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. 2021 Mar 10;2(1):100383.
doi: 10.1016/j.xpro.2021.100383. eCollection 2021 Mar 19.

Analysis workflow to assess de novo genetic variants from human whole-exome sequencing

Nicholas S Diab  1 , Spencer King  2   3 , Weilai Dong  1   4 , Garrett Allington  1 , Amar Sheth  5 , Samuel T Peters  2 , Kristopher T Kahle  5   6   7 , Sheng Chih Jin  2
Affiliations

Analysis workflow to assess de novo genetic variants from human whole-exome sequencing

Nicholas S Diab et al. STAR Protoc. .

Abstract

Here, we present a protocol to analyze de novo genetic variants derived from the whole-exome sequencing (WES) of proband-parent trios. We provide stepwise instructions for using existing pipelines to call de novo mutations (DNMs) and determine whether the observed number of such mutations is enriched relative to the expected number. This protocol may be extended to any human disease trio-based cohort. Cohort size is a limiting determinant to the discovery of high-confidence pathogenic DNMs. For complete details on the use and execution of this protocol, please refer to Dong et al. (2020).

Keywords: Bioinformatics; Genetics; Genomics; High-throughput screening; Sequence analysis; Sequencing.

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Conflict of interest statement

The authors declare no competing interests.

Figures

None
Graphical abstract
Figure 1
Figure 1
Example IGV plots for two DNM calls (A) A true-positive DNM in the gene GABRG1. (B) A false-positive DNM in the gene HTT. Color scheme: A is green, C is blue, G is brown, and T is red.
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References

    1. Dong W., Jin S.C., Allocco A., Zeng X., Sheth A.H., Panchagnula S., Castonguay A., Lorenzo L.É., Islam B., Brindle G. Exome sequencing implicates impaired GABA signaling and neuronal ion transport in trigeminal neuralgia. IScience. 2020;23:101552. - PMC - PubMed
    1. Homsy J., Zaidi S., Shen Y., Ware J.S., Samocha K.E., Karczewski K.J., DePalma S.R., McKean D., Wakimoto H., Gorham J. De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies. Science. 2015;350:1262–1266. doi: 10.1126/science.aac9396. - DOI - PMC - PubMed
    1. Jin S.C., Homsy J., Zaidi S., Lu Q., Morton S., DePalma S.R., Zeng X., Qi H., Chang W., Sierant M.C. Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nat. Genet. 2017;49:1593–1601. doi: 10.1038/ng.3970. - DOI - PMC - PubMed
    1. Kircher M., Witten D.M., Jain P., O'Roak B.J., Cooper G.M., Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat. Genet. 2014;46:310–315. - PMC - PubMed
    1. Lek M., Karczewski K.J., Minikel E.V., Samocha K.E., Banks E., Fennell T., O'DonnellLuria A.H., Ware J.S., Hill A.J., Cummings B.B. Analysis of proteincoding genetic variation in 60,706 humans. Nature. 2016;536:285–291. - PMC - PubMed

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