title: Discovery and genotyping of structural variation from long-read haploid genome sequence data.
abstract: In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes. By using an assembly-based approach (SMRT-SV), we systematically assessed each genome independently for structural variants (SVs) and indels resolving the sequence structure of 461,553 genetic variants from 2 bp to 28 kbp in length. We find that >89% of these variants have been missed as part of analysis of the 1000 Genomes Project even after adjusting for more common variants (MAF > 1%). We estimate that this theoretical human diploid differs by as much as ∼16 Mbp with respect to the human reference, with long-read sequencing data providing a fivefold increase in sensitivity for genetic variants ranging in size from 7 bp to 1 kbp compared with short-read sequence data. Although a large fraction of genetic variants were not detected by short-read approaches, once the alternate allele is sequence-resolved, we show that 61% of SVs can be genotyped in short-read sequence data sets with high accuracy. Uncoupling discovery from genotyping thus allows for the majority of this missed common variation to be genotyped in the human population. Interestingly, when we repeat SV detection on a pseudodiploid genome constructed in silico by merging the two haploids, we find that ∼59% of the heterozygous SVs are no longer detected by SMRT-SV. These results indicate that haploid resolution of long-read sequencing data will significantly increase sensitivity of SV detection.
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.|Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.
authors.forename: John
authors.initials: J
authors.lastname: Huddleston
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.
authors.forename: Mark J P
authors.initials: MJP
authors.lastname: Chaisson
authors.affiliation: McDonnell Genome Institute, Department of Medicine, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108, USA.
authors.forename: Karyn Meltz
authors.initials: KM
authors.lastname: Steinberg
authors.affiliation: McDonnell Genome Institute, Department of Medicine, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108, USA.
authors.forename: Wes
authors.initials: W
authors.lastname: Warren
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.
authors.forename: Kendra
authors.initials: K
authors.lastname: Hoekzema
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.|Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.
authors.forename: David
authors.initials: D
authors.lastname: Gordon
authors.affiliation: McDonnell Genome Institute, Department of Medicine, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108, USA.
authors.forename: Tina A
authors.initials: TA
authors.lastname: Graves-Lindsay
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.
authors.forename: Katherine M
authors.initials: KM
authors.lastname: Munson
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.
authors.forename: Zev N
authors.initials: ZN
authors.lastname: Kronenberg
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.
authors.forename: Laura
authors.initials: L
authors.lastname: Vives
authors.affiliation: Pacific Biosciences of California, Incorporated, Menlo Park, California 94025, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Peluso
authors.affiliation: Pacific Biosciences of California, Incorporated, Menlo Park, California 94025, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Boitano
authors.affiliation: Pacific Biosciences of California, Incorporated, Menlo Park, California 94025, USA.
authors.forename: Chen-Shin
authors.initials: CS
authors.lastname: Chin
authors.affiliation: Pacific Biosciences of California, Incorporated, Menlo Park, California 94025, USA.
authors.forename: Jonas
authors.initials: J
authors.lastname: Korlach
authors.affiliation: Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.|Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Evan E
authors.initials: EE
authors.lastname: Eichler
mesh_terms: D020451:Contig Mapping / Q000379:methods* / Q000592:standards; D015894:Genome, Human; D056914:Genomic Structural Variation; D006238:Haploidy; D016045:Human Genome Project; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards