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Recent technological advances in microarray technology have allowed whole-genome association studies to become possible and greatly expanded the ability to map complex genetic traits across the human genome. Current mapping array technologies offer unprecedented resolution to examine single-nucleotide polymorphisms (SNP) across the human genome. The resolution of these mapping arrays can be greatly increased by performing secondary screens using a targeted genotyping approach to further characterize SNPs discovered with the mapping arrays as well as include SNPs that are determined to be of interest in candidate genes or other genetic areas of importance.
Over the last several months, we have examined 2200 patient samples from the Shanghai Breast Cancer Study cohort using a combination of Affymetrix 500k mapping arrays and a custom 1700 SNP targeted genotyping array. Beginning with the analysis of 200 samples analyzed with the 500k mapping arrays and proceeding to 2200 samples analyzed using the custom targeted genotyping arrays, data regarding the automation of assay protocols and data analysis schemes to greatly increase the efficiency and speed of the analysis will be presented. Association statistics as well as chromosome copy number information has been produced. Data will be presented to illustrate the importance of automation, accurate sample tracking, and examination of existing data from the HapMap project in evaluating and analyzing the resulting genotyping datasets.