Quantification of offspring DNA contamination by a sibling. (A) GroupB single nucleotide polymorphisms (SNPs) are used for quantifying siblings’ DNA contamination in the DNA mixture. SNP variants are shown as stars; each bar represents a chromosome in the diploid genome. In the DNA mixture, the sibling's fraction is z, and the other offspring's fraction is 1−z. Meiotic recombination in one of the offspring's chromosomes is shown with alternating chromosome colors. Four possible SNP combinations between the offspring and the sibling (contamination) and their variant allele frequencies (VAFs) are shown on the right. (B) A density plot of GroupB SNP VAFs in a sample without contamination (offspring 100%) is shown. (C) A density plot of GroupB SNP VAFs in an offspring with 25% contamination from the sibling is shown. Additional peaks are shown with solid arrows. An additional peak near VAF = 0.5 is merged with the nearby heterozygous VAF = 0.5, which appears as one left-shifted peak. (D) True contaminated value versus estimated value for TrioMix (black circle), VerifyBamID2 (blue square), and GATK4 CalculateContamination (green triangle) for in silico simulated DNA contamination with sibling's DNA. Estimated values below 10−2.5 are shown on the plot's x-axis.
