Recommendations for whole genome sequencing in diagnostics for rare diseases

Erika Souche; Sergi Beltran; Erwin Brosens; John W Belmont; Magdalena Fossum; Olaf Riess; Christian Gilissen; Amin Ardeshirdavani; Gunnar Houge; Marielle van Gijn; Jill Clayton-Smith; Matthis Synofzik; Nicole de Leeuw; Zandra C Deans; Yasemin Dincer; Sebastian H Eck; Saskia van der Crabben; Meena Balasubramanian; Holm Graessner; Marc Sturm; Helen Firth; Alessandra Ferlini; Rima Nabbout; Elfride De Baere; Thomas Liehr; Milan Macek; Gert Matthijs; Hans Scheffer; Peter Bauer; Helger G Yntema; Marjan M Weiss

doi:10.1038/s41431-022-01113-x

Recommendations for whole genome sequencing in diagnostics for rare diseases

Erika Souche, Sergi Beltran, Erwin Brosens, John W Belmont, Magdalena Fossum, Olaf Riess, Christian Gilissen, Amin Ardeshirdavani, Gunnar Houge, Marielle van Gijn, Jill Clayton-Smith, Matthis Synofzik, Nicole de Leeuw, Zandra C Deans, Yasemin Dincer, Sebastian H Eck, Saskia van der Crabben, Meena Balasubramanian, Holm Graessner, Marc SturmHelen Firth, Alessandra Ferlini, Rima Nabbout, Elfride De Baere, Thomas Liehr, Milan Macek, Gert Matthijs, Hans Scheffer, Peter Bauer, Helger G Yntema, Marjan M Weiss

72 Citationer (Scopus)

Abstract

In 2016, guidelines for diagnostic Next Generation Sequencing (NGS) have been published by EuroGentest in order to assist laboratories in the implementation and accreditation of NGS in a diagnostic setting. These guidelines mainly focused on Whole Exome Sequencing (WES) and targeted (gene panels) sequencing detecting small germline variants (Single Nucleotide Variants (SNVs) and insertions/deletions (indels)). Since then, Whole Genome Sequencing (WGS) has been increasingly introduced in the diagnosis of rare diseases as WGS allows the simultaneous detection of SNVs, Structural Variants (SVs) and other types of variants such as repeat expansions. The use of WGS in diagnostics warrants the re-evaluation and update of previously published guidelines. This work was jointly initiated by EuroGentest and the Horizon2020 project Solve-RD. Statements from the 2016 guidelines have been reviewed in the context of WGS and updated where necessary. The aim of these recommendations is primarily to list the points to consider for clinical (laboratory) geneticists, bioinformaticians, and (non-)geneticists, to provide technical advice, aid clinical decision-making and the reporting of the results.

Originalsprog	Engelsk
Tidsskrift	European journal of human genetics : EJHG
Vol/bind	30
Udgave nummer	9
Sider (fra-til)	1017-1021
Antal sider	5
ISSN	1018-4813
DOI	https://doi.org/10.1038/s41431-022-01113-x
Status	Udgivet - sep. 2022

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Souche, E., Beltran, S., Brosens, E., Belmont, J. W., Fossum, M., Riess, O., Gilissen, C., Ardeshirdavani, A., Houge, G., van Gijn, M., Clayton-Smith, J., Synofzik, M., de Leeuw, N., Deans, Z. C., Dincer, Y., Eck, S. H., van der Crabben, S., Balasubramanian, M., Graessner, H., ... Weiss, M. M. (2022). Recommendations for whole genome sequencing in diagnostics for rare diseases. European journal of human genetics : EJHG, 30(9), 1017-1021. https://doi.org/10.1038/s41431-022-01113-x

Souche, E, Beltran, S, Brosens, E, Belmont, JW, Fossum, M, Riess, O, Gilissen, C, Ardeshirdavani, A, Houge, G, van Gijn, M, Clayton-Smith, J, Synofzik, M, de Leeuw, N, Deans, ZC, Dincer, Y, Eck, SH, van der Crabben, S, Balasubramanian, M, Graessner, H, Sturm, M, Firth, H, Ferlini, A, Nabbout, R, De Baere, E, Liehr, T, Macek, M, Matthijs, G, Scheffer, H, Bauer, P, Yntema, HG & Weiss, MM 2022, 'Recommendations for whole genome sequencing in diagnostics for rare diseases', European journal of human genetics : EJHG, bind 30, nr. 9, s. 1017-1021. https://doi.org/10.1038/s41431-022-01113-x

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abstract = "In 2016, guidelines for diagnostic Next Generation Sequencing (NGS) have been published by EuroGentest in order to assist laboratories in the implementation and accreditation of NGS in a diagnostic setting. These guidelines mainly focused on Whole Exome Sequencing (WES) and targeted (gene panels) sequencing detecting small germline variants (Single Nucleotide Variants (SNVs) and insertions/deletions (indels)). Since then, Whole Genome Sequencing (WGS) has been increasingly introduced in the diagnosis of rare diseases as WGS allows the simultaneous detection of SNVs, Structural Variants (SVs) and other types of variants such as repeat expansions. The use of WGS in diagnostics warrants the re-evaluation and update of previously published guidelines. This work was jointly initiated by EuroGentest and the Horizon2020 project Solve-RD. Statements from the 2016 guidelines have been reviewed in the context of WGS and updated where necessary. The aim of these recommendations is primarily to list the points to consider for clinical (laboratory) geneticists, bioinformaticians, and (non-)geneticists, to provide technical advice, aid clinical decision-making and the reporting of the results.",

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AU - Beltran, Sergi

AU - Brosens, Erwin

AU - Belmont, John W

AU - Fossum, Magdalena

AU - Riess, Olaf

AU - Gilissen, Christian

AU - Ardeshirdavani, Amin

AU - Houge, Gunnar

AU - van Gijn, Marielle

AU - Clayton-Smith, Jill

AU - Synofzik, Matthis

AU - de Leeuw, Nicole

AU - Deans, Zandra C

AU - Dincer, Yasemin

AU - Eck, Sebastian H

AU - van der Crabben, Saskia

AU - Balasubramanian, Meena

AU - Graessner, Holm

AU - Sturm, Marc

AU - Firth, Helen

AU - Ferlini, Alessandra

AU - Nabbout, Rima

AU - De Baere, Elfride

AU - Liehr, Thomas

AU - Macek, Milan

AU - Matthijs, Gert

AU - Scheffer, Hans

AU - Bauer, Peter

AU - Yntema, Helger G

AU - Weiss, Marjan M

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N2 - In 2016, guidelines for diagnostic Next Generation Sequencing (NGS) have been published by EuroGentest in order to assist laboratories in the implementation and accreditation of NGS in a diagnostic setting. These guidelines mainly focused on Whole Exome Sequencing (WES) and targeted (gene panels) sequencing detecting small germline variants (Single Nucleotide Variants (SNVs) and insertions/deletions (indels)). Since then, Whole Genome Sequencing (WGS) has been increasingly introduced in the diagnosis of rare diseases as WGS allows the simultaneous detection of SNVs, Structural Variants (SVs) and other types of variants such as repeat expansions. The use of WGS in diagnostics warrants the re-evaluation and update of previously published guidelines. This work was jointly initiated by EuroGentest and the Horizon2020 project Solve-RD. Statements from the 2016 guidelines have been reviewed in the context of WGS and updated where necessary. The aim of these recommendations is primarily to list the points to consider for clinical (laboratory) geneticists, bioinformaticians, and (non-)geneticists, to provide technical advice, aid clinical decision-making and the reporting of the results.

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KW - High-Throughput Nucleotide Sequencing/methods

KW - Humans

KW - Polymorphism, Single Nucleotide

KW - Rare Diseases/diagnosis

KW - Whole Genome Sequencing

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DO - 10.1038/s41431-022-01113-x

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JO - European journal of human genetics : EJHG

JF - European journal of human genetics : EJHG

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ER -

Recommendations for whole genome sequencing in diagnostics for rare diseases

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