1THE BIOMEDICAL SCIENTIST REPRINTED FROM APRIL 2016

INFORMATION TECHNOLOGY

Discovery of the genetic code, with itsunique signature for each living organism,has until recently had limited application in the routine clinical laboratory and littleimpact on the man in the street. However,this is set to change as advances ingenomics technology make it moreaccessible and as public awareness of itsbenefits grows.

Looking at DNA is highly specialised but technological advances includingautomation, miniaturisation and the costreductions that occur with scalability havemoved the utility of genetic information out of research and into mainstream clinicallaboratories. Affordable high-throughputgenomic technologies enable rapid provision of results and expandedcommercial platforms. This process islikely to accelerate, challenging the capacityof the clinical laboratories with new workprocesses and a requirement to storemassive amounts of genomics data andmaintain their integrity.

When the Human Genome Project wascompleted in 2003, the next obviousquestion was “what can we do with thisinformation?” Finding the causes of somecommon hereditary diseases (eg cysticfibrosis) was a logical starting point, but thishas since been broadened to include manyother common conditions. Research intovarious cancers and the push to find suitabletreatments for other previously difficult-to-treat diseases has also been targeted forinvestigation. Preventative strategies such as the surgical removal of non-essential,cancer-prone tissue (eg breast tissue) in

Genomics and its impact on information technology in the clinical laboratory

As the genomics age gathers pace, implementation of

advanced business management systems will ensure that

laboratory professionals across the breadth of pathology

remain firmly in the driving seat, as Gene Elliott explains.

are joining the discussion, as they believethere is a cost-benefit to testing forpreventative health before expensivecurative medicine is required. The caveat isthe ongoing ethical debate around whoshould have access to what information, the potential for discriminatory use, and theunintended consequences of knowing forthe patient. Not surprisingly, there is also an increased sensitivity to, and an awarenessof, security in the population in relation togenetic testing.

However, many of the everyday genomictests performed increasingly in clinicallaboratories will analyse the genetic make-upof tumours, not patients. Laboratories willhelp to deliver personalised medicine byidentifying a cancer down to its genetic code,

familial risk groups has now become popular.So, if it is written in our genes, we can nowknow and do something about it.

Genomics and personalised medicineThe interest in using genomics forpersonalised medicine has expanded rapidlyand even health funders in some countries

Infiltrating ductal breast cancer (immunocytochemistry for carcinoembryonic antigen). Preventative strategies suchas the surgical removal of cancer-prone tissue, such as breast, in familial risk groups has now become popular.

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‘Automation, miniaturisation and the cost reductions that occur

with scalability have moved the utility of genetic information out

of research and into mainstream clinical laboratories’

INFORMATION TECHNOLOGY

2 REPRINTED FROM APRIL 2016 THE BIOMEDICAL SCIENTIST

so clinicians can target the most appropriatetreatment. Using genomic analysis, manytumours can now be subtyped and matchedto treatments that yield the best clinicaloutcomes, and research is ongoing for anever-expanding range of cancers.

Genetic testing for pathogensThere is also the emergence of genetictesting of bacteria and other infectiousagents, with dramatic improvements inturnaround times. With genetic testing,traditional microbiology tests that take 48–72 hours can be reduced to hours so that prompt, targeted treatment can beassured. In the case of slow-growingmycobacterial organisms, there has been a massive reduction in turnaround time astests that used to take up to seven weeks are now performed through genomics in two hours.

As testing costs come down, there will be a fundamental change in how pathologydeals with tumours, microbiology tests, andeven blood grouping. DNA screening testsfor an individual that used to cost hundredsof thousands of dollars is now approachingUS$1000. And while genomic tests forcancers, for example, are still moreexpensive than this, the higher success rates of treatment can result in a compellingcost-benefit analysis.

Advances in technology have made DNA sequencing platforms, once solely the preserve of research departments,accessible to routine clinical laboratories.Hospitals that used to send colonic tumours away to specialised laboratories are now asking “why can’t we do that here?” As medical care decisions become moreprecise and personal, laboratoriesincreasingly will be required to providegenomic testing services, and this will also influence their choice of informationsystems.

Laboratory systems challengesThe need to incorporate genetic informationabout an individual into their electronicmedical record (EMR) will no longer simplybe nice to have, but necessary to deliver aclinical service. Dealing with the data in away that meets the exponential increase indemand for secure storage as well as readyaccessibility for analysis is also challengingclinical laboratory information managementsystems (LIMS).

Some of the key issues are alreadyaccommodated in current laboratory

processes, including security of patientdemographics, accurate identification oftissue and specimens, long-term storagerequirements of specimens, and someanalytics. However, traditional LIMS were not designed to cope with the newbioinformatics demands for storage oranalysis, as a typical genomics test cangenerate a file 30–70 megabytes in size.

Risk mitigation also requires traceabilityof all aspects of the process. Ensuring fullaudit ability and adherence to standardoperating procedures (SOPs) are crucialcriteria for a laboratory management system. When laboratories perform agenetics test, it must retain evidence of who handles the sample at every point ofprocessing, how it has been stored, and the complex workflows. Many current LIMS will not handle this type of complexrequirement for chain of custody.

New breed of system requiredProviding security of information andallowing access by authorised healthcareworkers via the EMR provides morecomplexity. All these considerations need tobe part of any evaluation of new systems aslegacy applications have not been designedto cope with this disruptive demand. This necessitates a new breed of system,termed a laboratory business managementsystem (LBMS; InterSystems). Features ofan LBMS required to support genomicstesting in clinical laboratories include:• support for connected care models, with

a contiguous pathology patient recordintegrated within the EMR, includinggenomics data

• configuration and enforcement of SOPs,

including sample preparation and chainof custody for genetics testing, with fullaudit ability within the system

• access to virtually unlimited amounts oflow-cost data storage, while maintaininghigh levels of system performance, fullycontrolled and secured within the system

• ability to perform complex analytics ongenomics data without the need topurchase or integrate with third-partysolutions.

The nature of laboratory business is changingdramatically and genetics testing is one of themajor drivers. Genomics testing is becomingmore prevalent, and its growth will accelerateas diagnostic and therapeutic use becomesever more evident. As a result, the ways inwhich clinical laboratories have traditionallyperformed their work will change significantlyover the next two to five years. While thepressure to deliver new services will intensify,advanced information technology solutionswill let laboratory professionals be the driversof change, not its victims. �

Gene Elliott is Physician Executive atInterSystems.

Mycobacterium avium-intracellulare (Ziehl-Neelsen stain). In the case of slow-growing mycobacterial organisms,genetic testing has resulted in a massive reduction in results turnaround time.

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‘As testing costs come down,

there will be a fundamental

change in how pathology deals

with tumours, microbiology

tests, and even blood grouping’

‘Genomics testing is becoming

more prevalent, and its growth

will accelerate as diagnostic

and therapeutic use becomes

ever more evident’