This cell line has been the subject of several large-scale genomic analyses including comprehensive exome sequencing to detect somatic point mutations and BAC sequencing to identify chromosome translocations, which thus allows direct comparison between the approaches ( 9– 11). Our primary interest was to determine whether we could use this technology to identify genomic alterations, specifically gene fusions, and thus contribute to an integrated view of the genome and transcriptome alterations within the breast cancer cell line HCC1954. Here, we use 454 Life Sciences pyrosequencing technology that enables relatively long sequence reads and deep transcriptome coverage.
However, the short tags that are used give a very limited view of the complete transcript set and variations therein such as through alternative splicing, translocations and point mutations. To address that issue, and to attain deep coverage of the transcriptome such that rare transcripts could be identified, tagging approaches such as SAGE ( 6), CAGE ( 7), and MPSS ( 8) have been used. However, cost has been a significant limitation. Large-scale Sanger-based cDNA sequencing approaches contributed significantly to deciphering transcriptome complexity ( 3– 5). Comprehensive analysis of the active genes comprising the transcriptome has resulted in advances in our ability to understand the pathways involved in the progression of cancer, serves as a tool to delineate molecular differences in cancers, even among those that are from the same body site and appear similar by traditional approaches. The onset of cancer results from genomic alterations in precursor cells, and changes in the surrounding microenvironment ( 1) including the immune system ( 2). An achievable goal of the oncology community is to perform comprehensive sequence analysis of the cancer genome and its transcripts toward the identification of new detection, diagnostic and intervention strategies.
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