WO2014160876A2

WO2014160876A2 - Brca2-specific modifier locus related to breast cancer risk

Info

Publication number: WO2014160876A2
Application number: PCT/US2014/032038
Authority: WO
Inventors: Kenneth Offit; Mia M. GAUDET; Karoline B. KUCHENBAECKER; Joseph VIJAI; Robert J. Klein; Antonis C. ANTONIOU
Original assignee: Memorial Sloan Kettering Cancer Center
Current assignee: Memorial Sloan Kettering Cancer Center
Priority date: 2013-03-27
Filing date: 2014-03-27
Publication date: 2014-10-02
Anticipated expiration: 2015-09-27
Also published as: WO2014160876A3; US20160251722A1

Abstract

The present invention relates to novel SNP biomarkers and to panels of biomarkers that may be used in assessing the risk that a patient carrying a BRCA2 mutation will develop breast cancer. It is based, at least in part, on the identification of a SNP located at 6p24 in the human genome which is associated with breast cancer risk in subjects carrying the BRCA2 mutation but not in the general population. In specific non-limiting embodiments, a SNP from the 6p24 region may be used alone or together with one or more breast cancer risk biomarker to evaluate the likelihood that a subject will develop breast cancer.

Description

BRCA2 -SPECIFIC MODIFIER LOCUS RELATED TO BREAST CANCER

RISK

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Patent Application

Serial No. 61/805,783, filed March 27, 2013, which is incorporated by reference herein in its entirety.

1 · INTRODUCTION

The present invention relates to novel single nucleotide polymorphism ("SNP") biomarkers and to panels of biomarkers that may be used in assessing the risk that a patient carrying a BRCA2 mutation will develop breast cancer. In particular non-limiting embodiments, the invention relates to biomarkers (minor alleles) in the human chromosome 6p24 region as indicators of decreased risk of developing breast cancer.

2. BACKGROUND OF THE INVENTION

The lifetime risk of breast cancer associated with carrying a BRCA2 mutation varies from 40 to 84% [1]. A genome- wide association study ("GWAS") of BRCA2 mutation carriers from the Consortium of Investigators of Modifiers of BRCAl/2 (CIMBA) was performed in order to determine whether common genetic variants modify breast cancer risk for BRCA2 mutation carriers [2]. Using the Affymetrix 6.0 platform, the discovery stage results were based on 899 young (<40 years) affected and 804 unaffected carriers of European ancestry. In a rapid replication stage wherein 85 discovery stage SNPs with the smallest P-values were genotyped in 2,486 additional BRCA2 mutation carriers, only published loci associated with breast cancer risk in the general population, including FGFR2 (10q26; rs2981575; P=1.2xl0-8), were associated with breast cancer risk at the genome-wide significance level among BRCA2 mutation carriers. Two other loci, in ZNF365

(rs 16917302) on 10q21 and a locus on 20ql3 (rs311499), were also associated with breast cancer risk in BRCA2 mutation carriers with P-values <10-4 (P=3.8xl0-5 and 6.6x10-5, respectively). A nearby SNP in ZNF365 was also associated with breast cancer risk in a study of unselected cases [3] and in a study of mammographic density [4], Additional follow-up replicated the findings for rsl 6917302, but not rs31 1499 [5] in a larger set of BRCA2 mutation carriers. There remained a need to identify additional breast cancer risk modifying loci for BRCA2 mutation carriers.

3. SUMMARY OF THE INVENTION

The present invention relates to novel SNP biomarkers and to panels of biomarkers that may be used in assessing the risk that a patient carrying a BRCA2 mutation will develop breast cancer. It is based, at least in part, on the identification of a SNP located at 6p24 in the human genome which is associated with breast cancer risk in subjects carrying the BRCA2 mutation but not in the general population. In specific non-limiting embodiments, a SNP from the 6p24 region may be used alone or together with one or more breast cancer risk biomarker to evaluate the likelihood that a subject will develop breast cancer.

4. BRIEF DESCRIPTION OF THE FIGURES

FIGURE 1. Associations between SNPs in the region surrounding rs9348512 on chromosome 6 and breast cancer risk for BRCA2 mutation carriers. Results based on imputed and observed genotypes. The blue spikes indicate the recombination rate at each position. Genotyped SNPs are represented by diamonds and imputed SNPs are represented by squares. Color saturation indicates the degree of correlation with the SNP rs9348512.

FIGURE 2. Predicted breast cancer risks for BRCA2 mutation carriers by the combined SNP profile distributions of the known breast cancer susceptibility loci at FGFR2, TOX3, 12pl 1, 5ql 1 , CDKN2A/B, LSP1, 8q24, ESR1, ZNF365, 3p24, 12q24, 5pl2, 1 Iql 3 and the newly identified BRCA2 modifier locus at 6p24. The figure shows the risks at the 5th and 95th percentiles of the combined genotyped distribution as well as minimum, maximum and average risks.

FIGURE 3A-C. Cluster plots for SNPs (A) rs9348512, (B) rs619373, and (C) rsl 84577.

FIGURE 4A-B. Multidimensional scaling plots of the top two principal components of genomic ancestry of all eligible BRCA2 iCOGS samples plotted with the HapMap CEU, ASI, and YRI samples: (A) samples from Finland and BRCA2 6174delT carriers highlighted, and (B) samples, indicated in red, with >19% non- European ancestry were excluded. FIGURE 5A-C. Quantile-quantile plot comparing expected and observed distributions of P-values. Results displayed (A) for the complete sample, (B) after excluding samples from the GWAS discovery stage, and (C) for the complete sample and a set of SNPs from the iCOGS array that were selected independent from the results of the BRCA2 mutation carriers.

FIGURE 6. Manhattan plot of P-values by chromosomal position for 18,086 SNPs selected on the basis of a previously published genome-wide association study of BRCA2 mutation carriers. Breast cancer associations results based on 4,330 breast cancer cases and 3,881 unaffected BRCA2 carriers.

FIGURE 7. Forest plot of the country-specific, per-allele hazard ratios

(HR) and 95% confidence intervals for the association between breast cancer and rs9348512 genotypes.

FIGURE 8A-B. Forest plot of the country-specific, per-allele hazard ratios (HR) and 95% confidence intervals for the association with breast cancer for (A) rs619373 and (B) rsl84577 genotypes.

5. DETAILED DESCRIPTION OF THE INVENTION

For clarity of disclosure and not by way of limitation the detailed description of the invention is divided into the following subsections:

(i) the BRCA2 Modifier Locus and its biomarkers;

(ii) risk assessment biomarker panels;

(iii) kits;

(iv) prognostic methods; and

(v) methods of treatment.

By way of introduction, the present invention relates to biomarkers which are allelic variations, allelic variants and/or single nucleotide polymorphisms. The biomarkers may be represented as nucleic acid molecules, for example SNPs, or may be represented as protein expression product of said nucleic acid.

The term "allelic variation" refers to the presence, in a population, of different forms of the same gene characterized by differences in their nucleotide sequences (sequences in genomic DNA). The variation may be in the form of one or more substitution, insertion, or deletion of a nucleotide. Different alleles may be functionally the same, or may be functionally different. In one subset of allelic variations, a single nucleotide is different between alleles and is referred to as a Single Nucleotide Polymorphism ("SNP"). Allelic variation in a known sequence may be identified by standard sequencing techniques. A "variation" or "variant," as those terms are used herein, is relative to the ancestral gene found in the majority of the population. Unless specified otherwise, the presence of a SNP means that at the single nucleotide position for which alleles have been identified, the nucleotide present is the variant nucleotide (also referred to as the "minor allele"), not the nucleotide found in the majority of the population (also referred to as the "major allele"). The variation (variant) is comprised of a substituted nucleotide or nucleotides or an insertion or deletion of a nucleotide or nucleotides. Herein, generally the ancestral nucleotide (major allele) is listed first and the variation (variant, minor allele) nucleotide is listed second (for example, in A/G A is the ancestral nucleotide and G is the variation (variant) nucleotide). If there is an insertion, the ancestral nucleotide is represented by a hyphen (e.g., -/G). If there is a deletion, the variation (variant) nucleotide is represented by a hyphen (e.g., G/-). Numerous allelic variations (variants), captured in SNPs, of genes are known in the art and catalogued (for example, in the National Center for Biotechnology

Information "Entrez SNP"). Allelic variations that are not SNPs include deletions or insertions or substitutions of multiple consecutive nucleotides.

In non-limiting embodiments of the invention, the presence of an allelic variation, for example a SNP, may be determined using a technique such as, but not limited to, primer extension or polymerase chain reaction, using primer(s) designed based on sequence in the proximity of the variation, followed by sequencing. For example, and not by way of limitation, the presence of a SNP may be determined by a method comprising using at least one primer sequence complementary to a sequence flanking the location of the SNP (for example, within 80 nucleotides, or within 50 nucleotides, or within 30 nucleotides, or within 20 nucleotides, or within 10 nucleotides, of the SNP) in a primer extension reaction or polymerase chain reaction to generate a test fragment that contains the location of the SNP and determining the nucleotide present at the location of the single nucleotide polymorphism, for example by sequencing all or a portion of the test fragment.

In addition to sequencing-based methods, other methods are known in the art for detecting one or more SNP including, but not limited to, methods that utilize hybridization, restriction fragment length polymorphism, enzyme-based methods, or electrophoresis, to name a few. Exemplary technologies for detecting SNPS include but are not limited to TaqMan® SNP Genotyping Assays, SNPlex™, Affymetrix Human SNP GeneChip (e.g. version 6.0), Sequenom MassArray sequencing, Illumina BeadArray products, and see, for example, De La Vega et al., 2005, Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 573:1 11-135; Larmy et al. 2006, Nucl. Acids Res. 34(14):el00 Shen et al., 2005, Mutat. Res. 573(l-2):70-82; Gaudet et al., 2009, Methods Mol. Biol. 578:415-424; Shen et al, 2009, Methods Mol. Biol. 578:293-306; Olivier, 2005, Mutat. Res. 573(1- 2X103-110; Duan et al., 2009, Biosens. Bioelectron 24(7): 2095-2099; Duan et al., 2009, Nat. Protoc. 4(6}:984-991 ; Hori et al, 2003, Curr. Pharm. Biotechnol. 4(6 :477- 484; Kwok and Chen, 2003, Curr. Isues Mol. Biol. 5:43-60; Kwok, 2002, Hum.

Mutat. 19(4):315-323 and Comen et al., 2011 , Breast Cancer Res. Treat. 127(2):479- 87.

Nucleic acid sequences of certain SNPs and the surrounding nucleic acids are set forth in TABLE 7 below.

In non-limiting embodiments where a biomarker is a protein, methods standard to the art may be used to detect the protein biomarker. Such methods include, but are not limited to, electrophoretic or chromatographic methods, mass spectrometry techniques, peptide sequencing, 1-D or 2-D gel-based analysis systems, protein microarray, immunofluorescence, Western blotting, enzyme linked immunosorbent assay ("ELISA"), radioimmunoassay (RIA), enzyme immunoassays (EIA) and other antibody-mediated detection methods known in the art.

A "subject" herein is a human subject. In particular non-limiting embodiments, the subject is a female. In particular non-limiting embodiments, the subject has a family history of breast cancer, for example, a mother, sister, grandmother, or aunt with breast cancer, for example occurring before the age of 40 or before the age of 50.

5.1 THE BRCA2 MODIFIER LOCUS AND ITS BIOMARKERS

In various embodiments a SNP (variant, minor allele) in the 6p24 region (also referred to herein as a "6p24 SNP") of the human genome may be used to assess the risk that a subject also carrying a BRCA2 mutation (variant, minor allele) may have or develop breast cancer, where the presence of the 6p24 SNP is associated with a lower risk that the subject has or will develop breast cancer relative to a subject having a BRCA2 mutation (also referred to as a BRCA2 biomarker) and the major allele at the 6p24 position. In certain non-limiting embodiments, the location of the SNP is between human chromosome 6 position 10540 kb and 10570 kb or between 10550 kb and 10565 kb or between 10560 kb and 10565 kb. In certain non-limiting embodiments, r² for the association between the SNP and breast cancer is at least 0.6 or at least 0.7 or at least 0.8.

In a specific non-limiting embodiment, the SNP is the minor allele at rs9348512, which, as illustrated in the working example below, was observed to be associated with a 15% decreased risk of breast cancer among BRCA2 mutation carriers (per allele HRH3.85, 95% CI 0.80-0.90) with no evidence of between-country heterogeneity (P=0.78, FIGURE 7). The association with rs9348512 did not differ by 6174delT mutation status (P for difference^.33), age (P=0.39), or estrogen receptor (ER) status of the breast tumor (P=0.78).

In a particular non-limiting embodiment, the presence of the major allele in a subject may be evaluated, for example as a means of determining heterozygosity or as a cross check when assessing whether the minor allele is present.

In other specific non-limiting embodiments, the SNP in the 6p24 region is a SNP listed in TABLE 5 below, where the minor alleles are shown. For example, but not by way of limitation, additional examples of 6p24 SNPs, which may be used according to the invention, include (minor alleles of) rs9358529, rs303067 and rs9366443.

5.2 RISK ASSESSMENT BIOMARKER PANELS A 6p24 SNP may be used alone or together with one or more additional biomarker (which together constitute a "panel") to assess the risk that a subject has or will develop breast cancer.

As the association for the 6p24 SNP with breast cancer is in the context of a BRCA2 mutation, a BRCA2 mutation, for example, but not limited to a BRCA2 SNP, may optionally be included in the panel so that the existence of BRCA2 mutation and 6p24 SNP may be assessed in the same assay or series of assays.

In addition, the panel may further comprise one or more biomarker in one or more or two or more or three or more or four or more or five or more or six or more or seven or more or eight or more or nine or more or ten or more or eleven or more or twelve or thirteen of the following genes and/or loci ("auxiliary biomarkers" in that they are other than a 6p24 SNP or a BRCA2 biomarker): 10q26 (FGFR2), 16ql2 (TOX3), 12pl l (PTHLH), 5ql l (MAP3K1), 9p21 (CDKN2A/B), l lpl5 (LSPl), 8q24, 6q25 (ESR1), 10q21 (ZNF365), 3p24 (SLC4A7, NEK!O), 12q24, 5pl2, and 1 l ql3. A non-limiting set of SNPs corresponding to these biomarkers is provided in TABLES 1 , 2, 5, and 6. TABLE 1 provides information regarding which biomarkers are associated with an increased risk of breast cancer and which biomarkers are associated with a decreased risk of breast cancer.

In certain non-limiting embodiments, a panel may comprise, in addition to a 6p24 SNP and optionally BRCA2, one or more biomarker selected from the biomarkers set forth in TABLES 1 , 2, and 6.

In certain non-limiting embodiments, the panel may comprise, in addition to a 6p24 SNP and optionally BRCA2, one or both of the following biomarkers: 10q26 (FGFR2) and/or 16ql2 (TOX3).

In certain non-limiting embodiments, the panel may comprise, in addition to a 6p24 SNP and optionally BRCA2, one, two, three, four, five or six of the following biomarkers: 10q26 (FGFR2), 16ql2 (TOX3), 5ql 1 (MAP3K1), 1 lpl 5 (LSPl) and/or 3p24 (SLC4A 7, NEKIO).

In a specific non-limiting embodiment, a panel comprises a biomarker of 10q26 (FGFR2) which is the SNP rs2420946.

In a specific, non-limiting embodiment, a panel comprises a biomarker of 16ql2 (TOX3) which is the SNP rs3803662.

In a specific non-limiting embodiment, a panel comprises a biomarker of 12pl 1 (PTHLH) which is the SNP rs27633.

In a specific non-limiting embodiment, a panel comprises a biomarker of 5ql 1 (MAP3K1) which is the SNP rsl 68861 13.

In a specific non-limiting embodiment, a panel comprises a biomarker of 10q26 (CDKN2A/B) which is the SNP rsl0965163.

In a specific non-limiting embodiment, a panel comprises a biomarker of 8q24 which is the SNP rs4733664.

In a specific non-limiting embodiment, a panel comprises a biomarker of 6q25 (ESR1) which is the SNP rs2253407.

In a specific non-limiting embodiment, a panel comprises a biomarker of 10q21 (ZNF365) which is the SNP rsl7221319.

In non-limiting embodiments, the above-described panel of biomarkers may constitute at least 10% or at least 20% or at least 30% or at least 40% or at least 50% or at least 60% or at least 70% or at least 80% or at least 90% or at least 95% or 100% of the biomarkers tested in a panel.

Biomarkers, which are not SNPs, may be detected using methods known in the art. Materials for such methods are discussed in the kits section below.

5.3 KITS

In non-limiting embodiments, the present invention provides for a kit for determining whether a subject has an increased risk of having or developing breast cancer comprising a means for detecting a 6p24 SNP and one or more biomarker selected from BRCA2, and an auxiliary biomarker selected from the group of 10q26 (FGFR2), 16ql2 (TOX3), 12pl l (PTHLH), 5ql l (MAP3K1), 9p21 (CDKN2A/B), l lpl 5 (LSP1), 8q24, 6q25 (ESR1), 10q21 (ZNF365), 3p24 (SLC4A 7, NEK10), 12q24, 5pl2, and l lql3.

Types of kits include, but are not limited to, packaged probe and primer sets (e.g. TaqMan probe/primer sets), arrays/microarrays, biomarker-specific antibodies and beads, which further contain one or more probes, primers, or other detection reagents for detecting one or more biomarkers of the present invention.

In a specific, non-limiting embodiment, a kit may comprise a pair of oligonucleotide primers, suitable for polymerase chain reaction (PCR) or nucleic acid sequencing, for detecting the biomarker(s) to be identified. A pair of primers may comprise nucleotide sequences complementary to a biomarker set forth above, and be of sufficient length to selectively hybridize with said biomarker. Alternatively, the complementary nucleotides may selectively hybridize to a specific region in close enough proximity 5' and/or 3' to the biomarker position to perform PCR and/or sequencing. Multiple biomarker-specific primers may be included in the kit to simultaneously assay large number of biomarkers. The kit may also comprise one or more polymerases, reverse transcriptase, and nucleotide bases, wherein the nucleotide bases can be further detectably labeled.

In non-limiting embodiments, a primer may be at least about 10 nucleotides or at least about 15 nucleotides or at least about 20 nucleotides in length and/or up to about 200 nucleotides or up to about 150 nucleotides or up to about 100 nucleotides or up to about 75 nucleotides or up to about 50 nucleotides in length.

In a specific, non-limiting embodiment, a kit may comprise at least one nucleic acid probe, suitable for in situ hybridization or fluorescent in situ hybridization, for detecting the biomarker(s) to be identified. Such kits will generally comprise one or more oligonucleotide probes that have specificity for various biomarkers.

In a further non-limiting embodiment, the oligonucleotide primers and/or probes may be immobilized on a solid surface or support, for example, on a nucleic acid microarray, wherein the position of each oligonucleotide primer and/or probe bound to the solid surface or support is known and identifiable.

In other non-limiting embodiments, a kit may comprise a primer for detection of a biomarker by primer extension.

In other non-limiting embodiments, a kit may comprise at least one antibody for immunodetection of the biomarker(s) to be identified. Antibodies, both polyclonal and monoclonal, specific for a biomarker, may be prepared using conventional immunization techniques, as will be generally known to those of skill in the art. The immunodetection reagents of the kit may include detectable labels that are associated with, or linked to, the given antibody or antigen itself. Such detectable labels include, for example, chemiluminescent or fluorescent molecules (rhodamine, fluorescein, green fluorescent protein, luciferase, Cy3, Cy5, or ROX), radiolabels ( H, ³⁵S, ³²P, ¹⁴C, ¹³¹I) or enzymes (alkaline phosphatase, horseradish peroxidase).

Alternatively, a detectable moiety may be comprised in a secondary antibody or antibody fragment which selectively binds to the first antibody or antibody fragment (where said first antibody or antibody fragment specifically recognizes a biomarker).

In a further non-limiting embodiment, the biomarker-specific antibody may be provided bound to a solid support, such as a column matrix, an array, or well of a microtiter plate. Alternatively, the support may be provided as a separate element of the kit.

In one specific non-limiting embodiment, a kit may comprise a primer, a pair of primers, a probe, microarray, or antibody suitable for detecting a 6p24 SNP biomarker.

In one specific non-limiting embodiment, a kit may comprise a primer, a pair of primers, a probe, microarray, or antibody suitable for detecting the rs9348512 SNP.

In certain non-limiting embodiments, a kit may comprise one or more pair of primers, primer, probe, microarray, or antibody suitable for detecting, in addition to a 6p24 SNP and optionally BRCA2, one, two, three, four, five or six of the following biomarkers: 10q26 (FGFR2), 16ql2 (TOX3), 5ql 1 (MAP3K1), 1 lpl5 (LSPi) and/or 3p24 (SLC4A7, NEK10).

In certain non-limiting embodiments, a kit may comprise a primer, a pair of primers, a probe, microarray, or antibody suitable for detecting, in addition to a 6p24 SNP and optionally BRCA2, one or more of the biomarkers shown in TABLES 1 , 2 and 6.

In a specific non-limiting embodiment, a kit may comprise a primer, a pair of primers, a probe, microarray, or antibody suitable for detecting a biomarker of 10q26 (FGFR2) which is the SNP rs2420946.

In a specific, non-limiting embodiment, a kit may comprise a primer, a pair of primers, a probe, microarray, or antibody suitable for detecting a biomarker of 16ql2 TOX3) which is the SNP rs3803662.

In a specific non-limiting embodiment, a kit may comprise a primer, a pair of primers, a probe, microarray, or antibody suitable for detecting a biomarker of 12pl 1 (PTHLH) which is the SNP rs27633.

In a specific non-limiting embodiment, a kit may comprise a primer, a pair of primers, a probe, microarray, or antibody suitable for detecting a biomarker of 5ql 1 (MAP3K1) which is the SNP rsl68861 13.

In a specific non-limiting embodiment, a kit may comprise a primer, a pair of primers, a probe, microarray, or antibody suitable for detecting a biomarker of 10q26 (CDKN2A/B) which is the SNP rs 10965163.

In a specific non-limiting embodiment, a kit may comprise a primer, a pair of primers, a probe, microarray, or antibody suitable for detecting a biomarker of 8q24 which is the SNP rs4733664.

In a specific non-limiting embodiment, a kit may comprise a primer, a pair of primers, a probe, microarray, or antibody suitable for detecting a biomarker of 6q25 (ESR1) which is the SNP rs2253407.

In a specific non-limiting embodiment, a kit may comprise a primer, a pair of primers, a probe, microarray, or antibody suitable for detecting a biomarker of 10q21 (ZNF365) which is the SNP rs 17221319.

In certain non-limiting embodiments, where the measurement means in the kit employs an array, the set of biomarkers set forth above may constitute at least 10 percent or at least 20 percent or at least 30 percent or at least 40 percent or at least 50 percent or at least 60 percent or at least 70 percent or at least 80 percent of the species of markers represented on the microarray.

In certain non-limiting embodiments, a biomarker detection kit may comprise one or more detection reagents and other components (e.g., a buffer, enzymes such as DNA polymerases or ligases, chain extension nucleotides such as deoxynucleotide triphosphates, and in the case of Sanger-type DNA sequencing reactions, chain terminating nucleotides, positive control sequences, negative control sequences, and the like) necessary to carry out an assay or reaction to detect a biomarker.

A kit may further contain means for comparing the biomarker with a standard, and can include instructions for using the kit to detect the biomarker of interest. Specifically, the instructions describes that the presence of a biomarker, set forth herein, is indicative of an increased or decreased risk that a subject has or will develop breast cancer.

5.4 PROGNOSTIC METHODS

In non-limiting embodiments, the present invention provides for a method for assessing the likelihood that a subject has or will develop breast cancer comprising determining whether the subject carries a 6p24 SNP biomarker and a BRCA2 biomarker, where the presence of both biomarkers indicates that while the subject has an increased risk of having or developing breast cancer relative to the general population, the risk is less than if the 6p24 biomarker were absent. In a non- limiting subset of embodiments, it is already known that the subject carries a BRCA2 biomarker (mutation, minor allele) so that the method need not necessarily re-test for the presence of that biomarker, although it may be desirable as confirmation or supporting information.

In non-limiting embodiments of said method, the 6p24 SNP biomarker is rs9348512 SNP.

In non-limiting embodiments, said method may further comprise determining whether the subject carries one or more auxiliary biomarker selected from the group of 10q26 (FGFR2), 16ql2 (TOX3), 12pl 1 (PTHLH), 5ql 1 {MAP SKI), 9p21 (CDKN2A/B), l lpl 5 (LSP1), 8q24, 6q25 (ESR1), 10q21 (ZNF365), 3p24 (SLC4A 7, NEK10), 12q24, 5pl2, and 1 Iql 3. The effect of the presence or absence of said biomarker(s) on the risk of having or developing breast cancer is presented in TABLE 1.

In certain non-limiting embodiments, said method may further comprise determining whether the subject carries one or more biomarker selected from the biomarkers shown in TABLES 1, 2, and 6. The effect of the presence or absence of said biomarker(s) on the risk of having or developing breast cancer is presented in TABLES 1, 2, and/or 6.

The presence of a biomarker may be determined in the subject in vivo or in a sample collected from the subject using methods known in the art. Non- limiting examples of a sample include, but are not limited to, a clinical sample, a tumor sample, cells in culture, cell supernatants, lymphocytes, an exudate, cell lysates, serum, blood plasma, biological fluid (e.g. , lymphatic fluid), and tissue samples. The source of the sample may be solid tissue (e.g., from a fresh, frozen, and/or preserved organ, tissue sample, biopsy, or aspirate), blood or any blood constituents, bodily fluids (such as, e.g., urine, lymph, cerebral spinal fluid, amniotic fluid, peritoneal fluid, saliva, or interstitial fluid), or cells from the individual, including circulating tumor cells.

Methods for determining the presence of biomarker are known in the art and are discussed above.

The foregoing method may comprise the further step, where the subject is found to carry a 6p24 SNP, of recommending or performing regular breast screening to monitor for the presence of cancer, for example by clinical breast exam, breast biopsy, mammography, ultrasound, magnetic resonance imaging, or similar techniques. Regular screening may, in non-limiting embodiments, be at least four times a year, at least twice a year, at least once a year, or every two years.

5.5 METHODS OF TREATMENT

In certain non-limiting embodiments, the present invention provides for a method of treating a subject who carries a BRCA2 biomarker (mutation), comprising determining whether the subject carries a 6p24 SNP biomarker and, where the 6p24 SNP biomarker is absent, advising the subject that she is at high risk for developing breast cancer relative to a subject carrying both the 6p24 SNP and BRCA2 biomarkers and to the general population. In a subset of non-limiting embodiments, the subject is previously known to carry the BRCA2 biomarker (mutation);

alternatively, both the 6p24 SNP and BRCA2 biomarkers may be assessed.

In certain non-limiting embodiments, the method may further comprise determining whether the subject carries one or more auxiliary biomarker selected from the group of 10q26 (FGFR2), 16ql2 (TOX3), 12pl 1 (PTHLH), 5ql 1 (MAP3K1), 9p21 (CDKN2A/B), 1 lpl 5 (LSP1), 8q24, 6q25 (ESR1), 10q21 (ZNF365), 3p24 (SLC4A7, NEK10), 12q24, 5pl2 and 1 lql3. The effect of the presence or absence of said biomarker(s) on the risk of having or developing breast cancer is presented in TABLE 1.

In certain non-limiting embodiments, the method may further comprise determining whether the subject carries one or more biomarker selected from the biomarkers shown in TABLES 1 , 2, and 6. The effect of the presence or absence of said biomarker(s) on the risk of having or developing breast cancer is presented in TABLES 1 , 2, and/or 6.

The presence of a biomarker may be determined in the subject in vivo or in a sample collected from the subject using methods known in the art. Non- limiting examples of a sample include, but are not limited to, a clinical sample, a tumor sample, cells in culture, cell supernatants, lymphocytes, an exudate, cell lysates, serum, blood plasma, biological fluid {e.g. , lymphatic fluid), and tissue samples. The source of the sample may be solid tissue (e.g., from a fresh, frozen, and/or preserved organ, tissue sample, biopsy, or aspirate), blood or any blood constituents, bodily fluids (such as, e.g., urine, lymph, cerebral spinal fluid, amniotic fluid, peritoneal fluid, saliva, or interstitial fluid), or cells from the individual, including circulating tumor cells.

The foregoing method may comprise the further step, where the subject is found not to carry the 6p24 SNP, of recommending or performing a mastectomy or oophorectomy, or initiating anti-estrogen therapy or chemoprevention. In addition the biomarker profile may serve to guide targeted therapies against tyrosine kinase pathways which are implicated by many of the biomarkers included in the panel, and which may down-modulate risk in BRCA2 mutation carriers. The protein products of the biomarkers themselves may serve as therapeutic targets to down-modulate breast cancer risk.

6. EXAMPLE: IDENTIFICATION OF A BRCA2-S?ECIFIC

MODIFIER LOCUS AT 6p24 RELATED TO BREAST CANCER RISK

6.1 MATERIALS AND METHODS

Ethics Statement. Each of the host institutions (TABLE 4) recruited under ethically-approved protocols. Written informed consent was obtained from all subjects.

Study subjects. The majority of BRCA2 mutation carriers were recruited through cancer genetics clinics and some came from population or community-based studies. Studies contributing DNA samples to these research efforts were members of the Consortium of Investigators of Modifiers of BRCAl/2 (CIMBA) with the exception of one study (NICCC). Eligible subjects were women of European descent who carried a pathogenic BRCA2 mutation, had complete phenotype information, and were at least 18 years of age. Harmonized phenotypic data included year of birth, age at cancer diagnosis, age at bilateral prophylactic mastectomy and oophorectomy, age at interview or last follow-up, BRCA2 mutation description, self-reported ethnicity, and breast cancer estrogen receptor status.

GWAS Discovery Stage Samples. Details of these samples have been described previously [2]. Data from 899 young (<40 years) affected and 804 older (>40 years) unaffected carriers of European ancestry from 14 countries were used to select SNPs for inclusion on the iCOGS array.

Samples genotyped in the extended replication set. Forty-seven studies from 24 different countries (including two East-Asian countries) provided DNA from a total of 10,048 BRCA2 mutations carriers. All eligible samples were genotyped using COGs, including those from the discovery stage.

Genotyping and quality control.

BRCA2 SNP Selection for Inclusion on iCOGS. The Collaborative Oncological Gene-Environment Study (COGS) consortium developed a custom genotyping array (referred to as the iCOGS array) to provide efficient genotyping of common and rare genetic variants to identify novel loci that are associated with risk of breast, ovarian, and prostate cancers as well as to fine-map known cancer

susceptibility loci. SNPs were selected for inclusion on iCOGS separately by each participating consortium: Breast Cancer Association Consortium (BCAC) [6], Ovarian Cancer Association Consortium (OCAC) [7], Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome (PRACTICAL) [8], and CIMBA. SNP lists from a BRCAI GWAS and SNPs in candidate regions were used together with the BRCA2 GWAS lists to generate a ranked CIMBA SNP list that included SNPs with the following nominal proportions: 55.5% from the BRCAI GWAS, 41.6% from the BRCA2 GWAS and fine mapping, 2.9% for CIMBA candidate SNPs. Each consortium was given a share of the array: nominally 25% of the SNPs each for BCAC, PRACTICAL and OCAC; 17.5% for CIMBA; and 7.5% for SNPs from commonly researched pathways (e.g., inflammation). For the CIMBA BRCA2 GWAS, we used the iCOGS array as the platform to genotype the extended replication set of the discovery GWAS stage [2]. SNPs were selected on the basis of the strength of their associations with breast cancer risk in the discovery stage [2], using imputed genotype data for 1.4M SNPs identified through CEU+TSI samples on HapMap3, release 2. A ranked list of SNPs was based on the 1 -df trend test statistic, after excluding highly correlated SNPs (r2>0.4). The final list included the 39,015 SNPs with the smallest p-values. An additional set of SNPs were selected for fine mapping of the regions surrounding the SNPs found to be associated with breast cancer in the discovery GWAS stage: rsl6917302 on 10q21 and rs311499 on 20ql3, including SNPs with a MAF >0.05 located 500kb in both directions of the SNP, based on HapMap 2 data. The final combined list of SNPs for the iCOGS array comprised 220,123 SNPs. Of these, 211,155 were successfully manufactured onto the array. The present analyses are based on the 19,029 SNPs selected on the basis of BRCA2 GWAS and fine mapping that were included on the iCOGS array.

Genotyping. The genotyping was performed on DNA samples from

10,048 BRCA2 mutation carriers at the McGill University and Genome Quebec Innovation Centre (Montreal, Canada). As a quality control measure, each plate included DNA samples from six individuals who were members of two CEPH trios. Some plates also contained three duplicate pairs of quality control samples.

Genotypes were called using GenCall [9]. Initial calling was based on a cluster file generated using 270 samples from Hapmap2. To generate the final calls, we first selected a subset of 3,018 individuals, including samples from each of the genotyping centers in the iCOGS project, each of the participating consortia, and each major ethnicity. Only plates with a consistent high call rate in the initial calling were used. We also included 380 samples of European, African, and Asian ethnicity genotyped as part of the Hapmap and 1000 Genomes project, and 160 samples that were known positive controls for rare variants on the array. This subset was used to generate a cluster file that was then applied to call the genotypes for the remaining samples.

Quality control of SNPs. Of the 211,155 SNPs on the iCOGS array, we excluded SNPs for the following reasons (TABLE 4): on the Y-chromosome, call rate <95%, deviations from Hardy- Weinberg equilibrium (P<10-7) using a stratified 1-d.f. test [10], and monomorphic. SNPs that gave discrepant genotypes among known duplicates were also excluded. After quality control filtering, 200,908 SNPs were available for analysis (TABLE 3); 18,086 of which were selected on the basis of the discovery BRCA2 GWAS [2]. Cluster plots of all reported SNPs were inspected manually for quality (FIGURE 3).

Description of imputation. Genotypes for SNPs identified through the 1000 Genomes Phase I data (released Jan 2012) [11] were imputed using all SNPs on the iCOGS chip in a region of 500 kb around the novel modifier locus at 6p24. The boundaries were determined according to the linkage disequilibrium (LD) structure in the region based on HapMap data. The imputation was carried out using IMPUTE 2.2 [12]. SNPs with imputation information/accuracy r²<0.30 were excluded in the analyses.

Quality Control of DNA Samples. Of 10,048 genotyped samples

(TABLE 3), 742 were excluded because they did not meet the phenotypic eligibility criteria or had self-reported non-CEU ethnicity (TABLE 4). Samples were then excluded for the following reasons: not female (XXY, XY), call rate <95%, low or high heterozygosity (P<10-6), discordant genotypes from previous CIMBA genotyping efforts, or discordant duplicate samples. For duplicates with concordant phenotypic data, or in cases of cryptic monozygotic twins, only one of the samples was included. Cryptic duplicates for which phenotypic data indicated different individuals were all excluded. Samples of non-European ancestry were identified using multi-dimensional scaling, after combining the BRCA2 mutation carrier samples with the HapMap2 CEU, CHB, JPT and YRI samples using a set of 37,120 uncorrelated SNPs from the iCOGS array. Samples with >19% non-European ancestry were excluded (FIGURE 4). A total of 4,330 affected and 3,881 unaffected BRCA2 mutation carrier women of European ancestry from 42 studies remained in the analysis (TABLE 4), including 3,234 breast cancer cases and 3,490 unaffected carriers that were not in the discovery set.

BRCA1 and BCAC Samples. Details of the sample collection, genotyping and quality control process for the BRCA1 and BCAC samples, are reported elsewhere [13,14].

Statistical methods. The associations between genotype and breast cancer risk were analyzed within a retrospective cohort framework with time to breast cancer diagnosis as the outcome [15]. Each BRCA2 carrier was followed until the first of: breast or ovarian cancer diagnosis, bilateral prophylactic mastectomy, or age at last observation. Only those with a breast cancer diagnosis were considered as cases in the analysis. The majority of mutation carriers were recruited through genetic counseling centers where genetic testing is targeted at women diagnosed with breast or ovarian cancer and in particular to those diagnosed with breast cancer at a young age.

Therefore, these women are more likely to be sampled compared to unaffected mutation carriers or carriers diagnosed with the disease at older ages. As a consequence, sampling was not random with respect to disease phenotype and standard methods of survival analysis (such as Cox regression) may lead to biased estimates of the associations [16]. We therefore conducted the analysis by modelling the retrospective likelihood of the observed genotypes conditional on the disease phenotypes. This has been shown to provide unbiased estimates of the associations [15]. The implementation of the retrospective likelihoods has been described in detail elsewhere [ 15,17], The associations between genotype and breast cancer risk were assessed using the 1 degree of freedom score test statistic based on the retrospective likelihood [15]. In order to account for non-independence between relatives, an adjusted version of the score test was used in which the variance of the score was derived taking into account the correlation between the genotypes [18]. P-values were not adjusted using genomic control because there was little evidence of inflation. Inflation w^ras assessed using the genomic inflation factor λ. Since this estimate is dependent on sample size, we also calculated λ adjusted to 1000 affected and 1000 unaffected samples. Per- allele and genotype-specific hazard-ratios (HR) and 95% confidence intervals (CI) were estimated by maximizing the retrospective likelihood. Calendar-year and cohort-specific breast cancer incidences for BRCA2 were used [1], All analyses were stratified by country of residence. The USA and Canada strata were further subdivided by reported Ashkenazi Jewish ancestry. The assumption of proportional hazards was assessed by fitting a model that includes a genotype-by-age interaction term. Between-country heterogeneity was assessed by comparing the results of the main analysis to a model with country- specific log-HRs. A possible survival bias due to inclusion of prevalent cases was evaluated by re-fitting the model after excluding affected carriers that were diagnosed >5 years prior to study recruitment. The associations between genotypes and tumor subtypes were evaluated using an extension of the retrospective likelihood approach that models the association with two or more subtypes simultaneously [19]. To investigate whether any of the significant SNPs were associated with ovarian cancer risk for BRCA2 mutation carriers and whether the inclusion of ovarian cancer patients as unaffected subjects biased our results, we also analyzed the data within a competing risks framework and estimated HR simultaneously for breast and ovarian cancer using the methods described elsewhere [15]. Analyses were carried out in R using the

GenABEL libraries [20] and custom-written software. The retrospective likelihood was modeled in the pedigree-analysis software MENDEL [21 ], as described in detail elsewhere [15].

TCGA Analysis. Affymetrix SNP 6.0 genotype calls for normal (non-tumor) breast DNA were downloaded for all available individuals from The Cancer Genome Atlas in September 2011. Analyses were limited to the 401 individuals of European ancestry based on principal component analysis. Expression levels in breast tumor tissue were adjusted for the top two principal components, age, gender (there are some male breast cancer cases in TCGA), and average copy number across the gene in the tumor. Linear regression was then used to test for association between the SNP and the adjusted gene expression level for all genes within one megabase.

Gene Set Enrichment Analysis. To investigate enrichment of genes associated with breast cancer risk, the gene-set enrichment approach was

implemented using Versatile Gene-based Association Study [22] based on the ranked P-values from retrospective likelihood analysis. Association List Go Annotator was also used to prioritize gene pathways using functional annotation from gene ontology (GO) [23] to increase the power to detect association to a pathway, as opposed to individual genes in the pathway. Both analyses were corrected for LD between SNPs, variable gene size, and interdependence of GO categories, where applicable, based on imputation. 100,000 Monte Carlo simulations were performed in VEGAS and 5000 replicate gene lists using random sampling of SNPs and 5000 replicate studies (sampling with replacement) were performed to estimate P-values.

Predicted absolute breast cancer risks by combined SNP profile. We estimated the absolute risks of developing breast cancer based on the joint distribution of SNPs associated with breast cancer for BRCA2 mutation carriers. The methods have been described elsewhere [24]. To construct the SNP profiles, we considered the single SNP from each region with the strongest evidence of association in the present dataset. We included all loci that had previously been found to be associated with breast cancer risk through GWAS in the general population and demonstrated associations with breast cancer risk for BRCA2 mutation carriers, and loci that had GWAS level of significance in the current study. We assumed that all loci in the profile were independent (i.e., they interact multiplicatively on BRCA2 breast cancer risk). Genotype frequencies were obtained under the assumption of Hardy- Weinberg Equilibrium. For each SNP, the effect of each allele was assumed to be consistent with a multiplicative model (log-additive). We assumed that the average, age -specific breast cancer incidences, over all associated loci, agreed with published breast cancer risk estimates for BRCA2 mutation carriers [1].

6.2 RESULTS

The genomic inflation factor (λ) based on the 18,086 BRCA2 GWAS

SNPs in the 6,724 BRCA2 mutation carriers not used for SNP discovery was 1.034 (λ adjusted to 1000 affected and 1000 unaffected: 1.01 , FIGURE 5). Multiple variants were associated with breast cancer risk in the combined discovery and replication datasets (FIGURE 6). SNPs in three independent regions had P-values <5xl0^"s; one was a region not previously associated with breast cancer.

The most significant associations were observed for known breast cancer susceptibility regions, rs2420946 (per allele P=2xl 0 ⁴) in FGFR2 and rs3803662 (P=5.4xl0^~n) near TOX3 (TABLE 1). Breast cancer risk associations with other SNPs reported previously for BRCA2 mutation carriers are summarized in TABLE 1. In this larger set of BRCA2 mutation carriers, we also identified novel SNPs in the 12pl 1 (PTHLH), 5ql 1 (MAP3K1), and 9p21 (CDKN2A/B) regions with smaller P-values for association than those of previously reported SNPs. These novel SNPs were not correlated with the previously reported SNPs (r <0.14). For one of the novel SNPs identified in the discovery GWAS [2], ZNF365 rs 16917302, there was weak evidence of association with breast cancer risk (P=0.01); however, an uncorrelated SNP, rsl 7221319 (r²<0.01), 54 kb upstream of rsl6917302, had stronger evidence of association (P=6xl 0-3).

One SNP, rs9348512 at 6p24, not known to be associated with breast cancer, had a combined P-value of association of 3.9x10^"8 amongst all BRCA2 samples (TABLE 2), with strong evidence of replication in the set of BRCA2 samples that were not used in the discovery stage (P=5.2xl 0^"3). The minor allele of rs9348512 (MAF=0.35) was associated with a 15% decreased risk of breast cancer among BRCA2 mutation carriers (per allele HR=0.85, 95% CI 0.80-0.90) with no evidence of between-country heterogeneity (P=0.78, FIGURE 7). None of the genotyped (n=68) or imputed (n=3,507) SNPs in that region showed a stronger association with risk (FIGURE 1 ; TABLE 5), but there were 40 SNPs with P<10^'4 (pairwise r²>0.38 with rs9348512, with the exception of rsl 1526201 for which r²=0.01 , TABLE 5). The association with rs9348512 did not differ by 6174delT mutation status (P for difference=0.33), age (P=0.39), or estrogen receptor (ER) status of the breast tumor (P=0.78). Exclusion of prevalent breast cancer cases (n=l,752) produced results (HR=0.83, 95% CI 0.77-0.89, P=3.40xl0^"7) consistent with those for all cases.

SNPs in two additional regions had P- values <10^"5 for breast cancer risk associations for BRCA2 mutation carriers (TABLE 2). The magnitude of associations for both SNPs was similar in the discovery and second stage samples. In the combined analysis of all samples, the minor allele of rs619373, located in FGF13 (Xq26.3), was associated with higher breast cancer risk (HR=1.30, 95% CI 1.17-1.45, P=3.1x10-6). The minor allele of rsl 84577, located in CYPlBl-ASl (2p22-p21), was associated with lower breast cancer risk (HR=0.85, 95% CI 0.79-0.91, P=3.6x10-6). These findings were consistent across countries (P for heterogeneity between country strata=0.39 and P=0.30, respectively; FIGURE 8). There was no evidence that the HR estimates for rs619373 and rsl 84577 change with age of the BRCA2 mutation carriers (P for the genotype-age interaction =0.80 and P=0.40, respectively) and no evidence of survival bias for either SNP (rs619373 : HR=1.35, 95% CI 1.20-1.53, P=1.5xl0-6 and rsl 84577: HR-0.86, 95% CI 0.79 -0.93, P=2.0xl0-4, after excluding prevalent cases). The estimates for risk of ER-negative and ER-positive breast cancer were not significantly different (P for heterogeneity between tumor subtypes =0.79 and 0.67, respectively). When associations were evaluated under a competing risks model, there was no evidence of association with ovarian cancer risk for SNPs rs9348 12 at 6p24, rs619373 in FGF13 or rsl 84577 at 2p22 and the breast cancer associations were virtually unchanged (TABLE 6).

Gene set enrichment analysis confirmed that strong associations exist for known breast cancer susceptibility loci and the novel loci identified here (gene- based P<lxl0^"5). The pathways most strongly associated with breast cancer risk that contained statistically significant SNPs included those related to ATP binding, organ morphogenesis, and several nucleotide bindings (pathway-based P<0.05).

To begin to determine the functional effect of rs9348512, we examined associations of expression levels of any nearby gene in breast tumors with the minor A allele. Using data from The Cancer Genome Atlas, we found that the A allele of rs9348512 was strongly associated with mRNA levels of GCNT2 in breast tumors (p=7.3xl0^"s).

6.3 DISCUSSION

In the largest assemblage of BRCA2 mutation carriers, we identified a novel locus at 6q24 that is associated with breast cancer risk, and noted two potential SNPs of interest at Xq26 and 2p22. We also replicated associations with known breast cancer susceptibility SNPs previously reported in the general population and in BRCA2 mutation carriers. For the 12pl 1 (PTHLH), 5ql 1 (MAP3K1), and 9p21 (CDKN2A/B), we found uncorrected SNPs that had stronger associations than the originally identified SNP in the breast cancer susceptibility region that should be replicated in the general population. In BRCA2 mutation carriers, evidence for a breast cancer association with genetic variants in PTHLH has been restricted previously to ER-negative tumors [25]; however, the novel susceptibility variant we reported here was associated with risk of ER+ and ER- breast cancer.

The novel SNP rs9348512 (6p24) is located in a region with no known genes (FIGURE 1). C6orf218, a gene encoding a hypothetical protein LOC221718, and a possible tumor suppressor gene, TFAP2A, are within lOOkb of rs9348512. TFAP2A encodes the AP-2a transcription factor that is normally expressed in breast ductal epithelium nuclei, with progressive expression loss from normal, to ductal carcinoma in situ, to invasive cancer [26,27]. AP-2a also acts as a tumor suppressor via negative regulation of MYC [28] and augmented p53-dependent transcription [29]. However, the minor allele of rs9348512 was not associated with gene expression changes of TFAP2A in breast cancer tissues in The Cancer Genome Atlas (TCGA) data; this analysis might not be informative since expression of TFAP2A in invasive breast tissue is low [26,27]. Using the TCGA data and a 1 Mb window, expression changes with genotypes of rs9348512 were observed for GCNT2, the gene encoding the enzyme for the blood group I antigen glucosaminyl (N-acetyl) transferase 2. GCNT2, recently found to be overexpressed in highly metastatic breast cancer cell lines [30] and basal-like breast cancer [31], interacts with TGF-β to promote epithelial-to-mesenchymal transition, enhancing the metastatic potential of breast cancer [31]. An assessment of alterations in expression patterns in normal breast tissue from BRCA2 mutation carriers by genotype are needed to further evaluate the functional implications of rs9348512 in the breast tumorigenesis of BRCA2 mutation carriers.

To determine whether the breast cancer association with rs9348512 was limited to BRCA2 mutation carriers, we compared results to those in the general population genotyped by BCAC and to BRCAl mutation carriers in CIMBA. No evidence of an association between rs9348512 and breast cancer risk was observed in the general population (OR=1.00, 95% CI 0.98-1.02, P=0.74) [14], nor in BRCAl mutation carriers (HR=0.99, 95% CI 0.94-1.04, P=0.75) [13]. Stratifying cases by ER status, there was no association observed with ER-subtypes in either the general population or among BRCAl mutation carriers {BCAC: ER positive P=0.89 and ER negative P=0.60; CIMBA BRCAl: P=0.49 and P=0.99, respectively). For the two

SNPs associated with breast cancer with P<10-5, neither rs619373, located in FGF13 (Xq26.3), nor rsl84577, located in CYPlBl-ASl (2p22-p21), was associated with breast cancer risk in the general population [14] or among BRCAl mutation carriers [13]. The narrow CIs for the overall associations in the general population and in BRCAl mutation carriers rule out associations of magnitude similar to those observed for BRCA2 mutation carriers. The consistency of the association in the discovery and replication stages and by country, the strong quality control measures and filters, and the clear cluster plot for rs9348512 suggest that our results constitute the discovery of a novel breast cancer susceptibility locus specific to BRCA2 mutation carriers rather than a false positive finding.

rs9348512 (6p24) is the first example of a common susceptibility variant identified through GWAS that modifies breast cancer risk specifically in BRCA2 mutation carriers. Previously reported Z?Z?C42-modifying alleles for breast cancer, including those in FGFR2, TOX3, MAP3K1, LSP1, 2q35, SLC4A7, 5pl2, lpl 1.2, ZNF365, and 19p 13.1 (ER-negative only) [18,32,33], are also associated with breast cancer risk in the general population and/or BRCA1 mutation carriers.

Taking into account all loci associated with breast cancer risk in BRCA2 mutation carriers from the current analysis, including the 6p24 locus, the 5% of the BRCA2 mutation carriers at lowest risk were predicted to have breast cancer risks by age 80 in the range of 21-47% compared to 83-100% for the 5% of mutation carriers at highest risk on the basis of the combined SNP profile distribution

(FIGURE 2). The breast cancer risk by age 50 is predicted to be 4-1 1% for the 5% of the carriers at lowest risk compared to 29-81% for the 5% at highest risk.

nd from the iCOG

here.

⁴ Stronger associations were originally reported for the SNP, assuming a dominant or recessive model of the 'risk allele'.

Active 15354791.1

Active 15354791.1

Table 3. Description of breast cancer affected and unaffected BRCA2 carriers included in the final analysis of the COGs array SNPs

Affected Unaffected

(n=4,330) (n=3,881)

Factor N % N %

Age at Censoring

<40 1 ,545 35.7 1 ,607 41.4

40-49 1 ,651 38 1 1 ,025 26.4

50-59 799 18.5 712 18.4

60+ 335 7.7 537 13.8

Ashkenazi Jewish Ancestry

No 3,988 92.1 3,433 88.5

Yes 342 7.9 448 1 1.5

i?«C42*6174delT Mutation Carrier

Yes 435 10.0 584 15.0

No 3,895 90.0 3,297 85.0

Country of Residence

Australia 288 6.7 200 5.2

Austria 123 2.8 77 2.0

Canada 153 3.5 150 3.9

Denmark & Sweden 158 3.6 198 5.1

Finland 66 1.5 55 1.4

France 491 1 1.3 209 5.4

Germany 365 8.4 198 5.1

Iceland 102 2.4 25 0.6

Israel 108 2.5 166 4.3

Italy- 353 8.2 174 4.5

South Africa 93 2.1 53 1.4

Spain 328 7.6 293 7.5

The Netherlands 260 6.0 492 12.7

United Kingdom &

Ireland 483 11.2 560 14.4

USA 959 22.1 1 ,03 1 26.6

Study

BCFR 197 4.5 152 3.9

BIDMC 4 0.09 5 0.1

BMBSA 93 2.1 53 1.4

BRICOH 48 1.1 80 2.1

CBCS 46 1.1 49 1.3

CNIO 113 2.6 1 13 2.9

COH 65 1.5 42 1.1

CONSIT TEAM 263 6.1 137 3.5

DFCI 55 1.3 79 2.0

DKFZ 14 0.3 11 0.3

EMBRACE 478 1 1.0 547 14.1

FCCC 19 0.4 35 0.9

GC-HBOC 351 8.1 186 4.8

GEMO 523 12.1 226 5.8

GOG 152 3.5 161 4.1 Affected Unaffected

(n=4,330) (n=3,881)

Factor N % N %

HCSC 59 1 ,4 54 1.4

HEBON 260 6.0 492 12.7

HEBCS 66 1.5 55 1.4

HVH 34 0.8 25 0.6

ICO 122 2.8 102 2.6

ILUH 103 2.4 26 0.7

INHERIT 26 0.6 23 0.6

IOVHBOCS 90 2.1 37 1.0 kConFab 254 5.9 182 4.7

MAGIC 8 0.2 22 0.6

MAYO 80 1 .8 61 1 .6

MCGILL 12 0.3 15 0.4

MSKCC 121 2.8 97 2.5

MUV 123 2.8 77 2.0

NCI 22 0.5 61 1.6

NICCC 61 1 .4 108 2.8

OCGN 65 1.5 1 12 2.9

OSU CCG 33 0.8 28 0.7

OUH 89 2.1 1 17 3.0

SMC 47 1.1 57 1.5

SWE-BRCA 23 0.5 31 0.8

UCHICAGO 25 0.6 12 0.3

UCLA 15 0.3 26 0.7

UCSF 16 0.4 1 1 0.3

UKGRFOCR 4 0.09 13 0.3

UPENN 134 3.1 105 2.7

WCP 17 0.4 54 1 .4

Table 4. Quality control filtering steps for BRCA2 mutation carriers and SNPs on the COGs array

Remaining Remaining

No. of No. of No. of No. of

Sample Data Cleaning Steps/Exclusion Reasons samples Samples Data Cleaning Steps for SNPs SNPs SNPs

Total Eligible Samples on Manifest with Genotype Data 10,048 Total SNPs on COGs Array 211,155

Ineligible based on phenotypic data 21 1 9,837 Y chromosome SNPs 79 21 1 ,076

Self-reported non-CEU ethnicity 531 9,306 Call rate <95% 4,446 206,630

Incorrect gender based on genotype 34 9,272 HWE(stratified) P-value <10^"7 1 ,845 204,785

Call rate <95% | Heterozygosity: P-value <10^"6 300 8,972 Monomorphic markers 3,853 200,932

> 19% inferred non-CEU ancestry 166 8,806 Unreliable SNP genotypes 1 200,931

Discordant with previous CIMBA genotyping 53 8,753 SNPs with high discordance rate among 23 200,908

Consistent duplicate pairs (one sample excluded 498 8,255 known duplicates (list obtained from all

Inconsistent duplicate pairs (both samples excluded) 44 8,21 1 members of COGs consortia)

Totals After Filtering 1 ,837 8,211 10,439 200,908

Active 1 5354791.1

Table 5. Breast cancer hazards ratios (HR) and 95% confidence intervals (CI) for all SNPs with P<10 in a

500Mb region around rs9348512 on 6p24 among BRCA2 mutation carriers

Minor

Minor r² with Allele r² P-

SNP Position Type¹ Major Allele Allele rs9348512 Freq. imputation value² rs9348512 10564692 typed C A 1.00 0.34 1.00 4.4x10^' rs9358529 10563215 imputed A C 0.86 0.3 1 0.96 8.2x10^" rs303067 10548212 imputed A T 0.71 0.40 0.95 1.9x10^' rsl 348 10557244 imputed T c 0.51 0.21 0.96 1.0x10^" rs9366443 10565096 imputed c T 0.72 0.41 0.94 3.7x10^" rs9460713 10555412 imputed c T 0.49 0.20 0.96 4.9x10^' rs9466289 10555931 imputed T c 0.50 0.20 0.97 5.4x10^'

6-10546956 10546956 imputed A AGG 0.48 0.41 0.84 5.9x10^' rs9466290 10555941 imputed G A 0.49 0.20 0.96 6.4x10^' rs3911709 10559876 imputed G A 0.45 0.26 0.96 7.3x10^"

6-10557995 10557995 imputed GTAT G 0.49 0,20 0.95 7.4x10^" rs9295542 10565669 imputed A G 0.61 0.46 0.91 8.2x10^" rs6908107 10559449 imputed C G 0.61 0.46 0.98 8.8x10^" rs35076407 10563463 imputed T C 0.62 0.45 0.98 9.2x10^" rs602199 10554912 imputed c G 0.60 0.39 0.94 9.3x10^' rs7738545 10563318 imputed c T 0.62 0.45 0.99 9.7x10^' rs303074 10560093 imputed G A 0.61 0.46 0.98 1.0x10^" rs781 13724 10543366 imputed G A 0.45 0.24 0.97 1.1x10^" rs303073 10560449 imputed A G 0.61 0.46 0.98 1.3x10^" rs4712668 10562060 typed G T 0.61 0.45 1.00 1.4x10^" rs75769093 10551514 imputed C A 0.54 0.47 0.90 1.5x10^" rs303070 10551 187 imputed G T 0.56 0.48 0.92 1.9x10^' rs9393239 10550632 imputed C T 0.43 0.21 0.98 2.0x10^" rs303061 10538157 typed T c 0.41 0.24 1.00 2.1x10^' rs4097280 10561081 imputed G A 0.58 0.44 0.95 2.3xl0^'4 rs4710998 10541811 typed A G 0.39 0.22 1.00 2.8x10^'4 rs6907578 10532198 imputed T A 0.53 0.43 0.86 3.7x10^'

6-10550552 10550552 imputed G T 0.55 0.47 0.90 3.9xl0^"4 rs56365413 10540162 imputed C T 0.40 0.20 0.98 4.0xl0^"4

6-10545251 10545251 imputed GTTGTTGTT G 0.38 0.21 0.99 4.4x10^' rs303068 10549297 imputed A C 0.56 0.48 0.92 4.5x10^"" rs6923826 10532295 imputed C G 0.50 0.42 0.86 4.8x10^"" rsl2175352 10545445 imputed T C 0.38 0.21 0.99 4.8xl0^"4 rs303065 10541072 imputed c T 0.39 0.20 0.99 5.0x10^"' rs303064 10540524 typed c T 0.38 0.20 1.00 5.2x10^"" rs9295535 10547954 typed T c 0.40 0.21 1.00 6.2X10"¹ rs 1 15262601 10526048 imputed A c 0.01 0.01 0.44 6.6x10 -4 rs6924202 10532454 imputed c T 0.56 0.39 0.80 6.7x10^' rs 12526269 10536199 imputed T A 0.37 0.21 0.98 7.1x10^'

6-10546510 10546510 imputed GC G 0.48 0.44 0.94 7.9x10^" rs303063 10538964 imputed C T 0.38 0.20 0.99 8.7x10^"

Type indicates whether the SNP was genotyped or imputed.

2p-value was calculated based on the 1 -degree of freedom score test

Active Table 6. Associations with SNPs at 6p24, FGF13 and 2p22 and breast and ovarian cancer risk using a competing risk analysis model

SNP rs No. No. unafNo. breast No. ovarian Ovarian cancer Breast cancer

Chr. fected cancer cancer HR (95%CI) p-value HR (95%CI) p-value rs9348512

6p24 3432 43 10 468 0.98 (0.84, 1.13) 0.74 0.84 (0.79,0,90) 8.7xl0^-8 rs619373

Xq26 3432 4307 468 0.98 (0.73,1.30) 0.88 1.29 (1.15,1.44) 7.1xl0^"6 rsl 84577

2p22 3432 431 1 468 1.01 (0.86, 1.19) 0.89 0.85 (0.79,0.92) 1.4xl0^"5

Active TABLE 7

>gnl I dbSNP I rs l 34 8

GAAAGTATTG ATGGTGAGTA ACTTTGGTAA AAGAAGGTCC AGGCATGTGG CTCATGCCTA TAATCCCAGC ACTTTGGGAG

GCCGAGGCAG GATAATTGCT TGAGGTCAGG AGTTCGAGAC TAGCCTAGGT AACATAGTAA AACCCTGCCC CTACAAAAAA TTAAAATATT AGCCAGGTGT GATGGTGCAC ATAGTCCTGT CATCCTAGCT ACTTGGGAGG CTGAGGCAGG AGGATTGCTT

GAGCCCAGGA ATTTGAGGCT ACAGTGAGCT ATGATTGTGT CACTGCACTC CAGCCTAGGC AACCGAGTGA GACTCCATTT

CTAAAAGAAA TTAATTAATT AATAAAAATG AAGAGAATGC TCAGCAGACT TCTGAATTCT TTGAGTGTTC ACAAGAAAAA

TAAATTCATG TATCACATGT CCTATAAAAG AAAAAGGGGT TGGGGTTGCT TTTGCATATA AAGCAAGCTA GTTTCAACCG AACTCTCTGT CCACTGGAGA R AAGTGCTTGC CACAGAAAAC TGTTTTTCTG GTTCACTGAG GTATAAT GA CAAATAACAA GTACATATAT CCAAGGTGCA

CAATGTGATG TTTTGATATA AGTATACACT GTGAAAGGAT TATTACAACC AATTTGTAGT AATTAACTTG ATGAATTAAC

ATATTCATCA AGTATATAGT ACATTATTAT TAACTGTAGT CACCATGCTG TGCTTTCCAT CTCAGAAAAC TTAGAGTATT

ACCCTAAAGT TAACTATGAC CATTTAGAAG TTTGCTTTAA AACACTGCTT TTCAAATTTT ACTGTGGAAA CAAATCGCTT

GGGGATCTTG TTAAAATTTG GATTCTGAAT CAGTAGGTCT AGAGTGGGGC CTGAGATTCT GTCTTTCTGA CAATCTCCCC AGGTGACACC AATGCTGCTG GTCCCTGAAG CACGCTTTTG GTGGCAAGGT TTCCAGAGAG CTGAGGCTCC TGTATTTCTT TACAATCCAG ACATCAGTTT

>gnl I dbSNP I rs 303061

CACCTGCTAC TGATACACAC TATAAACGTG GAAGATGATT TTCATTTTTG TAGTCATGAG CAGGATACTG TATAATGTAT

AATTGTTGGA CATTAAAGAA AACAAACTCC TTCTTGTCTC CTTAGGCTCA GAGCCACTCA GACATTGGGA AGCAAGTTTG

Active TCAAGATGAC AGAGAACCGA GGTAATGGAT TCGAGTGATG AAACAGGAAG TTCATTCATG

AGTTTTTGGC CACACCTCCA

AAGTGACGAC TTAGCCAGAA ATGGGATAAC TGGGTTTCCC TACTTCTCTT TTATCATCCT CAATGAGAGT GACCAAATAT

TAGAGCTAGA TGGAACCTTA GTGAAAATCT GGCTACTCGT CCCGTCCCAC CAGCCTGCCA CCCATTTCAA GTTTGAAGAG

ACAAAGACAC ATGGACCTTA TGTAATTACT GGGGATTACC CCAGGAGTCT GTGGCAAAAG TCAGCTTCTT CCCTCCCTGC TTCCCCGCCC TGTCTCTGGT R

CTTTCTACCA ACACTGGGCT GTTTCTGTGA TCACACTTAA GCGTACCTAA CCTGCGAATG CTGTATAGAA GGTGCTAATG

AACATGATTT AGCTTTAACA CTCAGTTTTC TAAAGGGACA CGTGGGGGCA GCAAATGTTT AGGCAAAAAC AATTCCAGTT

CTAGCCTCTA CTGTCTACAT ATGTGTATAC ATTTGGGAAA CGTTTGGGAA AGGGATATTT GAGAGCTTCT TTTTCTTTTT

TGTGGTTTAG TTATTTGATG ATATTGAGAT TGTTTCTGAG CCATGTGCTT CAACATCGGA TTGGGGATTT CAGAAAAAGT

TTTAGTCACT GTGATTCCAT TTAGCTTCCA AATGTGTCTC TGCTAAGAGA CTTAAAAGCA CTCATAAATA GCACGTGTGT

CTTCTTTGCA GTGTTTGCTA ATTTTGAGTC ACATCTTTTT AGAAAATCAT GAGATTTGGT GTCACAGAGA CTGGAATAAA TATAGTCAAA CTTATTGGTG

>gnl | dbSNP | rs 303063

CACGTCTGTC ACTCTAAAGC CTGTTCTAAG ATCACATCCC CTCTGGCTCT CCCTAGATAC TTCTGATTAT AGTTGGTAAT

CATGCCCATT AAATGTCTTT GGTTTCTTGG TACACAGAGA GAAGGTAAAT AATGGGTTCA TGATTTAGGT AAGAATACAC

AAATATTTTT CACACTATAA ATCTGTTTTC TATTCAGTTA AATATTAGAC CATCTGGTAA TGGAGAAAAT GTTTGAAAAT

CCACCTAGTT AACCTAAAAG TTTGCATTTC CTGCCTTTGG GGCTTTGAAT TTTTAAGTTA CATGTCTTCG TAGATGGTGA

TCAGGATAAA ACTAATATCT CTCTTAGATG AATCAAAATT CACCCCCTTG GGCAAGGGAG GGACCCAGCC TTTCTTTAAA

CATGTGGTTG CCTGAGAGTT GAACAAAACT GGAATAGGGA GAGAATGGCT TTGCCATGCT GATCATGGTA TTGTGGAGAT TTAAGAACTA GTGGCCAGGC R

Active 1 AGGTGGCTCA CGCCTGTAAT CCCAGCATTG TGAGAGGCCA AGGCAGGTGG ATCACTTGAG

GCCAGGATTT CGAGACCAGC

CCGGCCAACA TGATGACCCT GTTTTTACTA AAAATACAAA AATTAGCCGA GTGTGGTGGT GTGTGCCTGT AGTCCCAACT

GAGGCATGAG ACTTGCTTCA ACCCAGGAGG CGGGGGTTGC AGTGAGCCGA GATTGTGCCA CTGCACTCCA GCCTGGGTGA

CAGAGTGAGA CTCTGTCTCA AAAAAAAAAA AAAAAAAAAC TAGTCAGAGC TGTTGAGGTG TTGAGGCACC TGCTACTGAT

ACACACTATA AACGTGGAAG ATGATTTTCA TTTTTGTAGT CATGAGCAGG ATACTGTATA ATGTATAATT GTTGGACATT

AAAGAAAACA AACTCCTTCT TGTCTCCTTA GGCTCAGAGC CACTCAGACA TTGGGAAGCA AGTTTGTCAA GATGACAGAG AACCGAGGTA ATGGATTCGA

>gnl I dbSNP | rs303064

ATAGTGAGAT TCTGCCTCTA AAACAAAACA AAATAAAAGA CAAAACAACT AATTCTGTTT TTTAAAAAAA AAAAACACAC

AACAGCAAAC TTGACTATAA AGATTATTGC TGGGCACGGT GGCTCAGGCC TGTAATCCCA GCACTTTGGG AGGCTGAGGC

GGGTGGATCA CCTGAGGTCA GGAGCTCAAG ACCAGCCTGG CCAACATGGT GAAACCCTGT CTGTACTAAT AATACAAAAA

ATTAGCCGGG CATGGTGGTG CATGCCTGCA ATCCCAGCTA CTCGGGAGGA TGAGGCAGGA GAATCACTTG AACCTGGGAG

GTAGAGGTTG CAGTGAGCCG AGACTGCGCC ACTGCACTCC AGCCTGGGCA ACAAGAGCAA AACTCCGTGT CCAAAAAAAA

AAAAAAAAAA AAAGATTATT ATATATAATC ATTCAAGGCC TGTATGACTC AGTTCCCTTA GAAAAATGTC ATAATTTTTA TATTACTGAA TATTATTGGC R

TTATTTGTGT AGCCCACTTA AGTGAAGTCA ATAACATGAT TAAGTGGCAT ATTATCTTCA TGTCAGTCAA ACGTTATTTG

GATTTTATAA GTTAGGGTGA GATACAAATA AGTGAAAATA CTTTTTCTAA TGAATAATGA TGAATCTAAA ATAGGATTGA

CTTGGCTGGG CATAGTGGCT CGTGCTTGTA ACCCCAACAC TTTGGGAGGC TGAGGCAGTA GGATTACTTG AAACCAGGAG

TTTGAGACCA GCCTCGGCAA CAAAGGGAGA ACTCTTCTCT AATAAAAATA AGAATAAAAA ATTAGCCAGG TGTGGCAATG

TTCACCTGTG GTCCCAGCTA CTTGGGAAGC TGAGGCAGGA GGATCGTTGG AGCACAGGAG TTCAAGACTG CAGTTAGCGG TGACTGCACT CCAGCCTGGG CAATAGAGCA AGACCCTGTC TCTAAAAAAA AAATAATAAT

AAATAGGACT GGCTCGCATA TGTATGCAAC TATTTTGTTA

>gnl I dbSNP I rs 3030 65

rs=303065 I pos=501 | len=1001 ί taxid=9606 | mol= "genomic " ! cla s s=l ] alleles = "C/ T " | b ui ld=137 I suspect= ? | GMAF=T : 21 84 : 0 . 2083

ACTGAGTCAT ACAGGCCTTG AAT GAT TATA TATAATAATC TTTTTTTTTT TTTTTTTTTT TGGACACGGA GTTTTGCTCT

TGTTGCCCAG GCTGGAGTGC AGTGGCGCAG TCTCGGCTCA CTGCAACCTC TACCTCCCAG GTTCAAGTGA TTCTCCTGCC

TCATCCTCCC GAGTAGCTGG GATTGCAGGC ATGCACCACC ATGCCCGGCT AATTTTTTGT ATTATTAGTA CAGACAGGGT

TTCACCATGT TGGCCAGGCT GGTCTTGAGC TCCTGACCTC AGGTGATCCA CCCGCCTCAG CCTCCCAAAG TGCTGGGATT

ACAGGCCTGA GCCACCGTGC CCAGCAATAA TCTTTATAGT CAAGTTTGCT GTTGTGTGTT TTTTTTTTTT AAAAAACAGA

ATTAGTTGTT TTGTCTTTTA TTTTGTTTTG TTTTAGAGGC AGAATCTCAC TATGTTGCCC AGGCTTATTT TGCACCACTG GCCTCAAGCA GTCCTCCCAG Y

TCTGCCAAAT TTTAGACACC TGGACTTGGA AACCCATGAG AAGTTGGCCA GCGCTTCCTT TTGCATTTAT GCAGAGCAAT

GGTAAACGTC AGCAGCAAAT TTACAATCAA TCTTATTTTC CAGTGTCTCC AGAGATTTGA TTGTTTTGCT TATATGGCTT

ATGGCAATAC TTACCTCCAA TGTCTGATTT TTCAAAAAAA TTTCATCTAA TCCTTTGTGC AATGGTTTAC ATCTAATTTT

TTTTGTTCTG AGATGTAGAC AGCTATTAAG AACTGATCTT TGCACAGTAA ATTTTTCCTA TTCTTAGTCA TTATCCTTAG

GTGAGGCAAC ATGGTGCCAT TCAGTTATTC AGCAAATTCT CACATCTTCC GTGTGCCATG CATTGTTACA GGTTTTGAGC

CTAGAACCAT GAAAACAAAA GACAAAAATC TCTGCCCTTG TGGACTTTGT ATTCCAGAGG AGAGAAAATA AACAAGGTAA GTAAAATATA TAGTATGGTA

>gnl | dbSNP | rs 3030 67

rs=303067 | pos=50 1 I len=1001 I taxid=9606 I mol="genomic " I class=l | alleles= "A/T " | b ui ld=4 37 I suspect=? | GMAF=A : 218 4 : 0 . 4 98 6

TGTGTTCATT ATGACCACTG GGAAGATGAG TTTCACCCTT CACATGACTA TATGGTGAGA ACATGTTTCT CAGCTGAGAC

Active AAGATTTCAG GAAAGTTTGC AAGAACCGAG AGAAAATGGA AGAAAATGAA ATATTTGTTC

TTCAGAGTCA CCAGTTTTAT

TATATGCCTG GACTCTGTCA CTTATGTCAA TAAATTTACA AATGCAAAAT ACACATTTAA TTCCAGCGTG GTAGCATACA

CCTGTAGTCC TAGATACTCA GGAGGGTGAG TATCTAGGAC TACAGGTGTG TGCTACCACG CTTGAACTCA GGAGTTCAAG

GCCAGCCTGG ACAACACAGG GAGACCCCCT CTCTAAATGT ATATACACAC ATACACACAC ACACACACAC ACACACACAT

TCAAACATTG GAATCAGATG TCCTGGACAA AATGCTCAAA TCAGCTGAAC ACTTTGGAAT GCTTAACTTT TCTTTTTTTT AGATGTTTAT TTATTTATTT W

TTTTGTTTTT TATTTTATTA T TAT TAT ACT TTAAGTTTTA GGGTACATGT GCGCAATGTG CAGGTTTGTT ACATATGTAT

ACATGTGCCA TGTTGGTGTG CTGCACCCAT TAACTCGTCA TTTAGCATTA GGTATATCTC CAAATGCTAT CCCTCCCCCC

TCCCCCCACC CCACAACAGT CCCCGGAGTG TGATGTTCCC CTTCCTGTGT CCATGTGTTC TCATTGTTCA ATTCCCACCT

AT GAG T GAGA ACATGCGGTG TTTGGTTTTT TGTCCTTGTG ATAGTTTGCT GAGGATGATG GTTTCCAGTT TCATCCATGT

CCCTACAAAG GACATGAACT CATCATTTTT TATGGCTGCA TAGTATTCCA TGGTGTATAT GTGCCACATT TTCTTAATCC

AGTCTATCAT TGTTGGACAT TTGGGTTGGT TCCAAGTCTT TGCTATTGTG AATAGTGCCG CAATAAACCT ACGTGTGCAT GTGTCTTTAT AGCAGCATGA

>gnl I dbSNP I rs 3030 6 B

rs=303068 | pos=501 1 len= 1001 [ taxid=960 6 [ mol="genomic " | clas s=l i alleles="A/C " | b uild=137 I suspect=? | GMAF=A : 218 4 : 0 . 4 14 8

CACTGACTTC CACAATGGTT GAACTAGTTT ACGGTCCCAC CAACAGTGTA AAAGTGTTCC TATTTCTCCA CATCCTCTCC

AGCACCTGTT GTTTCCTGAC TTTTTAATGA TCACCATTCT AACTGGTGTG AGATGGTATC TCATTGTGGT TTTGATTTGC

ATTTCTCTGA TGGCCAGTGA TGATGAGCAT TTTTTCATGT GTTTTTTGGC TGCATAAATG TCTTCTTTTG AGAAGTGTCT

GTTCATATCC TTCGCCCACT TTTTGATGGG GTTGTTTATT TTTTTCTTGT AAATTTGTTT GAGTTCATTG TAGATTCTGG

ATATTAGCCC TTTGTCAGAT GAGTAGGTTG CAAAAATTTT CTCCCATTTC GTAGGTTGCT TGTTCACTCT GATGGTAGTT

TCTTTTGCTG GAATGCTTAA CTTTTCTTTC CTGCAAGAGG AAGACTGGGA GATTGAGAGG TGTGCCCAGG GTGTCAGCTC

Active 1 AGTGCCTGGT AGAGGCAGGT

M

ACATGAGCTT TGAGCCCTGG CCTGTGGATT GTGTTGTGCT TGGACTGGCC TGTTACGCCA TCTGCTTGCT TCTGCCTGAA ATTCCTGTAA CACAAGATAA AACCTCTCAT TCTGCAATTT ACCAATAAAC CTTATAAAAT CTGAGGCTAA GCCTTGTGAA ATGGCAAACC CTAGAAAGCC AGAGAGCTGG CATGCGGTAG TTCAGCAGTG GCTGCAGGAA ATAGAAGGAA AGGGAGTGAG GAGACAGGGT GCAAGCTGGA ATGTGATCAC AGGGGAGGGG GATCTCTGGA CTATGGGGGA ATGACGGGCA GCTTGAGGCC CTGAGATGAA AGACACTCCC TTTAAGAAAA ACGTCTGTGA CTCAGAGCCA CAAGGCGTGT CAGGAGAAAG TTCTGATGAA ACTGCATTCC ATTCCTGGAG GAATACGCAT TGCCATTGAA GTACAAACTC TAAAATGATG TAGGATTAAT AATTAAGGCA ACACTAGTAG TGGATGGTGG

>gnl | dbSNP | rs 303070

TTCTTTTAAA ACTAAACATA TACAGTTGTC CATCAGTATC TGCAGGGGAC TGGTTCCAGG TCTCCCTGCA AGTACCAAAA

TCACAGATGC TCAGGAATCT GATATAAAGC AGGGTAGTAC TTGCATATAA CCCACACACA TCCTCCTGTA TACTTTAAAT

CATCTCTAGA TTACTTATAA TACCTAGTAC AAGGTGAAGA CTATGTAAAC AGTTGTTATA CTGTATTTAA AAAAATAATT

TCCACTTTCA TTTTAGATTC AGGTGGTACA TATGCAGGTT TGTTATATAA GTGTATTGCA TGATGCTGAG GTTTGGAGTT

CAATTGATCC CATCACTCAG ATAGTGAGCA TAATTATACT GTATACAGTT TAGGAAATAA TAACAAGAAA AAAGTCTATA

CATATTCCAT AC G AC AT G A TCATCCTTTC CTCCCACCCC TTGATTTTTT ATTGAATTCA TGAATATTTG CTGAGTCCAT GAATGTGGAA CCCACGGATA K

GGAAGGCTGA CTGCACCTAC ATTATGACCT GGCAATTCCA CACCTAGGTT ACTCACCCGG GAGAAATAAA AGCATATGTC

CTCAAAGAGG CTTGTTCAAA AATGTCCATA GCTTTATTCA TAAATAACTG AAAGCTGAAA ACAACCAATA GGAGAATGAA

TAAACTAACT GTGGTAAATT CAGACAATGA AATACTACAC AATAAAAAAG GGAGGAACCG GCTGGGCGCG GTGGCTCACA

CCTGTAATCC CAGCACATTG GGAGGCCGAG GTGGGTGGAT CACCTGGGGT CAAGAGTTCG AGACCAGCCT GGCCAACATG

Active GTGAAACCCC ATCTCTACTA AAAATACAAA AATAGTCAGG TGTGGTGGCA CGCACCTCCA

ATCCCAGCTA CTCGAAAGGC

TGAGGCAGGA GAATCAGCTT GAATCCAGGA GGCAGAGGTT GCAGTGAGCT GAGATTGTGC CACTGCACTC CAGCCTGGGT GACTCTGTCT CAAAAAAAAA

>gnl ! dbSNP i rs 303073

ATGAACTAGG TTTTGAACTC CCCCATGCAT GACCCCTGCC TGTGGGGTCT GCCCTAGATG GATAATAAAT AGGTCATTAT

CAGTCTCATT TCAGTGTCCA CAGTGGAGAG ATTTTATTCT TCCCCTTGCT CTGGAACTGG CCCCTTTTCT CCTCCAAATC

CCAATCTTGG CCTAGAATTT TGAACTCTGC TTAGAATTCC AAATTGCCAC ATATATATGT CAGGAGATCA GACAGAGTTA

GCTGAGCAGG GAACAAGGCC GTGCTTTTCA GAAGTATGTA GGTCTGCTTC ACAAGAATAT GCCATTAACA ATATGGACAA

GGCTCACCAT AAATTTATGA GTGAAACAAC TTATTCCAAC TGCTCTCATG CCTGGCTTTA TACAGTCATC TACTTGTCCT

TCCCTGGGCC CAGCCAATGC TGCTCCCCCT TTAACAACTG CTTCTGAATG TCCCTGTGGT GTGGGCCAGA AAGGAGACTC TCTTCTTCCC CAAATCCACC Y

GCAGTATGGC AGAAACTAGA ATTCATGGTC CTCTCCCAAC CCATGCCCAC TTCCTTCTGC CACTTAAAGA AAACACCCAT

AAAGGGTGGG AAGAGAGAGC GTAACAGCAA GGTCTGTGCA TTCCCAGAGA TGTGATGCAA GGGGTGTGGG AGGCATGGCA

CTGCTTGACT CACGCTGGAG AGCGGGCACT TGGCCTGGCT TTCAGAGGAA ATGCTCCTTG GAATGCGGTC GGCCCCGGCT

GCACCCACGC CTGTGAGGGA GGGGCTTATG TGTCTGGCAC ATCATAGGTG GCTCCTGGGG TTTGCCATGA GTCTCAGCAC

AGCAGACCTG AGAGGAAAAA AATACAGACT GAACGCGTTT CTTCTATTCT CTCACCCAAC ACAGAAGACT TCTGTGGCCG

CATGTGTGGG GTTTTTTTTC CCCACATACC AAGAAGCAAA CAATTCTTCT GTGGACTCTA GCCGAGACTC TTCCAATTCA ATTCAATTCA GACACTAGCT

>gnl [ dbSNP | rs 303074

Active CAACTGCTCT CATGCCTGGC TTTATACAGT CATCTACTTG TCCTTCCCTG GGCCCAGCCA

ATGCTGCTCC CCCTTTAACA ACTGCTTCTG AATGTCCCTG TGGTGTGGGC CAGAAAGGAG ACTCTCTTCT TCCCCAAATC CACCTGCAGT ATGGCAGAAA CTAGAATTCA TGGTCCTCTC CCAACCCATG CCCACTTCCT TCTGCCACTT AAAGAAAACA CCCATAAAGG GTGGGAAGAG AGAGCGTAAC AGCAAGGTCT GTGCATTCCC AGAGATGTGA TGCAAGGGGT GTGGGAGGCA TGGCACTGCT TGACTCACGC TGGAGAGCGG GCACTTGGCC TGGCTTTCAG AGGAAATGCT CCTTGGAATG CGGTCGGCCC CGGCTGCACC CACGCCTGTG AGGGAGGGGC T ATGTGTCT GGCACATCAT AGGTGGCTCC TGGGGTTTGC CATGAGTCTC AGCACAGCAG ACCTGAGAGG AAAAAAATAC AGACTGAACG Y

GTTTCTTCTA TTCTCTCACC CAACACAGAA GACTTCTGTG GCCGCATGTG TGGGGTTTTT TTTCCCCACA TACCAAGAAG CAAACAATTC TTCTGTGGAC TCTAGCCGAG ACTCTTCCAA TTCAATTCAA TTCAGACACT AGCTACCTAG AGATAGTGTA AGAAGGCAC GGTTGAGGAC TCATTCCCCA AGACCACCCC TCACTCCTGA TGCCAACTGC AAGCTCCACG TTGTTTTATC TGTGCATCTG ACTGGCTATA AATCAGGGGT CCTATGGCCC CCTCCGGTGG CCCTTCCTTG GGTTTGATTA ATATGCTAGA GCAGCTCACA GAACTCAGGG AAACACCGAT TTATTATAAA GGATATTACA AAGGATAAAG ATTAATAGAT GCATAGGGTA AAGTATGGGG GAAGGCAGAA GCAGTTTCCA CGTCCTTCCC AAGCACCACA CCCTCCAGGA ACCTCCACGT GGTCAGCTAC CCAGAAGGTC TCCAAACATG

>gnl I dbSNP! rs602199

GCAGATGGGG CCTTTGGGAG GTGACTAGGA CATGAGGGTG GAGCACTTGT GAGTGGGATT AGTGCCCTTA CAGAGAGACT

GCAGAGAGCT CCCTTGCCCC TTCCACCATG TGAGGACACA GGGAGAAGAT GGCTGTCTGT GAACTGGGAA ACAGGCCCTC

ATCAGACACT GAGTCAGCTG AGGTATTGAT CTTGGACTTC CCAGCCTTCA GAACTGTGAG AAATAAATTT CTGTTTAAAA

GACACCCAGT TTCAGGTATT TTTGCCATAG TAGCCCAAAC AGACTAACAG TGGATATAAT TTTGTTGAGC CAGTTATAAA

ATCCAAGTCC AAGTCAAAAC TGCAGGCTGA TATTAGCTGG GCATGGTGGT GCATGCCTGT AGTTCCAGCT ACTCCAGAGG

Active CGGAGGTGGG AGGATGGCTT GGGCCCCAGA GGTCAAGGCT GCTGTGAGTG GTGATCACAC

CAATGCACAC CAGCCTGGGG GACAGAGCAA GACCCTGTCT S

AAAAACACAA AAATACAAAA AACTTGCAGG CTCCAAAACT ACCTGAACTT CAACCTACCT TCTTTCAATA CAATGCCCAG AACATAGTCT CTCTCAATGA CCCAGTCAAG CTTAAAAAAA AAAAAAAGAA AAAAAAAGCA TCACCACTTC TCTCTTCAAA ATCTAGCCTT GATATATATT TTGAGGGGAT GCATTCTGAA GTGTGTCAGC ATGATACATC GTATCATCTG CAACTTACTT TCAAATGGCT TAGGAAAAAA ATATGGTATC TGCTGTCTAT TTATCTACCT ACCTATCTAT CAAGAGATAA GCAAACATGA TGAAATAATA ACAGTTGTTA AATCCATGTG AGGGGTATTT GGCTGTTTGT GTGCTATTTT TCAGCTTTTC TGATTGAGCT TACTTTTTTA AAAAGGCAGG AAAAAGTATG TGGCCTTGAC TGTGAAGACA GACAAGAAAC AGCTGAGCCC CTCTTGTTTC TCGATACATC AAAAATGCGG

>gnl ! dbSNP | rs 3911709

ACACCCATAA AGGGTGGGAA GAGAGAGCGT AACAGCAAGG TCTGTGCATT CCCAGAGATG TGATGCAAGG GGTGTGGGAG

GCATGGCACT GCTTGACTCA CGCTGGAGAG CGGGCACTTG GCCTGGCTTT CAGAGGAAAT GCTCCTTGGA ATGCGGTCGG

CCCCGGCTGC ACCCACGCCT GTGAGGGAGG GGCTTATGTG TCTGGCACAT CATAGGTGGC TCCTGGGGTT TGCCATGAGT

CTCAGCACAG CAGACCTGAG AGGAAAAAAA TACAGACTGA ACGCGTTTCT TCTATTCTCT CACCCAACAC AGAAGACTTC

TGTGGCCGCA TGTGTGGGGT TTTTTTTCCC CACATACCAA GAAGCAAACA ATTCTTCTGT GGACTCTAGC CGAGACTCTT

CCAATTCAAT TCAATTCAGA CACTAGCTAC CTAGAGATAG TGTAAGAAGG CACAGGTTGA GGACTCATTC CCCAAGACCA CCCCTCACTC CTGATGCCAA Y

TGCAAGCTCC ACGTTGTTTT ATCTGTGCAT CTGACTGGCT ATAAATCAGG GGTCCTATGG CCCCCTCCGG TGGCCCTTCC

TTGGGTTTGA TTAATATGCT AGAGCAGCTC ACAGAACTCA GGGAAACACC GATTTATTAT AAAGGATATT ACAAAGGATA

AAGATTAATA GATGCATAGG GTAAAGTATG GGGGAAGGCA GAAGCAGTTT CCACGTCCTT CCCAAGCACC ACACCCTCCA

Active 1 GGAACCTCCA CGTGGTCAGC TACCCAGAAG GTCTCCAAAC ATGGTTCTTT TGGGCTTTGA

TGGAGGCTTT ATTATGTAGG CATGATTGAT TAAACTCTTG GTCATTGGTG ATTAACTTTA CTTCAGCCCC TCTTCCCTTC CCAGAGGTTG GGGGATGAGG CTGAAAGCCC CAACCCTCTA ACCATGGCTT AGCCTTTCCC ATGACCAGTC TCCGTTCTGA AGCTACCGAT GGGCTGCCGG CCATCTGTCA ACTCATCAGC

>gnl |dbS P(rs4097280

rs=4097280 |pos=501 | len=1001 I taxid=9606 I mol="genomic" | class=l I alIeles="C/T" build=137 I suspect=? I GMAF=A: 2184 : 0. 789

GCTGGTCTCA AATTCCTGAC CTGAAATGAT CCGCCCGCCT CGGCCTCCCA AAGTGCTGGG A ACAGGTG TAAGCCACCA

CGCCTGGCCT GCCCATCTCT TTTTCACTTG AGCCAAAGCT ATTTCTAGGA AGGCAGTGGC ATTTCCTGAG CTAAAATCAT

TTTCCCATTC CTGAGTCACA TTTCACATGG TCCCAGAGGT GAATTTAGTG GATTACATTT TAAAAAACAA ACAAAAACCT

CAGAGCCACA CATAGACCAG GTTTTGCCTT CTTCCTCTCC AACTCCCACT ATTCCTTCCT TTGCACGTTT GCTGAGCCAT

ACGGAAGTGC ATGGCCAACA GAGAAGAAAA AGGTTGATTA GTAGTAAAGA AGCCCTGCTG TTGCCTTGAA TGTCAGCACG

TGCACACACA CACACAGGTG CGCGCACACA CGGGCACACA CAGGTACGCG CACACACACA GGTGCAAGCA CACAGGTGCG CGCACACACA CAGATGCGCG Y

GCACACACAG GTACGCGCAC ACACACTTTT ATACCTGTCC ATTGCCAGTT TCTTTTGGTT CTTCAGGATT GCCCTTAGTG

TTCGTTTTCA TCTGATGTTG CCTAGACCAA AATCCTGGAG GAAAGAACCT GATGAACTAG GTTTTGAACT CCCCCATGCA

TGACCCCTGC CTGTGGGGTC TGCCCTAGAT GGATAATAAA TAGGTCATTA TCAGTCTCAT TTCAGTGTCC ACAGTGGAGA

GATTTTATTC TTCCCCTTGC TCTGGAACTG GCCCCTTTTC TCCTCCAAAT CCCAATCTTG GCCTAG7AATT TTGAACTCTG

CTTAGAATTC CAAATTGCCA CATATATATG TCAGGAGATC AGACAGAGTT AGCTGAGCAG GGAACAAGGC CGTGCTTTTC

AGAAGTATGT AGGTCTGCTT CACAAGAATA TGCCATTAAC AATATGGACA AGGCTCACCA TAAATTTATG AGTGAAACAA CTTATTCCAA CTGCTCTCAT >gnl I dbSNP I rs 47 10998

TTTTTTGTTC TGAGATGTAG ACAGCTATTA AGAACTGATC TTTGCACAGT AAATTTTTCC TATTCTTAGT CATTATCCTT

AGGTGAGGCA ACATGGTGCC ATTCAGTTAT TCAGCAAATT CTCACATCTT CCGTGTGCCA TGCATTGTTA CAGGTTTTGA

GCCTAGAACC ATGAAAACAA AAGACAAAAA TCTCTGCCCT TGTGGACTTT GTATTCCAGA GGAGAGAAAA TAAACAAGGT

AAGTAAAATA TATAGTATGG TAGATAATGA ATGGTATGGG CTGAAGGAAA AACATAAACA AAGACGTTAG GTAGTGCTGA

GAGGGAGGGT GGTTTGCAGT TGAGATAAGG ATGTCTCCAA GGATATGGTG GCATCTGCAT TACCAGAGAA ACATTCCAGG

CAGAGAAACC AGTGAGTGCA AAGGCCCTGA GGCAGAAGCA TGGCTGGCTT GTGTGGTAGG CATGAGTGAG CTAAGGACAG AGGAGCTACA GAGGACGCCA R

AGAGAAATTG AGAATTGAAG GGAGTTGGGG GATGGAGCTG TTGGTACCGA AG G GAG C AT TATAAAGACC TTAGCTTGGC

TGGGCACTGT GGCTCATGCC TGTAATCCCA GCACATTGGG AAGCCGAGGC AGGTGGATCA CCTGAGGTCA AGAGTTCGAG

ACCAGCCTGG CCAACATGGG GAAACCCCAT CTCTACTAAA AATACAAAAA TTAGCCGGGC GTGGTGGCGT GCACCTGTAA

TCCCAGCTAC TTGGGAGGCT GAGGCAAGAG AATCGCTTGA ACCCGGGAAG TGGAGGTTGC AGTGAGCCAA GATCACACCA

CTGCACTGCA GTCTGGGCAA CAAGAGTGAA ACTCCATCTC AAAAAAAAAA AAGACCTTAG CTTTTCCTCT GAGAGCAGAA

ACTTTGGAGG GGCTTGAGTC AAGCAATGGC GTGATCTGCT TCGTATCTTA ACAGAGTCAC CTTGGCTGCT CGGTCAGGGC AGGGGGACAA GTGTGGAGGC

> gnl i dbSNP | rs 4 7 1 2 668

AGGTCAGGAA TTTGAGACCA GCCTGGCTGA CATGGTGAAA CCCGGTCGCT ACTAAAAATT CCAAAAATTA GCCGGGCATC

GTGGCGGGCA CCTGTAGTCC CAGCTACTCA GGAGGCTGAG TCTGGAGAAT GGCTTGAACC CAGAAGATGG AGGCTGCAGT

GAGCCAAGAT CGTGCCACTG CACTCCAGCC TGGGCAACAG AGCGAGACTC CATCTTAAAA AAAAAAGAAA AGAAAGAAAA

Active AGAAATGGGC AAGACAAAAC CAAGTTTAAG AATGCAAGTT TATTACTTAT GAAATTATAG

ATTGCAGGAA CCAGAGACTT AAGTTTCTCC AGGCAGTAGT GTATATTATC AGGATGAGGT AAGGAACACC AGACCAACAG GGCAGACAGG TCTGATGAAG GAAAGGGACC TGAAGGTCAT TCTGAATCCA GTGGAGCTCT AAGTAGGTCA ACTTTTGGCC TCCTCAGACC AACATCCCTT TGTGGTGACT CAAGACCAAT K

TCTACCTCAG GGTCAGGCTG GTTTGGTCAA CCACCTCCAG TATGGCTGAC TTAGTTTTCA AATTCAGCCA CAAGGATCAC ATTGAGGAGT CTTTTTTTCA GAGACAGGGT CTTGCCCTGT TGCCCAGGCT GGAGTGCAAT GGTACAATCA TAACTCACTG CAGCCTCGAC CTCTTGGGCT CAAGCAATCC TCCTGCCTCA GCCTCCTGAG TAGCTGGGAC TAC GACACA CACCACCATG CCCAGCTATT TATTTTATTT TTGTAGAAAT GGGTCTTGCT ATGTTGCCCA GGCTGGTCTT CAACTCCTGA TCCTCCCATC TTGGCCTCCC AAAGTGCTGG GATTACAGGC ATGAGCCACC TTGCCCAGCT GATCTTGAGG AGTAGTTCTT TCTTTGCTCT GAAGCCCCAT GGCTTCATTT GAATGTATGA CTAAGCCCCT GTTAATGGTA ACCAGTGAAA TGAATTATTA TTTTTTTTAT CATTTTTATT TTTTTTTGAG

>gnl I dbSNP I r s 6907 578

TTGCACTTCT GTTTACAAAG CAATCCTGCC ATCAAAAGAG GAACAAAATC ACCACTTATC ACACCCTGTC ATAAAGTAAT

CTGCCCTGGA GGGAAACCCT TGTGGAGAAC TGCTGTGTGT GTGTGTGTGT GTGTGTGTGT GTGTGTGTGT GTGTGTTGGG

GGAGGGGGGA TGGAGGAAAG GGGGATTCTC CCAACTCTTC TGCAGAGTAA ATCGCTGGAA CGCGTGGTGT CCCAACCGGC

CTGGAAAGAC CGAGAGTACC ATGAGCTGTG AAGCTGGGGT GTGACAGGGA TGCCCGTCCA GGGCTGGCAA GAGTGCAGAA

TGGCTCTCTT GGATCTTTGG AATAGGCACA TCTGCAGACC CCGCTCCAAT GTTTACTTTC CTAGCGCCTT CGAAGATACT

CCCAAGGGCC CCCAAAATAG ATCAGCAAAA AGTGTTGGGG GTGGGGGGAG TGAAAAAGCC AGTTCTTGAA GACTGTAAGG TCCCCTTTCG CATCTCAGCA W

CTGGAGTGTG CAGGGAATTC CTGACCAGTG GTTTTGCTCC CTCCAATCCC TTGCCTCCCC CCTCCCATGT TATGCACTTG

Active TTCTTGGAGA GATGGACGTT AAAGAAGCGT CAAGCAGTTC TCACTGCAAA TAAATGGTGC

AGAAATAAGA GAGAGAGGAT

GAAAGCCTAG GAAGTTATAA GTGATCCTGA CCCGACCCAG CCACCAGGGG GTTATCTCTT TCCAGGTCCT GCCTTGTGTA

GAGTGAGGTG ATAAACGCTT TAGGCAGCCA AATCCAAGCA CAGCTGGGTG CCTGGCGGGG ATGGGGTGGG GGTGGTCCTA

TGTGGTGCCT CTGCCTCTGG AGTTACCTTT AGGAAAGGTC AAGAGAACTA TCCTCCCCTC CATGTCTGCT GAAAAGGGGC

TATTTTGCTA GTCTTGTTAT CAGTAATTCA CCACTTAATA TAACCAGGTT TTAGGTTTGT ATAT GAGCGA TCCTGGACAT CCAATACCAT CCCCCCAGTT

>gnl l dbSNP | rs 6908 107

r s=690 8 107 | pos =501 1 l en=1 001 1 t axid=960 6 | mol= *' genomi c " i cl a s s= l I al l ele s= "C/G " | bui ld= 137 | su spect=? I GMAF=C : 2 1 8 4 : 0 . 42 7 7

TGTCCTACTG CCCTTCCCAG CACCTGGCTT TAATTGGGGC TGCTCTGGGC CACTTTGCCA GGAATCCTGA AGTTGATTTG

TAGGGAACAG GGATTGAGTG ACCGGGCCCT ACCTCCGCTC CCCAAAAACA ATGTCCTGTT CTCATGTGCT GGCCCACCTC

CTCCCCAGGA CCTGGGTCCC TACGCTGAAC ACTGAGGTGG CTTTTGCTCA GCTAGTCTCC AAG C GCAC GAGCCTATTT

TGCCTATATT GGTAAGAGTA ATGGAGCTGT TCATTCCAGT TATCTTTCAC TGGACTGAAA GGATTGGCTT AAAAAATTAC

TGTACCCTAC TGCGATATTG AAAAATATAT ATTTCATCTT CCACCTTGTT TCCCTGTGTA CAACTCCTAA ATTCCTTGGA

ATCTCCAAAG TGATGTCTTT TTTGTGTGCT GATGAGTTGA CAGATGGCCG GCAGCCCATC GGTAGCTTCA GAACGGAGAC TGGTCATGGG AAAGGCTAAG S

CATGGTTAGA GGGTTGGGGC TTTCAGCCTC ATCCCCCAAC CTCTGGGAAG GGAAGAGGGG CTGAAGTAAA GTTAATCACC

AATGACCAAG AGTTTAATCA ATCATGCCTA CATAATAAAG CCTCCATCAA AGCCCAAAAG AACCATGTTT GGAGACCTTC

TGGGTAGCTG ACCACGTGGA GGTTCCTGGA GGGTGTGGTG CTTGGGAAGG ACGTGGAAAC TGCTTCTGCC TTCCCCCATA

CTTTACCCTA TGCATCTATT AATCTTTATC CTTTGTAATA TCCTTTATAA TAAATCGGTG TTTCCCTGAG TTCTGTGAGC

TGCTCTAGCA TATTAATCAA ACCCAAGGAA GGGCCACCGG AGGGGGCCAT AGGACCCCTG ATTTATAGCC AGTCAGATGC

ACAGATAAAA CAACGTGGAG CTTGCAGTTG GCATCAGGAG TGAGGGGTGG TCTTGGGGAA TGAGTCCTCA ACCTGTGCCT

Active i TCTTACACTA TCTCTAGGTA >gnl I dbSNP I rs 6923826

CCTTGTGGAG AACTGCTGTG TGTGTGTGTG TGTGTGTGTG TGTGTGTGTG TGTGTGTGTT GGGGGAGGGG GGATGGAGGA

AAGGGGGATT CTCCCAACTC TTCTGCAGAG TAAATCGCTG GAACGCGTGG TGTCCCAACC GGCCTGGAAA GACCGAGAGT

ACCATGAGCT GTGAAGCTGG GGTGTGACAG GGATGCCCGT CCAGGGCTGG CAAGAGTGCA GAATGGCTCT CTTGGATCTT

TGGAATAGGC ACATCTGCAG ACCCCGCTCC AATGTTTACT TTCCTAGCGC CTTCGAAGAT ACTCCCAAGG GCCCCCAAAA

TAGATCAGCA AAAAGTGTTG GGGGTGGGGG GAGTGAAAAA GCCAGTTCTT GAAGACTGTA AGGTCCCCTT TCGCATCTCA

GCATCTGGAG TGTGCAGGGA ATTCCTGACC AGTGGTTTTG CTCCCTCCAA TCCCTTGCCT CCCCCCTCCC ATGTTATGCA CTTGTTCTTG GAGAGATGGA S

GTTAAAGAAG CGTCAAGCAG TTCTCACTGC AAATAAATGG TGCAGAAATA AGAGAGAGAG GATGAAAGCC TAGGAAGTTA

TAAGTGATCC TGACCCGACC CAGCCACCAG GGGGTTATCT CTTTCCAGGT CCTGCCTTGT GTAGAGTGAG GTGATAAACG

CTTTAGGCAG CCAAATCCAA GCACAGCTGG GTGCCTGGCG GGGATGGGGT GGGGGTGGTC CTATGTGGTG CCTCTGCCTC

TGGAGTTACC TTTAGGAAAG GTCAAGAGAA CTATCCTCCC CTCCATGTCT GCTGAAAAGG GGCTATTTTG CTAGTCTTGT

TATCAG AAT TCACCACTTA ATATAACCAG GTTTTAGGTT TGTATATGAG CGATCCTGGA CATCCAATAC CATCCCCCCA

GTTCCCCAGC GCCACTCCTG GACATTCTAG ACACCAGCGA GGCTTCTTCT GCAGCCATTC CTAATGTAGC AGATCCATTT TGGGGGGAGT CTGGATGCAG

>gnl I dbSNP | rs 6924202

TACCATGAGC TGTGAAGCTG GGGTGTGACA GGGATGCCCG TCCAGGGCTG GCAAGAGTGC AGAATGGCTC TCTTGGATCT

TTGGAATAGG CACATCTGCA GACCCCGCTC CAATGTTTAC TTTCCTAGCG CCTTCGAAGA TACTCCCAAG GGCCCCCAAA

Active 1 ATAGATCAGC AAAAAGTGTT GGGGGTGGGG GGAGTGAAAA AGCCAGTTCT TGAAGACTGT

AAGGTCCCCT TTCGCATCTC

AGCATCTGGA GTGTGCAGGG AATTCCTGAC CAGTGGTTTT GCTCCCTCCA ATCCCTTGCC TCCCCCCTCC CATGTTATGC

ACTTGTTCTT GGAGAGATGG ACGTTAAAGA AGCGTCAAGC AGTTCTCACT GCAAATAAAT GGTGCAGAAA TAAGAGAGAG

AGGATGAAAG CCTAGGAAGT TATAAGTGAT CCTGACCCGA CCCAGCCACC AGGGGGTTAT CTCTTTCCAG GTCCTGCCTT GTGTAGAGTG AGGTGATAAA Y

GCTTTAGGCA GCCAAATCCA AGCACAGCTG GGTGCCTGGC GGGGATGGGG TGGGGGTGGT CCTATGTGGT GCCTCTGCCT

CTGGAGTTAC CTTTAGGAAA GGTCAAGAGA ACTATCCTCC CCTCCATGTC TGCTGAAAAG GGGCTATTTT GCTAGTCTTG

TTATCAGTAA TTCACCACTT AATATAACCA GGTTTTAGGT TTGTATATGA GCGATCCTGG ACATCCAATA CCATCCCCCC

AGTTCCCCAG CGCCACTCCT GGACATTCTA GACACCAGCG AGGCTTCTTC TGCAGCCATT CCTAATGTAG CAGATCCATT

TTGGGGGGAG TCTGGATGCA GGTGTGTGTG ATCCAGCCTG AATTTGAGAC TCTCAGTTTC TTTAACACCA GCTTGAAAAG

TCTGCAATCA CTAGCCCTGA GAGAGTACTT TGGTTCCTAA TGGGATATCC TGAGTCAGGG TGGCTGAAAG AGCTACCAGT TTACCTTGTA CATGGCAGGC gnl ] dbSNPI rs7738545

rs=7738545 | pos=501 | len=1001 | taxid=9606 |mol="genomic" | class=l I alleles="C/T" build=137 j suspect=? | GMAF=T: 218 : 0.4899

GCGTGAGCCA CCGAGCTTGG CCAGTGAAAT GAATTATTAA ACATTATTAA CCTTGGTATT GATATATCAA AATTAATTTA

CTAAAGAGTG TTGTGGCCCA CACCTGTAAT CCCAGCACTT TGGGAGGCCA AGGTGAGAGG ATTTCTTGAG CCCAGGAGTT

CAAGACCAGC CTGGGCAACA AGGCCAGACC CCATCCCTAC AAAAAATTTT TTTAAAAAAA TAGCCACCAG GTATGGTGGT

GCACGCCTGT GGTCTCAACT GCTTGGGAGG CTGAGGCAGG AGGAATGTTT GAGCCCAGAA GGTCGGGGCT GCAGCAGTGA

GCTGTGATCA CACCACTGCA TTCCAGCTTG GGTAACAGAG TGAGATCTTT TCTCAAACAA ACAAACAAAC AAACAAAAAA

AAGATTTGGA ATCAATATCC TAGCAAGACT CTGGGTTGCA ACTTTGCAAA TCTTCTGCTG TGCACGTTTG TTGTTGTTGT TGAGACACAG TCTCGCTCTG Y

Active TGCCCAGGCT GGAGTGCAGT GGCACAATCA TTGCTCACTG AAACCTCGAC CTCCTGGACT

CAAGCATTCC TCCCGCGTCA

GCCTCCCAAG TCTCTGGGAC TATAGGCGTG CACCACCACG CCTGGCTAAT TAAATAAAAA

ATTGTGGGTG CCAGGCGCGG

TGGCTCACGC CTATAATCCC AGCACTTTGG GAGGGCGAGG AGGGTGGATC ACGAGGTCAA

GAGATTGAGA CCATTCTGGC

CAACCTGGTG AAATCCAGTC TCTACTAAAA TTACAAAAAT TAGCCGGGCG TGGTGGCGCA

TGCCTGTAGT CCCGGCTACT

CGGGAGGCTG AGGCAGGAGA ATCACTTGAA GCCGGGAGGC AGAGGTTGCA GTGAGCCGAT

ATTGTACCAC TGCACTCCAG

CCTGGCGACA GAGCAAGACT TCGTTTCAGA AAAAGAAAAA AAATTTTTTT TTTTTGTAGA

AACAGAGTCT TTCTATGTTG

CCCAGGCTGA TCGCAAACTC

>gnl | dbSNP | rs 9295535

TTAAAGGCGT GCACCACCAT GCATGGCTAA TTTTTGTATT TTTAGTAGAG TCAGGATTTC GACGTGTTGG CCAGGCTGGT

CTCGAACTCC TGACCTCAGG TAATCCACCC TCCTCGGCCT CCCAAAGTAC TAGGATTACA GGCATGAGCC ACATTACCTG

GCCACATTTA AGCTTTTTAA CTAAAAGTTT ATTGGGAGAA TAAAGTGGAG GGCAGTTAAA ATCCCTCTAG TGGAAGAAAA

GACCTGGACA ATATGAGCTG TGTTCATTAT GACCACTGGG AAGATGAGTT TCACCCTTCA CATGACTATA TGGTGAGAAC

ATGTTTCTCA GCTGAGACAA GATTTCAGGA AAGTTTGCAA GAACCGAGAG AAAATGGAAG AAAATGAAAT ATTTGTTCTT

CAGAGTCACC AGTTTTATTA TATGCCTGGA CTCTGTCACT TATGTCAATA AATTTACAAA TGCAAAAT C ACATTTAATT CCAGCGTGGT AGCATACACC Y

GTAGTCCTAG ATACTCAGGA GGGTGAGTAT CTAGGACTAC AGGTGTGTGC TACCACGCTT GAACTCAGGA GTTCAAGGCC

AGCCTGGACA ACACAGGGAG ACCCCCTCTC TAAATGTATA TACACACATA CACACACACA CACACACACA CACACATTCA

AACATTGGAA TCAGATGTCC TGGACAAAAT GCTCAAATCA GCTGAACACT TTGGAATGCT TAACTTTTCT TTTTTTTAGA

TGTTTATTTA TTTATTTATT TTGTTTTTTA TTTTATTATT ATTATACTTT AAGTTTTAGG GTACATGTGC GCAATGTGCA

GGTTTGTTAC ATATGTATAC ATGTGCCATG TTGGTGTGCT GCACCCATTA ACTCGTCATT TAGCATTAGG TATATCTCCA

Active AATGCTATCC CTCCCCCCTC CCCCCACCCC ACAACAGTCC CCGGAGTGTG ATGTTCCCCT

TCCTGTGTCC ATGTGTTCTC ATTGTTCAAT TCCCACCTAT

>gnl I dbSNP I rs 92 95542

ATATCTCATG TATTGGGTAT CTACTATGTG CCAAGCCTTT TACTAGGTGC TTTACACACA CATTTATATT GTGCCACTTA

AAACTTATAG TAACTCTAAA AGATGATGGC TGGGTGCACT GGCCCACACC TGTAATCCCA GCAAGTTGGG AGCCCAAGGT

GGGAGGATGG CTTGAGGCCA GGAGTTTGAC ACCAGCAGGG AGAACATAGC AAGACCTCAT CTCTACAAAA TTAAAAAAAA

AAATACAAAA ATTAGCCGAG TGTGGTGGTG CACACCTGTA GTCCCAGGTA CTTGGGAGGT TGAGGTGGGA GGATCACTTG

AGCCCAGGAG GTTGAGGCTG CAGTGAGCTA TGATTGTACC ACTGCGCTCC AGCTCAGATA ACAGAGCCAG ACCCTATCTC

TAAAATTTAA ATAAATAAAT AAATAAATAA ATAAATAAAT AAATAAATAA TGTCTATTAT CCCCATTTTG AAAAAAAAAA AAAATCTGAG AGAAGGCCAG R

CACCATGGCT CAAACCTGTA GACAGAGACG GGCAGAAGGC TTGGl'CAAGA GTTCGAGACC

AGCCTGGCTA ACATGGTGAA

AACCCCTGCC TCTACTAAAA ATACAAAAAT TAGCCAAGTA TGATGGTGGC GCCTGCTATC CCAGCTACTT GGGAGGCTGA

GGCAGAATTG CTTGAACCCG GGAGGCAGAG GTTGCAGTGA GCTGAGATCA CACCACTGCA CTCCAGCCTG GGTGACAGAG

CGAGTATCCA TCTCAAAAAA AAAAAAAAAA AAAAGCCTGA GAGAGAAATC AAGCAATATG CCCCAAATTA CACTACTAGC

AAATAACAAA ATCAAAATTC AATCCCAAGT CTCAATTTTC TTTTCAAATT CTTCACTTAC TATATCCGTT TCCTGTTGCT

GCTGTAGCAC GTTACTGTGC ACTTTCTCAC GGTGCAGGAG ATGAGAAGTC TGAAATCAAG GAGTCAGCAA GGCCACAGTC CCTCCAGAGG CTCCAGGAGA

>gril ! dbSNP | rs 934 8512

ACTAATGCCT CTTCAAATGG AGGGTTTTGT TTGTTTGTTT GTTTATGGGA ATTTTAAGTA ATTTTCAGTG CCTGAGAATG

Active TTCTCCATAA AACCTGTAAC AAAACACATA ATAATGGTTC CAGTGAAAAT AGTTATCTCA

AAGTTGGATT GGATTTGAAA TTCTAAATAC CCTATGACTA GGGTATCAAA ATTTAAGGTT TGGTCAAATG TAACTTTTTA GGTGTCTTGT GTATGGTACA AGTTTGAAAG TGTTTATGTG CACTACCTGT TCCATTCATC ATATCTACCC ATATCTGTAT CACTTAAAAT GAATACTTTT AGGTTTATTA AAAAGTAACA CTTCAAGCAA GCAAATGGAA ATTATTTTGC AGTAACTACA AATAATAGAG AAGTAT TAAC ATAGAGTTGT GGGCCATGAC CTAGTGGGTT GTTTGTCACT GTTTATTTTC TGCCATTTCC TAGGGGTGAA TTGCATCCTG TACTGTTTAC AGCCTTATCT

CAACTTTTGC AGAGTCAAGA ATTTAAAAGC AGCAGGGCTT GGTGGCCCAT GCCTGTAATC CCAATATTTT GGGAGGCCGC AGCGGGAGGA TCACTTGAGG CCAGGAGTTC CAGACCTCCC TGGGCAACAT GATGAGACCA CATCTCTACA GAAAAATTAG CTGGGCATGC TGGCATGTGC CTGTAGTCCC AGCTCCTCAA GAGGCTGAGG TGGGAGGATC ACTTGAGCCC AGGAGGTCAA GGCTGCAGTG AGCTATGATC ACACCAATGC ACTCTAGCCT GGGGACACAG TGAGACCCTG TCTCAAAAAA AAAAAAAAGA GGAAT TTAAA AGCATTTACT ACTATCTAGT GTACTATATA CTTATTATTA GTTTATTTTT GGTCTCCCTC ACCAGAATGT AGGCTCCTTA AAGGCAGTAG TATTGCACAT AATAGGGACT AATATACCTT TATTGAATTA ATTAATGAGG GCCAAGATAT CTCATGTATT GGGTATCTAC

>gnl I dbSNP | rs 9358 52 9

r s = 93 58 52 9 [ po s=50 1 1 len=100 1 I taxid= 960 6 I mo L= " genomi c " ! c las s = l I al l e le s= "A/C " I bui ld= 137 j suspect = ? | GMAF=C : 2 1 84 : 0 . 28 1 6

AT TTTTAGTA GAGATGGGGT TTCACCACGT TGGCCAGGCT AGTCTCGATC TCCTGACCTC GTGATCCTCC CACCTCGGCC

TCCCCAAAGT GCTGGGATTA CAGGCGTGAG CCACCGAGCT TGGCCAGTGA AATGAATTAT TAAACATTAT TAACCTTGGT

ATTGATATAT CAAAATTAAT TTACTAAAGA GTGTTGTGGC CCACACCTGT AATCCCAGCA CTTTGGGAGG CCAAGGTGAG

AGGATTTCTT GAGCCCAGGA GTTCAAGACC AGCCTGGGCA ACAAGGCCAG ACCCCATCCC TACAAAAAAT TTTTTTAAAA

AAATAGCCAC CAGGTATGGT GGTGCACGCC TGTGGTCTCA ACTGCTTGGG AGGCTGAGGC AGGAGGAATG TTTGAGCCCA GAAGGTCGGG GCTGCAGCAG TGAGCTGTGA TCACACCACT GCATTCCAGC TTGGGTAACA GAGTGAGATC TTTTCTCAAA

Activ e CAAACAAACA AACAAACAAA

M

AAAAGATTTG GAATCAATAT CCTAGCAAGA CTCTGGGTTG CAACTTTGCA AATCTTCTGC TGTGCACGTT TGTTGT TGTT

GTTGAGACAC AGTCTCGCTC TGCTGCCCAG GCTGGAGTGC AGTGGCACAA TCATTGCTCA CTGAAACCTC GACCTCCTGG

ACTCAAGCAT TCCTCCCGCG TCAGCCTCCC AAGTCTCTGG GACTATAGGC GTGCACCACC ACGCCTGGCT AATTAAATAA

AAAATTGTGG GTGCCAGGCG CGGTGGCTCA CGCCTATAAT CCCAGCACTT TGGGAGGGCG AGGAGGGTGG ATCACGAGGT

CAAGAGATTG AGACCATTCT GGCCAACCTG GTGAAATCCA GTCTCTACTA AAATTACAAA AATTAGCCGG GCGTGGTGGC

GCATGCCTGT AGTCCCGGCT ACTCGGGAGG CTGAGGCAGG AGAATCACTT GAAGCCGGGA GGCAGAGGT T GCAGTGAGCC GATATTGTAC CACTGCACTC

>gnl ! dbSNP I rs 93 664 4 3

r s =93 664 4 3 | po s=5 0 1 | l en= 1 001 | t axi d= 960 6 | mol= " genomic " | cl a s s= l 1 a l l ele s =" C / T " bui ld= 13 7 I suspect = ? | GMAF=T : 2 1 84 : 0 . 38 37

AGTTGTGGGC CATGACCTAG TGGGTTGTTT GTCACTGTTT ATTTTCTGCC ATTTCCTAGG GGTGAATTGC ATCCTGTACT

GTTTACAGCC TTATCTCCAA CTTTTGCAGA GTCAAGAATT TAAAAGCAGC AGGGCTTGGT GGCCCATGCC TGTAAT CCCA

ATATTTTGGG AGGCCGCAGC GGGAGGATCA CTTGAGGCCA GGAGTTCCAG ACCTCCCTGG GCAACATGAT GAGACCACAT

CTCTACAGAA AAATTAGCTG GGCATGCTGG CATGTGCCTG TAGTCCCAGC TCCTCAAGAG GCTGAGGTGG GAGGATCACT

TGAGCCCAGG AGGTCAAGGC TGCAGTGAGC TATGATCACA CCAATGCACT CTAGCCTGGG GACACAGTGA GACCCTGTCT

CAAAAAAAAA AAAAAGAGGA ATTTAAAAGC ATTTACTACT ATCTAGTGTA CTATATACTT ATTATTAGTT TATTTTTGGT CTCCCTCACC AGAATGTAGG Y

TCCTTAAAGG CAGTAGTATT GCACATAATA GGGACTAATA TACCTTTATT GAATTAATTA ATGAGGGCCA AGATATCTCA

TGTATTGGGT ATCTACTATG TGCCAAGCCT TTTACTAGGT GCTTTACACA CACATTTATA TTGTGCCACT TAAAACTTAT

AGTAACTCTA AAAGATGATG GCTGGGTGCA CTGGCCCACA CCTGTAATCC CAGCAAGTTG GGAGCCCAAG GTGGGAGGAT

GGCTTGAGGC CAGGAGTTTG ACACCAGCAG GGAGAACATA GCAAGACCTC ATCTCTACAA AATTAAAAAA AAAAATACAA

Active AAATTAGCCG AGTGTGGTGG TGCACACCTG TAGTCCCAGG TACTTGGGAG GTTGAGGTGG

GAGGATCACT TGAGCCCAGG

AGGTTGAGGC TGCAGTGAGC TATGATTGTA CCACTGCGCT CCAGCTCAGA TAACAGAGCC AGACCCTATC TCTAAAATTT AAATAAATAA ATAAATAAAT

>gnl I dbSNP I rs 9393239

ATGAGAACTC ACTCACTATC ATGAGGACAG CAAGGGGGAA ATTCTCCCCC ATGAGCCAAT CACCTCCCAC CAGGTCCCTC

CCCCAACATT AGGAATTACA ATTTGCATGA GATTTGTGTG GCCACACGGA GCCAAACCAT ATCACATTGG TCAACCTATA

TAGTAATGTT TTTCTTAATC TAAATGTATA CTAAGTTAGT GTTTTATCGA TTTAAAAATA CATCTTGAAA AGGATTTTGC

AATTTACTTT TTTTTTTTTT TTGTGAGACA GAGTCTCACT CTTGTCCCCC AGGCTGGAGT GTAGTAGCGT GATCTTGGCT

CGCTGCAATC TCTGCCTCCC AGGTTCAAGC AATTCTCCTG CCTCAGCCTC CTGAGTAGCT TGGATTACAG GCGCCTGCCA CTACTCCCGG CTAATTTTTT GGTATTTTTA GTAGAGACAG GGTTTCACCA TGTTGGCCAG GCTGGTTTCA AACTCCTGAC CTCAAGTGAT CCGCCCACCT Y

GGCTTCCCAA AGTGCTAGGA TTACAGACGT GAGCCACCAT GCCCAGCCCA CAATTTCTTT TAA.AACTAAA CA TAC GT

TGTCCATCAG TATCTGCAGG GGACTGGTTC CAGGTCTCCC TGCAAGTACC AAAATCACAG ATGCTCAGGA ATCTGATATA

AAGCAGGGTA GTACTTGCAT ATAACCCACA CACATCCTCC TGTATACTTT AAATCATCTC TAGATTACTT ATAATACCTA GTACAAGGTG AAGACTATGT AAACAGTTGT TATACTGTAT TTAAAAAAAT AATTTCCACT TTCATTTTAG ATTCAGGTGG

TACATATGCA GGTTTGTTAT ATAAGTGTAT TGCATGATGC TGAGGTTTGG AGTTCAATTG ATCCCATCAC TCAGATAGTG

AGCATAATTA TACTGTATAC AGTTTAGGAA ATAATAACAA GAAAAAAGTC TATACATATT CCATACAGAC ATGATCATCC TTTCCTCCCA CCCCTTGATT

>gnl i dbSNP ! rs 94 60713

Active CAGACAGGGT CTTGCTCTGT CCCCCAGGCT GGTGTGCATT GGTGTGATCA CCACTCACAG

CAGCCTTGAC CTCTGGGGCC CAAGCCATCC TCCCACCTCC GCCTCTGGAG TAGCTGGAAC TACAGGCATG CACCACCATG CCCAGCTAAT ATCAGCCTGC AGTTTTGACT TGGACTTGGA TTTTATAACT GGCTCAACAA AATTATATCC ACTGTTAGTC TGTTTGGGCT ACTATGGCAA AAATACCTGA AACTGGGTGT CTTTTAAACA GAAATTTATT TCTCACAGTT CTGAAGGCTG GGAAGTCCAA GATCAATACC TCAGCTGACT CAGTGTCTGA TGAGGGCCTG TTTCCCAGTT CACAGACAGC CATCTTCTCC CTGTGTCCTC ACATGGTGGA AGGGGCAAGG GAGCTCTCTG CAGTCTCTCT GTAAGGGCAC TAATCCCACT CACAAGTGCT CCACCCTCAT GTCCTAGTCA CCTCCCAAAG GCCCCATCTG Y

TAATACCATC ACCTTGGGGA TTAGAATACC AGTGTATGAA TTTGGAGGGG AGATAAGCAT TC GTCCATT GCACCCTTAT TTCCAAGGCC CAGGGATAAC GCTGAGCTCC TCTGTGGGTG AAGCACATTC AGCTATAAAA CAGTATCTTA AGATTTTCTT CTCGAGTTAG ATTTGGTACG TAGATAACGA CCTTTAACTA TTTGCATCTA TGCAGCTTTT ACTTCCACCT CCTCAACCCA CTGTCTACAA TTCTCACATA GAATTAAGAA TAATTTTGCA TAGCAGATAA TTGGCTGAGC ATGCGGTATT CTTTTGACCC ATTCAAGTGA ATAAAATACT GTATAGGAAC ACTGTCACAA TTTAAATGAA ATTAAATTTC TTGCCCCTTT TCCTCCCCCG ACCATTTAGT CTTTGGGTAG CAACAGAGAT CACTAACATG ATATAACAAT TAATGTAGTT TTGTTTCAGG GCATTAATTT GATACAAATT GTAATTCTGT

>gnl I dbSNP i rs 94 66289

GATTAGAATA CCAGTGTATG AATTTGGAGG GGAGATAAGC ATTCAGTCCA TTGCACCCTT ATTTCCAAGG CCCAGGGATA

ACGCTGAGCT CCTCTGTGGG TGAAGCACAT TCAGCTATAA AACAGTATCT TAAGATTTTC TTCTCGAGTT AGATTTGGTA

CGTAGATAAC GACCTTTAAC TATTTGCATC TATGCAGCTT TTACTTCCAC CTCCTCAACC CACTGTCTAC AATTCTCACA

TAGAATTAAG AATAATTTTG CATAGCAGAT AATTGGCTGA GCATGCGGTA TTCTTTTGAC CCATTCAAGT GAATAAAATA

CTGTATAGGA ACACTGTCAC AATTTAAATG AAATTAAATT TCTTGCCCCT TTTCCTCCCC CGACCATTTA GTCTTTGGGT

Active AGCAACAGAG ATCACTAACA TGATATAACA ATTAATGTAG TTTTGTTTCA GGGCATTAAT

TT GAT AC AAA TTGTAATTCT GTTCTCATCA GTTCTGTAAA Y

TGCTTTACTG TAATTACACC AAGTATTTGA TCAAATATTG CCGATATTTC CATCTGTTTA GTGTATGGTA TTATGATTTC AAAATTGATT CTAGATTTAG TCCAATAATT TTTAGAATGT CTCTTTCTAT ATAAAAGTCA ATGCAGAAAT AATAATATTT TGAGATAAAA AATAAAGGCA TCTTCTAGTT AATATAACAG ATTTTAGTCA CATTTATATT CTTTAATGTT CAGTGTATGT ATCCACTACA TGAGAAACTC AAGAC C AA CAAAATGGTT ATATTTACTG CAACACTAAG CAATATGGAA CATTAAAAAG AATATGTATT CATAAACAAG ACAAAAGATG GTATAGCAAC ATAAAATTTA CAAGAACATT ATAGCTGGAC TGTATAGGAA GAGCTTGACT GATTTCTTTC CACAATGCAT TTTCATCAAA ACTCATACAT ATTCAGAGAT ACAAATAGCA TACCAGTGAA TTCAATGAAC TGCCACTGAA gnl ! dbSNP I rs 94 662 90

CCAGTGTATG AATTTGGAGG GGAGATAAGC ATTCAGTCCA TTGCACCCTT ATTTCCAAGG CCCAGGGATA ACGCTGAGCT

CCTCTGTGGG TGAAGCACAT TCAGCTATAA AACAGTATCT TAAGATTTTC TTCTCGAGTT AGATTTGGTA CGTAGATAAC

GACCTTTAAC TATTTGCATC TATGCAGCTT TTACTTCCAC CTCCTCAACC CACTGTCTAC AATTCTCACA TAGAA TAAG

AATAATTTTG CATAGCAGAT AATTGGCTGA GCATGCGGTA TTCTTTTGAC CCATTCAAGT GAATAAAATA CTGTATAGGA

ACACTGTCAC AATTTAAATG AAATTAAATT TCTTGCCCCT TTTCCTCCCC CGACCATTTA GTCTTTGGGT AGCAACAGAG

ATCACTAACA TGATATAACA ATTAATGTAG TTTTGTTTCA GGGCATTAAT TTGATACAAA TTGTAATTCT GTTCTCATCA GTTCTGTAAA TTGCTTTACT R

TAATTACACC AAGTATTTGA TCAAATATTG CCGATATTTC CATCTGTTTA GTGTATGGTA TTATGATTTC AAAATTGATT

CTAGATTTAG TCCAATAATT TTTAGAATGT CTCTTTCTAT ATAAAAGTCA ATGCAGAAAT AATAATATTT TGAGATAAAA

AATAAAGGCA TCTTCTAGTT AATATAACAG ATTTTAGTCA CATTTATATT CTTTAATGTT CAGTGTATGT ATCCACTACA

Active TGAGAAACTC AAGACACAAA CAAAATGGTT ATATTTACTG CAACACTAAG CAAT TGGAA

CATTAAAAAG AATATGTATT CATAAACAAG ACAAAAGATG GTATAGCAAC ATAAAATTTA CAAGAACATT ATAGCTGGAC TGTATAGGAA GAGCTTGACT GATTTCTTTC CACAATGCAT TTTCATCAAA ACTCATACAT ATTCAGAGAT ACAAATAGCA TACCAGTGAA TTCAATGAAC TGCCACTGAA ACCAAAACAT

>gnl I dbSNP I rs l2175352

AGAATTGTGT TTTACTGTAG TATACCATAC CTTATATGTT TAATAGAACA TATCTCATCT ATATTTTGTA ATTCATTTTT

ATAAAACTGC CTGTAAATAG AAAAATTTTA TTATCTCTTT CATGTCTACA GCTTCTACAT TTATGTCCCC TCTTACTTTT

TTTTTTTTTG GAGAGACAGT GTCTCACTAT GTTGCCTAGA CCAGTTTCAA ACTCCTGGGC TCAAGTGATC CTTCTGCCTC

AGCCTCCCAA AGCGTTGGAA CTACAGGTGT GAGCCAGCCC GCCTGGCCCC TCTTACATTC TTTGTTGTTG TTGTTTTGTT

GTTGTTGTCT TTGTTGTTTT TTGAAGCAGA GTCTCCCTCT GTGGCCCAGG CTGGAGTGCA GTGGCTTGAT CGTGGCTCAC

TGCAACCTCC GCCTCCCAGG TTCAAGCCAT TCTCCTGCCT CAGCTTCCCG AGTAGCTAGG ACTGTAGGCA TATGCCACCA CGCCCAGCTA ATTTTTTTTA Y

AATTTTAGTA GAGATGGGTT TTCACCATGT TGGCCAGGCT GGCCTCAAGC TCCTGACCTC CAGTGATCTT CCTGCCTTGG

CCTCCCAAAA TGCTGGGATT ACAGGCATGA GCCACTGGGC CGAGCCCCCT TACATTCTTA ATATAGTTTA TTTGTGTCCT

TTCTTTTTTC ACTTTTTCAC TCTTGCTTAC AGGTTTTTCA ATTGTGTTAG GCTTTTTAAA GAACTGCTTG TCTTTGTAAT

GCTCTATATT ATAAATTTTA GTTGTATTTA TTTACTTCTG CTCTTACATT AATTTTTCAT TTTTGATCTT TGAATTTATT

TTGCTGTTGT TTTCTAATTC TAATTTGGAT GACTAGCTAA TTAAAAAAAA TGTTTTCCCA CTTCTTAAAT GTCAGCATTT

ATAGGCTTTT GCGCTATACA TTTCACTCAA AGTAGATTTT GTGAAATGCC ACAATATTTG GCATGTGGCA TTTTCACAAT TGTCAATTCA AAATGTTTTC

Activ e >gnl [ dbSNP | rs l 252 6269

AGCTGTGATA TTGTGAATAT AAGAATTGTA CAATTTTCCT TTGAAATGTG CTGCTGAGAA GAATAAAAAT GAAGTTTTCT

CTCTGGAAAT GGCTGGAAAC AAACGTCAAA ACCTGACAAT TTACACACAC AGTTCTCTTT CTGACTTGAC TCACCCCTTT

GAGAATTACT TTTTAAAACA CCAAAGTTAT AGGATACTAA GTTAATTGTG GTCTTTCTAA TTCTGAAAAA CTGGTTTTCA

TTTGCCTCAA GAACTTTTAA GGCAAAGTTG TCTAAGATAC TTCCTTGAAC AAAGACTCAG ACAAAAGCAT TTGACTGCTT

TTAATTTCTC AGCATTTTTA CATTTTAAAA CTATAGCTTG AATGAAACTC AAGTGTCCTG AATAAAGAAT AAATACTTAA

AAATTGTTTA AATACATATT TTCTCCTTTC ATTGTTGGAG CATTCAAGCA AAGATTGTGT AAAATTCAGG TTAAGTAAAA TGTAAAAAAT ACATATCCAG W

TTACATTACA TATTCTTTTT GTGTACAAAT ATTTATACCA ATAAAAACCC CCTAAGATAT TTATATCTTT AACATCTATT

TTTCTTTTAC CTTTACTACT AGAAAGAGAA GCTAACAAAG GAAAGCCTCT TCAAAAAATG GGATTTCCTT GGCCTTAGCA

GTTCTGGTGT GTTCCACTGC CAACACTAGG TAGGAAAAAT CTGACTTGTG ATGTTGTGAT TAAATAGCGG CCTGGCTCAA

ACTGCCCAAA GAGAGGGAAT TCACTATGAG TTCCACAGTT TTATCTTGAG GAAGAAACTA GCAGAAACAC AGAATTTTAG

AGCCTTAGAG CTCTCATTAC AAAATGGCCC TCACTATAAA GTGGCATATA CTGAACCCAG CTTAGATGTG TGTACTGAGC

CCAGTACAAA TGTATATAGT GAACCCAGAG CTCTCATTAC AAAATGCCTC TCACTATAAA GTGGCATATA CTGAACCCAG CTTAGGTGTG TGTACTGAGC

>gnl I dbSNP | rs 3507 6407

TTGAGCCCAG GAGTTCAAGA CCAGCCTGGG CAACAAGGCC AGACCCCATC CCTACAAAAA ATTTTTTTAA AAAAATAGCC

ACCAGGTATG GTGGTGCACG CCTGTGGTCT CAACTGCTTG GGAGGCTGAG GCAGGAGGAA TGTTTGAGCC CAGAAGGTCG

GGGCTGCAGC AGTGAGCTGT GATCACACCA CTGCATTCCA GCTTGGGTAA CAGAGTGAGA TCTTTTCTCA AACAAACAAA

Active CAAACAAACA AAAAAAAGAT TTGGAATCAA TATCCTAGCA AGACTCTGGG TTGCAACTTT

GCAAATCTTC TGCTGTGCAC GTTTGTTGTT GTTGTTGAGA CACAGTCTCG CTCTGCTGCC CAGGCTGGAG TGCAGTGGCA CAATCATTGC TCACTGAAAC CTCGACCTCC TGGACTCAAG CATTCCTCCC GCGTCAGCCT CCCAAGTCTC TGGGACTATA GGCGTGCACC ACCACGCCTG GCTAATTAAA TAAAAAATTG Y

GGGTGCCAGG CGCGGTGGCT CACGCCTATA ATCCCAGCAC TTTGGGAGGG CGAGGAGGGT GGA CACGAG GTCAAGAGAT TGAGACCATT CTGGCCAACC TGGTGAAATC CAGTCTCTAC TAAAATTACA AAAATTAGCC GGGCGTGGTG GCGCATGCCT GTAGTCCCGG CTACTCGGGA GGCTGAGGCA GGAGAATCAC TTGAAGCCGG GAGGCAGAGG TTGCAGTGAG CCGATATTGT ACCACTGCAC TCCAGCCTGG CGACAGAGCA AGACTTCGTT TCAGAAAAAG AAAAAAAAT TTTTTTTTTT GTAGAAACAG AGTCTTTCTA TGTTGCCCAG GCTGATCGCA AACTCCTGGG CTCAAGGGAT CCTCTCACCT CCCAAAGTGC TGGGATTACA GGCCTGAGCC ACCTTCCCCA GCCCTATGCA CATTTTCACA AAGATATTTT GAACCCTAGC AGTGGGAAAG GATACTTTTT GACTGGTGAC ATCCCAGAGC

>gnl I dbSNP I rs 56365413

rs=563654 1 3 | pos=501 | len=1001 | taxid=9606 I mol= " genomic " | class=l | al leles="C/T " | build=137 [ suspect=? [ GMAF=T : 2 18 : 0 . 15 98

TAATGTAACA GGTAGGAAAC ACTCAATATT CGGGAATGCT GATGAGTTTC CTGAGTAGCA TGCGACTGGA ATGGGAAGAA

CAGGAATCTG GTATCAGCCT AGCCACAGGC TGGCTGTTAT GTCCTTGGGC AAGTTTCATC TTGTCTCTGG GTTGTATTTC

CTGACCTGTA ATGCAAGAGT ATCAGTCCCA ACCATCTCTG AGGCCCTTTC CAGCTCTCAG AGACTCTGGA ATCAGATTCA

TACATCTGTC AGCTGAGTTT CCAAACAACA CAGCCTGGAA ACAACAATTC TAAAAATAAA ACATACAACT AAGAAACCAG

TCACAAGACT AGAAAACATC ATCACATGTA TTCTGTCACT GGTAACAAAA TAGTTGCATA CATATGCGAG CCAGTCCTAT

TTATTATTAT TTTTTTTTTA GAGACAGGGT CTTGCTCTAT TGCCCAGGCT GGAGTGCAGT CACCGCTAAC TGCAGTCTTG AACTCCTGTG CTCCAACGAT Y

CTCCTGCCTC AGCTTCCCAA GTAGCTGGGA CCACAGGTGA ACATTGCCAC ACCTGGCTAA TTTTTTATTC TTATTTTTAT

Active 1 TAGAGAAGAG TTCTCCCTTT GTTGCCGAGG CTGGTCTCAA ACTCCTGGTT TCAAGTAATC

CTACTGCCTC AGCCTCCCAA

AGTGTTGGGG TTACAAGCAC GAGCCACTAT GCCCAGCCAA GTCAATCCTA TTTTAGATTC ATCATTATTC ATTAGAAAAA

GTATTTTCAC TTATTTGTAT CTCACCCTAA CTTATAAAAT CCAAATAACG TTTGACTGAC ATGAAGATAA TA GCCACTT

AATCATGTTA TTGACTTCAC TTAAGTGGGC TACACAAATA ACGCCAATAA TATTCAGTAA TATAAAAATT ATGACATTTT

TCTAAGGGAA CTGAGTCATA CAGGCCTTGA ATGATTATAT ATAATAATCT TTTTTTTTTT TTTTTTTTTT GGACACGGAG TTTTGCTCTT GTTGCCCAGG

>gnl I dbSNPI rs75769093

TCCCATCACT CAGATAGTGA GCATAATTAT ACTGTATACA GTTTAGGAAA TAATAACAAG AAAAAAGTCT ATACATATTC

CATACAGACA TGATCATCCT TTCCTCCCAC CCCTTGATTT TTTATTGAAT TCATGAATAT TTGCTGAGTC CATGAATGTG

G.AACCCACGG ATAGGGAAGG CTGACTGCAC CTACATTATG ACCTGGCAAT TCCACACCTA

GGTTACTCAC CCGGGAGAAA

TAAAAGCATA TGTCCTCAAA GAGGCTTGTT CAAAAATGTC CATAGCTTTA TTCATAAATA ACTGAAAGCT GAAAACAACC

AATAGGAGAA TGAATAAACT AACTGTGGTA AATTCAGACA ATGAAATACT ACACAATAAA AAAGGGAGGA ACCGGCTGGG

CGCGGTGGCT CACACCTGTA ATCCCAGCAC ATTGGGAGGC CGAGGTGGGT GGATCACCTG GGGTCAAGAG TTCGAGACCA GCCTGGCCAA CATGGTGAAA M

CCCATCTCTA CTAAAAATAC AAAAATAGTC AGGTGTGGTG GCACGCACCT CCAATCCCAG CTACTCGAAA GGCTGAGGCA

GGAGAATCAG CTTGAATCCA GGAGGCAGAG GTTGCAGTGA GCTGAGATTG TGCCACTGCA CTCCAGCCTG GGTGACTCTG

TCTCAAAAAA AAAGGGGGGG TGGGGGGAGG AACCATTGAT ACATACAACA TCATGATGAA TTCCAAAAAT GTTGTACTGA

ATGGAAGAAG CCTTACACAA GAAAGCACAT ACTGTTTATA TATTTATCAT CCTAGAACAA GCAAAACTAA TCTATGGACT

AATCTAAGGT GGGGGCAGGG GAATCCAGAG AAAGGGTTAC CTTTGGGAGT TGGGCCATGG GGTTGGGGAC CAGCTGTGCA

GGGGAGCTTT CAGGGCAGTC TTAAGGTACT GGATCTCACC AGGGGTTTGC CTTGCTTGTA TACATGGCCT TCCTTGCAAC

Active TTGCTGAATG GCACACTTAT >gnl | dbSNP | rs 78113724

TTGCAAACAT TTATTTTCTC ACAGTTCCGG AGGCTGGA¾G TCCAAGATGG AGCTGCTGTG

AGGGTTGGTT TCCGGTGAGG

CCTTTCTTCC TAGCTCGTAG ACAGCCACCT TCTCTCTGTG TCCTCACATG GCTTTTCTTT TGTGTCCATG CCGAGAGAGA

GGACTCTCTG AGGACTCTCC CTCTTCTTGT AAGGACACCA GTCCTATCAG ACTAGGGCCC CACTCTTATG ACCTCATTTA

ATTTAATTAT GTCTGTAAAG GCCCCTGCTC CAAATATAGT CACATTGAGG ATTATGGCTT CATAATCCTG TGACTCTGGG

GAGAGGACAC ATTTCAGTCC ATAACAAAGC CCTTAGTGTG TTTTAGTGCT CAAAACTGTT CATTCATACC TCGGTTATTC

CATTATTATT GCCTACGATA TTACCACTTC AGGGTTTTTG TTATTTTTTA CAATATAGAG CACAACGTAT AATAAACTAC ACATACGAAT TCTCATTGAG N

AATTACAGAA AATATATCTA TCGCGTCTAA CAAGGTTTAA TTAGCATCTT GGAAAAAAAA AAAAACACCT ACGTTTTTAA

GGAAAAAGTT GGCCAATACT GCCATCTGTT GGAATTTTGG TCAAAGCTCA TGTGTTGGAC TTTACTCATT CTTTGTCAAT

ATCTTTTCTT TCTTTCTTTC TTTCTTTTTT TCTGAGACGG AGCCTTGCTC TGTTACCCAG GCTGGAGTGT GGTGGCGCGA

TCTCGGCTCA CTGCAACCTC CGCCTCCTAG GTTCAAGCGA TTCTCCTGCC TTGGCCTCCT GAGTAGCTGG AATTACAGGC

ACGCGCCACC ACGCCCGGCT AATTTTTGTA TTTTTAGTAG AGACGGAGTT TCACCATGTT GGTCAGGCTG GTTTCGAACT

CCTGACCTCG TGATCCACCC ACCTCGGCCT CCCAAAGTGC TGGAATTACA GGCGTGAGCC ACCGCGCCCG GCCCTTTGTC AACATCTTAT ATGTTGCTGT

>gnl I dbSNP ! rs 1152 62601

r s=115262601 | pos=201 I len=401 i taxid=9606 i mol=" genomic " | class= l | al leles="A/ C " I build=132 | suspect = ? j GMAF=C : 2 184 : 0 . 00 6

GTGAGAGACA GAGTCACAAA GAGAAAGAGA CAGTGAGGGG CCAGAACGAC TCTCTTTTCT CCGATTGTCA ATGCCCAGTG

GGAGCCGGGA GCCCAACAGG CCCAGCCCAT CAGATTCGGC CCCTCCGGGC CCCAAATCCG CTCGCCCCAC CCGAGATCCA

GGCCTCCAGC CACTTGCCTA ACTGTGAGCC CGCAAGAGCC

Active M

GGCCCGCGGC TCCCTCCTTC CTCCTCCTGC GGCAGTCTCG CGGCTTTCAA ACCTTAGTCG AACCCACAGA AGGCCCAGTC

CCAGGCCAAA CCTACTCAAC AGGCACCTTC TCACGGCCTA GGAATTCTGC AGCGAAATTC ACTGGAATTT GAGGAGAAAA

CCCAAAGACT GCTCCGAAAG GACTCCCCCA GTCTTCAGCC

CTATGGAAGT TTCTCAAAAA AT AAAAAT GAACTACCAT GTGATCCAGA AATCCCACTG CTGGGTATTT ATCCAAAGGA AAAAAAATCA ATATATCAAA GGGAGACCTG CACTCCCATG TTTATTGCAG CACTATTCAC AATAGCCAAG ATACAGTATC AATCTAAGTG TCCATCAACA GATGAATGGA TAAAGCAAAT GTGATACACA CACACACACA CACACACACA CACACACACA ATGGAATACT ATTAAGCCGT AAAAAAGAAT GAAATTCTAT CATTTGCAGG AACATGTATG GAATTGAAGG GCATCTTGTT AAGTAAAATC AGCCAGGCAC CGAAAGACAA ATATTGCATA TTCTTACTCA TATGTGGGAG CTAAAAAGAT GGATCTCATG GAGGTAGAGA AAAGAATGGT AGCTACTAGA GGCTATGAAG GGTGTGTGGG ATGAAGAGAG GTTGGTTAAT AGGTACAGAC ATATAGTTAG ACGGAATAAG Y

GCTAGTATTC AGCCTCAAAG TAGGGTGACT ATAGTTAACA AAAACATATT GAGTATCTCA AAATAGCCAG AAGAGAAAAT TTGAAATGTT CCTAGCTCAA AGAAATGATA CATGTTCAAG GCGATGGATA TCCTAAATAC CCTGATTTGA TCATTACACA TTCTATGGCT GTGTCAAGAT ATCACAGATA CCCCATAAAT ATGTGTAATT ATTATGTATC AAAAACTTTA TATAAAAAAC ATTAATTTGC TGTATTTTTG ATTCTACAAT TGGGCAGCAC TTTATTCCAT AAAATAGAAT GAGTGTTCTG ATGAGCCAAG AAGAGGAGGT TGGTTTTACA GACAGAAAAG GGCTGTGGAA AGCAGAAAAA AACAAACAAA AAAAATGTGG ATTGGTCATT TCAAAGTTTC TTTTCATGTA AAGGTTAAAG CAGAGGGGAC TTTCTTGTCC TGCTGGCACT GGATCTAGGT CAGTGTTGGA GACGATGTCT GGGACTCAGG

TTTGGGGGCT GAGTGTTCTT CCAATCCTAA AAACAACTCT CTGTGGCCAA ATTGCTCCAG

R

CCTCCAACAT ATCCAACATA GCTATATGTG AATAGAGTCA TCAGCTTCTG CTGTTCGTAT

ADDITIONAL NOTES ABOUT TABLE 7:

Global Minor Allele Frequency (GMAF) [ie. G:0.262:330 <-- (allele : count : frequency) ]

(http : //www . ncbi . nlm . ih . go /pro j ects/SNP/docs/rs_at tributes . html#gmaf )

Active "G : 0.262 : 330 " . This means that for this rs, minor allele is 'G' and has a frequency of 26.2% in the lOOOGenome phase 1 population and that 'G' is observed 330 times in the sample population of 629 people (or 1258 chromosomes) .

7- REFERENCES

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14. Michailidou K, Hall P, Gonzalez-Neira A, Ghoussaini M, Dennis J, et al. (2012) Large-scale genotyping identifies 38 new breast cancer susceptibility loci. Nat Genet under review.

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18. Antoniou AC, Wang X, Fredericksen ZS, McGuffog L, Tarrell R, et al. (2010) A locus on 19pl3 modifies risk of breast cancer in BRCAl mutation carriers and is associated with hormone receptor-negative breast cancer in the general population. Nat Genet 42: 885- 892.

19. Mulligan AC, Couch FJ, Barrowdale D, Domchek SM, Eccles D, et al. (2011) Common breast cancer susceptibility alleles are associated with tumour subtypes in BRCAl and BRCA2 mutation carriers: results from the Consortium of Investigators of Modifiers of BRCAl/2. Breast Cancer Res 13: Rl 10.

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35. Antoniou AC, Kartsonaki C, Sinilnikova OM, Soucy P, McGuffog L, et al. (201 1) Common alleles at 6q25.1 and lpl 1.2 are associated with breast cancer risk for BRCAl and

BRCA2 mutation carriers. Hum Mol Genet 20: 3304-3321.

Various references are cited herein, the contents of which are hereby incorporated by reference in their entireties.

Active

Claims

WHAT IS CLAIMED IS:

1. A kit for determining whether a subject has an increased risk of having or developing breast cancer comprising a means for detecting a 6p24 SNP biomarker and one or more biomarker selected from BRCA2, 10q26 (FGFR2), 16ql2 (TOX3), 12pl 1 (PTHLH), 5ql 1 (MAP3K1), 9p21 (CDKN2A/B), l lpl 5 (LSP1), 8q24, 20ql3, 6q25 (ESR1), 10q21 (ZNF365), 3p24 (SLC4A 7, NEK10), 12q24, 5pl2 and 1 lql 3.

2. The kit according to claim 1 where the 6p24 SNP biomarker is rs9348512

SNP.

3. The kit according to claim 1 comprising a means for detecting one or more biomarker selected from 10q26 (FGFR2), 16ql2 (TOX3), 5ql 1 (MAP3K1), 1 lpl 5 (LSP1) and 3p24 (SLC4A 7, NEK10),

4. The kit according to claim 1 comprising a means for detecting a biomarker of 10q26 (FGFR2) which is the SNP rs2420946.

5. The kit according to claim 1 comprising a means for detecting a biomarker of 16ql2 (TOX3) which is the SNP rs3803662.

6. The kit according to claim 1 comprising a means for detecting a biomarker of 12pl 1 (PTHLH) which is the SNP rs27633.

7. The kit according to claim 1 comprising a means for detecting a biomarker of 5ql 1 (MAP 3 K J) which is the SNP rsl 6886113.

8. The kit according to claim 1 comprising a means for detecting a biomarker of

10q26 (CDKN2A/B) which is the SNP rs 10965163.

9. The kit according to claim 1 comprising a means for detecting a biomarker of 8q24 which is the SNP rs4733664.

10. The kit according to claim 1 comprising a means for detecting a biomarker of 6q25 (ESR1) which is the SNP rs2253407.

11. The kit according to claim 1 comprising a means for detecting a biomarker of 10q21 (ZNF365) which is the SNP rs 17221319.

12. A method for assessing the likelihood that a subject has or will develop breast cancer comprising determining whether the subject carries a 6p24 SNP biomarker and a BRCA2 biomarker, where the presence of both biomarkers indicates that while the subject has an increased risk of having or developing breast cancer relative to the general population, the risk is less than if the 6p24 biomarker were absent.

13. The method of claim 12, where the subject has previously been tested and known to carry a BRCA2 biomarker.

Active 1

14. The method of claim 12, where the 6p24 SNP biomarker is rs9348512 SNP.

15. The method of claim 12, further comprising determining whether the subject carries one or more auxiliary biomarker selected from the group of 10q26 (FGFR2), 16ql2 (mo), 12pl l (PTHLH), 5ql l (MAPSKl), 9p21 (CDKN2AIB), 1 lpl 5 (LSP1), 8q24, 6q25 (ESR1), 10q21 (ZNF365), 3p24 (SLC4A 7, NEK10), 12q24, 5pl2, and 1 lql3.

16. The method of claim 12, where the presence of the biomarker is determined in a sample taken from the subject.

17. The method of any of claims 12-16 comprising the further step, where the subject is found to carry a 6p24 SNP, of recommending or performing regular breast screening to monitor for the presence of cancer.

18. The method of claim 17 where screening is performed by a clinical breast exam, biopsy, mammography, ultrasound, magnetic resonance imaging, or similar techniques.

19. A method of treating a subject who carries a BRCA2 biomarker, comprising determining whether the subject carries a 6p24 SNP biomarker and, where the 6p24 SNP biomarker is absent, advising the subject that she is at high risk for developing breast cancer relative to a subject carrying both the 6p24 SNP and BRCA2 biomarkers and to the general population.

20. The method of claim 19, where the subject has previously been tested and known to carry a BRCA2 biomarker.

21. The method of claim 19, where the 6p24 SNP biomarker is rs9348512 SNP.

22. The method of claim 19, further comprising determining whether the subject carries one or more auxiliary biomarker selected from the group of 10q26 (FGFR2), 16ql2 (TOX3), 12pl l (PTHLH), 5ql l (MAP3K1), 9p21 (CDKN2A/B), l lpl5 (LSP1), 8q24, 6q25 (ESR1), 10q21 (ZNF365), 3p24 (SLC4A 7, NEK10), 12q24, 5pl 2, and 1 lql 3.

23. The method of claim 19, where the presence of the biomarker is determined in a sample taken from the subject.

24. The method of any of claims 19-23 comprising the further step, where the subject is found not to carry the 6p24 SNP, of recommending or performing a mastectomy or oophorectomy, or recommending or administering anti-estrogen therapy or chemoprevention.

25. A 6p24 SNP and one or more biomarker selected from BRCA2, 10q26 (FGFR2), 16ql2 (TOX3), 12pl l (PTHLH), 5ql l (MAP3K1), 9p21 (CDKN2AIB), l lpl S LSP1), 8q24, 6q25 (ESR1), 10q21 (ZNF365), 3p24 (SLC4A7, NEK10), 12q24, 5pl2 and 1 1 q 13 for use in assessing the likelihood that a subject has or will develop breast cancer.

Active

26. The biomarkers of claim 25, where the 6p24 SNP is rs9348512 SNP.

27. The biomarkers of claim 25, further comprising one or more biomarker selected from 10q26 (FGFR2), 16ql2 (TOX3), 5ql 1 (MAP 3 K J), l lp l 5 (LSPl) and 3p24 (SLC4A 7, NEK10).

Active