Skip to main content
Premium Trial:

Request an Annual Quote

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.

The Scan

ChatGPT Does As Well As Humans Answering Genetics Questions, Study Finds

Researchers in the European Journal of Human Genetics had ChatGPT answer genetics-related questions, finding it was about 68 percent accurate, but sometimes gave different answers to the same question.

Sequencing Analysis Examines Gene Regulatory Networks of Honeybee Soldier, Forager Brains

Researchers in Nature Ecology & Evolution find gene regulatory network differences between soldiers and foragers, suggesting bees can take on either role.

Analysis of Ashkenazi Jewish Cohort Uncovers New Genetic Loci Linked to Alzheimer's Disease

The study in Alzheimer's & Dementia highlighted known genes, but also novel ones with biological ties to Alzheimer's disease.

Tara Pacific Expedition Project Team Finds High Diversity Within Coral Reef Microbiome

In papers appearing in Nature Communications and elsewhere, the team reports on findings from the two-year excursion examining coral reefs.