Accurate and comprehensive sequencing of personal genomes

被引：140

作者：

Ajay, Subramanian S. ^{[1
]}

Parker, Stephen C. J. ^{[1
]}

Abaan, Hatice Ozel ^{[1
]}

Fajardo, Karin V. Fuentes ^{[2
]}

Margulies, Elliott H. ^{[1
]}

机构：

[1] NHGRI, Genome Informat Sect, Genome Technol Branch, NIH, Bethesda, MD 20892 USA

[2] NHGRI, Undiagnosed Dis Program, Off Clin Director, NIH, Bethesda, MD 20892 USA

来源：

GENOME RESEARCH | 2011年 / 21卷 / 09期

基金：

美国国家卫生研究院;

关键词：

SHORT-READ; DISCOVERY; PATIENT;

D O I：

10.1101/gr.123638.111

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

As whole-genome sequencing becomes commoditized and we begin to sequence and analyze personal genomes for clinical and diagnostic purposes, it is necessary to understand what constitutes a complete sequencing experiment for determining genotypes and detecting single-nucleotide variants. Here, we show that the current recommendation of similar to 30x coverage is not adequate to produce genotype calls across a large fraction of the genome with acceptably low error rates. Our results are based on analyses of a clinical sample sequenced on two related Illumina platforms, GAII(x) and HiSeq 2000, to a very high depth (126x). We used these data to establish genotype-calling filters that dramatically increase accuracy. We also empirically determined how the callable portion of the genome varies as a function of the amount of sequence data used. These results help provide a "sequencing guide'' for future whole-genome sequencing decisions and metrics by which coverage statistics should be reported.

引用

页码：1498 / 1505

页数：8

共 29 条

[1] Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries [J].

Aird, Daniel ;

Ross, Michael G. ;

Chen, Wei-Sheng ;

Danielsson, Maxwell ;

Fennell, Timothy ;

Russ, Carsten ;

Jaffe, David B. ;

Nusbaum, Chad ;

Gnirke, Andreas .

GENOME BIOLOGY, 2011, 12 (02)

[2] A map of human genome variation from population-scale sequencing [J].

Altshuler, David ;

Durbin, Richard M. ;

Abecasis, Goncalo R. ;

Bentley, David R. ;

Chakravarti, Aravinda ;

Clark, Andrew G. ;

Collins, Francis S. ;

De la Vega, Francisco M. ;

Donnelly, Peter ;

Egholm, Michael ;

Flicek, Paul ;

Gabriel, Stacey B. ;

Gibbs, Richard A. ;

Knoppers, Bartha M. ;

Lander, Eric S. ;

Lehrach, Hans ;

Mardis, Elaine R. ;

McVean, Gil A. ;

Nickerson, DebbieA. ;

Peltonen, Leena ;

Schafer, Alan J. ;

Sherry, Stephen T. ;

Wang, Jun ;

Wilson, Richard K. ;

Gibbs, Richard A. ;

Deiros, David ;

Metzker, Mike ;

Muzny, Donna ;

Reid, Jeff ;

Wheeler, David ;

Wang, Jun ;

Li, Jingxiang ;

Jian, Min ;

Li, Guoqing ;

Li, Ruiqiang ;

Liang, Huiqing ;

Tian, Geng ;

Wang, Bo ;

Wang, Jian ;

Wang, Wei ;

Yang, Huanming ;

Zhang, Xiuqing ;

Zheng, Huisong ;

Lander, Eric S. ;

Altshuler, David L. ;

Ambrogio, Lauren ;

Bloom, Toby ;

Cibulskis, Kristian ;

Fennell, Tim J. ;

Gabriel, Stacey B. .

NATURE, 2010, 467 (7319) :1061-1073

[3] Accurate whole human genome sequencing using reversible terminator chemistry [J].

Bentley, David R. ;

Balasubramanian, Shankar ;

Swerdlow, Harold P. ;

Smith, Geoffrey P. ;

Milton, John ;

Brown, Clive G. ;

Hall, Kevin P. ;

Evers, Dirk J. ;

Barnes, Colin L. ;

Bignell, Helen R. ;

Boutell, Jonathan M. ;

Bryant, Jason ;

Carter, Richard J. ;

Cheetham, R. Keira ;

Cox, Anthony J. ;

Ellis, Darren J. ;

Flatbush, Michael R. ;

Gormley, Niall A. ;

Humphray, Sean J. ;

Irving, Leslie J. ;

Karbelashvili, Mirian S. ;

Kirk, Scott M. ;

Li, Heng ;

Liu, Xiaohai ;

Maisinger, Klaus S. ;

Murray, Lisa J. ;

Obradovic, Bojan ;

Ost, Tobias ;

Parkinson, Michael L. ;

Pratt, Mark R. ;

Rasolonjatovo, Isabelle M. J. ;

Reed, Mark T. ;

Rigatti, Roberto ;

Rodighiero, Chiara ;

Ross, Mark T. ;

Sabot, Andrea ;

Sankar, Subramanian V. ;

Scally, Aylwyn ;

Schroth, Gary P. ;

Smith, Mark E. ;

Smith, Vincent P. ;

Spiridou, Anastassia ;

Torrance, Peta E. ;

Tzonev, Svilen S. ;

Vermaas, Eric H. ;

Walter, Klaudia ;

Wu, Xiaolin ;

Zhang, Lu ;

Alam, Mohammed D. ;

Anastasi, Carole .

NATURE, 2008, 456 (7218) :53-59

[4] Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing [J].

Campbell, Peter J. ;

Stephens, Philip J. ;

Pleasance, Erin D. ;

O'Meara, Sarah ;

Li, Heng ;

Santarius, Thomas ;

Stebbings, Lucy A. ;

Leroy, Catherine ;

Edkins, Sarah ;

Hardy, Claire ;

Teague, Jon W. ;

Menzies, Andrew ;

Goodhead, Ian ;

Turner, Daniel J. ;

Clee, Christopher M. ;

Quail, Michael A. ;

Cox, Antony ;

Brown, Clive ;

Durbin, Richard ;

Hurles, Matthew E. ;

Edwards, Paul A. W. ;

Bignell, Graham R. ;

Stratton, Michael R. ;

Futreal, P. Andrew .

NATURE GENETICS, 2008, 40 (06) :722-729

[5] Mapping translocation breakpoints by next-generation sequencing [J].

Chen, Wei ;

Kalscheuer, Vera ;

Tzschach, Andreas ;

Menzel, Corinna ;

Ullmann, Reinhard ;

Schulz, Marcel Holger ;

Erdogan, Fikret ;

Li, Na ;

Kijas, Zofia ;

Arkesteijn, Ger ;

Pajares, Isidora Lopez ;

Goetz-Sothmann, Margret ;

Heinrich, Uwe ;

Rost, Imma ;

Dufke, Andreas ;

Grasshoff, Ute ;

Glaeser, Birgitta ;

Vingron, Martin ;

Ropers, H. Hilger .

GENOME RESEARCH, 2008, 18 (07) :1143-1149

[6] High-resolution mapping of copy-number alterations with massively parallel sequencing [J].

Chiang, Derek Y. ;

Getz, Gad ;

Jaffe, David B. ;

O'Kelly, Michael J. T. ;

Zhao, Xiaojun ;

Carter, Scott L. ;

Russ, Carsten ;

Nusbaum, Chad ;

Meyerson, Matthew ;

Lander, Eric S. .

NATURE METHODS, 2009, 6 (01) :99-103

[7] Finishing the euchromatic sequence of the human genome [J].

Collins, FS ;

Lander, ES ;

Rogers, J ;

Waterston, RH .

NATURE, 2004, 431 (7011) :931-945

[8] A framework for variation discovery and genotyping using next-generation DNA sequencing data [J].

DePristo, Mark A. ;

Banks, Eric ;

Poplin, Ryan ;

Garimella, Kiran V. ;

Maguire, Jared R. ;

Hartl, Christopher ;

Philippakis, Anthony A. ;

del Angel, Guillermo ;

Rivas, Manuel A. ;

Hanna, Matt ;

McKenna, Aaron ;

Fennell, Tim J. ;

Kernytsky, Andrew M. ;

Sivachenko, Andrey Y. ;

Cibulskis, Kristian ;

Gabriel, Stacey B. ;

Altshuler, David ;

Daly, Mark J. .

NATURE GENETICS, 2011, 43 (05) :491-+

[9] Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing [J].

Fujimoto, Akihiro ;

Nakagawa, Hidewaki ;

Hosono, Naoya ;

Nakano, Kaoru ;

Abe, Tetsuo ;

Boroevich, Keith A. ;

Nagasaki, Masao ;

Yamaguchi, Rui ;

Shibuya, Tetsuo ;

Kubo, Michiaki ;

Miyano, Satoru ;

Nakamura, Yusuke ;

Tsunoda, Tatsuhiko .

NATURE GENETICS, 2010, 42 (11) :931-U39

[10] A highly annotated whole-genome sequence of a Korean individual [J].

Kim, Jong-Il ;

Ju, Young Seok ;

Park, Hansoo ;

Kim, Sheehyun ;

Lee, Seonwook ;

Yi, Jae-Hyuk ;

Mudge, Joann ;

Miller, Neil A. ;

Hong, Dongwan ;

Bell, Callum J. ;

Kim, Hye-Sun ;

Chung, In-Soon ;

Lee, Woo-Chung ;

Lee, Ji-Sun ;

Seo, Seung-Hyun ;

Yun, Ji-Young ;

Woo, Hyun Nyun ;

Lee, Heewook ;

Suh, Dongwhan ;

Lee, Seungbok ;

Kim, Hyun-Jin ;

Yavartanoo, Maryam ;

Kwak, Minhye ;

Zheng, Ying ;

Lee, Mi Kyeong ;

Park, Hyunjun ;

Kim, Jeong Yeon ;

Gokcumen, Omer ;

Mills, Ryan E. ;

Zaranek, Alexander Wait ;

Thakuria, Joseph ;

Wu, Xiaodi ;

Kim, Ryan W. ;

Huntley, Jim J. ;

Luo, Shujun ;

Schroth, Gary P. ;

Wu, Thomas D. ;

Kim, HyeRan ;

Yang, Kap-Seok ;

Park, Woong-Yang ;

Kim, Hyungtae ;

Church, George M. ;

Lee, Charles ;

Kingsmore, Stephen F. ;

Seo, Jeong-Sun .

NATURE, 2009, 460 (7258) :1011-U96

← 1 2 3 →