ArticleCancer genetics2011
Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines.
Article in Cancer genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Sample and Library Preparation for PacBio Long-Read Sequencing in Grapevine.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Proteomic Analysis of HCC-1954 and MCF-7 Cell Lines Highlights Crosstalk between αv and β1 Integrins, E-Cadherin and HER-2.International journal of molecular sciences · 2022Article
- In Vivo Modeling of Human Breast Cancer Using Cell Line and Patient-Derived Xenografts.Journal of mammary gland biology and neoplasia · 2022Review
- High-throughput long paired-end sequencing of a Fosmid library by PacBio.Plant methods · 2019Article
- Integrative detection and analysis of structural variation in cancer genomes.Nature genetics · 2018Article
- 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
- A Mutagenesis Assay for Reporter Gene Screening Using Partially Degenerate Oligonucleotides of the Tandems NNT and NNC.BioMed research international · 2015Article
- Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations.Genome research · 2014Article
- Discovery of recurrent structural variants in nasopharyngeal carcinoma.Genome research · 2014Article
- Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing.BMC genomics · 2013Article
- Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing.Scientific reports · 2013Article
- Structural analysis of the genome of breast cancer cell line ZR-75-30 identifies twelve expressed fusion genes.BMC genomics · 2012Article
- Paired-end sequencing of Fosmid libraries by Illumina.Genome research · 2012Article
- Are breast cancers driven by fusion genes?Breast cancer research : BCR · 2012Article
Corrections and comments
- Erratum issuedCoarfa, Cristian [added];Schoenherr, Caroline [added]
Authors and funding
13 authors.
Funding
Abstract
Cancer genomes frequently undergo genomic instability resulting in accumulation of chromosomal rearrangement. To date, one of the main challenges has been to confidently and accurately identify these rearrangements by using short-read massively parallel sequencing. We were able to improve cancer rearrangement detection by combining two distinct massively parallel sequencing strategies: fosmid-sized (36 kb on average) and standard 5 kb mate pair libraries. We applied this combined strategy to map rearrangements in two breast cancer cell lines, MCF7 and HCC1954. We detected and validated a total of 91 somatic rearrangements in MCF7 and 25 in HCC1954, including genomic alterations corresponding to previously reported transcript aberrations in these two cell lines. Each of the genomes contains two types of breakpoints: clustered and dispersed. In both cell lines, the dispersed breakpoints show enrichment for low copy repeats, while the clustered breakpoints associate with high copy number amplifications. Comparing the two genomes, we observed highly similar structural mutational spectra affecting different sets of genes, pointing to similar histories of genomic instability against the background of very different gene network perturbations.
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