Mapping 250K/500K SNP assay

Introduction
This chapter describes the general requirements for genomic DNA
sources and extraction methods. The success of this assay requires the
amplification of PCR fragments between 200 and 1100 bp in size
throughout the genome. To achieve this, the genomic DNA must be
of high quality, and must be free of contaminants that would affect the
enzymatic reactions carried out.
A genomic DNA control (Reference Genomic DNA, 103) is provided
in both of the GeneChip ® Mapping 250K Assay Kits (Nsp and Sty).
This control DNA meets the requirements outlined below. The size of
the starting genomic DNA can be compared with Ref103 DNA to
assess the quality. The control DNA should also be used as a routine
experimental positive control and for troubleshooting.
Assay performance may vary for genomic DNA samples that do not
meet the general requirements outlined below. However, the
reliability of any given result should be assessed in the context of
overall experimental design and goals.
General Requirements for Human Genomic DNA
1. DNA must be double-stranded (not single-stranded). This
requirement relates to the restriction enzyme digestion step in the
protocol.
2. DNA must be free of PCR inhibitors. Examples of inhibitors
include high concentrations of heme (from blood) and high
concentrations of chelating agents (i.e., EDTA). The genomic
DNA extraction/purification method should render DNA that is
generally salt-free because high concentrations of certain salts can
also inhibit PCR and other enzyme reactions. DNA should be
prepared as described in Chapter 4, 96-Well Plate Protocol or
Appendix C, Low Throughput Protocol as appropriate.
3. DNA must not be contaminated with other human genomic DNA
sources, or with genomic DNA from other organisms. PCR
amplification of the ligated genomic DNA is not human specific,
so sufficient quantities of non-human DNA may also be amplified
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