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High-Throughput Association Testing on DNA Pools to Identify Genetic Variants that Confer Susceptibility to Acute Myeloid Leukemia

¹ Leukaemia Research Fund Epidemiology and Genetics Unit, School of Medicine, University of Leeds, Leeds, LS2 9JT, United Kingdom; ² Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, California; and ³ Roche Molecular Systems, Alameda, California

Requests for reprints: Gareth J. Morgan, Academic Unit of Haematology and Oncology, Algernon Firth Building, Great George Street, University of Leeds, Leeds, LS2 9JT, United Kingdom. Phone: 44-113-3433372; Fax: 44-113-3433372. E-mail: Gareth.Morgan{at}egu.leeds.ac.uk

We have evaluated the use of allele-specific PCR (AS PCR) on DNA pools as a tool for screening inherited genetic variants that may be associated with risk of adult acute myeloid leukemia (AML). Two DNA pools were constructed, one of 444 AML cases, and another of 823 matched controls. The pools were validated using individual genotyping data for GSTP1 and LT variants. Allele frequencies for variants in GSTP1 and LT were estimated using quantitative AS PCR, and when compared to individual genotyping data, a high degree of concordance was seen. AS primer pairs were designed for nine candidate genetic variants in DNA repair and cell cycle/apoptotic regulatory genes, including Cyclin D1 [codon 870 splice site variant (A>G)]; BRCA1, P871L; ERCC2, K751Q; FAS –1377 (G>A); hMLH1 –93 (G>A) and V219I; p21, S31R; and the XRCC1 R194W and R399Q variants. For six of these assays, there was at least 95% concordance between AS PCR genotyping and an alternative approach carried out on individual samples. Furthermore, these six AS PCR assays all accurately estimated allele frequencies in the pools that had been calculated using individual genotyping data. A significant disease association was seen with AML for the –1377 variant in FAS (odds ratio 1.76, 95% confidence interval 1.26–2.44). These data suggest that quantitative AS PCR can be used as an efficient screening technique for disease associations of genetic variants in DNA pools made from case-control studies.