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Next PrecisionFDA Challenge Takes on Indel Calling from Oncopanel Sequencing Data

NEW YORK – The US Food and Drug Administration is preparing to open the next PrecisionFDA challenge, one looking at indel calling from oncopanel sequencing data.

The PrecisionFDA program is working with the FDA's National Center for Toxicological Research (NCTR) to challenge the bioinformatics community to develop, validate, benchmark, and optimize indel calling pipelines from data produced by the SEQC2 Oncopanel Sequencing Working Group. The working group is part of a six-year-old FDA effort called Sequencing Quality Control Phase 2 (SEQC2) to develop standard analysis protocols and quality control metrics regarding next-generation sequencing data to support regulatory science research and precision medicine.

NCTR will provide two unique oncopanel sequencing datasets as FASTQ and BED files, the latter for describing the targeted regions of each panel. Participants will then be asked to create pipelines optimized for either or both datasets. The submission period will run from May 2 through July 8.

An optional second phase, involving a third oncopanel sequencing dataset for first-phase participants to validate their pipelines, is scheduled for July 11-26.

"Given that indels have not been studied as much as single nucleotide variants (SNVs), it is important that the tools for indel calling be rigorously evaluated and optimized," the PrecisionFDA program said on its website.

NCTR and PrecisionFDA are taking preregistrations now. Winners will be announced in late August.