Evaluation of next generation sequencing platforms for population targeted sequencing studies

被引：471

作者：

Harismendy, Olivier ^{[2
]}

Ng, Pauline C. ^{[1
]}

Strausberg, Robert L. ^{[1
]}

Wang, Xiaoyun ^{[2
]}

Stockwell, Timothy B. ^{[1
]}

Beeson, Karen Y. ^{[1
]}

Schork, Nicholas J. ^{[2
]}

Murray, Sarah S. ^{[2
]}

Topol, Eric J. ^{[2
]}

Levy, Samuel ^{[1
]}

Frazer, Kelly A. ^{[2
]}

机构：

[1] J Craig Venter Inst, Rockville, MD 20850 USA

[2] Scripps Res Inst, Scripps Genom Med Scripps Translat Sci Inst, La Jolla, CA 92037 USA

来源：

GENOME BIOLOGY | 2009年 / 10卷 / 03期

关键词：

GENOME; IDENTIFICATION; SELECTION; SNPS; SETS;

D O I：

10.1186/gb-2009-10-3-r32

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 [微生物学]; 090105 [作物生产系统与生态工程];

摘要：

Background: Next generation sequencing (NGS) platforms are currently being utilized for targeted sequencing of candidate genes or genomic intervals to perform sequence-based association studies. To evaluate these platforms for this application, we analyzed human sequence generated by the Roche 454, Illumina GA, and the ABI SOLiD technologies for the same 260 kb in four individuals. Results: Local sequence characteristics contribute to systematic variability in sequence coverage (> 100-fold difference in per-base coverage), resulting in patterns for each NGS technology that are highly correlated between samples. A comparison of the base calls to 88 kb of overlapping ABI 3730xL Sanger sequence generated for the same samples showed that the NGS platforms all have high sensitivity, identifying > 95% of variant sites. At high coverage, depth base calling errors are systematic, resulting from local sequence contexts; as the coverage is lowered additional 'random sampling' errors in base calling occur. Conclusions: Our study provides important insights into systematic biases and data variability that need to be considered when utilizing NGS platforms for population targeted sequencing studies.

引用

页数：13

共 30 条

[1]

Direct selection of human genomic loci by microarray hybridization [J].

Albert, Thomas J. ;

Molla, Michael N. ;

Muzny, Donna M. ;

Nazareth, Lynne ;

Wheeler, David ;

Song, Xingzhi ;

Richmond, Todd A. ;

Middle, Chris M. ;

Rodesch, Matthew J. ;

Packard, Charles J. ;

Weinstock, George M. ;

Gibbs, Richard A. .

NATURE METHODS, 2007, 4 (11) :903-905

[2]

Microdeletions and microinsertions causing human genetic disease: Common mechanisms of mutagenesis and the role of local DNA sequence complexity [J].

Ball, EV ;

Stenson, PD ;

Abeysinghe, SS ;

Krawczak, M ;

Cooper, DN ;

Chuzhanova, NA .

HUMAN MUTATION, 2005, 26 (03) :205-213

[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]

Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes [J].

Bhangale, TR ;

Rieder, MJ ;

Livingston, RJ ;

Nickerson, DA .

HUMAN MOLECULAR GENETICS, 2005, 14 (01) :59-69

[5]

Estimating coverage and power for genetic association studies using near-complete variation data [J].

Bhangale, Tushar R. ;

Rieder, Mark J. ;

Nickerson, Deborah A. .

NATURE GENETICS, 2008, 40 (07) :841-843

[6]

Automating resequencing-based detection of insertion-deletion polymorphisms [J].

Bhangale, Tushar R. ;

Stephens, Matthew ;

Nickerson, Deborah A. .

NATURE GENETICS, 2006, 38 (12) :1457-1462

[7]

Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE) [J].

Bhinge, Akshay A. ;

Kim, Jonghwan ;

Euskirchen, Ghia M. ;

Snyder, Michael ;

Iyer, Vishwanath R. .

GENOME RESEARCH, 2007, 17 (06) :910-916

[8]

Genome sequencing in the fast lane [J].

Bonetta, L .

NATURE METHODS, 2006, 3 (02) :141-147

[9]

Identification of genetic variants using bar-coded multiplexed sequencing [J].

Craig, David W. ;

Pearson, John V. ;

Szelinger, Szabolcs ;

Sekar, Aswin ;

Redman, Margot ;

Corneveaux, Jason J. ;

Pawlowski, Traci L. ;

Laub, Trisha ;

Nunn, Gary ;

Stephan, Dietrich A. ;

Homer, Nils ;

Huentelman, Matthew J. .

NATURE METHODS, 2008, 5 (10) :887-893

[10]

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology [J].

Cronn, Richard ;

Liston, Aaron ;

Parks, Matthew ;

Gernandt, David S. ;

Shen, Rongkun ;

Mockler, Todd .

NUCLEIC ACIDS RESEARCH, 2008, 36 (19)

← 1 2 3 →