Highlights of PrecisionFDA Truth Challenge V2 and WASAI’s participation

TAIPEI, TAIWAN, Jun.30, 2022 - The publication of PrecisionFDA Truth Challenge V2 is finally out on Cell Genomics[1], two years after the challenge began. The challenge was aimed to evaluate the state of the art of variant calling in challenging genomic regions. Twenty organizations participated in the challenge by submitting variants called results for Illumina, PacBio HiFi, and/or Oxford Nanopore Technologies FASTQ datasets.

WASAI is honored to be one of the participants and joined the publishing of the results of our variant calling pipelines from the on-premise solution Lightning™ with the FPGA acceleration for BWA+GATK for small variants on short-read sequencing data.

The Genome-in-a-Bottle small variant benchmark also released v4.2.1[2] along with the publication of the challenge using long and linked reads for seven GIAB samples HG001~007. The challenge submissions were evaluated with these new GIAB benchmark sets and new genome stratifications and differed in performance and in challenging genomic regions, including difficult-to-map regions, segmental duplications, and the Major Histocompatibility Complex (MHC).

Resource: https://precision.fda.gov/challenges/10

As part of this challenge, WASAI demonstrated overall precision of 99.16% for INDEL and 99.01% for SNP on all benchmark regions with our FPGA acceleration of BWA+GATK. The genomics revolution has come to an analytics-driven era, and WASAI is here with the researchers and clinicians to face the challenge of managing exponentially-growing data with our comprehensive bioinformatics solution.


[1] PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

[2] Benchmarking challenging small variants with linked and long reads

About WASAI Technology Inc.

WASAI Technology's mission is to deliver acceleration technologies of High-Performance Data Analysis (HPDA) in future data centers for targeted vertical applications with massive volumes and high velocities of scientific data. To strengthen and advance scientific discovery and technological research via big data-intensive acceleration in high-performance computing, WASAI Technology aims to improve commercialization and commoditization of scientific and technological applications.


WASAI Tecnology Inc.

4F, No. 6, Zhiyuan 3rd Rd., Beitou Dist., Taipei 112025, Taiwan