Development of a Comprehensive Sequencing Assay for Inherited Cardiac Condition Genes
Author(s)
Type
Journal Article
Abstract
Inherited cardiac conditions (ICCs) are characterised
by marked genetic and allelic heterogeneity and require extensive
sequencing for genetic characterisation. We iteratively
optimised a targeted gene capture panel for ICCs that includes
disease-causing, putatively pathogenic, research and phenocopy
genes (n = 174 genes). We achieved high coverage of
the target region on both MiSeq (>99.8 % at ≥20× read depth,
n= 12) and NextSeq (>99.9 % at ≥20×, n= 48) platforms with
100 % sensitivity and precision for single nucleotide variants
and indels across the protein-coding target on the MiSeq. In the
final assay, 40 out of 43 established ICC genes informative in
clinical practice achieved complete coverage (100 % at ≥20×).
By comparison, whole exome sequencing (WES; ∼80×),
deep WES (∼500×) and whole genome sequencing
(WGS; ∼70×) had poorer performance (88.1, 99.2 and
99.3 % respectively at ≥20×) across the ICC target. The
assay described here delivers highly accurate and affordable
sequencing of ICC genes, complemented by accessible
cloud-based computation and informatics.
by marked genetic and allelic heterogeneity and require extensive
sequencing for genetic characterisation. We iteratively
optimised a targeted gene capture panel for ICCs that includes
disease-causing, putatively pathogenic, research and phenocopy
genes (n = 174 genes). We achieved high coverage of
the target region on both MiSeq (>99.8 % at ≥20× read depth,
n= 12) and NextSeq (>99.9 % at ≥20×, n= 48) platforms with
100 % sensitivity and precision for single nucleotide variants
and indels across the protein-coding target on the MiSeq. In the
final assay, 40 out of 43 established ICC genes informative in
clinical practice achieved complete coverage (100 % at ≥20×).
By comparison, whole exome sequencing (WES; ∼80×),
deep WES (∼500×) and whole genome sequencing
(WGS; ∼70×) had poorer performance (88.1, 99.2 and
99.3 % respectively at ≥20×) across the ICC target. The
assay described here delivers highly accurate and affordable
sequencing of ICC genes, complemented by accessible
cloud-based computation and informatics.
Date Issued
2016-02-17
Date Acceptance
2016-01-07
Citation
Journal of Cardiovascular Translational Research, 2016, 9 (1), pp.3-11
ISSN
1937-5395
Publisher
Springer Verlag (Germany)
Start Page
3
End Page
11
Journal / Book Title
Journal of Cardiovascular Translational Research
Volume
9
Issue
1
Copyright Statement
© The Author(s) 2016. This article is published with open access at Springerlink.com
License URL
Sponsor
British Heart Foundation
Wellcome Trust
Department of Health
Grant Number
SP/10/10/28431
HICF-R6-373
HICF-R6-373
Subjects
Science & Technology
Life Sciences & Biomedicine
Cardiac & Cardiovascular Systems
Medicine, Research & Experimental
Cardiovascular System & Cardiology
Research & Experimental Medicine
Inherited cardiac conditions
Targeted sequencing
Whole exome sequencing
Whole genome sequencing
Genetics
Diagnostics
DILATED CARDIOMYOPATHY
CLINICAL DIAGNOSTICS
ARRHYTHMIA SYNDROMES
CUSTOM AMPLISEQ
MUTATION
EXOME
SENSITIVITY
FRAMEWORK
VARIANTS
FEATURES
Publication Status
Published