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

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A comparative study of single nucleotide variant detection performance using three massively parallel sequencing methods. / Trudsø, Linea Christine; Andersen, Jeppe Dyrberg; Jacobsen, Stine Bøttcher; Christiansen, Sofie Lindgren; Congost-Teixidor, Clàudia; Kampmann, Marie-Louise; Morling, Niels.

In: PLoS ONE, Vol. 15, No. 9, e0239850, 2020.

Research output: Contribution to journalJournal articleResearchpeer-review

Harvard

Trudsø, LC, Andersen, JD, Jacobsen, SB, Christiansen, SL, Congost-Teixidor, C, Kampmann, M-L & Morling, N 2020, 'A comparative study of single nucleotide variant detection performance using three massively parallel sequencing methods', PLoS ONE, vol. 15, no. 9, e0239850. https://doi.org/10.1371/journal.pone.0239850

APA

Trudsø, L. C., Andersen, J. D., Jacobsen, S. B., Christiansen, S. L., Congost-Teixidor, C., Kampmann, M-L., & Morling, N. (2020). A comparative study of single nucleotide variant detection performance using three massively parallel sequencing methods. PLoS ONE, 15(9), [e0239850]. https://doi.org/10.1371/journal.pone.0239850

Vancouver

Trudsø LC, Andersen JD, Jacobsen SB, Christiansen SL, Congost-Teixidor C, Kampmann M-L et al. A comparative study of single nucleotide variant detection performance using three massively parallel sequencing methods. PLoS ONE. 2020;15(9). e0239850. https://doi.org/10.1371/journal.pone.0239850

Author

Trudsø, Linea Christine ; Andersen, Jeppe Dyrberg ; Jacobsen, Stine Bøttcher ; Christiansen, Sofie Lindgren ; Congost-Teixidor, Clàudia ; Kampmann, Marie-Louise ; Morling, Niels. / A comparative study of single nucleotide variant detection performance using three massively parallel sequencing methods. In: PLoS ONE. 2020 ; Vol. 15, No. 9.

Bibtex

@article{72b72c4b307b40da855849390beeee29,
title = "A comparative study of single nucleotide variant detection performance using three massively parallel sequencing methods",
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.",
keywords = "Alleles, Cardiomyopathies/genetics, Channelopathies/genetics, Exome, Genome, Human, Genotype, High-Throughput Nucleotide Sequencing/methods, Humans, Polymorphism, Single Nucleotide, Sensitivity and Specificity, Sequence Analysis, DNA/methods, Whole Exome Sequencing/methods",
author = "Truds{\o}, {Linea Christine} and Andersen, {Jeppe Dyrberg} and Jacobsen, {Stine B{\o}ttcher} and Christiansen, {Sofie Lindgren} and Cl{\`a}udia Congost-Teixidor and Marie-Louise Kampmann and Niels Morling",
year = "2020",
doi = "10.1371/journal.pone.0239850",
language = "English",
volume = "15",
journal = "P L o S One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "9",

}

RIS

TY - JOUR

T1 - A comparative study of single nucleotide variant detection performance using three massively parallel sequencing methods

AU - Trudsø, Linea Christine

AU - Andersen, Jeppe Dyrberg

AU - Jacobsen, Stine Bøttcher

AU - Christiansen, Sofie Lindgren

AU - Congost-Teixidor, Clàudia

AU - Kampmann, Marie-Louise

AU - Morling, Niels

PY - 2020

Y1 - 2020

N2 - 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.

AB - 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.

KW - Alleles

KW - Cardiomyopathies/genetics

KW - Channelopathies/genetics

KW - Exome

KW - Genome, Human

KW - Genotype

KW - High-Throughput Nucleotide Sequencing/methods

KW - Humans

KW - Polymorphism, Single Nucleotide

KW - Sensitivity and Specificity

KW - Sequence Analysis, DNA/methods

KW - Whole Exome Sequencing/methods

U2 - 10.1371/journal.pone.0239850

DO - 10.1371/journal.pone.0239850

M3 - Journal article

C2 - 32986766

VL - 15

JO - P L o S One

JF - P L o S One

SN - 1932-6203

IS - 9

M1 - e0239850

ER -

ID: 257872073