The Impact of HPC (High Performance Computing) on Development in Genomics in Trends

TAIPEI, TAIWAN, Nov. 30, 2020 – High Performance Computing (HPC) is a term that refers to supercomputers that utilize a variety of performance enhancing hardware components to calculate massive quantities of data in a fraction of the time that it takes a regular computer to process. In the field of genomics sequencing, advancements within the field of HPC computing is one of, if not, the most crucial areas that will continue to change how scientists are able to utilize genomic data for research. Within the last two decades, the time in which it takes to sequence genomes has dropped from years, to weeks, to days and to hours as a result of HPC advancements. These speeds allow researchers to tackle some of the most critical areas of health such as combating viruses and cancer.

Until 2014, there were very few systems that enabled sequencing processing to the extent of “text mining”. The advancements in FPGA changed this dramatically. Field-Programmable Gate Arrays use easily configurable logic blocks arranged in an array to process data. When used in genomic sequencing, FPGA HPC supercomputers have the potential to sequence entire human genomes in less than a day. In comparison, the very first fully sequenced human genome took 13 years and millions of dollars to complete back in 2003 with the Human Genome Project. In a decade, new computing architectures have emerged to efficiently process genomic data, such as GPU or FPGA. The utilization of FPGA has considerably slashed those times and cost, making the entire venture significantly more viable within scientific research. Being able to fully sequence entire genomes allows for a staggering degree of potential within the scientific community. Especially, as recent times have taught us, viruses are difficult to predict and even more difficult to combat. But, faster genome sequencing can provide humanity with the tools we need to fight back and ultimately, save lives.


Another example of the impact of HPC computing on the field of genetics is its use in cancer research. On November 10th of this year, the Tokyo Medical and Dental University in collaboration with Fujitsu Laboratories managed to fully sequence genes that are related to cancer mutations in a matter of hours by using HPC supercomputing. This process would have taken months to parse through the 20 thousand genes they sequenced in order to find relationships between them and the development of cancer cells. This very recent example of the impact of supercomputing on the field of genetic research shows just how much HPC has had an impact on the field as a whole. It is making what was thought to be impossible, not only possible, but truly viable in the span of hours instead of in the span of years. Companies like our own here at WASAI look at these examples and see the impact our work can mean to saving lives and bettering humanity.


The scientific community has been developing genome toolkits as open source toolkits to aid in collaboration and the efficiency of data analysis, to assist scientists in the development of accelerated genomic research. Due to the mega amount of data clusters in genomics, three analytical stages take place in the HPC environment of a cluster or supercomputer, including genome assembly, variant analyses, and downstream bioinformatics. The first stage is to assemble DNA letters and information; the second is to compare different genes within different people; the third stage is to measure effects of variations on disease and its function. Compared to GPU, FPGA has an incomparable function for flexibility due to its ability to be easily configured to the needs of the user. Since each stage contains numerous calculations back and forth, the rewritable programming function of FPGA is far more efficient and costs less.


In conclusion, the importance of HPC on the field of genomics has increased. While multiple programming methods are in use, FPGA has an incomparable function in this field in terms of both computation and cost efficiency. This allows researchers to do things that could only be dreamed of in the past and will continue to shape the future.


References:

[1] Accelerating High Performance Computing (HPC) for Population-level Genomics


[2] Intel® Select Solutions for Genomics Analytics


[3] A REVIVAL IN CUSTOM HARDWARE FOR ACCELERATED GENOMICS


[4] Teaching HPC and genomics side-by-side


[5] Fujitsu and Tokyo Medical and Dental University Leverage Fugaku for Cancer Gene Analysis Milestone



#NextGenerationSequencing #LightningSolution #Genomics #GATK #BWA #PrecisionMedicine



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.

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WASAI Tecnology Inc.

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WASAI Technology Inc. specializes in Big Data acceleration platforms, provides expert patented solutions to key problems for large data centers with both high quality and performance.


Founded in 2015.

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