Research

Evaluation of next generation sequencing platforms for population targeted sequencing studies

Olivier Harismendy^1* , Pauline C Ng^2* , Robert L Strausberg² , Xiaoyun Wang¹ , Timothy B Stockwell² , Karen Y Beeson² , Nicholas J Schork¹ , Sarah S Murray¹ , Eric J Topol¹ , Samuel Levy² and Kelly A Frazer¹

¹  Scripps Genomic Medicine - Scripps Translational Science Institute - The Scripps Research Institute, N. Torrey Pines Court, La Jolla, CA 92037, USA

²  The J Craig Venter Institute, Medical Center Drive, Rockville, MD 20850, USA

author email corresponding author email* Contributed equally

Genome Biology 2009, 10:R32doi:10.1186/gb-2009-10-3-r32

Published:	27 March 2009

Subject areas: Genetics, Genome studies, Methods

Abstract

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.