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  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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  • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
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  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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  • C12Q2600/00—Oligonucleotides characterized by their use
  • C12Q2600/156—Polymorphic or mutational markers

Definitions

• the present invention relates generally to the fields of pharmacogenetics and cancer therapy. More particularly, it concerns methods and compositions for predicting or anticipating the level of toxicity of irinotecan and other compounds glucuronidated by a UGT enzyme in a patient. Such methods and compositions can be used to evaluate whether irinotecan-based therapy or therapy involving a UGT substrate may pose toxicity problems if given to a particular patient. Alterations in suggested therapy may ensue if toxicity may pose a problem.
• Irinotecan is a topoisomerase I inhibitor that is approved worldwide for the treatment of metastatic colorectal cancer.
• Irinotecan has a well established role as single agent in 5- fluorouracil-refractory patients (Rougier et al., 1998; Cunningham et al., 1998), as well as in combination with 5-fluorouracil/leucovorin as a first-line therapy (Saltz et al., 2000; Rothenberg et al., 2001). Its role in the adjuvant setting is being explored.
• irinotecan treatment is associated with significant toxicity.
• the main severe toxicities of irinotecan are delayed diarrhea and myelosuppression.
• grade 3-4 diarrhea occurred in about one third of patients and was dose limiting (Negoro et al., 1991; Rothenberg et al., 1993). Its frequency varies from study to study and is also schedule dependent. The frequency of grade 3-4 diarrhea in the three- eekly regimen (19%) is significantly lower compared to the weekly schedule (36%, Fuchs et al., 2003).
• grade 3-4 neutropenia is also a common adverse event, with about 30-40% of the patients experiencing it in both weekly and three- weekly regimens (Fuchs et al., 2003; Nanhoefer et al., 2001). Fatal events during irinotecan treatment have been reported. A high mortality rate of 5.3 and 1.6% was reported in the weekly and three- weekly single agent irinotecan regimens, respectively (Fuchs et al., 2003). While some information may be known about how to predict the patients who will eventually suffer intolerable toxicities (Ratain, 2002), additional information can be useful.
• Irinotecan hydrolysis by carboxylesterase-2 is responsible for its activation to SN-38 (7-ethyl-10-hydroxycamptothecin), a topoisomerase I inhibitor of much higher potency than irinotecan (ref).
• the main inactivating pathway of irinotecan is the biotransformation of active SN-38 into inactive SN-38 glucuronide (SN-38G). Interpatient differences in systemic formation of SN-38G have been shown to have clear clinical consequences in patients treated with irinotecan.
• SN-38 is glucuronidated by UDP-glucuronosyltransferase 1A1 (UGTIAI) (Iyer et al., 1997)
• the UGTIAI genetic variation has been extensively investigated in relation to hyperbilirubinemic syndromes, as UGTIAI enzyme catalyzes the glucuronidation of bilirubin (ref).
• a variable number of repeats (5, 6, 1, and 8) have been found in the UGTIAI TATA box.
• Gene transcriptional efficiency has been inversely correlated to the number of TA repeats (Beutler et al., 1998).
• Homozygosity for the (TA) 7 allele has been associated with the classical picture of Gilbert's syndrome, a common mild hyperbilirubinemia (Burchell et al.; Monaghan et al.).
• Gilbert's syndrome has also been associated with missense coding variants in the UGTIAI gene, in particular in Asian populations where these variants are relatively common.
• UGTIAI is the candidate gene to be investigated in order to predict the events of severe toxicity after irinotecan treatment.
• the present invention is based on the observation that the nucleotide at position -3516 in the UGTIAI upstream region is correlated with irinotecan toxicity.
• An A at that position positively correlates with irinotecan toxicity while a G at that position correlates with tolerance to irinotecan.
• the present invention concerns methods and compositions for evaluating, predicting, and determining whether a patient will experience toxicity from irinotecan.
• Toxicity from irinotecan evidences itself as side effects from the drug, which are well known to oncologists and their patients.
• Methods involve determining the nucleic acid sequence of base -3516 in the UGTIAI promoter in one or both alleles of the patient.
• the presence of an A nucleotide indicates the person is at risk for irinotecan toxicity.
• An AA genotype is more closely correlated with grade 4 neutropenia than other genotypes at that position. Moreover, in some embodiments, this is unrelated to the genotype of the TA indel in the UGTIAI promoter.
• methods also include determining the sequence of other polymorphisms or indels (insertion/deletions) in linkage disequilibrium (LED) with the -3516 variant. Therefore, in some embodiments of the invention, the TA indel is evaluated to determine the number of repeats. Also, any other variant in UGTIAI or any other gene (the term "gene" includes non- coding regions that affect the expression or activity level of the encoded polypeptide) may be evaluated for variants in LED with the -3516 variant.
• Compositions of the invention include nucleic acids that can be used to determine the sequence at position -3516 of UGT 1 A or other reagents in that regard. Arrays and other assays for screening multiple samples are also included as part of the invention.
• Metabolism of SN-38, an active metabolite of irinotecan, via glucuronidation represents a mechanism to protect patients from the toxic effects of irinotecan, thus a reduction in SN-38 glucuronidation contributes to the probability that toxicity associated with irinotecan may be experienced in patients. While some genetic basis for reduced SN-38 glucuronidation have been identified, other basis have yet to be identified. Therefore, there remains a need for improved methods and compositions for evaluating polymorphisms in one or both UGTIAI genes of a patient and correlating a genotype with adverse effects of various therapies.
• the present invention is based on the fact that genetic variation is correlated with UGTIAI expression and has several important clinical implications.
• the improved methods and compositions of the present invention may be used in determining if a treatment has a propensity to adversely affect a patient or what treatment may be appropriate or inappropriate for a particular patient.
• UGTIAI basal transcription is affected by a polymorphic (TA) repeat (see Fig. 4, legend in Innocenti et al, 2002), in addition to a phenobarbital-responsive enhancer module (PBREM) that contains variants affecting inducible gene expression, as described herein.
• TA polymorphic
• PBREM phenobarbital-responsive enhancer module
• a "polymorphism” or “genetic polymorphism,” as referred to herein, is the existence of two or more variant forms of a particular characteristic, e.g., a single nucleotide or a repeat a nucleotide or nucleotides. Generally, variations are due to the addition, deletion, or substitution of one or more nucleotides at a site or a variation in the number of tandem repeats of a DNA sequence.
• other polymorphisms within or outside the UGT1 gene locus see Genbank accession number AF297093 which is incorporated herein by reference, may be used as long as an association of a polymorphism with a particular phenotype and/or haplotype can be established. Exemplary methods for genotyping a UGT1A gene may be found at least in U.S. Patents 6,479,236, 6,472,157 and 6,395,481, each of which is incorporated herein by reference.
• significant linkage disequilibrium between a (TA) polymorphism and variants in the PBREM, or other variants within or outside the UGT1 gene locus indicates that patients possessing such other variants may be at risk of irinotecan toxicity.
• “Significant” as used in respect to linkage disequilibrium is contemplated to be a statistical p or ⁇ value that may be 0.25 or 0.1 and may be 0.1, 0.05. 0.001, 0.00001 or less.
• Linkage disequilibrium refers to a situation where a particular combination of alleles (i.e., a variant form of a given gene) or polymorphisms at two loci appears more frequently than would be expected by chance.
• the relationship between PBREM-(TA) n haplotypes and the glucuronidation rate of the UGTIAI substrate SN-38 may be used to correlate the genotype (i.e., the genetic make up of an organism) to a phentoype (i.e., the physical traits displayed by an organism or cell).
• Haplotype is used herein to refer to a collective genotype of two or more closely linked loci.
• Each haplotype defines the sequence of alleles or polymorphisms along one of the homologous chromosomes.
• the polymorphisms may be 0.001, 0.01, 0.1, 0.2 cM or more within one another.
• Various embodiments of the invention include methods for evaluating the risk of toxicity from irinotecan, or other UGTIAI substrates, in a patient.
• a polymorphism may be a single nucleotide polymorphism (SNP) and may be in linkage disequilibrium with a (TA) n repeat, h certain embodiments, the methods include detecting one or more polymorphisms in one or both copies of the UGTIAI gene and/or one or both copies of any other gene located in the UGT1 gene locus of a patient. In particular embodiments a promoter polymorphism is detected. It is specifically contemplated that methods and compositions of the invention may be implemented to determine whether UGTIAI polymorphisms are present or absent in one or both alleles.
• a polymorphism may be a polymorphism that affects the transcription of UGTIAI, such as in the promoter region or 5' flanking region that affects transcription (which includes the promoter region), and in particular a polymorphism at nucleotide position -3440, -3401, -3279, -3177, -3175, or -3156 from the UGTIAI gene transcriptional start site, which is designated +1 with no nucleotide designated as 0.
• the number of TA repeats can be 5, 6, 1, 8 or more TA repeats.
• the polymorphism is the following: -3440C>A, -3401T>C, -3279G>T, -31770G, -
• the notation -3440C>A indicates that cytosine nucleotide (C) at the -3440 position is replaced by an Adenosine (A).
• Methods of the invention may include obtaining a nucleic acid sample from a patient and detecting one or more polymorphisms in the UGTIAI gene using various methods.
• polymorphism detection may include amplifying a nucleic acid containing all or part of a particular region of the UGTIAI gene to obtain amplification products; and/or analyzing the amplification products for the presence or absence of one or more polymorphisms.
• Other methods of polymorphism detection known in the art are also contemplated.
• a promoter polymorphism of a UGTIAI gene may be detected by performing one of a variety of known assays. These may include, but are not limited to hybridization assays, sequencing or microsequencing assays, allele-specific amplification assays or any other methods known for detecting nucleic acid polymorphisms, which may or may not include amplification of a nucleic acid. It is understood that "detecting" a polymorphism includes identifying the nucleotide sequence at that site and/or determining whether the polymorphism is present or absent.
• a correlation between one or more polymorphisms and the glucoronidation rate of irinotecan or other substrates of UGTIAI including but not limited to bilirubin, estriol, beta- estradiol, 2-hydroxyestriol, 2-hydroxyestrone, 2-hydroxyestradiol, thyroxme (T4), rT3, octyl gallate, propyl gallate, anthraflavic acid, quercitin, fisetin, naringenin, 1-naphtol, and ethynylestradiol, may be used to determine various aspects of a treatment regime, including irinotecan and/or other drugs or compounds metabolized directly or indirectly by UGTIAI.
• the methods also include analyzing the glucuronidation rate associated with the various polymorphisms and polymorphism combinations, for exemplary methods and compositions related to analysis of glucuronidation rates see U.S. Patent 6,319,678, which is incorporated herein by reference.
• the methods may also include determining the biliary transport capacity of the patient.
• the evaluation of the promoter polymorphism may be used to optimize the dose of irinotecan or other compounds for treatment of a patient or to reduce their toxicity.
• the methods of the invention may further include treating a patient by administering to the patient irinotecan in combination with other pharmaceutical agents at appropriate dosages, such that the toxicity of irinotecan or other substrates of UGTIAI are reduced.
• a second agent that reduces excretion of an active irinotecan species through the bile may administered in conjunction with irinotecan based upon determinations made using methods and compositions of the invention, for related methods and compositions see U.S. Patents 6,407,117, 6,287,834 and 5,786,344, each of which is incorporated herein by reference.
• the present invention is also based on the observation that the nucleotide at position -
• the present invention concerns methods and compositions for evaluating, predicting, and determining whether a patient will experience toxicity from irinotecan. Toxicity from irinotecan evidences itself as side effects from the drug, which are well known to oncologists and their patients.
• there are methods of predicting whether a patient may suffer or be subject to toxicity from irinotecan if given it involving determining the nucleic acid sequence of base -3516 in the UGTIAI 5' flanking region in one or both alleles of the patient.
• the presence of an A nucleotide indicates the person is at risk for irinotecan toxicity.
• An AA genotype is more closely correlated with grade 4 neutropenia than other genotypes at that position. Moreover, in some embodiments, this is unrelated to the genotype of the TA indel in the UGTIAI promoter.
• methods also include determimng the sequence of other polymorphisms or indels (insertion/deletions) in linkage disequilibrium (LD) with the -3516 variant. Therefore, in some embodiments of the invention, the TA indel is evaluated to determine the number of repeats. Also, any other variant in UGTIAI or any other gene (the term "gene" includes non-coding regions that affect the expression or activity level of the encoded polypeptide) may be evaluated for variants in LD with the -3516 variant.
• kits for evaluating the risk of irinotecan toxicity in a patient.
• the kit may include a variety of containers, reagents and the like.
• the kit may include an oligonucleotide primer to amplify a promoter region of a UGTIAI gene or genes, haplotype tag SNPs or allele specific amplification primers of the UGTIAI gene or any other primer within the UGT1 gene locus.
• the haplotype tag SNPs or allele specific primers may be used to amplify a polymorphism at one or more nucleotide positions of the UGTIAI gene or other UGT1 locus gene.
• the nucleotide position may be at -3440, -3401, -3279, -3177, -3175, or -3156, or a combination thereof, from the UGTIAI gene transcriptional start site.
• the kit may include the haplotype tag SNPs or allele specific amplification primers in multi-well assay plate.
• the kit may also include haplotype tag SNPs or allele specific hybridization probes for a variety of promoter polymorphisms.
• the haplotype tag SNPs or allele specific hybridization probes may detect polymorphisms at nucleotide position -3440, -3401, -3279, -3177, -3175, or -3156 from the UGTIAI gene transcriptional start site.
• the kit may include haplotype tag SNPs or allele specific hybridization probes comprised in an oligonucleotide array or microarray.
• compositions of the invention include nucleic acids that can be used to determine the sequence at position -3516 of UGT 1 A or other reagents in that regard. Arrays and other assays for screening multiple samples are also included as part of the invention. Such compositions may be incorporated into kits or as part of a kit, along with any other composition discussed herein.
• FIG. 2 Pre-treatment total bilirubin levels and distribution of the -3156 genotypes within each TA indel genotype.
• FIG. 3 Correlation between ln(ANC nadir) and pretreatment total bilirubin levels. Patients with bilirubin levels less than 0.6 mg/dl are depicted in squares. Those with bilirubin levels higher than 0.7 mg/dl are depicted in circles.
• the present invention provides improved methods and compositions for identifying the effects of various polymorphisms, promoter polymorphisms or any combination thereof on the expression of UGTIAI or the glucuronidation rate of UGTIAI for the evaluation of the potential or risk for irinotecan toxicity in an individual or patient.
• the development of these improved methods and compositions allows for the use of such an evaluation to optimize treatment of a patient and to lower the risk of toxicity.
• various combinations of promoter polymorphisms may be used in this evaluation, in particular, polymorphisms in the PBREM region and polymorphisms in the TA repeats may be used.
• UGTIAI basal transcription is affected by a polymorphic (TA) repeat.
• PBREM phenobarbital-responsive enhancer module
• the examples provided herein study the extent of linkage disequilibrium between the (TA) polymorphism and variants in the PBREM and UGTIAI promoter.
• the relationship between PBREM-(TA) n haplotypes and the glucuronidation rate of the UGTIAI substrate SN-38 is also addressed herein. Studies described in the Examples illustrate that SN-38G formation rates were correlated with (TA) genotypes and promoter variants. In vaious aspects particular (TA) variants are in linkage disequilibrium with various other polymorphisms.
• Certain aspects of the invention are based on, but not limited to, the observation and characterization of novel polymorphisms in the PBREM region of the UGTIAI gene. Due to the clinical implications of genetically modified regulation of UGTIAI activity, the PBREM region was sequenced and polymorphisms in the TATA box of the UGTIAI promoter genotyped, as described in the Examples section below.
• UGT enzymes are broadly classified into two distinct gene families.
• the UGT1 locus codes for multiple isoforms of UGT, all of which share a C-terminus encoded by a unique set of exons 2-5, but which have a variable N-terminus encoded by different first exons, each with its own independent promoter (Bosma et al, 1992; Ritter et al, 1992).
• the variable first exons confer the substrate specificity of the enzyme.
• Isoforms of the UGT2 family are unique gene products of which at least eight isozymes have been identified (Clarke et al. Handbook of Experimental Pharmacology 1994).
• the UGTIAI isoform is the major bilirubin glucuronidation enzyme. Genetic defects in the UGTIAI gene can result in decreased glucuronidation activity which leads to abnormally high levels of unconjugated serum bilirubin that may enter the brain and cause encephalopathy and kernicterus (Owens & Ritter, 1995). This condition is commonly known as Gilbert's syndrome.
• the molecular defect in Gilbert's Syndrome is a change in the TATA box within the UGTIAI promoter (Bosma et al, 1995 and Monaghan et al, 1996).
• This promoter usually contains a (TA) 6 TAA element, but another allele, termed UGT1A1*28 or allele 7, is also present in human populations at high frequencies, and contains the sequence (TA) 7 TAA.
• UGT1A1*28 or allele 7 is also present in human populations at high frequencies, and contains the sequence (TA) 7 TAA.
• This polymorphism in the promoter of the UGTIAI gene results in reduced expression of the gene and accounts for most cases of Gilbert's Syndrome (Bosma et al, 1995).
• gene expression levels for the UGTIAI promoter alleles are inversely related to the length of the TA repeat in the TATA box.
• UGTs have been shown to contribute to the detoxification and elimination of both exogenous and endogenous compounds.
• one typical role of the UGTIAI isoform is the glucuronidation of SN-38 (7-ethyl-10-hydroxycamptothecin) to the corresponding glucuronide (lO-O-glucuronyl-SN-38, SN-38G) as well as the glucuronidation of TAS-103 (6- [ [2-(dimethylamino)ethyl] amino] -3 -hydroxy-7H-indeno [2, 1 -c] quinoline-7-one dihydrochloride) to its corresponding glucuronide (TAS-103G).
• SN-38 is the active form of irinotecan (CPT-11, 7-ethyl-10-[4-(l-piperidino)-l-piperidino]carbonyloxycamptothecin), which is a camptothecin derivative used in the treatment of metastatic colorectal cancer and other malignancies.
• the metabolism of SN-38 and TAS-103 are merely illustrative of the present invention the metabolism of other UGTIAI substrates is also contemplated, such as estradiol, bilirubin, simple phenols, flavones, C18 steroids, complex phenols and coumarins.
• Irinotecan is biotransformed by tissue and serum carboxylesterases to an active metabolite, SN-38, which has a 100- 1,000-fold higher antitumor activity than irinotecan.
• SN- 38 is glucuronidated by hepatic uridine diphosphate glucuronosyltransferases (UGTs) to form SN-38 glucuronide (10O-glucuronyl-SN-38, SN-38G), which is inactive and excreted into the bile and urine although, SN-38G might be deconjugated to form SN-38 by intestinal ⁇ - glucuronidase enzyme (Kaneda et al, 1990).
• irinotecan-induced diarrhea can be serious and often does not respond adequately to conventional antidiarrheal agents (Takasuna et al, 1995).
• This diarrhea may be due to direct enteric injury caused by the active metabolite, SN-38, which has been shown to accumulate in the intestine after intra peritoneal administration of irinotecan in athymic mice (Araki et al, 1993).
• isoforms of the UGT1 family are the predominate isoforms involved in TAS-103 glucuronidation
• the isoform of the UGT2 family may also participate in TAS-103 glucuronidation. Failure to glucuronidate SN-38 and TAS-103 in these instances may result specifically from the genetic defect in UGT1 gene family.
• individuals with the 8 allele may also have differing susceptibility to xenobiotics when compared to other genotypes when those compounds are metabolized by UGTIAls.
• the presence of the 5 allele that correlates with increased gene expression and higher glucuronidation activity may result in the administration of less than optimum drug dosages.
• the increased glucuronidation activity may cause more of the drug to be converted into the inactive metabolite in a shorter period, thereby reducing the drug's effectiveness.
• decreased glucuronidation activity may cause less of the activated form of the drug or xenobiotic to be available.
• alleles 6 and 7 also appears to differ significantly across ethnic groups, with Asian and Amerindian populations showing the highest frequencies of allele 6. Conversely, alleles 6 and 7 occur at intermediate and similar frequencies among Caucasians and Sub-Saharan Africans.
• Several hypotheses may be proposed regarding the selective pressures that might be responsible for the observed pattern of inter-population variation at the UGTIAI promoter. It was previously proposed that the maintenance of intermediate levels of bilirubin is adaptive (Beutler et al, 1998), and that the alleles at this promoter would be maintained in the population by balancing selection. This hypothesis is based on the observation that bilirubin is a potent antioxidant likely to have physiological significance (Stocker et al, 1987).
• glucuronidation is an important detoxification step for many endogenous as well as exogenous compounds (Clarke & Burchell, 1994).
• UGTIAI is likely to act on other substrates present in the environment, e.g., dietary bomponents, environmental pollutants and carcinogens ⁇ which require detoxification as well as playing a role in the metabolism of bilirubin and other endogenous compounds.
• maintaining high levels of UGTIAI gene expression would ensure rapid elimination of toxic or endogenous compounds and be advantageous.
• pairwise linkage disequilibrium was separately assessed in Caucasians and African- Americans, highly significant linkage disequilibrium was similarly detected in Caucasians (P ⁇ 0.0001). In African-Americans, pairwise linkage disequilibrium was also detected between all sites, however, the level of significance varied greatly between the pairwise comparisons.
• Haplotypes I-V include the (TA) 6 allele, and haplotype I differs from haplotype II at position -3279 in the NR3 domain of PBREM.
• Haplotypes VI, VII and VIJJ include the (TA) 7 repeat and haplotypes VI and VII differ from each other at position -3156. There is a suggestion that the haplotype structure of the (TA) 6 allele is different in the African-American subsample.
• haplotypes were found in Caucasians. In Caucasians, the most frequent haplotype pairs are I/VI (0.35), I/I (0.24) and I/II (0.11), while in African-Americans, they are I/II (0.11), II/VI (0.11), II/VIII (0.08), I/VI (0.08), II/NII (0.08) and NLNI (0.08).
• the effective numbers of haplotypes which reflect how many relatively high frequency haplotypes are observed, were 5.2 and 2.6 in African- Americans and Caucasians, respectively (table below).
• diversity ( ⁇ SD) of (TA) 6 haplotypes was 0.555 ⁇ 0.070 and 0.262 ⁇ 0.065 in African-Americans and Caucasians, respectively (P ⁇ 0.05).
• Haplotype structure of promoter mutations and haplotype frequencies The effective number of haplotypes is also reported.
• UGTIAI activity was measured as S ⁇ -38 glucuronidation rates in 83 human liver microsomes. A 46% coefficient of variation (1.90 f 0.87 SN-38G/IS, mean f SD) and a 10- fold range in SN-38 glucuronidation were observed.
• Exonuclease I and shrimp alkaline phosphatase were purchased from USB (Cleveland, Ohio, USA).
• ABI Big Dye terminator cycle-sequencing kit was purchased from Applied Biosystems (Foster City, California, USA).
• Primers for amplification, sequencing of the PBREM, and amplification of the (TA) n polymo ⁇ hism were obtained from GibcoBRL (hivitrogen Co., Carlsbad, California, USA).
• SN-38 was kindly provided by Dr Kiyoshi Terada (Yakult Honsha Co., Ltd, Japan).
• Camptothecin, UDPGA, magnesium chloride, trizma base, potassium monohydrogen phosphate and 1-heptanesulfonic acid were purchased from Sigma-Aldrich (St. Louis, Missouri, USA). Acetonitrile, tetrahydrofuran and hydrochloric acid were obtained from Fisher Scientific (Hanover, Illinois, USA). b. Human livers
• PAAR Pharmacogenetics of Anticancer Agents Research
• liver samples consistently comprised in the 10th percentile of UGTIAI, UGT1A9 and UGT2B7 activities were sought.
• UGT1A9 and UGT2B7 activities were measured using specific probes (data not shown) (Ramirez et al, 2002 and Innocenti, et al, 2001).
• Out of eight samples within the 10th percentile of UGTIAI only one sample was comprised within the 10th percentile of activities of the other two enzyme activities.
• primers flank the polymo ⁇ hic TA locus in the promoter region of the UGTIAI gene and amplify a 98bp fragment when a (TA) 6 allele is present and a 100 bp fragment when a (TA) allele is present.
• 96 bp and 102 bp alleles are amplified.
• the reverse primer is labeled with a fluorescent dye at its 5'-end to permit visualization of the amplification product.
• the amplification reactions were performed in a lO ⁇ l volume consisting of 1.5 mmol Mg l 2 , 250 mmol dNTPs, 0.8 mmol of each primer and 0.5 U of Taq polymerase (Amplitaq Gold from Applied Biosystems).
• the polymerase was activated at 95°C for 10 min and DNA amplified for 35 cycles at 95°C for 30 sec, 55°C for 30 sec and 72°C for 30 sec, followed by a final extension at 72°C for 10 min.
• Control DNAs from individuals known to have a 616, 6/1 and 7/7 genotype were included in the PCR analysis. PCR fragments were subjected to gel electrophoresis on an ABI 377 DNA analyzer (Applied Biosystems).
• Amplified products were diluted in a formamide and dextran blue loading buffer and 1 ⁇ l combined with 1 ⁇ l of size standard (GS-350 from Applied Biosystems), denatured at 95°C, and loaded onto a 6% denaturing polyacrylamide gel. Electrophoresis was performed for 3.5 hours following manufacturers recommendations. The Genescan and Genotyper software (version 3.7, Applied Biosystems) was used to analyze fragments for size determination. d. Sequencing of PBREM
• a 606 bp region (-3641 to -3036) including PBREM was successfully PCR-amplified and sequenced in 81 of the 83 human liver DNAs and 22 of the 24 DNA samples from African- American individuals (Americans of African descent, born in the USA) included in the NIGMS HGCR Human NariationPanel (Coriell Institute for Medical Research, Camden, New Jersey, USA).
• the reference sequence shown in FIG. 4 is that deposited in the GenBank database (accession number AF313454).
• Amplification of the PCR product was performed in a 10 or 25-pl reaction volume using the following primers: 5'- CTGGGGATAAACATGGGATG-3' SEQ ID NO:4 (forward) and 5'- CACCACCACTTCTGGAACCT-3* SEQ ID NO:5 (reverse). These primers were designed using Primer3 software (Rozen et al, 1998). PCR conditions were 2 min at 94°C, 32 or 33 cycles of a three-step cycling program (30 sec at 94°C, 30 sec at 66.8°C and 1 min at 72°C) and 72°C for 3 min.
• this amplicon was then sequenced in the forward and reverse directions using the amplification primers, Big Dye terminator chemistry, and run on an ABI 3700 (Applied Biosystems) following the manufacturer's protocol. Sequences were analyzed and individuals genotyped using the Poly- Phred software (Nickerson et al, 1997). To determine the ancestral state of the polymo ⁇ hisms found in humans, the sequence was compared to that of baboon (accession number AC091778).
• SN- 38 glucuronidation assay in human liver microsomes Samples were phenotyped by using SN-38 as a substrate for UGTIAI.
• the incubation mixture consisted of 5 ⁇ mol SN-38, 10 mmol MgCl 2 , 1 mg/ml microsomes, 0.025 mol Tris- HC1 (pH 7.4) and 5 mmol UDP-GA. Samples were incubated for 30 min at 37°C. The reaction was stopped by the addition of methanol. These conditions were selected after previous optimization of the enzyme reaction (Iyer et al, 1998). Camptothecin (75 ng) was used as an internal standard.
• HPLC Hexachi Instruments Inc., San Jose, California, USA
• a ⁇ BondapakTM 8 column (3.9 X 300 mm, 10 ⁇ m; Waters Co ⁇ ., Milford, Massachusetts, USA) and ⁇ BondapakTM C 18 guardpak (Waters Co ⁇ .) were used.
• the eluent consisted of 30/70 acetonitrile/5 mmol sodium heptanesulfonic acid in 50 mmol potassium dihydrogen phosphate (pH 4).
• the flow rate was 0.9 ml/min.
• Retention times for SN-38G, SN-38 and camptothecin were 13.3, 18.4 and 19.3 min, respectively.
• SN-38 glucuronidation rates were reported as the ratios between SN-38 glucuronide (SN-38G) and internal standard (IS) peak heights.
• the intra-assay variability was determined by performing 10 incubations on the same day using a pool of human liver microsomes.
• the inter-assay variability was evaluated by incubating a pool of human liver microsomes in triplicate on three different days. The inter- and intra- assay variabilities were within 7%. f.
• Statistical analysis The significance of linkage disequilibrium between pairs of polymo ⁇ hic sites was assessed using genotypic data and a likelihood ratio test provided in ARLEQUTN, version 2 (Schneider et al, 2000). ARLEQUIN was also used to run a modified Markov-chain random walk algorithm to test for Hardy- Weinberg equilibrium. Next, multisite haplotypes were estimated using the program PHASE (Stephens et al, 2001). Because this program does not accept both bi- allelic and multi-allelic polymo ⁇ hic sites, haplotypes were estimated only for individuals with either the (TA) 6 or (TA) 7 alleles.
• haplotypes were determined manually by assuming that the chromosome with the (TA) 6 or (TA) 7 allele contained a haplotype previously identified by the PHASE analysis. In one case, this method would have resulted in a new (TA) 8 haplotype. However, it is more likely that this individual would instead have a novel (TA) 6 haplotype (V), which is consistent with the observation that the (TA) 6 allele is found on multiple haplotypes, including other rare ones. An incorrect assignment would have little or no affect on the subsequent analyses because the novel haplotype only occurs once out of 103 individuals and not in a sample used in studies of correlation with phenotype.
• the effective number of haplotypes was calculated as the reciprocal of the sum of the frequency squared.
• Diversity in (TA) 6 haplotypes in Caucasians and African-Americans based on the numbers and frequencies of haplotypes and adjusted by sample size, was estimated by DnaSP version 3.53 (Rozas et al.) as well as their SDs.
• Statistical significance was assessed using a t-test as previously described (Nei, 1987).
• the chi-square test was used to analyze the differences in genotype/haplotype frequencies between Caucasians and African- Americans .
• UGTIAI activity was phenotyped by measuring SN-38 glucuronidation rates of each liver as the mean ⁇ SD of a single experiment performed in triplicate.
• genotypes expressed as the sum of TA repeats in both chromosomes (i.e., in samples with ⁇ 12 (5/6, 6/6, 5/7), 13 (6/7) and ⁇ 14 (7/7, 6/8, 7/8) TA repeat genotypes).
• haplotype-phenotype relationship two-sided exact Wilcoxon tests were used to compare the S ⁇ -38 glucuronidation rates between two haplotypes.
• SAS system SAS Institute, hie, Gary, North Carolina
• StatXact-5 CYTEL Software Co ⁇ oration, Cambridge, Massachusetts, USA
• nucleic acids including promoters, amplification primers, oligonucleotide probes and other nucleic acid elements involved in the analysis of genomic DNA.
• a nucleic acid comprises a wild- type, a mutant, or a polymo ⁇ hic nucleic acid.
• nucleic acid is well known in the art.
• a “nucleic acid” as used herein will generally refer to a molecule (i.e., a strand) of DNA, RNA or a derivative or analog thereof, comprising a nucleobase.
• a nucleobase includes, for example, a naturally occurring purine or pyrimidine base found in DNA (e.g., an adenine "A,” a guanine “G,” a thymine “T” or a cytosine “C”) or RNA (e.g., an A, a G, an uracil "U” or a C).
• nucleic acid encompass the terms “oligonucleotide” and “polynucleotide,” each as a subgenus of the term “nucleic acid.”
• oligonucleotide refers to a molecule of between about 3 and about 100 nucleobases in length.
• polynucleotide refers to at least one molecule of greater than about 100 nucleobases in length.
• a “gene” refers to coding sequence of a gene product, as well as introns and the promoter of the gene product, h addition to the UGTIAI gene, other regulatory regions such as enhancers for UGTIAI are contemplated as nucleic acids for use with compositions and methods of the claimed invention.
• a nucleic acid may encompass a double-stranded molecule or a triple-stranded molecule that comprises one or more complementary strand(s) or "complement(s)" of a particular sequence comprising a molecule.
• a single stranded nucleic acid may be denoted by the prefix "ss”, a double stranded nucleic acid by the prefix "ds”, and a triple stranded nucleic acid by the prefix "ts.”
• a nucleic acid encodes a protein, polypeptide, or peptide.
• the present invention concerns novel compositions comprising at least one proteinaceous molecule.
• a "proteinaceous molecule,” “proteinaceous composition,” “proteinaceous compound,” “proteinaceous chain,” or “proteinaceous material” generally refers, but is not limited to, a protein of greater than about 200 amino acids or the full length endogenous sequence translated from a gene; a polypeptide of greater than about 100 amino acids; and/or a peptide of from about 3 to about 100 amino acids. All the "proteinaceous” terms described above may be used interchangeably herein. 1. Preparation of Nucleic Acids
• a nucleic acid may be made by any technique known to one of ordinary skill in the art, such as for example, chemical synthesis, enzymatic production or biological production.
• a synthetic nucleic acid e.g., a synthetic oligonucleotide
• Non-limiting examples of a synthetic nucleic acid include a nucleic acid made by in vitro chemical synthesis using phosphotriester, phosphite or phosphoramidite chemistry and solid phase techniques such as described in European Patent 266,032, inco ⁇ orated herein by reference, or via deoxynucleoside H-phosphonate intermediates as described by Froehler et al, 1986 and U.S.
• Patent 5,705,629 each inco ⁇ orated herein by reference, the methods of the present invention, one or more oligonucleotide may be used.
• oligonucleotide synthesis has been disclosed in for example, U.S. Patents 4,659,774, 4,816,571, 5,141,813, 5,264,566, 4,959,463, 5,428,148, 5,554,744, 5,574,146, 5,602,244, each of which is inco ⁇ orated herein by reference.
• a non-limiting example of an enzymatically produced nucleic acid include one produced by enzymes in amplification reactions such as PCRTM (see for example, U.S. Patent 4,683,202 and U.S. Patent 4,682,195, each inco ⁇ orated herein by reference), or the synthesis of an oligonucleotide described in U.S. Patent 5,645,897, inco ⁇ orated herein by reference.
• a non-limiting example of a biologically produced nucleic acid includes a recombinant nucleic acid produced (i.e., replicated) in a living cell, such as a recombinant DNA vector replicated in bacteria (see for example, Sambrook et al. 2001, inco ⁇ orated herein by reference).
• a nucleic acid may be purified on polyacrylamide gels, cesium chloride centrifugation gradients, chromatography columns or by any other means known to one of ordinary skill in the art (see for example, Sambrook et al, 2001, inco ⁇ orated herein by reference).
• a nucleic acid is a pharmacologically acceptable nucleic acid.
• Pharmacologically acceptable compositions are known to those of skill in the art, and are described herein.
• the present invention concerns a nucleic acid that is an isolated nucleic acid.
• isolated nucleic acid refers to a nucleic acid molecule (e.g., an RNA or DNA molecule) that has been isolated free of, or is otherwise free of, the bulk of the total genomic and transcribed nucleic acids of one or more cells.
• isolated nucleic acid refers to a nucleic acid that has been isolated free of, or is otherwise free of, bulk of cellular components or in vitro reaction components such as for example, macromolecules such as lipids or proteins, small biological molecules, and the like.
• nucleic acid is a nucleic acid segment.
• nucleic acid segment are fragments of a nucleic acid, such as, for a non-limiting example, those that encode only part of a UGT1 gene locus or a UGTIAI gene sequence.
• a “nucleic acid segment” may comprise any part of a gene sequence, including from about 2 nucleotides to the full length gene including promoter regions to the polyadenylation signal and any length that includes all the coding region.
• nucleic acid segments may be designed based on a particular nucleic acid sequence, and may be of any length.
• an algorithm defining all nucleic acid segments can be created: n to n + y where n is an integer from 1 to the last number of the sequence and y is the length of the nucleic acid segment minus one, where n + y does not exceed the last number of the sequence.
• the nucleic acid segments correspond to bases 1 to 10, 2 to 11, 3 to 12 ... and so on.
• nucleic acid segments correspond to bases 1 to 15, 2 to 16, 3 to 17 ... and so on.
• the nucleic segments correspond to bases 1 to 20, 2 to 21, 3 to 22 ... and so on.
• the nucleic acid segment may be a probe or primer.
• a probe generally refers to a nucleic acid used in a detection method or composition.
• a “primer” generally refers to a nucleic acid used in an extension or amplification method or composition. 4. Nucleic Acid Complements
• the present invention also encompasses a nucleic acid that is complementary to a nucleic acid.
• a nucleic acid is "complement(s)" or is “complementary” to another nucleic acid when it is capable of base-pairing with another nucleic acid according to the standard Watson-Crick, Hoogsteen or reverse Hoogsteen binding complementarity rules.
• another nucleic acid may refer to a separate molecule or a spatial separated sequence of the same molecule.
• a complement is a hybridization probe or amplification primer for the detection of a nucleic acid polymo ⁇ hism.
• complementary also refers to a nucleic acid comprising a sequence of consecutive nucleobases or semiconsecutive nucleobases (e.g., one or more nucleobase moieties are not present in the molecule) capable of hybridizing to another nucleic acid strand or duplex even if less than all the nucleobases do not base pair with a counte ⁇ art nucleobase.
• semiconsecutive nucleobases e.g., one or more nucleobase moieties are not present in the molecule
• completely complementary nucleic acids are preferred.
• Some embodiments of the invention concern identifying polymo ⁇ hisms in UGTIAI, correlating genotype or haplotype to phenotype, wherein the phenotype is lowered or altered UGTIAI activity or expression, and then identifying such polymo ⁇ hisms in patients who have or will be given irinotecan or related drugs or compounds.
• the present invention involves assays for identifying polymo ⁇ hisms and other nucleic acid detection methods. Nucleic acids, therefore, have utility as probes or primers for embodiments involving nucleic acid hybridization. They may be used in diagnostic or screening methods of the present invention.
• nucleic acids encoding UGTIAI as well as nucleic acids involved in the expression or stability of UGTIAI polypeptides or transcripts, are encompassed by the invention.
• General methods of nucleic acid detection methods are provided below, followed by specific examples employed for the identification of polymo ⁇ hisms, including single nucleotide polymo ⁇ hisms (SNPs).
• SNPs single nucleotide polymo ⁇ hisms
• a probe or primer of between 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 and 50, 60, 70, 80, 90, or 100 nucleotides, preferably between 17 and 100 nucleotides in length, or in some aspects of the invention up to 1-2 kilobases or more in length allows the formation of a duplex molecule that is both stable and selective.
• Molecules having complementary sequences over contiguous stretches greater than 20 bases in length are generally preferred, to increase stability and/or selectivity of the hybrid molecules obtamed.
• Such fragments may be readily prepared, for example, by directly synthesizing the fragment by chemical means or by introducing selected sequences into recombinant vectors for recombinant production.
• nucleotide sequences of the invention may be used for their ability to selectively form duplex molecules with complementary stretches of DNAs and/or RNAs or to provide primers for amplification of DNA or RNA from samples.
• relatively high stringency conditions For applications requiring high selectivity, one will typically desire to employ relatively high stringency conditions to form the hybrids.
• relatively low salt and/or high temperature conditions such as provided by about 0.02 M to about 0.10 M NaCl at temperatures of about 50°C to about 70°C.
• Such high stringency conditions tolerate little, if any, mismatch between the probe or primers and the template or target strand and would be particularly suitable for isolating specific genes or for detecting a specific polymo ⁇ hism. It is generally appreciated that conditions can be rendered more stringent by the addition of increasing amounts of formamide.
• hybridization to filter-bound DNA may be carried out in 0.5 M NaHPO 4 , 7% sodium dodecyl sulfate (SDS), 1 mM EDTA at 65°C, and washing in 0.1 x SSC/0.1% SDS at 68°C (Ausubel et al, 1989).
• Conditions may be rendered less stringent by increasing salt concentration and/or decreasing temperature.
• a medium stringency condition could be provided by about ⁇ .l to 0.25M NaCl at temperatures of about 37°C to about 55°C
• a low stringency condition could be provided by about 0.15M to about 0.9M salt, at temperatures ranging from about 20°C to about 55°C.
• the washing may be carried out for example in 0.2 x SSC/0.1% SDS at 42°C (Ausubel et al, 1989).
• Hybridization conditions can be readily manipulated depending on the desired results.
• hybridization may be achieved under conditions of, for example, 50mM Tris-HCl (pH 8.3), 75mM KC1, 3mM MgCL,, OmM dithiothreitol, at temperatures between approximately 20°C to about 37°C.
• Other hybridization conditions utilized could include approximately lOmM Tris-HCl (pH 8.3), 50mM KC1, 1.5mM MgCi2, at temperatures ranging from approximately 40°C to about 72°C.
• nucleic acids of defined sequences of the present invention in combination with an appropriate means, such as a label, for determining hybridization.
• appropriate indicator means include fluorescent, radioactive, enzymatic or other ligands, such as avidin/biotin, which are capable of being detected, hi preferred embodiments, one may desire to employ a fluorescent label or an enzyme tag such as urease, alkaline phosphatase or peroxidase, instead of radioactive or other environmentally undesirable reagents.
• colorimetric indicator substrates are known that can be employed to provide a detection means that is visibly or spectrophotometrically detectable, to identify specific hybridization with complementary nucleic acid containing samples.
• a particular nuclease cleavage site may be present and detection of a particular nucleotide sequence can be determined by the presence or absence of nucleic acid cleavage.
• the probes or primers described herein will be useful as reagents in solution hybridization, as in PCR, for detection of expression or genotype of corresponding genes, as well as in embodiments employing a solid phase.
• test DNA or RNA
• RNA is adsorbed or otherwise affixed to a selected matrix or surface.
• This fixed, single-stranded nucleic acid is then subjected to hybridization with selected probes under desired conditions.
• the conditions selected will depend on the particular circumstances (depending, for example, on the G+C content, type of target nucleic acid, source of nucleic acid, size of hybridization probe, etc.). Optimization of hybridization conditions for the particular application of interest is well known to those of skill in the art.
• hybridization is detected, and/or quantified, by determining the amount of bound label. Representative solid phase hybridization methods are disclosed in U.S.
• Patents 5,843,663, 5,900,481 and 5,919,626 Other methods of hybridization that may be used in the practice of the present invention are disclosed in U.S. Patents 5,849,481, 5,849,486 and 5,851,772. The relevant portions of these and other references identified in this section of the Specification are inco ⁇ orated herein by reference. B. Amplification of Nucleic Acids
• Nucleic acids used as a template for amplification may be isolated from cells, tissues or other samples according to standard methodologies (Sambrook et al, 2001). In certain embodiments, analysis is performed on whole cell or tissue homogenates or biological fluid samples with or without substantial purification of the template nucleic acid.
• the nucleic acid may be genomic DNA or fractionated or whole cell RNA. Where RNA is used, it may be desired to first convert the RNA to a complementary DNA.
• primer is meant to encompass any nucleic acid that is capable of priming the synthesis of a nascent nucleic acid in a template-dependent process.
• primers are oligonucleotides from ten to twenty and/or thirty base pairs in length, but longer sequences can be employed.
• Primers may be provided in double-stranded and/or single-stranded form, although the single-stranded form is preferred.
• Pairs of primers designed to selectively hybridize to nucleic acids corresponding to the UGT1 gene locus (Genbank accession AF279093), UGTIAI gene and/or SEQ ID NO:l or variants thereof, and fragments thereof are contacted with the template nucleic acid under conditions that permit selective hybridization.
• SEQ ID NO:l set forth a nucleotide sequence that includes a majority of the UGTIAI gene.
• SEQ ID NO:l includes nucleotides 169,831 to 187,313 of the UGT1 gene locus with nucleotide 1645 of SEQ ID NO:l corresponding to nucleotide -3565 from the transcriptional start of the UGTIAI gene, thus the transcriptional start is located at nucleotide 5212 of SEQ ID NO:l.
• high stringency hybridization conditions may be selected that will only allow hybridization to sequences that are completely complementary to the primers. In other embodiments, hybridization may occur under reduced stringency to allow for amplification of nucleic acids that contain one or more mismatches with the primer sequences.
• the template-primer complex is contacted with one or more enzymes that facilitate template- dependent nucleic acid synthesis. Multiple rounds of amplification, also referred to as "cycles,” are conducted until a sufficient amount of amplification product is produced.
• the amplification product may be detected, analyzed or quantified, h certain applications, the detection may be performed by visual means. In certain applications, the detection may involve indirect identification of the product via chemiluminescence, radioactive scintigraphy of inco ⁇ orated radiolabel or fluorescent label or even via a system using electrical and/or thermal impulse signals (Affymax technology; Bellus, 1994).
• PCRTM polymerase chain reaction
• LCR ligase chain reaction
• European Application No. 320 308 inco ⁇ orated herein by reference in its entirety.
• U.S. Patent 4,883,750 describes a method similar to LCR for binding probe pairs to a target sequence.
• a method based on PCRTM and oligonucleotide ligase assay (OLA) (described in further detail below), disclosed in U.S. Patent 5,912,148, may also be used.
• SDA Strand Displacement Amplification
• nucleic acid amplification procedures include transcription-based amplification systems (TAS), including nucleic acid sequence based amplification (NASBA) and 3SR (Kwoh et al, 1989; PCT Application WO 88/10315, inco ⁇ orated herein by reference in their entirety).
• TAS transcription-based amplification systems
• NASBA nucleic acid sequence based amplification
• 3SR 3SR
• European Application 329 822 disclose a nucleic acid amplification process involving cyclically synthesizing single-stranded RNA ("ssRNA”), ssDNA, and double- stranded DNA (dsDNA), which may be used in accordance with the present invention.
• ssRNA single-stranded RNA
• dsDNA double- stranded DNA
• PCT Application WO 89/06700 disclose a nucleic acid sequence amplification scheme based on the hybridization of a promoter region/primer sequence to a target single-stranded DNA ("ssDNA”) followed by transcription of many RNA copies of the sequence. This scheme is not cyclic, i.e., new templates are not produced from the resultant RNA transcripts.
• Other amplification methods include "RACE” and “one-sided PCR” (Frohman, 1990; Ohara et al, 1989).
• amplification products are separated by agarose, agarose-acrylamide or polyacrylamide gel electrophoresis using standard methods (Sambrook et al, 2001). Separated amplification products may be cut out and eluted from the gel for further manipulation. Using low melting point agarose gels, the separated band may be removed by heating the gel, followed by extraction of the nucleic acid.
• Separation of nucleic acids may also be effected by spin columns and/or chromatographic techniques known in art.
• chromatography There are many kinds of chromatography which may be used in the practice of the present invention, including adso ⁇ tion, partition, ion- exchange, hydroxylapatite, molecular sieve, reverse-phase, column, paper, thin-layer, and gas chromatography as well as HPLC.
• the amplification products are visualized, with or without separation.
• a typical visualization method involves staimng of a gel with ethidium bromide and visualization of bands under UV light.
• the separated amplification products can be exposed to x-ray film or visualized under the appropriate excitatory spectra.
• a labeled nucleic acid probe is brought into contact with the amplified marker sequence.
• the probe preferably is conjugated to a chromophore but may be radiolabeled.
• the probe is conjugated to a binding partner, such as an antibody or biotin, or another binding partner carrying a detectable moiety.
• detection is by Southern blotting and hybridization with a labeled probe.
• Methods used to detect point mutations include denaturing gradient gel electrophoresis
• DGGE restriction fragment length polymo ⁇ hism analysis
• RFLP restriction fragment length polymo ⁇ hism analysis
• SSCP single-strand conformation polymo ⁇ hism analysis
• RNA/DNA or RNA/RNA heteroduplexes are two methods of screening for point mutations.
• RNase cleavage of base pair mismatches in RNA/DNA or RNA/RNA heteroduplexes is based on RNase cleavage of base pair mismatches in RNA/DNA or RNA/RNA heteroduplexes.
• mismatch is defined as a region of one or more unpaired or mispaired nucleotides in a double-stranded RNA/RNA, RNA/DNA or DNA/DNA molecule. This definition thus includes mismatches due to insertion/deletion mutations, as well as single or multiple base point mutations.
• U.S. Patent 4,946,773 describes an RNase A mismatch cleavage assay that involves annealing single-stranded DNA or RNA test samples to an RNA probe, and subsequent treatment of the nucleic acid duplexes with RNase A. For the detection of mismatches, the single-stranded products of the RNase A treatment, electrophoretically separated according to size, are compared to similarly treated control duplexes. Samples containing smaller fragments (cleavage products) not seen in the control duplex are scored as positive.
• VNTRs variable nucleotide type polymo ⁇ hisms
• RFLPs restriction fragment length polymo ⁇ hisms
• RFLPs are been widely used in human and animal genetic analyses.
• Another class of polymo ⁇ hisms are generated by the replacement of a single nucleotide.
• Such single nucleotide polymo ⁇ hisms (SNPs) rarely result in changes in a restriction endonuclease site. Thus, SNPs are rarely detectable restriction fragment length analysis.
• SNPs are the most common genetic variations and occur once every 100 to 300 bases and several SNP mutations have been found that affect a single nucleotide in a protein- encoding gene in a manner sufficient to actually cause a genetic disease.
• SNP diseases are exemplified by hemophilia, sickle-cell anemia, hereditary hemochromatosis, late-onset alzheimer disease etc.
• polymo ⁇ hic mutations that affect the activity and/or levels of the UGTIAI gene products which are responsible for the glucuronidation of irinotecan and other chemotherapeutic and xenobiotic agents, will be determined by a series of screening methods.
• One set of screening methods is aimed at identifying SNPs that affect the inducibility, activity and/or level of the UGTIAI gene products in in vitro or in vivo assays.
• the other set of screening methods will then be performed to screen an individual for the occurrence of the SNPs identified above. To do this, a sample (such as blood or other bodily fluid or tissue sample) will be taken from a patient for genotype analysis.
• the presence or absence of SNPs will determine the ability of the screened individuals to metabolize irinotecan and other chemotherapeutic agents that are metabolized by the UGTIAI gene products. According to methods provided by the invention, these results will be used to adjust and/or alter the dose of irinotecan or other agent administered to an individual in order to reduce drug side effects.
• SNPs can be the result of deletions, point mutations and insertions and in general any single base alteration, whatever the cause, can result in a SNP.
• the greater frequency of SNPs means that they can be more readily identified than the other classes of polymo ⁇ hisms.
• the greater uniformity of their distribution permits the identification of SNPs "nearer" to a particular trait of interest.
• the combined effect of these two attributes makes SNPs extremely valuable. For example, if a particular trait (e.g., inability to efficiently metabolize irinotecan) reflects a mutation at a particular locus, then any polymo ⁇ hism that is linked to the particular locus can be used to predict the probability that an individual will be exhibit that trait.
• SNPs relating to glucuronidation of chemotherapeutic agents can be characterized by the use of any of these methods or suitable modification thereof.
• Such methods include the direct or indirect sequencing of the site, the use of restriction enzymes where the respective alleles of the site create or destroy a restriction site, the use of allele-specific hybridization probes, the use of antibodies that are specific for the proteins encoded by the different alleles of the polymo ⁇ hism, or any other biochemical inte ⁇ retation.
• the most commonly used method of characterizing a polymo ⁇ hism is direct DNA sequencing of the genetic locus that flanks and includes the polymo ⁇ hism. Such analysis can be accomplished using either the "dideoxy-mediated chain termination method,” also known as the “Sanger Method” (Sanger, F., et al, 1975) or the “chemical degradation method,” also known as the “Maxam-Gilbert method” (Maxam, A. M., et al, 1977). Sequencing in combination with genomic sequence-specific amplification technologies, such as the polymerase chain reaction may be utilized to facilitate the recovery of the desired genes (Mullis, K. et al, 1986; European Patent Application 50,424; European Patent Application.
• a primer complementary to allelic sequences immediately 3 '-to a polymo ⁇ hic site is used.
• the identity of the nucleotide of that site is determined using labeled dideoxynucleotide derivatives which are inco ⁇ orated at the end of the primer if complementary to the nucleotide of the polymo ⁇ hic site.
• PCT Application WO92/15712 describes a method that uses mixtures of labeled terminators and a primer that is complementary to the sequence 3' to a polymo ⁇ bic site.
• the labeled terminator that is inco ⁇ orated is complementary to the nucleotide present in the polymo ⁇ hic site of the target molecule being evaluated and is thus identified.
• the primer or the target molecule is immobilized to a solid phase.
• oligonucleotides capable of hybridizing to abutting sequences of a single strand of a target DNA are used.
• One of these oligonucleotides is biotinylated while the other is detectably labeled. If the precise complementary sequence is found in a target molecule, the oligonucleotides will hybridize such that their termini abut, and create a ligation substrate. Ligation permits the recovery of the labeled oligonucleotide by using avidin.
• Other nucleic acid detection assays, based on this method, combined with PCR have also been described (Nickerson et al, 1990).
• extended haplotypes may be determined at any given locus in a population, which allows one to identify exactly which SNPs will be redundant and which will be essential in association studies.
• the latter is referred to as 'haplotype tag SNPs (htSNPs)', markers that capture the haplotypes of a gene or a region of linkage disequilibrium.
• htSNPs 'haplotype tag SNPs
• the VDA-assay utilizes PCR amplification of genomic segments by long PCR
• Chip Assay uses PCR amplification of genomic segments by standard or long PCR protocols. Hybridization products are analyzed by VDA, Halushka et al, 1999, inco ⁇ orated herein by reference. SNPs are generally classified as “Certain” or “Likely” based on computer analysis of hybridization patterns. By comparison to alternative detection methods such as nucleotide sequencing, “Certain” SNPs have been confirmed 100%) of the time; and “Likely” SNPs have been confirmed 73%) of the time by this method.
• PCR-amplified Primers are designed from published or database sequences and PCR- amplification of genomic DNA is performed using the following conditions: 200 ng DNA template, 0.5 ⁇ M each primer, 80 ⁇ M each of dCTP, dATP, dTTP and dGTP, 5% formamide, 1.5mM MgCl , 0.5U of Taq polymerase and 0.1 volume of the Taq buffer. Thermal cycling is performed and resulting PCR-products are analyzed by PCR-single strand conformation polymo ⁇ hism (PCR-SSCP) analysis, under a variety of conditions, e.g, 5 or 10% polyacrylamide gel with 15% urea, with or without 5% glycerol. Electrophoresis is performed overnight. PCR-products that show mobility shifts are reamplified and sequenced to identify nucleotide variation. In a method called CGAP-GAI (DEMIGLACE), sequence and alignment data (from a)
• PHRAP.ace file quality scores for the sequence base calls (from PHRED quality files), distance information (from PHYLIP dnadist and neighbour programs) and base-calling data (from PHRED '-d' switch) are loaded into memory. Sequences are aligned and examined for each vertical chunk ('slice') of the resulting assembly for disagreement. Any such slice is considered a candidate SNP (DEMIGLACE). A number of filters are used by DEMIGLACE to eliminate slices that are not likely to represent true polymo ⁇ hisms.
• filters that: (i) exclude sequences in any given slice from SNP consideration where neighboring sequence quality scores drop 40% or more; (ii) exclude calls in which peak amplitude is below the fifteenth percentile of all base calls for that nucleotide type; (iii) disqualify regions of a sequence having a high number of disagreements with the consensus from participating in SNP calculations; (iv) removed from consideration any base call with an alternative call in which the peak takes up 25% or more of the area of the called peak; (v) exclude variations that occur in only one read direction.
• PHRED quality scores were converted into probability- of-error values for each nucleotide in the slice. Standard Baysian methods are used to calculate the posterior probability that there is evidence of nucleotide heterogeneity at a given location.
• PCR amplification is performed from DNA isolated from blood using specific primers for each SNP, and after typical cleanup protocols to remove unused primers and free nucleotides, direct sequencing using the same or nested primers.
• DEBNICK a comparative analysis of clustered EST sequences is performed and confirmed by fluorescent-based DNA sequencing.
• ERO ERO
• new primers sets are designed for electronically published STSs and used to amplify DNA from 10 different mouse strains.
• the amplification product from each strain is then gel purified and sequenced using a standard dideoxy, cycle sequencing technique with 33p_i a beled terminators. All the ddATP terminated reactions are then loaded in adjacent lanes of a sequencing gel followed by all of the ddGTP reactions and so on. SNPs are identified by visually scanning the radiographs.
• ERO RESEQ-HT
• new primers sets are designed for electronically published murine DNA sequences and used to amplify DNA from 10 different mouse strains.
• the amplification product from each strain is prepared for sequencing by treating with Exonuclease I and Shrimp Alkaline Phosphatase. Sequencing is performed using ABI Prism Big Dye Terminator Ready Reaction Kit (Perkin-Elmer) and sequence samples are run on the 3700 DNA Analyzer (96 Capillary Sequencer).
• FGU-CBT SCA2-SNP
• genomic DNA is amplified in a 50 ml reaction volume containing a final concentration of 5mM Tris, 25mM KC1, 0.75mM MgCl 2 , 0.05% gelatin, 20pmol of each primer and 0.5U of
• Taq DNA polymerase samples are denatured, annealed and extended and the PCR product is purified from a band cut out of the agarose gel using, for example, the QIAquick gel extraction kit (Qiagen) and is sequenced using dye terminator chemistry on an ABI Prism 377 automated DNA sequencer with the PCR primers.
• QIAquick gel extraction kit Qiagen
• JBLACK SEQ/RESTRICT
• two independent PCR reactions are performed with genomic DNA.
• Products from the first reaction are analyzed by sequencing, indicating a unique Fspl restriction site.
• the mutation is confirmed in the product of the second PCR reaction by digesting with Fsp I.
• KWOK(l) SNPs are identified by comparing high quality genomic sequence data from four randomly chosen individuals by direct DNA sequencing of PCR products with dye-terminator chemistry (see Kwok et al, 1996).
• SNPs are identified by comparing high quality genomic sequence data from overlapping large-insert clones such as bacterial artificial chromosomes (BACs) or Pl-based artificial chromosomes (PACs). An STS containing this SNP is then developed and the existence of the SNP in various populations is confirmed by pooled DNA sequencing (see Taillon-Miller et al, 1998).
• SNPs are identified by comparing high quality genomic sequence data from overlapping large-insert clones BACs or PACs. The SNPs found by this approach represent DNA sequence variations between the two donor chromosomes but the allele frequencies in the general population have not yet been determined.
• SNPs are identified by comparing high quality genomic sequence data from a homozygous DNA sample and one or more pooled DNA samples by direct DNA sequencing of PCR products with dye-terminator chemistry.
• the STSs used are developed from sequence data found in publicly available databases. Specifically, these STSs are amplified by PCR against a complete hydatidiform mole (CHM) that has been shown to be homozygous at all loci and a pool of DNA samples from 80 CEPH parents (see Kwok et al, 1994).
• CHM complete hydatidiform mole
• KWOK OverlapSnpDetectionWithPolyBayes
• SNPs are discovered by- automated computer analysis of overlapping regions of large-insert human genomic clone sequences.
• clone sequences are obtained directly from large-scale sequencing centers. This is necessary because base quality sequences are not present/available through GenBank.
• Raw data processing involves analyzed of clone sequences and accompanying base quality information for consistency. Finished ('base perfect', error rate lower than 1 in 10,000 bp) sequences with no associated base quality sequences are assigned a uniform base quality value of 40 (1 in 10,000 bp error rate). Draft sequences without base quality values are rejected. Processed sequences are entered into a local database.
• a version of each sequence with known human repeats masked is also stored. Repeat masking is performed with the program "MASKERAID.” Overlap detection: Putative overlaps are detected with the program "WUBLAST.” Several filtering steps followed in order to eliminate false overlap detection results, i.e. similarities between a pair of clone sequences that arise due to sequence duplication as opposed to true overlap. Total length of overlap, overall percent similarity, number of sequence differences between nucleotides with high base quality value "high-quality mismatches.” Results are also compared to results of restriction fragment mapping of genomic clones at Washington University Genome Sequencing Center, finisher's reports on overlaps, and results of the sequence contig building effort at the NCBI.
• SNP detection Overlapping pairs of clone sequence are analyzed for candidate SNP sites with the 'POLYBAYES' SNP detection software. Sequence differences between the pair of sequences are scored for the probability of representing true sequence variation as opposed to sequencing error. This process requires the presence of base quality values for both sequences. High-scoring candidates are extracted. The search is restricted to substitution-type single base pair variations. Confidence score of candidate SNP is computed by the POLYBAYES software.
• TaqMan assay In method identified by KWOK (TaqMan assay), the TaqMan assay is used to determine genotypes for 90 random individuals.
• PCR products are post- labeled with fluorescent dyes and analyzed by an automated capillary electrophoresis system under SSCP conditions (PLACE-SSCP).
• PLACE-SSCP automated capillary electrophoresis system under SSCP conditions
• PCR primers are tagged to have 5'-ATT or 5'-GTT at their ends for post-labeling of both strands.
• Samples of DNA (10 ng/ul) are amplified in reaction mixtures containing the buffer (lOmM Tris-HCl, pH 8.3 or 9.3, 50mM KC1, 2.0mM MgCl 2 ), 0.25 ⁇ M of each primer, 200 ⁇ M of each dNTP, and 0.025 units/ ⁇ l of Taq DNA polymerase premixed with anti-Taq antibody.
• the two strands of PCR products are differentially labeled with nucleotides modified with R110 and R6G by an exchange reaction of Klenow fragment of DNA polymerase I.
• the reaction is stopped by adding EDTA, and uninco ⁇ orated nucleotides are dephosphorylated by adding calf intestinal alkaline phosphatase.
• SSCP For the SSCP: an aliquot of fluorescently labeled PCR products and TAMRA-labeled internal markers are added to deionized formamide, and denatured. Electrophoresis is performed in a capillary using an ABI Prism 310 Genetic Analyzer. Genescan softwares (P-E Biosystems) are used for data collection and data processing. DNA of individuals (two to eleven) including those who showed different genotypes on SSCP are subjected for direct sequencing using big-dye terminator chemistry, on ABI Prism 310 sequencers. Multiple sequence trace files obtained from ABI Prism 310 are processed and aligned by Phred/Phrap and viewed using Consed viewer. SNPs are identified by PolyPhred software and visual inspection.
• KYUGEN Method2
• individuals with different genotypes are searched by denaturing HPLC (DHPLC) or PLACE-SSCP (Inazuka et al, 1997) and their sequences are determined to identify SNPs.
• PCR is performed with primers tagged with 5'-ATT or 5'-GTT at their ends for post-labeling of both strands.
• DHPLC analysis is carried out using the WAVE DNA fragment analysis system (Trans genomic). PCR products are injected into DNASep column, and separated under the conditions determined using WAVEMaker program (Transgenomic).
• the reaction is stopped by adding EDTA, and uninco ⁇ orated nucleotides are dephosphorylated by adding calf intestinal alkaline phosphatase.
• SSCP followed by electrophoresis is performed in a capillary using an ABI Prism 310 Genetic Analyzer. Genescan softwares (P-E Biosystems). DNA of individuals including those who showed different genotypes on DHPLC or SSCP are subjected for direct sequencing using big-dye terminator chemistry, on ABI Prism 310 sequencer.
• SNPs are identified by PolyPhred software and visual inspection. Trace chromatogram data of EST sequences in Unigene are processed with PHRED. To identify likely SNPs, single base mismatches are reported from multiple sequence alignments produced by the programs PHRAP, BRO and POA for each Unigene cluster. BRO corrected possible misreported EST orientations, while POA identified and analyzed non-linear alignment structures indicative of gene mixing/chimeras that might produce spurious SNPs.
• Bayesian inference is used to weigh evidence for true polymo ⁇ hism versus sequencing error, misalignment or ambiguity, misclustering or chimeric EST sequences, assessing data such as raw chromatogram height, sha ⁇ ness, overlap and spacing; sequencing error rates; context-sensitivity; cDNA library origin, etc.
• h method identified as MARSHFIELD(Method-B) overlapping human DNA sequences which contained putative insertion/deletion polymo ⁇ hisms are identified through searches of public databases.
• PCR primers which flanked each polymo ⁇ hic site are selected from the consensus sequences. Primers are used to amplify individual or pooled human genomic DNA. Resulting PCR products are resolved on a denaturing polyacrylamide gel and a Phosphorhnager is used to estimate allele frequencies from DNA pools.
• Aqueous compositions may have an effective amount of irinotecan and/or an effective amount of a compound (second agent) that increases conjugative enzyme activity, as represented by a compound that increases the activity of the phase II conjugative enzyme, glucuronosyltransferase or that decreases biliary transport.
• Such compositions will generally be dissolved or dispersed in a pharmaceutically acceptable carrier or aqueous medium.
• phrases "pharmaceutically or pharmacologically acceptable” refer to molecular entities and compositions that do not produce an adverse, allergic or other untoward reaction when administered to an animal, or human, as appropriate.
• pharmaceutically acceptable carrier includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and abso ⁇ tion delaying agents and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredients, its use in the therapeutic compositions is contemplated. Supplementary active ingredients, such as other anti-cancer agents, can also be inco ⁇ orated into the compositions.
• parenteral administration such as intravenous or intramuscular injection
• other pharmaceutically acceptable forms include, e.g., tablets or other solids for oral administration; time release capsules; and any other form currently used, including cremes, lotions, mouthwashes, inhalants and the like.
• the active compounds will often be formulated for parenteral administration, e.g., formulated for injection via the intravenous, intramuscular, sub-cutaneous, or ' even intraperitoneal routes.
• parenteral administration e.g., formulated for injection via the intravenous, intramuscular, sub-cutaneous, or ' even intraperitoneal routes.
• the preparation of an aqueous composition that contains irinotecan and a second agent as active ingredients will be known to those of skill in the art in light of the present disclosure.
• such compositions can be prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for using to prepare solutions or suspensions upon the addition of a liquid prior to injection can also be prepared; and the preparations can also be emulsified.
• Solutions of the active compounds as free base or pharmacologically acceptable salts can be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions can also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms.
• the pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions; formulations including sesame oil, peanut oil or aqueous propylene glycol; and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions, hi all cases the form must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
• the active compounds may be formulated into a composition in a neutral or salt form.
• Pharmaceutically acceptable salts include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like.
• the carrier can also be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils.
• the proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
• the prevention of the action of microorganisms can be brought about by various antibacterial ad antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, tbimerosal, and the like.
• isotonic agents for example, sugars or sodium chloride.
• Prolonged abso ⁇ tion of the injectable compositions can be brought about by the use in the compositions of agents delaying abso ⁇ tion, for example, aluminum monostearate and gelatin.
• Sterile injectable solutions are prepared by inco ⁇ orating the active compounds in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization.
• dispersions are prepared by inco ⁇ orating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above.
• the preferred methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
• solutions Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective.
• the formulations are easily administered in a variety of dosage forms, such as the type of injectable solutions described above, with even drug release capsules and the like being employable.
• aqueous solutions For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose.
• aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration.
• sterile aqueous media which can be employed will be known to those of skill in the art in light of the present disclosure.
• one dosage could be dissolved in lmL of isotonic NaCl solution and either added to lOOOmL of hypodermoclysis fluid or injected at the proposed site of infusion, (see for example, "Remington's Pharmaceutical Sciences" 15th Edition, pages
• active compounds may be administered orally. This is contemplated for agents which are generally resistant, or have been rendered resistant, to proteolysis by digestive enzymes. Such compounds are contemplated to include all those compounds, or drugs, that are available in tablet form from the manufacturer and derivatives and analogues thereof.
• the active compounds may be administered, for example, with an inert diluent or with an assimilable edible carrier, or they may be enclosed in hard or soft shell gelatin capsule, or compressed into tablets, or inco ⁇ orated directly with the food of the diet.
• the active compounds may be inco ⁇ orated with excipients and used in the form of ingestible tablets, buccal tables, troches, capsules, elixirs, suspensions, syrups, wafers, and the like.
• Such compositions and preparations should contain at least 0.1% of active compound.
• the percentage of the compositions and preparations may, of course, be varied and may conveniently be between about 2 to about 60% of the weight of the unit.
• the amount of active compounds in such therapeutically useful compositions is such that a suitable dosage will be obtained.
• the tablets, troches, pills, capsules and the like may also contain the following: a binder, as gum tragacanth, acacia, comstarch, or gelatin; excipients, such as dicalcium phosphate; a disintegrating agent, such as corn starch, potato starch, alginic acid and the like; a lubricant, such as magnesium stearate; and a sweetening agent, such as sucrose, lactose or saccharin may be added or a flavoring agent, such as peppermint, oil of wintergreen, or cherry flavoring.
• a binder as gum tragacanth, acacia, comstarch, or gelatin
• excipients such as dicalcium phosphate
• a disintegrating agent such as corn starch, potato starch, alginic acid and the like
• a lubricant such as magnesium stearate
• a sweetening agent such as sucrose, lactose or saccharin may be added or
• any material may be present as coatings or to otherwise modify the physical form of the dosage unit.
• tablets, pills, or capsules may be coated with shellac, sugar or both.
• a syrup of elixir may contain the active compounds sucrose as a sweetening agent methyl and propylparabens as preservatives, a dye and flavoring, such as cherry or orange flavor.
• any material used in preparing any dosage unit form should be pharmaceutically pure and substantially non-toxic in the amounts employed.
• the active compounds may be inco ⁇ orated into sustained-release preparation and formulations.
• the compounds Upon formulation, the compounds will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective.
• the formulations are easily administered in a variety of dosage forms, such as those described below in specific examples.
• liposomal formulations are contemplated.
• Liposomal encapsulation of pharmaceutical agents prolongs their half-lives when compared to conventional drug delivery systems. Because larger quantities can be protectively packaged, this allow the opportunity for dose-intensity of agents so delivered to cells. This would be particularly attractive in the chemotherapy of cervical cancer if there were mechanisms to specifically enhance the cellular targeting of such liposomes to these cells.
• "Liposome” is a generic term encompassing a variety of single and multilamellar lipid vehicles fo ⁇ ned by the generation of enclosed lipid bilayers. Phospholipids are used for preparing the liposomes according to the present invention and can carry a net positive charge, a net negative charge or are neutral.
• Dicetyl phosphate can be employed to confer a negative charge on the liposomes, and stearylamine can be used to confer a positive charge on the liposomes.
• Liposomes are characterized by a phospholipid bilayer membrane and an inner aqueous medium. Multilamellar liposomes have multiple lipid layers separated by aqueous medium. They form spontaneously when phospholipids are suspended in an excess of aqueous solution. The lipid components undergo self-rearrangement before the formation of closed structures and entrap water and dissolved solutes between the lipid bilayers (Ghosh and Bachhawat, 1991). Also contemplated are cationic lipid-nucleic acid complexes, such as lipofectamine-nucleic acid complexes
• compositions described herein may be comprised in a kit.
• reagents for determining the genotype of one or both UGTIAI genes are included in a kit.
• the kit may further include individual nucleic acids that can be amplify and/or detect particular nucleic acid sequences the UGTIAI gene. It may also include one or more buffers, such as a DNA isolation bufffers, an amplification buffer or a hybridization buffer.
• the kit may also contain compounds and reagents to prepare DNA templates and isolate DNA from a sample.
• the kit may also include various labeling reagents and compounds.
• kits may be packaged either in aqueous media or in lyophilized form.
• the container means of the kits will generally include at least one vial, test tube, flask, bottle, syringe or other container means, into which a component may be placed, and preferably, suitably aliquoted. Where there are more than one component in the kit (labeling reagent and label may be packaged together), the kit also will generally contain a second, third or other additional container into which the additional components may be separately placed. However, various combinations of components may be comprised in a vial.
• the kits of the present invention also will typically include a means for containing the nucleic acids, and any other reagent containers in close confinement for commercial sale. Such containers may include injection or blow-molded plastic containers into which the desired vials are retained.
• the liquid solution is an aqueous solution, with a sterile aqueous solution being particularly preferred.
• the components of the kit may be provided as dried powder(s).
• the powder can be reconstituted by the addition of a suitable solvent. It is envisioned that the solvent may also be provided in another container means.
• a kit will also include instructions for employing the kit components as well the use of any other reagent not included in the kit. Instructions may include variations that can be implemented.
• kits of the invention are embodiments of kits of the invention.
• Such kits are not limited to the particular items identified above and may include any reagent used directly or indirectly in the detection of polymo ⁇ hisms in the UGTIAI gene or the activity level of the UGTIAI polypeptide.
• Patients must have been off previous anticancer therapy, including radiation therapy, for at least 4 weeks (6 weeks if the previous treatment included a nitrosourea or mitomycin C) and off colony stimulating factor for at least 2 weeks.
• Patients with a history of inflammatory bowel disease requiring therapy, chronic diarrheal syndrome, paralytic ileus, or organ or stem cell transplant were excluded from the study.
• Concurrent use of medications that may be substrates of the UGTIAI enzyme or that may be inducers or inhibitors of UGTIAI activity was not permitted.
• Pregnant and lactating women were also excluded from participation, and those with reproductive potential were required to use an effective contraceptive method if sexually active.
• Irinotecan was supplied by the National Cancer Institute (NCI) as an intravenous solution with concentration 20 mg/ml in either 2 ml or 5 ml vials.
• the amount of irinotecan to be administered was removed aseptically from the vial and added to 500 ml of 0.9% saline or 5% dextrose injection, USP.
• irinotecan 350 mg/m 2 was administered as a 90 minute intravenous infusion once every 3 weeks — a standard dose and schedule.
• venous blood (4.5 ml) for genotyping was collected in pu ⁇ le top Vacutainer® tubes containing EDTA (Becton, Dickinson, and Company, Franklin Lakes, NJ) and stored at -80°C for no more than 5 days prior to analysis.
• Venous blood for pharmacokinetic analysis was collected on day 1 of cycle 1 for pharmacokinetic analysis.
• Samples of 7 ml were collected into green top sodium heparinized Vacutainer® tubes prior to the infusion; 30, 60, and 90 minutes during the infusion; and 10, 20, 30, 45, and 60 minutes and 1.5, 2, 4, 6, 12, and 24 hours after the infusion. Samples were centrifuged (2500 rpm, 20 min, 4°C) and the plasma was immediately separated, transferred as two aliquots into storage tubes, frozen at -80°C until analysis.
• UGTIAI Genotyping Assays were centrifuged (2500 rpm, 20 min, 4°C) and the plasma was immediately separated, transferred as two aliquots into
• the variants typed in this study are listed in Table 1.
• the UGTIAI (TA)nTAA polymo ⁇ hism was genotyped by PCR and product sizing as previously described (Te et al., 2000). Alleles with 6 TA repeats resulted in a 98 bp fragment while alleles with 7 TA repeats resulted in a 100 bp fragment. Alleles with 5 TA and 8 TA repeats resulted in 96 bp and 102 bp fragments respectively.
• the variants in the 5 'upstream region (-3279G>T and -3156G>A) and in exon 1 [211G>A (G71R) and 686C>A (P229Q)] were genotyped by single base extension (SBE) and separated on a denaturing high performance liquid chromatography (DHPLC) system (Devaney et al., 2001). Genotyping of the -3279G>T and -3156G>A variants was performed by PCR amplification of a 333 bp fragment in the UGTIAI 5' upstream region that contains both variants.
• PCR primers used were: 5'-ACC TCT AGT TAG ATA ACC TGA A-3' (forward primer) and 5'-AAT AAA CCC GAC CTC ACC AC-3' (reverse primer).
• PCRs were performed in a 15 ⁇ l volume containing 125 nM each primer, 2.5 mM MgCl 2 , 50 ⁇ M each dNTP and 0.375 U of AmpliTaq Gold polymerase (Applied Biosystems) in the buffer provided by the manufacturer.
• PCR cycling conditions were for 40 cycles at 95°C for 15 s, 58°C for 15 s and 72°C for 30 s in a 9600 thermal cycler (Applied Biosystems).
• PCR amplified products were purified using shrimp alkaline phosphatase and exonuclease I by incubating at 37°C for 45 min prior to the SBE reaction.
• SBE reactions were performed in duplex for genotyping of both variants in 10 ⁇ l volumes containing 1 ⁇ M of extension primer (5'-GCC AAG GGT AGA GTT CAG T-3' for -3279G>T and 5'-GAC CCC AGC CCA CCT GTC-3' for -3156G>A), 250 ⁇ M each ddNTP and 1.25 U thermosequenase (Amersham Pharmacia Biotech).
• Reactions were cycled at 96°C for 30 s, 55°C for 30 s and 60°C for 30 s for 60 cycles. Separation of the SBE products was performed on a WAVE 3500HT DHPLC system (Transgenomic ie) at 70°C after denaturation of the samples. The flow rate used was 1.5 ml/min and the run time for each sample was 2.5 min. The gradient used for elution of the SBE products was created by the software based on the length of the extended product and was adjusted from 24% to 34% buffer B over 2 min (buffer B contains 25% acetonitrile). Extended products were eluted in the order of C ⁇ G ⁇ T ⁇ A which is dependent on the hydrophobicity differences of the four bases.
• Genotyping of the 211G>A and 686C>A exon 1 variants was performed by PCR amplification of a 774 bp fragment that encompasses both variants.
• the PCR primers used were: 5'-ATG CTG GGA AGA TAC TGT TG-3' (forward primer) and 5'-TTT GGT GAA
• Plasma concentrations of irinotecan and its metabolites were determined as previously published (Iyer et al., 2001). Pharmacokinetic parameters for irinotecan, SN-38, and SN-38G were calculated using standard non-compartmental methods with WinNonlin 2.0 (Pharsight Co ⁇ oration, Mountain View, CA). The area under the plasma concentration-time curve (AUC) from time zero to the last measured concentration of irinotecan and metabolites was determined by the linear trapezoidal method. The glucuronidation ratio was expressed as the ratio of the SN-38G AUC over SN-38 AUC.
• Nonparametric trend tests were used to investigate how the genotype is related to pharmacokinetic parameters, pretreatment bilirubin levels and ANC nadir.
• the relationship between genotype and grade 4 neutropenia was assessed by the use of Fisher's exact test and calculation of the relative risks.
• Univariate regression analyses were performed to identify the potential predictors of ANC nadir. They were performed on the log scale for ANC to reduce skewness in the residuals.
• the pretreatment variables were also considered jointly via analysis of covariance (ANCOVA) models in order to identify the pretreatment measurements that can predict ln(ANC nadir).
• ANCOVA covariance
• the TA 5 and TA 8 alleles occurred exclusively in Black patients (one with 5/6, two patients with 6/8, and one patient with 7/8 genotype).
• -3279T and -3156A alleles had a frequency of 0.55 and 0.26, respectively.
• Table 3 shows the frequencies of promoter haplotypes comprising -3279, -3156, and the TA indel, based upon our previous publication on their linkage disequilibrium (Innocenti et al., 2002). The frequency of the haplotype pairs is shown in table 4. No exon 1 variants (211G>A and 686C>A) were detected in this patient population.
• the relative risk of grade 4 neutropenia was analyzed for the -3156 AA genotype (versus AG and GG combined) and 7/7 genotype (versus 5/6, 6/6, 6/7 and 6/8 combined).
• the predictive power of a genetic test in patients receiving irinotecan was evaluated for both the TA indel and the -3156 variant (Table 5).
• the predictive power of either 7/7 or - 3156 AA genotypes for grade 4 neutropenia was evaluated.
• the predictive power of either 6/6 or -3156 GG genotypes was evaluated in relation to the absence of grade 4 neutropenia (i.e., grade 0-3).
• the -3156 and the TA indel variants were correlated with total bilirubin by multiple regression analysis.
• the other common variant -3279G>T had no significant association with total bilirubin (data not shown).
• Table 6 describes the pharmacokinetic parameters of irinotecan and its metabolites stratified by 6/6, 6/7, and 7/7 genotypes.
• ln(pretreatment ANC) Other factors, such as ethnicity, number of prior regimens, performance status, and ln(pretreatment ANC) are not found to be significant predictors of ln(ANC nadir) after adjusting for -3156 genotype, gender and total bilirubin.
• the post- treatment measurements of irinotecan AUC, SN-38 AUC, SN-38G AUC, and glucuronidation ratio were added to the model as independent variables with the intention of determining the possible mechanism of how the variability in UGTIAI status affects m(ANC nadir).
• Toxic Death and Response One toxic death was reported, as the patient died of neutropenia-related sepsis. He was admitted to the hospital on day 7 of cycle 1 with fever and an no neutrophils detected (white blood cell count of 100 ⁇ f 1 ). He was empirically treated with ceftazadime, tobramycin, and fluconazole, though no infectious source was ever identified. Despite support with granulocyte colony stimulating factor, the patient remained neutropenic, became septic, and died on day 11. He had 7/7 genotype and the highest level of pretreatment total bilirubin observed in these patients (1.2 mg/dl).
• the haplotypes reflect the change of -3279, -3156, and the TA indel variants, such as the first base refers to —3279 variants, the second to -3156 variant and the number refers to the number of TA repeats.
• PPV positive predictive value.
• NPV negative predicted value.
• compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents that are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.

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