I will be using Axiom Genome-wide Human Origins 1 array. Is there a way to tell whether a sample is contaminated with DNA from another sample during the extraction stage (for example, excessive heterozygous calls)? Is there a way to eliminate alleles of the contaminant from the data? What is the minimimum proportion of contaminating DNA which can be detected by most SNP arrays?
Hi Jae Joseph Russell Beltran Rodriguez
the best should be to take a look at the allele frequencies since possible contamination would give low allelic frequencies for the contaminant SNP. If you're not working on cancer samples (harboring some clones in whole sample with fluctuating MAF), you must therefore select a threshold and discard what you think to be a contaminant.
fred
Hi, dear
The best to take a look at the allele frequencies, because contamination would give low allelic frequencies.
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