title: Computational techniques for human genome resequencing using mated gapped reads.
abstract: Unchained base reads on self-assembling DNA nanoarrays have recently emerged as a promising approach to low-cost, high-quality resequencing of human genomes. Because of unique characteristics of these mated pair reads, existing computational methods for resequencing assembly, such as those based on map-consensus calling, are not adequate for accurate variant calling. We describe novel computational methods developed for accurate calling of SNPs and short substitutions and indels (<100 bp); the same methods apply to evaluation of hypothesized larger, structural variations. We use an optimization process that iteratively adjusts the genome sequence to maximize its a posteriori probability given the observed reads. For each candidate sequence, this probability is computed using Bayesian statistics with a simple read generation model and simplifying assumptions that make the problem computationally tractable. The optimization process iteratively applies one-base substitutions, insertions, and deletions until convergence is achieved to an optimum diploid sequence. A local de novo assembly procedure that generalizes approaches based on De Bruijn graphs is used to seed the optimization process in order to reduce the chance of converging to local optima. Finally, a correlation-based filter is applied to reduce the false positive rate caused by the presence of repetitive regions in the reference genome.
authors.affiliation: Complete Genomics Inc., Mountain View, California 94043, USA.
authors.forename: Paolo
authors.initials: P
authors.lastname: Carnevali
authors.forename: Jonathan
authors.initials: J
authors.lastname: Baccash
authors.forename: Aaron L
authors.initials: AL
authors.lastname: Halpern
authors.forename: Igor
authors.initials: I
authors.lastname: Nazarenko
authors.forename: Geoffrey B
authors.initials: GB
authors.lastname: Nilsen
authors.forename: Krishna P
authors.initials: KP
authors.lastname: Pant
authors.forename: Jessica C
authors.initials: JC
authors.lastname: Ebert
authors.forename: Anushka
authors.initials: A
authors.lastname: Brownley
authors.forename: Matt
authors.initials: M
authors.lastname: Morenzoni
authors.forename: Vitali
authors.initials: V
authors.lastname: Karpinchyk
authors.forename: Bruce
authors.initials: B
authors.lastname: Martin
authors.forename: Dennis G
authors.initials: DG
authors.lastname: Ballinger
authors.forename: Radoje
authors.initials: R
authors.lastname: Drmanac
mesh_terms: D000465:Algorithms; D000483:Alleles; D001483:Base Sequence; D001499:Bayes Theorem; D002874:Chromosome Mapping; D003198:Computer Simulation; D020451:Contig Mapping / Q000379:methods*; D003627:Data Interpretation, Statistical; D015894:Genome, Human; D006801:Humans; D008957:Models, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*