Abstract
The problems of cross-contamination and swap samples are extremely relevant during large-scale genetic studies. In this study several approaches of detecting cross-contaminated DNA samples were checked: the ratio of reads per reference and alternative allele (allele ratio, AR), the amount of heterozygos to homozygous variants ratio, the CallRate value for the DNA microarrays data, the Picard CrosscheckFingerprints (CrossCheck) program. Contaminated samples (mixtures) were created by mixing ordinary “pure” DNA samples in different ratios. Samples’ quality parameters were analyzed after whole genome sequencing and genotyping with the Illumina microarray BeadArray technology CoreExome (CE) DNA microarray. It has been experimentally established that all of these approaches can be used to detect genotyping errors associated with sample contamination.
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