Journal Article

Understanding genetic variability: exploring large-scale copy number variants through non-invasive prenatal testing in European populations

Budis, Jaroslav, Kucharik, Marcel, Minarik, Gabriel, Hyblova, Michaela, Holesova, Zuzana, Gazdarica, Juraj, Szemes, Tomas, Pös, Ondrej

2024

Overview

Large-scale copy number variants (CNVs) are structural alterations in the genome that involve the duplication or deletion of DNA segments, contributing to genetic diversity and playing a crucial role in the evolution and development of various diseases and disorders, as they can lead to the dosage imbalance of one or more genes. Massively parallel sequencing (MPS) has revolutionized the field of genetic analysis and contributed significantly to routine clinical diagnosis and screening. It offers a precise method for detecting CNVs with exceptional accuracy. In this context, a non-invasive prenatal test (NIPT) based on the sequencing of cell-free DNA (cfDNA) from pregnant women’s plasma using a low-coverage whole genome MPS (WGS) approach represents a valuable source for population studies. Here, we analyzed genomic data of 12,732 pregnant women from the Slovak (9,230), Czech (1,583), and Hungarian (1,919) populations. We identified 5,062 CNVs ranging from 200 kbp and described their basic characteristics and differences between the subject populations. Our results suggest that re-analysis of sequencing data from routine WGS assays has the potential to obtain large-scale CNV population frequencies, which are not well known and may provide valuable information to support the classification and interpretation of this type of genetic variation. Furthermore, this could contribute to expanding knowledge about the central European genome without investing in additional laboratory work, as NIPTs are a relatively widely used screening method.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Accuracy / Analysis / Animal Genetics and Genomics / Biomedical and Life Sciences / Cell-Free Nucleic Acids / Chromosomes / Copy number / Copy number variation / Data analysis / Deoxyribonucleic acid / Developmental biology / DNA / DNA Copy Number Variations / DNA sequencing / Evolution / Female / Gene sequencing / Genes / Genetic analysis / Genetic aspects / Genetic diversity / Genetic research / Genetic Testing / Genetic variability / Genetic variation / Genomes / Genomics / Genomics - methods / Health aspects / Humans / Laboratories / Large-scale CNV frequency comparison / Life Sciences / Microarrays / Microbial Genetics and Genomics / Non-invasive prenatal testing / Nucleotide sequencing / Plant Genetics and Genomics / Plasma / Population studies / Population study / Populations / Pregnancy / Pregnant women / Prenatal diagnosis / Prenatal Diagnosis - methods / Proteomics / Whole genome sequencing / Whole Genome Sequencing - methods / Womens health