Mapping 250K/500K SNP assay

6 GeneChip ® Mapping 500K Assay Manual
The third-generation product in the mapping portfolio, the
GeneChip ® Human Mapping 500K Array Set, also uses the WGSA
assay that has been the hallmark characteristic of all previous mapping
arrays. An outline of the assay steps is shown in Figure 1.1 and Figure
1.2. By changing the choice of the restriction enzymes used in WGSA,
and therefore the complexity of the resulting PCR products, along
with an increase in the information capacity of the high-density arrays
themselves, genotyping of 500,000 SNPs has been enabled on two
arrays. This increase in the number of SNPs allows for higher density,
genome-wide mapping sets, which in turn will increase the amount of
information that can be extracted for association studies, the
identification of DNA copy number alterations, and population substructure.
Estimates for the number of SNPs that need to be genotyped
for whole-genome association studies using large population based
samples range from 100,000 to 1,000,000 depending on the disease,
population or number of samples being studied [63-66]. In order to
leverage the power of SNPs in genetic studies, we have developed a
DNA target preparation method that, when combined with allelic
discrimination via hybridization and with an automated genotype
calling algorithm [67], allows rapid and accurate genotypic
information at a fraction of the cost of current approaches. The
Mapping 500K Set thus provides a powerful, flexible, cost-effective
approach for scoring SNP genotypes in large numbers of samples and
will provide a new technological paradigm for the design of wholegenome
association studies.