Genetics in Medicine Features Baylor Genetics for Assessing The Scale of Low-level Parental Mosaicism in Exome Sequencing (ES) Databases

Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions

Tomasz Gambin, Qian Liu, Justyna A. Karolak, Christopher M. Grochowski, Nina G. Xie BS, Lucia R. Wu, Yan Helen Yan, Ye Cao, Zeynep H. Coban Akdemir, Theresa A. Wilson, Shalini N. Jhangiani, Ed Chen, Christine M. Eng, Donna Muzny, Jennifer E. Posey, Yaping Yang, David Y. Zhang, Chad Shaw, Pengfei Liu, James R. Lupski, Paweł Stankiewicz

Published: July 13, 2020 

Abstract

Purpose

The goal of this study was to assess the scale of low-level parental mosaicism in exome sequencing (ES) databases.

Methods

We analyzed approximately 2000 family trio ES data sets from the Baylor-Hopkins Center for Mendelian Genomics (BHCMG) and Baylor Genetics (BG). Among apparent de novo single-nucleotide variants identified in the affected probands, we selected rare unique variants with variant allele fraction (VAF) between 30% and 70% in the probands and lower than 10% in one of the parents.

Results

Of 102 candidate mosaic variants validated using amplicon-based next-generation sequencing, droplet digital polymerase chain reaction, or blocker displacement amplification, 27 (26.4%) were confirmed to be low- (VAF between 1% and 10%) or very low (VAF <1%) level mosaic. Detection precision in parental samples with two or more alternate reads was 63.6% (BHCMG) and 43.6% (BG). In nine investigated individuals, we observed variability of mosaic ratios among blood, saliva, fibroblast, buccal, hair, and urine samples.

Conclusion

Our computational pipeline enables robust discrimination between true and false positive candidate mosaic variants and efficient detection of low-level mosaicism in ES samples. We confirm that the presence of two or more alternate reads in the parental sample is a reliable predictor of low-level parental somatic mosaicism.

Genetics in Medicine (2020) 

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