Mapping 250K/500K SNP assay

Sources of Human Genomic DNA
chapter 3 | Genomic DNA General Requirements 29
The following sources of human genomic DNA have been successfully
tested in the laboratories at Affymetrix for DNA that meets the
requirements described in the section General Requirements for Human
Genomic DNA on page 27.
• blood
• cell line
Success with other types of samples such as formalin-fixed paraffinembedded
tissue will depend on quality (degree of degradation, degree
of inhibitors present, etc.), quantity of genomic DNA extracted, and
purity of these types of samples, as described in the section General
Requirements for Human Genomic DNA on page 27.
Genomic DNA Extraction/Purification Methods
DNA Cleanup
Genomic DNA extraction and purification methods that meet the
general requirements for genomic DNA outlined above should yield
successful results. Methods that include boiling or strong denaturants
are not acceptable, because the DNA would be rendered singlestranded.
Genomic DNA extracted using the following methods have
been tested at Affymetrix:
1. SDS/ProK digestion, phenol-chloroform extraction, Microcon ® or
Centricon ® (Millipore) ultrapurification and concentration.
2. QIAGEN; QIAamp ® DNA Blood Maxi Kit.
If a genomic DNA preparation is suspected to contain inhibitors, the
following cleanup procedure can be used:
1. Add 0.5 volumes of 7.5 M NH4OAc, 2.5 volumes of absolute
ethanol (stored at –20°C), and 0.5 µL of glycogen (5 mg/mL) to
250 ng genomic DNA.
2. Vortex and incubate at –20°C for 1 hour.
3. Centrifuge at 12,000 x g in a microcentrifuge at room temperature
for 20 minutes.