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Clin Biochem Rev [journal]
- Informatics and the clinical laboratory. [Journal Article, Review]
- Clin Biochem Rev 2014 Aug; 35(3):177-92.
The nature of pathology services is changing under the combined pressures of increasing workloads, cost constraints and technological advancement. In the face of this, laboratory systems need to meet new demands for data exchange with clinical electronic record systems for test requesting and results reporting. As these needs develop, new challenges are emerging especially with respect to the format and content of the datasets which are being exchanged. If the potential for the inclusion of intelligent systems in both these areas is to be realised, the continued dialogue between clinicians and laboratory information specialists is of paramount importance. Requirements of information technology (IT) in pathology, now extend well beyond the provision of purely analytical data. With the aim of achieving seamless integration of laboratory data into the total clinical pathway, 'Informatics' - the art and science of turning data into useful information - is becoming increasingly important in laboratory medicine. Informatics is a powerful tool in pathology - whether in implementing processes for pathology modernisation, introducing new diagnostic modalities (e.g. proteomics, genomics), providing timely and evidence-based disease management, or enabling best use of limited and often costly resources. Providing appropriate information to empowered and interested patients - which requires critical assessment of the ever-increasing volume of information available - can also benefit greatly from appropriate use of informatics in enhancing self-management of long term conditions. The increasing demands placed on pathology information systems in the context of wider developmental change in healthcare delivery are explored in this review. General trends in medical informatics are reflected in current priorities for laboratory medicine, including the need for unified electronic records, computerised order entry, data security and recovery, and audit. We conclude that there is a need to rethink the architecture of pathology systems and in particular to address the changed environment in which electronic patient record systems are maturing rapidly. The opportunity for laboratory-based informaticians to work collaboratively with clinical systems developers to embed clinically intelligent decision support systems should not be missed.
- Automation of molecular-based analyses: a primer on massively parallel sequencing. [Journal Article, Review]
- Clin Biochem Rev 2014 Aug; 35(3):169-76.
Recent advances in genetics have been enabled by new genetic sequencing techniques called massively parallel sequencing (MPS) or next-generation sequencing. Through the ability to sequence in parallel hundreds of thousands to millions of DNA fragments, the cost and time required for sequencing has dramatically decreased. There are a number of different MPS platforms currently available and being used in Australia. Although they differ in the underlying technology involved, their overall processes are very similar: DNA fragmentation, adaptor ligation, immobilisation, amplification, sequencing reaction and data analysis. MPS is being used in research, translational and increasingly now also in clinical settings. Common applications include sequencing of whole genomes, whole exomes or targeted genes for disease-causing gene discovery, genetic diagnosis and targeted cancer therapy. Even though the revolution that is occurring with MPS is exciting due to its increasing use, improving and emerging technologies and new applications, significant challenges still exist. Particularly challenging issues are the bioinformatics required for data analysis, interpretation of results and the ethical dilemma of 'incidental findings'.
- Existing and Emerging Technologies for Point-of-Care Testing. [Journal Article, Review]
- Clin Biochem Rev 2014 Aug; 35(3):155-67.
The volume of point-of-care testing (PoCT) has steadily increased over the 40 or so years since its widespread introduction. That growth is likely to continue, driven by changes in healthcare delivery which are aimed at delivering less costly care closer to the patient's home. In the developing world there is the challenge of more effective care for infectious diseases and PoCT may play a much greater role here in the future. PoCT technologies can be split into two categories, but in both, testing is generally performed by technologies first devised more than two decades ago. These technologies have undoubtedly been refined and improved to deliver easier-to-use devices with incremental improvements in analytical performance. Of the two major categories the first is small handheld devices, providing qualitative or quantitative determination of an increasing range of analytes. The dominant technologies here are glucose biosensor strips and lateral flow strips using immobilised antibodies to determine a range of parameters including cardiac markers and infectious pathogens. The second category of devices are larger, often bench-top devices which are essentially laboratory instruments which have been reduced in both size and complexity. These include critical care analysers and, more recently, small haematology and immunology analysers. New emerging devices include those that are utilising molecular techniques such as PCR to provide infectious disease testing in a sufficiently small device to be used at the point of care. This area is likely to grow with many devices being developed and likely to reach the commercial market in the next few years.
- Clinical Chemistry Laboratory Automation in the 21st Century - Amat Victoria curam (Victory loves careful preparation). [Journal Article, Review]
- Clin Biochem Rev 2014 Aug; 35(3):143-53.
The era of automation arrived with the introduction of the AutoAnalyzer using continuous flow analysis and the Robot Chemist that automated the traditional manual analytical steps. Successive generations of stand-alone analysers increased analytical speed, offered the ability to test high volumes of patient specimens, and provided large assay menus. A dichotomy developed, with a group of analysers devoted to performing routine clinical chemistry tests and another group dedicated to performing immunoassays using a variety of methodologies. Development of integrated systems greatly improved the analytical phase of clinical laboratory testing and further automation was developed for pre-analytical procedures, such as sample identification, sorting, and centrifugation, and post-analytical procedures, such as specimen storage and archiving. All phases of testing were ultimately combined in total laboratory automation (TLA) through which all modules involved are physically linked by some kind of track system, moving samples through the process from beginning-to-end. A newer and very powerful, analytical methodology is liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). LC-MS/MS has been automated but a future automation challenge will be to incorporate LC-MS/MS into TLA configurations. Another important facet of automation is informatics, including middleware, which interfaces the analyser software to a laboratory information systems (LIS) and/or hospital information systems (HIS). This software includes control of the overall operation of a TLA configuration and combines analytical results with patient demographic information to provide additional clinically useful information. This review describes automation relevant to clinical chemistry, but it must be recognised that automation applies to other specialties in the laboratory, e.g. haematology, urinalysis, microbiology. It is a given that automation will continue to evolve in the clinical laboratory, limited only by the imagination and ingenuity of laboratory scientists.
- The march of technology through the clinical laboratory and beyond. [Journal Article]
- Clin Biochem Rev 2014 Aug; 35(3):139-41.
- Protein Biomarker Research in UK Hospital Clinical Biochemistry Laboratories: A Survey of Current Practice and Views. [Journal Article]
- Clin Biochem Rev 2014 May; 35(2):115-33.
With the increasing drive for more and better disease biomarkers to underpin the stratified or personalised medicine agenda, clinical biochemistry laboratories should be ideally placed to play a major role in their translation into clinical practice. However, little is known about the current extent of biomarker-related research activity in UK National Health Service clinical biochemistry departments.In December 2010, an online questionnaire was sent to active UK members of the Association for Clinical Biochemistry (ACB) to determine the extent of their current research activity and involvement in protein biomarker discovery and translation, including an assessment of the awareness of proteomics.A total of 198 eligible responses (19% response rate) was received from across the UK. Of a further 50 eligible people who responded to a follow-up for initial non-responders, most cited insufficient knowledge about the topic as the reason for non-response (24% total response rate). The results illustrate the highly skilled nature of the workforce with many having experience in a research environment (75%) with postgraduate qualifications. However, more than half spend <10% of their time undertaking research in their current role, and many (61%) would like to be more research active. Encouragingly, approximately a third were involved in biomarker discovery activities, even though for <10% of their time, with slightly more reporting involvement in biomarker translation.Although there are people with the necessary skills and desire to be involved in biomarker research in clinical biochemistry departments, their involvement is small, predominantly due to issues with capacity and resources. It is likely that the majority of biomarker programmes will therefore continue to be carried out by a small number of academic groups, hopefully with collaborative input from hospital laboratories.
- Laboratory medicine best practice guideline: vitamins a, e and the carotenoids in blood. [Journal Article]
- Clin Biochem Rev 2014 May; 35(2):81-113.
Despite apparent method similarities between laboratories there appear to be confounding factors inhibiting uniform reporting and standardisation of vitamin assays. The Australasian Association of Clinical Biochemists (AACB) Vitamins Working Party, in conjunction with The Royal College of Pathologists of Australasia Quality Assurance Programs, has formulated a guideline to improve performance, reproducibility and accuracy of fat-soluble vitamin results. The aim of the guideline is to identify critical pre-analytical, analytical and post-analytical components of the analysis of vitamins A, E and carotenoids in blood to promote best practice and harmonisation. This best practice guideline has been developed with reference to the Centers for Disease Control and Prevention (CDC) "Laboratory Medicine Best Practices: Developing an Evidence-Based Review and Evaluation Process". The CDC document cites an evaluation framework for generating best practice recommendations that are specific to laboratory medicine. These 50 recommendations proposed herein, were generated from a comprehensive literature search and the extensive combined experience of the AACB Vitamins Working Party members. They were formulated based on comparison between an impact assessment rating and strength of evidence and were classified as either: (1) strongly recommend, (2) recommend, (3) no recommendation for or against, or (4) recommend against. These best practice recommendations represent the consensus views, in association with peer reviewed evidence of the AACB Vitamins Working Party, towards best practice for the collection, analysis and interpretation of vitamins A, E and carotenoids in blood.
- Challenges to the measurement of oestradiol: comments on an endocrine society position statement. [Journal Article, Review]
- Clin Biochem Rev 2014 May; 35(2):75-9.
- Estimated Glomerular Filtration Rate versus Albuminuria in the Assessment of Kidney Function: What's More Important? [Journal Article, Review]
- Clin Biochem Rev 2014 May; 35(2):67-73.
Clinical practice guidelines state that any evaluation of kidney disease requires the assessment of (1) kidney function in the form of the estimated glomerular filtration rate (eGFR) and (2) kidney damage by a quantitative assessment of proteinuria, preferably by the determination of the urine albumin-to-creatinine ratio. This review discusses the relative merits of each measurement, focusing on the strengths of each measurement in relationship to all-cause and cardiovascular mortality risk prediction as well as the prediction of kidney disease progression with loss of kidney function over time and the progression to end-stage kidney disease treated by dialysis or kidney transplantation.
- Uncertainty in measurement: a review of monte carlo simulation using microsoft excel for the calculation of uncertainties through functional relationships, including uncertainties in empirically derived constants. [Journal Article, Review]
- Clin Biochem Rev 2014 Feb; 35(1):37-61.
The Guide to the Expression of Uncertainty in Measurement (usually referred to as the GUM) provides the basic framework for evaluating uncertainty in measurement. The GUM however does not always provide clearly identifiable procedures suitable for medical laboratory applications, particularly when internal quality control (IQC) is used to derive most of the uncertainty estimates. The GUM modelling approach requires advanced mathematical skills for many of its procedures, but Monte Carlo simulation (MCS) can be used as an alternative for many medical laboratory applications. In particular, calculations for determining how uncertainties in the input quantities to a functional relationship propagate through to the output can be accomplished using a readily available spreadsheet such as Microsoft Excel. The MCS procedure uses algorithmically generated pseudo-random numbers which are then forced to follow a prescribed probability distribution. When IQC data provide the uncertainty estimates the normal (Gaussian) distribution is generally considered appropriate, but MCS is by no means restricted to this particular case. With input variations simulated by random numbers, the functional relationship then provides the corresponding variations in the output in a manner which also provides its probability distribution. The MCS procedure thus provides output uncertainty estimates without the need for the differential equations associated with GUM modelling. The aim of this article is to demonstrate the ease with which Microsoft Excel (or a similar spreadsheet) can be used to provide an uncertainty estimate for measurands derived through a functional relationship. In addition, we also consider the relatively common situation where an empirically derived formula includes one or more 'constants', each of which has an empirically derived numerical value. Such empirically derived 'constants' must also have associated uncertainties which propagate through the functional relationship and contribute to the combined standard uncertainty of the measurand.