TY  - JOUR
A1  - McKernan, Kevin Judd
A1  - Peckham, Heather E.
A1  - Costa, Gina L.
A1  - McLaughlin, Stephen F.
A1  - Fu, Yutao
A1  - Tsung, Eric F.
A1  - Clouser, Christopher R.
A1  - Duncan, Cisyla
A1  - Ichikawa, Jeffrey K.
A1  - Lee, Clarence C.
A1  - Zhang, Zheng
A1  - Ranade, Swati S.
A1  - Dimalanta, Eileen T.
A1  - Hyland, Fiona C.
A1  - Sokolsky, Tanya D.
A1  - Zhang, Lei
A1  - Sheridan, Andrew
A1  - Fu, Haoning
A1  - Hendrickson, Cynthia L.
A1  - Li, Bin
A1  - Kotler, Lev
A1  - Stuart, Jeremy R.
A1  - Malek, Joel A.
A1  - Manning, Jonathan M.
A1  - Antipova, Alena A.
A1  - Perez, Damon S.
A1  - Moore, Michael P.
A1  - Hayashibara, Kathleen C.
A1  - Lyons, Michael R.
A1  - Beaudoin, Robert E.
A1  - Coleman, Brittany E.
A1  - Laptewicz, Michael W.
A1  - Sannicandro, Adam E.
A1  - Rhodes, Michael D.
A1  - Gottimukkala, Rajesh K.
A1  - Yang, Shan
A1  - Bafna, Vineet
A1  - Bashir, Ali
A1  - MacBride, Andrew
A1  - Alkan, Can
A1  - Kidd, Jeffrey M.
A1  - Eichler, Evan E.
A1  - Reese, Martin G.
A1  - De La Vega, Francisco M.
A1  - Blanchard, Alan P.
T1  - Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding
Y1  - 2009/09/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1527 
EP  - 1541 
DO  - 10.1101/gr.091868.109 
VL  - 19 
IS  - 9 
UR  - http://genome.cshlp.org/content/19/9/1527.abstract 
N2  - 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 ∼18× haploid coverage of aligned sequence and close to 300× 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. 
ER  -