The Dynamic Model Mapping Algorithm - Newport iServer MicroServer iTHX-M Operator's Manual

The Dynamic Model Mapping Algorithm

Reference
.. .T A GG G GG TG A TT AT G AA C CT AC T AT TT A GG A .. .
Sequence
Probe
Sequences
Figure C.2
Offset interrogation positions
Seven offset position options are tested for the pairs of probe
quartet (-4, -2, -1, 0, +1, +3, +4). This results in fourteen probe
quartets being tested. Five offsets are chosen, selected to give the
best results for the particular SNP being tested by comparing their
performance across a selection of samples as a built-in redundancy
used to build confidence in a PM result. This results in ten probe
quartets being used.
The cells in a particular probe set are distributed on a 100K or 500K
mapping array set and may not be physically located next to each
other.
The Dynamic Model mapping algorithm is a likelihood model based
algorithm using Wilcoxon's signed-rank test
provides a genotype call for each SNP, along with quality information
for the call.
The Dynamic Model mapping algorithm compares the cell intensity
values for all the probe quartets for a SNP to the following models
(Figure C.3):
Appendix C | Dynamic Model Mapping Algorithm
SNP site
CC C CA C TA AT A CT TG G AT G AT AA A T
CCCCC ACTA ATAC T T GG A TG AT A AA
CCACT AATACT TGGAT GATAA ATCC
= changed base/interrogation position
offset
(see page 347). It
339
0
1
+2