ArticleNature genetics2022
Allelic imbalance of chromatin accessibility in cancer identifies candidate causal risk variants and their mechanisms.
Article in Nature genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 36 citations in OpenAlex.
- Multi-tissue analyses of allele-specific chromatin accessibility nominate likely functional variants for type 2 diabetes.medRxiv : the preprint server for health sciences · 2026Article
- Generation of a comprehensive epigenomic atlas in clear cell renal cell carcinoma informs kidney cancer progression and heritability.Cell reports · 2026Article
- A gene-specific variance-control approach corrects polygenicity-driven inflation observed in transcriptome-wide association studies.American journal of human genetics · 2026Article
- GENEasso: a curated resource of credible disease-gene associations across complex diseases from GWAS summary statistics.Nucleic acids research · 2026Article
- Circulating chromatin reveals the effects of disease-associated variants on gene regulation.bioRxiv : the preprint server for biology · 2025Article
- Single-cell multi-omics analysis reveals cancer regulatory elements of transcriptional programs and clinical implications.Cell death & disease · 2025Article
- Allelic expression imbalance of CDKN2A variants in childhood acute lymphoblastic leukemia.Cellular oncology (Dordrecht, Netherlands) · 2025Article
- Enhancing nonlinear transcriptome- and proteome-wide association studies via trait imputation with applications to Alzheimer's disease.PLoS genetics · 2025Article
- Statistical framework for calling allelic imbalance in high-throughput sequencing data.Nature communications · 2025Article
- Leveraging genome-wide association studies to better understand the etiology of cancers.Cancer science · 2025Review
- Impact of rare non-coding variants on human diseases through alternative polyadenylation outliers.Nature communications · 2025Article
- Multiome-wide Association Studies: Novel Approaches for Understanding Diseases.Genomics, proteomics & bioinformatics · 2024Review
- Pervasive polygenicity of complex traits inflates false positive rates in transcriptome-wide association studies.bioRxiv : the preprint server for biology · 2024Article
- Heterogeneous genetic architectures of prostate cancer susceptibility in sub-Saharan Africa.Nature genetics · 2024Article
- DNA-binding factor footprints and enhancer RNAs identify functional non-coding genetic variants.Genome biology · 2024Article
- Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements.Cellular and molecular life sciences : CMLS · 2024Review
- Decoding polygenic diseases: advances in noncoding variant prioritization and validation.Trends in cell biology · 2024Review
- Unveiling promising drug targets for autism spectrum disorder: insights from genetics, transcriptomics, and proteomics.Briefings in bioinformatics · 2024Article
- Regulome-wide association study identifies genetically driven accessible regions associated with pancreatic cancer risk.International journal of cancer · 2024Article
- Novel insight into the etiology of ischemic stroke gained by integrative multiome-wide association study.Human molecular genetics · 2024Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
While many germline cancer risk variants have been identified through genome-wide association studies (GWAS), the mechanisms by which these variants operate remain largely unknown. Here we used 406 cancer ATAC-Seq samples across 23 cancer types to identify 7,262 germline allele-specific accessibility QTLs (as-aQTLs). Cancer as-aQTLs had stronger enrichment for cancer risk heritability (up to 145 fold) than any other functional annotation across seven cancer GWAS. Most cancer as-aQTLs directly altered transcription factor (TF) motifs and exhibited differential TF binding and gene expression in functional screens. To connect as-aQTLs to putative risk mechanisms, we introduced the regulome-wide associations study (RWAS). RWAS identified genetically associated accessible peaks at >70% of known breast and prostate loci and discovered new risk loci in all examined cancer types. Integrating as-aQTL discovery, motif analysis and RWAS identified candidate causal regulatory elements and their probable upstream regulators. Our work establishes cancer as-aQTLs and RWAS analysis as powerful tools to study the genetic architecture of cancer risk.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.