Thailand’s biobank powers up genomic sequencing

Tasked to drive genomic medicine in thailand, the National Biobank of Thailand (NBT) has added a NVIDIA DGX A100 system and NVIDIA Clara Parabricks sequencing analysis software to accelerate its genomic sequencing research.

In 2019, the research institution was entrusted by the government to design and implement the IT infrastructure for the Genomics Thailand (GeTH) project which aims to introduce genomic medicine as a common medical service.

One of the GeTH’s flagship projects involves extracting genetic variations from 50,000 Thai volunteers’ whole genome sequencing (GeTH50K) data.

GeTH 50K harbours variants distributed across the entire human genome which are extremely useful in population genetics.

But, the biggest challenge is the sheer size of whole genome sequencing (WGS) data. The sequence data for an individual’s genome contains more than 100GB that must be sequentially aligned to a human genome reference to identify potential variants of the individual. This process results in an extra 100GB in total of more than 200GB per sample.

Identification of variant, called variant calling, is the required process in genomics medicine. Accurate and rapid processing of WGS data makes it possible for patients to be treated with precise and personalised care, improving quality of life by reducing hospital visits and associated costs.

Here’s where the parallel processing power of GPUs dramatically accelerates the variant calling process from WGS data. NVIDIA DGX A100 enables NBT to consolidate training, inference, and analytics into a unified AI infrastructure.

NBT also uses the NVIDIA Clara Parabricks computational pipelines, which support several genomics applications. Employing NVIDIA’s CUDA, HPC, AI and data analytics stacks, Clara Parabricks Pipelines empower researchers to build GPU-accelerated libraries, pipelines, and reference application workflows for primary, secondary and tertiary analysis. The complete portfolio of off-the-shelf solutions is coupled with a toolkit to support new application development to address the rapidly evolving needs of high throughput genomic labs.

“The accelerated solution from NVIDIA lets us carry out the WGS variant discovery process efficiently and with high confidence. By pairing NVIDIA DGX A100 with NVIDIA Clara Parabricks, we have been able to reduce our WGS data processing by four months. Processing time per individual user has also been shortened from more than 30 hours to just one to two hours,” said Sissades Tongsima, Director of NBT.