A Microarray-based DNA pooling study based on 100K GeneChip
Large-scale genome-wide genetic studies are useful to the dissection of complex disorders. Rapid promotion of biotechnique in the post-genome era hastens the developments of human genetics. However, the cost is still high owing to simultaneously genotyping a large quantity of markers for large samples, and therefore the initialization of these studies is deferred. The purpose of this study is to develop an affordable genetic typing method for genome-wide studies. The information extracted from such data can provide potential clues and suggestions for the next-stage confirmation studies. This method combines a microarray-based genotyping technique and pooled DNA analysis. The microarray-based genotyping technique is based on the Affymetrix 100K GeneChip platform, which provides genome-wide genotyping for each individual using two-primer arrays based on XbaI and HindIII restriction enzymes. The costs of primer design and assay reagents are reduced largely. Pooled DNA analysis involves mixing genomic DNAs from different study individuals to reduce the number of typings and hence lower typing cost in this study. The total number of samples was 87 and the number of SNPs was 116,204. To evaluate the performance of the microarray-based pooled DNA analysis, all samples were typed by both typing platforms: individual genotyping and pooled alleletyping. Allele frequency was estimated by allele-counting approach and intensity-ratio approach with an adjustment of unbalanced hybridization. All calculations were carried out based on the developed software PDA (Pooled DNA Analyzer) and the adjustment of unbalanced hybridization was based on our previously developed database. Comparative study shows the estimated allele frequencies from the two typing platforms were highly correlated (Pearson correlation coefficient is 0.99), suggesting the reliability of the microarray-based pooled DNA study.