Contamination check

VerifyBamID2

If DNA from several people is mixed, variants are called wrongly and analyses become unreliable. A contamination check estimates the fraction of foreign DNA before further interpretation. Genome runs this quality control as its own step.

Why it comes first

Every statement about variants, HLA, pharmacogenetics or haplogroups assumes the sample comes from one person. An unnoticed mixture creates apparent heterozygosity and false findings. That is why the contamination check belongs at the start of the analysis.

How Genome analyses

Genome uses VerifyBamID2, which estimates the foreign-DNA fraction ancestry-agnostically from the reads and population allele frequencies. An elevated value is a warning flag for the interpretation of all further reports.

What Genome measures. The estimated fraction of foreign DNA in the sample as a quality metric, independent of the ancestry of the people involved.

Related topics

EBV sequence traces

Sources

  1. 1Zhang et al., 2020 Ancestry-agnostic estimation of DNA sample contamination from sequence reads (VerifyBamID2). Genome Research 30:185–194. doi.org/10.1101/gr.246934.118
  2. 2Jun et al., 2012 Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data. American Journal of Human Genetics 91:839–848. doi.org/10.1016/j.ajhg.2012.09.004