A comparative study of single nucleotide variant detection performance using three massively parallel sequencing methods.

Linea Christine Trudsø,Marie-Louise Kampmann,Clàudia Congost-Teixidor,Stine Bøttcher Jacobsen,Sofie Lindgren Christiansen,Jeppe Dyrberg Andersen,Niels Morling,Tomohiko Ai

doi:10.1371/journal.pone.0239850

Linea Christine Trudsø, Marie-Louise Kampmann + Show 6 more

Open Access

https://doi.org/10.1371/journal.pone.0239850

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Journal: PloS one	Publication Date: Sep 28, 2020
Citations: 11	License type: CC BY 4.0

Affiliation: University of Copenhagen, University of Barcelona

Abstract

Massively parallel sequencing (MPS) has revolutionised clinical genetics and research within human genetics by enabling the detection of variants in multiple genes in several samples at the same time. Today, multiple approaches for MPS of DNA are available, including targeted gene sequencing (TGS) panels, whole exome sequencing (WES), and whole genome sequencing (WGS). As MPS is becoming an integrated part of the work in genetic laboratories, it is important to investigate the variant detection performance of the various MPS methods. We compared the results of single nucleotide variant (SNV) detection of three MPS methods: WGS, WES, and HaloPlex target enrichment sequencing (HES) using matched DNA of 10 individuals. The detection performance was investigated in 100 genes associated with cardiomyopathies and channelopathies. The results showed that WGS overall performed better than those of WES and HES. WGS had a more uniform and widespread coverage of the investigated regions compared to WES and HES, which both had a right-skewed coverage distribution and difficulties in covering regions and genes with high GC-content. WGS and WES showed roughly the same high sensitivities for detection of SNVs, whereas HES showed a lower sensitivity due to a higher number of false negative results.

Highlights

Parallel sequencing (MPS) has revolutionised clinical genetics and the research within human genetics
We found that whole genome sequencing (WGS) covered the largest proportion of the investigated cardiac gene regions (S2 Table)
As expected due to the PCR-free workflow, WGS resulted in normally distributed coverages, whereas PCR amplifications with whole exome sequencing (WES) and HaloPlex target enrichment sequencing (HES) protocols resulted in right skewed coverage distributions (Fig 2)

Summary

Introduction

Parallel sequencing (MPS) has revolutionised clinical genetics and the research within human genetics. MPS has significantly reduced the cost of sequencing per base compared with traditional Sanger sequencing and made it possible to efficiently investigate a large number of genes in several samples at the same time. Multiple approaches for MPS of DNA are available today. These include e.g. targeted gene sequencing (TGS) panels [1,2,3], whole exome sequencing (WES) [4,5,6,7], and whole genome sequencing (WGS) [8,9,10,11].

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