title: Identification of cancer-driver genes in focal genomic alterations from whole genome sequencing data.
abstract: DNA copy number alterations (CNAs) are the main genomic events that occur during the initiation and development of cancer. Distinguishing driver aberrant regions from passenger regions, which might contain candidate target genes for cancer therapies, is an important issue. Several methods for identifying cancer-driver genes from multiple cancer patients have been developed for single nucleotide polymorphism (SNP) arrays. However, for NGS data, methods for the SNP array cannot be directly applied because of different characteristics of NGS such as higher resolutions of data without predefined probes and incorrectly mapped reads to reference genomes. In this study, we developed a wavelet-based method for identification of focal genomic alterations for sequencing data (WIFA-Seq). We applied WIFA-Seq to whole genome sequencing data from glioblastoma multiforme, ovarian serous cystadenocarcinoma and lung adenocarcinoma, and identified focal genomic alterations, which contain candidate cancer-related genes as well as previously known cancer-driver genes.
authors.affiliation: Gwangju Institute of Science and Technology, School of Electrical Engineering and Computer Science, Gwangju, 500-712, South Korea.
authors.forename: Ho
authors.initials: H
authors.lastname: Jang
authors.affiliation: Yonsei University, Department of Mathematics, Seoul, 120-749, South Korea.
authors.forename: Youngmi
authors.initials: Y
authors.lastname: Hur
authors.affiliation: Gwangju Institute of Science and Technology, School of Electrical Engineering and Computer Science, Gwangju, 500-712, South Korea.
authors.forename: Hyunju
authors.initials: H
authors.lastname: Lee
mesh_terms: D056915:DNA Copy Number Variations / Q000235:genetics; D030541:Databases, Genetic; D066246:ErbB Receptors / Q000235:genetics; D018628:Gene Dosage; D052138:Genes, Neoplasm; D015894:Genome, Human; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D000073336:Whole Genome Sequencing
chemical_list: D066246:ErbB Receptors