Lifesaving whole genome sequencing could bring HPC to our daily lives

The impact of HPC in our daily lives is usually abstract and “for the good of humanity”. For example, accurate weather forecasting is important for those working at sea and for those in charge of the supply chains of strawberries and umbrellas at Wimbledon. However, most of us can take it for granted along with the safety of our cars, the progression in Formula 1 and the search for the Higgs boson.

By contrast, whole genome sequencing (WGS) is an area that has the potential to touch certain individuals and measurably improve their lives in ways that can be quantified and predicted before anyone has allocated time on a supercomputer.

Netflix does WGS

A good example of what WGS can do for someone is evident in the first episode of the Netflix docudrama Diagnosis. The series follows the real-life efforts to crowdsource a diagnosis for patients with rare disorders. The doctor behind the initiative was a consultant on the TV show House MD and presented each case through her New York Times column.

Episode 1 of Diagnosis presents the case of 23-year-old female nursing student Angel, who is constantly struck down with extremely painful episodes. On a good day she can study and spend time with friends. On a bad day she doesn’t get out of bed and on really bad days is hospitalised with extreme breakdowns of muscle tissue that threaten the health of internal organs.

While many individuals reached out to Angel with theories, it was an Italian hospital in Turin that specialised in paediatric metabolic disorders that offered the best hope. When a blood test for the top 100 disorders showed no results, they deployed WGS to find an answer.

How WGS works

WGS for diagnostic purposes is a twofold process. First, it involves sequencing the genome to get a raw sequence of nucleotides that come in four flavours: A, T, G and C. The DNA sequence comes out of the machine in short segments of varying quality and the first job is to match those against a reference genome.

This jigsaw is complex, but now sequencing software is capable of processing samples that contain multiple species of DNA, from soil samples and other sources, the process is compute intensive and fairly well understood. However, the size of the samples and the weight of the problem means that small file sizes and I/O operations can be only traded off against memory consumption, so while advances in HPC hardware continue to help to bring the price down for WGS, it remains very much an HPC problem.

The second stage for WGS is to analyse the genome for known genetic diseases or mutations. This is another area that can be dependent on HPC.

WGS could come to you

WGS used to be prohibitively expensive, but organisations are now starting to offer a service for under $1,000 there, which significantly lowers the barrier to entry. Even a nursing student in medical debt can raise that money if it was sure to provide some form of relief from the burden of not knowing.

The Netflix show has a happy ever after feeling as, along with a diagnosis, Angel is given a way of managing her condition with a strict diet and has the go ahead to start living her life and planning for a family of her own. The same is not true for all of those with rare genetic diseases, but swift diagnosis of conditions that are not curable can prevent patents from undergoing unnecessary painful treatments and can save grieving families from often life-changing debt.

WGS has the potential to change all our lives through personalised medicine and customised treatment, even for those of us lucky to be born without a serious genetic disease. It is an important part of the battle against cancer, micro-biologic threats and many other diseases and yet another reason to continue to support HPC.