Originally Published IVD Technology October 2002
Tools for molecular diagnostics
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| The I-Core module by Cepheid (Sunnyvale, CA) is a complete, integrated thermal cycler and optical-detection device capable of performing and continuously monitoring the PCR reaction for amplifying DNA to detectable levels. |
Molecular diagnostics is of critical importance to public health. This area of medical technology will facilitate the detection and characterization of disease, the monitoring of drug response, and the identification of genetic modifiers and disease susceptibility—all this just in the human clinical arena. Molecular diagnostics will also be used to identify food, water, and environmental contamination and—of particular interest this past year—the possible presence of biological warfare agents. And several nucleic acid–based methods are available to support DNA detection and analysis and to pinpoint changes in gene expression. Questions of practical implementation of these diagnostic technologies hinge on their cost-effectiveness, the choice of technology and equipment, the accuracy and reproducibility of the tests, the training required by users, reimbursement rates, and patent positions.
The molecular diagnostics market is estimated to stand now at $1.0 billion to $1.2 billion per year, with an annual growth rate of 20–40%. Approximately 90% of this market is infectious-disease assays. That leaves a market of $100 million or a bit more for other tests related to genetic disease, predictive testing, paternity testing, cancer screening, and so on. The non-infectious-disease market also has been growing more than 20% a year.
Total sales of all clinical diagnostic applications was estimated to be in excess of $21 billion in 2001. Of this total, nucleic acid–based diagnostics represented about 7%, or $1.5 billion. The clinical diagnostics industry as a whole is expected to exceed $35 billion by 2005. During that period, the nucleic acid segment is anticipated to grow at a much more rapid rate than that, as new technologies enable new procedures and cannibalize old testing methodologies.
Nucleic Acid Testing at the Point of Care
Nucleic acid testing (NAT), which is the most rapidly growing diagnostic sector, is predicted to quickly become a point-of-care (POC) technique. POC nucleic acid methodologies could play a pivotal role in the early diagnosis of diseases, facilitating their prompt treatment. The tests provide a powerful tool for identifying myriad microorganisms known to be associated with sexually transmitted diseases, infections of the immunocompromised host, and many other diseases. Further, these tests aid in the critical evaluation of disease predisposition.
Molecular diagnostic testing will need to overcome several challenges before it is fully accepted for POC work in a physician's office. First of all, it will have to be CLIA-waived; that is, it must have extremely low complexity. Perhaps even more critical will be the requirement that the test be completely self-contained so as to eliminate any risk of cross-contamination. And because the primary reasons for preferring POC testing to testing in a centralized laboratory are the time to result and lower cost, any POC test must be very rapid and cost-effective. Otherwise, the physician cannot justify bringing the testing in-house.
Several technologies are now under development for genetic testing. These include gene chips, DNA probe technology, microfluidics, and tandem mass spectrometry, among others. Nucleic acid probe–based tests introduced the application of molecular genetics in diagnostics. Owing to their speed, probe-based tests hold great appeal except in situations where sensitivity is an issue.
However, nucleic acid amplification techniques are the chief NAT methods because of the general need for high sensitivity. Typically, POC testing requires several elements: rapid capture of the target molecule from a readily available biologic sample, selective amplification of the target region of the molecule (which may also be used to label the product intended for detection), and specific detection of the amplified product. For NAT methods ever to win a place in POC testing, these three steps will have to be integrated into a very simple, self-contained device.
More than 50 biotechnology and diagnostics companies offer DNA amplification technologies. Some 30 different gene- and signal-amplification techniques, from polymerase chain reaction (PCR) and ligase chain reaction to transcription-mediated amplification and dendritic polymers, are being used for an ever increasing variety of applications in research and clinical settings.
The market for amplification technology is currently in the hundreds of millions of dollars, but as the need for genomic information increases and clinical diagnostic tools are developed, this market will grow. Although PCR is the dominant amplification technology now, others are emerging to challenge it in many areas. Forces driving the development of amplification technology and shaping this dynamic market are patents, testing costs, and the user-friendliness of new techniques.
Outside the realm of POC testing, genomics-based assays represent a different type of business opportunity. The test volumes here are too small and reimbursement rates too low to support the development of traditional FDA-cleared (Class II) or FDA-approved (Class III) diagnostic kits. In general, a market opportunity of $10 million to $50 million per year is necessary before a product can generate the positive return on investment that makes pursuit of FDA approval worthwhile. Only the highest-volume genomic tests, such as Factor V Leiden and cystic fibrosis panels, are believed to approach this market potential. This has resulted in the emergence of new, nontraditional diagnostic businesses that offer reagents labeled as Class I general-purpose reagents (GPRs) or analyte-specific reagents (ASRs) to CLIA high-complexity laboratories.
This trend can be contrasted with the more traditional strategies of molecular diagnostics companies competing for the larger molecular infectious-disease opportunities such as viral load testing, viral genotyping, and detection of sexually transmitted diseases. The purchase of GPR/ASR reagents rather than approved IVD kits has worked well for the commercial laboratories that are capable of developing and validating assays, as well as for patients who benefit from earlier availability of state-of-the-art testing.
Infectious Diseases
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| The DTS800 system by Gen-Probe Inc. (San Diego) is an automated nucleic acid pipetting system. |
For some time to come, infectious disease will remain the principal focus of molecular diagnostics. Infectious-disease testing demands high sensitivity and specificity with rapid turnaround, all of which are offered by NAT. The correlation between pathogenic microorganisms and human disease has been investigated longer than human diseases with genetic origins have. Because of this, and because the genomes of bacterial and viral agents are smaller and therefore easier to characterize than the human genome, infectious disease was the first area targeted by molecular diagnostics. Molecular diagnostics has proven invaluable in testing for pathogen identification, strain verification, viral load monitoring, and drug-resistant strains.
One day, infectious-disease NAT and pharmacogenomics will be used in concert. The capabilities of these tests will allow the physician not only to identify the illness-causing pathogen, but also to determine its resistance or susceptibility to a drug. Also, by analyzing the patient's DNA, the physician can know which drug will generate the best response.
Clinical Genetic Testing
Only a portion of non-infectious-disease testing can be considered genomic. Most molecular cancer-related testing is aimed at detecting tumor-associated changes in gene expression: translocations, loss of heterozygosity, or other abnormal patterns of expression. It is not clear yet whether developments in this area will involve detection of changes in gene expression through analysis of DNA or messenger RNA, or whether protein determinations will be the assays of choice.
Current strategies for prenatal testing rely primarily on biochemical assays and imaging methods for whole-chromosome analysis. The genomic testing associated with preimplantation genetic diagnosis is still new and limited to a few major centers. Paternity testing is based mostly on measuring the size of selected short tandem repeats, although some believe that this field will in time adopt testing for single-nucleotide polymorphisms (SNPs) as a more cost-effective approach. Many genetic diseases are detected through assays directed at proteins or metabolites rather than by characterizing DNA sequences. True genomic-based testing is largely limited to assays for thrombotic risk, cystic fibrosis, and certain other heritable genetic disorders, for human leukocyte antigen typing, and for predictive testing in selected populations.
Theranostics and Pharmacogenomics
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| Xtra Amp nucleic acid extraction kits by Xtrana Inc. (Broomfield, CO) are available for a wide variety of sample types and are based on a novel solid-phase extraction system that allows for extraction and amplification in the same tube or well. |
The greatest potential for genomic testing appears to be in theranostics, a shorthand term for therapy-specific diagnostics. This approach differs from traditional medical practice in which therapeutic choices follow a diagnosis that may be based on clinical signs alone or may also take into account results of an in vivo or in vitro diagnostic test. In traditional practice, neither the effectiveness of the prescribed drug therapy nor the likelihood of side effects can be predicted for individual patients in many cases. The primary current application of theranostic assays is to select patients for drug treatments that are likely to benefit them and unlikely to produce adverse effects. In addition, theranostics will provide an early indication of treatment efficacy for a particular patient. Personalized diagnostic tests thus will provide healthcare professionals with information useful for individualizing and optimizing the therapeutic regimen of each patient.
Theranostics represents a new generation of tests that promise to transform medical diagnosis and treatment into a predictive science. The potential market for theranostics is enormous and presents a commercial opportunity for both diagnostics and pharmaceutical companies.
Approximately 2.4 million SNPs have been identified in the human genome, most of which still await allelic frequency determination. Very likely, many SNPs will show great variation in allele frequency between different populations. In addition, while many diseases are monogenic—that is, involve mutations in a single gene (as certain inborn errors of metabolism)—more frequently, diseases are associated with polygenic genetic anomalies. This greatly complicates transforming the link between SNP and disease into a clinical diagnostic reality. SNP detection and analysis will initially be useful in drug discovery efforts. The data have not yet arisen that would warrant integrating SNP testing into even clinical trial screening as a routine component.
The magnitude of this opportunity ultimately will depend on the success of clinical validation and the speed with which new drug and diagnostic assay combinations can be moved through the approval process. Also, pharmacogenomic profiling may be able to be applied to existing drugs or may even be used to resurrect old drugs that were recalled owing to adverse effects in identifiable subgroups. It is generally accepted that the clinical validation and approvals required to move pharmacogenomics into routine diagnostic testing will take 5 to 10 years. The potential economic reward is huge: profits would come from sales of both the drug and the companion diagnostic test.
Establishing NAT as a routine component of POC testing will certainly take some time. While some companies have been quite open about their intentions to enter this new market, there are probably many others undertaking research in this area who have not disclosed their plans or projects publicly. The market is in its infancy. Some would say it does not exist. Its eventual size is a mystery. However, given the speed with which molecular diagnostic technologies are being developed and the vast quantity of genomic information coming to light, NAT will undoubtedly be an exciting arena to watch.
Shannon Beard and Roy Mondesire, Xtrana Inc. (Broomfield, CO)
Photos Courtesy Cepheid, Gen-Probe Inc., Xtrana Inc.
Copyright ©2002 IVD Technology
