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Open AccessCommunication

Identification of Structural Variation from NGS-Based Non-Invasive Prenatal Testing

1
Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia
2
Geneton Ltd., 841 04 Bratislava, Slovakia
3
Comenius University Science Park, 841 04 Bratislava, Slovakia
4
Slovak Center of Scientific and Technical Information, 811 04 Bratislava, Slovakia
5
Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(18), 4403; https://doi.org/10.3390/ijms20184403
Received: 31 July 2019 / Revised: 3 September 2019 / Accepted: 4 September 2019 / Published: 7 September 2019
(This article belongs to the Special Issue Cell-Free Nucleic Acids)
Copy number variants (CNVs) are an important type of human genome variation, which play a significant role in evolution contribute to population diversity and human genetic diseases. In recent years, next generation sequencing has become a valuable tool for clinical diagnostics and to provide sensitive and accurate approaches for detecting CNVs. In our previous work, we described a non-invasive prenatal test (NIPT) based on low-coverage massively parallel whole-genome sequencing of total plasma DNA for detection of CNV aberrations ≥600 kbp. We reanalyzed NIPT genomic data from 5018 patients to evaluate CNV aberrations in the Slovak population. Our analysis of autosomal chromosomes identified 225 maternal CNVs (47 deletions; 178 duplications) ranging from 600 to 7820 kbp. According to the ClinVar database, 137 CNVs (60.89%) were fully overlapping with previously annotated variants, 66 CNVs (29.33%) were in partial overlap, and 22 CNVs (9.78%) did not overlap with any previously described variant. Identified variants were further classified with the AnnotSV method. In summary, we identified 129 likely benign variants, 13 variants of uncertain significance, and 83 likely pathogenic variants. In this study, we use NIPT as a valuable source of population specific data. Our results suggest the utility of genomic data from commercial CNV analysis test as background for a population study. View Full-Text
Keywords: copy number variants; next generation sequencing; non-invasive prenatal testing; population study copy number variants; next generation sequencing; non-invasive prenatal testing; population study
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Pös, O.; Budis, J.; Kubiritova, Z.; Kucharik, M.; Duris, F.; Radvanszky, J.; Szemes, T. Identification of Structural Variation from NGS-Based Non-Invasive Prenatal Testing. Int. J. Mol. Sci. 2019, 20, 4403.

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