Mapping 250K/500K SNP assay

Introduction to Laboratory Setup
Please read this chapter before planning any experiments.
The GeneChip ® Human Mapping 500K Array Set has been optimized
to reliably and accurately detect greater than 500,000 SNPs in each
sample. The assay reduces the complexity of the genome by
preferentially amplifying approximately 200-1100 base pair (bp)
Nsp I fragments and approximately 200-1100 bp Sty I fragments
using a single PCR primer from only 250 ng DNA per restriction
enzyme. As with all genotyping applications, care should be taken to
minimize possible sources of contamination that would reduce
genotyping accuracy, call rate, and consequently, genetic power.
To reduce the possibility of cross-contamination, Affymetrix
recommends maintaining a single direction workflow.
The GeneChip ® Human Mapping 250K Nsp assay and the
GeneChip ® Human Mapping 250K Sty assay should be performed
separately to avoid sample mix up.
The most likely potential source of contamination for the
GeneChip ® Mapping 500K Assay is previously amplified PCR
product.
Maintain an ambient laboratory environment throughout the
procedure.
Steps should be taken to minimize the possibility of contaminating
pre-PCR steps with amplified PCR product. Suggested precautions
include:
• Store reagents in proper room according to the box label and manual
instructions.
• Restrict movements through labs containing amplified DNA.
• Use proper gowning procedures.
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