Title |
ClinSeK: a targeted variant characterization framework for clinical sequencing
|
---|---|
Published in |
Genome Medicine, March 2015
|
DOI | 10.1186/s13073-015-0155-1 |
Pubmed ID | |
Authors |
Wanding Zhou, Hao Zhao, Zechen Chong, Routbort J Mark, Agda K Eterovic, Funda Meric-Bernstam, Ken Chen |
Abstract |
Applying genomics to patient care demands sensitive, unambiguous and rapid characterization of a known set of clinically relevant variants in patients' samples, an objective substantially different from the standard discovery process, in which every base in every sequenced read must be examined. Further, the approach must be sufficiently robust as to be able to detect multiple and potentially rare variants from heterogeneous samples. To meet this critical objective, we developed a novel variant characterization framework, ClinSeK, which performs targeted analysis of relevant reads from high-throughput sequencing data. ClinSeK is designed for efficient targeted short read alignment and is capable of characterizing a wide spectrum of genetic variants from single nucleotide variation to large-scale genomic rearrangement breakpoints. Applying ClinSeK to over a thousand cancer patients demonstrated substantively better performance, in terms of accuracy, runtime and disk storage, for clinical applications than existing variant discovery tools. ClinSeK is freely available for academic use at http://bioinformatics.mdanderson.org/main/clinsek. |
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Geographical breakdown
Country | Count | As % |
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United States | 6 | 43% |
United Kingdom | 2 | 14% |
Germany | 1 | 7% |
Montenegro | 1 | 7% |
Unknown | 4 | 29% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 7 | 50% |
Scientists | 7 | 50% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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United States | 3 | 7% |
Sweden | 1 | 2% |
Unknown | 41 | 91% |
Demographic breakdown
Readers by professional status | Count | As % |
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Researcher | 13 | 29% |
Other | 7 | 16% |
Student > Ph. D. Student | 7 | 16% |
Student > Doctoral Student | 3 | 7% |
Student > Bachelor | 3 | 7% |
Other | 9 | 20% |
Unknown | 3 | 7% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 14 | 31% |
Biochemistry, Genetics and Molecular Biology | 11 | 24% |
Computer Science | 7 | 16% |
Medicine and Dentistry | 3 | 7% |
Engineering | 2 | 4% |
Other | 3 | 7% |
Unknown | 5 | 11% |