Evaluation of next generation sequencing platforms for population targeted sequencing studies

By Olivier Harismendy, Pauline Crystal Ng, R. Strausberg, Xiaoyun Wang, Timothy B. Stockwell, K. Beeson, Nicholas J. Schork, Sarah S. Murray, Eric J. Topol, S. Levy and 1 more. Genome Biology, 2009

658 citations recorded by the source corpus.

BackgroundNext 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.ResultsLocal 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.ConclusionsOur study provides important insights into systematic biases and data variability that need to be considered when utilizing NGS platforms for population targeted sequencing studies.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/992952bb900753a0bca51105e2e9e04dd1ae78ea

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In Genetics

Citations in the corpus

VarScan: variant detection in massively parallel sequencing of individual and pooled samples (2009, background): “There is considerable interest in applying high-throughput sequencing to targeted regions of the genome (Harismendy et al., 2009), particularly to identify sequence variants affecting human disease.”
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities (2015, background): “…are expected to have similar sequence 80 coverage, i.e. genome abundance, the coverage of contigs can vary significantly within a library 81 due to biases originated from the current sequencing technology (Benjamini & Speed 2012; 82 Harismendy et al. 2009; Nakamura et al. 2011; Ross et al. 2013).”
Computer simulations: tools for population and evolutionary genetics (2012, background): “…in efficiency do not suffice to simulate next-generation sequencing data sets properly; simulators should either model the genotyping errors and biases that are specific to this technology 88,89 , or they should at least produce raw data that can easily be modified by additional software modules.”
Characterizing and measuring bias in sequence data (2013, background): “Illumina sequencing [18] has been shown to lose coverage in regions of high or low GC [19-22], a phenomenon also seen in other ‘ next-generation ’ technologies [3,6].”
A Primer on Metagenomics (2010, background): “For further reading on second generation sequencing see [31–34].”
Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels (2012, background): “Sequencing errors occur on all MPS platforms, but the type of errors and the error rates vary across MPS platforms [18–25].”
Assembly Algorithms for Next-Generation Sequencing Data (2010, neutral): “There are published error profiles for the 454 GS 20 [11], the Illumina 1G Analyzer [12], and comparisons of three platforms [13].”
Sequencing technologies — the next generation (2010, neutral): “Genome analysis of Illumina/Solexa data has revealed an underrepresentation of AT-ric”
SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data (2012, background): “, [10,11,12,13]), but if the coverage is low, they will be sharing the basic features outlined here: a trade-off between including too many SNPs and under-calling true heterozygotes.”
The impact of next-generation sequencing on genomics (2011, background): “More detailed technical description of these platforms are available elsewhere (Mardis, 2008a,b, 2009; Schuster, 2008; Shendure and Ji, 2008; Ansorge, 2009; Harismendy et al., 2009; Tucker et al., 2009; Voelkerding et al., 2009; Metzker, 2010; Ng and Kirkness, 2010).”
High‐throughput DNA sequencing – concepts and limitations (2010, methodology): “Considerably higher coverage is needed to perform SNP calling with similar accuracy using the Illumina GA [64].”