title: Expanding the computational toolbox for mining cancer genomes.
abstract: High-throughput DNA sequencing has revolutionized the study of cancer genomics with numerous discoveries that are relevant to cancer diagnosis and treatment. The latest sequencing and analysis methods have successfully identified somatic alterations, including single-nucleotide variants, insertions and deletions, copy-number aberrations, structural variants and gene fusions. Additional computational techniques have proved useful for defining the mutations, genes and molecular networks that drive diverse cancer phenotypes and that determine clonal architectures in tumour samples. Collectively, these tools have advanced the study of genomic, transcriptomic and epigenomic alterations in cancer, and their association to clinical properties. Here, we review cancer genomics software and the insights that have been gained from their application.
authors.affiliation: 1] The Genome Institute, Washington University in St. Louis, 4444 Forest Park Ave., St. Louis, Missouri 63108, USA. [2] Department of Medicine, Washington University in St. Louis, 660 S. Euclid Ave., St. Louis, Missouri 63110, USA. [3] Department of Genetics, Washington University in St. Louis, 660 S. Euclid Ave., St. Louis, Missouri 63110, USA. [4] Siteman Cancer Center, Washington University in St. Louis, 4921 Parkview Place, St. Louis, Missouri 63110, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Ding
authors.affiliation: 1] The Genome Institute, Washington University in St. Louis, 4444 Forest Park Ave., St. Louis, Missouri 63108, USA. [2] Department of Genetics, Washington University in St. Louis, 660 S. Euclid Ave., St. Louis, Missouri 63110, USA. [3] Department of Mathematics, Washington University in St. Louis, 1 Brookings Drive, St. Louis, Missouri 63130, USA.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Wendl
authors.affiliation: The Genome Institute, Washington University in St. Louis, 4444 Forest Park Ave., St. Louis, Missouri 63108, USA.
authors.forename: Joshua F
authors.initials: JF
authors.lastname: McMichael
authors.affiliation: Department of Computer Science and Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, Rhode Island 02912, USA.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Raphael
mesh_terms: D000818:Animals; D057225:Data Mining / Q000379:methods*; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009154:Mutation; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism; D015398:Signal Transduction; D012984:Software