Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines
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 rea...
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| Veröffentlicht in: | Cancer genetics 2011-08, Vol.204 (8), p.447-457 |
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| container_title | Cancer genetics |
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| creator | Hampton, Oliver A Miller, Christopher A Koriabine, Maxim Li, Jian Den Hollander, Petra Carbone, Lucia Nefedov, Mikhail Ten Hallers, Boudewijn F.H Lee, Adrian V De Jong, Pieter J Milosavljevic, Aleksandar |
| description | 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. |
| doi_str_mv | 10.1016/j.cancergen.2011.07.009 |
| format | Article |
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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.</description><identifier>ISSN: 2210-7762</identifier><identifier>EISSN: 2210-7770</identifier><identifier>DOI: 10.1016/j.cancergen.2011.07.009</identifier><identifier>PMID: 21962895</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Breakpoints ; Breast Neoplasms - genetics ; Cell Line, Tumor ; Chromosome Aberrations ; Chromosome Mapping ; Copy number variation ; DNA, Neoplasm - analysis ; DNA, Neoplasm - genetics ; Female ; fosmid diTag ; gene fusion ; Genome, Human ; Genomic Instability ; Hematology, Oncology and Palliative Medicine ; High-Throughput Nucleotide Sequencing - methods ; Humans ; massively parallel sequencing ; Medical Education ; Mutation - genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA</subject><ispartof>Cancer genetics, 2011-08, Vol.204 (8), p.447-457</ispartof><rights>Elsevier Inc.</rights><rights>2011 Elsevier Inc.</rights><rights>Copyright © 2011 Elsevier Inc. All rights reserved.</rights><rights>2011 Elsevier Inc. All rights reserved. 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c561t-9b5aae0a9757f3fbce3b7f89fa0604c8f18bb3ddb87425e5ed8e8bb6f5ab6aed3</citedby><cites>FETCH-LOGICAL-c561t-9b5aae0a9757f3fbce3b7f89fa0604c8f18bb3ddb87425e5ed8e8bb6f5ab6aed3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.cancergen.2011.07.009$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>230,314,780,784,885,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21962895$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hampton, Oliver A</creatorcontrib><creatorcontrib>Miller, Christopher A</creatorcontrib><creatorcontrib>Koriabine, Maxim</creatorcontrib><creatorcontrib>Li, Jian</creatorcontrib><creatorcontrib>Den Hollander, Petra</creatorcontrib><creatorcontrib>Carbone, Lucia</creatorcontrib><creatorcontrib>Nefedov, Mikhail</creatorcontrib><creatorcontrib>Ten Hallers, Boudewijn F.H</creatorcontrib><creatorcontrib>Lee, Adrian V</creatorcontrib><creatorcontrib>De Jong, Pieter J</creatorcontrib><creatorcontrib>Milosavljevic, Aleksandar</creatorcontrib><title>Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines</title><title>Cancer genetics</title><addtitle>Cancer Genet</addtitle><description>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.</description><subject>Breakpoints</subject><subject>Breast Neoplasms - genetics</subject><subject>Cell Line, Tumor</subject><subject>Chromosome Aberrations</subject><subject>Chromosome Mapping</subject><subject>Copy number variation</subject><subject>DNA, Neoplasm - analysis</subject><subject>DNA, Neoplasm - genetics</subject><subject>Female</subject><subject>fosmid diTag</subject><subject>gene fusion</subject><subject>Genome, Human</subject><subject>Genomic Instability</subject><subject>Hematology, Oncology and Palliative Medicine</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Humans</subject><subject>massively parallel sequencing</subject><subject>Medical Education</subject><subject>Mutation - genetics</subject><subject>Polymerase Chain Reaction</subject><subject>Sequence Analysis, DNA</subject><issn>2210-7762</issn><issn>2210-7770</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNUk2P0zAQjRCIXS37F8A3Ti228-HkstJqxZdUiQNwthxnUqY4dvE4XfW38Gdx6FIBF_DF9vjN88y8VxQvBF8LLppXu7U13kLcgl9LLsSaqzXn3aPiUkrBV0op_vh8buRFcU2043lVNW9V-bS4kKJrZNvVl8X3TfDbVTR-C2wyRHgAd2R7E41z4HIoQb5hZATfZvAW_ZYNkMAmYgNSQm8Tm-ZkEgZPzPiBEU7oTMxpKUHMwTAySnG2ac6sP8E9OkxHhp6l-8D6CIYSOzXFLDjHHHqgZ8WT0TiC64f9qvj85vWnu3erzYe37-9uNytbNyKtur42BrjpVK3GcuwtlL0a2240vOGVbUfR9n05DH2rKllDDUMLOdKMtekbA0N5VdycePdzP8FgwadcqN5HnEw86mBQ__ni8YvehoMuRVvLrskELx8IYshToqQnpKUP4yHMpDteVZ1qhfgnss26SNWUMiPVCWljIIownusRXC820Dt9toFebKC50tkGOfP57-2c836JngG3JwDkoR4QoiaLWVsYMGZh9RDwPz65-YvDZs3QGvcVjkC7MEefNdNCk9Rcf1zcuJhRCM5FV5XlDxpX48M</recordid><startdate>20110801</startdate><enddate>20110801</enddate><creator>Hampton, Oliver A</creator><creator>Miller, Christopher A</creator><creator>Koriabine, Maxim</creator><creator>Li, Jian</creator><creator>Den Hollander, Petra</creator><creator>Carbone, Lucia</creator><creator>Nefedov, Mikhail</creator><creator>Ten Hallers, Boudewijn F.H</creator><creator>Lee, Adrian V</creator><creator>De Jong, Pieter J</creator><creator>Milosavljevic, Aleksandar</creator><general>Elsevier Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7TO</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>P64</scope><scope>RC3</scope><scope>5PM</scope></search><sort><creationdate>20110801</creationdate><title>Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines</title><author>Hampton, Oliver A ; 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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. 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| ispartof | Cancer genetics, 2011-08, Vol.204 (8), p.447-457 |
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| subjects | Breakpoints Breast Neoplasms - genetics Cell Line, Tumor Chromosome Aberrations Chromosome Mapping Copy number variation DNA, Neoplasm - analysis DNA, Neoplasm - genetics Female fosmid diTag gene fusion Genome, Human Genomic Instability Hematology, Oncology and Palliative Medicine High-Throughput Nucleotide Sequencing - methods Humans massively parallel sequencing Medical Education Mutation - genetics Polymerase Chain Reaction Sequence Analysis, DNA |
| title | Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines |
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