ClinSeK: a targeted variant characterization framework for clinical sequencing.
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.
Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.
Wanding
W
Zhou
Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.
Hao
H
Zhao
Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.
Zechen
Z
Chong
Department of Hematopathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.
Routbort J
RJ
Mark
Department of Systems Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA ; Institute of Personalized Cancer Therapy, the University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.
Agda K
AK
Eterovic
Institute of Personalized Cancer Therapy, the University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA ; Department of Investigational Cancer Therapy, the University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.
Funda
F
Meric-Bernstam
Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.
Ken
K
Chen