Accurate variant detection across non-amplified and whole genome amplified DNA using targeted next generation sequencing.

ElSharawy, Abdou, Warner, Jason, Olson, Jeff, Forster, Michael, Schilhabel, Markus B., Link, Darren R., Rose-John, Stefan, Schreiber, Stefan, Rosenstiel, Philip, Brayer, James and Franke, Andre (2012) Accurate variant detection across non-amplified and whole genome amplified DNA using targeted next generation sequencing. BMC Genomics, 13 . DOI 10.1186/1471-2164-13-500.

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Supplementary data:

Abstract

Background: Many hypothesis-driven genetic studies require the ability to comprehensively and efficiently target specific regions of the genome to detect sequence variations. Often, sample availability is limited requiring the use of whole genome amplification (WGA). We evaluated a high-throughput microdroplet-based PCR approach in combination with next generation sequencing (NGS) to target 384 discrete exons from 373 genes involved in cancer. In our evaluation, we compared the performance of six non-amplified gDNA samples from two HapMap family trios. Three of these samples were also preamplified by WGA and evaluated. We tested sample pooling or multiplexing strategies at different stages of the tested targeted NGS (T-NGS) workflow. Results: The results demonstrated comparable sequence performance between non-amplified and preamplified samples and between different indexing strategies [ sequence specificity of 66.0% +/- 3.4%, uniformity (coverage at 0.2x of the mean) of 85.6% +/- 0.6%]. The average genotype concordance maintained across all the samples was 99.5% +/- 0.4%, regardless of sample type or pooling strategy. We did not detect any errors in the Mendelian patterns of inheritance of genotypes between the parents and offspring within each trio. We also demonstrated the ability to detect minor allele frequencies within the pooled samples that conform to predicted models. Conclusion: Our described PCR-based sample multiplex approach and the ability to use WGA material for NGS may enable researchers to perform deep resequencing studies and explore variants at very low frequencies and cost.

Document Type: Article
Keywords: High-throughput targeted next-generation resequencing, Microdroplet-based multiplex PCR, Sample pooling or Multiplexing, Whole-genome amplified DNA samples, Cost reduction
Research affiliation: OceanRep > The Future Ocean - Cluster of Excellence
Kiel University
Refereed: Yes
Open Access Journal?: No
DOI etc.: 10.1186/1471-2164-13-500
ISSN: 1471-2164
Projects: Future Ocean
Date Deposited: 14 May 2014 10:14
Last Modified: 31 Jul 2019 06:48
URI: http://oceanrep.geomar.de/id/eprint/23909

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