PrecisionFDA Announces Truth Challenge Winners

June 29, 2016

By Bio-IT World Staff

June 29, 2016 | PrecisionFDA announced the results of its Truth Challenge today. Entries from Verily Life Sciences, Kinghorn Center for Clinical Genomics, Sentieon, and Sanofi-Genzyme won top recognition. In addition to the winners, DNAnexus, Roche, Real Time Genomics, Qunitiles, Macrogen, the Broad Institute, and others participated.

The precisionFDA platform was built as a test bed for the analytical tools that process raw DNA sequence data into useful information. Launched last year, the platform includes gold standard “truth sets” of genomic data that users can try to replicate; compute environments for running analytical pipelines on large volumes of sequence data; and a venue to share workflows and results with the broader scientific community. While the platform is managed by the FDA, its development was contracted out to the private company DNAnexus.

The first precisionFDA challenge focused on mapping and variant calling. Rafael Aldana and his team from Sentieon were recognized for Best Performance and Highest Reproducibility, and Deepak Grover from Sanofi-Genzyme was rewarded for Highest Accuracy.

PrecisionFDA’s second challenge offered genomics community members the chance to identify genetic variants in one known and one unknown sample dataset using their choice of genetic pipeline. The Truth Challenge provided entrants with sequencing reads datasets (FASTQ files) for two human samples: HG001 and HG002. During the challenge, participants had access to truth data for the first sample, but not for sample HG002. Entrants had the opportunity to fine tune their pipeline against the known sample, before making predictions for the unknown sample. Upon the closing of the Truth Challenge, the Genome in a Bottle (GiaB) consortium, led by the National Institute of Standards (NIST), released the HG002 truth data, as well as an updated version of the HG001 truth data.

Grover from Sanofi-Genzyme added two awards to his collection. His entry was recognized for highest indel performance and highest indel recall. Hanying Feng et al. from Sentieon won for highest indel precision.

The same three awards were granting for single nucleotide polymorphisms. Highest SNP performance went to Ryan Poplin et al. from Verily Life Sciences; highest SNP recall went to the entry submitted by Brendan Gallagher at Sentieon; and highest SNP precision was given to Aaron Statham et al. from Kinghorn Center for Clinical Genomics.

The full datasets as well as methodologies and score are available at the precisionFDA site.