Mapping 250K/500K SNP assay

28 GeneChip ® Mapping 500K Assay Manual
and could potentially result in compromised genotype calls.
Contaminated or mixed DNA may manifest as high detection rates
and low call rates.
4. DNA must not be highly degraded. For any particular SNP, the
genomic DNA fragment containing the SNP must have Nsp I (or
Sty I) restriction sites intact so that ligation can occur on both ends
of the fragment and PCR can be successful. The approximate
average size of genomic DNA may be assessed on a 1% or 2%
agarose gel using an appropriate size standard control. Reference
Genomic DNA 103 can be run on the same gel for side-by-side
comparison. High quality genomic DNA will run as a major band
at approximately 10-20 kb on the gel; assay performance may vary
with DNA that is substantially more degraded.
5. Pre-amplified genomic DNA has been tested with the Human
Mapping 500K Assay and found to give results comparable to the
standard DNA preparation methods. The Repli-G ® Kit (a Φ29
whole genome amplification kit; QIAGEN) was used to amplify
10 ng genomic DNA, and the amplified products were
immediately used in the subsequent protocol steps. This DNA
gave call rates between 96 and 98% (Nsp) and 95 and 98% (Sty),
and concordance greater than 99%. Other pre-amplification
methods or pre-digestion with restriction enzymes other than
Nsp I or Sty I have not been tested by Affymetrix. If these other
methods are desired, it is recommended that the user conduct
experiments to evaluate these other methods with the Mapping
500K Assay.