Abstract
Genetic testing is widely used in breast cancer and has identified a lot of susceptibility genes and single nucleotide polymorphisms (SNPs). However, for many SNPs, evidence of an association with breast cancer is weak, underlying risk estimates are imprecise, and reliable subtype-specific risk estimates are not in place. A recent genome-wide long non-coding RNA (lncRNA) association study in Chinese Han has verified a genetic association between rs12537 and breast cancer. This study is aimed at investigating the association between rs12537 and the phenotype. We collected the clinical information of 5,634 breast cancer patients and 6,308 healthy controls in the early study. And χ2 test was used for the comparison between different groups in genotype. The frequency of genotypic distribution among SNP rs12537 has no statistically significant correlation with family history (p = 0.8945), menopausal status (p = 0.3245) or HER-2 (p = 0.2987), but it is statistically and significantly correlated with ER (p = 0.004006) and PR (p = 0.01379). Most importantly, compared to the healthy control, rs12537 variant is significantly correlated with ER positive patients and the p-value has reached the level of the whole genome (p = 1.66E-08 <5.00E-08). Furthermore, we found rs12537 associated gene MTMR3 was lower expressed in breast cancer tissues but highly methylated. In conclusion, our findings indicate that rs12537 is a novel susceptibility gene in ER positive breast cancer in Chinese Han population and it may influence the methylation of MTMR3.
Highlights
The burden of breast cancer is increasing worldwide
By combining sequencing analysis with the clinical characteristics of breast cancer patients, more single nucleotide polymorphisms (SNPs)/genes that have a stronger correlation with clinical characteristics were identified, which provides important theoretical support for precision treatment of breast cancer [8, 11, 25]
genome-wide association studies (GWASs) have identified a lot of estrogen receptor (ER) positive breast cancer associated SNPs, such as rs112545418, rs17132398 in 4p16, rs116638271, rs77274510 and rs117564384 in 11q13 and rs10941679 in 5p12 [26, 27]
Summary
The burden of breast cancer is increasing worldwide. China is undergoing cancer transition with an increasing burden of breast cancer, and the incidence of breast cancer arrives at 18.41%. In China, female breast cancer patients took up approximately 18% of breast cancer deaths across the world [2]. Many sequencing methods such as genome-wide association studies (GWASs), exome and lncRNA sequencing are used to identify SNPs/loci/genes related to the occurrence, development, prognosis and drug resistance of breast cancer [3,4,5,6,7].
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