Newport iServer MicroServer iTHX-M Operator's Manual page 331

Evaluating Discrimination Scores
Having calculated the individual discrimination scores for the probe
pairs, the algorithm evaluates these scores to determine if the SNP
passes the detection filter:
The median discrimination scores are calculated for the forward
1.
and reverse strands for the A and B alleles:
DS(s,A) = median of the allele A sense strand probe pair
discrimination scores
DS(t,A) = median of the allele A antisense strand probe pair
discrimination scores
DS(s,B) = median of the allele B sense strand probe pair
discrimination scores
DS(t,B) = median of the allele B antisense strand probe pair
discrimination scores
The algorithm uses these median values to calculate a
2.
discrimination score for the SNP:
DSsnp =max [min [DS(s,A), DS(t,A)], min [DS(s,B), DS(t,B)]]
Where:
DSsnp = Discrimination score for the SNP
The algorithm evaluates the SNP discrimination score.
3.
When DSsnp > a predetermined threshold value, the SNP passes
the detection filter. Relative allele signal (RAS) scores are
calculated for the sense and antisense strands (see
used to calculate the call zone scores for the sample and make an
allele call for the SNP (see
If the SNP doesn't pass the discrimination filter, no call is given
for the SNP and the SNP call is not displayed in the Scatter Plot.
The Call Zone score for the SNP is set to 10 and the RAS scores for
the SNP are set to -2.
The Discrimination Score threshold can be adjusted by the user (see
MPAM Mapping Algorithm Settings, on page 331
Appendix B | MPAM Mapping Algorithm
page 325).
323
page 324) and
).