Genomics to disrupt business as usual in the clinical laboratory

The discovery of the genetic code, with its unique signature for every living organism, has until recently had limited application in the routine clinical laboratory and for the man in the street. This is set to change as advances in genomics technology make it more accessible and public awareness of its benefits grows.

Looking at DNA is highly specialised, but technology improvements including automation, miniaturisation and cost reductions that occur with scalability have moved the utility of genetic information out of research and into mainstream clinical laboratories. Affordable, high-throughput genomic technologies enable rapid provision of results and expanded commercial platforms. This process is likely to accelerate, challenging the capacity of the clinical laboratories with new work processes and a requirement to store massive amounts of genomics data and maintain its integrity.

When the human genome project was completed in 2003, the next obvious question was ‘what can we do with this information?’ Finding the causes of some of the common hereditary diseases like cystic fibrosis was a logical starting point, but has since then been broadened to include many other common conditions. Research into various cancers and the push to find suitable treatments for other previously difficult-to-treat diseases has also been targeted for investigation. Preventative strategies like surgical removal of non-essential, cancer-prone tissue like breasts in familial risk groups have now become popular. So if it is written in our genes, we can now know and do something about it.

Genomics and personalised medicine

The interest in using genomics for personalised medicine has expanded rapidly and even health funders in some countries are joining the discussion, as they believe there is a cost-benefit to do the testing for preventative health before expensive curative medicine is required. The caveat is the ongoing ethical debate around who should have access to what information, the potential for discriminatory use and unintended consequences of knowing for the patient. Not surprisingly, there is also an increased sensitivity to and awareness of security in the population around genetic testing.

However, many of the everyday genomic tests that will increasingly be performed in clinical laboratories will analyse the genetic make-up of tumours, not patients. Laboratories will help to deliver personalised medicine by identifying a cancer tumour down to its genetic code so clinicians can target the most appropriate treatment. With genomic analysis, many tumours can already be sub-typed and matched to treatments yielding the best clinical outcomes, and research is ongoing for an ever-expanding range of cancers.

Genetic testing of pathogens

There is also the emergence of genetic testing of bacteria and other infectious organisms, with dramatic improvements in turnaround times. With genetic testing, traditional microbiology tests that take 48–72 hours can be reduced to hours so that prompt, targeted treatment can be assured. In the case of slow-growing tuberculosis bacteria, there has been a massive reduction in turnaround time as tests that used to take up to seven weeks are now performed in two hours through genomics.

As the pricing comes down for these tests, there will be a fundamental change in how pathology will deal with tumours, microbiology tests and even blood groups. DNA screening tests for an individual that used to cost hundreds of thousands of dollars are now approaching US$1000. And while genomic tests for cancers, for example, are still more expensive than this, the higher success rates they result in for treatment can make for a compelling cost-benefit analysis.

Advances in technology have made DNA sequencing platforms accessible to clinical laboratories that were once solely the preserve of high-tech research laboratories. Hospitals that used to send colonic tumours away to highly specialised labs are now asking, ‘why can’t we do that here?’ As medical care decisions become more precise and personal, laboratories will increasingly be required to provide genomic testing services and this will also influence their choice of information systems.

Laboratory systems challenges

The need to incorporate genetic information about an individual into their electronic medical record will no longer be a nice to have, but necessary to deliver a clinical service. Dealing with the data in a way that meets the exponential increase in demand for secure storage as well as ready accessibility for analysis is also challenging clinical laboratory information management systems, or LIMS.

Some of the key issues are already accommodated in current laboratory processes. These include security of patient demographics, accurate identification of tissue and specimens, long-term storage requirements of specimens and some analytics. But traditional LIMS were not designed to cope with the new bioinformatics demands for storage or analysis, for example, with a typical genomics test generating a file 30–70 MB in size.

Risk mitigation also requires traceability of all aspects of the process. Ensuring full auditability and adherence to standard operating procedures are crucial criteria for a laboratory management system. When laboratories perform a genetic test, you must retain evidence of who handles the sample at every point of processing, how it has been stored and the complex workflows. Many LIMS today will not handle that sort of complex requirement for chain of custody.

New breed of system required

Providing security of the information and allowing access to authorised healthcare workers via the electronic medical record (EMR) provides more complexity. All these considerations need to be part of any evaluation of new systems as legacy applications have not been designed to cope with this disruptive demand. This is necessitating a new breed of system, which InterSystems calls a laboratory business management system (LBMS).

Features of an LBMS required to fully support genomic testing in clinical laboratories include:

• support for connected care models, with a contiguous pathology patient record integrated within the electronic medical record, including genomic data;
• configuration and enforcement of standard operating procedures (SOPs), including sample preparation and chain of custody for genetic testing, with full auditability within the system;
• access to virtually unlimited amounts of low-cost data storage, while maintaining high levels of system performance, fully controlled and secured within the system;
• the ability to perform complex analytics on genomics data without the requirement to purchase or integrate with third-party solutions.

The nature of the laboratory business is changing dramatically and genetic testing is one of the major drivers. Genomics is becoming more prevalent, and its growth will accelerate as its diagnostic and therapeutic use become even more evident. As a result, the ways in which clinical laboratories have traditionally performed their work will change significantly over the next 2–5 years. While the pressure to deliver new services will intensify, advanced information technology solutions will let laboratory professionals be the drivers of change, not the victims.

*Gene Elliott is the Johannesburg-based Physician Executive for InterSystems in South Africa.

^Martin Wilkinson is the Sydney-based Director of Product Introduction, Strategy and User Adoption for InterSystems. Originally trained as a biomedical scientist in the United Kingdom, he is global head of the company’s solutions for the laboratory market.