Resolving complex structural genomic rearrangements using a randomized approach.
Complex chromosomal rearrangements are structural genomic alterations involving multiple instances of deletions, duplications, inversions, or translocations that co-occur either on the same chromosome or represent different overlapping events on homologous chromosomes. We present SVelter, an algorithm that identifies regions of the genome suspected to harbor a complex event and then resolves the structure by iteratively rearranging the local genome structure, in a randomized fashion, with each structure scored against characteristics of the observed sequencing data. SVelter is able to accurately reconstruct complex chromosomal rearrangements when compared to well-characterized genomes that have been deeply sequenced with both short and long reads.
Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
Xuefang
X
Zhao
Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
Sarah B
SB
Emery
Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
Bridget
B
Myers
Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.|Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
Jeffrey M
JM
Kidd
Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA. remills@umich.edu.|Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA. remills@umich.edu.
Ryan E
RE
Mills
D000465:Algorithms; D056905:Chromosome Breakpoints; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D015321:Gene Rearrangement; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D015203:Reproducibility of Results; D012984:Software; D014178:Translocation, Genetic; D064878:Web Browser
Complex structural rearrangements; Copy number variant (CNV); Human; Sequence analysis; Structural variation (SV)