Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding.
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.
McKernan
Kevin Judd
KJ
Life Technologies, Beverly, Massachusetts 01915, USA. Kevin.McKernan@appliedbiosystems.com
Peckham
Heather E
HE
Costa
Gina L
GL
McLaughlin
Stephen F
SF
Fu
Yutao
Y
Tsung
Eric F
EF
Clouser
Christopher R
CR
Duncan
Cisyla
C
Ichikawa
Jeffrey K
JK
Lee
Clarence C
CC
Zhang
Zheng
Z
Ranade
Swati S
SS
Dimalanta
Eileen T
ET
Hyland
Fiona C
FC
Sokolsky
Tanya D
TD
Zhang
Lei
L
Sheridan
Andrew
A
Fu
Haoning
H
Hendrickson
Cynthia L
CL
Li
Bin
B
Kotler
Lev
L
Stuart
Jeremy R
JR
Malek
Joel A
JA
Manning
Jonathan M
JM
Antipova
Alena A
AA
Perez
Damon S
DS
Moore
Michael P
MP
Hayashibara
Kathleen C
KC
Lyons
Michael R
MR
Beaudoin
Robert E
RE
Coleman
Brittany E
BE
Laptewicz
Michael W
MW
Sannicandro
Adam E
AE
Rhodes
Michael D
MD
Gottimukkala
Rajesh K
RK
Yang
Shan
S
Bafna
Vineet
V
Bashir
Ali
A
MacBride
Andrew
A
Alkan
Can
C
Kidd
Jeffrey M
JM
Eichler
Evan E
EE
Reese
Martin G
MG
De La Vega
Francisco M
FM
Blanchard
Alan P
AP
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*
D008025:Ligases