Truth V2 Challenge on precisionFDA: Calling Variants in Difficult-to-Map Regions using short, long, and linked read sequencing

precisonFDA Truth Challenge

Four years ago, precisionFDA, in collaboration with The Genome in a Bottle (GIAB) Consortium led by the National Institute of Standards and Technology (NIST), successfully completed the Truth Challenge for human germline variant calling using a reference material HG002, also known as NA24385, the son of an Ashkenazi trio. This resulted in significant advances in variant calling accuracy, and enrichment of well-characterized benchmark datasets on precisionFDA with contributions from Illumina, Garvan, Macrogen, and NIST. The original challenge was timed such that a GIAB benchmark for reference material HG001 had been publicly released, but the benchmark for HG002, while complete, had not been made public. The HG002 benchmark was thus used as the blind truth set by which challenge submissions were graded based upon their results concordance with the HG002 benchmark produced by GIAB.

Recently, new long and linked read technologies and bioinformatics pipelines have enabled the characterization of increasingly challenging regions of the genome, such as an expanded benchmark developed by the GIAB for the parents of HG002 (HG003 and HG004). Another such propitious timing of benchmark releases has presented the opportunity for the Truth V2 Challenge,  focusing on variant calling in difficult-to-call genomic regions in GRCh38. While HG002 Benchmark V4.1 has been publicly released, the recently completed benchmarks for the parents of HG002, namely HG003 and HG004, have not yet been made public, and will be used as the blind truth set. This challenge aims to provide a common frame of reference for measuring performance aspects of participants’ pipelines on difficult-to-map regions, segmental duplications, and the Major Histocompatibility Complex.

precisionFDA Truth Challenge V2

Participants in the Truth V2 Challenge will be provided nine FASTQ files, three datasets for each of HG002, HG003, and HG004, produced by Illumina, PacBio HiFi, and Oxford Nanopore sequencing technologies. Participants will also be provided with the benchmark VCF and BED files for HG002 with which they can compare the results of their pipeline using the GA4GH Benchmark Comparator on precisionFDA. Submissions will include VCF files for HG002, HG003, and HG004, and the HG002 benchmark comparison results. Submissions will be graded on sensitivity and specificity independently and awards will be presented on precisionFDA for best concordance with the HG003 and HG004 Benchmarks which will be published simultaneously with the closing of the challenge.

The Truth V2 Challenge begins May 1, 2020 with a submission deadline of June 1, 2020. To pre-register for the challenge, visit our sign up!

Updated DNAnexus Impact Assessment for Cloudbleed: No evidence of exploitation.

As described in our February 27, 2017 blog post regarding the Cloudflare information leak (“Cloudbleed”), a  bug within the code running on Cloudflare edge servers was discovered by a Google security researcher.

Upon further investigation into the use of Cloudflare on DNAnexus we found, on February 27th at 2:39 PM PST, that contrary to what we had indicated in our blog post, HTTP requests to served by Cloudflare edge servers in some cases included session tokens with authentication information. We revoked all customer session tokens at 5:06 PM PST that same day, at which point all requests to DNAnexus required re-authentication. All existing tokens were unusable after this time.

On February 23rd Cloudflare provided their most recent update and stated that there was no evidence of exploitation; there have been no updates since that deviate from this information. Additionally, Cloudflare has completed analysis of edge server log data, and on March 3rd confirmed that was not found to have been impacted.

Our CDN usage design has been reviewed and we continue to believe no customer has been impacted by the incident. Any potential new exposure has been eliminated and there continues to be no evidence of exploitation.

We know how critical information security is to our customers so if you have any questions about your account, please do not hesitate to contact our customer support team at

DNAnexus Not Impacted by Cloudflare Information Leak (“Cloudbleed”)

A serious bug within the code running on Cloudflare edge servers may have leaked sensitive data from a large number of websites over many months. First, and most importantly, the DNAnexus Platform has not been impacted by this incident and no DNAnexus user data has been leaked.

Cloudflare provides Content Distribution Network (CDN) services, which enable providers of web content to enhance user experience by caching web content on edge servers geographically proximate to the web client. As part of a shared service, each edge server presents web content from multiple Cloudflare customers.

The bug led to a condition whereby the edge servers were returning content entirely unrelated to the requested web content, and that leaked content contained unencrypted private information such as HTTP cookies, authentication tokens, HTTP POST bodies, and other sensitive data. Search engines subsequently crawled and cached this leaked content, enabling it to be searched. For example, a web request to a ride sharing service could have resulted in leaked content being returned from a dating service.

DNAnexus uses the Cloudflare CDN service only to accelerate serving of public web content, such as web site images, help text, and html/css. DNAnexus does not serve any credentials, tokens, nor user data via the CDN and thus DNAnexus users are not impacted by this bug, and no DNAnexus user information has been leaked.

DNAnexus users do not need to change their DNAnexus password, unless they use similar passwords for other websites that were affected. We strongly recommend that users always choose a unique password for their DNAnexus account and that they configure their account to use two-factor authentication as described in the DNAnexus wiki documentation.

If you have any questions about your account, please contact our customer support team at