Whole genome amplification and DNA pooling strategies

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DESCRIPTION (provided by applicant): We propose to assess the utility of a recently developed variant of the whole genome amplification technique, multiple displacement amplification (MDA), for high-throughput genotyping of DNA samples for molecular epidemiology studies. We hypothesize that MDA products will be ideal for genotyping analysis when consistent DNA concentrations are required from samples that may be of uncertain concentrations and quality. To this end, we will amplify and genotype by various techniques a subset of buffy coat and buccal cell DNA samples ranging from low to high DNA concentrations from the Nurses Health Study (NHS) and the Health Professional Follow-up Study (HPFS) cohorts. Our genotyping analysis will include microsatellites, insertion/deletions and single nucleotide polymorphisms (SNPs) in GC-rich regions, markers that can be challenging to genotype. In addition, we will assess the utility of DNA pooling strategies to estimate allele frequencies in large nested case-control studies. We will use both DNA sources from the NHS and HPFS, as well as MDA-generated products to determine whether allele frequencies in pooled DNA will correlate strongly with those measured in individuals across a wide range of allele frequencies. Results from the pooling experiments will determine whether this method may be sensitive enough for use in nested case-control studies where a small difference in allele frequency is expected.