Low-coverage genome sequencing for the detection of clinically relevant copy-number and mtDNA variants

Abstract

Background: Compared to exome sequencing, genome sequencing is widely appreciated for its superior ability to detect a wide range of genetic variations including copy-number variants (CNVs) and mitochondrial (mtDNA) variants. We assessed whether low-coverage genome sequencing, a considerably cheaper approach, would detect clinically relevant CNVs and mtDNA variants and would thus be a cost-efficient supplement to exome sequencing in rare disease diagnostics. Methods: To assess the level of sequencing depth needed for variant detection, first, 30x mean coverage genome sequencing data were subsampled to 0.5x, 1x, 2x, and 4x coverage files in silico followed by CNV and mtDNA detection. Based on the analysis, 2x short-read sequencing was selected to be performed in 16 patients with putatively pathogenic CNVs or mtDNA variants to assess the empirical sensitivity. Results: For CNV calling, 2x coverage was sufficient to detect all heterozygous CNVs greater than 10kb in size from in silico subsampled data. In experimental data, the results were similar, although a 16kb heterozygous deletion was once not detected. Regarding mtDNA variants, 2x coverage sufficed for variant confident variant calling and heteroplasmy assessment for all samples. Conclusions: Low-coverage genome sequencing may be used to complement exome sequencing for simultaneous mtDNA variant and CNV detection.

Competing Interest Statement

The authors have declared no competing interest.

Funding Statement

This study was supported by European Regional Development Fund and the program Mobilitas Pluss grant MOBTP175. KO, TK, KTO, and MT received support from the Estonian Research Council grants PRG471 and PUT355. The high coverage genome sequencing used for methods development was provided by the Broad Institute of MIT and Harvard Center for Mendelian Genomics (Broad CMG) and was funded by the National Human Genome Research Institute, the National Eye Institute, and the National Heart, Lung and Blood Institute grant UM1 HG008900 and in part by National Human Genome Research Institute grant R01 HG009141.

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I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

Research Ethics Committee of the University of Tartu gave ethical approval for this work (approval date 11/18/2018 and number 287M-15, and 19/10/2020 327T-3).

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Data Availability

All data produced in the present study are available upon reasonable request to the authors.

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