Mapping 250K/500K SNP assay

Assessing Data Quality
194 GeneChip ® Mapping 500K Assay Manual
The purpose of this section is to help researchers establish guidelines
for evaluating results generated from Mapping experiments. The
Mapping Algorithm Report in GTYPE has a number of parameters
that must be checked for each array in order to assess the quality of the
data, and to identify outlier samples (Table 7.2). It is important to
check these parameters, and to create a running log for each project.
The Reference Genomic DNA 103, included in the GeneChip ®
Mapping 250K Assay Kits can serve as a positive control to ensure that
all steps of the assay are being performed correctly.
Table 7.2
Dynamic Model Mapping Algorithm Report Metrics
Metric Description
Call Rate (SNP Call) Good first pass evaluation. If the genomic DNA
sample is of equivalent quality and purity to the
Reference Genomic DNA 103, then the Call Rate
should be similar when analyzed at the same
algorithm settings.
Reference Genomic DNA
103 Call rate
Process control to show that assay steps are
being performed correctly.
MDR – MCR Difference can be used to identify sample
contamination.
Shared SNPs Evaluate possible sample mix ups.
Oligonucleotide controls Help evaluate hybridization, fluidics and
scanning steps.
Evaluation of a particular sample should be based on the examination
of all samples and array performance metrics.