{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T21:06:26Z","timestamp":1790024786354,"version":"4.0.1"},"reference-count":38,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2007,3,2]],"date-time":"2007-03-02T00:00:00Z","timestamp":1172793600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes Chromosomes &amp; Cancer"],"published-print":{"date-parts":[[2007,6]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>A BAC\u2010array platform for comparative genomic hybridization was constructed from a library of 32,433 clones providing complete genome coverage, and evaluated by screening for DNA copy number changes in 10 breast cancer cell lines (BT474, MCF7, HCC1937, SK\u2010BR\u20103, L56Br\u2010C1, ZR\u201075\u20101, JIMT1, MDA\u2010MB\u2010231, MDA\u2010MB\u2010361, and HCC2218) and one cell line derived from fibrocystic disease of the breast (MCF10A). These were also characterized by gene expression analysis and found to represent all five recently described breast cancer subtypes using the \u201cintrinsic gene set\u201d and centroid correlation. Three cell lines, HCC1937 and L56BrC1 derived from <jats:italic>BRCA1<\/jats:italic> mutation carriers and MDA\u2010MB\u2010231, were of basal\u2010like subtype and characterized by a high frequency of low\u2010level gains and losses of typical pattern, including limited deletions on 5q. Four estrogen receptor positive cell lines were of luminal A subtype and characterized by a different pattern of aberrations and high\u2010level amplifications, including <jats:italic>ERBB2<\/jats:italic> and other 17q amplicons in BT474 and MDA\u2010MB\u2010361. SK\u2010BR\u20103 cells, characterized by a complex genome including <jats:italic>ERBB2<\/jats:italic> amplification, massive high\u2010level amplifications on 8q and a homozygous deletion of <jats:italic>CDH1<\/jats:italic> at 16q22, had an expression signature closest to luminal B subtype. The effects of gene amplifications were verified by gene expression analysis to distinguish targeted genes from silent amplicon passengers. JIMT1, derived from an <jats:italic>ERBB2<\/jats:italic> amplified trastuzumab resistant tumor, was of the ERBB2 subtype. Homozygous deletions included other known targets such as <jats:italic>PTEN<\/jats:italic> (HCC1937) and <jats:italic>CDKN2A<\/jats:italic> (MDA\u2010MB\u2010231, MCF10A), but also new candidate suppressor genes such as <jats:italic>FUSSEL18<\/jats:italic> (HCC1937) and <jats:italic>WDR11<\/jats:italic> (L56Br\u2010C1) as well as regions without known genes. The tiling BAC\u2010arrays constitute a powerful tool for high\u2010resolution genomic profiling suitable for cancer research and clinical diagnostics. \u00a9 2007 Wiley\u2010Liss, Inc.<\/jats:p>","DOI":"10.1002\/gcc.20438","type":"journal-article","created":{"date-parts":[[2007,3,2]],"date-time":"2007-03-02T19:22:37Z","timestamp":1172863357000},"page":"543-558","source":"Crossref","is-referenced-by-count":153,"title":["High\u2010resolution genomic profiles of breast cancer cell lines assessed by tiling BAC array comparative genomic hybridization"],"prefix":"10.1002","volume":"46","author":[{"given":"G\u00f6ran","family":"J\u00f6nsson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johan","family":"Staaf","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eleonor","family":"Olsson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus","family":"Heidenblad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johan","family":"Vallon\u2010Christersson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazutoyo","family":"Osoegawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pieter","family":"de Jong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stina","family":"Oredsson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus","family":"Ringn\u00e9r","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mattias","family":"H\u00f6glund","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00c5ke","family":"Borg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2007,3,2]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddg261"},{"key":"e_1_2_6_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/sj.leu.2403749"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/labinvest.3700344"},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg230"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1002\/gcc.20366"},{"key":"e_1_2_6_7_1","first-page":"1919","article-title":"E\u2010cadherin is inactivated in a majority of invasive human lobular breast cancers by truncation mutations throughout its extracellular domain","volume":"13","author":"Berx G","year":"1996","journal-title":"Oncogene"},{"key":"e_1_2_6_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/sj.onc.1209254"},{"key":"e_1_2_6_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/sj.onc.1204694"},{"key":"e_1_2_6_10_1","first-page":"1972","article-title":"Mechanisms of inactivation of E\u2010cadherin in breast cancer cell lines","volume":"58","author":"Hiraguri S","year":"1998","journal-title":"Cancer Res"},{"key":"e_1_2_6_11_1","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1182\/blood.V87.1.324.324","article-title":"Molecular characterization of 12p abnormalities in hematologic malignancies: Deletion of KIP1,rearrangement of TEL, and amplification of CCND2","volume":"87","author":"Hoglund M","year":"1996","journal-title":"Blood"},{"key":"e_1_2_6_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng1307"},{"key":"e_1_2_6_13_1","doi-asserted-by":"publisher","DOI":"10.1002\/ijc.21934"},{"key":"e_1_2_6_14_1","doi-asserted-by":"publisher","DOI":"10.1097\/01.LAB.0000060030.10652.8C"},{"key":"e_1_2_6_15_1","doi-asserted-by":"publisher","DOI":"10.1093\/jnci\/dji280"},{"key":"e_1_2_6_16_1","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-05-0570"},{"key":"e_1_2_6_17_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1359641"},{"key":"e_1_2_6_18_1","first-page":"5323","article-title":"MYB oncogene amplification in hereditary BRCA1 breast cancer","volume":"60","author":"Kauraniemi P","year":"2000","journal-title":"Cancer Res"},{"key":"e_1_2_6_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh700"},{"key":"e_1_2_6_20_1","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-04-1992"},{"key":"e_1_2_6_21_1","doi-asserted-by":"publisher","DOI":"10.1186\/bcr1356"},{"key":"e_1_2_6_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/35021093"},{"key":"e_1_2_6_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/modpathol.3800621"},{"key":"e_1_2_6_24_1","first-page":"8861","article-title":"Patterns of chromosomal imbalances defines subgroups of breast cancer with distinct clinical features and prognosis. A study of 305 tumors by comparative genomic hybridization","volume":"63","author":"Rennstam K","year":"2003","journal-title":"Cancer Res"},{"key":"e_1_2_6_25_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2002-3-8-software0003"},{"key":"e_1_2_6_26_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1098918"},{"key":"e_1_2_6_27_1","doi-asserted-by":"publisher","DOI":"10.1186\/bcr1370"},{"key":"e_1_2_6_28_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng754"},{"key":"e_1_2_6_29_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0932692100"},{"key":"e_1_2_6_30_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng1571"},{"key":"e_1_2_6_31_1","doi-asserted-by":"publisher","DOI":"10.1158\/1535-7163.1585.3.12"},{"key":"e_1_2_6_32_1","first-page":"1222","article-title":"Distinct somatic genetic changes associated with tumor progression in carriers of BRCA1 and BRCA2 germ\u2010line mutations","volume":"57","author":"Tirkkonen M","year":"1997","journal-title":"Cancer Res"},{"key":"e_1_2_6_33_1","first-page":"3237","article-title":"Characterization of a breast cancer cell line derived from a germ\u2010line BRCA1 mutation carrier","volume":"58","author":"Tomlinson GE","year":"1998","journal-title":"Cancer Res"},{"key":"e_1_2_6_34_1","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.822.65.3"},{"key":"e_1_2_6_35_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng1407"},{"key":"e_1_2_6_36_1","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-03-2570"},{"key":"e_1_2_6_37_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1535-6108(02)00026-0"},{"key":"e_1_2_6_38_1","doi-asserted-by":"publisher","DOI":"10.1152\/physiolgenomics.00020.2001"},{"key":"e_1_2_6_39_1","article-title":"Within the fold: Assessing differential expression measures and reproducibility in microarray assays","volume":"3","author":"Yang IV","year":"2002","journal-title":"Genome Biol"}],"container-title":["Genes, Chromosomes and Cancer"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fgcc.20438","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/gcc.20438","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,29]],"date-time":"2023-09-29T01:18:26Z","timestamp":1695950306000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/gcc.20438"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,3,2]]},"references-count":38,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2007,6]]}},"alternative-id":["10.1002\/gcc.20438"],"URL":"https:\/\/doi.org\/10.1002\/gcc.20438","archive":["Portico"],"relation":{},"ISSN":["1045-2257","1098-2264"],"issn-type":[{"value":"1045-2257","type":"print"},{"value":"1098-2264","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,3,2]]}}}