L-R: Joe Copty, Dr Mark Cowley, Aaron Statham and Dr Mark Pinese
06 July 2016
A team from the Kinghorn Centre for Clinical Genomics (KCCG; Garvan Institute of Medical Research) was a top performer in last week’s precisionFDA ‘Truth Challenge’, an online competition designed to test the performance of genome informatics pipelines worldwide. The team – including Dr Mark Cowley, Aaron Statham, Joe Copty and Dr Mark Pinese – received the award for highest “SNP Precision” and several other commendations.
In the Truth Challenge, participating teams were given the opportunity to test the performance of their institution’s genomics pipeline on an individual genome sequence that had not previously been analysed. The Challenge aimed to identify the sensitivity and precision of each pipeline in two key areas of genomic analysis:
- detecting single-nucleotide polymorphisms (SNPs; where the DNA sequence being studied differs from a reference sequence by one nucleotide (A, T, G or C) only)
- detecting insertions and deletions (where the DNA sequence being studied has an additional stretch of DNA code included, or is missing a section of DNA code, relative to the reference sequence).
Among the 36 entries received, Garvan’s KCCG team achieved the highest overall precision in detecting SNPs in the unknown genome. The team’s precision level of over 99.98% earned them the “SNP Precision” award. In addition, the team gained several commendations for both sensitivity and precision in detecting insertions and deletions.
Dr Mark Cowley (Team Leader, Translational Genomics), who led the team that developed this pipeline at Garvan, says, “We’re thrilled to have won this award because it shows that despite the complexity in decoding an entire human genome, we can now do this with extraordinary sensitivity and precision. We needed to demonstrate that our pipeline works on new samples that we had not seen before, reflecting the real world scenario where each patient’s genome is unique.”
“We entered the Truth Challenge as a way of seeing how we compared to other leaders in the field, and obtaining feedback in areas that we could improve our pipeline. For us, performing this well in the Truth Challenge gives us further confidence that whole genome sequencing is indeed ready for the clinic.”
The ‘Truth Challenge’ is an initiative of precisionFDA, the US Food and Drug Administration (FDA)’s data analysis platform for the international genomics community. PrecisionFDA was set up by the FDA as an online research and development portal, with the aim of enabling researchers to test and validate bioinformatic approaches to processing genomic datasets. DNAnexus provides the cloud-based genomic analysis platform that the Garvan team uses for clinical genomic analysis, as well as the precisionFDA platform.
Truth Challenge winners were announced at the Festival of Genomics in Boston, MA on 29 June.