The Mpam Algorithm - Newport iServer MicroServer iTHX-M Operator's Manual

The MPAM 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 B.2
Offset interrogation positions
For each strand, there are seven offset position options for the probe
quartet pairs (-4, -2, -1, 0, +1, +3, +4). Five offsets are chosen,
selected to give the best results for the particular SNP being tested.
The cells in a particular probe set are distributed on the
mapping array and may not be physically located next to each
other.
GTYPE uses MPAM, a model-based algorithm, to determine which
allele is present at a particular SNP in the sample. Models of the RAS
values for each SNP and Genotype were developed by testing samples
from approximately 100 different individuals of different ethnicities
on the 10K mapping array (see
The MPAM mapping algorithm uses the following steps:
Evaluate specific and non-specific hybridization for a SNP's probe
1.
cells using the discrimination filter (see below).
Extract Median Relative Allele Signal (RAS) for Sense and
2.
Antisense directions for the SNP (see
Appendix B | MPAM 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
CC A CT AA T AC T TG GA T GA TA A AT C C
= changed base/interrogation position
Model Description, on page 325).
page 324).
321
offset
0
1
+2
10K