title: Improving the Power of Structural Variation Detection by Augmenting the Reference.
abstract: The uses of the Genome Reference Consortium's human reference sequence can be roughly categorized into three related but distinct categories: as a representative species genome, as a coordinate system for identifying variants, and as an alignment reference for variation detection algorithms. However, the use of this reference sequence as simultaneously a representative species genome and as an alignment reference leads to unnecessary artifacts for structural variation detection algorithms and limits their accuracy. We show how decoupling these two references and developing a separate alignment reference can significantly improve the accuracy of structural variation detection, lead to improved genotyping of disease related genes, and decrease the cost of studying polymorphism in a population.
authors: The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Computing and Information Systems, The University of Melbourne, Melbourne, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia.
authors: Jan
authors: J
authors: Schröder
authors: Genomic Sciences Institute of the Huck, The Pennsylvania State University, State College, United States of America; Department of Computer Science and Engineering, The Pennsylvania State University, State College, United States of America.
authors: Santhosh
authors: S
authors: Girirajan
authors: The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia.
authors: Anthony T
authors: AT
authors: Papenfuss
authors: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, United States of America; Genomic Sciences Institute of the Huck, The Pennsylvania State University, State College, United States of America; Department of Computer Science and Engineering, The Pennsylvania State University, State College, United States of America.
authors: Paul
authors: P
authors: Medvedev
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D015894:Genome, Human / Q000235:genetics*; D056914:Genomic Structural Variation; D005838:Genotype; D006801:Humans; D008565:Membrane Proteins / Q000235:genetics; D009419:Nerve Tissue Proteins / Q000235:genetics; D012016:Reference Values; D016415:Sequence Alignment / Q000379:methods*
chemical_list: C403049:CNTNAP2 protein, human; D008565:Membrane Proteins; D009419:Nerve Tissue Proteins