Integrative eQTL-based analyses reveal the biology of breast cancer risk loci.
paper
Cited
Public
- Authors
- Li, Qiyuan; Seo, Ji-Heui; Stranger, Barbara; McKenna, Aaron; Pe'er, Itsik; Laframboise, Thomas; Brown, Myles; Tyekucheva, Svitlana; Freedman, Matthew L
- Year
- 2013
- Journal
- Cell
- PMID
- 23374354
- DOI
- 10.1016/j.cell.2012.12.034
- PMCID
- PMC4165609
Germline determinants of gene expression in tumors are infrequently studied due to the complexity of transcript regulation caused by somatically acquired alterations. We performed expression quantitative trait locus (eQTL)-based analyses using the multi-level information provided in The Cancer Genome Atlas (TCGA). Of the factors we measured, cis-acting eQTLs accounted for 1.2% of the total variation of tumor gene expression, while somatic copy-number alteration and CpG methylation accounted for 7.3% and 3.3%, respectively. eQTL analyses of 15 previously reported breast cancer risk loci resulted in the discovery of three variants that are significantly associated with transcript levels (false discovery rate [FDR]Β < 0.1). Our trans-based analysis identified an additional three risk loci to act through ESR1, MYC, and KLF4. These findings provide a more comprehensive picture of gene expression determinants in breast cancer as well as insights into the underlying biology of breast cancer risk loci.
Effects of three determinants on gene expression in ER-positive breast cancer:cis-acting SNP loci, somatic copy number and CpG methylation. (a) Venn diagram shows the number of genes that are under regulation of one or multiple factors. (b) Pie chart shows the relative and absolute fraction of variance of gene expression explained by three factors. Please see also Figure S1, Figure S2, Table S1, Table S2, Table S3, Table S5.
Schematic of the hypothesis that risk alleles are cis-eQTLs of transcription factors. (A) A risk locus (blue triangle) cis-regulates a transcription factor (TF; red explosion). (B) the messenger RNA of the TF is translated into its active form and (C) binds to the target genes. (D) These target genes are associated with the risk allele, but not the TF because the TF is itself tightly regulated. (E) DNA sequences within DNaseI hypersensitive sites (yellow peak) are evaluated for TF binding motif enrichment. Please see also Table 1, Table S5.
Allelic imbalance (AI) of the ESR1, MYC, and KLF4 transcription factors by breast cancer risk genotypic status. Allelic specific expression measures of three TFs were derived from RNA-sequencing of 177 TCGA breast cancer samples. The association between ESR1, MYC and KLF4 and the corresponding risk loci of (A) 6q25 (rs2046210) (B) 8q24 (rs418269) and (C) 9q31 (rs471467) were evaluated using the F-test. Please see also Figure S3, Figure S4C.
Chromosome conformation capture (3C) demonstrates physical interactions between the 6q25 risk locus and the ESR1 promoter and the 9q21 risk locus and the KLF4 promoter. (A) The top panel shows screenshots of the restriction fragments used for the 6q25/ESR1 interaction. These fragments are separated by approximately 170 kb. The lower left panel shows the gel image of the ligation band. The 263 base pair band is visualized only in the sample with ligase (+Lg) and no band is seen in the negative control sample without ligase (-Lg). The lower right panel demonstrates sequence verification of the +Lg band, confirming this interaction. (B) The 9q21 risk locus and KLF4 physically interact over a distance of 640 kb. Please see also Figure 3, Table 1.
1β20 of 48
Next β
No entities extracted from this document yet.
No uploaded files.
Not in any collection.
In this knowledge base
External
| Title | Authors | Journal | Year | Link |
|---|---|---|---|---|
| eQTL analysis: A bridge from genome to mechanism. | Jia Z et al. | β | 2026 | β |
| Mixed-model and transcriptome-wide association analyses identify transcription factors and genes associated with colorectal cancer susceptibility. | Chen Z et al. | β | 2026 | β |
| Enhancing disease risk gene discovery by integrating transcription factor-linked trans-variants into transcriptome-wide association analyses. | He J et al. | β | 2025 | β |
| Genetic Control of tRNA-Derived Fragments Contributes to Cancer Risk. | Li B et al. | β | 2025 | β |
| Genetic Regulation of Alternative Polyadenylation Provides Novel Insights into Molecular Mechanisms Underlying Non-small Cell Lung Cancer. | Jin M et al. | β | 2025 | β |
| Systematically identification of survival-associated eQTLs in a Japanese kidney cancer cohort. | Song X et al. | β | 2025 | β |
| Epigenome-augmented eQTL-hotspots reveal genome-wide transcriptional programs in 36 human tissues. | Liu H et al. | β | 2024 | β |
| Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions. | Joosten SEP et al. | β | 2024 | β |
| Large-Scale Alternative Polyadenylation-Wide Association Studies to Identify Putative Cancer Susceptibility Genes. | Guo X et al. | β | 2024 | β |
| Selective Effect of DNA N6-Methyladenosine Modification on Transcriptional Genetic Variations in East Asian Samples. | Luan M et al. | β | 2024 | β |
| The rs2046210 Polymorphism Is Associated with Endometriosis Risk and Elevated Estrogen Receptor 1 Expression in the Eutopic Endometrium of Women with the Disease. | Proestling K et al. | β | 2024 | β |
| Towards functional maps of non-coding variants in cancer. | Wang Y et al. | β | 2024 | β |
| An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping. | Wang Z et al. | β | 2023 | β |
| A nomogram based on genotypic and clinicopathologic factors to predict the non-sentinel lymph node metastasis in Chinese women breast cancer patients. | Zhu L et al. | β | 2023 | β |
| Association of the Estrogen Receptor 1 Polymorphisms rs2046210 and rs9383590 with the Risk, Age at Onset and Prognosis of Breast Cancer. | Miedl H et al. | β | 2023 | β |
| Deciphering gene contributions and etiologies of somatic mutational signatures of cancer. | Ji X et al. | β | 2023 | β |
| Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human cancer risk. | Ying P et al. | β | 2023 | β |
| Imagine beyond: recent breakthroughs and next challenges in mammary gland biology and breast cancer research. | van Amerongen R et al. | β | 2023 | β |
| Profiling the Somatic Mutational Landscape of Breast Tumors from Hispanic/Latina Women Reveals Conserved and Unique Characteristics. | Ding YC et al. | β | 2023 | β |
| Promising therapeutic mechanism for Chinese herbal medicine in ameliorating renal fibrosis in diabetic nephropathy. | Wang S et al. | β | 2023 | β |
| Refined expression quantitative trait locus analysis on adenocarcinoma at the gastroesophageal junction reveals susceptibility and prognostic markers. | Zhong C et al. | β | 2023 | β |
| Rewired Metabolism Caused by the Oncogenic Deregulation of MYC as an Attractive Therapeutic Target in Cancers. | VΓzkeleti L et al. | β | 2023 | β |
| Allelic imbalance of HLA-B expression in human lung cells infected with coronavirus and other respiratory viruses. | Zhang Y et al. | β | 2022 | β |
| CCDC12 promotes tumor development and invasion through the Snail pathway in colon adenocarcinoma. | Du F et al. | β | 2022 | β |
| Dinucleotide tag-based parallel reporter gene assay method enables efficient identification of regulatory mutations. | Ren N et al. | β | 2022 | β |
| Functional annotation of breast cancer risk loci: current progress and future directions. | Romualdo Cardoso S et al. | β | 2022 | β |
| Genomic Variants Disrupt miRNA-mRNA Regulation. | Xi E et al. | β | 2022 | β |
| Integrating transcription factor occupancy with transcriptome-wide association analysis identifies susceptibility genes in human cancers. | He J et al. | β | 2022 | β |
| SBSA: an online service for somatic binding sequence annotation. | Jiang L et al. | β | 2022 | β |
| STAT3-mediated allelic imbalance of novel genetic variant Rs1047643 and B-cell-specific super-enhancer in association with systemic lupus erythematosus. | Zhang Y et al. | β | 2022 | β |
| The Expression Quantitative Trait Loci in Immune Response Genes Impact the Characteristics and Survival of Colorectal Cancer. | Chan RH et al. | β | 2022 | β |
| A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers. | Coignard J et al. | β | 2021 | β |
| An Integrative Co-localization (INCO) Analysis for SNV and CNV Genomic Features With an Application to Taiwan Biobank Data. | Yu QY et al. | β | 2021 | β |
| Common Susceptibility Loci for Male Breast Cancer. | Maguire S et al. | β | 2021 | β |
| DDRS: Detection of drug response SNPs specifically in patients receiving drug treatment. | Rong Y et al. | β | 2021 | β |
| Expression quantitative trait loci of genes predicting outcome are associated with survival of multiple myeloma patients. | Macauda A et al. | β | 2021 | β |
| Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells. | Shareef SJ et al. | β | 2021 | β |
| Functional Screenings Identify Regulatory Variants Associated with Breast Cancer Susceptibility. | Ren N et al. | β | 2021 | β |
| Genetic variations of DNA bindings of FOXA1 and co-factors in breast cancer susceptibility. | Wen W et al. | β | 2021 | β |
| Genome-wide association analysis reveals regulation of at-risk loci by DNA methylation in prostate cancer. | Liu Q et al. | β | 2021 | β |
| Genome-wide association and functional interrogation identified a variant at 3p26.1 modulating ovarian cancer survival among Chinese women. | Dai H et al. | β | 2021 | β |
| Long reads capture simultaneous enhancer-promoter methylation status for cell-type deconvolution. | Margalit S et al. | β | 2021 | β |
| MiR-3130-5p is an intermediate modulator of 2q33 and influences the invasiveness of lung adenocarcinoma by targeting NDUFS1. | Zhan J et al. | β | 2021 | β |
| Optimization of prediction methods for risk assessment of pathogenic germline variants in the Japanese population. | Senda N et al. | β | 2021 | β |
| Parallel Reporter Assays Identify Altered Regulatory Role of rs684232 in Leading to Prostate Cancer Predisposition. | Ren N et al. | β | 2021 | β |
| Rare Coding Variants Associated with Breast Cancer. | Han MR | β | 2021 | β |
| Rare variants regulate expression of nearby individual genes in multiple tissues. | Li J et al. | β | 2021 | β |
| Statistical method for modeling sequencing data from different technologies in longitudinal studies with application to Huntington disease. | Fuady AM et al. | β | 2021 | β |
| Supervised Dimension Reduction for Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards. | Spirko-Burns L et al. | β | 2021 | β |
| The Interaction Analysis of SNP Variants and DNA Methylation Identifies Novel Methylated Pathogenesis Genes in Congenital Heart Diseases. | Wang J et al. | β | 2021 | β |
| Variable expression quantitative trait loci analysis of breast cancer risk variants. | Wiggins GAR et al. | β | 2021 | β |
| ABC-GWAS: Functional Annotation of Estrogen Receptor-Positive Breast Cancer Genetic Variants. | Manjunath M et al. | β | 2020 | β |
| Allele-specific miRNA-binding analysis identifies candidate target genes for breast cancer risk. | Jacinta-Fernandes A et al. | β | 2020 | β |
| Cancer-specific expression quantitative loci are affected by expression dysregulation. | Sheng Q et al. | β | 2020 | β |
| eQTL Colocalization Analyses Identify NTN4 as a Candidate Breast Cancer Risk Gene. | Beesley J et al. | β | 2020 | β |
| Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes. | Fachal L et al. | β | 2020 | β |
| Genetic variants in epithelial-mesenchymal transition genes as predictors of clinical outcomes in localized prostate cancer. | Deng Y et al. | β | 2020 | β |
| <i>Cis</i>- and <i>Trans</i>-Acting Expression Quantitative Trait Loci of Long Non-Coding RNA in 2,549 Cancers With Potential Clinical and Therapeutic Implications. | Li W et al. | β | 2020 | β |
| Identification of Candidate Genes Associated with Susceptibility to Ovarian Clear Cell Adenocarcinoma Using <i>cis</i>-eQTL Analysis. | Kim J et al. | β | 2020 | β |
| Integrating germline and somatic genetics to identify genes associated with lung cancer. | Pattee J et al. | β | 2020 | β |
| Long Noncoding RNA LINC00261 Reduces Proliferation and Migration of Breast Cancer Cells via the NME1-EMT Pathway. | Guo G et al. | β | 2020 | β |
| Mapping Tumor-Specific Expression QTLs in Impure Tumor Samples. | Wilson DR et al. | β | 2020 | β |
| New insight into the significance of KLF4 PARylation in genome stability, carcinogenesis, and therapy. | Zhou Z et al. | β | 2020 | β |
| Non-coding RNAs underlie genetic predisposition to breast cancer. | Moradi Marjaneh M et al. | β | 2020 | β |
| Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function. | Fagny M et al. | β | 2020 | β |
| Novel CpG-SNPs in the gastric acid secretion pathway GNAI3 and susceptibility to gastric cancer. | Liu M et al. | β | 2020 | β |
| Regulation of KLF4 by posttranslational modification circuitry in endocrine resistance. | Zhou Z et al. | β | 2020 | β |
| Risk SNP-Mediated Enhancer-Promoter Interaction Drives Colorectal Cancer through Both <i>FADS2</i> and <i>AP002754.2</i>. | Tian J et al. | β | 2020 | β |
| SMDB: pivotal somatic sequence alterations reprogramming regulatory cascades. | Jiang L et al. | β | 2020 | β |
| Systematic analyses of genetic variants in chromatin interaction regions identified four novel lung cancer susceptibility loci. | Ji P et al. | β | 2020 | β |
| Tissue-Specific eQTL in Zebrafish. | Dobrinski KP | β | 2020 | β |
| Understanding oncogenicity of cancer driver genes and mutations in the cancer genomics era. | Porta-Pardo E et al. | β | 2020 | β |
| Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation. | Liu S et al. | β | 2020 | β |
| A cis-eQTL genetic variant in PLK4 confers high risk of hepatocellular carcinoma. | Meng L et al. | β | 2019 | β |
| Allelic Switching of <i>DLX5</i>, <i>GRB10</i>, and <i>SVOPL</i> during Colorectal Cancer Tumorigenesis. | Boot A et al. | β | 2019 | β |
| A transcriptome-wide association study of high-grade serous epithelial ovarian cancer identifies new susceptibility genes and splice variants. | Gusev A et al. | β | 2019 | β |
| Clonal Evolution of <i>TP53</i> c.375+1G>A Mutation in Pre- and Post- Neo-Adjuvant Chemotherapy (NACT) Tumor Samples in High-Grade Serous Ovarian Cancer (HGSOC). | Garziera M et al. | β | 2019 | β |
| Dysregulation of DNA methylation patterns may identify patients with breast cancer resistant to endocrine therapy: A predictive classifier based on differentially methylated regions. | Zhang F et al. | β | 2019 | β |
| Genetic associations of breast and prostate cancer are enriched for regulatory elements identified in disease-related tissues. | Chen H et al. | β | 2019 | β |
| Genome-wide Analysis of Common Copy Number Variation and Epithelial Ovarian Cancer Risk. | Reid BM et al. | β | 2019 | β |
| Genome-wide association studies identify susceptibility loci for epithelial ovarian cancer in east Asian women. | Lawrenson K et al. | β | 2019 | β |
| Identifying Putative Susceptibility Genes and Evaluating Their Associations with Somatic Mutations in Human Cancers. | Chen Z et al. | β | 2019 | β |
| Integration of methylation QTL and enhancer-target gene maps with schizophrenia GWAS summary results identifies novel genes. | Wu C et al. | β | 2019 | β |
| Laser capture microdissection of human pancreatic islets reveals novel eQTLs associated with type 2 diabetes. | Khamis A et al. | β | 2019 | β |
| Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response. | Xie X et al. | β | 2019 | β |
| Predicting stage-specific cancer related genes and their dynamic modules by integrating multiple datasets. | Aouiche C et al. | β | 2019 | β |
| Redefining the IBDs using genome-scale molecular phenotyping. | Furey TS et al. | β | 2019 | β |
| Reply. | Lu Y et al. | β | 2019 | β |
| Systems Metabolic Engineering Strategies: Integrating Systems and Synthetic Biology with Metabolic Engineering. | Choi KR et al. | β | 2019 | β |
| The Effect of Genetic Variation on the Placental Transcriptome in Humans. | Kikas T et al. | β | 2019 | β |
| The Need for Multi-Omics Biomarker Signatures in Precision Medicine. | Olivier M et al. | β | 2019 | β |
| A Comprehensive cis-eQTL Analysis Revealed Target Genes in Breast Cancer Susceptibility Loci Identified in Genome-wide Association Studies. | Guo X et al. | β | 2018 | β |
| A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. | Zhang W et al. | β | 2018 | β |
| A Mixed-Effects Model for Powerful Association Tests in Integrative Functional Genomics. | Su YR et al. | β | 2018 | β |
| A polymorphic MYC response element in KBTBD11 influences colorectal cancer risk, especially in interaction with an MYC-regulated SNP rs6983267. | Gong J et al. | β | 2018 | β |
| A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk. | Lu Y et al. | β | 2018 | β |
| A transcriptome-wide association study of 229,000 women identifies new candidate susceptibility genes for breast cancer. | Wu L et al. | β | 2018 | β |
| Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity. | Geeleher P et al. | β | 2018 | β |
| Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. | Kahles A et al. | β | 2018 | β |
| Deletion of the murine ortholog of the 8q24 gene desert has anti-cancer effects in transgenic mammary cancer models. | Homer-Bouthiette C et al. | β | 2018 | β |
| Elucidating the Underlying Functional Mechanisms of Breast Cancer Susceptibility Through Post-GWAS Analyses. | Rivandi M et al. | β | 2018 | β |
| Genetic Modifiers of the Breast Tumor Microenvironment. | Flister MJ et al. | β | 2018 | β |
| Genomic Effects of the Vitamin D Receptor: Potentially the Link between Vitamin D, Immune Cells, and Multiple Sclerosis. | Lu M et al. | β | 2018 | β |
| Germline genetic polymorphisms influence tumor gene expression and immune cell infiltration. | Lim YW et al. | β | 2018 | β |
| Germline genetic variants in somatically significantly mutated genes in tumors are associated with renal cell carcinoma risk and outcome. | Shu X et al. | β | 2018 | β |
| How Should Biobanks Prioritize and Diversify Biosample Collections? A 40-Year Scientific Publication Trend Analysis by the Type of Biosample. | Lee JE et al. | β | 2018 | β |
| Identification of an enhancer region within the TP63/LEPREL1 locus containing genetic variants associated with bladder cancer risk. | Dudek AM et al. | β | 2018 | β |
| Identification of nine new susceptibility loci for endometrial cancer. | O'Mara TA et al. | β | 2018 | β |
| Integrating RNA Expression Identifies Candidate Gene for Orofacial Clefts. | Ladd-Acosta C et al. | β | 2018 | β |
| Integrative Analysis of Omics Big Data. | Yu XT et al. | β | 2018 | β |
| Integrative expression quantitative trait locus-based analysis of colorectal cancer identified a functional polymorphism regulating SLC22A5 expression. | Zou D et al. | β | 2018 | β |
| Integrative Genomic Analysis Predicts Causative <i>Cis</i>-Regulatory Mechanisms of the Breast Cancer-Associated Genetic Variant rs4415084. | Zhang Y et al. | β | 2018 | β |
| Linking Race, Cancer Outcomes, and Tissue Repair. | Byun JS et al. | β | 2018 | β |
| Maximizing the Utility of Cancer Transcriptomic Data. | Xiang Y et al. | β | 2018 | β |
| Mechanistic interpretation of non-coding variants helps discover transcriptional regulators of drug response | Xie X et al. | β | 2018 | β |
| regQTLs: Single nucleotide polymorphisms that modulate microRNA regulation of gene expression in tumors. | Wilk G et al. | β | 2018 | β |
| A deep auto-encoder model for gene expression prediction. | Xie R et al. | β | 2017 | β |
| Allelic imbalance in human breast cancer. | French JD et al. | β | 2017 | β |
| Analyses of germline variants associated with ovarian cancer survival identify functional candidates at the 1q22 and 19p12 outcome loci. | Glubb DM et al. | β | 2017 | β |
| Association analysis identifies 65 new breast cancer risk loci. | Michailidou K et al. | β | 2017 | β |
| Common genetic variation drives molecular heterogeneity in human iPSCs. | Kilpinen H et al. | β | 2017 | β |
| Common genetic variation in the germline influences where and how tumors develop. | Carter H et al. | β | 2017 | β |
| Common, germline genetic variations in the novel tumor suppressor <i>BAP1</i> and risk of developing different types of cancer. | Lin M et al. | β | 2017 | β |
| Exploring the Link between the Germline and Somatic Genome in Cancer. | Geeleher P et al. | β | 2017 | β |
| Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue. | Quiroz-ZΓ‘rate A et al. | β | 2017 | β |
| FREQUENT SUBGRAPH MINING OF PERSONALIZED SIGNALING PATHWAY NETWORKS GROUPS PATIENTS WITH FREQUENTLY DYSREGULATED DISEASE PATHWAYS AND PREDICTS PROGNOSIS. | Durmaz A et al. | β | 2017 | β |
| Genome-wide association studies of cancer: current insights and future perspectives. | Sud A et al. | β | 2017 | β |
| Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer. | Phelan CM et al. | β | 2017 | β |
| Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer. | Milne RL et al. | β | 2017 | β |
| Identifying subtype-specific associations between gene expression and DNA methylation profiles in breast cancer. | Lee G et al. | β | 2017 | β |
| Impacts of somatic mutations on gene expression: an association perspective. | Jia P et al. | β | 2017 | β |
| Integrative eQTL analysis of tumor and host omics data in individuals with bladder cancer. | Pineda S et al. | β | 2017 | β |
| Integrative genomic analysis identifies ancestry-related expression quantitative trait loci on DNA polymerase Ξ² and supports the association of genetic ancestry with survival disparities in head and neck squamous cell carcinoma. | Ramakodi MP et al. | β | 2017 | β |
| Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. | Carter H et al. | β | 2017 | β |
| Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus. | Odhams CA et al. | β | 2017 | β |
| Potential Susceptibility Loci Identified for Renal Cell Carcinoma by Targeting Obesity-Related Genes. | Shu X et al. | β | 2017 | β |
| Precise Network Modeling of Systems Genetics Data Using the Bayesian Network Webserver. | Ziebarth JD et al. | β | 2017 | β |
| Promotor analysis of ESR1 in endometrial cancer cell lines, endometrial and endometriotic tissue. | Todorow V et al. | β | 2017 | β |
| SNP variants at the MAP3K1/SETD9 locus 5q11.2 associate with somatic PIK3CA variants in breast cancers. | Puzone R et al. | β | 2017 | β |
| Systematic identification of regulatory variants associated with cancer risk. | Liu S et al. | β | 2017 | β |
| The impact of methylation quantitative trait loci (mQTLs) on active smoking-related DNA methylation changes. | Gao X et al. | β | 2017 | β |
| The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers. | Amos CI et al. | β | 2017 | β |
| A functional polymorphism in lnc-LAMC2-1:1 confers risk of colorectal cancer by affecting miRNA binding. | Gong J et al. | β | 2016 | β |
| Association of breast cancer risk with genetic variants showing differential allelic expression: Identification of a novel breast cancer susceptibility locus at 4q21. | Hamdi Y et al. | β | 2016 | β |
| Association of germline variants in the APOBEC3 region with cancer risk and enrichment with APOBEC-signature mutations in tumors. | Middlebrooks CD et al. | β | 2016 | β |
| Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170. | Dunning AM et al. | β | 2016 | β |
| Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations. | Fehringer G et al. | β | 2016 | β |
| Data analysis in the post-genome-wide association study era. | Wang QL et al. | β | 2016 | β |
| Estrogen receptor alpha gene amplification in breast cancer: 25 years of debate. | Holst F | β | 2016 | β |
| Evaluation of potential regulatory function of breast cancer risk locus at 6q25.1. | Sun Y et al. | β | 2016 | β |
| Evidence that the 5p12 Variant rs10941679 Confers Susceptibility to Estrogen-Receptor-Positive Breast Cancer through FGF10 and MRPS30 Regulation. | Ghoussaini M et al. | β | 2016 | β |
| Expression quantitative trait analysis reveals fine germline transcript regulation in mouse lung tumors. | Cotroneo CE et al. | β | 2016 | β |
| Extraordinary Cancer Epigenomics: Thinking Outside the Classical Coding and Promoter Box. | Murtha M et al. | β | 2016 | β |
| Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer. | Shi J et al. | β | 2016 | β |
| Fine scale mapping of the 17q22 breast cancer locus using dense SNPs, genotyped within the Collaborative Oncological Gene-Environment Study (COGs). | Darabi H et al. | β | 2016 | β |
| Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus. | Lawrenson K et al. | β | 2016 | β |
| Genetic and Epigenetic Regulation of TOX3 Expression in Breast Cancer. | Han YJ et al. | β | 2016 | β |
| Genome-wide association study in East Asians identifies two novel breast cancer susceptibility loci. | Han MR et al. | β | 2016 | β |
| Identification of a functional variant for colorectal cancer risk mapping to chromosome 5q31.1. | Ke J et al. | β | 2016 | β |
| Identification of a Potential Regulatory Variant for Colorectal Cancer Risk Mapping to 3p21.31 in Chinese Population. | Ke J et al. | β | 2016 | β |
| Inherited variants affecting RNA editing may contribute to ovarian cancer susceptibility: results from a large-scale collaboration. | Permuth JB et al. | β | 2016 | β |
| Integrative bioinformatic analyses of an oncogenomic profile reveal the biology of endometrial cancer and guide drug discovery. | Wong HS et al. | β | 2016 | β |
| Integrative Functional Genomics Implicates EPB41 Dysregulation in Hepatocellular Carcinoma Risk. | Yang X et al. | β | 2016 | β |
| KLF4Ξ± stimulates breast cancer cell proliferation by acting as a KLF4 antagonist. | Ferralli J et al. | β | 2016 | β |
| Meta-dimensional data integration identifies critical pathways for susceptibility, tumorigenesis and progression of endometrial cancer. | Wei R et al. | β | 2016 | β |
| Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer. | Guo H et al. | β | 2016 | β |
| Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer. | Bailey SD et al. | β | 2016 | β |
| Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases. | Naz M et al. | β | 2016 | β |
| Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth. | Holst F et al. | β | 2016 | β |
| Regulators of genetic risk of breast cancer identified by integrative network analysis. | Castro MA et al. | β | 2016 | β |
| Role of non-coding sequence variants in cancer. | Khurana E et al. | β | 2016 | β |
| SPIRE, a modular pipeline for eQTL analysis of RNA-Seq data, reveals a regulatory hotspot controlling miRNA expression in C. elegans. | Kel I et al. | β | 2016 | β |
| STAT3 polymorphisms may predict an unfavorable response to first-line platinum-based therapy for women with advanced serous epithelial ovarian cancer. | Permuth-Wey J et al. | β | 2016 | β |
| The Expression Quantitative Trait Loci in Immune Pathways and their Effect on Cutaneous Melanoma Prognosis. | Vogelsang M et al. | β | 2016 | β |
| The Future is The Past: Methylation QTLs in Schizophrenia. | Hoffmann A et al. | β | 2016 | β |
| The miR-17βΌ92 microRNA Cluster Is a Global Regulator of Tumor Metabolism. | Izreig S et al. | β | 2016 | β |
| The role of enhancers in cancer. | Sur I et al. | β | 2016 | β |
| An argument for mechanism-based statistical inference in cancer. | Geman D et al. | β | 2015 | β |
| An integrated network of microRNA and gene expression in ovarian cancer. | Quitadamo A et al. | β | 2015 | β |
| Cell-type-specific enrichment of risk-associated regulatory elements at ovarian cancer susceptibility loci. | Coetzee SG et al. | β | 2015 | β |
| Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells. | Barutcu AR et al. | β | 2015 | β |
| Cis-eQTL analysis and functional validation of candidate susceptibility genes for high-grade serous ovarian cancer. | Lawrenson K et al. | β | 2015 | β |
| Common variants at the CHEK2 gene locus and risk of epithelial ovarian cancer. | Lawrenson K et al. | β | 2015 | β |
| Comprehensive genetic assessment of the ESR1 locus identifies a risk region for endometrial cancer. | O'Mara TA et al. | β | 2015 | β |
| Constitutional epimutation as a mechanism for cancer causality and heritability? | Hitchins MP | β | 2015 | β |
| Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. | Yao L et al. | β | 2015 | β |
| Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2. | Orr N et al. | β | 2015 | β |
| Fine-scale mapping of the 4q24 locus identifies two independent loci associated with breast cancer risk. | Guo X et al. | β | 2015 | β |
| Framework for the Integration of Genomics, Epigenomics and Transcriptomics in Complex Diseases. | Pineda S et al. | β | 2015 | β |
| Genome-wide significant risk associations for mucinous ovarian carcinoma. | Kelemen LE et al. | β | 2015 | β |
| Global transcription network incorporating distal regulator binding reveals selective cooperation of cancer drivers and risk genes. | Kim K et al. | β | 2015 | β |
| Inference of transcriptional regulation in cancers. | Jiang P et al. | β | 2015 | β |
| In-silico identification and functional validation of allele-dependent AR enhancers. | Garritano S et al. | β | 2015 | β |
| Integration Analysis of Three Omics Data Using Penalized Regression Methods: An Application to Bladder Cancer. | Pineda S et al. | β | 2015 | β |
| Integration of multiethnic fine-mapping and genomic annotation to prioritize candidate functional SNPs at prostate cancer susceptibility regions. | Han Y et al. | β | 2015 | β |
| Integrative network analysis for survival-associated gene-gene interactions across multiple genomic profiles in ovarian cancer. | Jeong HH et al. | β | 2015 | β |
| Interaction between common breast cancer susceptibility variants, genetic ancestry, and nongenetic risk factors in Hispanic women. | Fejerman L et al. | β | 2015 | β |
| Interplay between arginine methylation and ubiquitylation regulates KLF4-mediated genome stability and carcinogenesis. | Hu D et al. | β | 2015 | β |
| Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors. | Caswell JL et al. | β | 2015 | β |
| Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk. | Kar SP et al. | β | 2015 | β |
| Prostate cancer risk locus at 8q24 as a regulatory hub by physical interactions with multiple genomic loci across the genome. | Du M et al. | β | 2015 | β |
| Seasonal effects on gene expression. | Goldinger A et al. | β | 2015 | β |
| The 12p13.33/RAD52 locus and genetic susceptibility to squamous cell cancers of upper aerodigestive tract. | Delahaye-Sourdeix M et al. | β | 2015 | β |
| The role of regulatory variation in complex traits and disease. | Albert FW et al. | β | 2015 | β |
| A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer. | Al Olama AA et al. | β | 2014 | β |
| An eQTL analysis of the human glioblastoma multiforme genome. | Shpak M et al. | β | 2014 | β |
| An expressed retrogene of the master embryonic stem cell gene POU5F1 is associated with prostate cancer susceptibility. | Breyer JP et al. | β | 2014 | β |
| Applying genome-wide gene-based expression quantitative trait locus mapping to study population ancestry and pharmacogenetics. | Yang HC et al. | β | 2014 | β |
| A symbiotic liaison between the genetic and epigenetic code. | Heyn H | β | 2014 | β |
| Cancer: Directions for the drivers. | Gibson G | β | 2014 | β |
| Effects of long-term averaging of quantitative blood pressure traits on the detection of genetic associations. | Ganesh SK et al. | β | 2014 | β |
| Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation. | Hsieh CL et al. | β | 2014 | β |
| Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types. | Li Q et al. | β | 2014 | β |
| Expression QTL-based analyses reveal the mechanisms underlying colorectal cancer predisposition. | Zhang J et al. | β | 2014 | β |
| Functional annotation of colon cancer risk SNPs. | Yao L et al. | β | 2014 | β |
| Gene-centric meta-analysis in 87,736 individuals of European ancestry identifies multiple blood-pressure-related loci. | Tragante V et al. | β | 2014 | β |
| Genetic polymorphisms in the 9p21 region associated with risk of multiple cancers. | Li WQ et al. | β | 2014 | β |
| Genetic variation in mitotic regulatory pathway genes is associated with breast tumor grade. | Purrington KS et al. | β | 2014 | β |
| Genome-wide association studies and the clinic: a focus on breast cancer. | VΓ©ron A et al. | β | 2014 | β |
| Genomics meets proteomics: identifying the culprits in disease. | Stunnenberg HG et al. | β | 2014 | β |
| Laying a solid foundation for Manhattan--'setting the functional basis for the post-GWAS era'. | Zhang X et al. | β | 2014 | β |
| Linkage of DNA methylation quantitative trait loci to human cancer risk. | Heyn H et al. | β | 2014 | β |
| Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians. | Pierce BL et al. | β | 2014 | β |
| Metastasis-associated protein ribosomal RNA processing 1 homolog B (RRP1B) modulates metastasis through regulation of histone methylation. | Lee M et al. | β | 2014 | β |
| Molecular mechanisms of diabetic kidney disease. | Reidy K et al. | β | 2014 | β |
| Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. | Perry JR et al. | β | 2014 | β |
| Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins. | Postmus I et al. | β | 2014 | β |
| RNA-Seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations. | Munger SC et al. | β | 2014 | β |
| Serum microRNA expression patterns that predict early treatment failure in prostate cancer patients. | Singh PK et al. | β | 2014 | β |
| Single nucleotide variants in transcription factors associate more tightly with phenotype than with gene expression. | Sudarsanam P et al. | β | 2014 | β |
| Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types. | Fredriksson NJ et al. | β | 2014 | β |
| Systematic genetic analysis identifies Cis-eQTL target genes associated with glioblastoma patient survival. | Chen QR et al. | β | 2014 | β |
| TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile. | Huang YT et al. | β | 2014 | β |
| The 5p12 breast cancer susceptibility locus affects MRPS30 expression in estrogen-receptor positive tumors. | Quigley DA et al. | β | 2014 | β |
| The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts. | Wagner JR et al. | β | 2014 | β |
| Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C. | Dryden NH et al. | β | 2014 | β |
| Unmasking risk loci: DNA methylation illuminates the biology of cancer predisposition: analyzing DNA methylation of transcriptional enhancers reveals missed regulatory links between cancer risk loci and genes. | Aran D et al. | β | 2014 | β |
| Beyond GWASs: illuminating the dark road from association to function. | Edwards SL et al. | β | 2013 | β |
| Comprehensive functional annotation of seventy-one breast cancer risk Loci. | Rhie SK et al. | β | 2013 | β |
| Deconvoluting complex tissues for expression quantitative trait locus-based analyses. | Seo JH et al. | β | 2013 | β |
| DNA methylation of transcriptional enhancers and cancer predisposition. | Aran D et al. | β | 2013 | β |
| Fine-scale mapping of the FGFR2 breast cancer risk locus: putative functional variants differentially bind FOXA1 and E2F1. | Meyer KB et al. | β | 2013 | β |
| GWAS meets TCGA to illuminate mechanisms of cancer predisposition. | Kim HS et al. | β | 2013 | β |
| Hereditary breast cancer: ever more pieces to the polygenic puzzle. | Bogdanova N et al. | β | 2013 | β |
| Inherited susceptibility to chronic lymphocytic leukemia: evidence and prospects for the future. | Brown JR | β | 2013 | β |
| Master regulators of FGFR2 signalling and breast cancer risk. | Fletcher MN et al. | β | 2013 | β |
| Novel insights into breast cancer genetic variance through RNA sequencing. | Horvath A et al. | β | 2013 | β |
| The continuum of cancer immunosurveillance: prognostic, predictive, and mechanistic signatures. | Galon J et al. | β | 2013 | β |