ArticleBMC medical genomics2015
Massive interstitial copy-neutral loss-of-heterozygosity as evidence for cancer being a disease of the DNA-damage response.
Article in BMC medical genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 26 citations in OpenAlex.
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- Forward-reverse mutation cycles in cancer cell lines under chemical treatments.Human genomics · 2024Article
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- Comparison of the copy-neutral loss of heterozygosity identified from whole-exome sequencing data using three different tools.Genomics & informatics · 2022Article
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- Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds.eLife · 2021Article
- Genetic-variant hotspots and hotspot clusters in the human genome facilitating adaptation while increasing instability.Human genomics · 2021Article
- Genome-wide mapping of spontaneous genetic alterations in diploid yeast cells.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Genomic subtyping of liver cancers with prognostic application.BMC cancer · 2020Article
- Biomarkers for Bladder Cancer Diagnosis and Surveillance: A Comprehensive Review.Diagnostics (Basel, Switzerland) · 2020Review
- Dynamic Extreme Aneuploidy (DEA) in the vegetable pathogen Phytophthora capsici and the potential for rapid asexual evolution.PloS one · 2020Article
- Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas.Cell reports · 2019Article
- AluScanCNV2: An R package for copy number variation calling and cancer risk prediction with next-generation sequencing data.Genes & diseases · 2019Article
- Forward and reverse mutations in stages of cancer development.Human genomics · 2018Article
- MORC2, a novel oncogene, is upregulated in liver cancer and contributes to proliferation, metastasis and chemoresistance.International journal of oncology · 2018Article
- Feature co-localization landscape of the human genome.Scientific reports · 2016Article
- Integrated small copy number variations and epigenome maps of disorders of sex development.Human genome variation · 2016Article
- Intrinsic and chemically-induced daughter number variations in cancer cell lines.Cell cycle (Georgetown, Tex.)Article
Corrections and comments
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Authors and funding
25 authors at 7 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe presence of loss-of-heterozygosity (LOH) mutations in cancer cell genomes is commonly encountered. Moreover, the occurrences of LOHs in tumor suppressor genes play important roles in oncogenesis. However, because the causative mechanisms underlying LOH mutations in cancer cells yet remain to be elucidated, enquiry into the nature of these mechanisms based on a comprehensive examination of the characteristics of LOHs in multiple types of cancers has become a necessity.
methodsWe performed next-generation sequencing on inter-Alu sequences of five different types of solid tumors and acute myeloid leukemias, employing the AluScan platform which entailed amplification of such sequences using multiple PCR primers based on the consensus sequences of Alu elements; as well as the whole genome sequences of a lung-to-liver metastatic cancer and a primary liver cancer. Paired-end sequencing reads were aligned to the reference human genome to identify major and minor alleles so that the partition of LOH products between homozygous-major vs. homozygous-minor alleles could be determined at single-base resolution. Strict filtering conditions were employed to avoid false positives. Measurements of LOH occurrences in copy number variation (CNV)-neutral regions were obtained through removal of CNV-associated LOHs.
resultsWe found: (a) average occurrence of copy-neutral LOHs amounting to 6.9% of heterologous loci in the various cancers; (b) the mainly interstitial nature of the LOHs; and (c) preference for formation of homozygous-major over homozygous-minor, and transitional over transversional, LOHs.
conclusionsThe characteristics of the cancer LOHs, observed in both AluScan and whole genome sequencings, point to the formation of LOHs through repair of double-strand breaks by interhomolog recombination, or gene conversion, as the consequence of a defective DNA-damage response, leading to a unified mechanism for generating the mutations required for oncogenesis as well as the progression of cancer cells.
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