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

Авторлар: 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
Мекемелер:
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
Шығарылым: Том 59, № 7 (2023)
Беттер: 828-838
Бөлім: МАТЕМАТИЧЕСКИЕ МОДЕЛИ И МЕТОДЫ
URL: https://cardiosomatics.ru/0016-6758/article/view/666834
DOI: https://doi.org/10.31857/S0016675823060061
EDN: https://elibrary.ru/SSDAUO
ID: 666834

Дәйексөз келтіру

Толық мәтін

Ашық рұқсат
Рұқсат жабық

Рұқсат берілді
Рұқсат жабық

Рұқсат ақылы немесе тек жазылушылар үшін

Аннотация
Авторлар туралы
Әдебиет тізімі
Қосымша файлдар
Статистика

Аннотация

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.

Негізгі сөздер

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

Әдебиет тізімі

Dallavilla T., Marceddu G., Casadei A. et al. A fast, reliable and easy method to detect within-species DNA contamination // Acta Bio-Medica Atenei Parm. 2020. V. 91. № 13-S. https://doi.org/10.23750/abm.v91i13-S.10531
Wang J., Raskin L., Samuels D.C. et al. Genome measures used for quality control are dependent on gene function and ancestry // Bioinformatics. 2015. V. 31. № 3. P. 318–323. https://doi.org/10.1093/bioinformatics/btu668
Javed N., Farjoun Y., Fennell T.J. et al. Detecting sample swaps in diverse NGS data types using linkage disequilibrium // Nat. Commun.2020. V. 11. № 1. P. 3697. https://doi.org/10.1038/s41467-020-17453-5
Miller N.A., Farrow E.G., Gibson M. et al. A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases // Genome Med. 2015. V. 7. № 1. P. 100. https://doi.org/10.1186/s13073-015-0221-8
Kim S., Scheffler K., Halpern A.L. et al. Strelka2: Fast and accurate calling of germline and somatic variants // Nat. Methods. 2018. V. 15. № 8. P. 591–594. https://doi.org/10.1038/s41592-018-0051-x
Danecek P., Bonfield J.K., Liddle J. et al. Twelve years of SAMtools and BCFtools // GigaScience. 2021. V. 10. № 2. https://doi.org/10.1093/gigascience/giab008
Zhao H., Sun Z., Wang J. et al. CrossMap: A versatile tool for coordinate conversion between genome assemblies // Bioinforma. Oxf. Engl. 2014. V. 30. № 7. P. 1006–1007. https://doi.org/10.1093/bioinformatics/btt730