How laboratories can overcome the ‘big data’ challenge of genomics

The potential benefits to personalised medicine likely to be offered in the near future by genomics are huge. But to start realising them, laboratories need to overcome the challenge of ‘big data’ which could stop them embracing these new technologies, says Emma Huntridge of Clinisys.

It is hard to overstate the exciting pace of evolution in human genomics, despite being one of the most complex fields in modern healthcare. The first human genome was sequenced as recently as 2001, with a projected cost of $3 billion (£2.8 billion) over 15 years. Today, genomic tests can be carried out in a matter of weeks or months and have broken through the much anticipated £1,000 ceiling – a critical threshold that has allowed DNA sequencing to move out of the research laboratory and to be deployed at a greater scale to improve all manner of clinical outcomes.

Indeed, genomics has real potential to usher in a new era of personalised medicine, improving patient outcomes with individual risk information about major life-threatening diseases such as cancer, heart disease and obesity, as well as propensity to having certain adverse drug reactions.

However, while this burgeoning field has traversed a pivotal tipping point, laboratories’ ability to decode the vast amounts of information being produced from sequencing DNA is still catching up. Realising the many benefits and applications of genomics, therefore, does not hinge on any new scientific breakthroughs; but rather on innovation in the systems and processes laboratories use to process genetic results and data.

Unlocking the big data of genomics

The extraordinary complexity of the human genome means that the field is on track to become one of the biggest data producers on the planet. Each sequenced genome takes up 200 gigabytes – the size of some hard drives – and by some estimates would need an estimated 40 exabytes (an exabyte is a billion gigabytes) to store the data generated worldwide by 2025. This even rivals YouTube, the largest data consumer today.

Yet, many genomic laboratories still operate using spreadsheets and paper-based processes for handling results and data. By contrast, intelligent informatics systems have been used in other many other clinical diagnostic tests such as pathology and microbiology to help streamline workflows and order management for some time. Partially this is due to clinical use-cases for DNA sequencing only recently reaching a critical level of scale. But there is also a valid concern that traditional laboratory information systems are not fit for purpose to handle the complexities of a genomic testing environment.

Genomic laboratories need to change, however, and should look to adopt best-in-breed solutions that can provide bespoke solutions across the entire genomic spectrum, from conventional and molecular cytogenetics to molecular and tumour genetics. They should also be able to support new technologies such as next generation sequencing, which enables DNA to be fragmented into millions of pieces in parallel while improving speed and accuracy while reducing the cost. These customised solutions provide laboratories with the scalability that comes with greater automation, without the compromises of off-the-shelf solutions. Meanwhile, highly specialised tools can help interpret results, including generating maps of family relationship and genetic traits, as well as flexible reports and analytics dashboards for enhanced visibility.

Linking to electronic patient records to enable precision medicine

The other missing piece in the puzzle is ensuring effective storage and management to enable data from laboratories to flow through into electronic patient records to be called upon by clinicians when needed. This really helps drive the shift to precision medicine. This looks at all the factors that shape an individual’s health, from their genes to their environment and lifestyle. This allows doctors and clinicians to deploy the right treatments and preventative measures that are best suited for that individual.

Initiatives such as the NHS’ Genomic Medicine Service are really helping to drive this movement forward, which since 2018 has centralised genomic patient records and test ordering in the UK through seven Genomic Laboratory Hubs (GLH), each responsible for coordinating genetic testing services within their regional Genomic Medicine Service. Yet, this only works by having the underlying technology in place to join up all care providers in the network.

This means that software processing genomic data cannot just be a laboratory system used by laboratory staff. It needs to plug directly into hospitals’ electronic data systems to help clinicians working directly with patients to order tests electronically and manage their patients’ genomic records.

This is key as clinicians need to consider numerous types of patient data collated from different sources to consider whether a genomic test is suitable for a patient. These include factors such as a patient’s family history, medical record, phenotype and genotype-phenotype relationships. This is key to considering whether a genomic test is suitable for a patient. We may soon move to a future of personalised and precision medicine where everyone is screened from birth and this genetic data can be called upon when needed to address their health at each stage of life. However, the preponderance of data that will result from offering DNA sequencing to everyone at a national level requires the technology infrastructure that can transform laboratory workflows, and then connect them with clinicians to allow the real potential and benefits of genomics to be felt by end patients.