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Long-read sequencing and de novo assembly of a Chinese genome.
Shi, Lingling; Guo, Yunfei; Dong, Chengliang; Huddleston, John; Yang, Hui; Han, Xiaolu; Fu, Aisi; Li, Quan; Li, Na; Gong, Siyi; Lintner, Katherine E; Ding, Qiong; Wang, Zou; Hu, Jiang; Wang, Depeng; Wang, Feng; Wang, Lin; Lyon, Gholson J; Guan, Yongtao; Shen, Yufeng; Evgrafov, Oleg V; Knowles, James A; Thibaud-Nissen, Francoise; Schneider, Valerie; Yu, Chack-Yung; Zhou, Libing; Eichler, Evan E; So, Kwok-Fai; Wang, Kai.
Afiliação
  • Shi L; Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China.
  • Guo Y; Ministry of Education Joint International Research Laboratory of CNS Regeneration, Jinan University, Guangzhou 510632, China.
  • Dong C; Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China.
  • Huddleston J; Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90089, USA.
  • Yang H; Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90089, USA.
  • Han X; Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.
  • Fu A; Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90089, USA.
  • Li Q; Genetic, Molecular, and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA.
  • Li N; Wuhan Institute of Biotechnology, Wuhan 430000, China.
  • Gong S; Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90089, USA.
  • Lintner KE; Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China.
  • Ding Q; Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China.
  • Wang Z; Department of Pediatrics, The Ohio State University, and The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA.
  • Hu J; Wuhan Institute of Biotechnology, Wuhan 430000, China.
  • Wang D; Wuhan Institute of Biotechnology, Wuhan 430000, China.
  • Wang F; Nextomics Biosciences, Wuhan 430000, China.
  • Wang L; Nextomics Biosciences, Wuhan 430000, China.
  • Lyon GJ; School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430000, China.
  • Guan Y; Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Huazhong University of Science and Technology, Wuhan 430022, China.
  • Shen Y; Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, New York, New York 11797, USA.
  • Evgrafov OV; USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.
  • Knowles JA; Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, New York 10032, USA.
  • Thibaud-Nissen F; Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90089, USA.
  • Schneider V; Department of Psychiatry &Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA.
  • Yu CY; Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90089, USA.
  • Zhou L; Department of Psychiatry &Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA.
  • Eichler EE; National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, Maryland 20894, USA.
  • So KF; National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, Maryland 20894, USA.
  • Wang K; Department of Pediatrics, The Ohio State University, and The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA.
Nat Commun ; 7: 12065, 2016 06 30.
Article em En | MEDLINE | ID: mdl-27356984
ABSTRACT
Short-read sequencing has enabled the de novo assembly of several individual human genomes, but with inherent limitations in characterizing repeat elements. Here we sequence a Chinese individual HX1 by single-molecule real-time (SMRT) long-read sequencing, construct a physical map by NanoChannel arrays and generate a de novo assembly of 2.93 Gb (contig N50 8.3 Mb, scaffold N50 22.0 Mb, including 39.3 Mb N-bases), together with 206 Mb of alternative haplotypes. The assembly fully or partially fills 274 (28.4%) N-gaps in the reference genome GRCh38. Comparison to GRCh38 reveals 12.8 Mb of HX1-specific sequences, including 4.1 Mb that are not present in previously reported Asian genomes. Furthermore, long-read sequencing of the transcriptome reveals novel spliced genes that are not annotated in GENCODE and are missed by short-read RNA-Seq. Our results imply that improved characterization of genome functional variation may require the use of a range of genomic technologies on diverse human populations.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Genoma Humano / Povo Asiático Limite: Humans / Male Idioma: En Revista: Nat Commun Ano de publicação: 2016 Tipo de documento: Article
Texto completo
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Genoma Humano / Povo Asiático Limite: Humans / Male Idioma: En Revista: Nat Commun Ano de publicação: 2016 Tipo de documento: Article