Mapping 250K/500K SNP assay

198 GeneChip ® Mapping 500K Assay Manual
detection. The MPAM calling algorithm, used to make genotype calls
for the Mapping 10K array, is employed in this analysis to make
genotype calls on a subset of ~8,000 SNPs chosen for each of the
GeneChip ® Mapping 250K Nsp and 250K Sty Arrays. These SNPs
were chosen based upon the ability to be a suitable detector of sample
contamination across large data sets. Using this subset also allows the
software to quickly derive contamination metrics without the
additional computational burden of having to make an extra set of
calls on the entire array.
In a pure sample, the proportion of labeled DNA target for two alleles
of any SNP will typically be present at one of three allelic ratios,
100:0, 50:50 or 0:100. The models used to make genotype calls from
probe hybridization data apply this information to determine the
genotype call for each SNP, and assign a no call if the observed data
fall too far from these predicted ratios. If a mixed or contaminated
DNA sample is genotyped, the assumption of only three possible
allelic ratios will be violated for many SNPs, resulting in lower Call
Rates. However, whether or not the sample is contaminated, the
MPAM Detection Rate (MDR) will remain high as it is based only on
the extent to which PM probes are brighter than MM probes.
Therefore, a reduction in Call Rate (MCR < 0.94), accompanied by no
decrease in MDR (MDR > 0.99), is a characteristic indicator of sample
contamination (Figure 7.7 and Figure 7.8). Note that this
contamination metric does not apply if the MDR is < 99%.