FDA is launching the fourth precisionFDA challenge to continue its support of the genomics community in assessing, comparing, and improving techniques used for Next Generation Sequencing (NGS) analysis. This challenge will provide a unique opportunity for test developers to investigate the accuracy of their pipelines by testing the ability to find in silico injected variants in FASTQ files from exome sequencing of reference cell lines. It will be a warm up for the community ahead of a more difficult in silico challenge to come in the fall.
The challenge begins with a precisionFDA-provided input dataset (FASTQ file), corresponding to whole exome sequencing of NA12878 modified with specific variants blinded to challenge participants. This challenge will focus on detection of SNVs and InDels, not structural or copy number variants. Your mission is to process this FASTQ dataset, completely independently with no prior comparison, through your mapping and variation calling pipeline to create a VCF file. You can generate those results in your own environment, and upload them to precisionFDA, or you can reconstruct your pipeline on precisionFDA.
After submissions close, the precisionFDA team will then run and publish comparative results between each contestant's submitted VCF files and the known reference truth set. This will challenge a pipeline's ability to detect previously unknown genetic variants. The challenge runs until September 12, 2017.
Top performers will be recognized by FDA and advance to the next level of the challenge. To learn more visit: https://precision.fda.gov/challenges/