ArticleCancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology2014
Rare coding variants and breast cancer risk: evaluation of susceptibility Loci identified in genome-wide association studies.
Article in Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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15 citing papers in PubMed, 1 synthesis or guideline pooled it, 30 citations in OpenAlex.
- Exome chip meta-analysis identifies novel loci and East Asian-specific coding variants that contribute to lipid levels and coronary artery disease.Nature genetics · 2017Pooled it
- Emerging roles of RNA:DNA hybrid regulation by mammalian ribonuclease H2 in replication stress and cancer.Journal of cell science · 2025Review
- Refining breast cancer genetic risk and biology through multi-ancestry fine-mapping analyses of 192 risk regions.Nature genetics · 2025Observational
- Genetic variation in CCDC93 is associated with elevated central systolic blood pressure, impaired arterial relaxation, and mitochondrial dysfunction.PLoS genetics · 2024Article
- Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics.American journal of human genetics · 2022Article
- Exome-Wide Association Study Identifies East Asian-Specific Missense VariantFrontiers in genetics · 2021Article
- Aicardi-Goutières syndrome gene Rnaseh2c is a metastasis susceptibility gene in breast cancer.PLoS genetics · 2019Article
- Genetic Modifiers of the Breast Tumor Microenvironment.Trends in cancer · 2018Review
- Clinically Significant Unclassified Variants inCancer research and treatment · 2017Article
- Evaluating genetic variants associated with breast cancer risk in high and moderate-penetrance genes in Asians.Carcinogenesis · 2017Article
- Exome-chip association analysis reveals an Asian-specific missense variant in PAX4 associated with type 2 diabetes in Chinese individuals.Diabetologia · 2017Article
- Deregulation of F-box proteins and its consequence on cancer development, progression and metastasis.Seminars in cancer biology · 2016Review
- Exome-wide association analysis reveals novel coding sequence variants associated with lipid traits in Chinese.Nature communications · 2015Article
- Illumina human exome genotyping array clustering and quality control.Nature protocols · 2014Article
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Authors and funding
10 authors at 4 institutions in 3 countries.
Funding
Abstract
backgroundTo date, common genetic variants in approximately 70 loci have been identified for breast cancer via genome-wide association studies (GWAS). It is unknown whether rare variants in these loci are also associated with breast cancer risk.
methodsWe investigated rare missense/nonsense variants with minor allele frequency (MAF) ≤5% located in flanking 500 kb of each of the index single-nucleotide polymorphism (SNP) in 67 GWAS loci. Included in the study were 3,472 cases and 3,595 controls from the Shanghai Breast Cancer Study. Both single marker and gene-based analyses were conducted to investigate the associations.
resultsSingle marker analyses identified 38 missense variants being associated with breast cancer risk at P < 0.05 after adjusting for the index SNP. SNP rs146217902 in the EDEM1 gene and rs200340088 in the EFEMP2 gene were only observed in 8 cases (P = 0.004 for both). SNP rs200995432 in the EFEMP2 gene was associated with increased risk with an OR of 6.2 [95% confidence interval (CI), 1.4-27.6; P = 6.2 × 10(-3)]. SNP rs80358978 in the BRCA2 gene was associated with 16.5-fold elevated risk (95% CI, 2.2-124.5; P = 2.2 × 10(-4)). Gene-based analyses suggested eight genes associated with breast cancer risk at P < 0.05, including the EFEMP2 gene (P = 0.002) and the FBXO18 gene (P = 0.008).
conclusionOur results identified associations of several rare coding variants neighboring common GWAS loci with breast cancer risk. Further investigation of these rare variants and genes would help to understand the biologic mechanisms underlying the associations. IMPACT: Independent studies with larger sample size are warranted to clarify the relationship between these rare variants and breast cancer risk.
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