Mapping 250K/500K SNP assay

CALL RATE
chapter 7 | Analysis Workflow 195
Call Rate is displayed in the Dynamic Mapping Algorithm report
(Figure 7.6) in the SNP Call column. It is an indicator of the overall
performance of the assay. Using the Reference Genomic DNA 103
sample as the standard, a Call Rate in excess of 93% at a confidence
score of 0.33 indicates that all steps, from restriction digestion
through scanning, worked as expected. A reduced Call Rate may result
if an error in any of the assay steps occurs or if lower quality DNA
samples are processed. It is also common to observe lower Call Rates
in circumstances where a new operator is learning the assay or the
number of samples processed at one time increases. In these later
examples, it may be prudent to budget time for additional practice for
the operator in order to increase proficiency with the assay and achieve
higher performance. Some other factors that can lead to a reduced Call
Rate include:
• Deviation from the assay protocol
• Contaminated DNA
• Expired reagents
• Inaccurate quantitation
For a sample with a lower Call Rate, it is important to take into
consideration the reasons for the lower Call Rate as well as the degree
to which accuracy is compromised. It may be necessary to repeat target
preparation for that sample depending on the degree to which the
lower Call Rate and decrease in accuracy affects the overall
experimental goals. Please refer to Chapter 8 for detailed
troubleshooting tips.