Benjamin Darbro
Benjamin Darbro

A project team led by Benjamin Darbro, M.D., Ph.D., director of the Shivanand R. Patil Cytogenetics and Molecular Laboratory at the University of Iowa Hospital and Clinics, has won the inaugural Appistry Pipeline Challenge for developing and executing a pipeline designed to reduce the costs and turnaround times associated with next-generation sequencing (NGS)-based genomics testing. The team has won a complete hardware and software system from Appistry valued at approximately $70,000.

The winning pipeline, Appistry says, will integrate the results of a concurrently run NGS assay and a SNP-containing chromosomal microarray (CMA) to calculate patient specific, genome-wide, NGS-performance metrics (e.g., sensitivity, specificity, positive and negative predictive value) for different types of genetic variations detectable by the CMA platform—performance metrics intended to alleviate the need for confirmatory assays using conventional Sanger sequencing.

Appistry adds that the proposed pipeline will leverage NGS analysis tools provided by the firm—specifically the Genome Analysis Toolkit—along with other tools and a tool developed by the Cytogenetics and Molecular Laboratory called CNV-ROC. The Appistry tools are included as part of Appistry’s Ayrris On Ramp Program for NGS Analysis, a program that includes a developer workstation that can process 200 gigabases per day, Ayrris® software for developing and executing NGS pipelines, and preconfigured analysis tools and starter pipelines. The company is also providing Dr. Darbro a MacBook Air or iPad Air to help facilitate his personal research.

Rich Mazzarella, Ph.D., Appistry CSO and chair of the judging panel for the Pipeline Challenge, said in a statement that the firm’s goal in sponsoring the challenge was to inspire and support innovation that could advance the utility and impact of NGS in clinical labs. “There is enormous promise in the pipeline proposed by Dr. Darbro, and we look forward to assisting in its development over the coming year,” he added.

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