Abstract
BackgroundThe recommended genomic DNA input requirements for whole genome single nucleotide polymorphism microarrays can limit the scope of molecular epidemiological studies. We performed a large-scale evaluation of whole genome amplified DNA as input into high-density, whole-genome Illumina® Infinium® SNP microarray.ResultsOverall, 6622 DNA samples from 5970 individuals were obtained from three distinct biospecimen sources and genotyped using gDNA and/or wgaDNA inputs. When genotypes from the same individual were compared with standard, native gDNA input amount, we observed 99.94% mean concordance with wgaDNA input.ConclusionsOur results demonstrate that carefully conducted studies with wgaDNA inputs can yield high-quality genotyping results. These findings should enable investigators to consider expansion of ongoing studies using high-density SNP microarrays, currently challenged by small amounts of available DNA.
Highlights
The recommended genomic deoxyribonucleic acid (DNA) input requirements for whole genome single nucleotide polymorphism microarrays can limit the scope of molecular epidemiological studies
Whole genome amplification Based on completion and concordance rates between genomic DNA (gDNA) and whole genome amplified DNA (wgaDNA) generated by different with alleleWhole genome amplification (WGA) techniques in a previous study [17], we used the GE Healthcare’s illustraTM GenomiPhiTM V2 DNA Amplification Kit, based on the multiple displacement amplification (MDA) technology with φ29 DNA polymerase [18]
We obtained average yields of 5.1 μg of amplified DNA, with fragment sizes typically greater than 13 Kb. These values reflect the quality of the starting gDNA; we observed that the input wgaDNA should be of an average size of at least 2 kb for optimal genotyping with Infinium® microarrays [12]
Summary
The recommended genomic DNA input requirements for whole genome single nucleotide polymorphism microarrays can limit the scope of molecular epidemiological studies. We performed a large-scale evaluation of whole genome amplified DNA as input into high-density, whole-genome Illumina® Infinium® SNP microarray. Genome-wide association studies (GWAS) performed in the past decade have been instrumental in advancing the discovery of genetic variants associated with many human diseases and traits [1]. Oftentimes large sample sizes are necessary, especially in GWAS of rare variants as well as for the discovery of common variants with small estimated odds ratios (< 1.05). While success has been observed using whole genome amplified DNA (wgaDNA) as a suitable alternative to genomic DNA (gDNA) for lower-density microarrays [4,5,6,7], there has been no large methodological study published regarding the efficiency of wgaDNA using the newer high-density microarrays that include large numbers of rare or uncommon variants. Though it is an option to improve sample inclusion, many investigators have avoided using wgaDNA because of the potential for biased
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