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

N. V. Feliz; Фелиз Н. В.; S. M. Yudin; Юдин С. М.; A. A. Keskinov; Кескинов А. А.; V. S. Yudin; Юдин В. С.; E. A. Snigir; Снигирь Е. А.; A. A. Mkrtchian; Мкртчян А. А.; Yu. N. Akhmerova; Ахмерова Ю. Н.; P. G. Kazakova; Казакова П. Г.; T. A. Shpakova; Шпакова Т. А.; M. V. Erokhina; Ерохина М. В.; E. D. Maralova; Маралова Е. Д.; K. D. Konureeva; Конуреева К. Д.; P. A. Grebnev; Гребнев П. А.; S. I. Mitrofanov; Митрофанов С. И.; K. S. Grammatikati; Грамматикати К. С.; V. I. Skvortsova; Скворцова В. И.

doi:10.31857/S0016675823060061

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

Authors: Feliz N.V.¹, Yudin S.M.¹, Keskinov A.A.¹, Yudin V.S.¹, Snigir E.A.¹, Mkrtchian A.A.¹, Akhmerova Y.N.¹, Kazakova P.G.¹, Shpakova T.A.¹, Erokhina M.V.¹, Maralova E.D.¹, Konureeva K.D.¹, Grebnev P.A.¹, Mitrofanov S.I.¹, Grammatikati K.S.¹, Skvortsova V.I.²
Affiliations:
1. Federal State Budgetary Insntitution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency
2. The Federal Medical Biological Agency
Issue: Vol 59, No 7 (2023)
Pages: 828-838
Section: МАТЕМАТИЧЕСКИЕ МОДЕЛИ И МЕТОДЫ
URL: https://journals.rcsi.science/0016-6758/article/view/134621
DOI: https://doi.org/10.31857/S0016675823060061
EDN: https://elibrary.ru/SSDAUO
ID: 134621

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Abstract
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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.

Keywords

whole genome sequencing, contamination, microarray BeadArray technology, quality control.

References

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