A sequence-based survey of the complex structural organization of tumor genomes.

TitleA sequence-based survey of the complex structural organization of tumor genomes.
Publication TypeJournal Article
Year of Publication2008
AuthorsRaphael BJ, Volik S, Yu P, Wu C, Huang G, Linardopoulou EV, Trask BJ, Waldman F, Costello J, Pienta KJ, Mills GB, Bajsarowicz K, Kobayashi Y, Sridharan S, Paris PL, Tao Q, Aerni SJ, Brown RP, Bashir A, Gray JW, Cheng J-F, de Jong P, Nefedov M, Ried T, Padilla-Nash HM, Collins CC
JournalGenome Biol
Volume9
Issue3
PaginationR59
Date Published2008
ISSN1465-6914
KeywordsCarcinoma, Cell Line, Tumor, Chromosome Mapping, Chromosomes, Artificial, Bacterial, DNA Breaks, Gene Library, Gene Order, Genes, Neoplasm, Genome, Human, Humans, Polymorphism, Single Nucleotide, Recombination, Genetic, Sequence Analysis, DNA, Transcription, Genetic
Abstract

BACKGROUND: The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using end sequencing profiling, which relies on paired-end sequencing of cloned tumor genomes.

RESULTS: In the present study brain, breast, ovary, and prostate tumors, along with three breast cancer cell lines, were surveyed using end sequencing profiling, yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some rearrangements may be recurrent. Sequencing and fluorescence in situ hybridization confirmed translocations and complex tumor genome structures that include co-amplification and packaging of disparate genomic loci with associated molecular heterogeneity. Comparison of the tumor genomes suggests recurrent rearrangements. Some are likely to be novel structural polymorphisms, whereas others may be bona fide somatic rearrangements. A recurrent fusion transcript in breast tumors and a constitutional fusion transcript resulting from a segmental duplication were identified. Analysis of end sequences for single nucleotide polymorphisms revealed candidate somatic mutations and an elevated rate of novel single nucleotide polymorphisms in an ovarian tumor.

CONCLUSION: These results suggest that the genomes of many epithelial tumors may be far more dynamic and complex than was previously appreciated and that genomic fusions, including fusion transcripts and proteins, may be common, possibly yielding tumor-specific biomarkers and therapeutic targets.

DOI10.1186/gb-2008-9-3-r59
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/18364049?dopt=Abstract
PMCPMC2397511
Alternate JournalGenome Biol.
PubMed ID18364049