Data from: A study on genetic variants of Fibroblast Growth Factor Receptor 2 (FGFR2) and the risk of breast cancer from North India

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<0.05). In
per-allele model for rs2981582, rs1219648, rs7895676 and in dominant model
for rs2981578, association remained significant after bonferroni
correction (P<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<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.