Human genomic DNA can be limiting in molecular epidemiological and diagnostic analyses. Quality control of the MDA-amplified DNA is critical for high performance. These results suggest that MDA is an effective method of WGA with utility in molecular epidemiology. PCR on MDA-amplified DNA was routinely successful for challenging 10- and 12-kb segments with GC content ranging from 30% to 80%, demonstrating that rather long segments, which are difficult to amplify with PCR, are amplified well with MDA. The results of single-stranded conformation polymorphism (SSCP)-type of mutation scanning for seven MDA-amplified DNA samples in four genes were concordant with the genomic DNA samples. In contrast, one of four heterozygous loci was mistyped when lower quality MDA-amplified DNA samples were used. For heterozygotes, the relative intensity of peaks generated by the two alleles is highly similar for genomic and MDA-amplified genomic DNA, independent of GC content. Genotyping results demonstrate 100% accuracy. The GC content of these analyzed segments ranges from 30% to 69%.
Fifteen common polymorphisms from 10 genes located on 8 chromosomes were genotyped by direct sequencing of 300 PCR products from 115 high-quality MDA-amplified DNA samples extracted by different methods. The efficacy of the whole genome amplification (WGA) method, termed multiple displacement amplification (MDA), was assessed for detecting heterozygous sequence variants, mutation scanning, and PCR for challenging segments. Well-characterized epidemiological resources are generated with great effort, yet associated patient DNA samples can be limiting.
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