ArticleFrontiers in genetics2018
A Genome-Wide Study of Allele-Specific Expression in Colorectal Cancer.
Article in Frontiers in genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 42 citations in OpenAlex.
- Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples.Genome research · 2026Article
- Landscape of Allele-Specific Expression in Prostate Cancer Reveals Recurrent, Stage-Specific Events in AR Signaling and Resistance Pathways.Molecular cancer research : MCR · 2026Article
- NEXT-scASV: a Nextflow pipeline for allele-specific variant calling from single-cell RNA-seq data.GigaScience · 2026Article
- MutAnt: mutation annotation tool predicts deleteriousness of missense mutations and improves mutation calling from transcriptomics.Human genetics · 2025Article
- Geography, Ancestry, Age and Sex Shape Somatic Autosomal Mosaic Chromosomal Alterations in Blood.medRxiv : the preprint server for health sciences · 2025Article
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- Long-read RNA sequencing reveals allele-specificGenome research · 2025Article
- Statistical framework for calling allelic imbalance in high-throughput sequencing data.Nature communications · 2025Article
- Long-read RNA sequencing reveals allele-specific NbioRxiv : the preprint server for biology · 2024Article
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- Maximizing Small Biopsy Patient Samples: Unified RNA-Seq Platform Assessment of over 120,000 Patient Biopsies.Journal of personalized medicine · 2022Article
- Dominant complementation of biological pathways in maize hybrid lines is associated with heterosis.Planta · 2022Article
- Recombination affects allele-specific expression of deleterious variants in human populations.Science advances · 2022Article
- A guide for the diagnosis of rare and undiagnosed disease: beyond the exome.Genome medicine · 2022Review
- RNA-SSNV: A Reliable Somatic Single Nucleotide Variant Identification Framework for Bulk RNA-Seq Data.Frontiers in genetics · 2022Article
- Power calculator for detecting allelic imbalance using hierarchical Bayesian model.BMC research notes · 2021Article
- Genome-Wide Allele-Specific Expression in Obligately Asexual Daphnia pulex and the Implications for the Genetic Basis of Asexuality.Genome biology and evolution · 2021Article
- Allele-specific expression of GATA2 due to epigenetic dysregulation in CEBPA double-mutant AML.Blood · 2021Article
- Allelic Expression Imbalance Analysis IdentifiedCancers · 2021Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accumulating evidence from small-scale studies has suggested that allele-specific expression (ASE) plays an important role in tumor initiation and progression. However, little is known about genome-wide ASE in tumors. In this study, we conducted a comprehensive analysis of ASE in individuals with colorectal cancer (CRC) on a genome-wide scale. We identified 5.4 thousand genome-wide ASEs of single nucleotide variations (SNVs) from tumor and normal tissues of 59 individuals with CRC. We observed an increased ASE level in tumor samples and the ASEs enriched as hotspots on the genome. Around 63% of the genes located there were previously reported to contain complex regulatory elements, e.g., human leukocyte antigen (HLA), or were implicated in tumor progression. Focussing on the allelic expression of somatic mutations, we found that 37.5% of them exhibited ASE, and genes harboring such somatic mutations, were enriched in important pathways implicated in cancers. In addition, by comparing the expected and observed ASE events in tumor samples, we identified 50 tumor specific ASEs which possibly contributed to the somatic events in the regulatory regions of the genes and significantly enriched known cancer driver genes. By analyzing CRC ASEs from several perspectives, we provided a systematic understanding of how ASE is implicated in both tumor and normal tissues and will be of critical value in guiding ASE studies in cancer.
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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.