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High-resolution genomic profiles of breast cancer cell lines assessed by tiling BAC array comparative genomic hybridization.

  • Göran B Jönsson
  • Johan Staaf
  • Eleonor Olsson
  • Markus Heidenblad
  • Johan Vallon-Christersson
  • Kazutoyo Osoegawa
  • Pieter de Jong
  • Stina Oredsson
  • Markus Ringnér
  • Mattias Höglund
  • Åke Borg
Publishing year: 2007
Language: English
Pages: 543-558
Publication/Series: Genes, Chromosomes and Cancer
Volume: 46
Issue: 6
Document type: Journal article
Publisher: John Wiley and Sons Inc.

Abstract english

A BAC-array 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-BR-3, L56Br-C1, ZR-75-1, JIMTI, MDA-MB-231, MDA-MB-361, 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 '' intrinsic gene set '' and centroid correlation. Three cell lines, HCC 1937 and L56BrC1 derived from BRCA I mutation carriers and MDA-MB-23 1, were of basal-like subtype and characterized by a high frequency of low-level gains and losses of typical pattern, including limited deletions on Sq. Four estrogen receptor positive cell lines were of luminal A subtype and characterized by a different pattern of aberrations and high-level amplifications, including ERBB2 and other 17q amplicons in BT474 and MDA-MB-361. SK-BR-3 cells, characterized by a complex genome including ERBB2 amplification, massive high-level amplifications on 8q and a homozygous deletion of CDH1 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 ERBB2 amplified trastuzumab resistant tumor, was of the ERBB2 subtype. Homozygous deletions included other known targets such as PTEN (HCC1937) and CDKN2A (MDA-MB-231, MCF10A), but also new candidate suppressor genes such as FUSSEL18 (HCC1937) and WDR11 (L56Br-C1) as well as regions without known genes. The tiling BAC-arrays constitute a powerful tool for high-resolution genomic profiling suitable for cancer research and clinical diagnostics.


  • Cancer and Oncology
  • Medical Genetics


  • ISSN: 1045-2257
Stina Oredsson
E-mail: stina [dot] oredsson [at] biol [dot] lu [dot] se


Functional zoology

+46 46 222 94 97



Principal investigator

LUCC - Lund University Cancer Centre

Research group

Animal Physiology


Cell proliferation

Doctoral students and postdocs

PhD Students, main supervisor

Wendy Soria Sotillo

PhD Students, assistant supervisor

Atena Malakpour Permlid