Mapping 250K/500K SNP assay

chapter 7 | Analysis Workflow 207
We have chosen a confidence score value of 0.33 as the default because
it gives a good compromise between accuracy and Call Rate, especially
when the 85% per sample filter is applied. In cases where you see a
lower Call Rate, you may wish to consider reanalyzing the data at the
more stringent confidence score (e.g., 0.26), which will decrease the
Call Rate for the sample, but may increase the accuracy of the
genotypes.
Data Clean Up
For many genotyping applications, loss of accuracy can result in a
significant decrease in genetic power. Genotyping errors can be caused
by SNPs that give systematic errors, or by sporadic errors that occur
due to stochastic, sample or experimental factors. SNPs that
systematically give errors (e.g., out of Hardy Weinberg equilibrium)
have been removed through a SNP selection process 1 . Overall the
accuracy has been shown to be approximately 99.5% on the Mapping
500K Array Set based upon internal data.
Prior to downstream analysis, the user should consider taking steps to
identify and eliminate sporadic genotype errors. Steps may include
eliminating SNPs out of Hardy Weinberg equilibrium in control
samples from the population, or eliminating genotypes showing
Mendel inconsistency or unlikely genotypes. GTYPE has
functionality to identify SNPs showing Mendelian or Hardy
Weinberg errors in user defined samples. These genotyping errors can
be filtered out upon data export. Please consult the GeneChip ®
Genotyping Analysis Software User’s Guide for more information.
1 Matsuzaki H., Dong S., Loi H., Di X., Liu G., Hubbell E., Law J., Berntsen T., Chadha M., Hui H., Yang G., Kennedy
G., Webster T., Cawley S., Walsh P., Jones K., Fodor S., Mei R. Genotyping over 100,000 SNPs on a pair of oligonucleotide
arrays. Nat Methods 1:109-111 (2004).
2 Di X., Matsuzaki H., Webster T.A., Hubbell E., Liu G., Dong S., Bartell D., Huang J., Chiles R., Yang G., Shen M.M.,
Kulp D., Kennedy G.C., Mei R., Jones K.W., Cawley S. Dynamic model based algorithms for screening and genotyping
over 100K SNPs on oligonucleotide microarrays. Bioinformatics 21:1958-63 (2005).
1 See SNP Selection Criteria for the GeneChip Human Mapping 10K Array Xba 131 Technical Note. A similar process
was used for the Mapping 500K SNP selection.