NEW YORK (GenomeWeb) – Appistry said today that it is partnering with Washington University in St. Louis to integrate VarScan — variant detection software developed at the university's McDonnell Genome Institute — with GenomePilot, its solution for next-generation sequence data analysis.
Appistry's GenomePilot provides clinical laboratories with preconfigured NGS analysis tools and pipelines that can be deployed on local and cloud-based infrastructures. Paul Carter, business development director at Wash U's Office of Technology and Management, said in a statement that adding VarScan to the list of GenomePilot tools makes it easier for clinical labs to use the software in their bioinformatics pipelines.
"By selecting Appistry's GenomePilot as a distribution platform for VarScan, we are able to focus our scientific team on developing and validating innovative functionality," he added.
VarScan identifies variants in targeted, exome, and whole-genome resequencing data from sequencing instruments made by Illumina, Life Technologies, and other companies. "[It] uses a heuristic approach for variant calling that overcomes problems related to extreme read depth, pooled samples, contaminated, or impure samples," Dan Koboldt, analysis manager at the McDonnell Genome Institute, explained in the statement. "Our comparisons, and those of independent groups, have shown that it outperforms other mutation callers, particularly for low frequency variants in high-depth ... samples."
One such comparison was done last year by researchers from the National Institutes of Health's National Human Genome Research Institute. In a study published in BMC Bioinformatics, NHGRI researchers compared five variant detection programs, including VarScan, to evaluate their ability to detect variants in synthetically pooled sequences generated from single-sample sequencing data. The authors looked at overall run times and memory usage, balanced accuracy, and sensitivity and specificity for detecting true variants in samples.
"VarScan has been a staple of our tumor-normal analysis pipelines since it was first validated," Benjamin Darbro, director of the Cytogenetics and Molecular Laboratory at the University of Iowa Hospitals and Clinics and an Appistry customer, said in a statement. Its addition to GenomePilot "enhances an already very comprehensive suite of tools, providing us even more confidence in our analysis of genomic scale sequencing data."
VarScan is available in the current release of GenomePilot.