The Association Between Low-frequency Variants And Breast Cancer Prognosis In Chinese Women

Breast cancer remains to be the most common malignancy and is the leading cause of cancer death in women worldwide.Recently,with the improvement of China's economy and development of urbanization,the incidence of breast cancer has been increasing rapidly in China owing to the changes of breast feeding habits and life styles in females.It is estimated that 2.7 million women will be diagnosed with invasive breast cancer and 69,500 will die of the disease in China in 2015,which has been the most common cancer and ranks the sixth leading cause of cancer death in females.Therefore,breast cancer has become one of the greatest threats to female's health and needed to be resolved imminently.With the application of screening mammography and the development of comprehensive therapy for breast cancer,the prognosis of breast cancer has improved significantly during the past decades.However,the 5-year survival rate still remains less than 75%in China compared with 90%in developed countries.Therefore,the application of prognostic factors may predict clinical outcomes of breast cancer and optimize effective therapies for breast cancer patients.In clinical practice,classical prognostic factors for breast cancer patients include tumor size,lymph node status,histological grade,histopathological classification,lymphovascular invasion,and tumor-infiltrating lymphocytes.With the development of molecular biology and cancer genomics,a large number of proteins such as estrogen receptor(ER),progesterone receptor(PR),human epidermal growth factor receptor 2(HER2)and Ki-67,oncogenes(HER2,survivin and MYC),and tumor suppressor genes(TP53,PTEN and BCL2),have been found associated with breast cancer prognosis in recent years.Based on the results above,a variety of predictive tools have been developed,such as Oncotype DX,Prosigna and Mamma Print,helping clinicians evaluate patients'outcome and make optimized therapeutic strategy.However,the accuracy of these predictive tools above still need to be improved,and most models were generated from European and American population,which still lack effective evaluation in the Chinese population.In clinical practice,we always found that the outcomes of breast cancer patients were quite different from each other even with the same TNM stage,histopathological type,molecular characteristics and the same therapeutic regimen,suggesting that an individual'genetic background might be involved in the therapeutic response and breast cancer outcome.Nowadays,a great number of researches have been developed on identifying new genetic factors involved in breast cancer prognosis,which may be beneficial for providing individual precise treatment for patients.In recent years,genome-wide association study(GWAS)has been developed as one of the most powerful tools for association study of complex diseases,using tagging single nucleotide polymorphisms(tag SNPs)to represent all common variants in the genome through linkage disequilibrium analysis.To date,GWAS has identified several loci associated with breast cancer prognosis including1p13.2,1q23.3,2q24.3,5q14.3,10p14,10q21.1,10q22.3,11q24.2,14q24.1,15q22.2,15q25.1,16q22.3,16q24.1,17p13.1,19q13.41.These studies have provided valuable information on prognosis evaluation and therapeutic efficacy assessment for patients with breast cancer.Mainly based on the hypothesis of“common disease/common variants”,GWAS studies omit the role played by low-frequency or rare variants(minor allele frequency,MAF<5%)on breast cancer prognosis.Recently,more and more studies have discovered that low-frequency or rare variants usually have high penetrance and play an important role on susceptibility and prognosis of complex diseases.In 2012,Illumina developed a new high-throughput chip Infinium?Human Exome Beadchip,which was based on the whole-genome sequencing and exome sequencing of more than 12,000 individuals from different races(including African Americans,Americans,Asians and Europeans).More than 240,000 genetic variants were included on this chip,of which more than 93%were located at the exons and approximately 90%were low frequency variants.Based on this high-throughput exome chip,several studies have been successfully conducted to explore the association of low-frequency variants with susceptibility or prognosis of complex diseases including nonalcoholic fatty liver disease(NAFLD),coronary heart disease,endometrial cancer,esophageal squamous cell carcinoma,gastric cancer and lung cancer.To explore the association of low-frequency or rare variants with breast cancer susceptibility,we previously performed an exome-wide association study of breast cancer susceptibility in Chinese population.We identified two low-frequency variants rs200847762(6p21.33,KFBPL)and rs1045012(7q22.1,ARPC1B),which were significantly associated with breast cancer risk.In this study,we systematically explored the association between low-frequency variants and breast cancer survival by combining the clinical and prognostic information of patients from the previous research.Based on a case-only design,a total of 790 patients were enrolled in this study after integrating patients'genotype data,clinical and survival information.After systematic quality control,a total of56,688 variants in 776 cases were included in the following association analysis with Cox model.For missense or splicing variants with P<1×10^-3,we further replicated these associations using imputed genotype and gene expression data of 1,098 breast cancer patients from TCGA.After two-stage analysis,we identified a low-frequency missense variant in5q31.3(rs76571170 PCDHGA1,p.Asp187Asn:hazard ratio(HR)=3.37,P=2.19×10^-4)significantly associated with breast cancer prognosis,which was further replicated by TCGA samples(HR=1.82,P=0.023).In addition,we found another missense variant in 2q35(rs150878701 USP37,p.Pro328Arg:HR=2.62,P=7.43×10^-4)significantly increased breast cancer mortality,which was further replicated by its host gene USP37 expression in TCGA database(HR=1.33,P=0.003).USP37 expression was observed significantly upregulated in tumor tissues of breast cancer.In stratification analysis,we found that rs150878701 was only associated with PR-positive breast cancer(HR=5.99,P<0.001).Gene-based analysis revealed a total of 77 genes that might account for BC outcome(P<0.05).Overall,in our two-stage study,we identified two missense variants located at2q35 and 5q31.3 respectively associated with outcome of breast cancer patients and revealed a series of key genes which might play an important role in breast cancer prognosis.These results highlighted the importance of low-frequency variants and provide more evidences for prognosis prediction and decision making in individual treatment for breast cancer patients.