The Diploid Genome Sequence of an Individual Human Export

@article{levy:human, abstract = {Presented here is a genome sequence of an individual human. It was produced from \~{}32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb) of contiguous sequence with approximately 7.5-fold coverage for any given region. We developed a modified version of the Celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. Comparison of this genome and the National Center for Biotechnology Information human reference assembly revealed more than 4.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel) included 3,213,401 single nucleotide polymorphisms (SNPs), 53,823 block substitutions (2\^{a}€ ” 206 bp), 292,102 heterozygous insertion/deletion events (indels)(1\^{a}€ ” 571 bp), 559,473 homozygous indels (1\^{a}€ ” 82,711 bp), 90 inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22\% of all events identified in the donor, however they involve 74\% of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid genome structure. Moreover, 44\% of genes were heterozygous for one or more variants. Using a novel haplotype assembly strategy, we were able to span 1.5 Gb of genome sequence in segments >200 kb, providing further precision to the diploid nature of the genome. These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information.}, author = {Levy, Samuel and Sutton, Granger and Ng, Pauline C. and Feuk, Lars and Halpern, Aaron L. and Walenz, Brian P. and Axelrod, Nelson and Huang, Jiaqi and Kirkness, Ewen F. and Denisov, Gennady and Lin, Yuan and MacDonald, Jeffrey R. and Pang, Andy W. and Shago, Mary and Stockwell, Timothy B. and Tsiamouri, Alexia and Bafna, Vineet and Bansal, Vikas and Kravitz, Saul A. and Busam, Dana A. and Beeson, Karen Y. and McIntosh, Tina C. and Remington, Karin A. and Abril, Josep F. and Gill, John and Borman, Jon and Rogers, Yu-Hui and Frazier, Marvin E. and Scherer, Stephen W. and Strausberg, Robert L. and Venter, J. Craig}, citeulike-article-id = {1618977}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pbio.0050254}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17803354}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17803354}, day = {4}, doi = {10.1371/journal.pbio.0050254}, journal = {PLoS Biol}, keywords = {genome, human, thesis}, month = {September}, number = {10}, pages = {e254+}, posted-at = {2008-10-03 18:38:16}, priority = {2}, publisher = {Public Library of Science}, title = {The Diploid Genome Sequence of an Individual Human}, url = {http://dx.doi.org/10.1371/journal.pbio.0050254}, volume = {5}, year = {2007} }

TY - JOUR ID - levy:human L3 - citeulike-article-id:1618977 N2 - Presented here is a genome sequence of an individual human. It was produced from ~32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb) of contiguous sequence with approximately 7.5-fold coverage for any given region. We developed a modified version of the Celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. Comparison of this genome and the National Center for Biotechnology Information human reference assembly revealed more than 4.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel) included 3,213,401 single nucleotide polymorphisms (SNPs), 53,823 block substitutions (2–206 bp), 292,102 heterozygous insertion/deletion events (indels)(1–571 bp), 559,473 homozygous indels (1–82,711 bp), 90 inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid genome structure. Moreover, 44% of genes were heterozygous for one or more variants. Using a novel haplotype assembly strategy, we were able to span 1.5 Gb of genome sequence in segments >200 kb, providing further precision to the diploid nature of the genome. These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information. IS - 10 JF - PLoS Biol TI - The Diploid Genome Sequence of an Individual Human PB - Public Library of Science VL - 5 SP - e254 KW - genome KW - human KW - thesis AU - Levy, Samuel AU - Sutton, Granger AU - Ng, Pauline AU - Feuk, Lars AU - Halpern, Aaron AU - Walenz, Brian AU - Axelrod, Nelson AU - Huang, Jiaqi AU - Kirkness, Ewen AU - Denisov, Gennady AU - Lin, Yuan AU - MacDonald, Jeffrey AU - Pang, Andy AU - Shago, Mary AU - Stockwell, Timothy AU - Tsiamouri, Alexia AU - Bafna, Vineet AU - Bansal, Vikas AU - Kravitz, Saul AU - Busam, Dana AU - Beeson, Karen AU - McIntosh, Tina AU - Remington, Karin AU - Abril, Josep AU - Gill, John AU - Borman, Jon AU - Rogers, Yu-Hui AU - Frazier, Marvin AU - Scherer, Stephen AU - Strausberg, Robert AU - Venter, Craig PY - 2007/09/04/ UR - http://dx.doi.org/10.1371/journal.pbio.0050254 ER -