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Next generation diagnostics in inherited arrhythmia syndromes

Next generation diagnostics in inherited arrhythmia syndromes
Next generation diagnostics in inherited arrhythmia syndromes
Next-generation sequencing (NGS) provides an unprecedented opportunity to assess genetic variation underlying human disease. Here, we compared two NGS approaches for diagnostic sequencing in inherited arrhythmia syndromes. We compared PCR-based target enrichment and long-read sequencing (PCR-LR) with in-solution hybridization-based enrichment and short-read sequencing (Hyb-SR). The PCR-LR assay comprehensively assessed five long-QT genes routinely sequenced in diagnostic laboratories and "hot spots" in RYR2. The Hyb-SR assay targeted 49 genes, including those in the PCR-LR assay. The sensitivity for detection of control variants did not differ between approaches. In both assays, the major limitation was upstream target capture, particular in regions of extreme GC content. These initial experiences with NGS cardiovascular diagnostics achieved up to 89 % sensitivity at a fraction of current costs. In the next iteration of these assays we anticipate sensitivity above 97 % for all LQT genes. NGS assays will soon replace conventional sequencing for LQT diagnostics and molecular pathology
1937-5387
94-103
Ware, James S.
6e99bb22-caf5-489e-aa0a-27c1423a671e
John, Shibu
1fcbc011-2c50-42c6-aaf9-c01ada61373d
Roberts, Angharad M.
ff1e5c2c-db47-4224-9cbc-4dce0e57db43
Buchan, Rachel
ac625c05-2021-43db-bbd9-99695e176e18
Gong, Sungsam
b9faa19b-de03-432d-aceb-332476f770c3
Peters, Nicholas S.
94adcc5b-d577-4738-9bf8-98aa5a48b680
Robinson, David O.
9db1b26b-6c2b-4ac5-879e-20f8a2dc30ec
Lucassen, Anneke
2eb85efc-c6e8-4c3f-b963-0290f6c038a5
Behr, Elijah R.
0892c29b-6fed-41c9-ae16-3010859006f9
Cook, Stuart A.
2c9730f9-0c9b-4d81-a32b-2fa1180b8153
Ware, James S.
6e99bb22-caf5-489e-aa0a-27c1423a671e
John, Shibu
1fcbc011-2c50-42c6-aaf9-c01ada61373d
Roberts, Angharad M.
ff1e5c2c-db47-4224-9cbc-4dce0e57db43
Buchan, Rachel
ac625c05-2021-43db-bbd9-99695e176e18
Gong, Sungsam
b9faa19b-de03-432d-aceb-332476f770c3
Peters, Nicholas S.
94adcc5b-d577-4738-9bf8-98aa5a48b680
Robinson, David O.
9db1b26b-6c2b-4ac5-879e-20f8a2dc30ec
Lucassen, Anneke
2eb85efc-c6e8-4c3f-b963-0290f6c038a5
Behr, Elijah R.
0892c29b-6fed-41c9-ae16-3010859006f9
Cook, Stuart A.
2c9730f9-0c9b-4d81-a32b-2fa1180b8153

Ware, James S., John, Shibu, Roberts, Angharad M., Buchan, Rachel, Gong, Sungsam, Peters, Nicholas S., Robinson, David O., Lucassen, Anneke, Behr, Elijah R. and Cook, Stuart A. (2013) Next generation diagnostics in inherited arrhythmia syndromes. Journal of Cardiovascular Translational Research, 6 (1), 94-103. (doi:10.1007/s12265-012-9401-8). (PMID:22956155)

Record type: Article

Abstract

Next-generation sequencing (NGS) provides an unprecedented opportunity to assess genetic variation underlying human disease. Here, we compared two NGS approaches for diagnostic sequencing in inherited arrhythmia syndromes. We compared PCR-based target enrichment and long-read sequencing (PCR-LR) with in-solution hybridization-based enrichment and short-read sequencing (Hyb-SR). The PCR-LR assay comprehensively assessed five long-QT genes routinely sequenced in diagnostic laboratories and "hot spots" in RYR2. The Hyb-SR assay targeted 49 genes, including those in the PCR-LR assay. The sensitivity for detection of control variants did not differ between approaches. In both assays, the major limitation was upstream target capture, particular in regions of extreme GC content. These initial experiences with NGS cardiovascular diagnostics achieved up to 89 % sensitivity at a fraction of current costs. In the next iteration of these assays we anticipate sensitivity above 97 % for all LQT genes. NGS assays will soon replace conventional sequencing for LQT diagnostics and molecular pathology

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More information

Accepted/In Press date: 7 September 2012
Published date: February 2013
Organisations: Cancer Sciences, Human Development & Health

Identifiers

Local EPrints ID: 342782
URI: http://eprints.soton.ac.uk/id/eprint/342782
ISSN: 1937-5387
PURE UUID: 8c3afd7a-99ca-468a-a89d-8469284d575d
ORCID for Anneke Lucassen: ORCID iD orcid.org/0000-0003-3324-4338

Catalogue record

Date deposited: 13 Sep 2012 11:47
Last modified: 23 Jul 2022 01:49

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Contributors

Author: James S. Ware
Author: Shibu John
Author: Angharad M. Roberts
Author: Rachel Buchan
Author: Sungsam Gong
Author: Nicholas S. Peters
Author: David O. Robinson
Author: Anneke Lucassen ORCID iD
Author: Elijah R. Behr
Author: Stuart A. Cook

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