Newport iServer MicroServer iTHX-M, Operator'S Manual, Page: 22 / 414

14
Affymetrix GeneChip
®
Genotyping Analysis Software User’s Guide
• Import attributes such as pedigree data for the sample
(see Importing Pedigree/Attribute Information, on page 185 ).
• Use the SNP data and imported pedigree data for Mendelian error
checking (see Checking for Mendelian Inheritance Error, on page 201 ).
• Check the data for incorrectly labeled samples and other problems
with the Sample Mismatch report tool. See Using the Sample
Mismatch Report Tool (see page 208) .
• Export the SNP data and imported pedigree data in formats that
association and linkage analysis software can use (see Exporting
Data with the SNP Export Tool, on page 226 ).
• Perform comparisons between samples for loss of heterozygosity
(see Loss of Heterozygosity Analysis, on page 247 ).
10K MAPPING ARRAY
The Affymetrix GeneChip
®
Human Mapping 10K Array provides an
efficient method for genotyping 10,000 SNPs in a single experiment.
Each SNP that can be detected with the array has a group of probes,
known as a probe set, on the array. The Modified Partitioning Around
Medoids (MPAM) algorithm is used to make genotype calls for the
GeneChip 10K Array.
MPAM ( Modified Partitioning Around Medoids) Algorithm
The MPAM mapping algorithm makes the allele call for a SNP by
comparing the signal intensity value from the SNP’s probe set with a
model of the intensity values for different allele calls of the SNP. This
model is created by analyzing the cell intensity data from many
different samples. For more information about the algorithm and the
model, see
Appendix B, MPAM Mapping Algorithm, on page 317 .
GTYPE_manual.book Page 14 Wednesday, August 2, 2006 11:31 AM