Detection of low-level parental somatic mosaicism for clinically relevant SNVs and indels identified in a large exome sequencing dataset

Daniel D. Domogala, Tomasz Gambin, Roni Zemet, Chung Wah Wu, Katharina V. Schulze, Yaping Yang, Theresa A. Wilson, Ido Machol, Pengfei Liu, Paweł Stankiewicz*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Background: Due to the limitations of the current routine diagnostic methods, low-level somatic mosaicism with variant allele fraction (VAF) < 10% is often undetected in clinical settings. To date, only a few studies have attempted to analyze tissue distribution of low-level parental mosaicism in a large clinical exome sequencing (ES) cohort. Methods: Using a customized bioinformatics pipeline, we analyzed apparent de novo single-nucleotide variants or indels identified in the affected probands in ES trio data at Baylor Genetics clinical laboratories. Clinically relevant variants with VAFs between 30 and 70% in probands and lower than 10% in one parent were studied. DNA samples extracted from saliva, buccal cells, redrawn peripheral blood, urine, hair follicles, and nail, representing all three germ layers, were tested using PCR amplicon next-generation sequencing (amplicon NGS) and droplet digital PCR (ddPCR). Results: In a cohort of 592 clinical ES trios, we found 61 trios, each with one parent suspected of low-level mosaicism. In 21 parents, the variants were validated using amplicon NGS and seven of them by ddPCR in peripheral blood DNA samples. The parental VAFs in blood samples varied between 0.08 and 9%. The distribution of VAFs in additional tissues ranged from 0.03% in hair follicles to 9% in re-drawn peripheral blood. Conclusions: Our study illustrates the importance of analyzing ES data using sensitive computational and molecular methods for low-level parental somatic mosaicism for clinically relevant variants previously diagnosed in routine clinical diagnostics as apparent de novo.

Original languageEnglish
Article number72
JournalHuman Genomics
Volume15
Issue number1
DOIs
StatePublished - Dec 2021
Externally publishedYes

Funding

FundersFunder number
National Institutes of Health
National Institute of Child Health and Human DevelopmentR01HD087292
Eunice Kennedy Shriver National Institute of Child Health and Human Development

    Keywords

    • Clinical diagnostic testing
    • Mendelian genomics
    • Mosaicism carrier
    • Rare variants
    • Recurrence risk

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