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The diploid genome sequence of an individual human

PLoS biology, 2007-09, Vol.5 (10), p.e254-e254 [Peer Reviewed Journal]

2007 Levy et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. (2007) The Diploid Genome Sequence of an Individual Human. PLoS Biol 5(10): e254. doi:10.1371/journal.pbio.0050254 ;cc-by (c) Levy, S. et al., 2007 info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/3.0/es ;2007 Levy et al. 2007 ;ISSN: 1545-7885 ;ISSN: 1544-9173 ;EISSN: 1545-7885 ;DOI: 10.1371/journal.pbio.0050254 ;PMID: 17803354

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Title:
The diploid genome sequence of an individual human
Author: Levy, Samuel ; Sutton, Granger ; Ng, Pauline C ; Feuk, Lars ; Halpern, Aaron L ; Walenz, Brian P ; Axelrod, Nelson ; Huang, Jiaqi ; Kirkness, Ewen F ; Denisov, Gennady ; Lin, Yuan ; MacDonald, Jeffrey R ; Pang, Andy Wing Chun ; Shago, Mary ; Stockwell, Timothy B ; Tsiamouri, Alexia ; Bafna, Vineet ; Bansal, Vikas ; Kravitz, Saul A ; Busam, Dana A ; Beeson, Karen Y ; McIntosh, Tina C ; Remington, Karin A ; Abril, Josep F ; Gill, John ; Borman, Jon ; Rogers, Yu-Hui ; Frazier, Marvin E ; Scherer, Stephen W ; Strausberg, Robert L ; Venter, J Craig
Rubin, Edward M
Subjects: ADN ; Artificial chromosomes ; Base Sequence ; Bioinformatics ; Bioinformàtica ; Chromosome Mapping - instrumentation ; Chromosome Mapping - methods ; Chromosomes, Human ; Chromosomes, Human, Y - genetics ; Deoxyribonucleic acid ; Diploidy ; DNA ; Experiments ; Gene Dosage ; Genetics ; Genetics and Genomics ; Genoma humà ; Genome, Human ; Genomes ; Genomics ; Genotype ; Genòmica ; Haplotypes ; Human ; Human genome ; Human Genome Project ; Humans ; In Situ Hybridization, Fluorescence ; INDEL Mutation ; Male ; Mammals ; Medical research ; Microarray Analysis ; Middle Aged ; Molecular Sequence Data ; Pedigree ; Phenotype ; Polymorphism, Single Nucleotide ; Primates ; Reproducibility of Results ; Sequence Analysis, DNA - instrumentation ; Sequence Analysis, DNA - methods ; Software
Is Part Of: PLoS biology, 2007-09, Vol.5 (10), p.e254-e254
Description: Presented here is a genome sequence of an individual human. It was produced from approximately 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.
Publisher: United States: Public Library of Science
Language: English
Identifier: ISSN: 1545-7885
ISSN: 1544-9173
EISSN: 1545-7885
DOI: 10.1371/journal.pbio.0050254
PMID: 17803354
Source: Recercat
Geneva Foundation Free Medical Journals at publisher websites
MEDLINE
PubMed Central
Public Library of Science
ProQuest Central
DOAJ Directory of Open Access Journals

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The diploid genome sequence of an individual human

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