Keep it clean - Do everything you can to remove proteins and keep the DNA from degrading, Scherer says. "Sample preparation is critical. All problems, in some way, can be tracked back to the quality of the DNA."
Double up - If your lab can afford it, run samples with two types of arrays. Lo was able to confirm some dodgy-looking BAC findings with higher-density arrays, he says. SNP arrays can provide good backup to oligonucleotide arrays, and for any genetic studies, notes Scherer, "having both the SNP info and the CNV info is really advantageous." If two platforms are out of your price range, consider SNP arrays to detect both SNPs and CNVs. Be wary, however, of their whole-genome amplifications of starting DNA, since not all regions amplify at the same rate.
Choose a gold standard - Always use a standard sample DNA sequence to compare results between experiments. ...
