Harismendy, O., Ng, P. C., Strausberg, R. L., Wang, X., Stockwell, T. B., Beeson, K. Y., Schork, N. J., Murray, S. S., Topol, E. J., Levy, S., Frazer, K. A.
Evaluation of Next Generation Sequencing Platforms for Population Targeted Sequencing Studies
Genome Biol. 2009 Mar 27; 10(3): R32.
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 needs to be considered when utilizing NGS platforms for population targeted sequencing studies.