Decoding the human body with HPC.

What do human beings and the Universe have in common? They’re both incredibly complex and tough to figure out. 

Lucky for us, problem solving is embedded in our DNA. Rather than an outward exploration of the vast cosmos, 30 years ago  scientists turned inward and embarked on a voyage of discovery to sequence and map human genes – altogether known as the genome.

The Human Genome Project

2021 marks the 20th year since the first publication of the draft human genome sequence, under the Human Genome Project (HGP) launched back in 1990. Completed two years ahead of schedule, and at a cost less than the original estimated budget, this remarkable project gave us the ability, for the first time, to read nature’s complete genetic blueprint for building a human being. 

Upon publishing the results of the study, Francis Collin, then director of the National Human Genome Research Institute, noted that the genome can be envisioned as a “history book”. “It’s a narrative of the journey of our species through time. It’s a shop manual, with an incredibly detailed blueprint for building every human cell. And it’s a transformative textbook of medicine, with insights that will give health care providers immense new powers to treat, prevent and cure disease”

Transformative it was indeed. Still the largest collaborative biological project in history, we are constantly reaping the fruits of the HGP every day. It has allowed us to expand our horizons when it comes to understanding and innovating many avenues in biology, medicine and computation technology.

Wait, what? Computation technology?

What do genes have to do with computers?

The perfect combination of human and machine

While seemingly polar opposites, both fields of gene biology and data computing go together like bread and butter (yup, even bread is engulfed in the world of computing, check out this article). When the genome project unfolded, a revolution in computation took place simultaneously. Around Y2K, the internet was available, bandwidth was adequate to move genome data, and ample processing power was accessible. 

With the need to manage massive amounts of digital genome data, the rise of efficient data computing became instrumental in the success of the HGP.

Decoding genes with computer codes

In the present day, it is impossible to imagine decoding genes without using HPC, being one of the pillars supporting the realm of bioinformatics. Three out of four analysis stages in genomics take place in the HPC environment of a cluster or supercomputer. This has axed the time and cost required to sequence a partial or an entire genome, human or not. Today, genetic testing is ubiquitous and is typically doable in a matter of weeks.

What does that mean for the human race?

It enables researchers to map the genome of any individual to enable more precise medical treatment. Doctors can discover what medicine will work best on an individual patient. Physicians will have better, faster and more accurate resources to determine optimum treatment plans based on deep and broad databases of real-world genetic information. Chemists and biologists would be able to conduct more research ranging from boosting food production to helping us understand, diagnose, treat and cure a host of diseases including cancer. Early detection of various diseases such as breast cancer, colon cancer and Alzheimer’s is also possible.

Speaking of diseases, supercomputers are now being deployed in the battle against the SARS-CoV-2. With the end of the COVID-19 pandemic still not in sight, HPC might just be the light that we so desperately need at the end of the tunnel.

Editor’s note: if this article interested you, and you’d like to know more about HPC and its impact on bioinformatics research, register for our Data Science Week live discussion with Dr Elena Denisenko Research Associate at Harry Perkins Institute of Medical Science. Titled: “Data Science Evolution of HPC: The Cheetah is Changing its Spots”. 3pm-4pm May 13 at DUG’s Perth office. 

Main picture: An image celebrating the 20-year anniversary of publications reporting the draft human genome sequence. Photo credits: National Human Genome Research Institute.

 

By Mitchell Lim

Mitchell Lim is the latest addition to DUG’s science communication department. Currently completing his PhD in Chemical Engineering, Mitch is an expert in the fields of catalysis and ultrasonics. Full-time science geek, part-time fitness junkie, Mitch is living proof that brains and brawn are not mutually exclusive. His mission is to make science more accessible to you, while dreaming of having access to Martian land someday.

DUG