WO2014198893A2 - Prognostic relevance of aquired structural genetic abnormalities in acute myeloid leukemia - Google Patents

Abstract

The present invention concerns somatic genetic abnormalities present in acute myeloid leukaemia patients that are associated with treatment response. These chromosomal abnormalities, in particular present on chromosome 2, 11, 17, 21 and 16 allow giving a more distinct overall survival prognosis for AML patients and preferably to adapt the therapy to the prognosis.

Description

PROGNOSTIC RELEVANCE OF AQUIRED STRUCTURAL GENETIC

ABNORMALITIES IN ACUTE MYELOID LEUKEMIA

The present invention concerns somatic genetic abnormalities present in acute myeloid leukemia (AML) patients that are associated with treatment response. These chromosomal abnormalities allow an improved diagnosis and stratification of AML patients. Acute myeloid leukemia (AML) is a heterogeneous disease separated into several subtypes distinguished from each other by morphology, immunophenotype, cytogenetics, and molecular genetics, likely due to different leukemogenic mechanisms which cause variable responses to anti-leukemic treatment.

Traditional metaphase cytogenetics allowed the most important stratification of AML into three prognosis groups (i.e., favourable, intermediate and adverse), and detected balanced and unbalanced chromosomal defects (i.e., translocation, inversions, trisomies, deletions and amplifications).

Based on traditional cytogenetics, 50% of AML patients have no chromosomal abnormalities by cytogenetics and are classified as intermediate with large variable response to treatment. Moreover, traditional cytogenetics analyses chromosomes in metaphase of multiple dividing cells which fails in approximately 10% of AML cases.

Thus, a more accurate classification of AML especially among patients with normal cytogenetics, or among patients whose traditional cytogenetics analysis failed, is necessary.

Smaller size genetic abnormalities such as copy number variations (CNV) and loss of heterozygosity (LOH) are generally undetectable using cytogenetics.

These technical limitations may be overcome by the use of single-nucleotide polymorphism microarrays (SNP-A) as reported recently (Bullinger L. et al., 2010, Leukemia; 24 (2): 438-449; Yi J.H. et al. 201 1 , J Clin Oncol; 29 (35): 4702-4708).

Somatic genetic abnormalities in AML using high-resolution SNP-A have been previously detected with abnormalities being distributed over the whole genome (Yi J.H. et al. 201 1 , J Clin Oncol; 29 (35): 4702-4708, Tiu RV et al. 201 1 , Blood; 1 17(17): 4552-4560. Parkin B et al. 2010, Blood, 1 16(23):4958-4967).

Nevertheless, the inventors could show that all these genetic abnormalities were not usable as prognosis markers. Indeed, studies on the use of such genetic abnormalities as prognosis markers are so far controversy. For example, no significant association was found between clinical outcome and the presence or number of acquired abnormalities in the research performed by Bullinger et al. possibly due to the use of lower resolution SNP arrays, whereas others found a significant association for overall genomic alterations and clinical outcome of AML patients.

In contrast to these studies, the present inventors have provided for the first time evidence that certain chromosomal locations are especially bad prognosis indicators.

Recently, several genetic mutations such as those involving CEBPa, NPM1 and FLT3 have been identified and have further improved diagnostic classification of AML with normal cytogenetics. However, variability in treatment response remains in all cytogenetic subgroups for reasons largely unknown.

Therefore, there is a need of new methods of prognosis to better identify poor prognosis patients and to offer them alternative or novel treatment strategies.

In order to respond to this need of an improved patient stratification, the inventors performed high-resolution SNP-A analysis on paired tumour and remission samples of 1 19 AML patients. As a result, they unexpectedly identified specific somatic genetic abnormalities on chromosomes 2, 1 1 , 17, 21 and 16, which allowed a much better stratification of patients according to their expected treatment response than overall genomic alterations (Figure 5).

Additionally, the inventors validated these novel prognostic genomic markers in two additional cohorts of de novo adult AML (n=127, n=1 12) allowing to develop a further AML classification overcoming the limitations of the so far existing classification tools.

The inventors showed that a stratification of AML patients according to the presence of CNV on chromosomes 2, 1 1 , 17 and 21 allows to give a more distinct overall survival prognosis than stratifying the patients according to the overall number genomic SNP-A.

The inventors discovered furthermore that a higher frequency of copy number variations on chromosomes 2, 1 1 , 17 and 21 was associated with poor overall treatment response.

They further detected a similar relationship concerning the presence of abnormalities on chromosomes 2, 1 1 , 17 and 21 and an increased treatment relapse.

Furthermore, multivariate analysis confirmed independent prognostic impact of unfavourable SNP-A abnormalities with prognostic cytogenetics or with the European Leukaemia Net (ELN) classification. The present invention thus relates to an in vitro method for diagnosing AML in a subject, comprising determining, in a biological sample from the subject which includes nucleic acids, the presence and/or number of copy number variations on chromosomes 2, 1 1 , 17 and/or 21 , wherein the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject suffers from AML.

The present invention further relates to an in vitro method for determining survival prognosis in a subject suffering from AML, comprising:

determining, in a biological sample from the subject which includes nucleic acids, the presence and/or number of copy number variations on chromosomes 2, 1 1 , 17, 21 and/or 16,

wherein the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject has a reduced chance of overall survival after diagnosis than a subject suffering from AML who does not display any copy number variations on chromosomes 2, 1 1 , 17 and/or 21 , and/or

wherein the presence of at least one copy number variation on chromosome 16 indicates that the subject has an improved chance of survival than a subject suffering from AML who does not display any copy number variations on chromosome 16.

The invention also concerns a method for risk stratification of a subject suffering from AML, comprising:

a) determining, in a biological sample from the subject which includes nucleic acids, the presence and/or number of copy number variations on chromosomes 2, 1 1 , 17, 21 and/or 16, and

b) based on the number of copy number variations determined in step a), classifying the subject as being at high risk or at low risk of death,

wherein the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject is at high risk of death and the absence of any copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject is at low risk of death, and/or

wherein the presence of at least one copy number variation on chromosome 16 indicates that the subject is at low risk of death and the absence of any copy number variation on chromosomes 16 indicates that the subject is at high risk of death.

The invention further provides a method for predicting a clinical outcome in response to a treatment of AML in a subject comprising:

determining, in a biological sample from the subject which includes nucleic acids, the presence and/or number of copy number variations on chromosomes 2, 1 1 , 17, 21 and/or 16, wherein the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject has an increased risk of relapsing after being treated than a subject suffering from AML who does not display any copy number variations, and/or

wherein the presence of at least one copy number variation on chromosome 16 indicates that the subject has a decreased risk of relapsing after being treated than a subject suffering from AML who does not display any copy number variations.

The invention also provides a method for selecting a subject who suffers from AML which comprises:

a) determining, in a biological sample from the subject which includes nucleic acids, the presence and/or number of copy number variations on chromosomes 2, 1 1 , 17 and/or 21 ,

b) selecting the subject based on the presence or absence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 .

In one embodiment, said method is for selecting a subject with AML who is likely to be in need of a bone marrow transplant, and said subject is selected as likely to be in need of a bone marrow transplant if said subject harbours at least one copy number variation on chromosome 2, 1 1 , 17 and/or 21 .

Improved risk stratification advantageously allows better adapting the therapy to patients' needs. The invention thus relates to a method for treating AML in a subject in need thereof, comprising the steps of:

a) determining, in a biological sample from the subject which includes nucleic acids, the presence and/or number of copy number variations on chromosomes 2, 1 1 , 17 and/or 21 , and

b) if at least one copy number variation is determined on chromosomes 2, 1 1 , 17 and/or 21 at step a), performing a bone marrow transplant and/or intensified chemotherapy or a combination thereof in said subject.

Detailed description of the invention

"Acute myeloid leukemia" (AML) is also known under the synonyms "acute myelocytic leukemia", "acute myelogenous leukemia", "acute granulocytic leukemia" or "acute non-lymphocytic leukemia" and is characterized by the accumulation of large numbers of abnormal cells that fail to differentiate into granulocytes or monocytes. Acute myeloid leukemia leads to the replacement of normal bone marrow with leukemic cells causing a drop in red blood cells, platelets, and normal white blood cells. The symptoms associated with acute myeloid leukemia include fatigue, shortness of breath, easy bruising and bleeding, and increased risk of infection.

Several risk factors and chromosomal abnormalities have been identified, but the specific cause of AML is still unclear.

Subject

In the context of the invention, "subject" refers to an animal, preferably a non- human or human mammal. Examples of non-human mammals include rodents and primates. Most preferably, the subject is a human.

More preferably, the "subject" denotes herein an individual that is under medical care or treatment.

In one embodiment the subject suffers from symptoms of AML. In particular, the subject might suffer from symptoms selected from the group consisting of fever, bone pain, lethargy and fatigue, shortness of breath, pale skin, frequent infections, easy bruising, unusual bleeding, such as frequent nosebleeds and bleeding from the gums.

In the context of the invention, once the subject is under medical care and treatment, a blood count might be performed. The first indicator for the diagnosis of AML is typically an abnormal result on a complete blood count (CBC). While an excess of abnormal white blood cells (leukocytosis) is a common finding, and leukemic blasts are sometimes seen, AML can also present, in some individuals, decreases in platelets (thrombocytopenia), red blood cells (aneamia), neutrophils (neutropenia) or even with a low white blood cell count (leukopenia) (Abeloff, Martin et at., 2004, page: 2834). While a presumptive diagnosis of AML can be made via examination of the peripheral blood smear when there are circulating leukemic blasts, a definitive diagnosis usually requires an adequate bone marrow aspiration and/or biopsy for morphology studies, flow cytometry analysis, cytogenetics and molecular techniques.

In one embodiment, the subject thus has an abnormal result on a complete blood count.

An "abnormal result on a complete blood count" means the values obtained from the blood count for neutrophils and platelets differ from normal values.

The skilled in the art is able to deduce from his general knowledge which blood count values might suggest the presence of AML and which blood count values are supposed to be normal. Published guidelines to determine how many cells should be counted and which stains should be performed are disclosed for example by Vardiman, J. W., 2002, The American Society of Hematology, 100(7): 2292-2302. However, "normal values for neutrophils" might be between 1 .0x 1 0⁹/L to 8.0x 1 0⁹/L, "normal values for platelets" might be between 1 50 x 1 0⁹/L to 450x 1 0⁹/L, for white blood cells might be between 4.0 to 1 1 .0x 1 0⁹/L, and blast cells might be less than 5%. Peripheral blood has 0% of blast cells.

Therefore, in one embodiment, the subject has neutrophil values <1 .0x 1 0⁹/L and/or platelets <1 50x 1 0⁹/L and/or more than 5% blast cells, in particular more than 20%, preferably 20-80%, for example 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 65, 70, 75, 80%.

In a further embodiment, a bone marrow analysis in the subject may confirm >20% blast cells.

In another embodiment, a bone marrow analysis in the subject may indicate a myeloproliferative disease (MDS).

An abnormal result on a complete blood count might refer as well to the presence of cluster or collections of blast cells.

In a further embodiment the subject thus has clusters or collections of blast cells.

Abnormal results on a complete blood count are a first indicator for acute myeloid leukemia.

The inventors showed that it was possible to determine improved survival prognosis, risk stratification and predict clinical outcome in a subject having AML.

Therefore in several embodiments, the subject suffers from AML.

According to the standard techniques established so far, in order to determine if a subject suffers from AML, usually bone marrow or blood is examined via light microscopy. Furthermore flow cytometry might be used for diagnosing the presence of leukemia and to differentiate AML from other types of leukemia (e.g. acute lymphoblastic leukemia- ALL). A sample of marrow or blood is typically also tested for chromosomal abnormalities by routine cytogenetics and/or fluorescent in situ hybridization.

Therefore, in several embodiments, the subject suffering from AML has beforehand been classified, in particular using standard techniques.

Several guidelines have been established to classify AML wherein the best known are the world health organization (WHO) classification, the French-American-British (FAB) Cooperative Group classification and/or MRC classification.

In one embodiment the "subject having AML" has been beforehand classified according to the WHO classification and/or the FAB classification.

The "World Health Organization (WHO) classification" distinguishes acute myeloid leukemia (AML) via genetic, immunophenotypic, biological, and clinical features. In one embodiment, according to the WHO classification, the subject having AML is a subject having acute myeloid leukemia with recurrent genetic abnormalities; acute myeloid leukemia with t(8;21 )(q22;q22), (AML 1/ETO) ; acute myeloid leukemia with abnormal bone marrow eosinophils and inv(16)(p13q22) or t(16;16)(p13;q22), (CBF/MYH11); acute promyelocytic leukaemia with t(15;17)(q22;q12), (PML/RAR) and variants, acute myeloid leukaemia with 1 1 q23 (MLL) abnormalities, acute myeloid leukaemia with multilineage dysplasia following myelodysplastic syndrome (MDS) or myelodysplastic syndrome/myeloproliferative disease (MDS/MPD), acute myeloid leukemia without antecedent MDS or MDS/MPD, but with dysplasia in at least 50% of cells in 2 or more myeloid lineages; acute myeloid leukaemia and myelodysplastic syndromes, therapy related such as alkylating agent/radiation-related type and topoisomerase II inhibitor-related type (some may be lymphoid); acute myeloid leukaemia minimally differentiated; acute myeloid leukaemia without maturation, acute myeloid leukemia with maturation; acute myelomonocytic leukemia; acute monoblastic/acute monocytic leukemia; acute erythroid leukaemia (erythroid/myeloid and pure erythroleukemia); acute megakaryoblastic leukemia; acute basophilic leukemia; acute panmyelosis with myelofibrosis; myeloid sarcoma.

The "French-American-British (FAB) classification" system divides AML into eight subtypes, MO through to M7, based on the type of cell from which the leukemia developed and its degree of maturity. This is done by examining the appearance of the malignant cells with light microscopy and/or by using cytogenetics to characterize any underlying chromosomal abnormalities. The subtypes of FAB are published by Bennett J. et at., 1976, Br. J. Haematol. 33(4): 451-458 and have varying prognoses and responses to therapy.

Traditional metaphase cytogenetics allow the so far most important stratification of

AML according to the MRC cytogenetics classification criteria into three prognosis groups (i.e., favourable, intermediate and adverse), and detect balanced and unbalanced chromosomal defects (i.e., translocation, inversions, trisomies, deletions and amplifications) (Table 1 ).

MRC cytogenetics classification into favourable, intermediate and adverse AML patients allowed so far adapting the treatment strategy to a certain degree.

Therefore in one embodiment, the subject suffering from AML has beforehand been classified into favourable, intermediate or adverse category. Table 1 : MRC cytogenetics classification

The recently proposed European Leukemia Network (ELN) classification uses the presence of the FLT3-ITD mutation, as well as CEBPA and NPM1 mutation status, to stratify AML with intermediate-risk cytogenetics, including CN-AML. This classification uses the molecular markers to subdivide the intermediate-risk AML into a more favourable Intermediate- 1 and a less favourable Intermediate-ll category.

Therefore, in a further embodiment, subjects suffering from AML and being classified as intermediate might be further classified into a more favourable Intermediate-I or a less favourable Intermediate-ll category.

Nevertheless, based on traditional cytogenetics analysis, 50% of AML patients have no chromosomal abnormalities by cytogenetics and are classified as intermediate.

In a preferred embodiment, subjects suffering from AML are classified as intermediate.

Furthermore, traditional cytogenetics analyzes of chromosomes in metaphase of multiple dividing cells fails in approximately 10% of AML cases, due to lack of metaphases or poor quality preparations.

Therefore, in a further preferred embodiment the subject suffering from AML cannot be classified according to traditional cytogenetics into favourable, intermediate and adverse.

In one embodiment, AML has been diagnosed in a subject by cytogenetics and/or fluorescent in situ hybridization.

In some cases AML might be therapy-related and occurs as a complication after cytotoxic and/or radiation therapy. Two main groups have been described: (i) leukemia arising 5-7 years after therapy with alkylating agents or irradiation, and associated with abnormalities of chromosome arms 5q and/or 7q, and (ii) occurring with a shorter latency of 2-3 years, following treatment with agents targeting topoisomerase II: these are often associated with translocations involving 1 1 q23 (MLL gene) or 21 q22 (RUNX1 gene).

"Routine cytogenetics" refers in the context of the invention to "traditional metaphase cytogenetics", also known as "karyotyping" and may be used herein interchangeably. In a "traditional cytogenetic technique" known as karyotyping, metaphase chromosome spreads are prepared on a glass slide and stained with a dye revealing, once visualized under the microscope, a specific banding pattern for each chromosome.

A "band" is defined as the part of a chromosome which is clearly distinguishable from its adjacent segments by appearing darker or brighter with one or more banding techniques. The chromosomes are visualized as consisting of a continuous series of bright and dark bands.

The "banding techniques" fall into two principal groups:

1 ) a group resulting in bands distributed along the length of the whole chromosome, such as G-, Q- and R-bands and

2) a group staining a restricted number of specific bands or structures.

The latter includes methods which reveal centromeric bands, C-bands, and nucleolus organizer regions, NOR's (at terminal regions of areocentric chromosomes). C- banding methods do not permit identification of every chromosome in the somatic cell complement, but can be used to identify specific chromosomes.

In one embodiment, AML has been classified with traditional metaphase cytogenetics techniques.

In a further embodiment said traditional metaphase cytogenetics techniques are metaphase G-, Q- and R-banding analysis, in particular G-bands and/or R-bands.

Therefore, in a further embodiment, a subject suffering from AML has been classified by cytogenetic metaphase R-banding analysis.

G- and R bands might be bright field or fluorescent.

"Bright field G-bands", which take their name from the Giemsa dye, are most commonly used but can be produced with other dyes as well. In G-bands, the dark regions tend to be heterochromatic, late-replicating and AT rich. The bright regions tend to be euchromatic, early-replicating and GC rich.

"Bright field R-bands" are approximately the reverse of G-bands (the R stands for "reverse"). The dark regions are euchromatic and the bright regions are heterochromatic.

The "fluorescent G- and R-bands" are the photographic negative of the bright field versions, i.e. the reverse of the bright field G-bands and R-bands.

"Q-bands" are like fluorescent G-bands, but certain heterochromatic regions are more brightly stained with Q-banding.

Karyotyping might be supplemented with the molecular cytogenetic technique Fluorescent In Situ hybridization (FISH), which requires the use of fluorescently labelled DNA probes to target a specific chromosome region. Therefore, in a further embodiment, a subject suffering from AML has been classified by cytogenetic metaphase analysis supplemented with molecular cytogenetic technique, in particular Fluorescent In Situ hybridization (FISH).

In "Fluorescent In Situ hybridization" the chromosome preparations, such as metaphase spreads or interphase nuclei, are heat denatured. This denaturation is followed by application of the probe and hybridization at for example 37 °C. FISH can also be performed on interphase nuclei on non-cultured cells in less than 24h, but the chromosome structure cannot be visualized. On the other hand, metaphase FISH has the advantage of visualizing the entire karyotype at once and can detect potential abnormalities at a high resolution. However, the long analysis time and culturing required for metaphase FISH are important disadvantages.

Furthermore, DNA analysis, such as PCR amplification of a specific DNA region can be performed on non-cultured cells.

Therefore, in another embodiment, a subject suffering from AML has been classified by cytogenetic metaphase analysis supplemented with molecular cytogenetic technique, in particular Fluorescent In Situ hybridization (FISH) and/or PCR.

Interphase FISH and/or RT-PCR might also be considered when chromosome analysis are unsuccessful due to lack of metaphases or poor quality preparations.

If interphase FISH is required, then - in AML - it may be appropriate to include the following genes and rearrangements in the investigation: inv(16), t(15;17), t(8;21 ), MLL, 5q, 7q, TP53, 3q26. Fusion genes may be assessed also by RT-PCR analysis.

Nevertheless, FISH is rarely used as the first step in cytogenetic analysis, due to the high cost of the probes, need for skilled technicians and lengthy analysis protocol. Detection of copy number variations

In the context of the invention, copy number variations can be determined in a biological sample with techniques that are well known from the one skilled in the art. These methods include, without being limited, hybridization methods with DNA probes specific of marker sequences, such as comparative genomic hybridization (CGH), matrix- CGH, array-CGH, oligonucleotide arrays, representational oligonucleotide microarray (ROMA), high-throughput technologies for SNP genotyping such as DNA arrays, for example Affymetrix SNP chips, and amplification methods such as quantitative PCR.

The presence of at least one copy number variation can be determined in a preferred embodiment by DNA arrays, in particular by high-throughput single nucleotide polymorphism array (SNP-A). In particular, a "high-throughput single nucleotide polymorphism array" (SNP-A), such as for example the Affymetrix Genome-Wide Human SNP Array 6.0, is used in the context of the invention to detect structural abnormalities.

The inventors distinguished during their analysis "acquired structural abnormalities", which are used herein interchangeably with "somatic structural abnormalities", from "constitutional genetic abnormalities" allowing the identification of acquired structural abnormalities associated with AML.

In order to do so, the inventors compared DNA samples from subjects with complete remission as a DNA control to distinguish between acquired and germ line variants.

Acquired or somatic structural abnormalities were distinguished by comparing SNP-A abnormalities concurrent in the diagnostic and in the remission sample. As a result SNP-A abnormalities present in both samples were considered as germ line or constitutional and were excluded.

In the context of the invention, SNP-A may be used to detect acquired structural abnormalities.

The structural abnormalities in the context of the invention are therefore acquired structural abnormalities.

The "acquired structural abnormalities" or "somatic structural abnormalities", in the context of the invention are genomic abnormalities and/or alterations. Somatic genomic alterations detectable by SNP-A are single nucleotide polymorphisms (SNP), copy number variations (CNV), loss of heterozygosity (LOH) and uniparental disomies (UDP).

Herein, the term abnormality and alteration can be used interchangeably.

"Single nucleotide polymorphism" or "single nucleotide variation" refers to the variation of at least one nucleotide in the genome i.e. a site of the genome which is not identical in all individuals, such as a substitution, deletion, insertion and/or amplification.

"Uniparental disomies (UDP)" is a genomic abnormality which could not be associated with AML and is therefore excluded from the abnormalities detected according to the invention.

As used herein, the terms "copy number variation", "copy number alteration", "copy number variant" and "CNV" are used indifferently and refer to a DNA segment of at least 1 kb and present at variable copy number in comparison with a reference genome.

The terms "structural variant", "duplicon", "indel", "intermediate-sized structural variant (ISV)", "low copy repeat (LCR)", "multisite variant (MSV)", "paraloqous sequence variant (PSV)", "segmental duplication", "interchromosomal duplication", and "intrachromosomal duplication", found in the literature, are included herein in the term "CNV".

Most diploid cells, for example human somatic cells, contain two copies of the genome, one from each parent (chromosome pair). "Loss of heterozygosity" in the context of the invention describes thus the loss of one parental copy of a chromosomal segment.

The inventors detected, by using a high-throughput single nucleotide polymorphism array, that 57% of the de novo AML patients had 175 acquired structural abnormalities, in particular copy number variations.

The inventors showed that somatic genomic alterations, in particular copy number variations (CNV), can be associated with AML.

More particularly, they demonstrated that detecting the presence of at least one

CNV at specific chromosomal locations allowed an improved stratification of the patients and establishing a prognosis for the outcome of the disease.

According to the invention, an AML subject has therefore preferably at least one copy number variation on chromosomes 2, 1 1 , 17, 21 and/or 16, more preferably on chromosomes 2, 1 1 , 17 and/or 21 .

In particular embodiments, the presence of at least 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 ,

12, 13, 14, 15, 16, 17 18, 19 or 20 copy number variations on chromosomes 2, 1 1 , 17, 21 and/or 16, or on chromosomes 2, 1 1 , 17 and/or 21 , in particular of at least 2 or 3 copy number variations on chromosomes 2, 1 1 , 17, 21 and/or 16, or on chromosomes 2, 1 1 , 17 and/or 21 , is detected in the subject.

In one embodiment, said at least one copy number variation is at least one acquired or somatic copy number variation.

The inventors did not filter SNP-A abnormalities or LOH for segment minimal size since those were determined truly somatic if not present in the corresponding normal sample.

Therefore, in one embodiment the high-throughput single nucleotide polymorphism array is performed with a minimal size of segments for copy number variations of 50 kb.

In particular, the detected copy number variations were between 9kb and 191 Mb in length.

In one embodiment the copy number variation refers to a DNA fragment having a size of at least 1 kb, preferably at least 9kb, in particular 9kb- 200Mb, which is present at variable copy number in comparison with a reference genome.

Furthermore, the term copy number variation can refer herein to a DNA fragment including a single gene and/or including a contiguous set of genes. In one embodiment the copy number variation is thus a gene copy number variation.

The term "gene" means a DNA sequence that codes for, or corresponds to, a particular sequence of amino acids which comprises all or part of one or more proteins or enzymes, and may or may not include regulatory DNA sequences, such as promoter sequences, which determine for example the conditions under which the gene is expressed. Some genes, which are not structural genes, may be transcribed from DNA to RNA, but are not translated into an amino acid sequence. Other genes may function as regulators of structural genes or as regulators of DNA transcription. In particular, the term gene may be intended for the genomic sequence encoding a protein, i.e. a sequence comprising regulator, promoter, intron and exon sequences.

As used herein, the term "gene copy number" refers to the number of copies of a particular gene present in the cell. In diploid organisms, in a normal state, two copies of each nucleic sequence are naturally present in the genome. Therefore, the copy number is 2. In particular, the genome displays two alleles for each gene, one on each chromosome of a pair of homologous chromosomes (except for the genes localized on sexual chromosomes).

In the context of the invention, a "copy" of a sequence encompasses a sequence identical to said sequence but also allelic variations of said sequence.

In the context of the invention, a "mutated seguence" of a reference CNV refers to a sequence including insertion(s), deletion(s) or substitution(s) of one or more nucleotide(s), wherein said mutated sequence is at least 75% identical to the reference CNV.

The percentage is calculated by determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, U, or I) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Optimal alignment of sequences for comparison is conducted by global pairwise alignment, e.g. using the algorithm of Needleman and Wunsch J. Mol. Biol. 48: 443 (1970). The percentage of sequence identity can be readily determined for instance using the program Needle, with the BLOSUM62 matrix, and the following parameters gap-open=10, gap-extend=0.5.

Preferably, the mutated sequence is at least 80%, 85%, 90%, or 95% identical to the reference CNV. Preferably said mutated sequence of a reference sequence is an allelic variant of said reference sequence. As used herein, an "allelic variant" denotes any of two or more alternative forms of a gene occupying the same chromosome locus.

Copy number variations, in the context of the invention, may be amplifications and/or deletions.

In one embodiment, the copy number variations on chromosome 2 are in particular amplifications.

In a preferred embodiment, the CNV on chromosome 2 is situated at position from nucleotide 91 ,798,880 to nucleotide 92,193,296.

In a further embodiment, the at least one gene copy number variation on chromosome 2 is a gene copy number variation of at least one of the genes listed in Table 2 for chromosome 2.

In a preferred embodiment, the CNV on chromosome 1 1 is situated at position from nucleotide 55,362,386 to nucleotide 55,384,209 or is situated at position from nucleotide 3,641 ,337 to nucleotide 3,767,456.

In one embodiment the copy number variations on chromosome 1 1 situated at position from nucleotide 55,362,386 to nucleotide 55,384,209 are in particular amplifications.

In one further embodiment the copy number variations on chromosome 1 1 situated at position from nucleotide 3,641 ,337 to nucleotide 3,767,456 are in particular deletions.

In a further embodiment, the at least one gene copy number variation on chromosome 1 1 is a gene copy number variation of at least one of the genes listed in Table 2 for chromosome 1 1 .

In one embodiment the copy number variations on chromosome 17 are in particular amplifications.

In a preferred embodiment, the CNV on chromosome 17 situated at position from nucleotide 50,151 ,978 to nucleotide 50,589,177.

In a further embodiment, the at least one gene copy number variation on chromosome 17 is a gene copy number variation of at least one of the genes listed in Table 2 for chromosome 17.

In one embodiment the copy number variations on chromosome 21 are in particular amplifications.

In a preferred embodiment the CNV on chromosome 21 situated at position from nucleotide 39,837,306 to nucleotide 39,953,387. In a further embodiment the at least one gene copy number variation on chromosome 21 is a gene copy number variation of gene at least one of the genes listed in Table 2 for chromosome 21

Table 2: Correspondence between identified CNVs, the referenced chromosomal position on NCBI human genome sequence and the corresponding gene.

Nucleotide Position

Other

Gene Symbol Start End Name Aliases Gene ID

Chromosome 16

hect domain and RLD 2 pseudogene

HERC2P4 32162608 32163874 4 D16F37S5 440362

TP53TG3D 32264649 32267243 TP53 target 3D 729264 protein phosphatase 2, regulatory

LOC390705 32300867 32301302 subunit B", beta pseudogene 390705

Chromosome 2

lymphocyte-specific protein 1

LOC654342 91824708 91847975 pseudogene 654342 gamma-glutamyltransferase 8

GGT8P 91963367 91970153 pseudogene GGT1 P1 645367

ARP3 actin-related protein 3 homolog

ACTR3BP2 92129158 92130496 B (yeast) pseudogene 2 FKSG73 440888

Chromosome 17

CARPX, CA-

RPX,

CA10 49707673 50237377 carbonic anhydrase X HUCEP-15 56934

Chromosome 21

v-ets erythroblastosis virus E26

ERG 39739182 40033704 oncogene homolog (avian) p55, erg -3 2078

zinc finger and BTB domain

ZNF295 43406939 43430496 containing 21 ZNF295 49854

PRED87,

C21 orf121 ,

NCRNA0031

ZNF295-AS1 43442112 43445060 ZNF295 antisense RNA 1 8 150142

UMODL1 43483067 43563105 uromodulin-like 1 89766

chromosome 21 open reading frame

C21orf128 43522243 43528644 128 150147

ATP-binding cassette, sub-family G ABC8,

ABCG1 43619798 43717354 (WHITE), member 1 WHITE1 9619

ITF, P1 B,

TFF3 43731776 43735706 trefoil factor 3 (intestinal) TFI 7033

TFF2 43766466 43771208 trefoil factor 2 SP, SML1 7032

pS2, BCEI,

HPS2,

HP1.A, pNR-

TFF1 43782390 43786644 trefoil factor 1 2, D21 S21 7031

DFNB8,

DFNB10,

ECHOS1 ,

TMPRSS3 43791995 43816955 transmembrane protease, serine 3 TADG12 64699

TULA,

ubiquitin associated and SH3 domain CLIP4, STS-

UBASH3A 43823970 43867790 containing A 2, TULA-1 53347

TSA2,

RSP44,

radial spoke head 1 homolog TSGA2,

RSPH1 43892596 43916401 (Chlamydomonas) RSPH10A 89765 solute carrier family 37 (glycerol-3-

SLC37A1 43919741 44001550 phosphate transporter), member 1 G3PP 54020

PDE9A 44073861 44195618 phosphodiesterase 9A HSPDE9A2 5152

TRM82,

WDR4 44263189 44299699 WD repeat domain 4 TRMT82 10785

NADH dehydrogenase (ubiquinone) Cl-10k, Cl-

NDUFV3 44313377 44329773 flavoprotein 3, 10kDa 9KD 4731 Nucleotide Position

Other

Gene Symbol Start End Name Aliases Gene ID

PREP1 ,

PKNOX1 44394642 44453688 PBX/knotted 1 homeobox 1 pkonxlc 5316

CBS 44473300 44496472 cystathionine-beta-synthase HIP4 875

RN, FP793,

U2AF35,

U2 small nuclear RNA auxiliary factor U2AFBP,

U2AF1 44513065 44527688 1 RNU2AF1 7307

CRYA1 ,

CRYAA 44589140 44592913 crystallin, alpha A HSPB4 1409

Chromosome 11

transient receptor potential cation

channel, subfamily C, member 2,

TRPC2 3647689 3658789 pseudogene 7221

ART5 3659735 3663546 ADP-ribosyltransferase 5 ARTC5 116969

RT6, ART2,

ARTC1 ,

ART1 3666360 3685646 ADP-ribosyltransferase 1 CD296 417

cholinergic receptor, nicotinic, alpha

CHRNA10 3686816 3692614 10 (neuronal) 57053

ADIR2,

NUP96,

NUP98 3696239 3819022 nucleoporin 98kDa NUP196 4928

olfactory receptor, family 4, subfamily OR4C11 P,

OR4C11 55370829 55371874 C, member 11 OR11 -136 219429

In the context of the present invention, the positions of the nucleotides are indicated accordingly to the NCBI human genome sequence (according to the 6 June 2013). Furthermore, in the context of the invention reference sequences are obtainable under the listed Gene ID from the Genebank database (according to the 6 June 2013). It is known to the one skilled in the art, that a genome sequence is variable from an individual to another. Therefore, the positions defined herein may slightly change according to the human genome sequence used. However, methods to compare genomic sequences and nucleotide positions are well known to the one skilled in the art. Accordingly, CNVs of sequences situated on different nucleotide positions on another human genome than NCBI's reference sequence, but which sequence matches with the sequence delimited by the nucleotide positions defined above are within the scope of the invention. Biological sample

The term "nucleic acid" generally refers to at least one molecule or strand of DNA, RNA, miRNA or a derivative or mimic thereof, comprising at least one nucleobase, such as, for example, a naturally occurring purine or pyrimidine base found in DNA (e.g., adenine "A," guanine "G," thymine "T," and cytosine "C") or RNA (e.g. A, G, uracil "U," and C). The term "nucleic acid" encompasses the terms "oligonucleotide" and "polynucleotide".

The term "oligonucleotide" refers to at least one molecule of between about 3 and about 100 nucleobases in length.

The term "polynucleotide" refers to at least one molecule of greater than about 100 nucleobases in length. These definitions generally refer to at least one single-stranded molecule, but in specific embodiments will also encompass at least one additional strand that is partially, substantially or fully complementary to the at least one single-stranded molecule. Thus, a nucleic acid may encompass at least one double-stranded molecule that comprises one or more complementary strand(s) or "complement(s)" of a particular sequence comprising a strand of the molecule.

As used herein, the term "biological sample" means a substance of biological origin. In particular the biological sample comprises cells from the subject to be diagnosed. The biological samples comprises in particular nucleic acids. Examples of biological samples include, but are not limited to, blood and components thereof such as plasma, platelets, subpopulations of blood cells and the like; bone marrow samples, organs such as kidney, liver, heart, lung, and the like, saliva and mouth epithelial cells.

In a preferred embodiment of the invention, the biological sample is a bone marrow sample or a blood sample.

The preferred sample for chromosome analysis is bone marrow. In AML, if bone marrow is not available, e.g. unsuccessful aspiration, then blood samples can be used for cytogenetic analysis provided circulating blasts cells are present.

Therefore in a preferred embodiment, the sample is a bone marrow sample.

For DNA arrays such as SNP-A, DNA may be extracted from a sample of the subject and be analyzed by SNP-A.

In one example, DNA is extracted from typically bone marrow aspirates using for example with the QIAmp kit (Qiagen, Hilden, Germany) typically according to manufacturer recommendations.

In the following step the extracted DNA may be analyzed by a DNA-array, in particular, by a SNP-array, as defined in the section "Detection of CNV" above.

In one example, DNA samples (for example 250ng) are analyzed for example on the high-resolution Genome-wide Human SNP Array 6.0 (SNP-A) typically according to the manufacturer's protocol (Affymetrix, Santa Clara, USA). Primary data analysis might be done with Genotyping Console version 4.1 .3 software and Chromosome Analysis Suite 1 .2.2 (Affymetrix, Santa Clara, USA). Each array might be evaluated visually and quality control measures should be performed as recommended by the manufacturer (i.e., call rate, contrast QC and MAPD).

In another example, samples might be run on the Human Genome CGH Microarray 105k (Agilent Technologies, Les Ulis, France).

In one embodiment filtering criteria are for example that segments include at least

25 consecutive markers and the minimal size of segments might be larger than, for example, 50kb for CNV.

Method of diagnosis

As used herein the term "diagnosis" refers to the process of attempting to determine or identify a possible disease or disorder in a subject, as defined in the section "subject" herein above. In particular, "method of diagnosis" refers herein to a process of determining AML in a subject.

The inventors demonstrated that the presence of at least 3 copy number variations on the whole genome in subjects previously diagnosed as suffering from AML indicates an overall worse overall outcome.

Accordingly, in one embodiment the presence of at least three copy number variations on the overall genome indicates the presence of AML in a subject, as defined in the section "Subject" herein above.

Therefore in one embodiment, the presence of at least three copy number variations on the overall genome indicates that the subject suffers from AML.

The inventors demonstrated in particular that the presence of at least one copy number variation on chromosome 2, 1 1 , 17, 21 in subjects previously diagnosed as suffering from AML indicates an overall worse overall outcome.

Multivariate analysis confirmed independent prognostic impact of unfavourable SNP-A abnormalities with prognostic cytogenetics and EFL.

Accordingly, the presence of at least one copy number variation on chromosome 2, 1 1 , 17 and/or 21 indicates the presence of AML in a subject, as defined in the section "Subject herein above.

Therefore in one embodiment, the presence of at least one copy number variation on chromosome 2, 1 1 , 17 and/or 21 indicates that the subject suffers from AML.

In a further embodiment, the presence of at least three copy number variations on chromosome 2, 1 1 , 1 and/or 21 indicates that the subject suffers from AML.

In one embodiment the method of diagnosis is supplemented with an additional optional step to distinguish acute myeloid leukaemia (AML) from acute lymphoblastic leukemia (ALL). Techniques to distinguish AML from ALL are known to the skilled in the art.

In one example, AML can be distinguished from ALL by cytochemical stains on blood and bone marrow smears.

In another example, AML can be distinguished from ALL by myeloperoxidase or

Sudan black stain and in combination with a nonspecific esterase stain will provide the desired information in most cases. The myeloperoxidase or Sudan black reactions are most useful in establishing the identity of AML and distinguishing it from ALL. The nonspecific esterase stain is used to identify a monocytic component in AMLs and to distinguish poorly differentiated monoblastic leukemia from ALL. Specifically, myeloperoxidase >3% indicates AML (ALL is negative). In cases with <3% myeloperoxidase subsequent flow cytometry is used to distinguish between either poorly differentiated AML or ALL.

In another embodiment, the method of diagnosis is supplemented with a further step to distinguish acute myeloid leukemia (AML) from acute promyelocytic leukemia (APL). Techniques to distinguish AML from APL are known to the skilled in the art.

APL is commonly detected by cytology techniques (morphology) which are known the skilled in the art. In one example cells of a patient having APL are promyelocytes hypergranulated with bundles of Auer rods.

Survival prognosis

As used herein, the term "prognosis" refers to a statistical process for predicting the outcome of the disease for subjects suffering from AML, wherein outcome refers to the likelihood of having an improved or reduced chance of survival when treated.

The inventors assessed the prognostic relevance of SNP-A analysis on diagnostic and remission samples of 1 19 adult AML patients comparing the results with conventional cytogenetics and molecular diagnostics. Furthermore the findings were validated on two additional cohorts.

Initially a higher frequency of CNV on the whole genome was discovered in subjects suffering from AML and could be correlated with a reduced overall survival.

Accordingly, in one embodiment the presence of at least three copy number variations on the overall genome indicates that the subject has a reduced chance of survival after diagnosis than a subject suffering from AML who does not display any copy number variation. Furthermore, the presence of at least three copy number variations on the overall genome indicates that the subject has a 5-year overall survival (OS) chance of less than 40%, in particular less than 35%, for example between 35% and 5%, particularly, 5, 7, 8, 10, 12, 14, 16, 18, 19, 20, 22, 24, 26, 28, 30, 32, 34, 35%.

A higher frequency of unfavourable CNV was discovered on chromosome 2, 1 1 ,

17 and 21 and could be correlated with a worse overall treatment response and a worse relapse free survival.

Furthermore, the inventors could correlate CNV on chromosome 16 with a positive overall treatment response and a positive relapse free survival.

Therefore, in one embodiment, the presence of at least one copy number variation, as defined in the section "Detection of CNV" above, on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject has a reduced chance of overall survival after diagnosis than a subject suffering from AML who does not display any copy number variations on chromosomes 2, 1 1 , 17 and/or 21 .

"Overall survival" (OS) is defined herein as the fate of the patient after diagnosis, regardless of whether the patient has a recurrence of AML. It therefore corresponds to the total amount of time that a patient survives after diagnosis, regardless of whether the patient has a recurrence of AML. "Relapse-free survival" (RFS) is herein defined as the lack of AML recurrence and/or spread and the fate of a patient after diagnosis, for example, a patient who is alive without AML recurrence. It therefore corresponds to the total amount of time that a patient survives after diagnosis without any relapse.

The "relapse" is defined as the reoccurrence of AML after complete remission. "Complete remission" or "CR" is defined as follows: normal values for neutrophil (>1 .0^*10⁹/L), haemoglobin level of 10g/dL and platelet count (>100^*10⁹/L) and independence from red cell transfusion; blast cells less than 5%, no clusters or collections of blasts, and absence of Auer rods on bone marrow examination; and normal maturation of blood cells (morphology; myelogramme) and absence of extramedullar leukemia.

In a further embodiment, the presence of at least one copy number variation on chromosome 16 indicates that the subject has an improved chance of survival than a subject suffering from AML who does not display any copy number variations on chromosome 16.

In one embodiment, the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject has a 2-year overall survival (OS) chance, preferably a 3-year, 4-year, 5-year, 6-year, 7-year, 8-year, 9-year or 10-year OS chance, of less than 70%, in particular less than 60%, less than 50%, for example between 45% and 10%, particularly, 10, 12, 14,16, 18, 19, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, ,40, 42, or 44% .

In a preferred embodiment, the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject has a 2-year overall survival (OS) chance, preferably a 3-year, 4-year, 5-year, 6-year, 7-year, 8-year, 9-year or 10-year OS chance, of less than 20%, for example between 5% and 20%, particularly, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13, 14, 15, 1 -, 17, 18, 19, or 20%.

In another embodiment, the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject has a reduced chance of relapse-free survival after diagnosis than a subject suffering from AML who does not display any copy number variations on chromosomes 2, 1 1 , 17 and/or 21 ; and/or the presence of at least one copy number variation on chromosome 16 indicates that the subject has an improved chance of relapse-free survival than a subject suffering from AML who does not display any copy number variations on chromosome 16.

In one embodiment, the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject has a 2-year relapse free survival (RFS) chance, preferably a 3-year, 4-year, 5-year, 6-year, 7-year, 8-year, 9-year or 10-year RFS chance, of less than 50%, in particular less than 40%, for example between 1 % and 30%, particularly, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 25, 26, 27, 28, 29 or 30 %.

Risk stratification

As used herein, the term "risk stratification" refers to a statistical process for separating subjects suffering from AML who are highly likely of not responding to treatments, and therefore of dying (high risk) from those who are less likely of not responding to treatment, and therefore of dying (low risk).

In a particular embodiment of the method for risk stratification of the invention, the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject is at high risk of death and the absence of any copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject is at low risk of death, and/or the presence of at least one copy number variation on chromosome 16 indicates that the subject is at low risk of death and the absence of any copy number variation on chromosomes 16 indicates that the subject is at high risk of death.

"High risk of death" in the context of the invention means in particular that the subject has a 2-year overall survival (OS) chance, preferably a 3-year, 4-year, 5-year, 6- year, 7-year, 8-year, 9-year or 10-year OS chance, of less than 70%, in particular less than 60%, less than 50%, for example between 45% and 5%, particularly, 10, 12, 14, 16, 18, 19, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42 or 44%.

"Low risk of death" means in particular that the subject has a 2-year overall survival (OS) chance, preferably a 3-year, 4-year, 5-year, 6-year, 7-year, 8-year, 9-year or 10-year OS chance, of more than 50%, in particular more than 50 to 80%, particularly more than 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 74, 76, 78 or 80%.

Prediction of clinical outcome

In the context of the invention, the term "clinical outcome" refers to the risk of relapsing or dying after treatment.

In a particular embodiment, the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject has an increased risk of relapsing after being treated than a subject suffering from AML who does not display any copy number variations, and/or the presence of at least one copy number variation on chromosome 16 indicates that the subject has a decreased risk of relapsing after being treated than a subject suffering from AML who does not display any copy number variations.

In the context of the invention an "increased risk of relapsing" defines that the subject has a 2-year relapse free survival (RFS) chance, preferably a 3-year, 4-year, 5- year, 6-year, 7-year, 8-year, 9-year or 10-year RFS chance, of less than 50%, in particular less than 40%, for example between 1 % and 30%, particularly, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 25, 26, 27, 28, 29 or 30 %.

Furthermore, a "decreased risk of relapsing" defines that that the subject has a 2- year relapse free survival (RFS) chance, preferably a 3-year, 4-year, 5-year, 6-year, 7- year, 8-year, 9-year or 10-year RFS chance, of less more than 50% in particular more than 50 to 80%, particularly more than 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 74, 76, 78 or 80%.

Treatment of AML

In the context of the invention, the term "treating" or "treatment", as used herein, means reversing, alleviating, inhibiting the progress of, or preventing the disorder or condition to which such term applies, or one or more symptoms of such disorder or condition. By the term "treatment of AML" as used herein is meant the inhibition of the increase of cell abnormalities. In one embodiment the abnormal result on a complete blood count will thus, as a result of the treatment, stay stable. Such treatment can also lead to the normalization of the blood count and therefore to complete remission.

Treatment of acute myeloid leukemia (AML) comprises usually two phases:

a) remission induction therapy called just induction and

b) consolidation therapy (post-remission therapy).

In one embodiment, the treatment of AML is chosen from the group consisting of bone marrow transplant, chemotherapy and/or radiation therapy.

In "chemotherapy" a chemo drug is usually given in cycles, wherein a period of treatment is followed by a rest period to allow the body time to recover.

The "chemo drugs" used most often to treat AML are cytarabine (cytosine arabinoside or ara-C) and the anthracycline drugs (such as daunorubicin/daunomycin, idarubicin, and mitoxantrone), gemtuzumab, clofarabine, cladribine, hydroxyurea (hydrea®), etoposide, amsacrine, FLT3-inhibitors, and demethylating agents (5- azacytidine and decitabine). ,

Chemotherapy in the context of the invention comprises intensive chemotherapy, investigational chemotherapy, low dose chemotherapy.

In one embodiment, "intensive chemotherapy" comprises for example the combination of cytarabine with anthracyclines, cytarabine with mitoxanthrone, cytarabine with idarubicin, cytarabine with daunorobucin or high dose cytarabine.

"Investigational chemotherapy" might comprise for example the combination of cytarabine with gemtuzumab, cytarabine with clofarabine and gemtuzumab.

"Low dose chemotherapy" might comprises for example the combination of decitabine/5-azacytidine, low dose cyratabine and hydroxyurea, triapine-fludarabine and/or chloretazine

In some cases, people with AML may have very high numbers of leukemia cells in their blood when they are diagnosed, which can cause problems with normal circulation. Chemotherapy may not lower the number of cells until a few days after the first dose therefore in the meantime leukapheresis may be used until the chemotherapy has an effect.

"Induction" is the first phase of treatment. The goal is to clear the blood of leukemia cells (blasts) and to reduce the number of blasts in the bone marrow to normal.

"Consolidation" is chemo given after the patient has recovered from induction. In consolidation therapy the aim is to eliminate the left over leukemia cells. In some embodiments the AML treatment might optionally further comprise a maintenance phase.

In context of the invention, "maintenance" involves giving a low dose of a chemo drug for months or years after consolidation is finished. This is often used for AML M3, but rarely used for other types of AML.

"Radiation therapy" or "radiation" uses high-energy radiation to remove cancer cells. Radiation therapy is usually not part of the main treatment for people with acute myeloid leukemia (AML), but it might be used in exceptional situations.

In one embodiment, radiation therapy may be used to help treating leukemia that has spread to the brain and/or spinal fluid and/or to the testicles.

In another embodiment, radiation therapy might be used before a bone marrow or peripheral blood stem cell transplant.

In another embodiment, radiation therapy can also be used to reduce pain in an area of bone that is invaded by leukemia, if chemotherapy was not effective.

"Bone marrow transplant" might be an autologous stem cell transplants or an allogeneic transplant.

In an "autologous transplant", a patient's own stem cells are removed from his or her bone marrow or peripheral blood. They are frozen and stored while the person gets treatment (high-dose chemotherapy and/or radiation). A process called "purging" may be used to try to remove any leukemia cells in the samples. The stem cells are then reinfused into the patient's blood after treatment. Autologous transplants are sometimes used for people with AML who are in remission after initial treatment and who don't have a matched donor for an allogeneic transplant.

"Allogeneic transplants" are transplants from a matched donor. The advantage of allogenic bone marrow transplants is that the transplanted cells from the donor might establish a new immune system, which might detect leukaemia cells as foreign and removes them. The disadvantage of the allogeneic transplants is the limitation of matching donors and the side effects.

However, in a preferred embodiment, the bone marrow transplant is an allogenic transplant.

In one embodiment, if at least one copy number variations is determined on chromosomes 2, 1 1 , 17 and/or 21 performing a bone marrow transplant and/or intensified chemotherapy or a combination thereof in said subject would be recommended.

"Intensified chemotherapy" in the context of the invention refers to the use of chemo drugs specified under "intensive chemotherapy" such as the combinations of Cytarabine with Anthracyclines, Cytarabine with Mitoxanthrone, Cytarabine with Idarubicin, Cytarabine with Daunarobucin, AcDVP or high dose cytarabine.

Throughout the instant application, the term "comprising" is to be interpreted as encompassing all specifically mentioned features as well optional, additional, unspecified ones. As used herein, the use of the term "comprising" also discloses the embodiment wherein no features other than the specifically mentioned features are present (i.e. "consisting of").

The present invention will be further illustrated by the following figures and examples.

Brief description of the figures

Figure 1 is a set of pie charts representing the result of conventional metaphase cytogenetics and the overlap with SNP-A abnormalities: A) distribution of 1 19 AML samples stratified by conventional metaphase cytogenetics (MC) according to MRC classification criteria into adverse, favourable, intermediate and non-informative karyotypes, B) overlap between MC (n=98) and SNP-A (n=154) abnormalities.

The percentages were calculated based on the sum of 169 unique abnormalities. Thus 19% were detected by both methods (SNP-A MC), 27% abnormalities only detected by MC and 54% only detected by SNP-A.

Figure 2 shows in graphs of Kaplan-Meier estimates of OS and RFS by cytogenetics and SNP-A abnormalities.

A) OS (P =0.0015 logrank test) and B) RFS (P =0.0043 logrank test) are stratified by cytogenetics into favourable karyotype (dashed line), intermediate (dotted line) and adverse (full line) for the entire cohort of 109 patients. Not shown are the non-informative karyotypes (n=10).

C) OS (P =0.015 logrank test) and D) RFS (P =0.9 logrank test) stratified by overall number of genomic SNP-A abnormalities by none to three abnormalities (full line) and by four and more abnormalities (dashed line) for the entire cohort of 1 19 patients. Numbers at risk per year are given for each panel.

Figure 3 shows in a bar chart the chromosomal distribution of CNA detected by SNP-A. A) Frequencies of amplifications (AMP) and deletions (DEL) on the different chromosomes are presented and B) normalized by the size in megabase (Mb) of the respective chromosome (x-axis).

Figure 4 shows in a bar chart the frequency of SNP-A abnormalities on chromosomes (x- axis) in the case of event defined as death of any case or in the case of no_event defined as alive or censored because of bone marrow transplantation in A) and in the case of relapse or no_relapse or censored because of bone marrow transplantation in B). The chromosomes with high densities of SNP-A abnormalities occurring in patients with dismal outcome (bottom arrow) and with those chromosomes with high densities of SNP-A abnormalities occurring in patients with favorable outcome (top arrow) are presented. C) Shows in a pie chart the information obtained by conventional metaphase cytogenetics (MC), the additional information obtained by SNP-A analysis and those that are classified as unfavorable (SNP-Aunfav) detected by SNP-A only and those detected by both SNP-A and MC (SNP-Aunfav_MC). E) The bar chart illustrates the composition by conventional cytogenetics (intermediate (I), non-informative (NF), favourable (F), adverse (A)) of the three prognostic SNP-A groupings "no unfavorable abnormalities", "one unfavorable abnormality" and "two to six unfavorable abnormalities".

Figure 5 shows graphs for Kaplan-Meier estimates of OS and RFS survival by number of SNP-A abnormalities on negative chromosomes:

A) OS (P =0.284 logrank test) and B) RFS (P =0.193 logrank test) stratification by overall number of genomic SNP-A abnormalities by none (full line) and one to 17 abnormalities (dashed line) for the entire cohort of 1 19 patients. Numbers at risk per year are given for each panel.

C) OS (P <0.0001 logrank test) and D) RFS (P =0.0043 logrank test) stratification by number of abnormalities on chromosomes 2, 1 1 , 17, 21 into none (full line) and more than one abnormality (dashed) for the entire cohort of 1 19 patients.

E) OS (P <0.0001 logrank test) and F) RFS (P =0.9 logrank test) stratification into none (dotted line), one (dashed line) and more than one alterations (full line). Numbers at risk per year are given for each panel.

Stratification according to none or more abnormalities on chromosome 2, 1 1 , 17, 21 (B, C) is improved in comparison to the stratification according to none or more abnormalities present on all chromosomes (A, B).

Figure 6 shows graphs of Kaplan-Meier estimates of OS and RFS survival by karyotype and by number of SNP-A abnormalities on negative chromosomes in the validation cohort. A) OS (P =0.031 logrank test) and B) RFS (P =0.0039 logrank test) stratification by cytogenetics into favourable karyotype (dashed line), intermediate (dotted line) and adverse (full line) for the entire cohort of 1 17 patients. Not shown are the non-informative karyotypes (n=10).

C) OS (P <0.0001 logrank test) and D) RFS (P =0.0063 logrank test) stratification by number of abnormalities on chromosomes 2, 1 1 , 17, 21 into none (full line) and more than one abnormality (dashed line) for the entire cohort of 127 patients. Numbers at risk per year are given for each panel. EXAMPLE

The following example describes somatic genetic abnormalities present in acute myeloid leukaemia patients, in particular present on chromosome 2, 1 1 , 17, 21 and 16 and their association with treatment response and overall survival prognosis for AML patients.

1. Methods 1.1 Patients

Patients with de novo diagnosis of acute myeloid leukemia participated in or were treated according to the Acute Leukemia French Association (ALFA) 9801 and 9802 trials which was conducted between 1999 and 2006 and used daunorubicin and cytarabine for remission induction therapy commonly known as the 3+7 regimen (Pautas C. et at., J Clin Oncol 2010, 28(5): 808-814; Thomas X. et al., Blood 201 1 ; 1 18(7): 1754-1762). Patients were classified according to MRC cytogenetics as favourable (n=26), intermediate (n=70), adverse (n=13), and non informative karyotypes (n=10). Patients were aged from 13 to 66 years with a median of 42 years and distributed across all French-American-British (FAB) classes (6% M0, 50% M1/M2, 39% M4/M5, 2% M6, 3 unclassified), and FAB class M3 were excluded (Table 3).

Because of analyzing acquired genomic alterations by SNP-A, only patients who achieved complete remission after induction therapy were included in the discovery cohort.

The validation cohort consisted of 127 independent diagnostic AML samples from a subsequent ALFA study equally treated with the 3+7 regimen and of similar FAB type distribution (6% M0; 49% M1 /M2; 17% M4/M5; 2% M6). The median age was higher 62 years (range: 50 to 71 ), and inversion of chromosome 16 and other core-binding factor (CBF) AML were excluded, i.e., fewer M4 cases. A signed informed consent was obtained at diagnosis from all patients.

Table 3: Patients' characteristics

Patients without

Patients with

All patients alterations by P-value alterations by SNP-A

SNP-A

N (%) 119 63 (53) 56 (47)

Sex ratio (F/M) 0.92 (57/62) 0.85 (29/34) 1.0 (28/28) 0.72

Age (years)¹ 42 [13-66] 42 [13-66] 41 [14-63] 0.23

Hemoglobin (g/dl)¹ 8.8 [3.2-15.7] 9.1 [4.8-15.7] 8.7 [3.2-15.0] 0.48

Leukocyte count 21.1 [0.8-284] 22.3 [0.8-284] 20.5 [1 .0-209] 0.33

Platelet count (G/l)¹ 63 [3-355] 73.5 [5-355] 53 [3-253] 0.25 Patients without

Patients with

All patients alterations by P-value alterations by SNP-A

SNP-A

FAB classification n (%) 0.04

LAMO 7 (6%) 1 (2%) 6 (1 1 %)

LAM1 26 (22%) 17 (27%) 9 (16%)

LAM2 34 (28%) 20 (32%) 14 (25%)

LAM4 36 (30%) 16 (25%) 20 (36%)

LAM5 11 (9%) 7 (1 1 %) 4 (7%)

LAM6 2 (2%) 2 (3%) 0 (0%)

unclassified 3 (3%) 0 (0%) 3 (5%)

Cytogenetics, n (%) < 0.0001 adverse 13 (1 1 %) 1 (2%) 12 (21 %)

favourable 26 (22%) 6 (10%) 20 (36%)

non informative 10 (8%) 4 (6%) 6 (1 1 %)

intermediate 70 (59%) 52 (82%) 18 (32%)

Mutations within intermediate n (%) 0.27

CEBPa 9 (13%) 6 (12%) 3 (17%)

FLT3-ITD ± NPM1 20 (28%) 17 (33%) 3 (17%)

NPM1 18 (26%) 15 (29%) 3 (17%)

None 23 (33%) 14 (27%) 9 (50%)

Median [range]

1.2 Conventional metaphase cytogenetics and molecular diagnosis

Cytogenetic metaphase R-banding analysis (MC) was performed on 1 19 diagnostic bone marrow samples using standard methods with at least 20 bone marrow metaphase cells. The karyotypes were described according to recommendations of the 2009 International System for Human Cytogenetic Nomenclature and classified according to the revised MRC criteria into three groups (i.e., favourable, intermediate and adverse; Table 1 ). Ten karyotypes were not feasible and described as non-informative MC. Within the group with normal cytogenetics, 23 patients (33%) presented no mutations in CEPBa, FLT3-ITD or NPM1 (Table 3).

1.3 DNA extraction

DNA was extracted from bone marrow aspirates obtained at diagnosis (n=1 19), and after achieving complete remission (paired samples n=1 17), using the QIAmp kit (Qiagen, Hilden, Germany) according to manufacturer's recommendations. The median percentage of blasts at diagnosis was 74% (range: 33-100%). For the validation cohort no paired samples were required. DNA quality was evaluated by standard BET agarose gel electrophoresis; DNA purity and quantification was assessed by UV spectroscopy (NanoDrop, Wilmington, USA and the Qubit fluorometer (Invitrogen, St. Aubin, France). 1.4 Acquired SNP-array abnormalities

High-quality paired DNA samples (250ng) were analyzed on the high-resolution Genome-wide Human SNP Array 6.0 (SNP-A) according to the manufacturer's protocol (Affymetrix, Santa Clara, USA) to distinguish acquired from constitutional genetic abnormalities. This microarray contains more than 1 .8 million markers resulting in a median inter-marker spacing of 680 bases. Primary data analysis was done with Genotyping Console version 4.1 .3 software and Chromosome Analysis Suite 1 .2.2 (Affymetrix, Santa Clara, USA). Each array was analyzed visually and quality control measures were performed as recommended by the manufacturer (i.e., call rate, contrast QC and MAPD). Nine samples taken at complete remission were run on the Human Genome CGH Microarray 105k (Agilent Technologies, Les Ulis, France) and two unpaired samples did not have any SNP-A abnormalities at diagnosis. Initial marker filtering criteria were that segments include at least 25 consecutive markers and the minimal size of segments is larger than 50kb for CNA and larger than 5Mb for LOH segments. All SNP-A abnormalities concurrent in the diagnostic and in the remission sample were excluded and considered as germ line. Subsequently, all acquired copy number abnormalities (CNA) and copy neutral loss of heterozygosity or uniparental disomy (UPD) were verified by visual inspection and annotated based on the University of California, Santa Cruz (UCSC) hg19 human genome assembly. 1.5 Statistical analysis

Statistical analyses were executed using R version 15.0 http://www.r-project.org/ (Gentleman R.C. et at., 2004, Genome Biol; 5(10): R80). The Cox proportional hazard regression model was used to relate genetic abnormalities to treatment outcome, with karyotype or European Leukemia Net (ELN) classification (Mrozek K et at., J Clin Oncol 2012; 30(36): 4515-4523; Rollig C et al., J Clin Oncol 201 1 ; 29(20): 2758-2765) included as the second covariate. Time was censored at transplantation date if bone marrow transplantation was performed. Overall survival (OS) was defined as the time interval from date of diagnosis to death from any cause or to last follow up. Kaplan-Meier estimator of the survival function was used and the comparisons between survival distributions were made using log-rank test. Relapse-free survival (RFS) was defined as the time interval from date of diagnosis to first relapse and was similarly censored if bone marrow transplantation was performed at the time of transplant. The median follow-up time for the discovery cohort was 2.9 years (range: 0.13 to 10.45) and for the validation cohort 0.91 years (range: 0.01 to 3.29). Circos plots were generated using the online version of Circos (at: http://circos.ca/; Krzywinski M et al. Genome Res 2009; 19(9): 1639-1645) and the karyotypic representation of SNP-A abnormalities was generated with the IdeogramBrowser Software (Muller A et ai, Bioinformatics 2007; 23(4): 496-497)

2. Results 2.1 SNP-A detection of somatic genomic alterations in AML and comparison with conventional diagnostic cytogenetics

A total of 175 acquired structural abnormalities were detected in 57% of de novo AML (68 of 1 19). Abnormalities included mostly 154 copy number alterations [CNA] and 21 uniparental disomies [UPD]. UPD was found in 16% of AML (19 of 1 19), thereof two patients had two UPDs each. In 10% of AML (n=12) one UPD was the only genomic abnormality identified and in 43% of AML (n=51 ) no SNP-A abnormalities were detected. This resulted in 2.56 abnormalities on average ranging from 1 to 17 abnormalities per AML subject. Among CNAs, deletions were three-times more frequent than gains (1 15 vs. 39). CNA spanned from 9kb to 191 Mb in length (median of gains 25Mb, median of losses 2Mb). UPDs spanned from 15 to 151 Mb in length (median 38Mb).

Patients' characteristics (sex, age, haemoglobin, leukocyte and platelet counts) were similar between patients in whom acquired genetic CNA was detected by SNP-A compared with those in whom it was not (Table 3). Interestingly, less differentiated AML was more likely to have SNP-A abnormalities (2 vs. 1 1 %, P =0.04) and all M0 cases were of intermediate karyotype.

Adverse and favourable karyotypes were significantly associated with the presence of SNP-A abnormalities (2 vs. 21 % and 10 vs. 36%, P <0.0001 , Table 3). SNP- A abnormalities were more likely present in patients with abnormal karyotypes (P <0.0001 , Table 3). Nevertheless, among the 56 patients with CNA, 18 had an intermediate karyotype and of those seven were of normal karyotype by conventional cytogenetics. Within the intermediate cytogenetic group no significant association of known prognostic mutations in CEBPa, NPM1 and FLT3 and SNP-A alterations was observed (P =0.27).

Somatic SNP-A abnormalities were highly associated with abnormal cytogenetics. Therefore, the inventors aimed to evaluate if the two techniques were redundant or complementary with regards to prognosis. Using conventional metaphase cytogenetics (MC) on the 1 19 patients included in this study, it was found that 50 (42%) cases of normal karyotype and 59 (50%) cases were abnormal. According to the ISCN classification, the present study included 26 (22%) favourable and 13 (1 1 %) adverse. 70 (59%) were classified intermediate, and 10 (8%) karyotypes were non-informative (Figure 1 A). 95 abnormalities were detected by MC and 41 (43%) of those were confirmed by SNP-A. More importantly, of the 154 CNAs detected by SNP-A a large proportion 1 13 (73%) was not detected by conventional cytogenetic methods (Figure 1 B) underlining the novelty of the SNP-A technique. Of note, 60% (6 of 10) of patients with unsuccessful or non-informative karyotypes presented with SNP-A abnormalities.

Somatic SNP-A abnormalities were frequent and occurred in more than half of the adult AML cases. They were more frequent in M0 and in AML with adverse and favourable cytogenetics, and also detectable in AML with normal cytogenetics. Certain cytogenetic abnormalities were not detectable by SNP-A, but in all cytogenetic groups a large number of additional abnormalities was detected by SNP-A. 2.2 Prognostic impact of abnormalities detected by SNP-A

The accumulation of acquired genetic abnormalities may be fundamentally involved in the processes of leukemogenesis, leukemia progression or relapse. Thus, the inventors evaluated the association of the total number of SNP-A abnormalities with clinical outcome.

With regards to prognostic cytogenetic karyotypes the study cohort resembled a typical cohort of AML with an inferior 5-year overall survival (OS) of the adverse karyotype of 23% compared to intermediate 61 % or favourable karyotypes 88% and inferior 5-year relapse-free survival (RFS) of the adverse karyotype of 12% compared to intermediate 60% or favourable 69% (P =0.0004, HR =9.07, 95%CI =2.71 -30.35 and P =0.0026, HR =4.60, 95%CI =4.1 1 -5.15; Figures 2A and 2B). No other clinical parameter (age, sex, platelet count, molecular subtype) was associated with either OS or RFS.

Nevertheless, the total number of somatic SNP-A abnormalities was significantly associated to overall survival (P =0.016, HR =1 .15, 95%CI =1 .03-1 .30; Tables 4 and 5). Table 4. Univariate and multivariate analysis for OS of two independent cohorts by number of unfavourable SNP-A abnormalities detected.

P -value¹ HR¹ 95% CI¹ P -value² HR² 95% CI² t

negative alterations <0.0001 ^* 1 .64 1 .33 -2.02 <0.0001 ^* 1 .38 1 .20 -1 .59

MC - adverse - - - - - -

MC - intermediate 0.44 0.66 0.23 - 2.71 0.053 0.50 0.25 - 1 .01

classification, ¹discovery cohort (n=1 1 9) , Validation cohort (n=127) Table 5. Univariate and multivariate analysis for OS of the discovery cohort by number of SNP-A abnormalities detected.

Continuous variable, * p<0.05, MC: metaphase cytogenetics,

Multivariate analysis was not significant when adjusted by prognostic MC karyotype classification (i.e., adverse, intermediate, favourable, P =0.40).

Finally, the presence of three or more CNA was significantly associated to 5-years overall survival (32% vs 66%; P =0.019, HR =2.54, 95%CI =1 .17-5.51 ; Figure 2C and 2D). No significance was detected for RFS. The presence or absence of UPDs had no adverse effect on survival in our cohort of patients (OS, P =0.125).

A significant association of the total number of SNP-A abnormalities with OS was found. However, this was not independent from the known prognostic cytogenetic classification.

2.3 Chromosomal location of somatic SNP-A abnormalities

SNP-A abnormalities (i.e., CNA and UPD) were located on all chromosomes, but were small and/or infrequent on chromosomes 14 and 15 (Figure 3). Of the 21 UPDs three were found on chromosomes 1 1 and 13, respectively. No UPDs were detected on 1 1 of 24 chromosomes (i.e., 3, 4, 5, 10, 14, 15, 18, 20, 21 , 22, Y) and, on all other chromosomes, either one or two UPDs were located.

CNAs were separated into amplifications and deletions to gain further insight on their effect on treatment response. Figure 3A shows their not random distribution across chromosomes. Deletions were more frequent and were mainly located on chromosomes 2, 7, 1 1 , 12, 16, 17 and 21 with chromosome 7 having the highest density of deletions. Of those chromosomes 16, 17 and 21 presented with a larger density of deleterious abnormalities relative to size of the chromosomes, (Figure 3B). Eight chromosomes presented only deletions, namely chromosomes 3, 7, 12, 14, 15, 16, 18, and 20 (Figure 3A, B).

Amplifications occurred mainly on chromosomes 8, 1 1 , 17 and 21 with chromosome 21 having the highest density of amplifications (Figure 3A). Only chromosome ten had solely amplifications (Figure 3A, B). Finally, a large proportion of patients presented with abnormalities on one or two chromosomes 41 of 56 (73%), 10 with abnormalities on 3 or 4 (18%) and only five (9%) of the patients had abnormalities on 5 to 8 different chromosomes. SNP-A abnormalities involving multiple chromosomes within the same patient was a relatively rare event and is associated with abnormal karyotype and interestingly with non-informative karyotype.

The inventors showed that deletions were more frequent than amplifications, the distribution of SNP-A abnormalities was non-random across the genome and AML with SNP-A abnormalities on multiple chromosomes was relatively rare.

2.4 SNP-A abnormalities have distinct effects on treatment outcome depending on chromosomal location

An association of overall survival with total number of SNP-A abnormalities was found which was not independent of prognostic cytogenetics. Furthermore, it was found that chromosomal location of the SNP-A abnormalities was not random. Therefore, the inventors hypothesized that chromosomal location may explain the varying effect of somatic genomic abnormalities on survival. It was identified a higher frequency of abnormalities on chromosomes 2, 1 1 , 17 and 21 associated with dismal overall treatment response versus higher frequency of abnormalities on chromosome 16 associated with favourable overall treatment response. Similar chromosomes related to treatment relapse were found, with the exception of a less important effect of chromosome 21 and a more important effect of chromosome 7. Nevertheless, the top 4 chromosomes 2, 1 1 , 16 and 17 were the same for OS and for RFS. Of the 154 CN SNP-A abnormalities, 54 (35%) were classified as unfavourable and 13 (8%) as favourable. The SNP-A classification newly classified 21 % of the abnormalities as unfavourable.

To gain further insight into the relationship between SNP-A abnormalities and treatment outcome, co-occurrence of SNP-A abnormalities on different chromosomes were analyzed. As a result it was found that unfavourable chromosomal SNP-A abnormalities on chromosomes 2 and 1 1 frequently co-occurred in AML and that chromosome 7 abnormalities often co-occurred with unfavourable abnormalities on chromosomes 1 1 , 17 and 21 . It was further found that favourable SNP-A abnormalities on chromosome 16 were frequently associated with abnormalities on chromosomes 6, 8 and Y. Thus this favourable effect may occur more frequently in men. Eight of the nine patients with favourable SNP-A abnormalities were male and had favourable cytogenetics [inv(16)] and one patient was female (P =0.015) and classified as normal karyotype with no adverse gene mutations. This observation was linked to the high number of patients (13%) with inversion of chromosome 16 (n=15), a subgroup known to have better OS (Byrd JC et at., 2004, J Clin Oncol 22(6):1087-1094; Larson RA et ai, 1986, Blood 68(6):1242-1249; Marcucci G et al., 2005, J. Clin. Oncol.;23(24):5705-5717).

However, within the favourable karyotypes (n=26) eight patients with favourable (3- year OS: 88%) and two patients with unfavourable SNP-A abnormalities (3-year OS: 50%; P <0.0001 ) were identified.

It is clinically important to identify patients with dismal prognosis besides the ones who have adverse cytogenetics. Thus, novel classification into none, one and more than one unfavourable SNP-A abnormalities was proposed by the inventors. The new adverse classification to known prognostic cytogenetics were compared. This showed that these prognostic markers overlapped. Favourable AML did not have unfavourable SNP-A abnormalities and adverse AML had more unfavourable SNP-A abnormalities. Intermediate AML was found in all prognostic SNP-A categories. Interestingly, non- informative karyotype AML was found to have multiple unfavourable SNP-A abnormalities.

In conclusion, the new classification refines prognosis of all cytogenetic subgroups but in particular intermediate and the non-informative AML are much better classified. In summary, this emphasizes the benefit of SNP-A analysis in AML diagnostics and the new classification by SNP-A abnormalities may serve as a new stratification methods complementary to conventional cytogenetics.

2.5 Prognostic impact of unfavourable SNP-A abnormalities

Unfavourable acquired genomic SNP-A abnormalities located on chromosomes 2,

1 1 , 17 and 21 were linked to bad prognosis (Figure 4A and B). Survival of patients with at least one unfavourable SNP-A abnormality was worse than those without any SNP-A abnormalities or without any on chromosomes 2, 1 1 , 17 and 21 with respect to OS (5-year OS of 19% vs. 72%, P <0.0001 , HR =1 .64, 95%CI =1 .33-2.02; Figure 5C, Table 6) and with respect to RFS (5-year RFS of 27% vs. 64%, P =0.0022, HR =1 .39, 95%CI = 1 .13- 1 .72; Figure 5D).

Patients with multiple unfavourable SNP-A abnormalities had very poor overall outcome (23% vs. 72%, P =0.0005, HR =4.51 , 95%CI =1 .93-10.53; Figure 5E) and similarly were more likely to relapse (26% vs. 64%, P =0.026, HR =2.73, 95%CI =1 .13- 6.59; Figure 5F). Multivariate analysis (Table 6) confirmed the independent prognostic impact of unfavourable SNP-A abnormalities on OS after adjusting for prognostic cytogenetics (P =0.013, HR =1 .43, 95%CI =1 .08-1 .90) or after adjusting for ELN classification (P =0.013, HR =1 .45, 95%CI =1 .08-194). Independent significance was not detected for RFS. Table 6. Univariate and multivariate analysis for overall survival of the discovery cohort by number of SNP-A abnormalities detected.

This association remained significant in a multivariate analysis including MC karyotype (i.e., normal, abnormal, non-informative) (P =0.021 ).

A validation of the prognostic classification was performed in an independent subsequent cohort treated with an equivalent induction remission regimen (n=127) and similar response of prognostic cytogenetic subgroups (OS P =0.016 logrank test and RFS P= 0.013 logrank test; Figure 6A and B). The same SNP-A analysis criteria was used with the exception that potential somatic abnormalities were not verified in a corresponding remission sample. Thus, the second cohort included induction failures and very adverse cases i.e., with deletions on chromosome 5. Finally, the median age was higher (62 vs. 42 years) and chromosome 16 abnormalities were less frequent because of a separate treatment protocol for inv16 and other core-binding factor (CBF) AML. Nevertheless, worse outcome of patients with unfavourable SNP-A abnormalities for OS and RFS was confirmed (P <0.0001 , HR =1 .38, 95%CI =1 .20-1 .59 and P =0.002, HR =1 .71 , 95%CI =1 .23-2.46, Figure 6C and D). One year OS was 31 % vs. 75%, and one year RFS was 28% vs. 64%. Multivariate analysis (Table 6) confirmed the independent prognostic impact of unfavourable SNP-A abnormalities on OS after adjusting for prognostic cytogenetics (P =0.0082, HR =1 .26, 95%CI =1 .06-1 .50) or after adjusting for ELN classification (P =0.0051 , HR =1 .28, 95%CI =1 .08-1 .51 ). Independent significance was not detected for RFS.

The inventors have thus shown and validated independent prognostic significance of novel unfavourable SNP-A abnormalities on OS in a total of three different cohorts of AML. 2.6 Genes affected by recurrent negative SNP-A abnormalities

Several candidate genes affected recurrently by SNP-A abnormalities were identified. Six patients presented abnormalities on chromosome 2 DNMT3A (DNA (cytosine-5-)-methyltransferase 3 alpha) which is located at 2p23 and ASXL2 (additional sex combs like 2) at 2p24.1 . SNP-A abnormalities were also recurrent at 1 1 p13, a region containing the genes PAX6 (paired box gene 6) and WT1 (Wilms tumor 1 ). On chromosome 17, three patients had deletion of TP53 (tumor protein p53) at 17p13.1 . Finally, region 21 q22.12 was found affected in seven patients. This region contains RUNX1 (runt-related transcription factor 1 ) and SETD4 (SET domain containing 4). 3. Discussion

In this example, the prognostic relevance of acquired SNP-A abnormalities in AML was evaluated and it's potential to improve recognized risk classification.

Somatic genetic abnormalities in AML using high-resolution SNP-A have been previously detected by others and by the inventors. Similar to the inventors study, somatic SNP-A abnormalities were frequent and occurred in 57% of AML. Interestingly, they were more frequent in undifferentiated AML FAB M0. AML with adverse and favourable cytogenetics were expected to have more SNP-A abnormalities. Furthermore, abnormalities were detectable in AML with normal cytogenetics as it was shown (Walter M.J. et ai, 2009, Proc Natl Acad Sci U S A, 106(31 ): 12950-12955). Certain metaphase cytogenetic abnormalities were undetectable by SNP-A; and balanced chromosomal alterations are known to be difficult to identify by SNP-A. More importantly, in all cytogenetic subgroups a large number of additional abnormalities by SNP-A was identified by the inventors.

Previous study showed that UPD occurs at a frequency of 12 to 29% in AML samples which is consistent with finding in the present cohort (16% of UPD). In the present study, the presence of UPD was not associated with outcome and did not add any prognostic significance to CNA detected by SNP-A, which is in contrast to a previous report.

Consistent with recent publications the inventors found an association of the total number of SNP-A abnormalities with overall survival (P =0.016, HR =1 .15, 95%CI =1 .03- 1 .30). Furthermore, three or more SNP-A abnormalities detected were found to be significantly associated to inferior overall survival (P =0.019, HR =2.54, 95%CI =1 .17- 5.51 ) but this was not independent of known prognostic cytogenetics. No significance was found for RFS. Two studies only used the diagnostic sample which is prone to include extra false positives. Stringent characteristics for the initial study cohort were applied and included DNA samples from complete remission as DNA control to distinguish between acquired and germ line variants. Thus this cohort consisted of good prognosis patients i.e., achievement of complete remission after induction therapy, and relatively young age and therefore did not include remission induction failures and very bad prognosis patients. Alternatively, peripheral T-lymphocytes and buccal DNA has been used to control for germline variation. In which case bad prognosis patients are included in the study and statistical significance is easier to attain. Another smaller study of AML used skin biopsies as normal DNA controls did not find any association of total number of SNP-A abnormalities and outcome.

More importantly, the hypothesis of the inventors was that not all genetic abnormalities are equally causing worse prognosis. Specifically, higher frequency of these unfavourable abnormalities found on chromosomes 2, 1 1 , 17 and 21 was associated with worse overall treatment response (OS, P <0.0001 , HR =1 .64, 95%CI =1 .33-2.02) and with worse relapse-free survival (RFS, P =0.0022, HR =1 .39, 95%CI = 1 .13-1 .72). Multivariate analysis confirmed independent prognostic impact of unfavourable SNP-A abnormalities with prognostic cytogenetics (P =0.013, HR =1 .43, 95%CI =1 .08-1 .90) or with the European Leukemia Net (ELN) classification (P =0.013, HR =1 .45, 95%CI =1 .08-194). The number of unfavourable SNP-A abnormalities was significantly associated with OS and RFS in both validation cohorts of adult AML (P <0.0001 , HR =1 .38, 95%CI =1 .20-1 .59 and P =0.002, HR =1 .71 , 95%CI =1 .23-2.46). Multivariate analysis was validated similarly with prognostic cytogenetics (P =0.0082, HR =1 .26, 95%CI =1 .06-1 .50) or with ELN classification (P =0.0051 , HR =1 .28, 95%CI =1 .08-1 .51 ) in both cohorts.

Failure of conventional cytogenetics occurs in about 10% of AML at diagnosis, as actively dividing cells ex vivo are necessary to obtain metaphase chromosomes. Interestingly, 60% of patients with unsuccessful or non-informative cytogenetics in the cohort had abnormalities detected by SNP-A. Moreover, it was found that non-informative cytogenetics was associated with SNP-A abnormalities implicating multiple chromosome within the same patient. This underlines the interesting hypothesis that karyotyping failure may be due to increased genomic instability in AML cells and thus may not be just a technical problem. Furthermore, identification of abnormalities by SNP-A is easily accessible for samples for which classical cytogenetic methods fail and which are thus non-informative.

SNP array analysis may be useful to better define prognostic subgroups in addition to conventional cytogenetics and may identify candidate genes implicated in leukemogenesis or disease progression. New potentially disease-causing genetic alterations may be found enhancing treatment stratification and identifying potential new candidate genes involved in leukemogenesis and/or disease progression for targeted therapy.

In conclusion, the inventors showed independent relevance of unfavourable SNP- A abnormalities compared to conventional cytogenetics and molecular diagnosis. The new classification refines prognosis of all cytogenetic subgroups but in particular intermediate and the non-informative AML are much better classified. These findings suggest concurrent SNP-A analysis may improve current prognostic risk stratification of AML, in particular in cases where conventional cytogenetics is unsuccessful.

Claims

An in vitro method for diagnosing acute myeloid leukemia (AML) in a subject, comprising determining, in a biological sample from the subject which includes nucleic acids, the presence and/or number of copy number variations on chromosomes 2, 1 1 , 17, 21 and wherein the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject suffers from AML.

An in vitro method for determining survival prognosis in a subject suffering from acute myeloid leukemia (AML), comprising determining, in a biological sample from the subject which includes nucleic acids, the presence and/or number of copy number variations on chromosomes 2, 1 1 , 17, 21 and/or 16,

wherein the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject has a reduced chance of overall survival after diagnosis than a subject suffering from AML who does not display any copy number variations on chromosomes 2, 1 1 , 17 and/or 21 , and/or

wherein the presence of at least one copy number variation on chromosome 16 indicates that the subject has an improved chance of survival than a subject suffering from AML who does not display any copy number variations on chromosome 16.

The method according to claim 2, wherein the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject has a 2- year overall survival (OS) chance of less than 70%.

The method according to claim 2 or 3, wherein the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject has a reduced chance of relapse-free survival after diagnosis than a subject suffering from AML who does not display any copy number variations on chromosomes 2, 1 1 , 17 and/or 21 ; and/or

wherein the presence of at least one copy number variation on chromosome 16 indicates that the subject has an improved chance of relapse-free survival than a subject suffering from AML who does not display any copy number variations on chromosome 16.

The method according to claim 4,

wherein the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject has a 2-year relapse free survival (RFS) chance of less than 50%.

A method for risk stratification of a subject suffering from AML, comprising:

a) determining, in a biological sample from the subject which includes nucleic acids, the presence and/or number of copy number variations on chromosomes 2, 1 1 , 17, 21 and/or 16, and

b) based on the number of copy number variations determined in step a), classifying the subject as being at high risk or at low risk of death,

wherein the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject is at high risk of death and the absence of any copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject is at low risk of death, and/or

wherein the presence of at least one copy number variation on chromosome 16 indicates that the subject is at low risk of death and the absence of any copy number variation on chromosomes 16 indicates that the subject is at high risk of death.

A method for predicting a clinical outcome in response to a treatment of AML in a subject comprising

determining, in a biological sample from the subject which includes nucleic acids, the presence and/or number of copy number variations on chromosomes 2, 1 1 , 17, 21 and/or 16,

wherein the presence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 indicates that the subject has an increased risk of relapsing after being treated than a subject suffering from AML who does not display any copy number variations, and/or

wherein the presence of at least one copy number variation on chromosome 16 indicates that the subject has a decreased risk of relapsing after being treated than a subject suffering from AML who does not display any copy number variations.

8. The method according to claim 7, wherein the treatment of AML is chosen from the group consisting of bone marrow transplant, chemotherapy and/or radiation therapy.

9. A method for selecting a subject who suffers from AML which comprises:

a) determining, in a biological sample from the subject which includes nucleic acids, the presence and/or number of copy number variations on chromosomes 2, 1 1 , 17 and/or 21 , and

b) selecting the subject based on the presence or absence of at least one copy number variation on chromosomes 2, 1 1 , 17 and/or 21 .

10. The method according to claim 9,

wherein said method is for selecting a subject with AML who is likely to be in need of a bone marrow transplant, and said subject is selected as likely to be in need of a bone marrow transplant if said subject harbours at least one copy number variation on chromosome 2, 1 1 , 17 and/or 21 .

1 1 . The method according to any of claims 2 to 10, wherein the subject suffering from AML has beforehand been classified by cytogenetic metaphase R-banding analysis.

12. The method according to any of claim 1 to 13, wherein the presence and/or number of copy number variations on chromosomes 2, 1 1 , 17, 21 and/or 16 is determined using a high-throughput single nucleotide polymorphism array.

13. The method according to claim 12, wherein the high-throughput single nucleotide polymorphism array is performed with a minimal size of segments for copy number variations of 50 kB.

14. The method according to any one of claims 1 to 13, wherein the at least one copy number variation is an acquired or somatic copy number variation.

15. A method for treating AML in a subject in need thereof, comprising the steps of: a) determining, in a biological sample from the subject which includes nucleic acids, the presence and/or number of copy number variations on chromosomes 2, 1 1 , 17 and/or 21 , and

b) if at least one copy number variation is determined on chromosomes 2, 1 1 , 17 and/or 21 at step a), performing a bone marrow transplant and/or intensified chemotherapy or a combination thereof in said subject.