ArticleMolecular systems biology2014
Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs.
Article in Molecular systems biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
13 citing papers in PubMed, 26 citations in OpenAlex.
- Identification of candidate causal variants and target genes at 41 breast cancer risk loci through differential allelic expression analysis.Scientific reports · 2024Article
- Micronutrients intake and genetic variants associated with premature ovarian insufficiency; MASHAD cohort study.BMC women's health · 2024Article
- Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function.British journal of cancer · 2020Article
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- Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome.Genome biology · 2017Article
- Association of breast cancer risk in BRCA1 and BRCA2 mutation carriers with genetic variants showing differential allelic expression: identification of a modifier of breast cancer risk at locus 11q22.3.Breast cancer research and treatment · 2017Article
- Article
- Article
- Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells.BMC medical genomics · 2016Article
- GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information.Scientific reports · 2016Article
- Genomic approaches for understanding the genetics of complex disease.Genome research · 2015Article
- Tools and best practices for data processing in allelic expression analysis.Genome biology · 2015Article
- The role of regulatory variation in complex traits and disease.Nature reviews. Genetics · 2015Review
Corrections and comments
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Authors and funding
17 authors at 7 institutions in 5 countries.
Funding
Abstract
Most complex disease-associated genetic variants are located in non-coding regions and are therefore thought to be regulatory in nature. Association mapping of differential allelic expression (AE) is a powerful method to identify SNPs with direct cis-regulatory impact (cis-rSNPs). We used AE mapping to identify cis-rSNPs regulating gene expression in 55 and 63 HapMap lymphoblastoid cell lines from a Caucasian and an African population, respectively, 70 fibroblast cell lines, and 188 purified monocyte samples and found 40-60% of these cis-rSNPs to be shared across cell types. We uncover a new class of cis-rSNPs, which disrupt footprint-derived de novo motifs that are predominantly bound by repressive factors and are implicated in disease susceptibility through overlaps with GWAS SNPs. Finally, we provide the proof-of-principle for a new approach for genome-wide functional validation of transcription factor-SNP interactions. By perturbing NFκB action in lymphoblasts, we identified 489 cis-regulated transcripts with altered AE after NFκB perturbation. Altogether, we perform a comprehensive analysis of cis-variation in four cell populations and provide new tools for the identification of functional variants associated to complex diseases.
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Registered trials
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.