ArticleBreast cancer research : BCR2012
A common copy-number breakpoint of ERBB2 amplification in breast cancer colocalizes with a complex block of segmental duplications.
Article in Breast cancer research : BCR, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 34 citations in OpenAlex.
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- Aneuploidy and complex genomic rearrangements in cancer evolution.Nature cancer · 2024Review
- Double-strand breaks induce inverted duplication chromosome rearrangements by a DNA polymerase δ-dependent mechanism.Nature communications · 2023Article
- Multi-omic cross-sectional cohort study of pre-malignant Barrett's esophagus reveals early structural variation and retrotransposon activity.Nature communications · 2022Article
- Genomic and transcriptomic analyses reveal a tandem amplification unit of 11 genes and mutations in mismatch repair genes in methotrexate-resistant HT-29 cells.Experimental & molecular medicine · 2021Article
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- Functional Common and RareCancer prevention research (Philadelphia, Pa.) · 2021Article
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- Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs.eLife · 2020Article
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- Progression inference for somatic mutations in cancer.Heliyon · 2017Article
- Palindromic amplification of the ERBB2 oncogene in primary HER2-positive breast tumors.Scientific reports · 2017Article
- A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers.Nature communications · 2016Article
- Mre11-Sae2 and RPA Collaborate to Prevent Palindromic Gene Amplification.Molecular cell · 2015Article
- Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments.BMC genomics · 2014Article
- Targeted next-generation sequencing at copy-number breakpoints for personalized analysis of rearranged ends in solid tumors.PloS one · 2014Article
- Homology-mediated end-capping as a primary step of sister chromatid fusion in the breakage-fusion-bridge cycles.Nucleic acids research · 2013Article
- Distribution of copy number variations and rearrangement endpoints in human cancers with a review of literature.Mutation researchReview
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10 authors at 4 institutions in 1 country.
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Abstract
introductionSegmental duplications (low-copy repeats) are the recently duplicated genomic segments in the human genome that display nearly identical (> 90%) sequences and account for about 5% of euchromatic regions. In germline, duplicated segments mediate nonallelic homologous recombination and thus cause both non-disease-causing copy-number variants and genomic disorders. To what extent duplicated segments play a role in somatic DNA rearrangements in cancer remains elusive. Duplicated segments often cluster and form genomic blocks enriched with both direct and inverted repeats (complex genomic regions). Such complex regions could be fragile and play a mechanistic role in the amplification of the ERBB2 gene in breast tumors, because repeated sequences are known to initiate gene amplification in model systems.
methodsWe conducted polymerase chain reaction (PCR)-based assays for primary breast tumors and analyzed publically available array-comparative genomic hybridization data to map a common copy-number breakpoint in ERBB2-amplified primary breast tumors. We further used molecular, bioinformatics, and population-genetics approaches to define duplication contents, structural variants, and haplotypes within the common breakpoint.
resultsWe found a large (> 300-kb) block of duplicated segments that was colocalized with a common-copy number breakpoint for ERBB2 amplification. The breakpoint that potentially initiated ERBB2 amplification localized in a region 1.5 megabases (Mb) on the telomeric side of ERBB2. The region is very complex, with extensive duplications of KRTAP genes, structural variants, and, as a result, a paucity of single-nucleotide polymorphism (SNP) markers. Duplicated segments are varied in size and degree of sequence homology, indicating that duplications have occurred recurrently during genome evolution.
conclusionsAmplification of the ERBB2 gene in breast tumors is potentially initiated by a complex region that has unusual genomic features and thus requires rigorous, labor-intensive investigation. The haplotypes we provide could be useful to identify the potential association between the complex region and ERBB2 amplification.
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