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Variant discovery in targeted resequencing using whole genome amplified DNA

Amit R Indap1*, Regina Cole2, Christina L Runge3, Gabor T Marth1 and Michael Olivier4

Author Affiliations

1 Department of Biology, Boston College, Chestnut Hill, MA, USA

2 Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI, USA

3 Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, WI, USA

4 Texas Biomedical Research Intitute, San Antonio, Texas, USA

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BMC Genomics 2013, 14:468  doi:10.1186/1471-2164-14-468

Published: 10 July 2013



Next generation sequencing and advances in genomic enrichment technologies have enabled the discovery of the full spectrum of variants from common to rare alleles in the human population. The application of such technologies can be limited by the amount of DNA available. Whole genome amplification (WGA) can overcome such limitations. Here we investigate applicability of using WGA by comparing SNP and INDEL variant calls from a single genomic/WGA sample pair from two capture separate experiments: a 50 Mbp whole exome capture and a custom capture array of 4 Mbp region on chr12.


Our results comparing variant calls derived from genomic and WGA DNA show that the majority of variant SNP and INDEL calls are common to both callsets, both at the site and genotype level and suggest that allele bias plays a minimal role when using WGA DNA in re-sequencing studies.


Although the results of this study are based on a limited sample size, they suggest that using WGA DNA allows the discovery of the vast majority of variants, and achieves high concordance metrics, when comparing to genomic DNA calls.

Whole genome amplified DNA; Capture sequencing; Next generation sequencing; Variant discovery