WO2012049279A1 - MEANS AND METHODS APPLYING SINGLE NUCLEOTIDE PRIMER EXTENSION WITH ION PAIR-, REVERSED-PHASE HPLC (SIRPH) FOR THE DIAGNOSIS OF SNPs - Google Patents

MEANS AND METHODS APPLYING SINGLE NUCLEOTIDE PRIMER EXTENSION WITH ION PAIR-, REVERSED-PHASE HPLC (SIRPH) FOR THE DIAGNOSIS OF SNPs Download PDF

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WO2012049279A1
WO2012049279A1 PCT/EP2011/067953 EP2011067953W WO2012049279A1 WO 2012049279 A1 WO2012049279 A1 WO 2012049279A1 EP 2011067953 W EP2011067953 W EP 2011067953W WO 2012049279 A1 WO2012049279 A1 WO 2012049279A1
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c13
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nucleotide
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Sascha Tierling
Joern Walter
Christine Sers
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Universitaet Des Saarlandes
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    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869Methods for sequencing

Abstract

The present invention relates to a method for detecting one or more single nucleotide polymorphisms (SNPs) in a gene of interest by applying multiplex single nucleotide primer extension (SNuPE) and multiplex separation of primer extension products by IP/RP HPLC (SIRPH) as well as uses of that method in the detection of SNPs in cancer-related loci such as KRAS. Thus, the present invention provides adiagnostic and prognostic assay for determining a predisposition of colorectalcancer (CRC) as well as for determining the therapeutic potential of EGFR inhibitors for the treatment of CRC.

Description

MEANS AND METHODS APPLYING SINGLE NUCLEOTIDE PRIMER EXTENSION WITH ION PAIR-, REVERSED-PHASE HPLC (SIRPH) FOR THE DIAGNOSIS OF SNPs

TECHNICAL FIELD OF THE INVENTION

[0001] The present invention relates to a method for detecting one or more single nucleotide polymorphisms (SNPs) in a gene of interest by applying multiplex single nucleotide primer extension (SNuPE) and multiplex separation of primer extension products by IP/RP HPLC (SIRPH) as well as uses of that method in the detection of SNPs in cancer-related loci such as KRAS. Thus, the present invention provides a diagnostic and prognostic assay for determining a predisposition of colorectal cancer (CRC) as well as for determining the therapeutic potential of EGFR inhibitors for the treatment of CRC.

BACKGROUND OF THE INVENTION

[0002] One of the outcomes of the Human Genome Project is the discovery of millions of DNA sequence variants in the human genome. The majority of these variants are single nucleotide polymorphisms (SNPs). A dense set of SNP markers opens up the possibility of studying the genetic basis of complex diseases by population approaches.

[0003] A SNP is a single base change including a substitution, deletion or insertion in a DNA sequence that occurs in a significant proportion (more than 1 percent) of a population. SNPs are scattered throughout the genome and are found in both coding and non-coding regions. SNPs can cause silent, harmless, harmful, or latent effects. They occur with a certain frequency, with estimates ranging from about 1 in 1000 bases to 1 in 100 to 300 bases. This means that there could be millions of SNPs in each human genome. The abundance of SNPs and the ease with which they can be measured make these genetic variations significant.

[0004] A number of genotyping methods are currently in use (see, for example, WO 91/13075). However, no single genotyping method is ideally suited for all applications although a number of good genotyping methods are available to meet the needs of many study designs. The challenges for SNP genotyping in the near future include increasing the speed of assay development, reducing the cost of the assays, and performing multiple assays in parallel. A standard method is amplification of the nucleotide sequence or a region thereof and sequencing of the amplification product. The thus obtained sequence is compared with a reference (wild-type) sequence in order to determine a SNP. A somewhat easier and faster diagnostic tool for the analysis of SNPs that might be responsible for a phenotype is a 'fingerprinting' tool such as single nucleotide primer extension (SNupE).

[0005] SNuPE benefits from the high fidelity of DNA polymerases while incorporating nucleotides or nucleotide analogues, resulting in a highly specific distinction of sequence variants. When a specific primer hybridizes upstream from the target nucleotide position, a DNA polymerase incorporates a labelled nucleoside triphosphate, which terminates the reaction and results in a labelled extended primer. This labelling provides information about the nucleotide of interest in the opposite strand. The high accuracy of this incorporation is due to (i) preferential binding of the dNTP substrate to the enzyme-DNA complex, (ii) faster phosphodiester bond formation of the correct enzyme-DNA-dNTP complex, and (iii) a more rapid rate of PPi release in the case of correct dNTP incorporation. In addition, the proofreading activity of a DNA polymerase contributes to the fidelity of the reaction.

For example, SNuPE is applied for genotyping of SNPs in combination with HPLC (Hoogendoorn et al., 1999). Specifically, a SNP in the proneurotensin gene, a SNP in the 5HT2a receptor gene and a SNP at a polymorphism at about 1500 bp upstream of the 5HT2a receptor gene were analysed by multiple primer extension. The primer extension products were then separated by HPLC. However, Hoogendoorn et al. did neither analyse more than one SN P in the same gene nor did these authors analyse the resulting primer extension products by multiplex HPLC. Rather Hoogendoorn et al. focuses on multiplex primer extension and on single run HPLC. A similar approach is described in US 2006/0057566 by using a bacteriophage lambda polymorphism for testing the combined use of primer extension and HPLC separation. The combined use of multiplex PCR and single run HPLC as established by Hoogendoorn et al., was also applied by Giordano et al. , 2005). Giordano et al. analysed a SNP in the GLAST gene and at the genomic locus STS WI-12996. Hung et al. , 2005) applied primer extension and HPLC for the quantification of the relative gene dosage between the SMN 1 and SMN2 gene. However, Hung et al. applies a combined multiplex primer extension approach with separation of the resulting PCR products by HPLC, but does not teach or suggest that SNPs in one and the same gene could be analysed by multiplex primer extension and subsequent HPLC.

[0006] Most SNPs occur in non-coding regions and do, apart from some exceptions, not alter genes and thus cause a phenotype. The remaining SNPs occur in coding regions. They could alter the protein made by that coding region, which in turn could influence a person's health. In particular, SNPs are known which are, so to say, associated with the onset of cancer. For example, SNPs in the BRCA1 and BRCA2 gene are known to be associated with a high likelihood of a woman to develop breast cancer. There are other examples of SNPs that are associated with likelihood to develop other cancers such as colorectal cancer. [0007] In fact, mutations in the KRAS gene are known to represent one of the most important diagnostic and prognostic markers in tumorigenesis, especially in colorectal cancer development.

[0008] KRAS is a member of small G proteins that are involved in intracellular signalling by being activated through signal cascades initiated by cell surface receptor kinases (Malumbres and Barbacid, 2003). One of these is the epidermal growth factor receptor (EGFR) that activates signalling pathways like the Ras-Raf-Mek kinase pathway, that are responsible for cell cycle control (Schubbert et al. , 2007). Being mutated, the KRAS protein is unable to switch to its inactive form so that cell cycle progression is promoted. Former studies showed that mutations in the KRAS codons 12 and 13 are frequent in colorectal cancer patients and of clinical importance.

[0009] Indeed, the introduction of epidermal growth factor receptor inhibitors (EGFR-I) for therapy increased clinical benefit, however, only for a subset of patients treated. Recent publications revealed that a subset of tumors are insensitive to these inhibitors (Cunningham et al., 2004, Jonker et al. , 2007, van Cutsem et al., 2007, WO 2008/1 12274)) escaping clinical benefit. Retrospective studies correlated those tumors with being mutated in the KRAS gene. Including KRAS mutation screening into routine CRC diagnostics therefore helps to improve the selection of patients which are candidates for EGFR-I treatment. In fact, identification of KRAS mutations in codon 12 and 13 rises importance as a prognostic marker that allows to choose the therapy with the highest success rate.

[0010] To date, several methods are used to detect the most common mutations of the KRAS gene Bjorheim et al., 1998, Lin et al., 1993, Lleonart et al., 2004, McKinzie and Parsons, 2002, Poehlmann et al., 2007, Taback et al., 2004, van Heek et al. , 2005, Chang et al., 2009, Chang et al., 2010), some of them commercialized. However, the most frequently used techniques, allele-specific PCR or, especially, direct sequencing, are not standardized and often fail to detect low amounts of tumor cells in a paraffin-embedded tissue-block leading to a high number of false-negatives.

[0011] For example, successful direct sequencing is highly dependent on template quality and quantity which is challenging when working with formaldehyde-fixed paraffin-embedded tissue blocks. Moreover, it is difficult to detect less than 20% of mutated tumor DNA within a tissue block since signals do not rise beyond background noise. In consequence, these samples are classified as WT although they are not.

[0012] Pondering the above, there is still a need to provide reliable, fast, cost-effective, sensitive and robust diagnostic methods to detect SNPs, in particular SNPs in genes which could cause cancer (i.e., mutated tumor DNA in an excess of WT cells). The identification or confirmation of SNPs would, for example, allow to choose if a growing tumor such as a colorectal tumor might be sensitive (or resistant) to treatment with an anti-cancer agent such as an EGFR-I inhibitor.

[0013] Accordingly, the technical problem of the present invention is to comply with this need.

DESCRIPTION OF THE INVENTION

[0014] The present invention addresses this need and thus provides as a solution to the technical problem embodiments pertaining to methods for detecting SNPs in a gene of interest, in particular in a proto-oncogene and/or tumor suppressor gene, more particularly in the KRAS gene and/or B-raf gene, methods for determining a predisposition for a tumor, in particular a tumor caused by a proto-oncogene and/or tumor suppressor gene, more particularly a tumor caused by a mutated KRAS gene such as a tumor in the etiology of colorectal cancer (CRC) (i.e., a KRAS gene containing one or more SNPs as described herein) as well as methods for evaluating whether an EGFR-I inhibitor may be beneficial for a subject that suffers from colorectal cancer (including metastatic colorectal cancer) by determining whether said subject has one or more SNPs in the KRAS gene that is associated with the development of colorectal cancer.

[0015] Specifically, the present inventors found that the application of a multiplex single primer extension-based approach (SNuPE) with subsequent multiplex ion pair, reversed phase (IP/RP) HPLC separation (SIRPH) provides a reliable, fast, cost-effective and sensitive assay for the detection of SNPs in a gene of interest, in particular for the detection of SNPs in the KRAS gene and optionally in the B-raf gene.

[0016] More specifically, the present inventors found that a primer extension-based assay with subsequent IP/RP-HPLC separation allows the selective detection of all 12 clinically relevant variants known for codons 12 and 13 of the KRAS gene. Advantageously, the assay does not require complex chemistry or labelling and can be optimized to analyze up to 50 individual DNAs within a couple of hours, usually within 24 hours, preferably without the need of re-analyzing because of unclear signals. To this end, comparing direct sequencing, which is the commonly applied method for the purpose of detecting SNPs in the KRAS gene that are associated with cancer, to primer extension data the present inventors improved the sensitivity by 10-fold. Since the assay can preferably be almost entirely automatized, a minimum of human resources is required. This makes the assay a fast, simple, robust, sensitive and cost-effective assay that can be used in routine diagnostics for detecting SNPs in a gene of interest, in particular in a proto-oncogene and/or a tumor suppressor gene, more particularly in the KRAS gene. Accordingly, the assay of the present invention for the detection of one or more SNPs in the KRAS gene that are associated with colorectal cancer might serve as diagnostic tool, in particular in early colorectal cancer screening. That assay is topped off by simultaneously analysing the B-raf gene for a SNP in codon 600. Accordingly, the present invention provides fast, robust and cost-efficient methods for covering all known KRAS mutations in codons 12 and 13 as well as the most prominent B-raf mutation in codon 600 that are indicative as to whether or not a subject will respond to a therapy with EGFR-I inhibitors such as panitumumab or cetuximab.

[0017] Accordingly, in a first aspect the present invention provides a method for detecting one or more single nucleotide polymorphisms (SNP), i.e., SNPs in a gene of interest comprising

(a) amplifying a nucleotide sequence of said gene of interest suspected or known to comprise one or more SNPs;

(b) simultaneously (multiplex) extending multiple primers annealed downstream of said one or more SNPs such that each of said SNPs is contained in a separate extension product formed thereby (i.e., a plurality of extension products from one and the same gene is formed);

(c) simultaneously (multiplex) separating said extension product by IP/RP-HPLC (i.e., a plurality of extension products is simultaneously separated by IP/RP-HPLC); and

(d) detecting said one or more SNPs by comparing the extension product of said gene of interest with the extension product from the corresponding wild-type gene.

Preferably, the SNPs are in the coding region of said gene of interest which is preferably a proro-oncogene or a tumor suppressor gene. More preferably, said SNPs are next to each other, i.e., in codons which are within a distance of 300, 200, 100, 50, 25, or 10 nucleotides. It is also preferred that the primers are designed in a way such that their base composition is different to such an extent that they are distinguishable by IP/RP HPLC.

[0018] It must be noted that as used herein, the singular forms "a", "an", and "the", include plural references unless the context clearly indicates otherwise. Thus, for example, reference to "a reagent" includes one or more of such different reagents and reference to "the method" includes reference to equivalent steps and methods known to those of ordinary skill in the art that could be modified or substituted for the methods described herein.

[0019] All publications and patents cited in this disclosure are incorporated by reference in their entirety. To the extent the material incorporated by reference contradicts or is inconsistent with this specification, the specification will supersede any such material.

[0020] Unless otherwise indicated, the term "at least" preceding a series of elements is to be understood to refer to every element in the series. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the present invention.

[0021] Throughout this specification and the claims which follow, unless the context requires otherwise, the word "comprise", and variations such as "comprises" and "comprising", will be understood to imply the inclusion of a stated integer or step or group of integers or steps but not the exclusion of any other integer or step or group of integer or step. When used herein the term "comprising" can be substituted with the term "containing" or sometimes when used herein with the term "having".

[0022] When used herein "consisting of" excludes any element, step, or ingredient not specified in the claim element. When used herein, "consisting essentially of" does not exclude materials or steps that do not materially affect the basic and novel characteristics of the claim.

[0023] In each instance herein any of the terms "comprising", "consisting essentially of" and "consisting of" may be replaced with either of the other two terms.

[0024] Several documents are cited throughout the text of this specification. Each of the documents cited herein (including all patents, patent applications, scientific publications, manufacturer's specifications, instructions, etc.), whether supra or infra, are hereby incorporated by reference in their entirety. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.

[0025] A "SNP" (Single Nucleotide Polymorphism) when used herein is defined as any variation (nucleotide variation) of (a) base pair(s)/nucleotide(s) in a nucleotide sequence of a gene of interest. Accordingly, rather than the term "SNP", the term "mutation" or "mutated (nucleotide) sequence" is sometimes used herein. As such these terms are used interchangeably herein.

Each SNP reflects the possibility of having two or more different bases in the same position in the nucleotide sequence of a gene of interest (also sometimes referred to herein as "candidate gene"), resulting in the fact that at least two different alleles of the candidate gene may be found in the genome of individuals.

[0026] Also, a SNP reflects the possibility of having one or more additional nucleotide (insertions) or one or more deletions of nucleotides in the nucleotide sequence of a gene of interest in comparison to a reference (wild-type) nucleotide sequence. Preferably, a SN P may be situated on a gene of interest (coding and/or regulating nucleotide sequence). In the sense of the invention, a SN P may be a change in the nature of a nucleotide (including preferably a nucleotide substitution, for example a base transition or base transversion), a deletion and/or an insertion such as a repetition of one or more nucleotides in the nucleotide sequence of a gene of interest in comparison to a reference (wild-type) nucleotide sequence. [0027] A SN P is preferably associated with a phenotype. For example, a SNP may lead to an altered nucleotide sequence and, thus, as a result to a modified protein which may not function properly. Similarly, a SNP may cause a mutation leading to a truncated protein. Alternatively, a SNP may cause over-or under-expression of a gene. Each of these "abnormal" (i.e, an activity or feature which differs from a normal activity or feature) conditions may cause a phenotype that can be diagnosed. "One or more SNPs" means more than one SNP. Accordingly , "One or more" SNPs includes more than one SNP, i.e., two, three, four, five, six, seven or eight SNPs; with two, three, four, five or six SNPs being preferred.

[0028] Accordingly, the method for detecting one or more SNPs in a gene of interest is equally suitable for the detection of a predisposition of a disease, preferably of a tumor or cancer as described herein. [0029] For example, a SNP known in the art may also be known or suspected to be correlated/associated with the phenotype of a disease, for example, a metabolic disorder/disturbance or development of a tumor or cancer. Indeed, as described herein a gene of interest as applied in the methods of the present invention may be a proto-oncogene or a tumor suppressor gene. Many of these two groups of genes are known to comprise one or more SN Ps that are associated with a predisposition to develop a tumor or cancer.

[0030] As mentioned, in some preferred embodiments, the SNP is suspected or known to be associated with a tumorigenic phenotype of a subject, i.e., the subject may develop a tumor and thus cancer in those cells/that tissue which is afflicted with the SNP. Put it differently, the SNP in the afflicted gene may render the gene to become capable of causing a tumor. For example, a SN P may cause an amino acid change and, thus, a proto-oncogene may then encode a constitutive active protein which renders cells to not arrest in cell cycle or to have a permanent active receptor which triggers expression of otherwise inactive genes which may render resting cells to become active at a point of time where they should not be active and the like.

[0031] Hence, in view of the fact that a SNP that can be diagnosed by the means and methods of the present invention may be associated with a tumorigenic phenotype, it is a more preferred embodiment that the presence of one or more SNPs in the nucleotide sequence of a gene of interest at a position in comparison to the respective position of the nucleotide sequence of the wild-type gene is indicative for a predisposition for a tumor. [0032] The term "predisposition of a disease (preferably a tumor or cancer)" includes a tendency or susceptibility to develop a certain disease that can be triggered under certain conditions, e.g. influence of the environment, personal circumstances of a subject, such as the nutritional behavior of a subject. The tendency or susceptibility to develop a certain disease is associated with a genotype that increases the risk for developing a disease, if other certain conditions, such as those mentioned above, are present. Genetic testing is able to identify subjects who are genetically predisposed to certain health problems. The disease for which a subject has a tendency or susceptibility to develop is preferably a disease related to the presence of a SNP in a proto-oncogene and/or tumor suppressor gene as described herein, with KRAS as proto-oncogene being particularly preferred.

[0033] Accordingly, a particularly preferred use of the methods of the present invention is for the detection of a predisposition of tumor or cancer because of the presence of one or more SNPs in the KRAS gene as described herein in detail elsewhere.

[0034] The term "position" when used in accordance with the present invention means the position of a nucleotide within the nucleotide sequence of a gene of interest. The position of a nucleotide within a gene of interest may vary due to deletions or additions of nucleotides elsewhere in the nucleotide sequence of a gene of interest (mutant or wild-type) including the promoter and/or any other regulatory sequences or exons and introns. Thus, the position of a nucleotide within a nucleotide sequence of a gene of interest, for the purpose of the present invention corresponds to a position of a nucleotide within a nucleotide sequence of a reference (wild-type) sequence (gene). Of note, a "position" does not only encompass a single nucleotide, it may also encompass more than a single nucleotide, for example, two, three, four, five, six, etc. nucleotides, i.e., a region/stretch, if the SNP may be an addition or deletion of nucleotides, respectively.

[0035] The term "corresponding" or a grammatical variant thereof when used in the context of the position of SNPs within the nucleotide sequence of a gene of interest includes that a position is not only determined by the number of the preceding and/or succeeding nucleotides. Thus, under a "corresponding position" in accordance with the present invention it is preferably to be understood that nucleotides may differ in the indicated number but may still have similar neighbouring nucleotides. Said nucleotides which may be exchanged, deleted or added are also comprised by the term "corresponding position".

[0036] In order to determine whether a nucleotide (residue) in a gene of interest (mutant or wild-type) corresponds to a certain position in a reference (wild type) sequence, the skilled person can use means and methods well-known in the art, e.g., alignments, either manually or by using computer programs such as BLAST2.0, which stands for Basic Local Alignment Search Tool or ClustalW or any other suitable program which is suitable to generate sequence alignments. [0037] A SNP, in a nucleotide sequence, can be coding, silent or non-coding. A coding SNP is a polymorphism in the coding sequence of a nucleotide sequence that involves a modification of at least one amino acid in the sequence of amino acids encoded by this nucleotide sequence. In this case, the term SN P applies equally, by extension, to a variation in an amino acid sequence. A silent SNP is a polymorphism included in the coding sequence of a nucleotide sequence that does not involve a modification of any amino acid in the amino acid sequence encoded by this nucleotide sequence. A non-coding SNP is a polymorphism included in the non-coding sequence of a nucleotide sequence. This polymorphism can notably be found in an intron, a splicing site, a promoter or an enhancer or a silencer sequence.

[0038] "Mutated nucleotide sequence" thus refers to the nucleotide sequence of a candidate gene comprising a sequence variation such as one or more SNPs. This mutated nucleotide sequence may correspond to a new allele of the gene revealed by the identification of a SNP in this sequence and that is preferably unknown in the prior art. By extension, a mutated protein corresponds to a protein encoded by said mutated nucleotide sequence.

[0039] Accordingly, the term "mutated" when applied to nucleotide sequences means that nucleotides in a nucleic acid sequence may be inserted, deleted or changed compared to a reference nucleotide sequence. A single alteration may be made at a locus (a point mutation) or multiple nucleotides may be inserted, deleted or changed at a single locus. In addition, one or more alterations may be made at any number of loci within a nucleic acid sequence.

[0040] The method for detecting one or more SNPs in a gene of interest as described herein can also be used for the identification of a yet unknown (i.e. new) SN P in a gene of interest. For example, if the variants A (WT) and G (mutation) are already known for a certain position, the primer would be extended by a T (WT) or a C (mutation). Providing all ddNTPs in the primer extension reaction would allow detecting new variants (C or T) at the respective position by detecting a G- or A-specific primer extension signals during HPLC separation.

[0041] "Functionality" is the biological activity of a protein or a nucleotide sequence coding for said protein and/or the expression (level of expression) of a protein or a nucleotide sequence coding for said protein. The biological activity may, for example, be linked to the affinity or to the absence of affinity to a ligand or a receptor of a protein encoded by the nucleotide sequence of the preselected candidate gene. The functionality of the preselected candidate gene may be known or determined by a skilled person in the art.

[0042] "Functional SNP" is defined as a SNP, such as previously defined, which is included in the nucleotide sequence of a candidate gene, and which modifies the functionality of the candidate gene. A functional SNP may increase, reduce or suppress the biological activity and/or the expression of the protein encoded by the nucleotide sequence of the preselected candidate gene or of this latter nucleotide sequence. A functional SNP can equally induce a change in the nature of the biological activity of the polypeptide encoded by the nucleotide sequence of the preselected candidate gene or of this latter nucleotide sequence. A functional SNP, for example located in the coding part of the nucleotide sequence that encodes for the signal peptide of the protein(s), may affect the activity at the proper localization and/or the localization of the protein(s) encoded by these genes. A functional SNP may modify the expression of the candidate gene (at the level of transcription and/or translation) or of the protein(s) encoded by the gene (post-translational changes such as glycosylation for example). A functional SNP may affect the expression and/or activity of the preselected candidate gene when it is positioned in a regulator sequence of the gene such as, for example, in the promoter or enhancer. A functional SNP is also any natural variation, situated in the coding sequence of a candidate gene and identified in the genome of one or more individuals of a random population, which causes either a stopping of translation (introduction of a STOP codon) or a change in the nature of an amino acid of the protein(s) encoded by this gene, if it or they exist, and which changes the activity of said protein(s). In this case, a variability in the activity (also called functionality) of the protein(s) encoded by the candidate gene in the random population is revealed. [0043] When used herein a "gene of interest" (sometimes also referred to herein as "candidate (preselected) gene" or "target sequence" or "target nucleotide sequence") includes any gene, preferably a gene from a mammalian subject, more preferably from a human subject. A "gene of interest" is generally a nucleotide sequence of interest in which a SNP is suspected or known to reside, including copies of such target nucleic acid generated by amplification or primer extension, i.e., the gene of interest is thus suspected to comprise one or more SNPs. Accordingly, the term "suspected to comprise one or more SNPs" means that the nucleotide sequence of a gene of interest is known or has a likelihood to comprise one or more SNPs at a position/region of interest. [0044] The term "gene of interest" when referred to herein preferably means that said gene of interest encodes a corresponding protein (protein of interest). Said protein can be functional or non-functional, for example, it can be truncated or mutated, thus rendering the protein non-functional. A "gene" when used herein is, so to say, a species of a nucleotide sequence and comprises a coding sequence for a protein/polypeptide, and optionally a 5'- UTR (containing, for example, expression control elements such as a promoter) and/or 3'- UTR (containing, for example, a termination signal sequence). The gene may be composed of exons and introns or may be free of introns, thus merely composed of exons. It may be composed of DNA, genomic DNA or cDNA.

[0045] In a preferred embodiment the gene of interest is a proto-oncogene or a tumor suppressor gene, respectively. More preferably, the gene of interest is the KRAS gene and/or the B-raf gene.

[0046] Most, if not all, cancer cells contain genetic damage that appears to be the responsible event leading to tumorigenesis. The genetic damage present in a parental tumorigenic cell is maintained (i.e. not correctable) such that it is a heritable trait of all cells of subsequent generations. Genetic damage found in cancer cells is of two types:

1. Dominant and the genes have been termed proto-oncogenes

[0047] The distinction between the terms proto-oncogene and oncogene relates to the activity of the protein product of the gene. A proto-oncogene is a gene whose protein product has the capacity to induce cellular transformation given it sustains some genetic insult. An oncogene is a gene that has sustained some genetic damage and, therefore, produces a protein capable of cellular transformation.

[0048] The process of activation of proto-oncogenes to oncogenes can include retroviral transduction or retroviral integration (see below), point mutations, insertion mutations, gene amplification, chromosomal translocation and/or protein-protein interactions.

Proto-oncogenes can be classified into many different groups based upon their normal function within cells or based upon sequence homology to other known proteins. As predicted, proto-oncogenes have been identified at all levels of the various signal transduction cascades that control cell growth, proliferation and differentiation. Proto- oncogenes that were originally identified as resident in transforming retroviruses were initially designated as c- indicative of the cellular origin as opposed to v- to signify original identification in retroviruses.

2. Recessive and the genes variously termed tumor suppressors, growth suppressors, recessive oncogenes or anti-oncogenes.

[0049] Given the complexity of inducing and regulating cellular growth, proliferation and differentiation, it was suspected for many years that genetic damage to genes encoding growth factors, growth factor receptors and/or the proteins of the various signal transduction cascades would lead to cellular transformation. This suspicion has proven true with the identification of numerous genes, whose products function in cellular signaling, that are involved in some way in the genesis of the tumorigenic state. The majority of these proto- oncogenes were identified by either of two means: as the transforming genes (oncogenes) of transforming retroviruses or through transfection of DNA from tumor cell lines into non- transformed cell lines and screening for resultant tumorigenesis.

[0050] In some more preferred embodiments, the proto-oncogene is a gene selected from the group consisting of growth factors, Receptor Tyrosine Kinases, Membrane Associated Non-Receptor Tyrosine Kinases, G protein coupled receptors, Membrane Associated G- Proteins, Serine-Threonine Kinases, and Nuclear DNA-Binding/Transcription Factors.

[0051] In some particularly preferred embodiments the proto-oncogene is at least one gene selected from the group of genes consisting of KRAS (also referred to herein as "KRAS"), B- raf RAS, WNT, MYC, ERK, B-raf, TRK, met, ret, ErB2/Her2/neu, Bcl-2 and c-myc, with KRAS and B-raf being particularly preferred.

[0052] In some other preferred embodiments, the tumor suppressor gene is a Breast and Ovarian Cancer Susceptibility Gene or a Hereditary Cancer Syndrome Gene.

[0053] In some more preferred embodiments, the tumor suppressor gene is a gene selected from the group consisting of BRCA1 , BRCA2, ATM, CHEK2, BRIP1 , PALB2, and RAD51 C. [0054] In some other more preferred embodiments the tumor suppressor gene is a Hereditary Cancer Syndrome Gene selected from the group consisting of p53, WT1 , NF1 , NF2, APC, TSC1 , TSC2, DPC4, DCC, STK1 1 , MSH1 , MLH2, VHL, CDKN2, PTEN, MEN1 and MEN2. [0055] "Nucleotides" are referred to by their commonly accepted single- letter codes following lUPAC nomenclature: A (Adenine), C (Cytosine), T (Thymine), G (Guanine), U (Uracil), W (A or T), R (A or G), K (G or T), Y (C or T), S (C or G), M (A or C), B (C, G or T), H (A, C, or T), D (A, G, or T), V (A, C, or G), N (A, C, G, or T).

[0056] The term "nucleotide sequence" or" nucleic acid molecule" refers to a polymeric form of nucleotides (i.e. polynucleotide) of at least 10 bases in length which are usually linked from one deoxyribose or ribose to another. The term includes DNA molecules (e.g., cDNA or genomic or synthetic DNA) and RNA molecules (e.g., mRNA or synthetic RNA), as well as analogs of DNA or RNA containing non-natural nucleotide analogs, non-native internucleoside bonds, or both. The term "nucleotide sequence" does not comprise any size restrictions and also encompasses nucleotides comprising modifications, in particular modified nucleotides, e.g., as described herein. The term "nucleotide sequence" includes single and double stranded forms of DNA. A nucleic acid molecule of this invention may include both sense and antisense strands of RNA, cDNA, genomic DNA, and synthetic forms and mixed polymers of the above. They may be modified chemically or biochemically or may contain non-natural or derivatized nucleotide bases, as will be readily appreciated by those of skill in the art. Such modifications include, for example, labels, methylation, substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications such as uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoramidates, carbamates, etc.), charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), pendent moieties (e.g., polypeptides), intercalators (e.g., acridine, psoralen, etc.), chelators, alkylators, and modified linkages (e.g., alpha anomeric nucleic acids, etc.) Also included are synthetic molecules that mimic polynucleotides in their ability to bind to a designated sequence via hydrogen bonding and other chemical interactions. Such molecules are known in the art and include, for example, those in which peptide linkages substitute for phosphate linkages in the backbone of the molecule.

[0057] The nucleotide sequences of the invention are preferably "isolated" or "substantially pure". An "isolated" or "substantially pure" nucleotide sequence or nucleic acid (e.g., RNA, DNA or a mixed polymer) is one which is substantially separated from other cellular components that naturally accompany the native polynucleotide in its natural host cell, e.g., ribosomes, polymerases, and genomic sequences with which it is naturally associated. The term embraces a nucleotide sequence or nucleic acid that (1) has been removed from its naturally occurring environment, (2) is not associated with all or a portion of a polynucleotide in which the "isolated nucleotide sequence" is found in nature, (3) is operatively linked to a polynucleotide which it is not linked to in nature, or (4) does not occur in nature. The term "isolated" or "substantially pure" also can be used in reference to recombinant or cloned DNA isolates, chemically synthesized polynucleotide analogs, or polynucleotide analogs that are biologically synthesized by heterologous systems.

[0058] However, "isolated" does not necessarily require that the nucleotide sequence or nucleic acid so described has itself been physically removed from its native environment. For instance, an endogenous nucleotide sequence in the genome of an organism is deemed "isolated" herein if a heterologous sequence (i.e., a sequence that is not naturally adjacent to this endogenous nucleic acid sequence) is placed adjacent to the endogenous nucleic acid sequence, such that the expression of this endogenous nucleic acid sequence is altered. By way of example, a non- native promoter sequence can be substituted (e.g., by homologous recombination) for the native promoter of a gene in the genome of a human cell, such that this gene has an altered expression pattern. This gene would now become "isolated" because it is separated from at least some of the sequences that naturally flank it. [0059] A nucleotide sequence is also considered "isolated" if it contains any modifications that do not naturally occur to the corresponding nucleic acid in a genome. For instance, an endogenous coding sequence is considered "isolated" if it contains an insertion, deletion or a point mutation introduced artificially, e.g., by human intervention. An "isolated nucleotide sequence" includes a nucleic acid integrated into a host cell chromosome at a heterologous site, a nucleic acid construct present as an episome. Moreover, an "isolated nucleotide sequence" can be substantially free of other cellular material or substantially free of culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.

[0060] A nucleotide sequence to be applied in the methods of the present invention is preferably contained in a sample. In accordance with the present invention by the term "sample" is intended any biological sample obtained from a subject, cell line, tissue culture, or other source containing nucleic acids or polypeptides or portions thereof. As indicated, biological samples include body fluids (such as blood, sera, plasma, urine, synovial fluid and spinal fluid) and tissue sources (such as a tumor biopsy) found to express a gene of interest. The source of the tissue or cell sample may be solid tissue as from a fresh, frozen and/or preserved organ or tissue sample. Optionally, the tissue or cell sample is obtained from a disease tissue/organ. The tissue sample may contain compounds which are not naturally intermixed with the tissue in nature such as preservatives, anticoagulants, buffers, fixatives, nutrients, antibiotics, or the like. A "reference sample", "reference cell", "reference tissue", "control sample", "control cell", or "control tissue", as used herein, refers to a sample, cell or tissue obtained from a source known, or believed, not to comprise one or more SNPs or afflicted with a disease. For the purposes herein a "section" of a tissue sample is meant a single part or piece of a tissue sample, e.g. a thin slice of tissue or cells cut from a tissue sample. Methods for obtaining tissue biopsies and body fluids from mammals are well known in the art. A biological sample which includes genomic DNA, mRNA or proteins is preferred as a source. Collection and analysis of cells from bodily fluids is well known to the art; see for example, Rodak, "Haematology: Clinical Principles & Applications" second ed., WB Saunders Co, 2002; Brunzel, "Fundamentals of Urine and Body Fluids Analysis", WB Saunders Co, 1994; Herndon and Brumback (Ed.), "Cerebrospinal Fluid", Kluwer Academic Pub., 1989. In addition, methods for DNA isolation are well described in the art; see, for example, Sambrook et al., cited herein. [0061] In the context of the present invention the term "subject" is preferably a mammal, particularly preferred a human. The term "subject" also includes a horse, a camel, a dog, a cat, a pig, a cow, a goat, a fowl, a rabbit, a mouse or a rat. [0062] When used herein "amplifying" a nucleotide sequence encompasses any technique, means and methods that can be applied to amplify (multi-copy) a nucleotide sequence. Preferably the amplification is linear or exponential (exponential being preferred) so that a sufficient amount of the nucleotide sequence of a gene of interest is available for appropriately performing the methods of the present invention.

A number of template dependent processes are available to amplify the nucleotide sequence of a gene of interest (here: a template sample).

[0063] The amplification of a nucleotide sequence of the present invention can in principle be performed by using any nucleic acid amplification system. Amplification systems include the Polymerase Chain Reaction (PCR; US 4,683, 195, 4,683,202, and 4,800, 159), RT-PCR, Ligase Chain Reaction (LCR; EP 320 308), Self- Sustained Sequence Replication (3SR), Strand Displacement Amplification (SDA; US 5,270, 184, and 5,455, 166), Transcriptional Amplification System (TAS), Q-Beta Replicase, Rolling Circle Amplification (RCA; US 5,871 ,921 ), transcription-based amplification systems including Nucleic Acid Sequence Based Amplification (NASBA), Cleavage Fragment Length Polymorphism (US 5,719,028), Isothermal and Chimeric Primer-initiated Amplification of Nucleic Acid (ICAN), Ramification- extension Amplification Method (RAM; US 5,719,028 and 5,942,391 ) or other suitable methods for amplification of DNA.

[0064] As mentioned hereinabove, PCR is the preferred method for amplifying a nucleotide sequence to be applied in the methods of the present invention. In a particularly preferred embodiment, amplification of a gene of interest comprising one or more SNPs should be perfomed using detergent-free PCR buffers. In a further particularly preferred embodiment, chromosomal DNA is used as template for the amplification of a gene of interest. Preferably, the amount of chromosomal DNA is about 50 ng. The volume of the amplification reaction is preferably about 30 μΙ. The number of cycles of a PCR is preferably about 30-35. Advantageously, the success of PCR should be checked by loading a small amount (such as 5 μΙ) of the PCR reaction onto, for example, a 1 -1 .5% agarose gel.

[0065] When performing the present invention, in particular the methods disclosed herein, more particularly the amplification of a nucleotide sequence it is preferred to purify the amplification product (amplicon), preferably before pooling with preferably a 1 : 10 mixture of Exonuclease I and Shrimp Alkaline Phosphatase to achieve maximum template amount.

[0066] Alternatively, it is preferred that the amplicon can be excised from an agarose gel used to purify the amplicon and can be further purified using ion exchange columns. [0067] Once a nucleotide sequence of a gene of interest has been provided (isolated), various oligonucleotides or primers spanning one or more SNPs comprised by the gene of interest may be designed in order to amplify the region containing a SNP, preferably by Polymerase Chain Reaction (PCR). Conventional methods for designing, synthesizing, producing said oligonucleotide primers and performing PCR amplification may be found in standard textbooks, see, for example Agrawal (Ed.), "Protocols for Oligonucleotides and Analogs: Synthesis and Properties (Methods in Molecular Biology, 20)", Humana Press, 1993; Innis et al. (Ed.), "PCR Applications: Protocols for Functional Genomics", Academic Press, 1999; Chen and Janes (Ed.), "PCR Cloning Protocols: From Molecular Cloning to Genetic", 2nd edition, Humana Press, 2002. For example, preferred primers for the detection of SNPs in the KRAS gene are given in the appended examples.

[0068] The term "oligonucleotide" refers to a short sequence of nucleotide monomers (usually 6 to 100 nucleotides) joined by phosphorous linkages (e.g., phosphodiester, alkyl and aryl-phosphate, phosphorothioate), or non- phosphorous linkages (e.g., peptide, sulfamate and others). An oligonucleotide may contain modified nucleotides having modified bases (e.g., 5-methyl cytosine) and modified sugar groups (e.g., 2'-0-methyl ribosyl, 2'-0- methoxyethyl ribosyl, 2'-fluoro ribosyl, 2'-amino ribosyl, and the like). Oligonucleotides may be naturally- occurring or synthetic molecules of double- and single-stranded DNA and double- and single- stranded RNA with circular, branched or linear shapes and optionally including domains capable of forming stable secondary structures (e.g., stem-and-loop and loop-stem-loop structures).

[0069] The term "primer" as used herein refers to an oligonucleotide which is capable of annealing to the amplification target allowing a DNA polymerase to attach thereby serving as a point of initiation of DNA synthesis when placed under conditions in which synthesis of primer extension product which is complementary to a nucleic acid strand is induced, i.e., in the presence of nucleotides and an agent for polymerization such as DNA polymerase and at a suitable temperature and pH. The (amplification) primer is preferably single stranded for maximum efficiency in amplification. Preferably, the primer is an oligodeoxy ribonucleotide.

[0070] The primer must be sufficiently long to prime the synthesis of extension products in the presence of the agent for polymerization. The exact lengths of the primers will depend on many factors, including temperature and source of primer. A "pair of bi- directional primers" as used herein refers to one forward and one reverse primer as commonly used in the art of DNA amplification such as in PCR amplification, and may be directed to the coding strand of the DNA or the complementary strand. Preferred PCR primer for the amplification of KRAS are shown in SEQ ID No: 3 and 4. [0071] The term "primer" also includes primers applied for the simultaneous (multiple) extension of the same. Specifically, the methods of the present invention apply multiple primer extension, more specifically, multiple single nucleotide primer extension (SNuPE). In SNuPE a primer anneals upstream from the nucleotide sequence of the gene of interest (target sequence). Taq DNA polymerase incorporates a labelled or unlabelled ddNTP, which terminates the reaction and results in a product. During the SNuPE a primer annealed downstream of a SNP is extended, thereby the SNP is, so to say, contained (i.e. copied) in the primer extension product.

[0072] It is preferred that the primer applied for primer extension is annealed directly downstream in front of the suspected or known SNP. This means that the primer is merely extended by one nucleotide (ddNTP). Though less preferred, it is contemplated that the primer may anneal downstream of the suspected or known SNP so that one or more nucleotides (preferably 1 , 2 or 3) are extended before the SNP is "copied" via primer extension. In that less preferred embodiment, it is necessary that, apart from that ddNTP that is complementary to the nucleotide at the position of the SNP, dNTPs are present in the primer extension reaction so that the primer can be extended up to the position of the SNP where the reaction will terminate because of the incorporation of a ddNTP Accordingly, it is preferred in that embodiment that all dNTPS are present, except for the dNTP that is complementary to the suspected or known SNP nucleotide(s). For that, the corresponding (complementary) ddNTP is present.

[0073] Preferred SNuPE primers for KRAS are shown in SEQ ID Nos: 5 - 8.

[0074] "Copied" means that the primer because of its binding (annealing) to the complementary strand of the nucleotide sequence of a gene of interest is extended to detect the SNP, thereby it "images" (i.e., reflects/mirrors) the SNP, i.e., the primer contains the complementary base (in case the SNP is a single nucleotide exchange) or complementary nucleotide sequence of the SNP either containing additional nucleotides (in case the SNP is an addition/insertion) or lacking nucleotides (in case the SNP is a deletion).

[0075] In case of multiplex primer extension, it is preferred that each primer extension product merely contains one SNP. Put it differently, the primer to be extended is designed such that it can merely "images" one SNP.

[0076] However, the use of (multiple) primers that anneal to the top and bottom strand, respectively, allows detecting SNPs that are next to each other. "Next to each other" means SNPs are in codons which are within a distance of 300, 200, 100, 50, 25, or 10 nucleotides. In fact, multiple extended primers can then be quickly and cost-efficiently separated and unambiguously separated by IP/RP-HPLC separation. Accordingly, the use of primers that anneal to the top and bottom strand, respectively, is a preferred embodiment. [0077] Hence, "multiple" in the context of primers that are extended in the method of the present invention means that more than one primer(s), for example, two, three, four, five, six, seven, eight, nine, ten, eleven or twelve primers - with two, three, four, five, six or seven primers being preferred - are simultaneously extended, i.e., the primer extension is performed by way of multiplexing (i.e., simultaneous extension of primers). The multiple primers may anneal to the same strand in order to detect more than one SNP or they may anneal to the top (sence) and bottom (anti-sense or complementary) strand, respectively. In order to achieve a subsequent separation of the primer extension products, the primers to be extended are designed in a way such that their base composition is different to such an extent that they are distinguishable by IP/RP HPLC. This is so because IP/RP HPLC is able to separate nucleotide sequences (here primer extension products) by length (size) and, in case of similar length (size), by hydrophobicity of the nucleotide sequence (because of differences in the charge of the base composition of the nucleotide sequence). The skilled person is aware of the principle of IP/RP HPLC and can thus readily design the primers applied for SNuPE:

[0078] It is advantageously and thus preferred to use HPLC-purified primers in the primer extension reaction in order to avoid disturbing signals (noise) in the subsequent separation step, for example, caused by primer synthesis.

[0079] Similarly, though any enzyme can be used in the primer extension reaction that is capable of polymerizing dNTPs and/or ddNTPs such as DNA polymerase or Taq Polymerase, it is particularly preferred to use the TermiPol enzyme from Solis BioDyne (Tartu, Estonia). That enzyme proved to achieve maximum efficiency in incorporating ddNTPs.

[0080] It is particularly preferred to apply at least 3.6 pmol of each primer in the SNuPE reaction, since this amount of primer allows a highly efficient reaction performance and a sufficient amount of the then-extended primer to achieve a readily detectable signal in the subsequent separation step.

[0081] Once primers are multiply extended, their extension product is simultaneously separated, i.e., multiplexed by ion-pair, reversed phase HPLC (IP/RP-HPLC).

Primer design for Multiplex-SNuPE (and SIRPH) is a decisive issue in developing a diagnostic primer extension assay.

[0082] Accordingly, it is preferred that the (multiple) primers are chosen to be specific for one or more SNPs to be detected in accordance with the methods of the present invention. [0083] It is also preferred that the (multiple) primers have a length of at least 9, 10, 1 1 , 12, 13, 14, 15 nucleotides. In particular, dependent on how many mutations should be analysed in one reaction (and later in one H PLC run for the separation of primer extension products) it is preferred to use primers that differ in least one nucleotide length, more preferably in at least two or three nucleotides length. For example, in the latter embodiment starting with at least 9 bp primers one would chose primers of 1 1 bp, 13 bp, 15 bp, 17 bp, 19 bp, 21 bp or 23 bp or primers of 12 bp, 15 np, 18 bp, 21 bp, etc. However, in certain embodiments it is particularly preferred that the maximum length of a primer is 21 , 23 or 25 bp. [0084] Generally, it is preferred that during the SNuPE unlabelled ddNTPs are incorporated by a DNA polymerase. However, though less preferred, also labelled ddNTPs can be applied and would thus be incorporated by a DNA polymerase. In that less preferred embodiment, a fluorescence detector is preferably applied for the detection of the incorporated ddNTPs. [0085] It is a preferred embodiment of the method of the present invention that the primers applied in the (multiple) primer extension can be labelled. Yet, it is more preferred that these primers are unlabelled.

[0086] In a yet further preferred embodiment, the (multiple) primer extension step (reaction) is performed on a single amplification product encompassing one or more SNPs.

For example, if SNPs are located quite close to each other the primer extension reaction can be performed on one single PCR product encompassing the mutations.

[0087] However, it is likewise a preferred embodiment that the (multiple) primer extension step (reaction) is performed on two or more amplification products encompassing one or more SNPs. For example, if mutations are located in different exons (or introns) of the gene one would perform separate PCR reactions for each mutation and pool the amplicons before primer extension reaction.

[0088] Once primers have been multiply extended in accordance with the present invention such that primer extension products are obtained, these extension products are subject to simultaneous separation by ion pair, reversed phase (IP RP) HPLC.

Though IP/RP HPLC is known in the art, it was neither disclosed nor suggested to be applied for multiple (simultaneous) separation of primer extension products, in particular in the context of a method of the present invention. In fact, up to the present invention, a double multiplex step (i.e., multiplex primer extension and multiplex separation by IP/RP HPLC) method for detecting one or more SNPs in a gene of interest was neither known nor envisaged. However, the double multiplex step methods of the present invention allow a fast, robust, sensitive and reliable method for detecting SNPs in a gene of interest. This method is suitable for a high throughput format. Indeed, SNuPE is an established method that provides sensitive and reliable results, since a specific primer is extended by merely one nucleotide (ddNTP). In view of the fact that the amplification of a nucleotide sequence of a gene of interest can be achieved within hours and primer extension does not require much time, it is possible to run a high number of samples to be analyzed in a short period of time.

[0089] In the separation step, an automated high performance liquid chromatography system coupled with ion-pair/reverse-phase columns, in particular C18 columns is preferably used for the separation of primer extension products. The term "primer extension products" when used herein includes "a multitude" of primer extension products. A "multitude" includes more than one primer extension products, e.g., two, three, four, five, six, seven or eight. IP/RP- HPLC is a form of chromatography particularly suited to the analysis of nucleotide sequences, e.g., in the form of DNA, and is characterized by the use of a reverse phase (i.e., hydrophobic) stationary phase and a mobile phase that includes an alkylated cation (e.g., triethylammonium) that is believed to form a bridging interaction between the negatively charged DNA and non-polar stationary phase. The alkylated cation-mediated interaction of DNA and stationary phase can be modulated by the polarity of the mobile phase, conveniently adjusted by means of a solvent that is less polar than water, e. g., acetonitrile.

[0090] IP/RP-HPLC is a form of chromatography particularly suited to the analysis of nucleotide sequences such as DNA, and is characterized by the use of a reverse phase (i.e., hydrophobic) stationary phase and a mobile phase that includes an alkylated cation (e.g., triethylammonium) that is believed to form a bridging interaction between the negatively charged DNA and non-polar stationary phase. The alkylated cation-mediated interaction of DNA and stationary phase can be modulated by the polarity of the mobile phase, conveniently adjusted by means of a solvent that is less polar than water, e. g., acetonitrile. It is preferred that the organic solvent used for elution of the SNuPE products is acetonitril (HPLC grade). Preferably, a gradient of 3% - 10% acetonitril is applied, preferably over 30 min time. This gradient conveniently allows the inclusion of up to 5 differentially extended primers and to evaluate the potential retention times of the respective SNuPE products. However, the application of a different gradient will readily allow the inclusion of more than five extended primers.

[0091] The particularly preferred system for IP/RP HPLC is the DNASep™ cartridge from Transgenomic (Omaha, USA), preferably on an analytical size (e.g., inner dimensions 50 x 4.6 mm) using a WAVE nucleic acid analysis system (Transgenomic, Inc.). The stationary phase of the DNASep™ column comprises octadecyl modified, nonporous poly (ethylvinylbenzene-divinylbenzene) beads, as described in U. S. Patent No. 6,066,258. In view of the fact that the separation step by multiplex IP/RP HPLC may require different separation temperatures, the use of a DHPLC system is advantageous and thus preferred (e.g., WAVE™ system, Transgenomic, Omaha, USA). [0092] The primer extension products may preferably be purified prior to multiplex separation, however, it is more preferred to not purify them by means and methods known in the art.

For an IP/RP HPLC run it is preferred to include standards in every run to exclude errors and to unambiguously detect and identify the respective SNP. These standards ideally represent a signal composition of potential extension products but only with one ddNTP included into each reaction and run, respectively. Thus, every signal can be assigned to its respective SNP. Of course, it is preferred that every analysis has to be accompanied by a no template control (NTC) representing the SNuPE reaction components only without including the purified PCR product(s). By that, unextended primers can be clearly distinguished from extended primers and contaminations can be excluded.

[0093] Using optimized assay conditions no enhancement of detection, like using fluorescence-labelled primers, is necessary. However, it is nevertheless envisaged in certain embodiments that labelled primers are applied. Standard UV detection of signals at 254 nm is sufficient to achieve intense and assessable signals.

[0094] The term "detection" includes any means of detecting, including direct and indirect detection, identifying the presence or absence of the SNP to be detected. Detection may comprise the demonstration of the presence, in absolute terms or in relative terms (e.g., relative intensity of signals), or of the absence of the marker in (a sample of) a subject.

[0095] Generally, when applied in the method of the present invention, IP/RP HPLC produces electropherograms by applying UV light and detecting its absorption by the DNA (here primer extension products) separated by IP/RP HPLC (i.e., absorption spectra are generated and analysed). The electropherograms allow a qualitative analysis of the primer extension products so as to assign a specific electropherogram to each of the separated primer extension products, thereby allowing the detection of a SNP (when comparing the electropherogram of a primer extension product to that of the primer extension product of a wild-type (reference) primer extension product). Specifically, as mentioned herein above, primers applied for (multiple) primer extension are designed such that they differ in at least one, two, three, etc. nucleotide(s) in length. Preferably, these primers also differ in their base composition. Accordingly, because of the difference in length (ant thus size), it is possible to assign an electropherogram to a specific primer extension product, thereby a suspected or known SNP is "tagged" (i.e., assigned to a specific primer applied for SNuPE). Additionally, because of the different base composition of a primer extension product (e.g., a single difference in the base composition is sufficient to separate primer extension products by IP/RP HPLC), it is possible to distinguish even primer extension products of the same size. The sensitivity of the separation achieved by IP/RP HPLC allows the determination of a SNP such as a single nucleotide exchange. For example, assuming that the wild-type sequence is an "A", the primer extension product would be a "T". Assuming that the SNP is a "G", the primer extension product would be a "C". Thus, IP/RP HPLC is able to discriminate between primer extension products of the same length (size) that merely differ in the "extended" nucleotide (i.e., the "copied" SNP or wild-type nucleotide, respectively).

[0096] In the context of the method for detecting one or more SNPs in a gene of interest, the detection of one or more SNPs is achieved by comparing the extension product of a gene of interest with the extension product from the corresponding wild-type gene. For example, if a SNP is present at a certain position in a nucleotide sequence of a gene of interest, it would be different in comparison to the corresponding position of the nucleotide sequence of a wild- type gene. Thus, the detection is then made by comparison of the nucleotide sequences via the analysis of electropherograms as described above.

[0097] Alternatively, the detection of a SNP could also be achieved by comparing the length of the primer extension product with that of a corresponding primer extension product of a wild-type gene. For example, a primer extension product of a gene of interest may be shorter or longer than that of a wild type gene, if the SNP is a deletion or addition, respectively.

[0098] A further alternative, in case, for example, an unknown SNP or a suspected SNP is to be detected by the application of the method of the present invention and it is thus unknown which ddNTP would be incorporated by a DNA polymerase, the detection of a SNP can be achieved on the basis of hydrophobicity of the primer extension products. Namely, different ddNTPs have a different hydrophobicity in IP/RP HPLC and can thus be separated and identified (as described above).

[0099] In a second aspect, the present invention provides a use of the method of the present invention for detecting one or more single nucleotide polymorphisms (SNP) in the KRAS gene comprising

(a) amplifying a nucleotide sequence of said KRAS gene comprising one or more of said SNPs;

(b) simultaneously (multiplex) extending multiple primers annealed downstream of the (i) first base of codon 12 (C12-1), (ii) second base of codon 12 (C12-2), (iii) first base of codon 13 (C13-1) and/or (iv) second base of codon 13 (C13-2) of the KRAS gene such that each of said SNPs is contained in a separate extension product formed thereby; (c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and

(d) detecting said one or more SN Ps,

wherein the presence of a SNP at a position corresponding to C12-1 , C12-2, C13-1 and/or C13-2 of the KRAS gene (nucleotide sequence) shown in SEQ ID NO: 1 is indicative for a predisposition for a tumor. The tumor may result in colorectal cancer.

[0100] In a preferred aspect, the above method further comprises

in step (a) amplifying a nucleotide sequence of the B-raf gene comprising one or more of said SN Ps;

- in step (b) simultaneously (multiplex) extending a primer annealed downstream of the second base of codon 600 (C600-2) such that said SN Ps is contained in a separate extension products formed thereby;

in step (c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and

- in step (d) detecting said one or more SNPs,

wherein the presence of a SNP at a position corresponding to C600-2 of the B-raf gene shown in SEQ I D NO: 16 is indicative for a predisposition for a tumor.

[0101] Preferably, the multiple primer extension step (b) is carried out as follows: in one reaction primers for C12-1 and C13-1 are extended and in a separate, further separate reaction primers for C12-2 and 13-2 as well as the primer for C600-2 are extended.

[0102] SEQ I D No: 1 is the nucleotide sequence of GenBank Accession Number NM_004985 (Version NM_004985.3) and SEQ I D No:2 is the corresponding amino acid sequence.

[0103] The term "first/second base of... " means the position of a base within the indicated codon, i.e. , within codon 12 or 13, respectively, of the KRAS sequence shown in NM_004985 (SEQ ID No: 1) (nucleotide sequence) or in SEQ ID No:2 (GenBank Accession Number NP_004976, Version NM_004976.2) (amino acid sequence). In the present case, the position of the codon equals with the amino acid position (shown in SEQ ID No:2). The respective nucleotide position can be taken from the overview provided below.

[0104] The genomic sequence of KRAS is shown in GenBank accession no. NG_007524. The skilled person can readily determine the exons and introns by way of the nucleotide sequence shown in SEQ ID No:1. [0105] By "C12-... " is meant the position of the codon and the position of the base within the codon, i.e., position 1 or 2, for example, C12-1 , C12-2, C13-1 or C13-2.

[0106] Likewise, the term "second base of ..." when used in the context of the B-raf gene means the position of a base within the indicated codon, i.e., within codon 600 of the B-raf sequence shown in SEQ ID No: 16 (nucleotide sequence) or in SEQ ID No:17 (amino acid sequence). In the present case, the position of the codon equals with the amino acid position (shown in SEQ ID No:17).

[0107] SEQ ID No: 16 is the nucleotide sequence of the B-raf gene, while SEQ ID No: 17 is the corresponding amino acid sequence.

[0108] By "C600-2" is meant the position of the codon and the position of the base within the codon, i.e., position 2. [0109] Put differently, the present invention provides a method for detecting one or more SNPs in the KRAS gene comprising

(a) amplifying a nucleotide sequence of said KRAS gene comprising one or more of said SNPs;

(b) simultaneously (multiplex) extending multiple primers annealed downstream of the (i) first base of codon 12 (C12-1), (ii) second base of codon 12 (C12-2), (iii) first base of codon 13 (C13-1) and/or (iv) second base of codon 13 (C13-2) of the KRAS gene such that each of said SNPs is contained in a separate extension product formed thereby;

(c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and (d) detecting said one or more SNPs,

wherein the presence of a SNP at a position corresponding to C12-1 , C12-2, C13-1 and/or C13-2 of the KRAS gene (nucleotide sequence) shown in SEQ ID NO: 1 (NM_004985) is indicative for a predisposition for a tumor, preferably a solid tumor. The tumor may be developed during the etiology of colorectal cancer (including metastatic colorectal cancer) and may result in the same.

[0110] Preferably, said method further comprises

in step (a) amplifying a nucleotide sequence of the B gene comprising at least codon 600 as determined from the B-raf gene shown in SEQ ID No: 16 with the first codon starting as nucleotide position 1 ; in step (b) simultaneously (multiplex) extending a primer annealed downstream of the second base of codon 600 (C600-2) such that said SNPs is contained in a separate extension products formed thereby;

in step (c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and

in step (d) determining whether at a position corresponding to C600-2 of the B- raf gene shown in SEQ ID NO: 16 a nucleotide different from that shown in SEQ ID No: 16 is present,

wherein the presence of a SNP at a position corresponding to C600-2of the B-raf gene shown in SEQ ID NO:16 is indicative for a predisposition for a tumor, preferably a solid tumor.

The tumor may be developed during the etiology of colorectal cancer (including metastatic colorectal cancer) and may result in the same.

[0111] Preferably, the multiple primer extension step (b) is carried out as follows: in one reaction primers for C12-1 and C13-1 are extended and in a separate, further separate reaction primers for C12-2 and 13-2 as well as the primer for C600-2 are extended.

[0112] Mutations in the KRAS gene represent one of the most important diagnostic and prognostic markers in tumorigenesis, especially in colorectal cancer development. Identification of KRAS mutations in codon 12 and 13 rises importance as a prognostic marker that allows to choose the therapy with the highest success rate. To date, several methods are used to detect the most common mutations, some of them commercialized. However, the most frequently used techniques, allele-specific PCR or direct sequencing, are not standardized and often fail to detect low amounts of tumor cells in a paraffin-embedded tissue-block leading to a high number of false-negatives. The same is true for the B-raf gene and the identification of a mutation in codon 600 as a prognostic marker. Indeed, a mutation in that codon which results in a change from valine to glutamate is indicative that a therapy with an EGFR-I inhibitor would not be beneficial for a subject. [0113] Accordingly, with its second aspect, the present invention provides a primer extension-based approach with subsequent IP/RP-HPLC separation that detects selectively all 12 clinically relevant variants known for codons 12 and 13 of the KRAS gene. Of note, that approach does not require complex chemistry or labelling and is optimized to analyze up to 50 and even more individual DNAs within about 24 hours without the need of re-analyzing because of unclear signals. When that approach is compared to direct sequencing, the method of the second aspect of the present invention improves sensitivity by 10fold; see the appended Examples. The workflow of the method of the second aspect of the present invention can be almost entirely automatized and, thus, a minimum of human resources is required.

[0114] Also, the present invention provides in a preferred aspect a primer extension-based approach with subsequent IP/RP-HPLC separation that detects selectively the relevant variant known for codon 600 of the B-raf gene. Thus, the present invention provides a combined primer extension-based approach with subsequent IP/RP-HPLC separation that detects selectively all 12 clinically relevant variants known for codons 12 and 13 of the KRAS gene and the relevant variant known for codon 600 of the B-raf gene (see Figures 4 and 5).

[0115] To date, 12 nucleotide variants are known for KRAS codons 12 and 13. Interestingly, they are limited to the first two bases of the codons leaving the third position unchanged (Fig. lA). For codon 12, position 1 and 2 (C12-1 , C12-2) the WT nucleotide G can be replaced by the nucleotides A, G or T. In codon 13, only two variants for the positions 1 (C13-1 ) and 2 (C13-2) are known: C13-1 : G (WT) and T (tumor), and C13-2: G (WT) and A (tumor). In total, the present inventors designed four different primers to detect all of these variations (Fig. l B). The first primer, detecting variations in C12-1 , binds to the lower strand of the PCR product with its 3'-end directly in front of C12-1 . The second primer also binds on the lower strand but with its 3'-end directly in front of C12-2. A G was chosen as the last base of this primer (binding at C12-1) since all other nucleotides at C12-1 are neighboured by a G at C12-2. So if there is no G at C12-1 , there is always a G at C12-2. The third primer, detecting the nucleotide at C13-2, binds to the upper strand and ends with its 3'end directly on position C13-3, being constant in all cases so far known. Consequently, the fourth primer also binds to the upper strand, ends with its 3'-end at C13-2 and detects the base information of C13-1 .

[0116] It is thus a preferred embodiment of the above method that the primer which anneals downstream of (i) C12-1 is designed such that it anneals with its 3'-end directly in front of C12-1 , (ii) C12-2 is designed such that it anneals with its 3'-end directly in front of C12-2, (iii) C13-1 is designed such that it anneals with its 3'-end directly in fron of C13-1 and/or (iv) C13- 2 is designed such that it anneals with its 3'-end directly in front of C13-2. [0117] For the B-raf gene one important mutation is known that occurs in codon 600 and which causes a valine to glutamate change, since at position 2 of said codon 600 a T is mutated to A. The primer that is to be applied for the detection of that SN P binds on the upper strand with its 3'-end directly in front of C600-2. [0118] To detect the SNP at the corresponding position, primers are extended by a single, unlabeled dideoxynucleotide dependent on the complementary base information. After the reaction, primers have different lengths and hydrophobicities (caused by the incorporated base) making them suitable for separation on an IP/RP-HPLC (here: WAVE system, Transgenomic). Detection was rendered by UV light; additional labelling or signal enhancement was considered to be unnecessary. As shown in Figure 2 the optimized assay analyses two positions (C12-1 + C13-2 and C12-2 + C13-1) in one primer extension reaction and in the very same H PLC run.

[0119] In a third aspect, the present invention relates to a use of the method of detecting one or more SNPs in a gene of interest in determining a predisposition for a tumor, preferably a solid tumor, comprising

(a) amplifying a nucleotide sequence of the KRAS gene comprising at least codons 12 and 13 as determined from the KRAS gene shown in SEQ ID NO:1 (NM_004985) with the first codon starting at nucleotide position 182 ;

(b) simultaneously (multiplex) extending multiple primers annealed downstream of (i) C12-1 , (ii) C12-2, (iii) C13-1 and/or (iv) C13-2 of the KRAS gene such that at least each of C12-1 , C12-2, C13-1 and/or C13-2 nucleotides is contained in a separate extension product formed thereby;

(c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and

(d) determining whether at a position corresponding to C12-1 , C12-2, C13-1 and/or C13- 2 of the KRAS gene shown in SEQ ID NO:1 a nucleotide different from that shown in SEQ ID NO:1 is present,

wherein the presence of at least one nucleotide difference is indicative for a predisposition for a tumor, preferably a solid tumor.

[0120] Preferably, said method further comprises

in step (a) amplifying a nucleotide sequence of the B gene comprising at least codon 600 as determined from the B-raf gene shown in SEQ ID No: 16 with the first codon starting as nucleotide position 1 ;

in step (b) simultaneously (multiplex) extending a primer annealed downstream of the second base of codon 600 (C600-2) such that said SNPs is contained in a separate extension products formed thereby;

in step (c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and

in step (d) determining whether at a position corresponding to C600-2 of the B- raf gene shown in SEQ ID NO: 16 a nucleotide different from that shown in SEQ ID No: 16 is present,

wherein the presence of a SNP at a position corresponding to C600-2of the B-raf gene shown in SEQ ID NO: 16 is indicative for a predisposition for a tumor, preferably a solid tumor. [0121] Preferably, the multiple primer extension step (b) is carried out as follows: in one reaction primers for C12-1 and C13-1 are extended and in a separate, further separate reaction primers for C12-2 and 13-2 as well as the primer for C600-2 are extended. [0122] The solid tumor may be developed by a subject suffering from colorectal cancer. Accordingly, the subject may, because of the presence of one or more of the SNPs described herein in the KRAS gene codons 12 and 13 (see SEQ ID No:2 or GenBank accession no. NM_004985), be at a risk of developing a solid tumor or colorectal cancer, respectively, or may even have developed such a tumor or colorectal cancer (including metastatic colorectal cancer).

[0123] Since the potential mutilations in codon 12 and 13, respectively, are also known to be associated with leukemia, especially AML, pancreatic cancer and/or lung cancer, the above and below method for (use in) determining a predisposition for a tumor is in a preferred aspect a method for use in determining a predisposition for colorectal cancer, leukemia, especially AML, pancreatic cancer and/or lung cancer.

[0124] Put differently, the present invention relates to a method for determining a predisposition for a tumor, preferably a solid tumor, comprising

(a) amplifying a nucleotide sequence of the KRAS gene comprising at least codons 12 and 13 as determined from the KRAS gene shown in SEQ ID NO: 1 (NM_004985) with the first codon starting at nucleotide position 182;

(b) simultaneously (multiplex) extending multiple primers annealed downstream of (i) C12-1 , (ii) C12-2, (iii) C13-1 and/or (iv) C13-2 of the KRAS gene such that at least each of C12-1 , C12-2, C13-1 and/or C13-2 nucleotides is contained in a separate extension product formed thereby;

(c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and

(d) determining whether at a position corresponding to C12-1 , C12-2, C13-1 and/or C13- 2 of the KRAS gene shown in SEQ ID NO:1 a nucleotide different from that shown in SEQ ID NO:1 is present,

wherein the presence of at least one nucleotide difference is indicative for a predisposition for a tumor, preferably a solid tumor. As described herein above, it is also envisaged for that method that a potential SNP at position 2 of codon 600 is analyzed. [0125] During their studies, the present inventors prepared DNA from 50 different tissue blocks obtained from colonoscopy of 50 different colorectal cancer patients. Histology of these tissue blocks was assessed by immunostaining resulting in a tumor/WT mix ranging from 10:90% to 60:50%. To show that the method of the present invention and its use in the herein described applications is robust and reliable these 50 different DNAs were screened for KRAS mutations (i.e., SNPs in the KRAS gene). In parallel, the present inventors performed direct sequencing and compared the results with those of the method of the present invention. In all analysed samples yielding a peak for a SNP (mutation) after direct sequencing, they also detected the SNP with the double multiplex method (see Table 1). As presented in Figure 3, the assay provided strong signals for the mutation even if the total amount of affected cells are quite low (10 or 15%). This makes the method of the present invention a much more sensitive and reliable tool in the detection of early cancer development (colorectal cancer including metastatic colorectal cancer). Moreover, the methods of the present invention are even more valuable, since they also allow in parallel the analysis of position 2 of codon 600 of the B-raf gene. Accordingly, the skilled person gets simultaneously results for the two most prominent biomarkers for prognosis of cancer, in particular those cancers mentioned herein, most preferably colorectal cancer (see Figures 4 and 5).

[0126] Indeed, by analysing 2 potentially mutated base positions in one reaction and HPLC run it was possibel to genotype 47 DNAs in a 96 well format within about 24 hours. None of the samples had to be repeated because of unsufficient signal quality or quantity. Moreover, the method of the present invention, in particular the use thereof in determining a predisposition for a tumor, preferably a solid tumor provides a sensitivity of down to 30 pg or 5% mutated template being detected in an excess of WT background. Sensitivity of regularly applied methos, like direct sequencing, does usually not go beyond 20% and reanalysing the sample is often required. In a pilot study on 30 DNAs from different colorectal cancer patients we confirmed the applicability of the approach, obtaining 100% concordance with direct sequencing results. In some samples even mutations at several positions in codons 12 and 13 were detected that had not been detected before.

[0127] KRAS is a member of small G proteins that are involved in intracellular signalling by being activated through signal cascades initiated by cell surface receptor kinases (Malumbres and Barbacid, 2003). One of these is the epidermal growth factor receptor (EGFR) that activates signalling pathways like the Ras-Raf-Mek kinase pathway, that are responsible for cell cycle control (Schubbert et a\., 2007). Being mutated, the KRAS protein is unable to switch to its inactive form so that cell cycle progression is promoted. Former studies showed that mutations in the KRAS codons 12 and 13 are frequent in colorectal cancer patients and of clinical importance. Indeed, the introduction of epidermal growth factor receptor inhibitors (EGFR or EGFR-I as used herein) for therapy increased clinical benefit, however, only for a subset of patients treated. Recent publications revealed that a subset of tumors are insensitive to these inhibitors (Cunningham et al., 2004, Jonker et al., 2007, van Cutsem et al., 2007) escaping clinical benefit. Retrospective studies correlated those tumors with being mutated in the KRAS gene. Including KRAS mutation screening into routine CRC diagnostics therefore helps to improve the selection of patients which are candidates for EGFR-I treatment. In fact, identification of KRAS mutations in codon 12 and 13 rises importance as a prognostic marker that allows to choose the therapy with the highest success rate. Similarly, B-raf is the second most important marker for the prognosis of an appropriate therapy. In fact, when position 2 of codon 600 of the B-raf gene is mutated such that an amino acid change from valine to glutamate occurs, a subject has usually a bad prognosis as regards a therapy with an EGFR inhibitor. It is interestingly known that once a subject has one of the SNPs in the KRAs gene, it would not have a SNP in the B-raf gene as described herein (Di Nicolantonia et al., 2008)

[0128] Accordingly, in view of the fact that SNPs in the KRAS gene may be associated with a tumorigenic phenotype, KRAS mutational analysis is commercially available from a number of laboratories. In July 2009, the US Food and Drug Administration (FDA) updated the labels of two anti-EGFR monoclonal antibody drugs (panitumumab (Vectibix) and cetuximab (Erbitux)) indicated for treatment of metastatic colorectal cancer to include information about KRAS mutations. Hence, since the method of the present invention is more reliable than commonly applied methods for detecting SNPs, including SNPs in the KRAS gene, the present invention provides an interesting alternative that may even be improved in comparison to prior art methods.

[0129] That alternative is materialized in the fourth aspect of the present invention. In particular, in a fourth aspect, the present invention provides a use of the method for detecting one or more SNPs in a gene of interest in evaluating whether an EGFR-I inhibitor may be beneficial for the treatment of colorectal cancer (including metastatic colorectal cancer) of a subject comprising

(a) amplifying a nucleotide sequence of a KRAS gene comprising at least codons 12 and 13 as calculated from the KRAS gene shown in SEQ ID NO: 1 (NM_004985) with +1 at nucleotide position 182 or as calculated from the KRAS protein shown in SEQ ID

No:2 (NM_004986);

(b) simultaneously (multiplex) extending multiple primers annealed downstream of (i) C12-1 , (ii) C12-2, (iii) C13-1 and/or (iv) C13-2 of the KRAS gene such that at least each of C12-1 , C12-2, C13-1 and/or C13-2 nucleotides is contained in a separate extension product formed thereby;

(c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and (d) determining whether at a position corresponding to C12-1 , C12-2, C13-1 and/or C13- 2 of the KRAS gene shown in SEQ ID NO:1 a nucleotide different from that shown in SEQ ID NO:1 is present,

wherein the presence of at least one nucleotide difference is indicative that an EGFR-I inhibitor may not be beneficial for the treatment of colorectal cancer (including metastatic colorectal cancer) or any of the other cancers disclosed herein above of a subject (Lievre et al. (2006); Tarn et al. (2006).

[0130] The monoclonal antibodies panitumumab and cetuximab that target the epidermal growth factor receptor (EGFR) have expanded the range of treatment options for metastatic colorectal cancer. Initial evaluation of these agents as monotherapy in patients with EGFR- expressing chemotherapy-refractory tumors yielded response rates of approximately 10%. The realization that detection of positive EGFR expression by immunostaining does not reliably predict clinical outcome of EGFR-targeted treatment has led to an intense search for alternative predictive biomarkers. Oncogenic activation of signaling pathways downstream of the EGFR, such as mutation of KRAS, BRAF, or PIK3CA oncogenes, or inactivation of the PTEN tumor suppressor gene is central to the progression of colorectal cancer. Tumor KRAS mutations, which may be present in 35%-45% of patients with colorectal cancer, have emerged as an important predictive marker of resistance to panitumumab or cetuximab treatment. In addition, among colorectal tumors carrying wild-type KRAS, mutation of BRAF or PIK3CA or loss of PTEN expression may be associated with resistance to EGFR-targeted monoclonal antibody treatment. Additional knowledge of the molecular basis for sensitivity or resistance to EGFR-targeted monoclonal antibodies will allow the development of new treatment algorithms to identify patients who are most likely to respond to treatment and could also provide rationale for combining therapies to overcome primary resistance. The use of KRAS mutations as a selection biomarker for anti-EGFR monoclonal antibody (eg, panitumumab or cetuximab) treatment is the first major step toward individualized treatment for patients with metastatic colorectal cancer.

[0131] Accordingly, in order to obtain even more prognostic information as to whether or not an EGFR-I inhibitor may be beneficial for a subject, the above method preferably further comprises

in step (a) amplifying a nucleotide sequence of the B gene comprising at least codon 600 as determined from the B-raf gene shown in SEQ ID No:16 with the first codon starting as nucleotide position 1 ;

in step (b) simultaneously (multiplex) extending a primer annealed downstream of the second base of codon 600 (C600-2) such that said SNPs is contained in a separate extension products formed thereby; in step (c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and

in step (d) determining whether at a position corresponding to C600-2 of the B-raf gene shown in SEQ ID NO:16 a nucleotide different from that shown in SEQ ID No:16 is present,

wherein the presence of at least one nucleotide difference is indicative that an EGFR-I inhibitor may not be beneficial for the treatment of colorectal cancer of a subject.

[0132] Put differently, the present invention provides a method for evaluating whether an EGFR-I inhibitor may be beneficial for the treatment of colorectal cancer (including metastatic colorectal cancer) of a subject comprising

(a) amplifying a nucleotide sequence of a KRAS gene comprising at least codons 12 and 13 as calculated from the KRAS gene shown in SEQ ID NO:1 (NM_004985) with +1 at nucleotide position 182 or as calculated from the KRAS protein shown in SEQ ID No:2 (NM_004986);

(b) simultaneously (multiplex) extending multiple primers annealed downstream of (i) C12-1 , (ii) C12-2, (iii) C13-1 and/or (iv) C13-2 of the KRAS gene such that at least each of C12-1 , C12-2, C13-1 and/or C13-2 nucleotides is contained in a separate extension product formed thereby;

(c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and (d) determining whether at a position corresponding to C12-1 , C12-2, C13-1 and/or C13- 2 of the KRAS gene shown in SEQ ID NO:1 a nucleotide different from that shown in SEQ ID NO:1 is present,

wherein the absence of at least one nucleotide difference is indicative that an EGFR-I inhibitor may be beneficial for the treatment of colorectal cancer (including metastatic colorectal cancer) of a subject. Also, as mentioned above, that method comprises in a preferred embodiment that also the second position of codon 600 is analysed for the presence or absence of a mutation.

[0133] EGFR-I inhibitors are, for example, the antibodies panitumumab (Vectibix), cetuximab (Erbitux) or lapatinib (Tykerb/Ty erb).

It is believed that the methods of the present invention are not only suitable for the KRAS locus but should be applicable to other known single base variations throughout the genome, in particular for analyzing the B-raf gene as described herein. For example, as described herein above, it is believed that other cancer-related loci of, for example, proto-oncogenes or tumor suppressor genes can be subjected to analysis for one or more SNPs by applying the teaching and methods and uses thereof. The potential of the methods of the present invention is thus not limited to KRAS and/or B-raf. Rather, even the combination of different cancer-related loci within one reaction/run is feasible such as the combined analysis of KRAS and B-raf as described herein. Moreover, recently initiated whole-genome sequencing will help to identify further mutations being potential candidates for high-throughput screening using primer extension/H PLC approaches.

[0134] In some preferred embodiments, the SNP at a position corresponding to C12-1 , C12- 2, C13-1 and/or C13-2 of the KRAS gene (nucleotide sequence) shown in SEQ ID NO:1 (NM_004985) is a nucleotide substitution. [0135] In other preferred embodiments, the nucleotide substitution at a position corresponding to the position

(i) C12-1 of the KRAS gene is a G→ A, C or T substitution;

(ii) C12-2 of the KRAS gene is a G→ A, C or T substitution;

(iii) C13-1 of the KRAS gene is a G→ A, C or T substitution; and/or

(iv) C13-2 of the KRAS gene is a G→ A, C or T substitution.

Of note, any possible combination of nucleotide substitutions is envisaged:

Figure imgf000034_0001

n = mutation at C12-1. C12-2, C13-1 and C13-2

k = number of mutations chosen from n.

[0136] Specifically, the above nucleotide substitutions have the following consequences: mutation mutation

(by amino acid position) by nucleotide position

(SEQ ID No:2) (SEQ ID No:1) mutated ("new") codon

G12V Mutation 35G>T gtt (V) (codon 12)

G12S Mutation 34G>A agt (S) (codon 12)

G12R Mutation 34G>C cgt (R) (codon 12)

G12C Mutation 34G>T tgt (C) (codon 12)

G12D Mutation 35G>A gat (D) (codon 12)

G12A Mutation 35G>C get (A) (codon 12)

G13S Mutation 37G>A age (S) (codon 13) G13R Mutation 37G>C cgc (R) (codon 13)

G13C Mutation 37G>T tgc (C) (codon 13)

G13D Mutation 38G>A gac (D) (codon 13)

G13A Mutation 38G>C gcc (A) (codon 13)

G 13V Mutation 38G>T gtc (V) (codon 13)

(underlined is the mutated nucleotide in comparison to the wild-type nucleotide at the respective position; the thus encoded amino acid is written in parenthesis)

[0137] In other preferred embodiments, the nucleotide substitution at a position corresponding to the position C600-2 of the B-raf gene is a T -» A substitution. Specifically, the above nucleotide substitution has the following consequence: mutation mutation

(by amino acid position) by nucleotide position

(SEQ I D No: 17) (SEQ ID No: 16) mutated ("new") codon

V600E Mutation 1799 T>A gag. (E) (codon 600)

[0138] In a fifth aspect, the present invention relates to the combined use of multiplex primer extension and multiplex IP/RP-HPLC, both described herein, for detecting one or more single nucleotide polymorphisms (SNP) in a gene of interest. The gene of interest is preferably a proto-oncogene or tumor suppressor gene, most preferably KRAS. That use is achieved by applying the methods of the present invention. [0139] A sixth aspect of the present invention is a combined use of multiplex primer extension and multiplex IP/RP-HPLC for determining a predisposition for a tumor, preferably a solid tumor, more preferably a tumor developed by colorectal cancer. Hence, in the determination of a predisposition for a tumor is particularly preferred the determination of a predisposition of colorectal cancer including metastatic colorectal cancer. That use is achieved by applying the methods of the present invention.

[0140] In a seventh aspect the present invention provide a use of DNA Sep® Cartridges for the simultaneous separation of multiple primer extension products, each primer extension product comprising a SN P of a gene of interest. The gene of interest is preferably a proto- oncogene or tumor suppressor gene, most preferably KRAS. That use is achieved by applying the methods of the present invention. [0141] All embodiments described herein in the context of the methods of the present invention are equally applicable and thus pertain to the fifth, sixth and seventh aspect of the present invention, mutatis mutandis.

[0142] In an eighth aspect the present invention relates to a kit for performing the method of any one of the preceding claims comprising:

(a) means for multiplex primer extension reactions;

(b) means for multiplex IP/RP-HPLC; and

(c) optionally means for amplifying a nucleotide sequence of a gene of interest.

[0143] Means for multiplex primer extension preferably include primers, dNTPs, ddNTPs and the like. Means for multiplex IP/RP-HPLC preferably include DNA Sep® Cartridges from Transgenomic.

All embodiments described herein in the context of the methods of the present invention are equally applicable and thus pertain to the eighth aspect of the present invention, mutatis mutandis.

***

[0144] In sum, the present invention the present invention may be characterized by the following aspects:

1. A method for detecting one or more single nucleotide polymorphisms (SNP) in a gene of interest comprising

(a) amplifying a nucleotide sequence of said gene of interest suspected or known to comprise one or more SNPs;

(b) simultaneously (multiplex) extending multiple primers annealed downstream of said one or more SNPs such that each of said SNPs is contained in a separate extension product formed thereby;

(c) simultaneously (multiplex) separating said extension product by IP/RP-HPLC; and

(d) detecting said one or more SNPs by comparing the extension product of said gene of interest with the extension product from the corresponding wild-type gene.

2. The method of item 1 , wherein said SNP is a nucleotide substitution, addition and/or deletion.

3. The method of any one of the preceding items, wherein said one or more SNPs are suspected or known to be associated with a tumorigenic phenotype

4. The method of item 1 , wherein said gene of interest is a proto-oncogene. The method of any one of the preceding items which is for use in detecting one or more single nucleotide polymorphisms (SNP) in the KRAS gene comprising

(a) amplifying a nucleotide sequence of said KRAS gene comprising one or more of said SNPs;

(b) simultaneously (multiplex) extending multiple primers annealed downstream of the (i) first base of codon 12 (C12-1), (ii) second base of codon 12 (C12-2), (iii) first base of codon 13 (C13-1) and/or (iv) second base of codon 13 (C13-2) of the KRAS gene such that each of said SNPs is contained in separate extension products formed thereby;

(c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and

(d) detecting said one or more SNPs,

wherein the presence of a SNP at a position corresponding to C12-1 , C12-2, C13-1 and/or C13-2 of the KRAS gene shown in SEQ ID NO: 1 is indicative for a predisposition for a tumor.

The method of item 1 , wherein said gene of interest is a tumor suppressor gene. The method of any one of the preceding items which is for use in determining a predisposition for a tumor.

The method of anyone of items 1 to 4 which is for use in determining a predisposition for a tumor comprising

(a) amplifying a nucleotide sequence of the KRAS gene comprising at least codons 12 and 13 as determined from the KRAS gene shown in SEQ ID NO:1 with the first codon starting at nucleotide position 182 ;

(b) simultaneously (multiplex) extending multiple primers annealed downstream of (i) C12-1 , (ii) C12-2, (iii) C13-1 and/or (iv) C13-2 of the KRAS gene such that at least each of C12-1 , C12-2, C13-1 and/or C13-2 nucleotides is contained in a separate extension product formed thereby;

(c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and

(d) determining whether at a position corresponding to C12-1 , C12-2, C13-1 and/or C13-2 of the KRAS gene shown in SEQ ID NO:1 a nucleotide different from that shown in SEQ ID No:1 is present,

wherein the presence of at least one nucleotide difference is indicative for a predisposition for a tumor.

The method of anyone of items 1 to 4 which is for use in evaluating whether an EGFR-I inhibitor may be beneficial for the treatment of colorectal cancer of a subject comprising (a) amplifying a nucleotide sequence of said KRAS gene comprising at least codons 12 and 13 as calculated from the KRAS gene shown in SEQ ID NO:1 with +1 at nucleotide position 182;

(b) simultaneously (multiplex) extending multiple primers annealed downstream of (i) C12-1 , (ii) C12-2, (iii) C13-1 and/or (iv) C13-2 of the KRAS gene such that at least each of C12-1 , C12-2, C13-1 and/or C13-2 nucleotides is contained in a separate extension product formed thereby;

(c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and

(d) determining whether at a position corresponding to C12-1 , C12-2, C13-1 and/or C13-2 of the KRAS gene shown in SEQ ID NO:1 a nucleotide different from that shown in SEQ ID NO: 1 is present,

wherein the presence of at least one nucleotide difference is indicative that an EGFR- I inhibitor may be beneficial for the treatment of colorectal cancer of a subject.

The method of any one of items 5, 8 and 9, wherein the SNP at a position corresponding to C12-1 , C12-2, C13-1 and/or C13-2 of the KRAS gene shown in SEQ ID NO: 1 is a nucleotide substitution.

The method of any one of items 5, 8, 9 and 10, wherein the nucleotide substitution at a position corresponding to the

(i) C12-1 of the KRAS gene is a G→A, C or T substitution;

(ii) C12-2 of the KRAS gene is a G→ A, C or T substitution;

(iii) C13-1 of the KRAS gene is a G→ A, C or T substitution; and/or

(iv) C13-2 of the KRAS gene is a G→ A, C or T substitution.

The combined use of multiplex primer extension and multiplex IP/RP-HPLC for detecting one or more single nucleotide polymorphisms (SNP) in a gene of interest The combined use of multiplex primer extension and multiplex IP/RP-HPLC for determining a predisposition for a tumor.

Use of DNA Sep® Cartridges for the simultaneous separation of multiple primer extension products, each primer extension product comprising a SNP of a gene of interest.

A kit for performing the method of any one of the preceding items comprising:

(a) means for multiplex primer extension reactions;

(b) means for multiplex IP/RP-HPLC; and

(c) optionally means for amplifying a nucleotide sequence. FIGURES

The Figures show: [0145] Figure 1 : KRAS-Multiplex-SIRPH assay design

A) First 20 codons of wild-type KRAS cDNA are shown with all so far detected mutations in codons 12 and 13 (see SEQ ID Nos: 9 and 10)

B) SNuPE primer positions and their possible extension products; primers detecting the base information in C13-1 and C13-2 anneal onto the top strand, primers detecting mutations in C12-1 and C12-2 anneal onto the bottom strand.

[0146] Figure 2: Electropherograms of KRAS-Multiplex-SIRPH standards

A) standard for simultaneous mutation detection in C12-1/C13-1 and C12-2/C13-2 showing all possible eventually occurring peaks; on top, the incorporated ddNTP during SNuPE and the the respective base information is given

B) representative picture for WT KRAS. P1 = unextended primers C12-1 and C12-2, respectively, P2 = unextended primers C13-1 and C13-2, respectively

[0147] Figure 3: Examples for KRAS double blind study results obtained by sequencing and Multiplex-SIRPH

Percentage of chromosomes possessing the respective mutation and the subsequent amino acid are shown on the left followed by the direct sequencing electropherogram; arrows within the HPLC diagrams highlight the peaks representative for the respective mutation; P1 = unextended primer for C12-1 and C12-2, respectively, P2 = unextended primer for C13-1 and C13-2, respectively.

[0148] Figure 4: KRAS C12-2+C13-2 und BRAF C600-2 Multiplexed Primer-Extension Standard [0149] Figure 5: KRAS C12-2+C13-2 und BRAF C600-2 Multiplexed Primer-Extension WT-Probe EXAMPLES

[0150] The invention will now be described by reference to the following Examples which are merely illustrative and are not construed as a limitation of the scope the present invention.

Tissue block preparation and histology

[0151] Preparation of DNA from FFPE samples was described in detail recently in Schewe et al., 2006 and Petersen et al., 2007. Four 3 m sections were cut from every tissue sample. The first slide was stained for H&E and a histopathologic diagnosis was rendered by a pathologist. Subsequently, the tumor area was marked and the percentage of tumor in relation to the whole block was documented. Distribution of cell content in the marked area was evaluated and the percentage of tumor cells, stromal cells, necrosis, fat tissue and normal tissue (either normal colon mucosa, normal liver or normal lung) was noted. Inflammation was graded as either none, weak, moderate or strong. In addition, every tumor was graded according to WHO criteria and the percentage of mucinous tumor areas was evaluated. When biopsies were referred, one additional tissue slide was prepared at the end to ensure that the respective unstained slides still contained tumor. DNA was prepared using the Tissue QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) and DNA amount was estimated with the Nanodrop 1000 Spectrophotometer (Peqlab, Erlangen, Germany). .

PCR and direct sequencing

[0152] Prior to direct sequencing PCRs were performed in 50 μΙ reaction volume in the presence of 3 mM Tris-HCI, pH 8.8, 0.7 mM (NH4)2S04, 50 mM KCL, 2.5 mM MgCI2, 0.06 mM of each dNTP, 0.2 μΜ of each primer (forward: 5'-aaggcctgctgaaaatgactg-3' (SEQ I D No: 1 1 ), reverse: 5'-agaatggtcctgcaccagtaa-3' (SEQ I D No: 12)) 3 U HotFire DNA polymerase (Solis BioDyne, Tartu, Estonia) and 2.5 μΙ (approx. 100 ng) template. After the initial denaturation of 5 minutes at 95°C, 40 cycles of 94° C 1 min, 60° C 1 min and 72° C 1 min followed by a final extension of 72°C for 7 minutes were performed. 8,5 ng of the purified PCR products were used for sequencing with Big Dye Terminator Cycle Sequencing Mix v1.1 (Applied Biosystems) according to the manufacturer's instructions. Sequencing reactions were performed for both DNA strands with the PCR oligonucleotides (5 pM) as respective primers. Sequence analysis was done on a 3130 Genetic Analyzer, software Sequencing Analysis 5.2, (Applied Biosystems). The obtained files were aligned and examined for mutations in codon 12 and 13 of the KRAS gene by SeqScape 2.6 Software (Applied Biosystems). Primer extension and HPLC separation

[0153] 50 ng genomic DNA was used as template in a 30 μΙ reaction volume in presence of 3 mM Tris-HCI, pH 8.8, 0.7 mM (NH4)2S04, 50 mM KCL, 2.5 mM MgCI2, 0.06 mM of each dNTP, 3 U HotFire DNA polymerase (Solis BioDyne, Tartu, Estonia) and 1 μΜ primers (KRAS forward 5'-ggcctgctgaaaatgactgaata-3' (SEQ ID No:3), KRAS reverse 5'- ctcatgaaaatggtcagagaaacct-3' (SEQ ID No:4), BRAF forward: 5'-tcataatgcttgctctgatagga-3' (SEQ ID No: 13), BRAF reverse: 5'-ggccaaaaatttaatcagtgg-3') (SEQ ID No: 14). 5μΙ of PCR product were treated with 1 μΙ of ExoSAP (1 : 10 mixture of Exonuclease I and Shrimp Alkaline Phosphatase obtained from USB) for 30min at 37° C. To inactivate the ExoSAP enzymes the reaction was incubated 15 min at 80° C.

To the PCR product/ExoSAP-mix 14 μΙ primer extension mastermix (50 mM Tris-HCL, pH9.5, 2.5 mM MgCI2, 0.05 mM of all four ddNTPs, 2 x 3.6 μΜ SNuPE primer, 2.5 U Termipol (Solis BioDyne, Tartu, Estonia)) was added. HPLC-purified SNuPE primers have the following sequences: C12-1 5'-tagttggagct-3' (SEQ ID No:5), C13-1 5'-gcactcttgcctacgc-3' (SEQ ID No:6) (put into one reaction), C12-2 5'-gttggagctg-3' (SEQ ID No:7), C13-2 5 -actcttgcctacg- 3' (SEQ ID No:8), BRAF C600-2 5 -actccatcgagatttc-3' (SEQ ID No: 15) (put into one reaction). SNuPE reactions were performed with 96° C/2min followed by 50 cycles 96° C/30sec, 50° C/30sec, 60° C/1 min. Separation of SNuPE products was conducted at 50° C by continuously mixing buffer B (0.1 M TEAA, 25% acetonitril) to buffer A (0.1 M TEAA), either over 13 min: 21-29% (C12-1 + C13-1), or 21 min: 12-24% (C12-2, C13-2, BRAF 600-2). Results are shown in Figures 4 and 5.

Assay design

[0154] To date, 12 nucleotide variants are known for KRAS codons 12 and 13. Interestingly, they are limited to the first two bases of the codons leaving the third position unchanged (Fig. lA). For codon 12, position 1 and 2 (C12-1 , C12-2) the WT nucleotide G can be replaced by the nucleotides A, G or T. In codon 13, only two variants for the positions 1 (C13-1 ) and 2 (C13-2) are known: C13-1 : G (WT) and T (tumor), and C13-2: G (WT) and A (tumor). In total, we designed four different primers to detect all of these variations (Fig.l B). The first primer, detecting variations in C12-1 , binds to the lower strand of the PCR product with its 3'-end directly in front of C12-1 . The second primer also bind on the lower strand but with its 3'-end directly in front of C12-2. We chose a G for the last base of this primer (binding at C12-1 ) since all other nucleotides at C12-1 are neighboured by a G at C12-2. So if there's no G at C12-1 , there is always a G at C12-2. The third primer, detecting the nucleotide at C13-2, binds to the upper strand and ends with its 3'end directly on position C13-3, being constant in all cases so far known. Consequently, the fourth primer also binds to the upper strand, ends with its 3'-end at C13-2 and detects the base information of C13-1. To detect the mutation at the corresponding position, primers are extended by a single, unlabeled dideoxynucleotide dependent on the complementary base information. After the reaction, primers have different lengths and hydrophobicities (caused by the incorporated base) making them suitable for separation on an I P/RP-HPLC (here: WAVE™ system, Transgenomic). Detection was rendered by UV light; additional labelling or signal enhancement was considered to be unnecessary. As shown in Fig. 2 the optimized assay analyses two positions (C12-1 + C13-2 and C12-2 + C13-1) in one primer extension reaction and in the very same HPLC run. Assay sensitivity

[0155] To define the mutation detection limit of the assay the KRAS amplicons from mixed WT/cancerous tissues were cloned. Templates with mutated and WT genotype were diluted and mixed from 1 : 1 to 1 : 100 which equates to 600 pg to 6 pg mutated KRAS in an excess of WT background. For each of the eight known mutations in codons 12 and 13 the detection limit was defined. Table 1 shows that all mutations could be detected to a threshold of 1 :20 (30 pg template including either mutation). Interestingly, analysis of C12-1 showed the most sensitive (1 : 100 (6 pg)), analysis of C13 the least sensitive detection limit (1 :20 (30 pg)). To show the advantage of the assay versus the common direct sequencing method, we analysed DNA samples extracted from formaldehyde-fixed, paraffin-embedded tissue blocks as this represents the common application. In these tissue blocks, tumor cells are neighboured by healthy areas so that WT and tumorous genotypes are detected simultaneously. Looking at all possible changes at codons 12 and 13, signals obtained after primer extension and HPLC separation were robust - irrespective of the tumor/WT cell ratios ranging from 10:90 to 70:30% (data not shown). Comparing samples with tumor/WT cell ratios of 30:70, 20:80, 10:90 and 5:95% with direct sequencing results, we observed samples below 30% of tumor cells fail to provide signals above background noise in direct sequencing but show clear tumor-specific peaks down to 5% within the HPLC electropherogram. This makes our approach a much more reliable tool in detecting early stages of cancerogenesis. Pilot study to test assay reliability

[0156] DNA was prepared from 50 different tissue blocks obtained from colonoscopy of 50 different colorectal cancer patients. Histology of these tissue blocks was assessed by immunostaining resulting in a tumor/WT mix ranging from 10:90% to 60:50%. To show that the here presented assay is robust and reliable we screened the 50 different DNAs for KRAS mutations. In parallel, we performed direct sequencing and compared the results with those of the primer extension assay. In all analysed samples yielding a peak for mutation after direct sequencing, we also detected the mutation with the primer extension/HPLC assay (see Table 1). As presented in Figure 3, the assay provided strong signals for the mutation even if the total amount of affected cells are quite low (10 or 15%). This makes the primer extension/HPLC approach a much more sensitive and reliable tool in the detection of early cancer development.

Table 1 : Detection limits obtained after spiking mutated template into WT background prior to PCR

Mutation template was spiked in different concentrations into an excess of WT background DNA. After Multiplex-SIRPH peaks were detected (V) or not (-) depending on template quantity and primer extension efficiency.

Figure imgf000044_0001

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Claims

Claims
1. A method for detecting single nucleotide polymorphisms (SNPs) in the coding region of a gene of interest encoding a protein comprising
(a) amplifying a nucleotide sequence of said gene of interest suspected or known to comprise said SNPs;
(b) simultaneously (multiplex) extending multiple primers annealed downstream of said SNPs such that each of said SNPs is contained in a separate extension product formed thereby;
(c) simultaneously (multiplex) separating said extension product by IP/RP-HPLC; and
(d) detecting said SNPs by comparing the extension product of said gene of interest with the extension product from the corresponding wild-type gene, wherein the primers are designed in a way such that their base composition is different to such an extent that they are distinguishable by IP/RP HPLC.
2. The method of claim 1 , wherein said SNPs are next to each other.
The method of claim 1 or 2, wherein said SNP is a nucleotide substitution, addition and/or deletion.
The method of any one of the preceding claims, wherein said SNPs are suspected or known to be associated with a tumorigenic phenotype
The method of claim 4, wherein the presence of said SNPs in the nucleotide sequence of a gene of interest at a position in comparison to the respective position of the nucleotide sequence of the wild-type gene is indicative for a predisposition for a tumor.
The method of claim 1 , wherein said gene of interest is a proto-oncogene.
The method of claim 6, wherein said proto-oncogene is selected from the group consisting of growth factors, Receptor Tyrosine Kinases, Membrane Associated Non- Receptor Tyrosine Kinases, G protein coupled receptors, Membrane Associated G- Proteins, Serine-Threonine Kinases, and Nuclear DNA-Binding/Transcription Factors.
8. The method of claim 6 or 7, wherein said proto-oncogene is at least one selected from the group consisting of KRAS, B-raf RAS, WNT, MYC, ERK, B-raf, TRK, met, ret, ErB2/Her2/neu, Bcl-2 and c-myc.
The method of any one of the preceding claims which is for use in detecting one or more single nucleotide polymorphisms (SNP) in the KRAS gene comprising
(a) amplifying a nucleotide sequence of said KRAS gene comprising one or more of said SNPs;
(b) simultaneously (multiplex) extending multiple primers annealed downstream of the (i) first base of codon 12 (C12-1 ), (ii) second base of codon 12 (C12-2), (iii) first base of codon 13 (C13-1 ) and/or (iv) second base of codon 13 (C13-2) of the KRAS gene such that each of said SNPs is contained in separate extension products formed thereby;
(c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and
(d) detecting said one or more SN Ps,
wherein the presence of a SN P at a position corresponding to C12-1 , C12-2, C13-1 and/or C13-2 of the KRAS gene shown in SEQ ID NO: 1 is indicative for a predisposition for a tumor.
The method of claim 9, wherein the primer which anneals downstream of (i) C12-1 is designed such that it anneals with its 3'-end directly in front of C12-1 , (ii) C12-2 is designed such that it anneals with its 3'-end directly in front of C12-2, (iii) C13-1 is designed such that it anneals with its 3'-end directly in front of C13-1 and/or (iv) C13- 2 is designed such that it anneals with its 3'-end directly in front of C13-2.
1 1. The method of claim 9 or 10 further comprising
in step (a) amplifying a nucleotide sequence of the B gene comprising one or more of said SNPs;
- in step (b) simultaneously (multiplex) extending a primer annealed downstream of the second base of codon 600 (C600-2) such that said SN Ps is contained in a separate extension products formed thereby;
in step (c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and
- in step (d) detecting said one or more SNPs,
wherein the presence of a SNP at a position corresponding to C600-2 of the B-raf gene shown in SEQ I D NO: 16 is indicative for a predisposition for a tumor.
The method of claim 1 , wherein said gene of interest is a tumor suppressor gene.
The method of claim 12, wherein said tumor suppressor gene is a Breast or Ovarian Cancer Susceptibility Gene or a Hereditary Cancer Syndrome Gene.
The method of claim 13, wherein said Breast and Ovarian Cancer Susceptibility Gene is selected from the group consisting of BRCA1 , BRCA2, ATM, CHEK2, BRIP1 , PALB2 and RAD51 C.
The method of claim 14, wherein said Hereditary Cancer Syndrome Gene is selected from the group consisting of p53, WT1 , NF1 , NF2, APC, TSC1 , TSC2, DPC4, DCC, STK11 , MSH 1 , MLH2, VHL, CDKN2, PTEN, MEN1 and MEN2.
The method of any one of the preceding claims which is for use in determining a predisposition for a tumor.
The method of anyone of claims 1 to 8 which is for use in determining a predisposition for a tumor comprising
(a) amplifying a nucleotide sequence of the KRAS gene comprising at least codons 12 and 13 as determined from the KRAS gene shown in SEQ ID NO:1 with the first codon starting at nucleotide position 182 ;
(b) simultaneously (multiplex) extending multiple primers annealed downstream of (i) C12-1 , (ii) C12-2, (iii) C13-1 and/or (iv) C13-2 of the KRAS gene such that at least each of C12-1 , C12-2, C13-1 and/or C13-2 nucleotides is contained in a separate extension product formed thereby;
(c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and
(d) determining whether at a position corresponding to C12-1 , C12-2, C13-1 and/or C13-2 of the KRAS gene shown in SEQ ID NO: 1 a nucleotide different from that shown in SEQ ID No:1 is present,
wherein the presence of at least one nucleotide difference is indicative for a predisposition for a tumor.
The method of claim 17 further comprising
in step (a) amplifying a nucleotide sequence of the B gene comprising at least codon 600 as determined from the B-raf gene shown in SEQ ID No: 16 with the first codon starting as nucleotide position 1 ; in step (b) simultaneously (multiplex) extending a primer annealed downstream of the second base of codon 600 (C600-2) such that said SNPs is contained in a separate extension products formed thereby;
in step (c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and
in step (d) determining whether at a position corresponding to C600-2 of the B- raf gene shown in SEQ ID NO: 16 a nucleotide different from that shown in SEQ ID No: 16 is present,
wherein the presence of a SNP at a position corresponding to C600-2of the B-raf gene shown in SEQ ID NO: 16 is indicative for a predisposition for a tumor.
The method of anyone of claims 1 to 8 which is for use in evaluating whether an EGFR-I inhibitor may be beneficial for the treatment of colorectal cancer of a subject comprising
(a) amplifying a nucleotide sequence of said KRAS gene comprising at least codons 12 and 13 as calculated from the KRAS gene shown in SEQ ID NO:1 with +1 at nucleotide position 182;
(b) simultaneously (multiplex) extending multiple primers annealed downstream of (i) C12-1 , (ii) C12-2, (iii) C13-1 and/or (iv) C13-2 of the KRAS gene such that at least each of C12-1 , C12-2, C13-1 and/or C13-2 nucleotides is contained in a separate extension product formed thereby;
(c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and
(d) determining whether at a position corresponding to C12-1 , C12-2, C13-1 and/or C13-2 of the KRAS gene shown in SEQ ID NO: 1 a nucleotide different from that shown in SEQ ID NO: 1 is present,
wherein the presence of at least one nucleotide difference is indicative that an EGFR- I inhibitor may not be beneficial for the treatment of colorectal cancer of a subject.
The method of claim 19 further comprising
in step (a) amplifying a nucleotide sequence of the B gene comprising at least codon 600 as determined from the B-raf gene shown in SEQ ID No: 16 with the first codon starting as nucleotide position 1 ;
in step (b) simultaneously (multiplex) extending a primer annealed downstream of the second base of codon 600 (C600-2) such that said SNPs is contained in a separate extension products formed thereby; in step (c) simultaneously (multiplex) separating said extension products by IP/RP HPLC; and
in step (d) determining whether at a position corresponding to C600-2 of the B- raf gene shown in SEQ ID NO: 16 a nucleotide different from that shown in SEQ ID No: 16 is present,
wherein the presence of at least one nucleotide difference is indicative that an EGFR- I inhibitor may not be beneficial for the treatment of colorectal cancer of a subject.
The method of any one of claims 9, 10, 17 and 19, wherein the SNP at a position corresponding to C12-1 , C12-2, C13-1 and/or C13-2 of the KRAS gene shown in SEQ ID NO: 1 is a nucleotide substitution.
The method of any one of claims 9, 10, 17, 19, and 21 , wherein the nucleotide substitution at a position corresponding to the position
(i) C12-1 of the KRAS gene is a G→ A, C or T substitution;
(ii) C12-2 of the KRAS gene is a G→ A, C or T substitution;
(iii) C13-1 of the KRAS gene is a G→ A, C or T substitution; and/or
(iv) C13-2 of the KRAS gene is a G→ A, C or T substitution.
The method of any of claim 11 , 18, and 20, wherein the SNP at a position corresponding to C600-2 of the B-raf gene shown in SEQ ID NO: 16 is a nucleotide substitution.
The method of any of claim 1 1 , 18, 20 and 22, wherein the nucleotide substitution at a position corresponding to the position C600-2 of the B-raf gene is a T-> A substitution.
The method of any one of the preceding claims, wherein said multiple primers are chosen to be specific for said one or more SNPs.
The method of any one of the preceding claims, wherein said multiple primers have a length of at least 9 nucleotides.
The method of any one of the preceding claims, wherein said multiple primers differ from each other by at least 1 nucleotide in length.
The method of any one of the preceding claims, wherein said primers can be labelled.
The method of any one of the preceding claims, wherein step (b) is performed on a single amplification product encompassing said SNPs.
The method of any one of the preceding claims, wherein step (b) is performed on two or more amplification products encompassing said SNPs.
31. The combined use of multiplex primer extension and multiplex IP/RP-HPLC for detecting single nucleotide polymorphisms (SNP) in the coding region of a proto- oncogene or tumor suppressor gene.
32. The combined use of multiplex primer extension and multiplex IP/RP-HPLC for determining a predisposition for a tumor.
33. Use of DNA Sep® Cartridges for the simultaneous separation of multiple primer extension products, each primer extension product comprising a SNP of the coding region of a proto-oncogene or tumor suppressor gene.
34. A kit for performing the method of any one of the preceding claims comprising:
(a) means for multiplex primer extension reactions;
(b) means for multiplex IP/RP-HPLC; and
(c) optionally means for amplifying a nucleotide sequence.
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