Improving mapping and SNP-calling performance in ... - BioMed Central
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Improving mapping and SNP-calling performance in ... - BioMed Central
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ElSharawy et al. BMC Genomics 2012, 13:417 http://www.biomedcentral.com/1471-2164/13/417
RESEARCH ARTICLE
Open Access
Improving mapping and SNP-calling performance in multiplexed targeted next-generation sequencing Abdou ElSharawy1†, Michael Forster1†, Nadine Schracke2, Andreas Keller3, Ingo Thomsen1, Britt-Sabina Petersen1, Björn Stade1, Peer Stähler2, Stefan Schreiber1,4, Philip Rosenstiel1 and Andre Franke1*
Abstract Background: Compared to classical genotyping, targeted next-generation sequencing (tNGS) can be custom-designed to interrogate entire genomic regions of interest, in order to detect novel as well as known variants. To bring down the per-sample cost, one approach is to pool barcoded NGS libraries before sample enrichment. Still, we lack a complete understanding of how this multiplexed tNGS approach and the varying performance of the ever-evolving analytical tools can affect the quality of variant discovery. Therefore, we evaluated the impact of different software tools and analytical approaches on the discovery of single nucleotide polymorphisms (SNPs) in multiplexed tNGS data. To generate our own test model, we combined a sequence capture method with NGS in three experimental stages of increasing complexity (E. coli genes, multiplexed E. coli, and multiplexed HapMap BRCA1/2 regions). Results: We successfully enriched barcoded NGS libraries instead of genomic DNA, achieving reproducible coverage profiles (Pearson correlation coefficients of up to 0.99) across multiplexed samples, with
