DOI: 10.5061/dryad.13f6n
title: Data from: A study on genetic variants of Fibroblast Growth Factor Receptor 2 (FGFR2) and the risk of breast cancer from North India

description: Genome-Wide Association Studies (GWAS) have identified Fibroblast growth
 factor receptor 2 (FGFR2) as a candidate gene for breast cancer with
 single nucleotide polymorphisms (SNPs) located in intron 2 region as the
 susceptibility loci strongly associated with the risk. However, replicate
 studies have often failed to extrapolate the association to diverse ethnic
 regions. This hints towards the existing heterogeneity among different
 populations, arising due to differential linkage disequilibrium (LD)
 structures and frequencies of SNPs within the associated regions of the
 genome. It is therefore important to revisit the previously linked
 candidates in varied population groups to unravel the extent of
 heterogeneity. In an attempt to investigate the role of FGFR2
 polymorphisms in susceptibility to the risk of breast cancer among North
 Indian women, we genotyped rs2981582, rs1219648, rs2981578 and rs7895676
 polymorphisms in 368 breast cancer patients and 484 healthy controls by
 Polymerase chain reaction-Restriction fragment length polymorphism
 (PCR-RFLP) assay. We observed a statistically significant association with
 breast cancer risk for all the four genetic variants (P&lt;0.05). In
 per-allele model for rs2981582, rs1219648, rs7895676 and in dominant model
 for rs2981578, association remained significant after bonferroni
 correction (P&lt;0.0125). On performing stratified analysis,
 significant correlations with various clinicopathological as well as
 environmental and lifestyle characteristics were observed. It was evident
 that rs1219648 and rs2981578 interacted with exogenous hormone use and
 advanced clinical stage III (after Bonferroni correction,
 P&lt;0.000694), respectively. Furthermore, combined analysis on these
 four loci revealed that compared to women with 0–1 risk loci, those with
 2–4 risk loci had increased risk (OR = 1.645, 95%CI = 1.152–2.347, P =
 0.006). In haplotype analysis, for rs2981578, rs2981582 and rs1219648,
 risk haplotype (GTG) was associated with a significantly increased risk
 compared to the common (ACA) haplotype (OR = 1.365, 95% CI = 1.086–1.717,
 P = 0.008). Our results suggest that intron 2 SNPs of FGFR2 may contribute
 to genetic susceptibility of breast cancer in North India population.
description: Table
 S1Supplementary Table S1:
 Clinical, lifestyle and other demographic details of cases (N=368) and
 controls (N=484) in the present study.Table
 S2Supplementary Table S2:
 Details of the SNPs selected for present study.Table
 S3Supplementary Table S3:
 Distribution of risk loci for the studied FGFR2 SNPs (rs7895676,
 rs2981578, rs2981582 and rs1219648) in cases and controls of North
 India.Table
 S4Supplementary Table S4:
 One Way ANOVA for relative risk assessment of different number of risk
 loci for the studied FGFR2 SNP combinations.Table
 S5Supplementary Table S5:
 Frequencies of inferred haplotypes of various FGFR2 SNPs combinations
 taken two at a time in breast cancer cases and
 controls.Figure
 S1.tifSupplementary Figure 1:
 Linkage disequilibrium analysis {a) D′ value and b) r2 value} of the four
 intronic FGFR2 SNPs in the studied population of North
 India.