Molecular typing of human leukocyte antigen and related polymorphisms following whole genome amplification


*Dr Richard A. Kaslow or J. Tang
Program in Epidemiology of Infection and Immunity
Schools of Medicine and Public Health
University of Alabama at Birmingham
1665 University Boulevard
RPHB Room 220 A
AL 35294-0022, USA
Tel.: +1 205 975 8698
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Abstract:  Reliable, high-resolution genotyping of human leukocyte antigen (HLA) polymorphisms is often compromised by DNA samples of suboptimal quality or limited quantity. We tested the feasibility of molecular typing for variants at HLA and neighboring loci using whole genome amplification (WGA) strategy facilitated by the Φ29 DNA polymerase. With little (5–100 ng) starting genomic DNA of varying quality and source materials, WGA was deemed successful in 167 of 169 DNA from 47 cell lines, 100 European Americans, and 22 native Africans. The Φ29-processed DNA provided adequate templates for polymerase chain reaction (PCR)-based analyses of several HLA (A, B, C, DRB1, and DQB1) and related loci (HFE, MICA, and 10 microsatellites) in the 6p24.3–6p21.3 region, with PCR amplicons ranging from 92 to 2200 bp. Five different genotyping techniques resolved and confirmed 364 genotypes when both original and Φ29-processed DNA worked in PCRs. General population genetic analyses provided additional evidence that WGA may represent a reliable and simple approach to securing ample genomic DNA for typing HLA, MICA, and related variants.