Application of Restriction Site-Associated DNA Sequencing (RAD-Seq) for Copy Number Variation and Triploidy Detection in Human
Autor: | Xiao-yan Ma, Jian-Chun He, Qing Li, Wen-zhi He, Min-Cong Zhang, Bo Liang, Qin Xia, Guo-Xin Ye, Jia-jia Xian, Yan-Chao Wang, Shao-ying Li |
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Rok vydání: | 2021 |
Předmět: |
DNA Copy Number Variations
Restriction Mapping Aneuploidy Biology DNA sequencing Cell Line Genetics medicine Humans Copy-number variation Molecular Biology Allele frequency reproductive and urinary physiology Genetics (clinical) Whole genome sequencing Whole Genome Sequencing fungi High-Throughput Nucleotide Sequencing food and beverages Sequence Analysis DNA medicine.disease Triploidy genomic DNA Restriction site STR analysis |
Zdroj: | Cytogenetic and Genome Research. 161:406-413 |
ISSN: | 1424-859X 1424-8581 |
Popis: | At present, low-pass whole-genome sequencing (WGS) is frequently used in clinical research and in the screening of copy number variations (CNVs). However, there are still some challenges in the detection of triploids. Restriction site-associated DNA sequencing (RAD-Seq) technology is a reduced-representation genome sequencing technology developed based on next-generation sequencing. Here, we verified whether RAD-Seq could be employed to detect CNVs and triploids. In this study, genomic DNA of 11 samples was extracted employing a routine method and used to build libraries. Five cell lines of known karyotypes and 6 triploid abortion tissue samples were included for RAD-Seq testing. The triploid samples were confirmed by STR analysis and also tested by low-pass WGS. The accuracy and efficiency of detecting CNVs and triploids by RAD-Seq were then assessed, compared with low-pass WGS. In our results, RAD-Seq detected 11 out of 11 (100%) chromosomal abnormalities, including 4 deletions and 1 aneuploidy in the purchased cell lines and all triploid samples. By contrast, these triploids were missed by low-pass WGS. Furthermore, RAD-Seq showed a higher resolution and more accurate allele frequency in the detection of triploids than low-pass WGS. Our study shows that, compared with low-pass WGS, RAD-Seq has relatively higher accuracy in CNV detection at a similar cost and is capable of identifying triploids. Therefore, the application of this technique in medical genetics has a significant potential value. |
Databáze: | OpenAIRE |
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