title: Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding.
abstract: We describe the genome sequencing of an anonymous individual of African origin using a novel ligation-based sequencing assay that enables a unique form of error correction that improves the raw accuracy of the aligned reads to >99.9%, allowing us to accurately call SNPs with as few as two reads per allele. We collected several billion mate-paired reads yielding approximately 18x haploid coverage of aligned sequence and close to 300x clone coverage. Over 98% of the reference genome is covered with at least one uniquely placed read, and 99.65% is spanned by at least one uniquely placed mate-paired clone. We identify over 3.8 million SNPs, 19% of which are novel. Mate-paired data are used to physically resolve haplotype phases of nearly two-thirds of the genotypes obtained and produce phased segments of up to 215 kb. We detect 226,529 intra-read indels, 5590 indels between mate-paired reads, 91 inversions, and four gene fusions. We use a novel approach for detecting indels between mate-paired reads that are smaller than the standard deviation of the insert size of the library and discover deletions in common with those detected with our intra-read approach. Dozens of mutations previously described in OMIM and hundreds of nonsynonymous single-nucleotide and structural variants in genes previously implicated in disease are identified in this individual. There is more genetic variation in the human genome still to be uncovered, and we provide guidance for future surveys in populations and cancer biopsies.
authors: Life Technologies, Beverly, Massachusetts 01915, USA. Kevin.McKernan@appliedbiosystems.com
authors: Kevin Judd
authors: KJ
authors: McKernan
authors: Heather E
authors: HE
authors: Peckham
authors: Gina L
authors: GL
authors: Costa
authors: Stephen F
authors: SF
authors: McLaughlin
authors: Yutao
authors: Y
authors: Fu
authors: Eric F
authors: EF
authors: Tsung
authors: Christopher R
authors: CR
authors: Clouser
authors: Cisyla
authors: C
authors: Duncan
authors: Jeffrey K
authors: JK
authors: Ichikawa
authors: Clarence C
authors: CC
authors: Lee
authors: Zheng
authors: Z
authors: Zhang
authors: Swati S
authors: SS
authors: Ranade
authors: Eileen T
authors: ET
authors: Dimalanta
authors: Fiona C
authors: FC
authors: Hyland
authors: Tanya D
authors: TD
authors: Sokolsky
authors: Lei
authors: L
authors: Zhang
authors: Andrew
authors: A
authors: Sheridan
authors: Haoning
authors: H
authors: Fu
authors: Cynthia L
authors: CL
authors: Hendrickson
authors: Bin
authors: B
authors: Li
authors: Lev
authors: L
authors: Kotler
authors: Jeremy R
authors: JR
authors: Stuart
authors: Joel A
authors: JA
authors: Malek
authors: Jonathan M
authors: JM
authors: Manning
authors: Alena A
authors: AA
authors: Antipova
authors: Damon S
authors: DS
authors: Perez
authors: Michael P
authors: MP
authors: Moore
authors: Kathleen C
authors: KC
authors: Hayashibara
authors: Michael R
authors: MR
authors: Lyons
authors: Robert E
authors: RE
authors: Beaudoin
authors: Brittany E
authors: BE
authors: Coleman
authors: Michael W
authors: MW
authors: Laptewicz
authors: Adam E
authors: AE
authors: Sannicandro
authors: Michael D
authors: MD
authors: Rhodes
authors: Rajesh K
authors: RK
authors: Gottimukkala
authors: Shan
authors: S
authors: Yang
authors: Vineet
authors: V
authors: Bafna
authors: Ali
authors: A
authors: Bashir
authors: Andrew
authors: A
authors: MacBride
authors: Can
authors: C
authors: Alkan
authors: Jeffrey M
authors: JM
authors: Kidd
authors: Evan E
authors: EE
authors: Eichler
authors: Martin G
authors: MG
authors: Reese
authors: Francisco M
authors: FM
authors: De La Vega
authors: Alan P
authors: AP
authors: Blanchard
mesh_terms: D000349:Africa; D020029:Base Pairing; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D014644:Genetic Variation; D015894:Genome, Human; D023281:Genomics; D005838:Genotype; D006579:Heterozygote; D006720:Homozygote; D006801:Humans; D008025:Ligases; D020641:Polymorphism, Single Nucleotide; D012015:Reference Standards; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D008025:Ligases