V617F negative and/or positive post-MPN AML.

In one embodiment, the subject is at risk of having, or has post-MPN AML, e.g.,

JAK2V617F negative and/or positive post-MPN AML.

In other embodiments, the mutation is detected in a nucleic acid molecule by a method chosen from one or more of: nucleic acid hybridization assay, amplification-based assays (e.g., polymerase chain reaction (PCR)), PCR-RFLP assay, real-time PCR, sequencing, screening analysis, SSP, HPLC or mass-spectrometric genotyping.

In one embodiment, the method includes: contacting a nucleic acid sample, e.g., a genomic DNA sample (e.g., a chromosomal sample or a fractionated, enriched or otherwise pre-treated sample) or a gene product (mRNA, cDNA), obtained from the subject, with a nucleic acid fragment (e.g., a probe or primer as described herein (e.g., an exon-specific probe or primer) under conditions suitable for hybridization, and determining the presence or absence of the mutated nucleic acid molecule. The method can, optionally, include enriching a sample for the gene or gene product.

Alternatively, or in combination with the methods described herein, the invention features a method for determining the presence of a mutated nucleic acid molecule. The method includes: acquiring a sequence for a position in a nucleic acid molecule, e.g., by sequencing at least one nucleotide of the nucleic acid molecule (e.g., sequencing at least one nucleotide in the nucleic acid molecule that comprises the mutation), thereby determining that the mutation is present in the nucleic acid molecule. Optionally, the sequence acquired is compared to a reference sequence, or a wild type reference sequence. In one embodiment, the nucleic acid molecule is from a cell (e.g., a circulating cell), a tissue, or any sample from a subject (e.g., blood or plasma sample). In other embodiments, the nucleic acid molecule from a tumor sample (e.g., a tumor or cancer sample) is sequenced. In one embodiment, the sequence is determined by a next generation sequencing method. The method further can further include acquiring, e.g., directly or indirectly acquiring, a sample, e.g., a post-MPN AML (e.g., JAK2V617F and/or positive post- MPN AML).

In another aspect, the invention features a method of analyzing a tumor or a circulating tumor cell. The method includes acquiring a nucleic acid sample from the tumor or the circulating cell; and sequencing, e.g., by a next generation sequencing method, a nucleic acid molecule, e.g., a nucleic acid molecule that includes an alteration as described herein.

In yet other embodiment, a polypeptide comprising an alteration described herein is detected. The method includes: contacting a protein sample with a reagent which specifically binds to a polypeptide comprising an alteration described herein; and detecting the formation of a complex of the polypeptide and the reagent. In one embodiment, the reagent is labeled with a detectable group to facilitate detection of the bound and unbound reagent. In one embodiment, the reagent is an antibody molecule, e.g., is selected from the group consisting of an antibody, and antibody derivative, and an antibody fragment.

In yet another embodiment, the level (e.g., expression level) or activity the polypeptide comprising an alteration described herein is evaluated. For example, the level (e.g.,

expression level) or activity of the polypeptide (e.g., mRNA or polypeptide) is detected and (optionally) compared to a pre-determined value, e.g., a reference value (e.g., a control sample).

In yet another embodiment, the alteration is detected prior to initiating, during, or after, a treatment in a subject having an alteration described herein.

In one embodiment, the alteration is detected at the time of diagnosis with a cancer. In other embodiment, the alteration is detected at a pre-determined interval, e.g., a first point in time and at least at a subsequent point in time.

In certain embodiments, responsive to a determination of the presence of the alteration, any of the methods described herein further include one or more of: (1) stratifying a patient population (e.g., assigning a subject, e.g., a patient, to a group or class);

(2) identifying or selecting the subject as being likely or unlikely to respond to a treatment, e.g., an inhibitor treatment as described herein;

(3) selecting a treatment option, e.g., administering or not administering a preselected therapeutic agent, e.g., an inhibitor as described herein; or

(4) prognosticating the time course of the disease in the subject (e.g., evaluating the likelihood of increased or decreased patient survival).

In certain embodiments, responsive to the determination of the presence of a mutation, the subject is classified as a candidate to receive treatment with a therapy disclosed herein. In one embodiment, responsive to the determination of the presence of a mutation, the subject, e.g., a patient, can further be assigned to a particular class if a mutation is identified in a sample of the patient. For example, a patient identified as having a mutation can be classified as a candidate to receive treatment with a therapy disclosed herein. In one embodiment, the subject, e.g., a patient, is assigned to a second class if the mutation is not present. For example, a patient who has a tumor that does not contain a mutation, may be determined as not being a candidate to receive a therapy disclosed herein.

In another embodiment, responsive to the determination of the presence of the

alteration, the subject is identified as likely to respond to a treatment that comprises a therapy disclosed herein.

In yet another embodiment, responsive to the determination of the presence of the alteration, the method includes administering an agent, e.g., a therapeutic agent as described herein, e.g., an inhibitor, to the subject.

Method of Evaluating a Tumor or a Subject

In another aspect, the invention features a method of evaluating a subject (e.g., a patient), e.g., for risk of having or developing a cancer, e.g., e.g., JAK2V617F negative and/or positive post-MPN AML. The method includes: acquiring information or knowledge of the presence of a mutation as described herein in a subject (e.g., acquiring genotype information of the subject that identifies a mutation as being present in the subject); acquiring a sequence for a nucleic acid molecule identified herein (e.g., a nucleic acid molecule that includes a mutation sequence); or detecting the presence of a nucleic acid or polypeptide in the subject), wherein the presence of the mutation is positively correlated with increased risk for, or having, a cancer associated with such a mutation.

The method can further include acquiring, e.g., directly or indirectly, a sample from a patient and evaluating the sample for the present of an alteration as described herein.

The method can further include the step(s) of identifying (e.g., evaluating, diagnosing, screening, and/or selecting) the subject as being positively correlated with increased risk for, or having, a cancer associated with the alteration.

In another embodiment, a subject identified as having the alteration is identified or selected as likely or unlikely to respond to a treatment, e.g., a therapy disclosed herein. The method can further include treating the subject with a therapy disclosed herein.

In a related aspect, a method of evaluating a patient or a patient population is provided. The method includes: identifying, selecting, or obtaining information or knowledge that the patient or patient population has participated in a clinical trial; acquiring information or knowledge of the presence of an alteration (e.g., an alteration as described herein) in the patient or patient population (e.g., acquiring genotype information of the subject that identifies an alteration as being present in the subject); acquiring a sequence for a nucleic acid molecule identified herein (e.g., a nucleic acid molecule that includes an alteration sequence); or detecting the presence of a mutated nucleic acid or polypeptide in the subject), wherein the presence of the alteration identifies the patient or patient population as being likely to respond to an agent as described herein (e.g., a NRAS inhibitor, a MAPK inhibitor, a MEK inhibitor, an IDH2 inhibitor and/or an MLL inhibitor).

In some embodiments, the method further includes treating the subject with an agent as described herein (e.g., a NRAS inhibitor, a MAPK inhibitor, a MEK inhibitor, an IDH2 inhibitor and/or an MLL inhibitor).

Reporting

Methods described herein can include providing a report, such as, in electronic, web- based, or paper form, to the patient or to another person or entity, e.g., a caregiver, e.g., a physician, e.g., an oncologist, a hospital, clinic, third-party payor, insurance company or government office. The report can include output from the method, e.g., the identification of nucleotide values, the indication of presence or absence of an alteration as described herein, or wildtype sequence. In one embodiment, a report is generated, such as in paper or electronic form, which identifies the presence or absence of an alteration described herein, and optionally includes an identifier for the patient from which the sequence was obtained.

The report can also include information on the role of a mutation as described herein, or wildtype sequence, in disease. Such information can include information on prognosis, resistance, or potential or suggested therapeutic options, e.g., an agent as described herein (e.g., a NRAS inhibitor). The report can include information on the likely effectiveness of a therapeutic option, the acceptability of a therapeutic option, or the advisability of applying the therapeutic option to a patient, e.g., a patient having a sequence, alteration or mutation identified in the test, and in embodiments, identified in the report. For example, the report can include information, or a recommendation on, the administration of a drug, e.g., the administration at a preselected dosage or in a preselected treatment regimen, e.g., in combination with other drugs, to the patient. In one embodiment, not all mutations identified in the method are identified in the report. For example, the report can be limited to mutations in genes having a preselected level of correlation with the occurrence, prognosis, stage, or susceptibility of the cancer to treatment, e.g., with a preselected therapeutic option. The report can be delivered, e.g., to an entity described herein, within 7, 14, or 21 days from receipt of the sample by the entity practicing the method.

In another aspect, the invention features a method for generating a report, e.g., a personalized cancer treatment report, by obtaining a sample, e.g., a tumor sample, from a subject, detecting a mutation as described herein in the sample, and selecting a treatment based on the mutation identified. In one embodiment, a report is generated that annotates the selected treatment, or that lists, e.g., in order of preference, two or more treatment options based on the mutation identified. In another embodiment, the subject, e.g., a patient, is further administered the selected method of treatment.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and the example are illustrative only and not intended to be limiting.

The details of one or more embodiments featured in the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages featured in the invention will be apparent from the description and drawings, and from the claims.

BRIEF DESCRIPTION OF THE DRAWING

FIG. 1 shows the spectrum of genomic alterations found in JAK2V617F positive post- MPN AML (JAK2V617F) and JAK2V617F negative post-MPN AML (JAK2 wildtype).

FIG. 2 shows genomic mutations found in (a) de novo AML and (b) post-MPN AML.

FIG. 3 shows ASXL1 mutations result in impaired survival in patients with

JAK2V617F negative post-MPN AML (JAK2 wildtype).

FIG. 4 shows the spectrum of genomic alterations found in JAK2V617F positive post- MPN AML (JAK2V617F) and JAK2V617F negative post-MPN AML (JAK2 wildtype).

DETAILED DESCRIPTION

The invention is based, at least in part, on the discovery of alterations in post- myeloproliferative neoplasms (MPNs), such as post-MPN acute myeloid leukemia (AML) (referred to herein as "post-MPN AML"). In certain embodiments, the post-MPN AML has a mutation in JAK2, e.g., a mutation at position 617 (e.g., JAK2V617F), referred to herein as "JAK2V617F positive post-MPN AML." In other embodiments, the post-MPN AML does not have a mutation in JAK2 at position 617, e.g., has a wild-type JAK2, referred to herein as "JAK2V617F negative post-MPN AML. Additionally described herein is a genomic analysis of a series of patients with post-MPN AML e.g., JAK2V617F negative post-MPN AML and/or JAK2V617F positive post-MPN AML. As shown in FIG. 2, post-MPN and de novo AML have different driver genetic mutations. For example, post-MPN AML samples do not show detectable mutations in FLT3, NPM1 or DNMT3A, which are seen in de novo AML.

In certain embodiments, Applicants have identified, of 33 post-MPN AML cases analyzed (of which 17 were JAK2V617F positive and 16 were JAK2V617F negative), about 37.5% of the JAK2V617F negative cases had an alteration in NRAS; the NRAS and the JAK2 alterations were mutually exclusive in the entire cohort examined. KRAS mutations were found to coexist with JAK2 (in the subclones examined). Additional alterations identified in JAK2V617F negative post-MPN AML cases include alterations in ASXLl (at a frequency of about 56.3%), alterations in SETBP1 (at a frequency of about 19%), as well as those

alterations shown in FIG. 1 or Table 1. The SETBP1 mutation was mutually exclusive with the JAK2 mutation. Mutations in NRAS and KRAS largely coexist with ASXLl mutations.

In other embodiments, about 41.2% of the JAK2V617F positive cases had an alteration in IDH2. Additional alterations in JAK2V617F positive cases identified include alterations in ASXLl, TP53, as well as those alterations shown in FIG. 1 or Table 1. Mutations in RUNXl largely coexist with JAK2.

Alterations in MLL were observed in both JAK2V617F negative and JAK2V617F positive cases. Mutations in splicing factors (SRSF2, U2AF1 and SF3B1) were mutually exclusive.

Therefore, the invention provides, at least in part, methods for treating MPNs and related disorders, e.g., post-MPN AML. In one embodiment, a JAK2V617F negative post- MPN AML is treated with an agent that targets and/or inhibits a MAPK pathway gene or gene product. In other embodiments, a JAK2V617F positive post-MPN AML is treated with an agent that targets and/or inhibits an IDH2 gene or gene product. In yet other embodiments, a post-MPN AML (e.g., a JAK2V617F negative and/or JAK2V617F positive post-MPN AML) is an agent that targets and/or inhibits an MLL gene or gene product. Methods and reagents for identifying, assessing or detecting an alteration as described herein, e.g., a NRAS, IDH2, MLL, ASXLl mutation, and/or the alterations described in FIG. 1 or Table 1, in post-MPN AML are also discosed.

Certain terms are defined below and throughout the specification.

As used herein, the articles "a" and "an" refer to one or to more than one (e.g., to at least of the grammatical object of the article.

The term "or" is used herein to mean, and is used interchangeably with, the term "and/or' unless context clearly indicates otherwise.

"About" and "approximately" shall generally mean an acceptable degree of error for the quantity measured given the nature or precision of the measurements. Exemplary degrees of err< within 20 percent (%), typically, within 10%, and more typically, within 5% of a given value or ran of values.

"Acquire" or "acquiring" as the terms are used herein, refer to obtaining possession of a physical entity, or a value, e.g., a numerical value, by "directly acquiring" or "indirectly acquiring" the physical entity or value. "Directly acquiring" means performing a process (e.g., performing a synthetic or analytical method) to obtain the physical entity or value. "Indirectly acquiring" refers to receiving the physical entity or value from another party or source (e.g., a third party laboratory that directly acquired the physical entity or value). Directly acquiring a physical entity includes performing a process that includes a physical change in a physical substance, e.g., a starting material. Exemplary changes include making a physical entity from two or more starting materials, shearing or fragmenting a substance, separating or purifying a substance, combining two or more separate entities into a mixture, performing a chemical reaction that includes breaking or forming a covalent or non-covalent bond. Directly acquiring a value includes performing a process that includes a physical change in a sample or another substance, e.g., performing an analytical process which includes a physical change in a substance, e.g., a sample, analyte, or reagent (sometimes referred to herein as "physical analysis"), performing an analytical method, e.g., a method which includes one or more of the following: separating or purifying a substance, e.g., an analyte, or a fragment or other derivative thereof, from another substance; combining an analyte, or fragment or other derivative thereof, with another substance, e.g., a buffer, solvent, or reactant; or changing the structure of an analyte, or a fragment or other derivative thereof, e.g., by breaking or forming a covalent or non-covalent bond, between a first and a second atom of the analyte; or by changing the structure of a reagent, or a fragment or other derivative thereof, e.g., by breaking or forming a covalent or non-covalent bond, between a first and a second atom of the reagent.

"Acquiring a sequence" as the term is used herein, refers to obtaining possession of a nucleotide sequence or amino acid sequence, by "directly acquiring" or "indirectly acquiring" the sequence. "Directly acquiring a sequence" means performing a process (e.g., performing a synthetic or analytical method) to obtain the sequence, such as performing a sequencing method (e.g., a Next Generation Sequencing (NGS) method). "Indirectly acquiring a sequence" refers to receiving information or knowledge of, or receiving, the sequence from another party or source (e.g., a third party laboratory that directly acquired the sequence). The sequence acquired need not be a full sequence, e.g., sequencing of at least one nucleotide, or obtaining information or knowledge that identifies a mutation disclosed herein as being present in a subject constitutes acquiring a sequence.

Directly acquiring a sequence includes performing a process that includes a physical change in a physical substance, e.g., a starting material, such as a tissue sample, e.g., a biopsy, or an isolated nucleic acid (e.g., DNA or RNA) sample. Exemplary changes include making a physical entity from two or more starting materials, shearing or fragmenting a substance, such as a genomic DNA fragment; separating or purifying a substance (e.g., isolating a nucleic acid sample from a tissue); combining two or more separate entities into a mixture, performing a chemical reaction that includes breaking or forming a covalent or non-covalent bond. Directly acquiring a value includes performing a process that includes a physical change in a sample or another substance as described above.

"Acquiring a sample" as the term is used herein, refers to obtaining possession of a sample, e.g., a tissue sample or nucleic acid sample, by "directly acquiring" or "indirectly acquiring" the sample. "Directly acquiring a sample" means performing a process (e.g., performing a physical method such as a surgery or extraction) to obtain the sample. "Indirectly acquiring a sample" refers to receiving the sample from another party or source (e.g., a third party laboratory that directly acquired the sample). Directly acquiring a sample includes performing a process that includes a physical change in a physical substance, e.g., a starting material, such as a tissue, e.g., a tissue in a human patient or a tissue that has was previously isolated from a patient. Exemplary changes include making a physical entity from a starting material, dissecting or scraping a tissue; separating or purifying a substance (e.g., a sample tissue or a nucleic acid sample); combining two or more separate entities into a mixture; performing a chemical reaction that includes breaking or forming a covalent or non-covalent bond. Directly acquiring a sample includes performing a process that includes a physical change in a sample or another substance, e.g., as described above.

An "alteration" as used herein, of a gene or gene product (e.g., a NRAS, IDH2, and/or MLL gene or gene product) refers to the presence of a mutation or mutations within the gene or gene product, e.g., a mutation, which affects amount or activity of the gene or gene

product, as compared to the normal or wild-type gene. The alteration can be in amount, structure, and/or activity in a cancer tissue or cancer cell, as compared to its amount, structure, and/or activity, in a normal or healthy tissue or cell (e.g., a control), and is associated with a disease state, such as cancer. For example, a gene or gene product which is associated with cancer, or predictive of responsiveness to anti-cancer therapeutics, can have an altered nucleotide sequence (e.g., a mutation), amino acid sequence, chromosomal translocation, intra-chromosomal inversion, copy number, expression level, protein level, protein activity, or methylation status, in a cancer tissue or cancer cell, as compared to a normal, healthy tissue or cell. Exemplary mutations include, but are not limited to, point mutations (e.g., silent, missense, or nonsense), deletions, insertions, inversions, linking mutations, duplications, translocations, inter- and intra-chromosomal rearrangements. Mutations can be present in the coding or non-coding region of the gene. In certain embodiments, the alterations are

associated (or not associated) with a phenotype, e.g., a cancerous phenotype (e.g., one or more of cancer risk, cancer progression, cancer treatment or resistance to cancer treatment).

"Binding entity" means any molecule to which molecular tags can be directly or indirectly attached that is capable of specifically binding to an analyte. The binding entity can be an affinity tag on a nucleic acid sequence. In certain embodiments, the binding entity allows for separation of the nucleic acid from a mixture, such as an avidin molecule, or an antibody that binds to the hapten or an antigen-binding fragment thereof. Exemplary binding entities include, but are not limited to, a biotin molecule, a hapten, an antibody, an antibody binding fragment, a peptide, and a protein.

"Complementary" refers to sequence complementarity between regions of two nucleic acid strands or between two regions of the same nucleic acid strand. It is known that an adenine residue of a first nucleic acid region is capable of forming specific hydrogen bonds ("base pairing") with a residue of a second nucleic acid region which is antiparallel to the first region if the residue is thymine or uracil. Similarly, it is known that a cytosine residue of a first nucleic acid strand is capable of base pairing with a residue of a second nucleic acid strand which is antiparallel to the first strand if the residue is guanine. A first region of a nucleic acid is complementary to a second region of the same or a different nucleic acid if, when the two regions are arranged in an antiparallel fashion, at least one nucleotide residue of the first region is capable of base pairing with a residue of the second region. In certain embodiments, the first region comprises a first portion and the second region comprises a second portion, whereby, when the first and second portions are arranged in an antiparallel fashion, at least about 50%, at least about 75%, at least about 90%, or at least about 95% of the nucleotide residues of the first portion are capable of base pairing with nucleotide residues in the second portion. In other embodiments, all nucleotide residues of the first portion are capable of base pairing with nucleotide residues in the second portion.

The term "cancer" or "tumor" is used interchangeably herein. These terms refer to the presence of cells possessing characteristics typical of cancer-causing cells, such as uncontrolled proliferation, immortality, metastatic potential, rapid growth and proliferation rate, and certain characteristic morphological features.

The term "neoplasm" or "neoplastic" cell refers to an abnormal proliferative stage, e.g., a hyperproliferative stage, in a cell or tissue that can include a benign, pre-malignant, malignant (cancer) or metastatic stage.

Cancer is "inhibited" if at least one symptom of the cancer is alleviated, terminated, slowed, or prevented. As used herein, cancer is also "inhibited" if recurrence or metastasis of the cancer is reduced, slowed, delayed, or prevented.

"Chemo therapeutic agent" means a chemical substance, such as a cytotoxic or cytostatic agent that is used to treat a condition, particularly cancer.

As used herein, "cancer therapy" and "cancer treatment" are synonymous terms.

As used herein, "chemotherapy" and "chemotherapeutic" and "chemotherapeutic agent" are synonymous terms.

The terms "homology" or "identity," as used interchangeably herein, refer to sequence similarity between two polynucleotide sequences or between two polypeptide sequences, with identity being a more strict comparison. The phrases "percent identity or homology" and "% identity or homology" refer to the percentage of sequence similarity found in a comparison of two or more polynucleotide sequences or two or more polypeptide sequences. "Sequence similarity" refers to the percent similarity in base pair sequence (as determined by any suitable method) between two or more polynucleotide sequences. Two or more sequences can be anywhere from 0-100% similar, or any integer value there between. Identity or similarity can be determined by comparing a position in each sequence that can be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same nucleotide base or amino acid, then the molecules are identical at that position. A degree of similarity or identity between polynucleotide sequences is a function of the number of identical or matching nucleotides at positions shared by the polynucleotide sequences. A degree of identity of polypeptide sequences is a function of the number of identical amino acids at positions shared by the polypeptide sequences. A degree of homology or similarity of polypeptide sequences is a function of the number of amino acids at positions shared by the polypeptide sequences. The term "substantially identical," as used herein, refers to an identity or homology of at least 75%, at least 80%, at least 85%, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more.

"Likely to" or "increased likelihood," as used herein, refers to an increased probability that an item, object, thing or person will occur. Thus, in one example, a subject that is likely to respond to treatment with a kinase inhibitor, alone or in combination, has an increased probability of responding to treatment with the inhibitor alone or in combination, relative to a reference subject or group of subjects.

"Unlikely to" refers to a decreased probability that an event, item, object, thing or person will occur with respect to a reference. Thus, a subject that is unlikely to respond to treatment with a kinase inhibitor, alone or in combination, has a decreased probability of responding to treatment with a kinase inhibitor, alone or in combination, relative to a

reference subject or group of subjects.

"Sequencing" a nucleic acid molecule requires determining the identity of at least 1 nucleotide in the molecule. In embodiments, the identity of less than all of the nucleotides in a molecule is determined. In other embodiments, the identity of a majority or all of the nucleotides in the molecule is determined.

"Next-generation sequencing or NGS or NG sequencing" as used herein, refers to any sequencing method that determines the nucleotide sequence of either individual nucleic acid molecules (e.g., in single molecule sequencing) or clonally expanded proxies for individual nucleic acid molecules in a highly parallel fashion (e.g., greater than 10⁵ molecules are sequenced simultaneously). In one embodiment, the relative abundance of the nucleic acid species in the library can be estimated by counting the relative number of occurrences of their cognate sequences in the data generated by the sequencing experiment. Next generation sequencing methods are known in the art, and are described, e.g., in Metzker, M. (2010) Nature

Biotechnology Reviews 11:31-46, incorporated herein by reference. Next generation sequencing can detect a variant present in less than 5% of the nucleic acids in a sample. "Sample," "tissue sample," "patient sample," "patient cell or tissue sample" or

"specimen" each refers to a collection of similar cells obtained from a tissue of a subject or patient. The source of the tissue sample can be solid tissue as from a fresh, frozen and/or preserved organ, tissue sample, biopsy, or aspirate; blood or any blood constituents; bodily fluids such as cerebral spinal fluid, amniotic fluid, peritoneal fluid or interstitial fluid; or cells from any time in gestation or development of the subject. The tissue sample can contain compounds that are not naturally intermixed with the tissue in nature such as preservatives, anticoagulants, buffers, fixatives, nutrients, antibiotics or the like. In one embodiment, the sample is preserved as a frozen sample or as formaldehyde- or paraformaldehyde-fixed paraffin-embedded (FFPE) tissue preparation. For example, the sample can be embedded in a matrix, e.g., an FFPE block or a frozen sample.

A "tumor nucleic acid sample" as used herein, refers to nucleic acid molecules from a tumor or cancer sample. Typically, it is DNA, e.g., genomic DNA, or cDNA derived from RNA, from a tumor or cancer sample. In certain embodiments, the tumor nucleic acid sample is purified or isolated (e.g., it is removed from its natural state).

A "control" or "reference" "nucleic acid sample" as used herein, refers to nucleic acid molecules from a control or reference sample. Typically, it is DNA, e.g., genomic DNA, or cDNA derived from RNA, not containing the alteration or variation in the gene or gene product, e.g., not containing a mutation. In certain embodiments, the reference or control nucleic acid sample is a wild type or a non-mutated sequence. In certain embodiments, the reference nucleic acid sample is purified or isolated (e.g., it is removed from its natural state). In other

embodiments, the reference nucleic acid sample is from a non-tumor sample, e.g., a blood control, a normal adjacent tumor (NAT), or any other non-cancerous sample from the same or a different subject.

"Adjacent to the interrogation position," as used herein, means that a site sufficiently close such that a detection reagent complementary with the site can be used to distinguish between a mutation, e.g., an alteration described herein, and a reference sequence, e.g., a non- mutant or wild- type sequence, in a target nucleic acid. Directly adjacent, as used herein, is where 2 nucleotides have no intervening nucleotides between them.

"Associated mutation," as used herein, refers to a mutation within a preselected distance, in terms of nucleotide or primary amino acid sequence, from a definitional mutation, e.g., a mutant as described herein. In embodiments, the associated mutation is within n, wherein n is 2, 5, 10, 20, 30, 50, 100, or 200 nucleotides from the definitional mutation (n does not include the nucleotides defining the associated and definitional mutations). In embodiments, the associated mutation is a translocation mutation.

"Interrogation position," as used herein, comprises at least one nucleotide (or, in the case of polypeptides, an amino acid residue) which corresponds to a nucleotide (or amino acid residue) that is mutated in a mutation of interest, e.g., a mutation being identified, or in a nucleic acid (or protein) being analyzed, e.g., sequenced, or recovered.

A "reference sequence," as used herein, e.g., as a comparator for a mutant sequence, is a sequence which has a different nucleotide or amino acid at an interrogation position than does the mutant(s) being analyzed. In one embodiment, the reference sequence is wild-type for at least the interrogation position.

As used herein, "Myeloproliferative neoplasms" or "MPN" refers to blood cancers, e.g., clonal blood cancers, initiated one or more abnormal mutations in a bone marrow stem cell. The mutation typically leads to an overproduction of any combination of white blood cells, red blod cells and platelets. MPNs are commonly divided into two major subtypes: Philadelphia-chromosome positive (e.g., chronic myelogenous leukemia (CML)) and

Philadelphia-chromosome negative (e.g., polycythemia vera (PV), essential thrombocytosus (ET), and myelofibrosis (MF)).

Post-MPN acute myeloid leukemia (AML) (post-MPN AML) develops in a subset of patients with the Philadelphia-chromosome negative myeloproliferative neoplasms (MPNs), such as polycythemia vera (PV), essential thrombocytosus (ET), and myelofibrosis (MF). The JAK2 mutation, JAK2V617F, is a unifying, although not universal, genetic abnormality found in MPNs (Heaney, supra). However, in approximately 50% of cases, patients with

JAK2V617F mutant chronic-phase MPN transform to JAK2 wildtype AMLs, indicating that diverse genomic paths lead to development of post-MPN AML.

"Janus kinase 2," "JAK2" or "JAK2" (also known as JTK10 and THCYT3) refers to a JAK2 molecule (e.g., a nucleic acid or protein). The JAK2 protein refers to a protein, typically human JAK2 that is encoded by the JAK2 gene. JAK2 is a protein tyrosine kinase involved in a specific subset of cytokine receptor signaling pathways. Upon receptor activation JAKs phosphorylate the transcription factors known as STATs and initiate the JAK-STAT signaling pathway. The JAK2 amino and nucleotide sequences are known in the art. An exemplary amino acid and nucleotide sequence for human JAK2 are described in, e.g., Wilks, A.F. et al. (1991) Mol. Cell. Biol. 11 (4), 2057-2065; and NCBI Reference Sequence: NP_004963.1 and NM_004972.3, respectively, each of which are incorporated herein by reference. In one embodiment, the JAK2 gene or gene product comprises a mutation at position 617 {e.g., a JAK2V617F, also interchangeably referred to herein as "JAK2V617F").

A "MAPK pathway gene or gene product" as used herein, refers to a gene or a gene product that is directly or indirectly involved in intracellular signaling via a mitogen activated protein kinases (MAPK). In some embodiments, this direct and/or indirect involvement can comprise a gene and/or a gene product upstream and/or downstream of MAPK. MAP kinases can be mediators of cancer-related disease mechanisms (Chen et al., Chem Rev (2001) 101:2449-76; Pearson et al., Endocr Rev (2001) 22: 153-83; English et al., Trends Pharmacol Sci (2002) 23:40-45; Kohno et al., Prog Cell Cycle Res (2003) 5:219-24; and Sebolt-Leopold, Oncogene (2000) 19:6594-99). In one embodiment, a MAPK pathway comprises RAS, RAF, MEK, and ERK (MAPK) {e.g., Ras, Raf-1, A-Raf, B-Raf (BRAF)), MEK1 and/or MEK2. In some embodiments, MAPK pathway gene or gene product can also refer to either or both of the wild type or native gene, as well as or alternatively, certain mutations thereof {e.g., activating mutations thereof), and variants derived from any source {e.g., humans and other mammals), as described herein. In some embodiments, MAPK pathway gene product refers to mRNA, polypeptides and/or fragments thereof, of the encoding MAPK pathway gene.

"Neuroblastoma RAS vial (v-ras) oncogene homolog," "NRAS" or "NRAS" (also known as ALP64, NS4, N-Ras Protein Part 4, and HRAS) refers to a NRAS molecule {e.g., a nucleic acid or protein). The NRAS protein refers to a protein, typically human NRAS that is encoded by the NRAS gene. NRAS is an N-ras oncogene encoding a membrane protein that shuttles between the Golgi apparatus and the plasma membrane. The encoded NRAS protein has intrinsic GTPase activity and is activated by a guanine nucleotide-exchange factor and inactivated by a GTPase activating protein. The NRAS amino and nucleotide sequences are known in the art. An exemplary amino acid and nucleotide sequence for human NRAS are described in, e.g., Hall, A. and Brown, R. (1985) Nucleic Acids Res. 13 (14), 5255-5268; and SEQ ID NO: l and SEQ ID NO:2, respectively. NCBI Reference Sequence: NP_002515

1 MTEYKLVVVG AGGVGKSALT IQLIQNHFVD EYDPTIEDSY RKQVVIDGET CLLDILDTAG

61 QEEYSAMRDQ YMRTGEGFLC VFAINNSKSF ADINLYREQI KRVKDSDDVP MVLVGNKCDL

121 PTRTVDTKQA HELAKSYGIP FIETSAKTRQ GVEDAFYTLV REIRQYRMKK LNSSDDGTQG 181 CMGLPCVVM

(SEQ ID NO: l)

NCBI Reference Sequence: NM_002524.4

1 gaaacgtccc gtgtgggagg ggcgggtctg ggtgcggcct gccgcatgac tcgtggttcg

61 gaggcccacg tggccggggc ggggactcag gcgcctgggg cgccgactga ttacgtagcg 121 ggcggggccg gaagtgccgc tccttggtgg gggctgttca tggcggttcc ggggtctcca 181 acatttttcc cggctgtggt cctaaatctg tccaaagcag aggcagtgga gcttgaggtt 241 cttgctggtg tgaaatgact gagtacaaac tggtggtggt tggagcaggt ggtgttggga 301 aaagcgcact gacaatccag ctaatccaga accactttgt agatgaatat gatcccacca 361 tagaggattc ttacagaaaa caagtggtta tagatggtga aacctgtttg ttggacatac 421 tggatacagc tggacaagaa gagtacagtg ccatgagaga ccaatacatg aggacaggcg 481 aaggcttcct ctgtgtattt gccatcaata atagcaagtc atttgcggat attaacctct 541 acagggagca gattaagcga gtaaaagact cggatgatgt acctatggtg ctagtgggaa 601 acaagtgtga tttgccaaca aggacagttg atacaaaaca agcccacgaa ctggccaaga 661 gttacgggat tccattcatt gaaacctcag ccaagaccag acagggtgtt gaagatgctt 721 tttacacact ggtaagagaa atacgccagt accgaatgaa aaaactcaac agcagtgatg 781 atgggactca gggttgtatg ggattgccat gtgtggtgat gtaacaagat acttttaaag 841 ttttgtcaga aaagagccac tttcaagctg cactgacacc ctggtcctga cttccctgga 901 ggagaagtat tcctgttgct gtcttcagtc tcacagagaa gctcctgcta cttccccagc 961 tctcagtagt ttagtacaat aatctctatt tgagaagttc tcagaataac tacctcctca 1021 cttggctgtc tgaccagaga atgcacctct tgttactccc tgttattttt ctgccctggg 1081 ttcttccaca gcacaaacac acctctgcca ccccaggttt ttcatctgaa aagcagttca 1141 tgtctgaaac agagaaccaa accgcaaacg tgaaattcta ttgaaaacag tgtcttgagc 1201 tctaaagtag caactgctgg tgattttttt tttcttttta ctgttgaact tagaactatg 1261 ctaatttttg gagaaatgtc ataaattact gttttgccaa gaatatagtt attattgctg 1321 tttggtttgt ttataatgtt atcggctcta ttctctaaac tggcatctgc tctagattca 1381 taaatacaaa aatgaatact gaattttgag tctatcctag tcttcacaac tttgacgtaa 1441 ttaaatccaa ctttcacagt gaagtgcctt tttcctagaa gtggtttgta gacttccttt 1501 ataatatttc agtggaatag atgtctcaaa aatccttatg catgaaatga atgtctgaga 1561 tacgtctgtg acttatctac cattgaagga aagctatatc tatttgagag cagatgccat 1621 tttgtacatg tatgaaattg gttttccaga ggcctgtttt ggggctttcc caggagaaag 1681 atgaaactga aagcacatga ataatttcac ttaataattt ttacctaatc tccacttttt 1741 tcataggtta ctacctatac aatgtatgta atttgtttcc cctagcttac tgataaacct 1801 aatattcaat gaacttccat ttgtattcaa atttgtgtca taccagaaag ctctacattt 1861 gcagatgttc aaatattgta aaactttggt gcattgttat ttaatagctg tgatcagtga 1921 ttttcaaacc tcaaatatag tatattaaca aattacattt tcactgtata tcatggtatc 1981 ttaatgatgt atataattgc cttcaatccc cttctcaccc caccctctac agcttccccc 2041 acagcaatag gggcttgatt atttcagttg agtaaagcat ggtgctaatg gaccagggtc 2101 acagtttcaa aacttgaaca atccagttag catcacagag aaagaaattc ttctgcattt 2161 gctcattgca ccagtaactc cagctagtaa ttttgctagg tagctgcagt tagccctgca 2221 aggaaagaag aggtcagtta gcacaaaccc tttaccatga ctggaaaact cagtatcacg 2281 tatttaaaca tttttttttc ttttagccat gtagaaactc taaattaagc caatattctc 2341 atttgagaat gaggatgtct cagctgagaa acgttttaaa ttctctttat tcataatgtt 2401 ctttgaaggg tttaaaacaa gatgttgata aatctaagct gatgagtttg ctcaaaacag 2461 gaagttgaaa ttgttgagac aggaatggaa aatataatta attgatacct atgaggattt 2521 ggaggcttgg cattttaatt tgcagataat accctggtaa ttctcatgaa aaatagactt 2581 ggataacttt tgataaaaga ctaattccaa aatggccact ttgttcctgt ctttaatatc 2641 taaatactta ctgaggtcct ccatcttcta tattatgaat tttcatttat taagcaaatg 2701 tcatattacc ttgaaattca gaagagaaga aacatatact gtgtccagag tataatgaac 2761 ctgcagagtt gtgcttctta ctgctaattc tgggagcttt cacagtactg tcatcatttg 28 21 taaatggaaa ttctgctttt ctgtttctgc tccttctgga gcagtgctac tctgtaattt 28 81 tcctgaggct tatcacctca gtcatttctt ttttaaatgt ctgtgactgg cagtgattct 29 41 ttttcttaaa aatctattaa atttgatgtc aaattaggga gaaagatagt tactcatctt 30 01 gggctcttgt gccaatagcc cttgtatgta tgtacttaga gttttccaag tatgttctaa 30 61 gcacagaagt ttctaaatgg ggccaaaatt cagacttgag tatgttcttt gaatacctta 31 21 agaagttaca attagccggg catggtggcc cgtgcctgta gtcccagcta cttgagaggc 31 81 tgaggcagga gaatcacttc aacccaggag gtggaggtta cagtgagcag agatcgtgcc 32 41 actgcactcc agcctgggtg acaagagaga cttgtctcca aaaaaaaagt tacacctagg 33 01 tgtgaatttt ggcacaaagg agtgacaaac ttatagttaa aagctgaata acttcagtgt 33 61 ggtataaaac gtggttttta ggctatgttt gtgattgctg aaaagaattc tagtttacct 34 21 caaaatcctt ctctttcccc aaattaagtg cctggccagc tgtcataaat tacatattcc 34 81 ttttggtttt tttaaaggtt acatgttcaa gagtgaaaat aagatgttct gtctgaaggc 35 41 taccatgccg gatctgtaaa tgaacctgtt aaatgctgta tttgctccaa cggcttacta 36 01 tagaatgtta cttaatacaa tatcatactt attacaattt ttactatagg agtgtaatag 36 61 gtaaaattaa tctctatttt agtgggccca tgtttagtct ttcaccatcc tttaaactgc 37 21 tgtgaatttt tttgtcatga cttgaaagca aggatagaga aacactttag agatatgtgg 37 81 ggttttttta ccattccaga gcttgtgagc ataatcatat ttgctttata tttatagtca 38 41 tgaactccta agttggcagc tacaaccaag aaccaaaaaa tggtgcgttc tgcttcttgt 39 01 aattcatctc tgctaataaa ttataagaag caaggaaaat tagggaaaat attttatttg 39 61 gatggtttct ataaacaagg gactataatt cttgtacatt atttttcatc tttgctgttt 40 21 ctttgagcag tctaatgtgc cacacaatta tctaaggtat ttgttttcta taagaattgt 40 81 tttaaaagta ttcttgttac cagagtagtt gtattatatt tcaaaacgta agatgatttt 41 41 taaaagcctg agtactgacc taagatggaa ttgtatgaac tctgctctgg agggagggga 42 01 ggatgtccgt ggaagttgta agacttttat ttttttgtgc catcaaatat aggtaaaaat 42 61 aattgtgcaa ttctgctgtt taaacaggaa ctattggcct ccttggccct aaatggaagg 43 21 gccgatattt taagttgatt attttattgt aaattaatcc aacctagttc tttttaattt 43 81 ggttgaatgt tttttcttgt taaatgatgt ttaaaaaata aaaactggaa gttcttggct 44 41 tagtcataat tctt

(SEQ ID NO:2)

"Mitogen- activated protein kinase kinase 1," "MEK1" or "MEK1" (also known as PRKMKl, MKKl, MAPKKl, ERK activator kinase 1, MAP kinase kinase 1, and MAK/ERK kinase 1) refers to a MEK1 molecule (e.g., a nucleic acid or protein). The MEK1 protein refers to a protein, typically human MEK1 that is encoded by the MEK1 gene. MEK1 functions in the MAPK/ERK cascade, and catalyzes the concomitant phosphorylation of a threonine and a tyrosine residue in a Thr-Glu-Tyr sequence located in the extracellular signal- regulated kinases MAPK3/ERK1 and MAPK1/ERK2, leading to their activation and further transduction of the signal within the MAPK/ERK cascade. Depending on the cellular context, this pathway mediates diverse biological functions, including, inter alia, cell growth, adhesion, survival and differentiation, predominantly through the regulation of transcription, metabolism and cytoskeletal rearrangements. The MEK1 amino acid and nucleotide sequences are known in the art. An exemplary amino acid and nucleotide sequence for human MEK1 are disclosed in, e.g., Seger et al, (1992) J. Biol. Chem. 267 (36), 25628-25631; and NCBI Reference Sequence: NP_002746.1 and NM_002755.3, respectively, each of which are incorporated herein by reference.

"Mitogen- activated protein kinase kinase 2," "MEK2" or "MEK2" (also known as PRKMK2, MKK2, MAPKK2, ERK activator kinase 2, MAP kinase kinase 2, and MAK/ERK kinase 2) refers to a MEK2 molecule (e.g., a nucleic acid or protein). The MEK2 protein refers to a protein, typically human MEK2 that is encoded by the MEK2 gene. MEK2 is a member of the dual specificity protein kinase family, which acts as a MAP kinase kinase. MAP kinases, also known as ERKs, act as an integration point for multiple biochemical signals. MEK2 functions in the MAPK/ERK cascade, and catalyzes the concomitant phosphorylation of a threonine and a tyrosine residue in a Thr-Glu-Tyr sequence located in the extracellular signal-regulated kinases MAPK3/ERK1 and MAPK1/ERK2, leading to their activation and further transduction of the signal within the MAPK/ERK cascade. Depending on the cellular context, this pathway mediates diverse biological functions, including, inter alia, cell growth, adhesion, survival and differentiation, predominantly through the regulation of transcription, metabolism and cytoskeletal rearrangements. The MEK2 amino and nucleotide sequences are known in the art. An exemplary amino acid and nucleotide sequence for human MEK2 are described in, e.g., Rauen, K.A. (1993) Cardiofaciocutaneous syndrome in GENEREVIEWS. (Pagon R.A., Adam M.P, Ardinger H. H, Bird T.D., Dolan C.R., Fong C.T., Smith RJH and Stephens K. (Eds.)); and NCBI Reference Sequence: NP_109587.1 and NM_030662.3, each of which are respectively, incorporated herein by reference.

"Isocitrate dehydrogenase 2 (NADP+) mitochondrial," "IDH2," or "7DH2" (also known as oxalosuccinate decarboxylase, ICD-M, ICD-H, IDP, NADP(+)-Specific ICDH, D2HGA2, and MNADP-IDH) refers to an IDH2 molecule (e.g., a nucleic acid or protein). The IDH2 protein refers to a protein, typically human IDH2 that is encoded by the IDH2 gene. IDH2 is the NADP(+)-dependent isocitrate dehydrogenase found in the mitochondria. It plays a role in intermediary metabolism and energy production. The IDH2 amino and nucleotide sequences are known in the art. An exemplary amino acid and nucleotide sequence for human IDH2 are described in Holmen,S.L. and Colman,H. (2013) Curr Neurol Neurosci Rep 13 (5), 345; Liang,D.C, et al. (2013) Blood 121 (15), 2988-2995, respectively; all of which are incorporated herein by reference. "Myeloid/Lymphoid or mixed-lineage leukemia" (trithorax homolog, drosophila), "MLL" or "MLL" (also known as HRX, ALL-1, CXXC7, KMT2A, TRX1, HTRX1, MLLA1, MLLl, Lysine N-Methyltransferase 2A, Trithorax-Like Protein, MLL/GAS7, TETl-MLL, or WDSTS) refers to a MLL molecule (e.g., a nucleic acid or protein). The MLL protein refers to a protein, typically human MLL that is encoded by the MLL gene. The MLL gene encodes a transcriptional coactivator that plays an essential role in regulating gene expression during early development and hematopoiesis. The encoded MLL protein contains multiple conserved functional domains. One of these domains, the SET domain, is responsible for its histone H3 lysine 4 (H3K4) methyltransf erase activity, which mediates chromatin modifications

associated with epigenetic transcriptional activation. This protein is processed by the enzyme Taspase 1 into two fragments, MLL-C and MLL-N. These fragments reassociate and further assemble into different multiprotein complexes that regulate the transcription of specific target genes, including many of the HOX genes. The MLL amino and nucleotide sequences are known in the art. An exemplary amino acid of isoform 1 and isoform 2, and nucleotide sequence of isoform 1 and isoform 2 for human MLL are described in Ziemin-van der Poel S. et al, (1991) Proc. Natl. Acad. Sci. U.S.A. 88 (23); 10735-10739; and NCBI Reference

Sequence: NP_001184033.1 (MLL isoform precursor 1 amino acid), NP_005924.2 (MLL isoform precursor 2 amino acid), NM_001197104 (MLL isoform precursor 1 nucleic acid), and NM_005933.3(MLL isoform precursor 2 nucleic acid), respectively; each of which are incorporated herein by reference.

Headings, e.g., (a), (b), (i) etc, are presented merely for ease of reading the specification and claims. The use of headings in the specification or claims does not require the steps or elements be performed in alphabetical or numerical order or the order in which they are presented.

Various aspects featured in the invention are described in further detail below. Additional definitions are set out throughout the specification.

Therapeutic Methods and Agents

Methods for treating a post-MPN AML, e.g., JAK2V617F negative post-MPN AML and/or JAK2V617F positive post-MPN AML, in a subject are disclosed. In certain

embodiments, the methods include treatment of post-MPN AML, e.g., JAK2V617F negative post-MPN AML and/or JAK2V617F positive post-MPN AML, harboring an alteration described herein (e.g., a NRAS, IDH2, and/or MLL alteration described herein). The methods include administering to the subject a therapeutic agent, e.g., an agent that antagonizes the function of a MAPK signaling pathway (e.g., NRAS or MEK), IDH2, and/or MLL.

In other embodiment, the cancer, e.g., the post-MPN AML, e.g., JAK2V617F negative post-MPN AML and/or JAK2V617F positive post-MPN AML, comprises, or is identified or determined as having, an alteration in NRAS, IDH2, and/or MLL, e.g., an alteration as described herein.

"Treat," "treatment," and other forms of this word refer to the administration of an agent, e.g., a therapeutic agent, alone or in combination with a second agent in an amount effective to impede growth of a cancer, to cause a cancer to shrink by weight or volume, to extend the expected survival time of the subject and or time to progression of the tumor or the like. In those subjects, treatment can include, but is not limited to, inhibiting tumor growth, reducing tumor mass, reducing size or number of metastatic lesions, inhibiting the

development of new metastatic lesions, prolonged survival, prolonged progression-free survival, prolonged time to progression, and/or enhanced quality of life. A cancer is "treated" if at least one symptom of the cancer is alleviated, terminated, slowed or prevented. A cancer is also "treated" if recurrence or metastasis of the cancer is reduced, slowed, delayed or prevented.

As used herein, unless otherwise specified, the terms "prevent," "preventing" and "prevention" contemplate an action that occurs before a subject begins to suffer from the re- growth of the cancer and/or which inhibits or reduces the severity of the cancer.

As used herein, and unless otherwise specified, a "therapeutically effective amount" of an agent is an amount sufficient to provide a therapeutic benefit in the treatment or management of the cancer, or to delay or minimize one or more symptoms associated with the cancer. A therapeutically effective amount of a compound means an amount of therapeutic agent, alone or in combination with other therapeutic agents, which provides a therapeutic benefit in the treatment or management of the cancer. The term "therapeutically effective amount" can encompass an amount that improves overall therapy, reduces or avoids symptoms or causes of the cancer, or enhances the therapeutic efficacy of another therapeutic agent. As used herein, and unless otherwise specified, a "prophylactically effective amount" of an agent is an amount sufficient to prevent re-growth of the cancer, or one or more

symptoms associated with the cancer, or prevent its recurrence. A prophylactically effective amount of an agent means an amount of the agent, alone or in combination with other

therapeutic agents, which provides a prophylactic benefit in the prevention of the cancer. The term "prophylactically effective amount" can encompass an amount that improves overall prophylaxis or enhances the prophylactic efficacy of another prophylactic agent.

The term "patient" or "subject" includes a human (e.g., a male or female of any age group, e.g., a pediatric patient (e.g., infant, child, adolescent) or adult patient (e.g., young adult, middle-aged adult or senior adult). When the term is used in conjunction with

administration of a compound or drug, then the patient has been the object of treatment, observation, and/or administration of the compound or drug.

These treatments can be provided to a patient having had an unsatisfactory response to a different (e.g., non-NRAS, non-IDH2, and/or non-MLL) therapeutic agent or therapeutic modality. In one embodiment, the subject is undergoing or has undergone treatment with a different (e.g., non-NRAS, non-IDH2, and/or non-MLL) therapeutic agent or therapeutic modality. In one embodiment, the non-NRAS, non-IDH2, and/or non-MLL therapeutic agent or therapeutic modality is a chemotherapy or a surgical procedure. In one embodiment, the non- NRAS, non-IDH2, and/or non-MLL therapeutic agent or therapeutic modality comprises one or more of: an anthracycline, idarubicin, daunorubicin/daunomycin, anthracenedione, mitoxantrone, cytarabine (cytosine arabinose, ara-C), idarubicin, cladribine (Leustatin, 2-CdA), fludarabine (Fludara), topotecan, etoposide (VP-16), 6-thioguanine (6-TG), hydroxyurea (Hydrea), corticosteroid drugs (e.g., prednisone or dexamethasone (Decadron)), methotrexate (MTX), 6- mercaptopurine (6-MP), azacitidine (Vidaza), clofarabine (Colar), decitabine (Dacogen), stem cell transplantation, gemtuzumab ozogamicin, and bone marrow transplantation.

An agent, e.g., therapeutic agent, described herein can be administered, alone or in combination, e.g., in combination with other chemotherapeutic agents or procedures, in an amount sufficient to reduce or inhibit the tumor cell growth, and/or treat or prevent the cancer(s), in the subject.

The agent, e.g., therapeutic agent, can be a small molecule, a protein, a polypeptide, a peptide, an antibody molecule, a nucleic acid (e.g., a siRNA, an antisense or a micro RNA), a small molecule, or an immune cell therapy. Exemplary agents and classes of agents are described herein.

In some embodiments, the agent is a MEK inhibitor. A MEK inhibitor can include an agent that inhibits MEKl and/or MEK2. In some embodiments, the MEK inhibitor is chosen from: ARRY- 162 (MEK162), Trametinib (GSK1120212), Selumetinib (AZD6244,

ARRY142886), XL518 (GDC-0973), CI- 1040 (PD184352), PD035901, U0126-EtOH, PD198306, PD98059, BIX 02189, TAK-733, Honokiol, AZD8330 (ARRY-424704),

PD318088, BIX 02188, AS703026 (Pimasertib), RG7167, E6201 ; MSC2015103,

MSC 1936369, WX554 and/or SL327.

In one embodiment, the inhibitor MEK is ARRY-162 (MEK 162). ARRY- 162 is a potent, orally bioavailable and non-ATP competitive inhibitor of MEKl/2 (IC50 = 12 nM) and cellular pERK (IC50 = 11 nM). It shows ex vivo inhibition of cytokine production such as IL- 1, TNF and IL-6 in clinical trials. ARRY- 162 has the chemical name: 5-((4-bromo-2- fluorophenyl)amino)-4-fluoro-N-(2-hydroxyethoxy)- l-methyl-lH-benzo[d]imidazole-6- carboxamide; and has the following structure:

ARRY-162 Chemical Structure

Molecular Weight: 441.22681.

In one embodiment, the MEK inhibitor is Trametinib (GSK1120212). Trametinib is a highly specific and potent MEKl/2 inhibitor with IC50 of 0.92 nM/1.8 Nm. Trametinib does not inhibit the kinase activities of c-Raf, B-Raf, ERKl/2. Trametinib has the chemical name: /V-(3-{ 3-Cyclopropyl-5-[(2-fluoro-4-iodophenyl)amino]-6,8-dimethyl-2,4,7-trioxo-3,4,6,7- tetrahydropyrido[4,3-d]pyrimidin- l(2H)-yl}phenyl)acetamide; and has the following structure:

Trametinib Chemical Structure

Molecular Weight: 615.39.

In one embodiment, the MEK inhibitor is Selumetinib (AZD6244, ARRY 142886). Selumetinib is a potent, highly selective MEKl inhibitor with IC50 of 14 nM, also inhibits ERKl/2 phosphorylation with IC50 of 10 nM. Selumetinib has the chemical name: 6-(4- bromo-2-chloroanilino)-7-fluoro-N-(2-hydroxyethoxy)-3-methylbenzimidazole-5- carboxamide; and has the following structure:

Selumetinib Chemical Structure

Molecular Weight: 457.68.

In one embodiment, the MEK inhibitor is XL518 (GDC-0973). XL518 a potent, selective, orally bioavailable inhibitor of MEKl. XL518has the chemical name: [3,4- difluoro-2-[(2-fluoro-4-iodophenyl)amino]phenyl][3-hydroxy-3-[(2S)-2-piperidinyl]-l- azetidinyl]methanone; and has the following structure:

XL518 Chemical Structure

Molecular Weight: 531.31.

In one embodiment, the MEK inhibitor is CI- 1040 (PD 184352). CI- 1040 is an ATP noncompetitive MEK1/2 inhibitor with IC50 of about 17 nM, 100-fold more selective for MEK1/2 than MEK5. CI- 1040 has the chemical name: 2-(2-chloro-4-iodophenylamino)-N- (cyclopropylmethoxy)-3,4-difluorobenzamide; and has the following structure:

CI- 1040 Chemical Structure

Molecular Weight: 478.67.

In one embodiment, the MEK inhibitor is PD035901. PD0325901 is selective and non ATP-competitive MEK inhibitor with IC50 of about 0.33 nM, roughly 500-fold more potent than CI- 1040 on phosphorylation of ERKl and ERK2. PD035901 has the chemical name: (R)-N-(2,3-dihydroxypropoxy)-3,4-difluoro-2-(2-fluoro-4-iodophenylamino)benzamide; and has the following structure:

PD035901 Chemical Structure

Molecular Weight: 482.19. In one embodiment, the MEK inhibitor is U0126-EtOH. U0126-EtOH is a highly selective inhibitor of MEKl/2 with IC50 of about 0.07 μΜ/0.06 μΜ, 100-fold higher affinity for AN3-S218E/S222D MEK than PD098059. PD098059 has the chemical name: (2Z,3Z)- 2,3-bis(amino(2-aminophenylthio)methylene)succinonitrile,ethanol; and has the following structure:

EtOH

U0126-EtOH Chemical Structure

Molecular Weight: 426.56.

In one embodiment, the MEK inhibitor is PD198306. PD198306 is a cell-permeable and highly selective MEK inhibitor with IC50 of 8 nM. PD198306 has the chemical name: Benzamide, N-(cyclopropylmethoxy)-3,4,5-trifluoro-2-[(4-iodo-2-methylphenyl)amino]-; and has the following structure:

PD 198306 Chemical Structure

Molecular Weight: 476.23.

In one embodiment, the MEK inhibitor is PD98059. PD98059 is a non-ATP competitive MEK inhibitor with IC50 of 2 μΜ, specifically inhibits MEK- 1 -mediated activation of MAPK. PD98059 does not directly inhibit ERKl or ERK2. PD98059 has the chemical name: 2-(2-amino-3-methoxyphenyl)-4H-chromen-4-one; and has the following structure:

PD98059 Chemical Structure

Molecular Weight: 267.28.

In one embodiment, the MEK inhibitor is BIX 02189. BIX 02189 is a selective inhibitor of MEK5 with IC50 of 1.5 nM, also inhibits ERK5 catalytic activity with IC50 of 810 nM. BIX 02189 does not inhibit closely related kinases MEKl, MEK2, ERK2, and JNK2. BIX 02189 has the chemical name: (Z)-3-((3-((dimethylamino)methyl)phenylamino)

BIX 02189 Chemical Structure

Molecular Weight: 440.54.

In one embodiment, the MEK inhibitor is TAK-733. TAK-733 is a potent and selective MEK allosteric site inhibitor for MEKl with IC50 of about 3.2 nM. TAK-733 is inactive to Abll, AKT3, c-RAF, CamKl, CDK2, c-Met. TAK-733 has the chemical name: (R)-3-(2,3-dihydroxypropyl)-6-fluoro-5-(2-fluoro-4-iodophenylamino)-8-methylpyrido[2,3- d]pyrimidine-4,7(3H,8H)-dione; and has the following structure:

TAK-733 Chemical Structure

Molecular Weight: 267.28.

In one embodiment, the MEK inhibitor is Honokiol. Honokiol is the active principle of magnolia extract that inhibits Akt-phosphorylation and promotes ERK1 ^phosphorylation. Honokiol has the chemical name: 2-(4-hydroxy-3-prop-2-enyl-phenyl)- 4-prop-2-enyl-phenol; and has the following structure:

Honokiol Chemical Structure

Molecular Weight: 266.334.

In one embodiment, the MEK inhibitor is AZD8330 (ARRY-424704). AZD8330 is a novel, selective, non-ATP competitive MEK 1/2 inhibitor with IC50 of about 7 nM.

AZD8330 has the chemical name: 2-(2-fluoro-4-iodophenylamino)-N-(2-hydroxyethoxy)-l,5- dimethyl-6-oxo-l,6-dihydropyridine-3-carboxamide; and has the following structure:

AZD8330 Chemical Structure Molecular Weight: 461.23.

In one embodiment, the MEK inhibitor is PD318088. PD318088 is a non-ATP competitive allosteric MEKl/2 inhibitor. PD318088 has the chemical name: 5-bromo-N-(2,3- dihydroxypropoxy)-3,4-difluoro-2-(2-fluoro-4-iodophenylamino)benzamide; and has the following structure:

PD318088 Chemical Structure

Molecular Weight: 561.09.

In some embodiments, the MEK inhibitor is BIX 02188. BIX02188 is a selective inhibitor of MEK5 with IC50 of about 4.3 nM, also inhibits ERK5 catalytic activity with IC50 of 810 nM. BIX 02188 does not significantly inhibit closely related kinases MEKl, MEK2, ERK2, and JNK2. BIX02188 has the chemical name: (Z)-3-((3-

((dimethylamino)methyl)phenylamino) (phenyl)methylene)-2-oxoindoline-6-carboxamide; and has the following structure:

BIX02188 Chemical Structure

Molecular Weight: 426.51. In one embodiment, the MEK inhibitor is AS703026 (Pimasertib). AS-703026 is a highly selective, potent, ATP non-competitive allosteric inhibitor of MEK 1/2 with IC50 of about 0.005-2 μΜ in MM cell lines. AS703026 has the chemical name: (S)-N-(2,3- dihydroxypropyl)-3-(2-fluoro-4-iodophenylamino)isonicotinamide; and has the following structure:

AS703026 Chemical Structure

Molecular Weight: 431.20.

In one embodiment, the MEK inhibitor is SL327. SL327 is a selective inhibitor for MEKl/2 with IC50 of about 0.18 μΜ/ 0.22 μΜ. SL327 has no activity towards Erkl, MKK3, MKK4, c-JUN, PKC, PKA, or CamKII. SL327 is capable of transport through the blood-brain barrier. SL327 has the chemical name: (Z)-3-amino-3-(4-aminophenylthio)-2-(2- (trifluoromethyl)phenyl)acrylonitrile; and has the following structure:

SL327 Chemical Structure

Molecular Weight: 335.35.

In one embodiment, the MEK inhibitor is RG7167. RG7167 is a potent, orally bioavailable, highly selective MEK inhibitor. It potently inhibits the MAPK signaling pathway activation and tumor cell growth.

In one embodiment, the MEK inhibitor is E6201. E6201 is a synthetic, fungal metabolite analogue inhibitor of mitogen- activated protein kinase kinase 1 (MEK-1) and mitogen- activated protein kinase kinase kinase 1 (MEKK-1) with potential antipsoriatic and antineoplastic activities. MEK- l/MEKK-1 inhibitor E6201 specifically binds to and inhibits the activities of MEK- 1 and MEKK- 1, which may result in the inhibition of tumor cell proliferation. MEK- 1 and MEKK-1 are key components in the RAS/RAF/MEK/MAPK signaling pathway, which regulates cell proliferation and is frequently activated in human cancers. E6201 has the chemical name: ([(3S,4R,5Z,8S,9S, l lE)-14-(ethylamino)-8,9,16- trihydroxy-3,4-dimethyl-3,4,9, 19-tetrahydro- lH-2-benzoxacyclotetradecine- 1 ,7(8H)-dione] ; and has the following structure:

E6201 Chemical Structure

Molecular Weight: 389.44.

In one embodiment, the MEK inhibitor is MSC2015103. MSC2015103 is an orally bio-available, selective, and highly potent small molecule inhibitor of MEK 1/2.

In one embodiment, the MEK inhibitor is WX-554. WX-554 is an orally available small molecule mitogen- activated protein kinase kinase (MAP2K, MAPK/ERK kinase, or MEK) inhibitor, with potential antineoplastic activity.

Compositions, e.g., pharmaceutical compositions, comprising one or more of the agents, e.g., the therapeutic agents described herein, for use, e.g., in treating post-MPN AML, e.g., JAK2V617F negative and/or JAK2V617F positive post-MPN AML, as described herein are also disclosed.

Additionally, kits comprising the agents, e.g., the therapeutic agents (and compositions thereof), with instructions for use in treating post-MPN AML, e.g., JAK2V617F negative and/or JAK2V617F positive post-MPN AML, and/or determining the presence of an alteration described herein are also provided. In another aspect, the invention features a kit comprising one or more detection

reagents (e.g., probes, primers, antibodies), capable, e.g., of specific detection of a nucleic acid or protein comprising an alteration described herein.

The agents, e.g., the therapeutic agents described herein, can be administered in

combination with a second therapeutic agent or a different therapeutic modality, e.g., anticancer agents, and/or in combination with surgical and/or radiation procedures.

By "in combination with," it is not intended to imply that the therapy or the

therapeutic agents must be administered at the same time and/or formulated for delivery

together, although these methods of delivery are within the scope of the invention. The

pharmaceutical compositions can be administered concurrently with, prior to, or subsequent to, one or more other additional therapies or therapeutic agents. In general, each agent will be administered at a dose and/or on a time schedule determined for that agent. In will further be appreciated that the additional therapeutic agent utilized in this combination can be

administered together in a single composition or administered separately in different

compositions. The particular combination to employ in a regimen will take into account

compatibility of the inventive pharmaceutical composition with the additional therapeutically active agent and/or the desired therapeutic effect to be achieved.

Nucleic Acid Inhibitors

In yet another embodiment, the agent, e.g., the therapeutic agent, inhibits the expression of a nucleic acid encoding an alteration described herein. Examples of such agents include nucleic acid molecules, for example, antisense molecules, ribozymes, siRNA, triple helix molecules that hybridi to a nucleic acid encoding a mutation, or a transcription regulatory region, and blocks or reduces mRNA expression of the mutation.

In one embodiment, the nucleic acid antagonist is a siRNA that targets mRNA encoding a mutation. Other types of antagonistic nucleic acids can also be used, e.g., a dsRNA, a ribozyme, a triple-helix former, or an antisense nucleic acid. Accordingly, isolated nucleic acid molecules that i nucleic acid inhibitors, e.g., antisense, RNAi, to a mutation-encoding nucleic acid molecule are provided. An "antisense" nucleic acid can include a nucleotide sequence which is complementary to a "sense" nucleic acid encoding a protein, e.g., complementary to the coding strand of a double- stranded cDNA molecule or complementary to an mRNA sequence. The antisense nucleic acid can be complementary to an entire mutation coding strand, or to only a portion thereof. In another embodiment, the antisense nucleic acid molecule is antisense to a "noncoding region" of the coding strand of a nucleotide sequence encoding mutation (e.g., the 5' and 3' untranslated regions). Anti- sense agents can include, for example, from about 8 to about 80 nucleobases (i.e., from about 8 to about 80 nucleotides), e.g., about 8 to about 50 nucleobases, or about 12 to about 30 nucleobases. Anti-sense compounds include ribozymes, external guide sequence (EGS) oligonucleotides (oligozymes), and other short catalytic RNAs or catalytic oligonucleotides which hybridize to the target nucleic acid and modulate its expression. Anti-sense compounds can include a stretch of at least eight consecutive nucleobases that are complementary to a sequence in the target gene. An oligonucleotide need not be 100% complementary to its target nucleic acid sequence to be specifically hybridizable. An oligonucleotide is specifically hybridizable when binding of the oligonucleotide to the target interferes with the normal function of the target molecule to cause a los of utility, and there is a sufficient degree of complementarity to avoid non-specific binding of the oligonucleotide to non-target sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment or, in the case c in vitro assays, under conditions in which the assays are conducted.

Hybridization of antisense oligonucleotides with mRNA can interfere with one or more of tl normal functions of mRNA. The functions of mRNA to be interfered with include all key functions such as, for example, translocation of the RNA to the site of protein translation, translation of protei from the RNA, splicing of the RNA to yield one or more mRNA species, and catalytic activity whic may be engaged in by the RNA. Binding of specific protein(s) to the RNA may also be interfered with by antisense oligonucleotide hybridization to the RNA.

Exemplary antisense compounds include DNA or RNA sequences that specifically hybridizt to the target nucleic acid, e.g., the mRNA encoding a mutation described herein. The complementar region can extend for between about 8 to about 80 nucleobases. The compounds can include one or more modified nucleobases. Modified nucleobases are known in the art. Descriptions of modified nucleic acid agents are also available. See, e.g., U.S. Patent Nos. 4,987,071; 5,116,742; and 5,093,246; Woolf et al. (1992) Proc Natl Acad Sci USA; Antisense RNA and DNA, D.A. Melton, Ed Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1988); 89:7305-9; Haselhoff and Gerla< (1988) Nature 334:585-59; Helene, C. (1991) Anticancer Drug Des. 6:569-84; Helene (1992) Am. N. Y. Acad. Sci. 660:27-36; and Maher (1992) Bioassays 14:807- 15.

The antisense nucleic acid molecules are typically administered to a subject {e.g., by direct injection at a tissue site), or generated in situ such that they hybridize with or bind to cellular mRN and/or genomic DNA encoding a mutation to thereby inhibit expression of the protein, e.g., by inhibiting transcription and/or translation. Alternatively, antisense nucleic acid molecules can be modified to target selected cells and then be administered systemically. For systemic administratioi antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecules to peptides or antibodies which bind to cell surface receptors or antigens. The antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations of the antisense molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong pol II or pol III promoter are preferred.

In yet another embodiment, the antisense nucleic acid molecule is an cc-anomeric nucleic aci molecule. An cc-anomeric nucleic acid molecule forms specific double- stranded hybrids with complementary RNA in which, contrary to the usual β-units, the strands run parallel to each other (Gaultier et al. (1987) Nucleic Acids. Res. 15:6625-6641). The antisense nucleic acid molecule can also comprise a 2'-o-methylribonucleotide (Inoue et al. (1987) Nucleic Acids Res. 15:6131-6148) or chimeric RNA-DNA analogue (Inoue et al. (1987) FEBS Lett. 215:327-330).

siRNAs are small double stranded RNAs (dsRNAs) that optionally include overhangs. For example, the duplex region of an siRNA is about 18 to 25 nucleotides in length, e.g., about 19, 20, 1 22, 23, or 24 nucleotides in length. Typically, the siRNA sequences are exactly complementary to the target mRNA. dsRNAs and siRNAs in particular can be used to silence gene expression in mammalian cells (e.g., human cells). siRNAs also include short hairpin RNAs (shRNAs) with 29- base-pair stems and 2-nucleotide 3' overhangs. See, e.g., Clemens et al. (2000) Proc. Natl. Acad. St USA 97:6499-6503; Billy et al. (2001) Proc. Natl. Sci. USA 98: 14428-14433; Elbashir et al. (2001) Nature. 411 :494-8; Yang et al. (2002) Proc. Natl. Acad. Sci. USA 99:9942-9947; Siolas et al. (2005 Nat. Biotechnol. 23(2):227-31 ; 20040086884; U.S. 20030166282; 20030143204; 20040038278; anc 20030224432. In still another embodiment, an antisense nucleic acid featured in the invention is a ribozyme A ribozyme having specificity for a mutation-encoding nucleic acid can include one or more sequences complementary to the nucleotide sequence of a mutation cDNA disclosed herein (i.e., SE ID NO:6), and a sequence having known catalytic sequence responsible for mRNA cleavage (see U.S. Pat. No. 5,093,246 or Haselhoff and Gerlach (1988) Nature 334:585-591). For example, a derivative of a Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence oi the active site is complementary to the nucleotide sequence to be cleaved in a mutation-encoding mRNA. See, e.g., Cech et al. U.S. Patent No. 4,987,071; and Cech et al. U.S. Patent No. 5,116,742 Alternatively, mutation mRNA can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel, D. and Szostak, J.W. (1993) Science 261: 1411-1418.

Inhibition of a mutated gene can be accomplished by targeting nucleotide sequences complementary to the regulatory region of the mutation to form triple helical structures that prevent transcription of the mutated gene in target cells. See generally, Helene, C. (1991) Anticancer Drug Des. 6:569-84; Helene, C. i (1992) Am. N Y. Acad. Sci. 660:27-36; and Maher, L.J. (1992) Bioassa 14:807-15. The potential sequences that can be targeted for triple helix formation can be increased creating a so-called "switchback" nucleic acid molecule. Switchback molecules are synthesized in ; alternating 5'-3', 3'-5' manner, such that they base pair with first one strand of a duplex and then the other, eliminating the necessity for a sizeable stretch of either purines or pyrimidines to be present c one strand of a duplex.

The invention also provides detectably labeled oligonucleotide primer and probe molecules. Typically, such labels are chemiluminescent, fluorescent, radioactive, or colorimetric.

A mutated nucleic acid molecule can be modified at the base moiety, sugar moiety or phosphate backbone to improve, e.g., the stability, hybridization, or solubility of the molecule. For non-limiting examples of synthetic oligonucleotides with modifications see Toulme (2001) Nature Biotech. 19: 17 and Faria et al. (2001) Nature Biotech. 19:40-44. Such phosphoramidite

oligonucleotides can be effective antisense agents.

For example, the deoxyribose phosphate backbone of the nucleic acid molecules can be modified to generate peptide nucleic acids (see Hyrup B. et al. (1996) Bioorganic & Medicinal Chemistry 4: 5-23). As used herein, the terms "peptide nucleic acid" or "PNA" refers to a nucleic acid mimic, e.g., a DNA mimic, in which the deoxyribose phosphate backbone is replaced by a pseudopeptide backbone and only the four natural nucleobases are retained. The neutral backbone ( a PNA can allow for specific hybridization to DNA and RNA under conditions of low ionic strengtl The synthesis of PNA oligomers can be performed using standard solid phase peptide synthesis protocols as described in Hyrup B. et al. (1996) supra and Perry-O'Keefe et al. Proc. Natl. Acad. Sc 93: 14670-675.

PNAs of mutated nucleic acid molecules can be used in therapeutic and diagnostic applications. For example, PNAs can be used as antisense or antigene agents for sequence- specific modulation of gene expression by, for example, inducing transcription or translation arrest or inhibiting replication. PNAs of mutated nucleic acid molecules can also be used in the analysis of single base pair mutations in a gene, {e.g., by PNA-directed PCR clamping); as 'artificial restriction enzymes' when used in combination with other enzymes, {e.g., SI nucleases (Hyrup B. et al. (1996^* supra)); or as probes or primers for DNA sequencing or hybridization (Hyrup B. et al. (1996) supra Perry-O'Keefe supra).

In other embodiments, the oligonucleotide may include other appended groups such as peptides {e.g., for targeting host cell receptors in vivo), or agents facilitating transport across the eel membrane (see, e.g., Letsinger et al. (1989) Proc. Natl. Acad. Sci. USA 86:6553-6556; Lemaitre et <

(1987) Proc. Natl. Acad. Sci. USA 84:648-652; W088/09810) or the blood-brain barrier (see, e.g., V 89/10134). In addition, oligonucleotides can be modified with hybridization-triggered cleavage agents (see, e.g., Krol et al. (1988) Bio-Techniques 6:958-976) or intercalating agents {See, e.g., Zoi

(1988) Pharm. Res. 5:539-549). To this end, the oligonucleotide may be conjugated to another molecule, {e.g., a peptide, hybridization triggered cross-linking agent, transport agent, or hybridization-triggered cleavage agent). In some embodiments, a nucleic acid inhibitor described herein is provided for the inhibition of expression of a nucleic acid comprising the alteration in vitrc

Evaluation of Subjects

Subjects, e.g., patients, can be evaluated for the presence of an alteration, e.g., an

alteration as described herein. A patient can be evaluated, for example, by determining the genomic sequence of the patient, e.g., by an NGS method. Alternatively, or in addition,

evaluation of a patient can include directly assaying for the presence of a mutation in the patient, such as by an assay to detect a mutated nucleic acid {e.g., DNA or RNA), such as by, Southern blot, Northern blot, or RT-PCR, e.g., qRT-PCR. Alternatively, or in addition, a patient can be evaluated for the presence of a protein mutation, such as by immunohistochemistry, Western blot, immunoprecipitation, or immunomagnetic bead assay.

In one aspect, the results of a clinical trial, e.g., a successful or unsuccessful clinical trial, can be repurposed to identify agents that target an alteration disclosed herein, e.g., a

NRAS, IDH2, and/or MLL mutation. By one exemplary method, a candidate agent used in a clinical trial can be reevaluated to determine if the agent in the trial targets a mutation, or is effective to treat a tumor containing a particular mutation. For example, subjects who

participated in a clinical trial for an agent, such as a kinase inhibitor, can be identified.

Patients who experienced an improvement in symptoms, e.g., cancer (e.g., post-MPN AML, e.g., JAK2V617F negative post-MPN AML and/or JAK2V617F positive post-MPN AML) symptoms, such as decreased tumor size, or decreased rate of tumor growth, can be evaluated for the presence of a mutation. Patients who did not experience an improvement in cancer symptoms can also be evaluated for the presence of a mutation. Where patients carrying a mutation are found to have been more likely to respond to the test agent than patients who did not carry such a mutation, then the agent is determined to be an appropriate treatment option for a patient carrying the mutation.

"Reevaluation" of patients can include, for example, determining the genomic sequence of the patients, or a subset of the clinical trial patients, e.g., by an NGS method. Alternatively, or in addition, reevaluation of the patients can include directly assaying for the presence of a mutation in the patient, such as by an assay to detect a mutated nucleic acid (e.g., RNA), such as by RT-PCR, e.g., qRT-PCR. Alternatively, or in addition, a patient can be evaluated for the presence of a protein mutation, such as by immunohistochemistry, Western blot,

immunoprecipitation, or immunomagnetic bead assay.

Methods for Detection of Nucleic Acids and Polypeptides

Methods for evaluating a mutated gene, mutations and/or gene products are known to those of skill in the art. In one embodiment, the mutation is detected in a nucleic acid

molecule by a method chosen from one or more of: nucleic acid hybridization assay, SSP, HPLC or mass-spectrometric genotyping.

Additional exemplary methods include traditional "direct probe" methods such as Southern blots and "comparative probe" methods such as comparative genomic hybridization (CGH), e.g., cDNA-based or oligonucleotide-based CGH, can be used. The methods can be used in a wide variety of formats including, but not limited to, substrate (e.g., membrane or glass) bound methods or array-based approaches.

In certain embodiments, the evaluation methods include probes/primers against the alterations described herein.

In one embodiment, probes/primers can be designed to detect a mutation or a reciprocal thereof. These probes/primers are suitable, e.g., for PCR amplification. Probes are used that contain DNA segments that are essentially complementary to DNA base sequences existing in different portions of chromosomes. Examples of probes useful according to the invention, and labeling and hybridization of probes to samples are described in two U.S. patents to Vysis, Inc. U.S. Patent Nos. 5,491,224 and 6,277,569 to Bittner, et al.

Chromosomal probes are typically about 50 to about 10⁵ nucleotides in length.

Longer probes typically comprise smaller fragments of about 100 to about 500 nucleotides in length. Probes that hybridize with centromeric DNA and locus-specific DNA are available commercially, for example, from Vysis, Inc. (Downers Grove, 111.), Molecular Probes, Inc. (Eugene, Oreg.) or from Cytocell (Oxfordshire, UK). Alternatively, probes can be made non- commercially from chromosomal or genomic DNA through standard techniques. For example, sources of DNA that can be used include genomic DNA, cloned DNA sequences, somatic cell hybrids that contain one, or a part of one, chromosome (e.g., human

chromosome) along with the normal chromosome complement of the host, and chromosomes purified by flow cytometry or microdissection. The region of interest can be isolated through cloning, or by site- specific amplification via the polymerase chain reaction (PCR). See, for example, Nath and Johnson, Biotechnic Histochem., 1998, 73(l):6-22, Wheeless et al., Cytometry 1994, 17:319-326, and U.S. Patent No. 5,491,224.

The probes to be used hybridize to a specific region of a chromosome to determine whether a cytogenetic abnormality is present in this region. One type of cytogenetic abnormality is a deletion. Although deletions can be of one or more entire chromosomes, deletions normally involve loss of part of one or more chromosomes. If the entire region of a chromosome that is contained in a probe is deleted from a cell, hybridization of that probe to the DNA from the cell will normally not occur and no signal will be present on that chromosome. If the region of a chromosome that is partially contained within a probe is deleted from a cell, hybridization of that probe to the DNA from the cell can still occur, but less of a signal can be present. For example, the loss of a signal is compared to probe hybridization to DNA from control cells that do not contain the genetic abnormalities which the probes are intended to detect. In some embodiments, at least 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, or more cells are enumerated for presence of the cytogenetic abnormality.

Cytogenetic abnormalities to be detected can include, but are not limited to, non- reciprocal translocations, balanced translocations, intra-chromosomal inversions, point mutations, deletions, gene copy number changes, gene expression level changes, and germ line mutations. In particular, one type of cytogenetic abnormality is a duplication.

Duplications can be of entire chromosomes, or of regions smaller than an entire chromosome. If the region of a chromosome that is contained in a probe is duplicated in a cell, hybridization of that probe to the DNA from the cell will normally produce at least one additional signal as compared to the number of signals present in control cells with no abnormality of the chromosomal region contained in the probe.

Chromosomal probes are labeled so that the chromosomal region to which they hybridize can be detected. Probes typically are directly labeled with a fluorophore, an organic molecule that fluoresces after absorbing light of lower wavelength/higher energy. The fluorophore allows the probe to be visualized without a secondary detection molecule. After covalently attaching a fluorophore to a nucleotide, the nucleotide can be directly incorporated into the probe with standard techniques such as nick translation, random priming, and PCR labeling. Alternatively, deoxycytidine nucleotides within the probe can be transaminated with a linker. The fluorophore then is covalently attached to the transaminated deoxycytidine nucleotides. See, U.S. Patent No. 5,491,224.

U.S. Patent No. 5,491,224 describes probe labeling as a number of the cytosine residues having a fluorescent label covalently bonded thereto. The number of fluorescently labeled cytosine bases is sufficient to generate a detectable fluorescent signal while the individual so labeled DNA segments essentially retain their specific complementary binding (hybridizing) properties with respect to the chromosome or chromosome region to be detected. Such probes are made by taking the unlabeled DNA probe segment, transaminating with a linking group a number of deoxycytidine nucleotides in the segment, covalently bonding a fluorescent label to at least a portion of the transaminated deoxycytidine bases.

Probes can also be labeled by nick translation, random primer labeling or PCR labeling. Labeling is done using either fluorescent (direct)-or haptene (indirect)-labeled nucleotides. Representative, non-limiting examples of labels include: AMCA-6-dUTP, CascadeBlue-4-dUTP, Fluorescein- 12-dUTP, Rhodamine-6-dUTP, TexasRed-6-dUTP, Cy3- 6-dUTP, Cy5-dUTP, Biotin(BIO)-l l-dUTP, Digoxygenin(DIG)-l l-dUTP or Dinitrophenyl (DNP)-l l-dUTP.

Probes also can be indirectly labeled with biotin or digoxygenin, or labeled with

32 3

radioactive isotopes such as P and H, although secondary detection molecules or further processing then is required to visualize the probes. For example, a probe labeled with biotin can be detected by avidin conjugated to a detectable marker. For example, avidin can be conjugated to an enzymatic marker such as alkaline phosphatase or horseradish peroxidase. Enzymatic markers can be detected in standard colorimetric reactions using a substrate and/or a catalyst for the enzyme. Catalysts for alkaline phosphatase include 5-bromo-4-chloro-3- indolylphosphate and nitro blue tetrazolium. Diaminobenzoate can be used as a catalyst for horseradish peroxidase.

Probes can also be prepared such that a fluorescent or other label is not part of the DNA before or during the hybridization, and is added after hybridization to detect the probe hybridized to a chromosome. For example, probes can be used that have antigenic molecules incorporated into the DNA. After hybridization, these antigenic molecules are detected using specific antibodies reactive with the antigenic molecules. Such antibodies can themselves incorporate a fluorochrome, or can be detected using a second antibody with a bound fluorochrome.

However treated or modified, the probe DNA is commonly purified in order to remove unreacted, residual products (e.g., fluorochrome molecules not incorporated into the DNA) before use in hybridization.

Prior to hybridization, chromosomal probes are denatured according to methods well known in the art. Probes can be hybridized or annealed to the chromosomal DNA under hybridizing conditions. "Hybridizing conditions" are conditions that facilitate annealing between a probe and target chromosomal DNA. Since annealing of different probes will vary depending on probe length, base concentration and the like, annealing is facilitated by varying probe concentration, hybridization temperature, salt concentration and other factors well known in the art.

Hybridization conditions are facilitated by varying the concentrations, base compositions, complexities, and lengths of the probes, as well as salt concentrations, temperatures, and length of incubation. For example, in situ hybridizations are typically performed in hybridization buffer containing l-2x SSC, 50-65% formamide and blocking DNA to suppress non-specific hybridization. In general, hybridization conditions, as described above, include temperatures of about 25° C to about 55° C, and incubation lengths of about 0.5 hours to about 96 hours.

Non-specific binding of chromosomal probes to DNA outside of the target region can be removed by a series of washes. Temperature and concentration of salt in each wash are varied to control stringency of the washes. For example, for high stringency conditions, washes can be carried out at about 65° C to about 80° C, using 0.2x to about 2x SSC, and about 0.1% to about 1% of a non-ionic detergent such as Nonidet P-40 (NP40). Stringency can be lowered by decreasing the temperature of the washes or by increasing the concentration of salt in the washes. In some applications it is necessary to block the hybridization capacity of repetitive sequences. Thus, in some embodiments, tRNA, human genomic DNA, or Cot-I DNA is used to block non-specific hybridization. After washing, the slide is allowed to drain and air dry, then mounting medium, a counterstain such as DAPI, and a coverslip are applied to the slide. Slides can be viewed immediately or stored at -20° C. before examination.

In CGH methods, a first collection of nucleic acids (e.g., from a sample, e.g., a possible tumor) is labeled with a first label, while a second collection of nucleic acids (e.g., a control, e.g., from a healthy cell/tissue) is labeled with a second label. The ratio of hybridization of the nucleic acids is determined by the ratio of the two (first and second) labels binding to each fiber in the array. Where there are chromosomal deletions or multiplications, differences in the ratio of the signals from the two labels will be detected and the ratio will provide a measure of the copy number. Array-based CGH can also be performed with single-color labeling (as opposed to labeling the control and the possible tumor sample with two different dyes and mixing them prior to hybridization, which will yield a ratio due to competitive hybridization of probes on the arrays). In single color CGH, the control is labeled and hybridized to one array and absolute signals are read, and the possible tumor sample is labeled and hybridized to a second array (with identical content) and absolute signals are read. Copy number difference is calculated based on absolute signals from the two arrays. Hybridization protocols suitable for use with the methods featured in the invention are described, e.g., in Albertson (1984) EMBO J. 3: 1227-1234; Pinkel (1988) Proc. Natl. Acad. Sci. USA 85: 9138-9142; EPO Pub. No. 430,402; Methods in Molecular Biology, Vol. 33: In situ Hybridization Protocols, Choo, ed., Humana Press, Totowa, N.J. (1994), etc. In one embodiment, the hybridization protocol of Pinkel, et al. (1998) Nature Genetics 20: 207-211, or of Kallioniemi (1992) Proc. Natl Acad Sci USA 89:5321-5325 (1992) is used. Array-based CGH is described in U.S. Patent No. 6,455,258, the contents of each of which are

incorporated herein by reference.

In still another embodiment, amplification-based assays can be used to measure presence/absence and copy number. In such amplification-based assays, the nucleic acid sequences act as a template in an amplification reaction {e.g., Polymerase Chain Reaction (PCR). In a quantitative amplification, the amount of amplification product will be proportional to the amount of template in the original sample. Comparison to appropriate controls, e.g., healthy tissue, provides a measure of the copy number.

Methods of "quantitative" amplification are well known to those of skill in the art. For example, quantitative PCR involves simultaneously co-amplifying a known quantity of a control sequence using the same primers. This provides an internal standard that can be used to calibrate the PCR reaction. Detailed protocols for quantitative PCR are provided in Innis, et al. (1990) PCR Protocols, A Guide to Methods and Applications, Academic Press, Inc. N.Y.). Measurement of DNA copy number at microsatellite loci using quantitative PCR analysis is described in Ginzonger, et al. (2000) Cancer Research 60:5405-5409. The known nucleic acid sequence for the genes is sufficient to enable one of skill in the art to routinely select primers to amplify any portion of the gene. Fluorogenic quantitative PCR can also be used. In fluorogenic quantitative PCR, quantitation is based on amount of fluorescence signals, e.g., TaqMan and sybr green.

Other suitable amplification methods include, but are not limited to, ligase chain reaction (LCR) (see Wu and Wallace (1989) Genomics 4: 560, Landegren, et al. (1988) Science 241: 1077, and Barringer et al. (1990) Gene 89: 117), transcription amplification (Kwoh, et al. (1989) Proc. Natl. Acad. Sci. USA 86: 1173), self- sustained sequence replication (Guatelli, et al. (1990) Proc. Nat. Acad. Sci. USA 87: 1874), dot PCR, and linker adapter PCR, etc.

Nucleic Acid Samples

A variety of tissue samples can be the source of the nucleic acid samples used in the present methods. Genomic or subgenomic DNA fragments can be isolated from a subject's sample (e.g., a tumor sample, a normal adjacent tissue (NAT), a blood sample or any normal control)). In certain embodiments, the tissue sample is preserved as a frozen sample or as formaldehyde- or paraformaldehyde-fixed paraffin-embedded (FFPE) tissue preparation. For example, the sample can be embedded in a matrix, e.g., an FFPE block or a frozen sample. The isolating step can include flow-sorting of individual chromosomes; and/or micro-dissecting a subject's sample (e.g., a tumor sample, a NAT, a blood sample).

Protocols for DNA isolation, fragmentation and processing from a tissue sample are known in the art as described, e.g., in WO 2012/092426, entitled "Optimization of Multigene Analysis of Tumor Samples," incorporated herein by reference in its entirety. Additional methods to isolate nucleic acids (e.g., DNA) from formaldehyde- or paraformaldehyde-fixed, paraffin-embedded (FFPE) tissues are disclosed, e.g., in Cronin M. et al., (2004) Am J Pathol. 164(l):35-42; Masuda N. et al., (1999) Nucleic Acids Res. 27 (22): 4436-4443; Specht K. et al., (2001) Am J Pathol. 158(2):419-429, Ambion RecoverAU™ Total Nucleic Acid Isolation Protocol (Ambion, Cat. No. AM1975, September 2008), and QIAamp® DNA FFPE Tissue Handbook (Qiagen, Cat. No. 37625, October 2007). RecoverAU™ Total Nucleic Acid Isolation Kit uses xylene at elevated temperatures to solubilize paraffin-embedded samples and a glass- fiber filter to capture nucleic acids. QIAamp® DNA FFPE Tissue Kit uses QIAamp® DNA Micro technology for purification of genomic and mitochondrial DNA.

Design of Baits

A bait can be a nucleic acid molecule, e.g., a DNA or RNA molecule, which can hybridize to (e.g., be complementary to), and thereby allow capture of a target nucleic acid. In one embodiment, a bait is an RNA molecule. In other embodiments, a bait includes a binding entity, e.g., an affinity tag, that allows capture and separation, e.g., by binding to a binding entity, of a hybrid formed by a bait and a nucleic acid hybridized to the bait. In one embodiment, a bait is suitable for solution phase hybridization. Baits can be produced and used by methods and hybridization conditions as described in US 2010/0029498 and Gnirke, A. et al. (2009) Nat Biotechnol. 27(2): 182- 189, and WO 2012/092426, entitled "Optimization of Multigene Analysis of Tumor Samples, incorporated herein by reference.

Sequencing

The invention also includes methods of sequencing nucleic acids. In one

embodiment, any of a variety of sequencing reactions known in the art can be used to directly sequence at least a portion of a mutation. In one embodiment, the mutated sequence is compared to a corresponding reference (control) sequence.

In one embodiment, the sequence of the nucleic acid molecule comprising an alteration described herein is determined by a method that includes one or more of: hybridizing an oligonucleotide, e.g., an allele specific oligonucleotide for one mutation described herein to said nucleic acid; hybridizing a primer, or a primer set (e.g., a primer pair), that amplifies a region comprising the mutation of the allele; amplifying, e.g., specifically amplifying, a region comprising the mutation of the allele; attaching an adapter oligonucleotide to one end of a nucleic acid that comprises the mutation of the allele; generating an optical, e.g., a colorimetric signal, specific to the presence of the one of the mutation; hybridizing a nucleic acid comprising the mutation to a second nucleic acid, e.g., a second nucleic acid attached to a substrate; generating a signal, e.g., an electrical or fluorescent signal, specific to the presence of the mutation; and incorporating a nucleotide into an oligonucleotide that is hybridized to a nucleic acid that contains the mutation.

In another embodiment, the sequence is determined by a method that comprises one or more of: determining the nucleotide sequence from an individual nucleic acid molecule, e.g., where a signal corresponding to the sequence is derived from a single molecule as opposed, e.g., from a sum of signals from a plurality of clonally expanded molecules; determining the nucleotide sequence of clonally expanded proxies for individual nucleic acid molecules;

massively parallel short-read sequencing; template-based sequencing; pyrosequencing; real-time sequencing comprising imaging the continuous incorporation of dye-labeling nucleotides during DNA synthesis; nanopore sequencing; sequencing by hybridization; nano-transistor array based sequencing; polony sequencing; scanning tunneling microscopy (STM) based sequencing; or nanowire-molecule sensor based sequencing. Any method of sequencing known in the art can be used. Exemplary sequencing reactions include those based on techniques developed by Maxam and Gilbert (Proc. Natl Acad Sci USA (1977) 74:560) or Sanger (Sanger et al. (1977) Proc. Nat. Acad. Sci 74:5463). Any of a variety of automated sequencing procedures can be utilized when performing the assays (Biotechniques (1995) 19:448), including sequencing by mass spectrometry (see, for example, U.S. Patent Number 5,547,835 and international patent application Publication

Number WO 94/16101, entitled DNA Sequencing by Mass Spectrometry by H. Koster; U.S. Patent Number 5,547,835 and international patent application Publication Number WO

94/21822 entitled DNA Sequencing by Mass Spectrometry Via Exonuclease Degradation by H. Koster), and U.S. Patent Number 5,605,798 and International Patent Application No.

PCT/US96/03651 entitled DNA Diagnostics Based on Mass Spectrometry by H. Koster;

Cohen et al. (1996) Adv Chromatogr 36: 127-162; and Griffin et al. (1993) Appl Biochem

Biotechnol 38: 147-159).

Sequencing of nucleic acid molecules can also be carried out using next-generation sequencing (NGS). Next-generation sequencing includes any sequencing method that determines the nucleotide sequence of either individual nucleic acid molecules or clonally expanded proxies for individual nucleic acid molecules in a highly parallel fashion (e.g., greater than 10⁵ molecules are sequenced simultaneously). In one embodiment, the relative abundance of the nucleic acid species in the library can be estimated by counting the relative number of occurrences of their cognate sequences in the data generated by the sequencing experiment. Next generation sequencing methods are known in the art, and are described, e.g., in Metzker, M. (2010) Nature Biotechnology Reviews 11:31-46, incorporated herein by reference.

In one embodiment, the next-generation sequencing allows for the determination of the nucleotide sequence of an individual nucleic acid molecule (e.g., Helicos Biosciences' HeliScope Gene Sequencing system, and Pacific Biosciences' PacBio RS system). In other embodiments, the sequencing method determines the nucleotide sequence of clonally expanded proxies for individual nucleic acid molecules (e.g., the Solexa sequencer, Illumina Inc., San Diego, Calif; 454 Life Sciences (Branford, Conn.), and Ion Torrent), e.g., massively parallel short-read sequencing (e.g., the Solexa sequencer, Illumina Inc., San Diego, Calif.), which generates more bases of sequence per sequencing unit than other sequencing methods that generate fewer but longer reads. Other methods or machines for next-generation sequencing include, but are not limited to, the sequencers provided by 454 Life Sciences (Branford, Conn.), Applied Biosystems (Foster City, Calif.; SOLiD sequencer), and Helicos Biosciences Corporation (Cambridge, Mass.). Platforms for next-generation sequencing include, but are not limited to, Roche/454' s Genome Sequencer (GS) FLX System, Illumina/Solexa's Genome Analyzer (GA), Life/APG's Support Oligonucleotide Ligation Detection (SOLiD) system, Polonator' s G.007 system, Helicos Biosciences' HeliScope Gene Sequencing system, and Pacific Biosciences' PacBio RS system. NGS technologies can include one or more of steps, e.g., template preparation, sequencing and imaging, and data analysis as described in WO 2012/092426, entitled "Optimization of Multigene Analysis of Tumor Samples, incorporated herein by reference.

Data analysis

After NGS reads have been generated, they can be aligned to a known reference sequence or assembled de novo. For example, identifying genetic variations such as single-nucleotide polymorphism and structural variants in a sample (e.g., a tumor sample) can be accomplished by aligning NGS reads to a reference sequence (e.g., a wild-type sequence). Methods of sequence alignment for NGS are described e.g., in Trapnell C. and Salzberg S.L. Nature Biotech., 2009, 27:455-457. Examples of de novo assemblies are described, e.g., in Warren R. et ah,

Bioinformatics, 2007, 23:500-501; Butler J. et ah, Genome Res., 2008, 18:810-820; and Zerbino D.R. and Birney E., Genome Res., 2008, 18:821-829. Sequence alignment or assembly can be performed using read data from one or more NGS platforms, e.g., mixing Roche/454 and Illumina/Solexa read data. Algorithms and methods for data analysis are described in WO 2012/092426, entitled "Optimization of Multigene Analysis of Tumor Samples, incorporated herein by reference.

Detection of Mutated Polypeptide

The activity or level of a mutated polypeptide (e.g., a NRAS, IDH2, and/or MLL mutation) can also be detected and/or quantified by detecting or quantifying the expressed polypeptide. The mutated polypeptide can be detected and quantified by any of a number of means known to those of skill in the art. These can include analytic biochemical methods such as electrophoresis, capillary electrophoresis, high performance liquid chromatography

(HPLC), thin layer chromatography (TLC), hyperdiffusion chromatography, and the like, or various immunological methods such as fluid or gel precipitin reactions, immunodiffusion (single or double), Immunoelectrophoresis, radioimmunoassay (RIA), enzyme-linked

immunosorbent assays (ELISAs), immunofluorescent assays, Western blotting,

immunohistochemistry (IHC) and the like. A skilled artisan can adapt known

protein/antibody detection methods.

Another agent for detecting a mutated polypeptide is an antibody molecule capable of binding to a polypeptide corresponding to a polypeptide, e.g., an antibody with a detectable label. Techniques for generating antibodies are described herein. The term "labeled", with regard to the probe or antibody, is intended to encompass direct labeling of the probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as indirect labeling of the probe or antibody by reactivity with another reagent that is directly labeled. Examples of indirect labeling include detection of a primary antibody using a fluorescently labeled secondary antibody and end-labeling of a DNA probe with biotin such that it can be detected with fluorescently labeled streptavidin.

In another embodiment, the antibody is labeled, e.g., a radio-labeled, chromophore- labeled, fluorophore-labeled, or enzyme-labeled antibody. In another embodiment, an antibody derivative (e.g., an antibody conjugated with a substrate or with the protein or ligand of a protein-ligand pair { e.g., biotin- streptavidin} ), or an antibody fragment (e.g., a single- chain antibody, an isolated antibody hypervariable domain, etc.) which binds specifically with a mutated protein, is used.

Mutated polypeptides from cells can be isolated using techniques that are known to those of skill in the art. The protein isolation methods employed can, for example, be such as those described in Harlow and Lane (Harlow and Lane, 1988, Antibodies: A Laboratory

Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York).

Means of detecting proteins using electrophoretic techniques are well known to those of skill in the art (see generally, R. Scopes (1982) Protein Purification, Springer- Verlag, N.Y.; Deutscher, (1990) Methods in Enzymology Vol. 182: Guide to Protein Purification, Academic Press, Inc., N.Y.).

In another embodiment, Western blot (immunoblot) analysis is used to detect and quantify the presence of a polypeptide in the sample. In another embodiment, the polypeptide is detected using an immunoassay. As used herein, an immunoassay is an assay that utilizes an antibody to specifically bind to the analyte. The immunoassay is thus characterized by detection of specific binding of a polypeptide to an anti-antibody as opposed to the use of other physical or chemical properties to isolate, target, and quantify the analyte.

The mutated polypeptide is detected and/or quantified using any of a number of immunological binding assays (see, e.g., U.S. Patent Nos. 4,366,241; 4,376,110; 4,517,288; and 4,837,168). For a review of the general immunoassays, see also Asai (1993) Methods in Cell Biology Volume 37: Antibodies in Cell Biology, Academic Press, Inc. New York; Stites & Terr (1991) Basic and Clinical Immunology 7th Edition.

Kits

In one aspect, the invention features, a kit, e.g., containing an oligonucleotide having an alteration described herein, e.g., a NRAS, IDH2, and/or MLL mutation. Optionally, the kit can also contain an oligonucleotide that is the wildtype counterpart of the mutant oligonucleotide.

A kit can include a carrier, e.g., a means being compartmentalized to receive in close confinement one or more container means. In one embodiment the container contains an oligonucleotide, e.g., a primer or probe as described above. The components of the kit are useful, for example, to diagnose or identify a mutation in a tumor sample in a patient. The probe or primer of the kit can be used in any sequencing or nucleotide detection assay known in the art, e.g., a sequencing assay, e.g., an NGS method, RT-PCR, or in situ hybridization.

In some embodiments, the components of the kit are useful, for example, to diagnose or identify a mutation in a tumor sample in a patient, and to accordingly identify an appropriate therapeutic agent to treat the cancer.

A kit featured in the invention can include, e.g., assay positive and negative controls, nucleotides, enzymes (e.g., RNA or DNA polymerase or ligase), solvents or buffers, a stabilizer, a preservative, a secondary antibody, e.g., an anti-HRP antibody (IgG) and a detection reagent.

An oligonucleotide can be provided in any form, e.g., liquid, dried, semi-dried, or lyophilized, or in a form for storage in a frozen condition. Typically, an oligonucleotide, and other components in a kit are provided in a form that is sterile. An oligonucleotide, e.g., an oligonucleotide that contains a mutation, described herein, or an oligonucleotide complementary to an alteration described herein, is provided in a liquid solution, the liquid solution generally is an aqueous solution, e.g., a sterile aqueous solution. When the oligonucleotide is provided as a dried form, reconstitution generally is accomplished by the addition of a suitable solvent. The solvent, e.g., sterile buffer, can optionally be provided in the kit.

The kit can include one or more containers for the composition containing an

oligonucleotide in a concentration suitable for use in the assay or with instructions for dilution for use in the assay. In some embodiments, the kit contains separate containers, dividers or compartments for the oligonucleotide and assay components, and the informational material. For example, the oligonucleotides can be contained in a bottle or vial, and the informational material can be contained in a plastic sleeve or packet. In other embodiments, the separate elements of the kit are contained within a single, undivided container. For example, an oligonucleotide composition is contained in a bottle or vial that has attached thereto the informational material in the form of a label. In some embodiments, the kit includes a plurality (e.g., a pack) of individual containers, each containing one or more unit forms (e.g., for use with one assay) of an

oligonucleotide. For example, the kit includes a plurality of ampoules, foil packets, or blister packs, each containing a single unit of oligonucleotide for use in sequencing or detecting a mutation in a tumor sample. The containers of the kits can be air tight and/or waterproof. The container can be labeled for use.

For antibody-based kits, the kit can include: (1) a first antibody (e.g., attached to a solid support) which binds to a mutated polypeptide; and, optionally, (2) a second, different antibody which binds to either the polypeptide or the first antibody and is conjugated to a detectable agent.

In one embodiment, the kit can include informational material for performing and interpreting the sequencing or diagnostic. In another embodiment, the kit can provide guidance as to where to report the results of the assay, e.g., to a treatment center or healthcare provider. The kit can include forms for reporting the results of a sequencing or diagnostic assay described herein, and address and contact information regarding where to send such forms or other related information; or a URL (Uniform Resource Locator) address for reporting the results in an online database or an online application (e.g., an app). In another embodiment, the informational material can include guidance regarding whether a patient should receive treatment with a particular chemotherapeutic drug, depending on the results of the assay. The informational material of the kits is not limited in its form. In many cases, the informational material, e.g., instructions, is provided in printed matter, e.g., a printed text, drawings, and/or photographs, e.g., a label or printed sheet. However, the informational material can also be provided in other formats, such as computer readable material, video recording, or audio recording. In another embodiment, the informational material of the kit is contact information, e.g., a physical address, email address, website, or telephone number, where a user of the kit can obtain substantive information about the sequencing or diagnostic assay and/or its use in the methods described herein. The informational material can also be provided in any combination of formats.

In some embodiments, a biological sample is provided to an assay provider, e.g., a service provider (such as a third party facility) or a healthcare provider, who evaluates the sample in an assay and provides a read out. For example, in one embodiment, an assay provider receives a biological sample from a subject, such as a blood or tissue sample, e.g., a biopsy sample, and evaluates the sample using an assay described herein, e.g., a sequencing assay or in situ hybridization assay, and determines that the sample contains a mutation. The assay provider, e.g., a service provider or healthcare provider, can then conclude that the subject is, or is not, a candidate for a particular drug or a particular cancer treatment regimen.

Other embodiments of the invention include the following.

Nucleic Acid Molecules, Detection and Capturing Reagents

The invention also features an isolated nucleic acid molecule, or an isolated preparation of nucleic acid molecules, that includes an alteration described herein. Such nucleic acid molecules or preparations thereof can include an alteration described herein or can be used to detect, e.g., sequence, an alteration.

The invention also features a nucleic acid molecule, e.g., nucleic acid fragment, suitable as probe, primer, bait or library member that includes, flanks, hybridizes to, which are useful for identifying, or are otherwise based on, an alteration described herein. In certain embodiments, the probe, primer or bait molecule is an oligonucleotide that allows capture, detection or isolation of a nucleic acid molecule containing an alteration described herein, e.g., an alteration in NRAS, IDH2, MLL, and/or an alteration in FIG. 1. The oligonucleotide can comprise a nucleotide sequence substantially complementary to nucleic acid molecules or fragments of nucleic acid molecules comprising an alteration described herein. The sequence identity between the nucleic acid molecule, e.g., the oligonucleotide, and the target sequence need not be exact, so long as the sequences are sufficiently complementary to allow the capture, detection or isolation of the target sequence. In one embodiment, the nucleic acid fragment is a probe or primer that includes an oligonucleotide between about 5 and 25, e.g., between 10 and 20, or 10 and 15 nucleotides in length. In other embodiments, the nucleic acid fragment is a bait that includes an oligonucleotide between about 100 to 300 nucleotides, 130 and 230 nucleotides, or 150 and 200 nucleotides, in length.

In one embodiment, the nucleic acid fragment can be used to identify or capture, e.g., by hybridization, a nucleic acid molecules comprising an alteration described herein, e.g., an alteration in NRAS, IDH2, MLL, and/or an alteration in FIG. 1. For example, the nucleic acid fragment can be a probe, a primer, or a bait, for use in identifying or capturing, e.g., by hybridization, an alteration described herein.

The probes or primers described herein can be used, for example, PCR amplification. In one exemplary embodiment where detection is based on PCR, amplification of the mutation can be performed using a primer or a primer pair, e.g., for amplifying a sequence flanking an alteration described herein.

In other embodiments, the nucleic acid fragment includes a bait that comprises a nucleotide sequence that hybridizes to a nucleic acid molecules comprising an alteration described herein, and thereby allows the capture or isolation said nucleic acid molecule. In one embodiment, a bait is suitable for solution phase hybridization. In other embodiments, a bait includes a binding entity, e.g., an affinity tag, that allows capture and separation, e.g., by binding to a binding entity, of a hybrid formed by a bait and a nucleic acid hybridized to the bait.

In other embodiments, the nucleic acid fragment includes a library member comprising a nucleic acid molecule described herein. In one embodiment, the library member includes a mutation, e.g., a base substitution, that results in an alteration described herein. The nucleic acid fragment can be detectably labeled with, e.g., a radiolabel, a fluorescent label, a bioluminescent label, a chemiluminescent label, an enzyme label, a binding pair label, or can include an affinity tag; a tag, or identifier (e.g., an adaptor, barcode or other sequence identifier). Polypeptides

In another aspect, the disclosure features a polypeptide comprising an alteration described herein {e.g., a purified polypeptide comprising an alteration described herein), a biologically active or antigenic fragment thereof, as well as reagents {e.g., antibody molecules that bind to a polypeptide comprising an alteration described herein), methods for modulating the activity of a polypeptide comprising an alteration described herein and detection of a polypeptide comprising an alteration described herein.

In another embodiment, the polypeptide or fragment is a peptide, e.g., an immunogenic peptide or protein that contains an alteration described herein. Such immunogenic peptides or proteins can be used to raise antibodies specific to the polypeptide or protein comprising an alteration described herein. In other embodiments, such immunogenic peptides or proteins can be used for vaccine preparation. The vaccine preparation can include other components, e.g., an adjuvant.

In another aspect, the invention features antibody molecules that bind to a polypeptide comprising an alteration described herein or fragment described herein. In embodiments the antibody can distinguish wild type from the mutated polypeptide, e.g., the polypeptide comprising an alteration described herein. Techniques for generating antibody molecules are known in the art, and are described, for example, in WO 2012/092426, entitled "Optimization of Multigene Analysis of Tumor Samples, incorporated herein by reference.

Detection Reagents

In another aspect, the invention features a detection reagent, e.g., a purified or an isolated preparation thereof. Detection reagents can distinguish a nucleic acid, or protein sequence, having an alteration described herein, e.g., of a nucleic acid molecule comprising an alteration described herein, e.g., an alteration in NRAS, IDH2, MLL, and/or an alteration in

FIG. 1.

Detection reagents, e.g., nucleic acid-based detection reagents, can be used to identify mutations in a target nucleic acid, e.g., DNA, e.g., genomic DNA or cDNA, or RNA, e.g., in a sample, e.g., a sample of nucleic acid derived from a post-MPN AML, e.g., JAK2V617F negative post-MPN AML and/or JAK2V617F positive post-MPN AML. Detection reagents, e.g., antibody-based detection reagents, can be used to identify mutations in a target protein, e.g., in a sample, e.g., a sample of protein derived from, or produced by, post-MPN AML, e.g., JAK2V617F negative post-MPN AML and/or JAK2V617F positive post-MPN AML cell.

Nucleic Acid-based Detection Reagents

In one embodiment, the detection reagent comprises a nucleic acid molecule, e.g., a DNA, RNA or mixed DNA/RNA molecule, comprising sequence which is complementary with a nucleic acid sequence on a target nucleic acid (the sequence on the target nucleic acid that is bound by the detection reagent is referred to herein as the "detection reagent binding site" and the portion of the detection reagent that corresponds to the detection reagent binding site is referred to as the "target binding site"). In one embodiment, the detection reagent binding site is disposed in relationship to the interrogation position such that binding (or in embodiments, lack of binding) of the detection reagent to the detection reagent binding site allows differentiation of mutant and reference sequences for a mutant described herein (nucleic acid molecule comprising an alteration described herein, e.g., an alteration in NRAS, IDH2, MLL, and/or an alteration in FIG. 1. The detection reagent can be modified, e.g., with a label or other moiety, e.g., a moiety that allows capture.

In one embodiment, the detection reagent comprises a nucleic acid molecule, e.g., a DNA, RNA or mixed DNA/RNA molecule, which, e.g., in its target binding site, includes the interrogation position and which can distinguish (e.g., by affinity of binding of the detection reagent to a target nucleic acid or the ability for a reaction, e.g., a ligation or extension reaction with the detection reagent) between a mutation, e.g., a translocation described herein, and a reference sequence. In embodiments, the interrogation position can correspond to a terminal, e.g., to a 3' or 5' terminal nucleotide, a nucleotide immediately adjacent to a 3' or 5' terminal nucleotide, or to another internal nucleotide, of the detection reagent or target binding site.

In embodiments, the difference in the affinity of the detection reagent for a target nucleic acid comprising the alteration described herein and that for a target nucleic acid comprising the reference sequence allows determination of the presence or absence of the mutation (or reference) sequence. Typically, such detection reagents, under assay conditions, will exhibit substantially higher levels of binding only to the mutant or only to the reference sequence, e.g., will exhibit substantial levels of binding only to the mutation or only to the reference sequence.

In embodiments, binding allows (or inhibits) a subsequent reaction, e.g., a subsequent reaction involving the detection reagent or the target nucleic acid. E.g., binding can allow ligation, or the addition of one or more nucleotides to a nucleic acid, e.g., the detection reagent, e.g., by DNA polymerase, which can be detected and used to distinguish mutant from reference. In embodiments, the interrogation position is located at the terminus, or

sufficiently close to the terminus, of the detection reagent or its target binding site, such that hybridization, or a chemical reaction, e.g., the addition of one or more nucleotides to the detection reagent, e.g., by DNA polymerase, only occurs, or occurs at a substantially higher rate, when there is a perfect match between the detection reagent and the target nucleic acid at the interrogation position or at a nucleotide position within 1, 2, or 3 nucleotides of the interrogation position.

In one embodiment, the detection reagent comprises a nucleic acid, e.g., a DNA, RNA or mixed DNA/RNA molecule wherein the molecule, or its target binding site, is adjacent (or flanks), e.g., directly adjacent, to the interrogation position, and which can distinguish between a mutation described herein, and a reference sequence, in a target nucleic acid.

In embodiments, the detection reagent binding site is adjacent to the interrogation position, e.g., the 5' or 3'terminal nucleotide of the detection reagent, or its target binding site, is adjacent, e.g., between 0 (directly adjacent) and 1,000, 500, 400, 200, 100, 50, 10, 5, 4, 3, 2, or 1 nucleotides from the interrogation position. In embodiments, the outcome of a reaction will vary with the identity of the nucleotide at the interrogation position allowing one to distinguish between mutant and reference sequences. E.g., in the presence of a first nucleotide at the interrogation position a first reaction will be favored over a second reaction. E.g., in a ligation or primer extension reaction, the product will differ, e.g., in charge, sequence, size, or susceptibility to a further reaction (e.g., restriction cleavage) depending on the identity of the nucleotide at the interrogation position. In embodiments the detection reagent comprises paired molecules (e.g., forward and reverse primers), allowing for amplification, e.g., by PCR amplification, of a duplex containing the interrogation position. In such embodiments, the presence of the mutation can be determined by a difference in the property of the

amplification product, e.g., size, sequence, charge, or susceptibility to a reaction, resulting from a sequence comprising the interrogation position and a corresponding sequence having a reference nucleotide at the interrogation positions. In embodiments, the presence or absence of a characteristic amplification product is indicative of the identity of the nucleotide at the interrogation site and thus allows detection of the mutation.

In embodiments, the detection reagent, or its target binding site, is directly adjacent to the interrogation position, e.g., the 5' or 3'terminal nucleotide of the detection reagent is directly adjacent to the interrogation position. In embodiments, the identity of the nucleotide at the interrogation position will determine the nature of a reaction, e.g., a reaction involving the detection reagent, e.g., the modification of one end of the detection reagent. E.g., in the presence of a first nucleotide at the interrogation position a first reaction will be favored over a second reaction. By way of example, the presence of a first nucleotide at the interrogation position, e.g., a nucleotide associated with a mutation, can promote a first reaction, e.g., the addition of a complementary nucleotide to the detection reagent. By way of example, the presence of an A at the interrogation position will cause the incorporation of a T, having, e.g., a first colorimetric label, while the presence of a G and the interrogation position will cause the incorporation for a C, having, e.g., a second colorimetric label. In one embodiment, the presence of a first nucleotide at the nucleotide will result in ligation of the detection reagent to a second nucleic acid. For example, in an embodiment a third nucleic acid can be hybridized to the target nucleic acid sufficiently close to the interrogation site that if the third nucleic acid has an exact match at the interrogation site it will be ligated to the detection reagent.

Detection of the ligation product, or its absence, is indicative of the identity of the nucleotide at the interrogation site and thus allows detection of the mutation.

A variety of readouts can be employed. For example, in an embodiment binding of the detection reagent to the mutant or reference sequence can be followed by a moiety, e.g., a label, associated with the detection reagent, e.g., a radioactive or enzymatic label. In embodiments the label comprises a quenching agent and a signaling agent and hybridization results in altering the distance between those two elements, e.g., increasing the distance and un-quenching the signaling agent. In embodiments, the detection reagent can include a moiety that allows separation from other components of a reaction mixture. In embodiments, binding allows cleavage of the bound detection reagent, e.g., by an enzyme, e.g., by the nuclease activity of the DNA polymerase or by a restriction enzyme. The cleavage can be detected by the appearance or disappearance of a nucleic acid or by the separation of a quenching agent and a signaling agent associated with the detection reagent. In embodiments, binding protects, or renders the target susceptible, to further chemical reaction, e.g., labeling or degradation, e.g., by restriction enzymes. In embodiments binding with the detection reagent allows capture separation or physical manipulation of the target nucleic acid to thereby allow for identification. In embodiments binding can result in a detectable

localization of the detection reagent or target, e.g., binding could capture the target nucleic acid or displace a third nucleic acid. Binding can allow for the extension or other size change in a component, e.g., the detection reagent, allowing distinction between mutant and reference sequences. Binding can allow for the production, e.g., by PCR, of an amplicon that distinguishes mutant from reference sequence.

In one embodiment the detection reagent, or the target binding site, is between 5 and 500, 5 and 300, 5 and 250, 5 and 200, 5 and 150, 5 and 100, 5 and 50, 5 and 25, 5 and 20, 5 and 15, or 5 and 10 nucleotides in length. In one embodiment the detection reagent, or the target binding site, is between 10 and 500, 10 and 300, 10 and 250, 10 and 200, 10 and 150, 10 and 100, 10 and 50, 10 and 25, 10 and 20, or 10 and 15, nucleotides in length. In one embodiment the detection reagent, or the target binding site, is between 20 and 500, 20 and 300, 20 and 250, 20 and 200, 20 and 150, 20 and 100, 20 and 50, or 20 and 25 nucleotides in length. In one embodiment the detection reagent, or the target binding site, is sufficiently long to distinguish between mutant and reference sequences and is less than 100, 200, 300, 400, or 500 nucleotides in length.

Preparations of Nucleic Acids and Uses Thereof

In another aspect, the invention features purified or isolated preparations of a neoplastic or tumor cell nucleic acid, e.g., DNA, e.g., genomic DNA or cDNA, or RNA, containing an interrogation position described herein, useful for determining if a mutation disclosed herein is present. The nucleic acid includes the interrogation position, and typically additional sequence on one or both sides of the interrogation position. In addition the nucleic acid can contain heterologous sequences, e.g., adaptor or priming sequences, typically attached to one or both terminus of the nucleic acid. The nucleic acid also includes a label or other moiety, e.g., a moiety that allows separation or localization. In embodiments, the nucleic acid is between 20 and 1,000, 30 and 900, 40 and 800, 50 and 700, 60 and 600, 70 and 500, 80 and 400, 90 and 300, or 100 and 200 nucleotides in length (with or without heterologous sequences). In one embodiment, the nucleic acid is between 40 and 1,000, 50 and 900, 60 and 800, 70 and 700, 80 and 600, 90 and 500, 100 and 400, 110 and 300, or 120 and 200 nucleotides in length (with or without heterologous sequences). In another embodiment, the nucleic acid is between 50 and 1,000, 50 and 900, 50 and 800, 50 and 700, 50 and 600, 50 and 500, 50 and 400, 50 and 300, or 50 and 200 nucleotides in length (with or without heterologous sequences). In embodiments, the nucleic acid is of sufficient length to allow sequencing (e.g., by chemical sequencing or by determining a difference in T_m between mutant and reference preparations) but is optionally less than 100, 200, 300, 400, or 500 nucleotides in length (with or without heterologous sequences).

Such preparations can be used to sequence nucleic acid from a sample, e.g., a neoplastic or tumor sample. In one embodiment the purified preparation is provided by in situ amplification of a nucleic acid provided on a substrate. In embodiments the purified preparation is spatially distinct from other nucleic acids, e.g., other amplified nucleic acids, on a substrate.

In one embodiment, the purified or isolated preparation of nucleic acid is derived from a post-MPN AML, e.g., JAK2V617F negative post-MPN AML and/or JAK2V617F positive post-MPN AML. Such preparations can be used to determine if a sample comprises mutant sequence, e.g., an alteration described herein.

In another aspect, the invention features, a method of determining the sequence of an interrogation position for an alteration described herein, comprising:

providing a purified or isolated preparations of nucleic acid, e.g., DNA, e.g., genomic DNA or cDNA, or RNA, containing an interrogation position described herein,

sequencing, by a method that breaks or forms a chemical bond, e.g., a covalent or non- covalent chemical bond, e.g., in a detection reagent or a target sequence, the nucleic acid so as to determine the identity of the nucleotide at an interrogation position. The method allows determining if an alteration described herein is present.

In one embodiment, sequencing comprises contacting the nucleic acid comprising an alteration described herein with a detection reagent described herein. In one embodiment, sequencing comprises determining a physical property, e.g., stability of a duplex form of the nucleic acid comprising an alteration described herein, e.g., T_m, that can distinguish mutant from reference sequence.

In one embodiment, the nucleic acid comprising an alteration described herein is derived from a post-MPN AML, e.g., JAK2V617F negative post-MPN AML and/or

JAK2V617F positive post-MPN AML.

Reaction Mixtures and Devices

In another aspect, the invention features, purified or isolated preparations of a nucleic acid, e.g., DNA, e.g., genomic DNA or cDNA, or RNA, containing an interrogation position described herein, useful for determining if a mutation disclosed herein is present, disposed in sequencing device, or a sample holder for use in such a device. In one embodiment, the nucleic acid is derived from a post-MPN AML, e.g., JAK2V617F negative post-MPN AML and/or JAK2V617F positive post-MPN AML.

In another aspect, the invention features, purified or isolated preparations of a nucleic acid, e.g., DNA, e.g., genomic DNA or cDNA, or RNA, containing an interrogation position described herein, useful for determining if a mutation disclosed herein is present, disposed in a device for determining a physical or chemical property, e.g., stability of a duplex, e.g., T_m or a sample holder for use in such a device. In one embodiment, the device is a calorimeter. In one embodiment the nucleic acid comprising an alteration described herein is derived from a post-MPN AML, e.g., JAK2V617F negative post-MPN AML and/or JAK2V617F positive post-MPN AML.

The detection reagents described herein can be used to determine if an alteration described herein is present in a sample. In embodiments, the sample comprises a nucleic acid that is derived from a post-MPN AML, e.g., JAK2V617F negative post-MPN AML and/or JAK2V617F positive post-MPN AML. The cell can be from a neoplastic or a tumor sample, e.g., a biopsy taken from the neoplasm or the tumor; from circulating tumor cells, e.g., from peripheral blood; or from a blood or plasma sample. In one embodiment, the nucleic acid is derived from a post-MPN AML, e.g., JAK2V617F negative post-MPN AML and/or

JAK2V617F positive post-MPN AML. Accordingly, in one aspect, the invention features a method of making a reaction mixture, comprising:

combining a detection reagent, or purified or isolated preparation thereof, described herein with a target nucleic acid derived from a post-MPN AML, e.g., JAK2V617F negative post-MPN AML and/or JAK2V617F positive post-MPN AML, which comprises a sequence having an interrogation position for an alteration described herein.

In another aspect, the invention features a reaction mixture, comprising:

a detection reagent, or purified or isolated preparation thereof, described herein; and a target nucleic acid derived from a post-MPN AML, e.g., JAK2V617F negative post- MPN AML and/or JAK2V617F positive post-MPN AML cell, which comprises a sequence having an interrogation position for an alteration described herein.

In one embodiment of the reaction mixture, or the method of making the reaction mixture:

the detection reagent comprises a nucleic acid, e.g., a DNA, RNA or mixed

DNA/RNA, molecule which is complementary with a nucleic acid sequence on a target nucleic acid (the detection reagent binding site) wherein the detection reagent binding site is disposed in relationship to the interrogation position such that binding of the detection reagent to the detection reagent binding site allows differentiation of mutant and reference sequences for a mutation sequence or event described herein.

In one embodiment of the reaction mixture, or the method of making the reaction mixture: the target nucleic acid sequence is derived from a post-MPN AML, e.g., JAK2V617F negative post-MPN AML and/or JAK2V617F positive post-MPN AML, as described herein. In one embodiment of the reaction mixture, or the method of making the reaction mixture: the mutation is an alteration described herein, including: a substitution, e.g., a substitution described herein.

An alteration described herein, can be distinguished from a reference, e.g., a non- mutant or wildtype sequence, by reaction with an enzyme that reacts differentially with the mutation and the reference. E.g., they can be distinguished by cleavage with a restriction enzyme that has differing activity for the mutant and reference sequences. E.g., the invention includes a method of contacting a nucleic acid comprising an alteration described herein with such an enzyme and determining if a product of that cleavage which can distinguish mutant form reference sequence is present.

In one aspect the inventions provides, a purified preparation of a restriction enzyme cleavage product which can distinguish between mutant and reference sequence, wherein one end of the cleavage product is defined by an enzyme that cleaves differentially between mutant and reference sequence. In one embodiment, the cleavage product includes the interrogation position.

Protein-based Detection Reagents, Methods, Reaction Mixtures and Devices

A mutant protein described herein can be distinguished from a reference, e.g., a non- mutant or wild-type protein, by reaction with a reagent, e.g., a substrate, e.g, a substrate for catalytic activity or functional activity, or an antibody, that reacts differentially with the mutant and reference protein. In one aspect, the invention includes a method of contacting a sample comprising a mutant protein described herein with such reagent and determining if the mutant protein is present in the sample.

In another embodiment, the invention features, an antibody that can distinguish a mutant protein described herein, or a fragment thereof, from a reference, e.g., a non-mutant or wild type protein.

Accordingly, in one aspect, the invention features a method of making a reaction mixture comprising:

combining a detection reagent, or purified or isolated preparation thereof, e.g., a substrate, e.g., a substrate for phosphorylation or other activity, or an antibody, described herein with a target protein derived from a post-MPN AML, e.g., JAK2V617F negative post- MPN AML and/or JAK2V617F positive post-MPN AML cell, which comprises a sequence having an interrogation position for an alteration described herein.

In another aspect, the invention features, a reaction mixture comprising:

a detection reagent, or purified or isolated preparation thereof, e.g., a substrate, e.g., a substrate for phosphorylation or other activity, or an antibody, described herein; and

a target protein derived from a post-MPN AML, e.g., JAK2V617F negative post-MPN AML and/or JAK2V617F positive post-MPN AML cell, which comprises a sequence having an interrogation position for an alteration described herein. In one embodiment of the reaction mixture, or the method of making the reaction mixture:

the detection reagent comprises an antibody specific for a mutant protein described herein.

In one embodiment of the reaction mixture, or the method of making the reaction mixture that includes a post-MPN AML, e.g., JAK2V617F negative post-MPN AML and/or JAK2V617F positive post-MPN AML cell.

In one embodiment of the reaction mixture, or the method of making the reaction mixture: the mutation is an alteration described herein (e.g., a NRAS, IDH2, and/or MLL mutation described herein).

Screening Methods

In another aspect, the invention features a method, or assay, for screening for agents that modulate, e.g., inhibit, the expression or activity of a nucleic acid or polypeptide or protein comprising a mutation as described herein. The method includes contacting a nucleic acid or polypeptide or protein comprising an alteration described herein, or a cell expressing a nucleic acid or polypeptide or protein comprising an alteration described herein, with a candidate agent; and detecting a change in a parameter associated with a nucleic acid or polypeptide or protein comprising an alteration described herein, e.g., a change in the expression or an activity of the nucleic acid or polypeptide or protein comprising an alteration described herein. The method can, optionally, include comparing the treated parameter to a reference value, e.g., a control sample (e.g., comparing a parameter obtained from a sample with the candidate agent to a parameter obtained from a sample without the candidate agent). In one embodiment, if a decrease in expression or activity of the nucleic acid or polypeptide or protein comprising an alteration described herein is detected, the candidate agent is identified as an inhibitor. In another embodiment, if an increase in expression or activity of the nucleic acid or polypeptide or protein comprising an alteration described herein is detected, the candidate agent is identified as an activator.

In one embodiment, the contacting step is effected in a cell-free system, e.g., a cell lysate or in a reconstituted system. In other embodiments, the contacting step is effected in a cell in culture, e.g., a cell expressing an alteration described herein (e.g., a mammalian cell, a tumor cell or cell line, a recombinant cell). In yet other embodiments, the contacting step is effected in a cell in vivo (a -expressing cell present in a subject, e.g., an animal subject (e.g., an in vivo animal model).

Exemplary parameters evaluated include one or more of:

(i) a change in binding activity, e.g., direct binding of the candidate agent to a polypeptide comprising an alteration described herein; a binding competition between a known ligand and the candidate agent to a polypeptide comprising an alteration described herein;

(ii) a change in enzymatic activity, e.g., dehydrogenase activity, GTPase activity or kinase activity. In one embodiment, a change in kinase activity is detected by measuring

phosphorylation levels of a polypeptide comprising an alteration described herein (e.g., an increased or decreased autophosphorylation); or a change in a target of a polypeptide comprising an alteration described herein, In certain embodiments, a change in kinase activity, e.g., phosphorylation, is detected by any of Western blot (e.g., using an antibody which binds to a polypeptide comprising an alteration described herein, mass spectrometry, immunoprecipitation, immunohistochemistry, immunomagnetic beads, among others;

(iii) a change in an activity of a cell containing a tumor cell or a recombinant cell, e.g., a change in proliferation, morphology or tumorigenicity of the cell;

(iv) a change in tumor present in an animal subject, e.g., size, appearance, proliferation, of the tumor; or

(v) a change in the level, e.g., expression level, of a nucleic acid or polypeptide or protein comprising an alteration described herein.

In one embodiment, a change in a cell free assay in the presence of a candidate agent is evaluated. For example, an activity of a nucleic acid or polypeptide or protein comprising an alteration described herein, or interaction of a nucleic acid or polypeptide or protein comprising an alteration described herein with a downstream ligand can be detected. In one embodiment, the polypeptide or protein comprising an alteration described herein is contacted with a ligand, e.g., in solution, and a candidate agent is monitored for an ability to modulate, e.g., inhibit, an interaction, e.g., binding, between the nucleic acid or polypeptide or protein comprising an alteration described herein and the ligand.

In other embodiments, a change in an activity of a cell is detected in a cell in culture, e.g., a cell expressing a mutation (e.g., a mammalian cell, a tumor cell or cell line, a recombinant cell). In one embodiment, the cell is a recombinant cell that is modified to express a nucleic acid comprising an alteration described herein, e.g., is a recombinant cell transfected with a nucleic acid comprising an alteration described herein. The transfected cell can show a change in response to the expressed mutation, e.g., increased proliferation, changes in morphology, increased tumorigenicity, and/or acquired a transformed phenotype. A change in any of the activities of the cell, e.g., the recombinant cell, in the presence of the candidate agent can be detected. For example, a decrease in one or more of: proliferation, tumorigenicity, transformed morphology, in the presence of the candidate agent can be indicative of an inhibitor of a nucleic acid or polypeptide or protein comprising an alteration described herein. In other embodiments, a change in binding activity or phosphorylation as described herein is detected.

In yet other embodiment, a change in a tumor present in an animal subject (e.g., an in vivo animal model) is detected. In one embodiment, the animal model is a tumor containing animal or a xenograft comprising cells expressing a nucleic acid or polypeptide or protein comprising an alteration described herein (e.g., tumorigenic cells expressing a nucleic acid or polypeptide or protein comprising an alteration described herein). The candidate agent can be administered to the animal subject and a change in the tumor is detected. In one embodiment, the change in the tumor includes one or more of a tumor growth, tumor size, tumor burden, survival, is evaluated. A decrease in one or more of tumor growth, tumor size, tumor burden, or an increased survival is indicative that the candidate agent is an inhibitor.

In other embodiments, a change in expression of a nucleic acid or polypeptide or protein comprising an alteration described herein can be monitored by detecting the nucleic acid or protein levels, e.g., using the methods described herein.

In certain embodiments, the screening methods described herein can be repeated and/or combined. In one embodiment, a candidate agent that is evaluated in a cell-free or cell-based described herein can be further tested in an animal subject.

In one embodiment, the candidate agent is a small molecule compound, e.g., a kinase inhibitor, a nucleic acid (e.g., antisense, siRNA, aptamer, ribozymes, microRNA), an antibody molecule (e.g., a full antibody or antigen binding fragment thereof that binds to the mutation). The candidate agent can be obtained from a library (e.g., a commercial library of kinase inhibitors) or rationally designed.

In other embodiments, the method, or assay, includes providing a step based on proximity- dependent signal generation, e.g., a two-hybrid assay that includes a first mutation protein (e.g., a mutated protein), and a second mutated protein (e.g., a ligand), contacting the two-hybrid assay witl a test compound, under conditions wherein said two hybrid assay detects a change in the formation and/or stability of the complex, e.g., the formation of the complex initiates transcription activation c a reporter gene.

In one non-limiting example, the three-dimensional structure of the active site of a polypeptide or protein comprising an alteration described herein is determined by crystallizing the complex formed by the polypeptide or protein and a known inhibitor. Rational drug design is then used to identify new test agents by making alterations in the structure of a known inhibitor or by designing small molecule compounds that bind to the active site of the polypeptide or protein.

The candidate agents can be obtained using any of the numerous approaches in combinatori; library methods known in the art, including: biological libraries; peptoid libraries (libraries of molecules having the functionalities of peptides, but with a novel, non-peptide backbone which are resistant to enzymatic degradation but which nevertheless remain bioactive; see, e.g., Zuckermann, R.N. et al. (1994) J. Med. Chem. 37:2678-85); spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the 'one-bead one-compound' library method; and synthetic library methods using affinity chromatography selection. The biological library and peptoid library approaches are limited to peptide libraries, while the other fou approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compounc (Lam (1997) Anticancer Drug Des. 12: 145).

Examples of methods for the synthesis of molecular libraries can be found in the art, for example in: DeWitt et al. (1993) Proc. Natl. Acad. Sci. U.S.A. 90:6909; Erb et al. (1994) Proc. Na Acad. Sci. USA 91: 11422; Zuckermann et al. (1994). J. Med. Chem. 37:2678; Cho et al. (1993) Science 261: 1303; Carrell et al. (1994) Angew. Chem. Int. Ed. Engl. 33:2059; Carell et al. (1994) Angew. Chem. Int. Ed. Engl. 33:2061; and Gallop et al. (1994) J. Med. Chem. 37: 1233.

Libraries of compounds may be presented in solution (e.g., Houghten (1992) Biotechniques 13:412-421), or on beads (Lam (1991) Nature 354:82-84), chips (Fodor (1993) Nature 364:555-556 bacteria (Ladner, U.S. Patent No. 5,223,409), spores (Ladner U.S. Patent No. 5,223,409), plasmids (Cull et al. (1992) Proc Natl Acad Sci USA 89: 1865-1869) or on phage (Scott and Smith (1990) Science 249:386-390; Devlin (1990) Science 249:404-406; Cwirla et al. (1990) Proc. Natl. Acad. Sc 87:6378-6382; Felici (1991) J. Mol. Biol. 222:301-310; Ladner supra.). The interaction between two molecules can also be detected, e.g., using fluorescence energy transfer (FET) (see, for example, Lakowicz et al., U.S. Patent No. 5,631,169; Stavrianopoulos, et al U.S. Patent No. 4,868,103). An FET binding event can be conveniently measured through standard fluorometric detection means known in the art {e.g., using a fluorimeter).

In another embodiment, determining the ability of the mutated protein to bind to a target molecule can be accomplished using real-time Biomolecular Interaction Analysis (BIA) {see, e.g., Sjolander, S. and Urbaniczky, C. (1991) Anal. Chem. 63:2338-2345 and Szabo et al. (1995) Curr. Opin. Struct. Biol. 5:699-705). "Surface plasmon resonance" or "BIA" detects biospecific interactions in real time, without labeling any of the interactants {e.g., BIAcore). Changes in the mass at the binding surface (indicative of a binding event) result in alterations of the refractive index of light near the surface (the optical phenomenon of surface plasmon resonance (SPR)), resulting in a detectable signal which can be used as an indication of real-time reactions between biological molecules.

EXAMPLES

Example 1. High-throughput mutational profiling of post-myeloproliferative neoplasm acute myeloid leukemia reveals frequent mutations in NRAS in JAK2V617F-negative post-MPN

AML.

Background:

A subset of patients with the Philadelphia-chromosome negative myeloproliferative neoplasms (MPNs) transform to AML, and the prognosis of post-MPN AML patients is very poor. As such, new genomic insights are needed to define the mechanisms that govern

transformation from MPN to AML, and to identify new therapeutic targets for clinical

intervention in this poor-risk myeloid neoplasm. Patients with JAK2V617F mutant chronic- phase MPN disease can transform to JAK2 wildtype AMLs in approximately half of cases, indicating that diverse genomic paths lead to transformation. The following example

characterizes the genomic alterations, including point mutations, short indels, translocations, and copy number alterations, in 33 post-MPN AML samples.

Methods: Genomic DNA and total RNA was isolated from formalin fixed paraffin embedded (FFPE) tissue, blood and bone marrow aspirates, Adaptor ligated sequencing libraries were captured by solution hybridization using two custom baitsets targeting 374 cancer-related genes and 24 genes frequently rearranged for DNA-seq, and 272 genes frequently rearranged for RNA-seq. Ail captured libraries were sequenced to high depth (illumina HiSeq), averaging >590X for DNA and >20,000,000 total pairs for RNA, to enable the sensitive and specific detection of genomic alterations, A mean coverage depth of 51 Ix (range 405-645) was achieved.

Results:

The most common genomic alterations identified in post-MPN AML samples were mutations in JAK2 (51.5%), ASXL1 (48.5%), and IDH2 (30.3%). Mutually exclusive mutations in the genes of spliceosome components SRSF2, U2AF1, and SF3B1 were identified in 39% of patients in this cohort, suggesting that somatic mutations in splicing factors are a common genomic event in transformation from MPN to AML. These data were in contrast to de-novo AML, in which mutations in FLT3, NPMl, and DNMT3A are the most common disease alleles (NEJM 2013; 368: 2059), suggesting that the spectrum of genomic alteration in post-MPN AML differs from that in de novo AML.

Within this cohort of post-MPN AML samples, 52% of the patients had JAK2V617F positive AML and 48% of the cohort presented with JAK2 wildtype AML. Notably, the two subsets of post-MPN AML had distinct mutational patterns. In the JAK2V617F mutant subgroup, we identified frequent mutations in ASXL1 (41.2%), TP53 (41.2%), and IDH2 (41.2%). In JA£2-wildt pe AML subgroup frequent ASXL1 mutations (56.3%) and NRAS point mutations (37.5%) were identified. NRAS mutations were exclusive of JAK2 mutations in the entire cohort, consistent with alternate disease alleles which activate signaling in JAK2V617F positive AML and in JAK2 wildtype AML. SETBP1 mutations were found in 19% of patients with JAK2 wildtype post-MPN AML but not in any patients with

JAK2V617F-positiwe post-MPN AML.

Several alterations not previously described in post-MPN AML, were identified in this cohort including MLL, which was observed in both JAK2V617F and wildtype JAK2 patients. Copy number analysis of our high-depth sequencing data allowed us to identify homozygous deletions of TET2 and ETV6 and MYC amplifications in post-MPN AML. Univariate analysis demonstrated TP53 mutations were associated with significantly impaired overall survival (p<0.001). IDH2 mutations were associated with higher peripheral blood blast count

(p=0.017).

Conclusions:

The spectrum of genomic alterations in post-MPN AML is distinct from de novo AML. Furthermore, capture-based sequencing shows there are important differences in the mutational profile of JAK2V617F and JAK2 wildtype post-MPN AML. NRAS mutations can represent driver mutations in JAK2V617F negative post-MPN AML.

Example 2. Integrated Genetic Profiling of JAK2 wild-type chronic-phase myeloproliferative neoplasms.

Background:

The Myeloproliferative Neoplasms (MPNs), including Polycythemia Vera (PV), Essential Thrombocythemia (ET), and Primary Myelofibrosis (PMF) are clonal hematopoietic disorders. JAK2V617F mutations are observed in approximately 90-95% of PV cases, but only 40-50% of ET and PMF cases. Although JAK2 exon 12 and LNK mutations are observed in the majority of JAK2V617F- negative PV patients, candidate gene and exome sequencing studies to date have not identified activating oncogenes in the majority of JAK2V617F- negative ET/PMF patients. Thus, further genetic investigations are needed to define the mutational architecture of these JAK2 wildtype MPNs in order to gain insight into the biology of these diseases, the clinical implications of genetic events that do occur, and the elucidation of potential therapeutic targets. This example characterizes the spectrum of genetic alterations in JAK2 wildtype chronic-phase myeloproliferative neoplasms.

Methods:

32 identified patients with a confirmed diagnosis of an MPN (per 2008 WHO criteria), including MF, PV and ET, who were negative for JAK2V617F using a CLIA-certified allele specific assay for the JAK2 disease allele were confrmed. Genomic DNA and total RNA was isolated from formalin fixed paraffin embedded (FFPE) tissue, blood and bone marrow aspirates. Adaptor ligated sequencing libraries were captured by solution hybridization using two custom baitsets targeting 374 cancer-related genes and 24 genes frequently rearranged for DNA-seq, and 258 genes frequently rearranged for RNA-seq. All captured libraries were sequenced to high depth (Illumina HiSeq), averaging >590X for DNA and >20,000,000 total pairs for RNA, to enable the sensitive and specific detection of genomic alterations.

Results:

High coverage sequencing allowed us to identify JAK2V617F mutations in two patients (allele burden 3-5%) that were below the limit of detection of the CLIA assay. The most common mutations observed in JAK2V617F- negative MPN were in ASXL1 (22% of patients) and in TET2 (9%). Taken together, mutations in known epigenetic modifiers (ASXL1, TET2, DNMT3A, EZH2, MLL) were observed in 43% of samples, including a MLL mutation in one patient with PMF. We identified mutations in spliceosome components (SRSF2, U2AF1), in a subset of patients, consistent with previous reports, and in each case mutations in spliceosome components were mutually exclusive.

Mutations in the JAK-STAT pathway (MPL, TYK2) and the RAS pathway

components (KRAS, NF1) were identified in 9% of this patient cohort, suggesting that there are alternate disease alleles that activate signaling in JAK2V617F-negative MPN. RNA- sequencing identified a ETV6-ABL1 fusion in one patient, and amplification of PIK3CA in one patient in the cohort was identified; these data suggest fusion genes and amplifications activate signaling in a subset of patients with JAK2V617F-negative MPN. Novel mutations in MPN patients which have not been reported to date were also identified, including mutations in DNA repair genes (ATM and BRCA) in 25% of cases and mutations in the Notch signaling pathway (NOTCHl-4) in 31% of cases. The functional implications of these novel mutations remain to be elucidated.

In univariate analysis, ASXL1 mutations were found to associate with impaired overall survival (FIG. 3, p=0.049). These findings are consistent with data demonstrating an impaired survival in patients with MDS and PMF, and suggest that ASXL1 mutations represent an important biomarker for adverse outcome in JAK2V617F-negative MPN. Conclusions:

These data demonstrate that the mutational spectra of JAK2V617F-negative MPN includes genes implicated in epigenetic regulation, novel mutations which activate gene signaling, and fusion genes/copy number alterations which provide a novel mechanism of oncogenic activation not previously reported in MPN. ASXLl mutations occur frequently in JAK2 wild-type Philadelphia-Chromosome negative MPNs, and are associated with impaired overall survival. Collectively, these findings support the importance of ASXLl mutations in predicting outcome in JAK2V617F- negative MPN, demonstrate that mutations in signaling effectors and in epigenetic regulators are common in MPN, and illustrate the genetic heterogeneity of

MPN.

Table 1: Exemplary mutations found in post- MPN AML samples include:

SMARCA4_c.4909G>T_p.E1637*,

SUZ12_c.506-2A>G_p.splice

Sample: Bone marrow EZH2_c.2069G>A_p.R690H, ARID2_c.79_79delC_p.H27fs*31 MF to AML NRAS_c.38G>A_p.G13D,

ASXLl_c.l934_1935insG_p.G646fs*12

Sample: Bone marrow CEBPA_c.63_63delC_p.P23fs*137 BCOR_c.2811_2812insC_p.T938fs*8, MF to AML NRAS_c.34G>A_p.G12S(0.51,684), BCOR_c.2514_2515insC_p.K839fs*5,

TP53_c.455_456insC_p.P153fs*28, EZH2_c.786_787insC_p.N263fs*8 ASXLl_c.l934_1935insG_p.G646fs*12

Sample: Bone marrow IDH2_c.419G>A_p.R140Q,

MF to AML KRAS_c.71T>A_p.I24N,

PTCHl_c.2333C>T_p.T778M,

PTPN1 l_c.l472C>T_p.P491L,

U2AFl_c.470A>G_p.Q 157R,

JAK2_c.l849G>T_p.V617F,

ASXLl_c.l934_1935insG_p.G646fs*12

Sample: Bone marrow IDH2_c.515G>A_p.R172K, ASXLl_c.2383_2383delT_p.S795fs*23 MF to AML MLL2_c.9260G>T_p.R3087L,

TP53_c.824G>A_p.C275Y,

JAK2_c.1849G>T_p. V617F

Sample: Bone marrow IDH2_c.419G>A_p.R140Q, ASXLl_c.l756A>T_p.K586* ET to MF to AML TP53_c.743G>A_p.R248Q,

JAK2_c.1849G>T_p. V617F

Sample: Blood IDH2_c.419G>A_p.R140Q, RUNXl_c.l329_1329delC_p.S445fs*3 PV to AML SRSF2_c.284C>G_p.P95R, 7+, TP53_c.996_996delC_p.R333fs*12

JAK2_c.1849G>T_p. V617F

ET = Essential Thrombocythemia; MF = Myelofibrosis; PV = polycythemia vera.

EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments described herein. Such equivalents are intended to be encompassed by the following claims.

Claims

CLAIMS We Claim:

1. A method of treating a subject having a post-myeloproliferative neoplasm (MPN) acute myeloid leukemia (AML), comprising administering to the subject an effective amount of a MAPK pathway inhibitor chosen from a MEK inhibitor, an NRAS inhibitor, or a combination thereof, thereby treating the post-MPN AML.

2. The method of claim 1, further comprising acquiring knowledge of the presence or absence of an alteration in NRAS in the subject, or a cancer sample derived from the subject having the post-MPN AML.

3. The method of claim 1 or 2, further comprising acquiring knowledge of one or both of:

(i) the presence or absence of an alteration in NRAS; or

(ii) the presence or absence of an alteration in JAK2.

4. The method of claim 1 or 2, further comprising identifying the subject, or a cancer sample from the subject, as having one or both of:

(i) the presence (or absence) of an alteration in NRAS; or

(ii) the presence (or absence) of an alteration in JAK2.

5. A method of treating a subject having a post-myeloproliferative neoplasm (MPN) acute myeloid leukemia (AML), comprising:

acquiring knowledge of:

(i) the presence or absence of an alteration in NRAS; or

(ii) the absence of a an alteration in JAK2, in the subject, or a cancer sample from the subject; and

administering to the subject an effective amount of a MAPK pathway inhibitor chosen from a MEK inhibitor, an NRAS inhibitor, or a combination thereof,

thereby treating the post-MPN AML.

6. The method of claim 2, wherein the inhibitor is administered responsive to a determination of the presence of the NRAS alteration, in the subject, or the cancer sample from the subject.

7. The method of claim 1, wherein the post-MPN AML comprises, or is identified as having, an alteration in NRAS that results in an increased activity of a NRAS gene product, compared to a wild type activity of NRAS.

8. The method of claim 2, wherein the alteration in NRAS is chosen from:

(i) a substitution,

(ii) a deletion,

(iii) an insertion,

(iv) a missense mutation,

(v) a point mutation; or

(vi) an alteration in Table 1.

9. The method of claim 1, wherein the subject is identified, or has been previously identified, as having a post-MPN AML, comprising a NRAS alteration, wherein the alteration in NRAS is chosen from:

(i) a substitution,

(ii) a deletion,

(iii) an insertion;

(iv) a missense mutation,

(v) a point mutation;

(vi) an alteration in Table 1.

10. The method of claim 1, wherein the subject is a human having, or is at risk of having, the post-MPN AML.

11. The method of claim 1, wherein the subject is identified, or has been previously identified, as having the post-MPN AML.

12. The method of claims 10 or 11, wherein the subject is undergoing or has undergone treatment with a non-MAPK pathway inhibitor therapeutic agent or therapeutic modality.

13. The method of claim 12, wherein the non-MAPK pathway inhibitor therapeutic agent or therapeutic modality comprises one or more of: an anthracycline, idarubicin, daunorubicin/daunomycin, anthracenedione, mitoxantrone, cytarabine (cytosine arabinose, ara-C), idarubicin, cladribine (Leustatin, 2-CdA), fludarabine (Fludara), topotecan, etoposide (VP-16), 6-thioguanine (6-TG), hydroxyurea (Hydrea), corticosteroid drugs (e.g., prednisone or dexamethasone (Decadron)), methotrexate (MTX), 6-mercaptopurine (6-MP), azacitidine (Vidaza), clofarabine (Colar), decitabine (Dacogen), stem cell transplantation, gemtuzumab ozogamicin, or bone marrow transplantation.

14. The method of claim 13, wherein, responsive to the determination of the presence of the NRAS alteration, the non-MAPK pathway inhibitor therapeutic agent or therapeutic modality is discontinued.

15. The method of claim 12, wherein the MAPK pathway inhibitor is administered

(i) after cessation of the non- MAPK pathway inhibitor therapeutic agent or therapeutic modality; or

(ii) in combination with a non-MAPK pathway inhibitor therapeutic agent or therapeutic modality selected from the group of: an anthracycline, idarubicin, daunorubicin/daunomycin, anthracenedione, mitoxantrone, cytarabine (cytosine arabinose, ara-C), idarubicin, cladribine (Leustatin, 2-CdA), fludarabine (Fludara), topotecan, etoposide (VP-16), 6-thioguanine (6-TG), hydroxyurea (Hydrea), corticosteroid drugs (e.g., prednisone or dexamethasone (Decadron)), methotrexate (MTX), 6-mercaptopurine (6-MP), azacitidine (Vidaza), clofarabine (Colar), decitabine (Dacogen), stem cell transplantation, gemtuzumab ozogamicin, and bone marrow transplantation.

16. The method of claim 1, wherein the MAPK pathway inhibitor reduces the activity or expression of a MEK gene product, wherein the MAPK pathway inhibitor is a MEK inhibitor.

17. The method of claim 16, wherein the MEK inhibitor is chosen from one or more of: ARPvY-162 (MEK162), Trametinib (GSK1120212), Selumetinib (AZD6244,

PD318088, BIX 02188, AS703026 (Pimasertib) or SL327.

18. The method of claim 1, wherein the MAPK pathway inhibitor reduces the activity or expression of an NRAS gene or gene product.

19. The method of claim 18, wherein the MAPK pathway inhibitor is chosen from a multi- specific GTPase inhibitor or a small molecule inhibitor that is selective for NRAS.

20. The method of claim 1, wherein the MAPK pathway inhibitor is chosen from one or more of: an antisense molecule, a ribozyme, a double stranded RNA, or a triple helix molecule that hybridizes to and/or inhibits a MAPK pathway nucleic acid.

21. The method of claim 2, wherein the determination of the presence of the alteration in NRAS comprises sequencing.

22. A method of determining the presence of a NRAS alteration in a post-MPN AML, comprising (i), or (ii), or both (i)-(ii):

(i) acquiring knowledge that a nucleic acid molecule comprising the NRAS alteration is present in a sample from a subject;

(ii) acquiring knowledge of the presence or absence of an alteration in JAK2in a sample from a subject, wherein the acquiring step in (i) or (ii) comprises directly acquiring the knowledge, e.g., comprises sequencing or directly obtaining the an alteration in JAK2.

23. The method of claim 22, further comprising administering the MAPK pathway inhibitor, to the subject responsive to the determination of the presence of the NRAS alteration and/or the absence of an alteration in JAK2, in the sample from the subject.

24. A method of determining the presence of a NRAS alteration in post-MPN AML, comprising (i), (ii) or both (i)-(ii):

(i) acquiring knowledge that a nucleic acid molecule comprising the NRAS alteration is present in a tumor sample from a subject; and/or

(ii) acquiring knowledge of a presence or absence of an alteration in JAK2, in a cancer sample from a subject; and

responsive to a determination of the presence of the NRAS alteration and/or alteration in JAK2, the method further comprises one or more of:

(1) stratifying a patient population;

(2) identifying or selecting the subject as likely or unlikely to respond to a treatment, e.g., a NRAS inhibitor treatment as described herein;

(3) selecting a treatment option comprising a MAPK pathway inhibitor;

(4) administering a MAPK pathway inhibitor; or

(5) prognosticating the time course of the disease in the subject.

25. The method of claim 22-24, wherein the acquiring step comprising sequencing the alteration in NRAS.

26. A composition, e.g., a pharmaceutical composition, comprising one or more MAPK pathway inhibitors, for use in treating a post-MPN AML.

27. A kit comprising one or more MAPK pathway inhibitors with instructions for use in treating a post-MPN AML, and/or determining the presence of an NRAS alteration.

28. A kit comprising one or more detection reagents, capable, e.g., of specific detection of a nucleic acid or protein comprising an NRAS alteration in post-MPN AML.

29. A purified or an isolated preparation of a nucleic acid derived from a post-MPN AML, containing an interrogation position described herein, useful for determining if a mutation disclosed herein is present, disposed in sequencing device, or a sample holder for use in such a device.

30. The preparation of claim 29, which is obtained from a post-MPN AML sample.

31. A reaction mixture, comprising:

a detection reagent, or purified or isolated preparation thereof, described herein; and a target nucleic acid derived from a post-MPN AML cell, which comprises a sequence having an interrogation position for an alteration described herein.

32. A method of making a reaction mixture, comprising:

combining a detection reagent, or purified or isolated preparation thereof, described herein with a target nucleic acid derived from a post-MPN AML, which comprises a sequence having an interrogation position for an alteration described herein.

33. The reaction mixture of claim 31 wherein:

the detection reagent comprises a nucleic acid molecule which is complementary with a nucleic acid sequence on a target nucleic acid wherein the detection reagent binding site is disposed in relationship to the interrogation position such that binding of the detection reagent to the detection reagent binding site allows differentiation of mutant and reference sequences for a mutation sequence or event described herein.

34. The reaction mixture of claim 31 wherein:

the target nucleic acid sequence is derived from a post-MPN AML as described herein; and

the mutation is an alteration described herein.

35. The method of claim 1, 2, 5, 9, 11, 22, 24, 26, 27, 28, 29, 31, 32, 34, wherein the post-MPN AML is JAK2V617F negative.

36. The method of claim 3, wherein the JAK2 alternation is a JAK2V617F alternation.

37. The method of claim 4, wherein the JAK2 alternation is a JAK2V617F alternation.

38. The method of claim 5, 22, 23, 24, wherein the JAK2 alternation is a JAK2V617F alternation.

39. The method of claim 20, wherein the MAPK pathway nucleic acid encodes an alteration.

40. The method of claim 20, wherein the MAPK pathway nucleic acid encodes a transcription regulatory region that blocks or reduces mRNA expression of an alteration.

41. The method of claims 39, wherein the alteration is a JAK2 alternation.

42. The method of claims 40, wherein the alteration is a JAK2 alternation.

43. The method of claim 41 or 42, wherein the alteration is a JAK2 alternation is a JAK2V617F alternation.

44. The kit of claim 28, wherein the one or more detection reagents comprise one or more of: probes, primers, or antibodies.

45. The purified or isolated preparation of the nucleic acid of claim 29, wherein the nucleic acid comprises one or more of: genomic DNA, cDNA, or RNA.

46. The method of making the reaction mixture of claim 32, wherein:

47. The reaction mixture of claim 33 or 46, wherein the nucleic acid molecule is chosen from: a DNA, RNA or mixed DNA/RNA moelecule.

48. The reaction mixture of claim 33 or 46, wherein the detection reagent binds the target nucleic acid.

49. The method of making the reaction mixture of claim 32, wherein:

the mutation is an alteration described herein.

50. The reaction mixture of claim 34 or 49, wherein the mutation is an alteration in Table 1.