Mapping 250K/500K SNP assay

Table 7.1
Dynamic Model Mapping Algorithm Report Components
Report Component Description
Total number of SNPs Number of SNPs on array.
Total number of QC Probes Number of QC SNPs on array.
Probe array type Affymetrix probe array model number.
chapter 7 | Analysis Workflow 187
SNP Performance A list of the analyzed samples, with the following
information:
Sample An identifier assigned to the analyzed samples.
Gender Gender of the sample determined by the DM algorithm.
SNP Call Rate Number of SNP calls/Total number of SNPs on the array.
AA Call Rate The number of AA calls for the sample/Total number of
SNPs on the array.
AB Call Rate The number of AB calls for the sample/Total number of
SNPs on the array.
BB Call Rate The number of BB calls for the sample/Total number of
SNPs on the array.
QC Performance A list of the analyzed samples, with the following
information:
Sample An identifier assigned to the analyzed samples.
Median PM
(QC Probe Set ID)
MCR
(DM Mapping only)
MDR
(DM Mapping only)
Common SNP Patterns
(DM Mapping only)
Median Intensity Value for perfect match cells for the QC
probe sets.
MPAM algorithm Call Rate. This is used to determine
whether a sample is contaminated.
MPAM algorithm Discrimination Rate. This is used to
determine whether a sample is contaminated.
Calls for a selected set of SNPs, displayed as a list of the
analyzed samples with the allele calls for the common
SNPs.