Dataset Information

High positive predictive value of CNVs detected by clinical exome sequencing in suspected genetic diseases.

ABSTRACT:

Background

Genetic disorders often manifest as abnormal fetal or childhood development. Copy number variations (CNVs) represent a significant genetic mechanism underlying such disorders. Despite their importance, the effectiveness of clinical exome sequencing (CES) in detecting CNVs, particularly small ones, remains incompletely understood. We aimed to evaluate the detection of both large and small CNVs using CES in a substantial clinical cohort, including parent-offspring trios and proband only analysis.

Methods

We conducted a retrospective analysis of CES data from 2428 families, collected from 2018 to 2021. Detected CNV were categorized as large or small, and various validation techniques including chromosome microarray (CMA), Multiplex ligation-dependent probe amplification assay (MLPA), and/or PCR-based methods, were employed for cross-validation.

Results

Our CNV discovery pipeline identified 171 CNV events in 154 cases, resulting in an overall detection rate of 6.3%. Validation was performed on 113 CNVs from 103 cases to assess CES reliability. The overall concordance rate between CES and other validation methods was 88.49% (100/113). Specifically, CES demonstrated complete consistency in detecting large CNV. However, for small CNVs, consistency rates were 81.08% (30/37) for deletions and 73.91% (17/23) for duplications.

Conclusion

CES demonstrated high sensitivity and reliability in CNV detection. It emerges as an economical and dependable option for the clinical CNV detection in cases of developmental abnormalities, especially fetal structural abnormalities.

SUBMITTER: Zeng Y

PROVIDER: S-EPMC11234535 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature

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Publications

High positive predictive value of CNVs detected by clinical exome sequencing in suspected genetic diseases.

Zeng Yimo Y Ding Hongke H Wang Xingwang X Huang Yanlin Y Liu Ling L Du Li L Lu Jian J Wu Jing J Zeng Yukun Y Mai Mingqin M Zhu Juan J Yu Lihua L He Wei W Guo Fangfang F Peng Haishan H Yao Cuize C Qi Yiming Y Liu Yuan Y Li Fake F Yang Jiexia J Hu Rong R Liang Jie J Wang Jicheng J Wang Wei W Zhang Yan Y Yin Aihua A

Journal of translational medicine 20240709 1

<h4>Background</h4>Genetic disorders often manifest as abnormal fetal or childhood development. Copy number variations (CNVs) represent a significant genetic mechanism underlying such disorders. Despite their importance, the effectiveness of clinical exome sequencing (CES) in detecting CNVs, particularly small ones, remains incompletely understood. We aimed to evaluate the detection of both large and small CNVs using CES in a substantial clinical cohort, including parent-offspring trios and prob ...[more]

PMID: 38982507

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Dataset Information

High positive predictive value of CNVs detected by clinical exome sequencing in suspected genetic diseases.

Background

Methods

Results

Conclusion

Publications

High positive predictive value of CNVs detected by clinical exome sequencing in suspected genetic diseases.

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