Year: 2013
Type: article
Abstract: BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.
Source: BMC Genomics
Language: English
Topic: Genomics and Rare Diseases
Subfield: Genetics
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,090
Awards: Genotype-Phenotype Relationships in Auditory Neuropathy, Software Tools for Next-Generation Sequencer Data, Wisconsin Center of Excellence in Genomics Science, G516049965, Robust Software Tools for Variant Identification and Functional Assessment, Genomic dissection of a QTL affecting the lipid profile, G9000269208
OpenAlex ID: W2126480703