Use of dried blood spots for the determination of genetic variation of interleukin-10, killer immunoglobulin-like receptor and HLA class I genes

Optimal methods for using dried blood spots (DBSs) for population genetics‐based studies have not been well established. Using DBS stored for 8 years from 21 pregnant South African women, we evaluated three methods of gDNA extraction with and without whole‐genome amplification (WGA) to characterize...

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Bibliographic Details
Published in:Tissue antigens 2012-02, Vol.79 (2), p.114-122
Main Authors: Ndlovu, B. G., Danaviah, S., Moodley, E., Ghebremichael, M., Bland, R., Viljoen, J., Newell, M.-L., Ndung'u, T., Carr, W. H.
Format: Article
Language:English
Subjects:
Adolescent
Adult
Blood
DNA - analysis
DNA - genetics
DNA Fingerprinting - methods
Dried Blood Spot Testing
dried blood spots
Female
Genetic diversity
Genetic Variation
Genotype
Genotyping
Histocompatibility antigen HLA
Histocompatibility Antigens Class I - genetics
Histocompatibility Antigens Class I - immunology
human leukocyte antigen class I
Humans
Immunoglobulin-like receptors
Interleukin 10
Interleukin-10 - genetics
Interleukin-10 - immunology
Killer cell immunoglobulin-like receptors
killer immunoglobulin-like receptor genotyping
Middle Aged
Polymerase Chain Reaction
Population genetics
Population studies
Potassium channels (inwardly-rectifying)
Pregnancy
Primers
Protein Isoforms - genetics
Protein Isoforms - immunology
Receptors, KIR - genetics
Receptors, KIR - immunology
Sensitivity and Specificity
whole-genome amplification
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Summary:Optimal methods for using dried blood spots (DBSs) for population genetics‐based studies have not been well established. Using DBS stored for 8 years from 21 pregnant South African women, we evaluated three methods of gDNA extraction with and without whole‐genome amplification (WGA) to characterize immune‐related genes: interleukin‐10 (IL‐10), killer immunoglobulin‐like receptors (KIRs) and human leukocyte antigen (HLA) class I. We found that the QIAamp DNA mini kit yielded the highest gDNA quality (P< 0.05; Wilcoxon signed rank test) with sufficient yield for subsequent analyses. In contrast, we found that WGA was not reliable for sequence‐specific primer polymerase chain reaction (SSP‐PCR) analysis of KIR2DL1, KIR2DS1, KIR2DL5 and KIR2DL3 or high‐resolution HLA genotyping using a sequence‐based approach. We speculate that unequal template amplification by WGA underrepresents gene repertoires determined by sequence‐based approaches.
ISSN:0001-2815
1399-0039
DOI:10.1111/j.1399-0039.2011.01807.x