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Evaluating Whole Genome Amplification via Multiply-Primed Rolling Circle Amplification for SNP Genotyping of Samples With Low DNA Yield

Published online by Cambridge University Press:  21 February 2012

Kaisa Silander*
Affiliation:
Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland. kaisa.silander@ktl.fi
Kati Komulainen
Affiliation:
Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland.
Pekka Ellonen
Affiliation:
Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland.
Minttu Jussila
Affiliation:
Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland.
Mervi Alanne
Affiliation:
Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland.
Minna Levander
Affiliation:
Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland.
Päivi Tainola
Affiliation:
Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland.
Kari Kuulasmaa
Affiliation:
Department of Epidemiology and Health Promotion, National Public Health Institute, Helsinki, Finland.
Veikko Salomaa
Affiliation:
Department of Epidemiology and Health Promotion, National Public Health Institute, Helsinki, Finland.
Markus Perola
Affiliation:
Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland.
Leena Peltonen
Affiliation:
Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland.
Janna Saarela
Affiliation:
Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland.
*
*Address for correspondence: Kaisa Silander, PhD, Department of Molecular Medicine, National Public Health Institute, Biomedicum, Haartmaninkatu 8, 00251 Helsinki, Finland.

Abstract

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The amount of available DNA is often a limiting factor in pursuing genetic analyses of large-scale population cohorts. An association between higher DNA yield from blood and several phenotypes associated with inflammatory states has recently been demonstrated, suggesting that exclusion of samples with very low DNA yield may lead to biased results in statistical analyses. Whole genome amplification (WGA) could present a solution to the DNA concentration-dependent sample selection. The aim was to thoroughly assess WGA for samples with low DNA yield, using the multiply-primed rolling circle amplification method. Fifty-nine samples were selected with the lowest DNA yield (less than 7.5µg) among 799 samples obtained for one population cohort. The genotypes obtained from two replicate WGA samples and the original genomic DNA were compared by typing 24 single nucleotide polymorphisms (SNPs). Multiple genotype discrepancies were identified for 13 of the 59 samples. The largest portion of discrepancies was due to allele dropout in heterozygous genotypes in WGA samples. Pooling the WGA DNA replicates prior to genotyping markedly improved genotyping reproducibility for the samples, with only 7 discrepancies identified in 4 samples. The nature of discrepancies was mostly homozygote genotypes in the genomic DNA and heterozygote genotypes in the WGA sample, suggesting possible allele dropout in the genomic DNA sample due to very low amounts of DNA template. Thus, WGA is applicable for low DNA yield samples, especially if using pooled WGA samples. A higher rate of genotyping errors requires that increased attention be paid to genotyping quality control, and caution when interpreting results.

Type
Articles
Copyright
Copyright © Cambridge University Press 2005