Title |
Development of a Comprehensive Sequencing Assay for Inherited Cardiac Condition Genes
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Published in |
Journal of Cardiovascular Translational Research, February 2016
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DOI | 10.1007/s12265-016-9673-5 |
Pubmed ID | |
Authors |
Chee Jian Pua, Jaydutt Bhalshankar, Kui Miao, Roddy Walsh, Shibu John, Shi Qi Lim, Kingsley Chow, Rachel Buchan, Bee Yong Soh, Pei Min Lio, Jaclyn Lim, Sebastian Schafer, Jing Quan Lim, Patrick Tan, Nicola Whiffin, Paul J. Barton, James S. Ware, Stuart A. Cook |
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. See Editorial in this issue (DOI: 10.1007/s12265-015-9667-8 ). |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United Kingdom | 12 | 24% |
United States | 7 | 14% |
Netherlands | 3 | 6% |
Saudi Arabia | 1 | 2% |
India | 1 | 2% |
Austria | 1 | 2% |
France | 1 | 2% |
Germany | 1 | 2% |
Australia | 1 | 2% |
Other | 0 | 0% |
Unknown | 22 | 44% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 34 | 68% |
Scientists | 9 | 18% |
Practitioners (doctors, other healthcare professionals) | 4 | 8% |
Science communicators (journalists, bloggers, editors) | 3 | 6% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 1 | <1% |
Unknown | 118 | 99% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 24 | 20% |
Student > Ph. D. Student | 22 | 18% |
Student > Bachelor | 15 | 13% |
Other | 13 | 11% |
Student > Master | 11 | 9% |
Other | 20 | 17% |
Unknown | 14 | 12% |
Readers by discipline | Count | As % |
---|---|---|
Medicine and Dentistry | 33 | 28% |
Biochemistry, Genetics and Molecular Biology | 29 | 24% |
Agricultural and Biological Sciences | 25 | 21% |
Engineering | 3 | 3% |
Computer Science | 2 | 2% |
Other | 12 | 10% |
Unknown | 15 | 13% |