ArticlePloS one2013
Comprehensive functional annotation of seventy-one breast cancer risk Loci.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 43 citations in OpenAlex.
- Chronic lymphocytic leukemia (CLL) risk is mediated by multiple enhancer variants within CLL risk loci.Human molecular genetics · 2020Article
- Genetic associations of breast and prostate cancer are enriched for regulatory elements identified in disease-related tissues.Human genetics · 2019Article
- MCF-7 as a Model for Functional Analysis of Breast Cancer Risk Variants.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2019Article
- Brain Banks Spur New Frontiers in Neuropsychiatric Research and Strategies for Analysis and Validation.Genomics, proteomics & bioinformatics · 2019Review
- Functional intronic variant of SLC5A10 affects DRG2 expression and survival outcomes of early-stage non-small-cell lung cancer.Cancer science · 2018Article
- Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation.Science advances · 2018Article
- CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops.Genome biology · 2018Article
- Positional integration of lung adenocarcinoma susceptibility loci with primary human alveolar epithelial cell epigenomes.Epigenomics · 2018Article
- LEM-3 is a midbody-tethered DNA nuclease that resolves chromatin bridges during late mitosis.Nature communications · 2018Article
- Functional Prediction of Chronic Kidney Disease Susceptibility Gene PRKAG2 by Comprehensively Bioinformatics Analysis.Frontiers in genetics · 2018Article
- A catalog of potential putative functional variants in psoriasis genome-wide association regions.PloS one · 2018Article
- Ovarian cancer variant rs2072590 is associated with HOXD1 and HOXD3 gene expression.Oncotarget · 2017Article
- Identification of breast cancer associated variants that modulate transcription factor binding.PLoS genetics · 2017Article
- Characterizing Genetic Susceptibility to Breast Cancer in Women of African Ancestry.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2017Article
- Molecular mechanisms underlying noncoding risk variations in psychiatric genetic studies.Molecular psychiatry · 2017Review
- Functional annotation of sixty-five type-2 diabetes risk SNPs and its application in risk prediction.Scientific reports · 2017Article
- SNP variants at the MAP3K1/SETD9 locus 5q11.2 associate with somatic PIK3CA variants in breast cancers.European journal of human genetics : EJHG · 2017Article
- Epigenetic Combinatorial Patterns Predict Disease Variants.Frontiers in genetics · 2017Article
- The importance of detailed epigenomic profiling of different cell types within organs.Epigenomics · 2016Review
- Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Breast Cancer (BCa) genome-wide association studies revealed allelic frequency differences between cases and controls at index single nucleotide polymorphisms (SNPs). To date, 71 loci have thus been identified and replicated. More than 320,000 SNPs at these loci define BCa risk due to linkage disequilibrium (LD). We propose that BCa risk resides in a subgroup of SNPs that functionally affects breast biology. Such a shortlist will aid in framing hypotheses to prioritize a manageable number of likely disease-causing SNPs. We extracted all the SNPs, residing in 1 Mb windows around breast cancer risk index SNP from the 1000 genomes project to find correlated SNPs. We used FunciSNP, an R/Bioconductor package developed in-house, to identify potentially functional SNPs at 71 risk loci by coinciding them with chromatin biofeatures. We identified 1,005 SNPs in LD with the index SNPs (r(2)≥0.5) in three categories; 21 in exons of 18 genes, 76 in transcription start site (TSS) regions of 25 genes, and 921 in enhancers. Thirteen SNPs were found in more than one category. We found two correlated and predicted non-benign coding variants (rs8100241 in exon 2 and rs8108174 in exon 3) of the gene, ANKLE1. Most putative functional LD SNPs, however, were found in either epigenetically defined enhancers or in gene TSS regions. Fifty-five percent of these non-coding SNPs are likely functional, since they affect response element (RE) sequences of transcription factors. Functionality of these SNPs was assessed by expression quantitative trait loci (eQTL) analysis and allele-specific enhancer assays. Unbiased analyses of SNPs at BCa risk loci revealed new and overlooked mechanisms that may affect risk of the disease, thereby providing a valuable resource for follow-up studies.
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