Results
Title

Experimental Evaluation of the Possibility to Detect Cross-Contaminated DNA Samples Based on Genetic Data.

Authors

Feliz, N. V.; Grammatikati, K. S.; Mitrofanov, S. I.; Grebnev, P. A.; Konureeva, K. D.; Maralova, E. D.; Erokhina, M. V.; Shpakova, T. A.; Kazakova, P. G.; Akhmerova, Yu. N.; Mkrtchian, A. A.; Snigir, E. A.; Yudin, V. S.; Keskinov, A. A.; Yudin, S. M.; Skvortsova, V. I.

Abstract

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

Subjects

GENETIC variation; WHOLE genome sequencing; MICROARRAY technology; QUALITY control; SAMPLING errors

Publication

Russian Journal of Genetics, 2023, Vol 59, Issue 7, p719

ISSN

1022-7954

Publication type

Academic Journal

DOI

10.1134/S1022795423060066