Reliability of high‐throughput genotyping of whole genome amplified DNA in SNP genotyping studies

Abstract

Whole genome amplification (wga) of DNA is being widely implemented in many laboratories to extend the life of samples only available in limited quantities for genetic analysis. We determined the reliability of wgaDNA genotypes in three sets of replicates from the same individuals: (i) 23 pairs of genomic DNA (gDNA), (ii) 43 pairs gDNA versus wgaDNA, and (iii) 29 pairs of independently amplified wgaDNA. Amplification was performed using multiple displacement amplification (MDA). Genotyping was successful for both DNA types for 1268 out of 1534 SNPs from 164 cardiovascular candidate genes assayed in a single Illumina panel. Amplified DNA failed for 77 SNPs (6%) that were genotyped successfully with genomic material. Percent of successful SNP calls, and concordance between pairs and kappa statistics (kappa) were determined. A total of 54 110 genotypes from gDNA-wgaDNA pairs were available for concordance analysis. Mean kappa for gDNA-wgaDNA pairs was 0.99. Concordance between gDNA-wgaDNA pairs was higher than amongst wgaDNA pairs (mean kappa for the 29 independently amplified pairs of wgaDNA was 0.95; interquartile range: 0.93-1.00). A statistical analysis of those SNPs which failed to genotype from amplified DNA only revealed that those loci were more likely to be closer to the telomeres and in locally GC-rich sequences. In summary, the MDA method produces wgaDNA samples that can be genotyped using high-throughput technology with a very high reproducibility to the original DNA but with slightly lower call rates. DNA amplification methodologies provide a useful solution for current and future large-scale genetic analyses especially with limited quantities of samples and DNA.

Concordance Study of 3 Direct-to-Consumer Genetic-Testing Services

“…Concerns have been voiced over the lack of involvement of a clinician or genetic counselor in such testing (7 ), the regulation of such tests (8,9 ), ethical and legal issues (10,11 ), the variance in and the validity of risk (2,12 ), and the reliability of the overall analytical process and the possibility of genotyping errors (13)(14)(15). Our study found a Ͼ99.6% concordance in SNP genotypes among 3 DTC services (23andMe, deCODEme, Navigenics) and a genomics-analysis service (Expression Analysis).…”

Genotyping Performance Assessment of Whole Genome Amplified DNA with Respect to Multiplexing Level of Assay and Its Period of Storage

“…The validity of wgaDNA for ordinary use has been well justified [7], [14] and wgaDNA has previously been tested on medium-throughput MassARRAY platform with iPLEX GOLD chemistry [17]. However, to our knowledge, this study is the first one that made use of the variable multiplexing ability of the same genotyping technology to study the relationship between genotyping performance and multiplexing level of the assays using wgaDNA, and to examine whether the storage of wgaDNA would reduce the genotyping efficiency.…”

“…It can generate products with average size >10 kb, and the relatively consistent product yield is less sensitive to the amount of starting material [7], [11]. Whole genome amplified DNA (wgaDNA) from MDA methods can be used in a variety of applications including high-throughput genotyping [7], [14], e.g., Affymetrix array [15] and Illumina BeadArray [16]. In addition, the starting DNA sample for WGA needs not to be fresh [17].…”

Construction of a high-density linkage map and fine mapping of QTLs for growth and gonad related traits in blunt snout bream

“…In present study, we constructed the first high-resolution genetic map of M. amblycephala using SNPs, which represent the most common type of genome DNA polymorphism and are amenable to high-throughput genotyping31. Finally, an integrated map consisting of 24 LGs, which corresponded to 5,676 effective loci, was constructed based on 14,648 SNPs.…”