title: Decoding the fine-scale structure of a breast cancer genome and transcriptome.
abstract: A comprehensive understanding of cancer is predicated upon knowledge of the structure of malignant genomes underlying its many variant forms and the molecular mechanisms giving rise to them. It is well established that solid tumor genomes accumulate a large number of genome rearrangements during tumorigenesis. End Sequence Profiling (ESP) maps and clones genome breakpoints associated with all types of genome rearrangements elucidating the structural organization of tumor genomes. Here we extend the ESP methodology in several directions using the breast cancer cell line MCF-7. First, targeted ESP is applied to multiple amplified loci, revealing a complex process of rearrangement and co-amplification in these regions reminiscent of breakage/fusion/bridge cycles. Second, genome breakpoints identified by ESP are confirmed using a combination of DNA sequencing and PCR. Third, in vitro functional studies assign biological function to a rearranged tumor BAC clone, demonstrating that it encodes anti-apoptotic activity. Finally, ESP is extended to the transcriptome identifying four novel fusion transcripts and providing evidence that expression of fusion genes may be common in tumors. These results demonstrate the distinct advantages of ESP including: (1) the ability to detect all types of rearrangements and copy number changes; (2) straightforward integration of ESP data with the annotated genome sequence; (3) immortalization of the genome; (4) ability to generate tumor-specific reagents for in vitro and in vivo functional studies. Given these properties, ESP could play an important role in a tumor genome project.
authors.affiliation: Department of Urology, and Cancer Research Institute, University of California San Francisco Comprehensive Cancer Center, San Francisco, California 94115, USA.
authors.forename: Stanislav
authors.initials: S
authors.lastname: Volik
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Raphael
authors.forename: Guiqing
authors.initials: G
authors.lastname: Huang
authors.forename: Michael R
authors.initials: MR
authors.lastname: Stratton
authors.forename: Graham
authors.initials: G
authors.lastname: Bignel
authors.forename: John
authors.initials: J
authors.lastname: Murnane
authors.forename: John H
authors.initials: JH
authors.lastname: Brebner
authors.forename: Krystyna
authors.initials: K
authors.lastname: Bajsarowicz
authors.forename: Pamela L
authors.initials: PL
authors.lastname: Paris
authors.forename: Quanzhou
authors.initials: Q
authors.lastname: Tao
authors.forename: David
authors.initials: D
authors.lastname: Kowbel
authors.forename: Anna
authors.initials: A
authors.lastname: Lapuk
authors.forename: Dmitri A
authors.initials: DA
authors.lastname: Shagin
authors.forename: Irina A
authors.initials: IA
authors.lastname: Shagina
authors.forename: Joe W
authors.initials: JW
authors.lastname: Gray
authors.forename: Jan-Fang
authors.initials: JF
authors.lastname: Cheng
authors.forename: Pieter J
authors.initials: PJ
authors.lastname: de Jong
authors.forename: Pavel
authors.initials: P
authors.lastname: Pevzner
authors.forename: Colin
authors.initials: C
authors.lastname: Collins
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics*; D045744:Cell Line, Tumor; D022202:Chromosomes, Artificial, Bacterial / Q000378:metabolism; D002877:Chromosomes, Human; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D015894:Genome, Human; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D014158:Transcription, Genetic