Identification of large-scale genomic variation in cancer genomes using in silico reference models.
Identifying large-scale structural variation in cancer genomes continues to be a challenge to researchers. Current methods rely on genome alignments based on a reference that can be a poor fit to highly variant and complex tumor genomes. To address this challenge we developed a method that uses available breakpoint information to generate models of structural variations. We use these models as references to align previously unmapped and discordant reads from a genome. By using these models to align unmapped reads, we show that our method can help to identify large-scale variations that have been previously missed.
Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, 6, Avenue Swing, Belvaux L-4367, Luxembourg.
Sarah
S
Killcoyne
Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, 6, Avenue Swing, Belvaux L-4367, Luxembourg antonio.delsol@uni.lu.
Antonio
A
Del Sol
D000465:Algorithms; D045744:Cell Line, Tumor; D002869:Chromosome Aberrations; D002874:Chromosome Mapping; D003198:Computer Simulation; D014644:Genetic Variation; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D008954:Models, Biological; D009369:Neoplasms / Q000235:genetics*