ArticleGenome research2009
A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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Who cites it
77 citing papers in PubMed, 130 citations in OpenAlex.
- Overview of Optical Fiber Biosensors for the Detection of Cancer Biomarkers in the Past Decade.ACS omega · 2026Review
- Sample and Library Preparation for PacBio Long-Read Sequencing in Grapevine.Methods in molecular biology (Clifton, N.J.) · 2024Article
- maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.PLoS computational biology · 2023Article
- Deep whole genome sequencing identifies recurrent genomic alterations in commonly used breast cancer cell lines and patient-derived xenograft models.Breast cancer research : BCR · 2022Article
- Article
- Inhibition of the translesion synthesis polymerase REV1 exploits replication gaps as a cancer vulnerability.Science advances · 2020Article
- Cancer cell lines show high heritability for motility but not generation time.Royal Society open science · 2020Article
- FusionPro, a Versatile Proteogenomic Tool for Identification of Novel Fusion Transcripts and Their Potential Translation Products in Cancer Cells.Molecular & cellular proteomics : MCP · 2019Article
- High expression of the vacuole membrane protein 1 (VMP1) is a potential marker of poor prognosis in HER2 positive breast cancer.PloS one · 2019Article
- Stem cells, immortality, and the evolution of metastatic properties in breast cancer: telomere maintenance mechanisms and metastatic evolution.Journal of cancer metastasis and treatment · 2019Article
- Forskolin increases the effect of everolimus on aromatase inhibitor-resistant breast cancer cells.Oncotarget · 2018Article
- Resource competition promotes tumour expansion in experimentally evolved cancer.BMC evolutionary biology · 2017Article
- SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads.BMC genomics · 2017Article
- Patient-derived xenograft (PDX) models in basic and translational breast cancer research.Cancer metastasis reviews · 2016Review
- Identifying fusion transcripts using next generation sequencing.Wiley interdisciplinary reviews. RNA · 2016Review
- RWCFusion: identifying phenotype-specific cancer driver gene fusions based on fusion pair random walk scoring method.Oncotarget · 2016Article
- Rad51C-ATXN7 fusion gene expression in colorectal tumors.Molecular cancer · 2016Article
- Mapping of deletion breakpoints at the CDKN2A locus in melanoma: detection of MTAP-ANRIL fusion transcripts.Oncotarget · 2016Article
- Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing.Nucleic acids research · 2015Article
- PacBio Sequencing and Its Applications.Genomics, proteomics & bioinformatics · 2015Review
17 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors at 1 institution in 1 country.
Funding
Abstract
By applying a method that combines end-sequence profiling and massively parallel sequencing, we obtained a sequence-level map of chromosomal aberrations in the genome of the MCF-7 breast cancer cell line. A total of 157 distinct somatic breakpoints of two distinct types, dispersed and clustered, were identified. A total of 89 breakpoints are evenly dispersed across the genome. A majority of dispersed breakpoints are in regions of low copy repeats (LCRs), indicating a possible role for LCRs in chromosome breakage. The remaining 68 breakpoints form four distinct clusters of closely spaced breakpoints that coincide with the four highly amplified regions in MCF-7 detected by array CGH located in the 1p13.1-p21.1, 3p14.1-p14.2, 17q22-q24.3, and 20q12-q13.33 chromosomal cytobands. The clustered breakpoints are not significantly associated with LCRs. Sequences flanking most (95%) breakpoint junctions are consistent with double-stranded DNA break repair by nonhomologous end-joining or template switching. A total of 79 known or predicted genes are involved in rearrangement events, including 10 fusions of coding exons from different genes and 77 other rearrangements. Four fusions result in novel expressed chimeric mRNA transcripts. One of the four expressed fusion products (RAD51C-ATXN7) and one gene truncation (BRIP1 or BACH1) involve genes coding for members of protein complexes responsible for homology-driven repair of double-stranded DNA breaks. Another one of the four expressed fusion products (ARFGEF2-SULF2) involves SULF2, a regulator of cell growth and angiogenesis. We show that knock-down of SULF2 in cell lines causes tumorigenic phenotypes, including increased proliferation, enhanced survival, and increased anchorage-independent growth.
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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.