Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

Abstract

Human cancers often carry many somatically acquired genomic rearrangements, some of which may be implicated in cancer development. However, conventional strategies for characterizing rearrangements are laborious and low-throughput and have low sensitivity or poor resolution. We used massively parallel sequencing to generate sequence reads from both ends of short DNA fragments derived from the genomes of two individuals with lung cancer. By investigating read pairs that did not align correctly with respect to each other on the reference human genome, we characterized 306 germline structural variants and 103 somatic rearrangements to the base-pair level of resolution. The patterns of germline and somatic rearrangement were markedly different. Many somatic rearrangements were from amplicons, although rearrangements outside these regions, notably including tandem duplications, were also observed. Some somatic rearrangements led to abnormal transcripts, including two from internal tandem duplications and two fusion transcripts created by interchromosomal rearrangements. Germline variants were predominantly mediated by retrotransposition, often involving AluY and LINE elements. The results demonstrate the feasibility of systematic, genome-wide characterization of rearrangements in complex human cancer genomes, raising the prospect of a new harvest of genes associated with cancer using this strategy.Somatic genetic changes involved in cancer causation include point mutations, genomic rearrangements and changes in copy number1. Most of the currently identified genes © 2008 Nature Publishing Group Correspondence should be addressed to M.R.S. (mrs@sanger.ac.uk) or P. A.F. (paf@sanger.ac.uk).. 4 These authors contributed equally to this work. AUTHOR CONTRIBUTIONS P.J.C. and P.J.S. equally contributed to generating and analysing sequencing, copy number, PCR and breakpoint data, and wrote the manuscript. E.D.P. coordinated the bioinformatic analyses with support for mapping from H.L. and A.C. and for pipelining from L.A.S., C.L., A.M. and J.W.T. S.O., S.E. and C.H. performed the confirmatory PCRs and Sanger sequencing. T.S. and P.A.W.E. performed FISH and SKY experiments. I.G. and M.A.Q. undertook library production from the cell lines, and C.M.C. and D.J.T. ran the massively parallel sequencing instruments. C.B., R.D. and M.E.H. contributed to the analysis and interpretation of data. G.R.B., M.R.S. and P.A.F. coordinated the research, interpreted the data and wrote the manuscript. URLs Europe PMC Funders Author ManuscriptsEurope PMC Funders Author Manuscripts associated with cancer contribute to oncogenesis as a result of somatic rearrangements that result either in fusion transcripts or in transcriptional deregulation by apposing enhancer or promoter elements to intact protein coding sequences1. The large majority of the known somatically rearranged genes associated with cancer are found in the small minority of human cancers comprising leukemias, lymphomas and soft tissue tumors (see URLs section in Methods). Fus...

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