An interview with Ilsa Gomez-Curet, PhD, bioscience consultant, Thermo Scientific NanoDrop Products

Ilsa Gomez-Curet, PhD

With the identification of new biomarkers and the development of new molecular techniques, the field of molecular diagnostics has seen significant transformation and evolution. Companies such as Thermo Fisher are working to develop instruments and tests to optimize these new molecular diagnostic techniques and processes. Clinical Lab Products sat down with Ilsa Gomez-Curet, PhD, bioscience consultant, Thermo Scientific NanoDrop Products, Wilmington, Del, to discuss current trends in the molecular diagnostics field, where the field is headed, and some solutions Thermo Fisher is working on.

CLP: What are some cutting-edge applications of molecular diagnostics?

Gomez-Curet: Cutting-edge applications have emerged due to the development of current and new molecular technologies. For example, proteomic-based tests can be used to determine the association between a patient’s protein-expression profile and the onset or progression of disease. Metabolomics tests can be used for disease diagnosis, drug therapy, and monitoring the response to treatment. These technologies are improving and/or facilitating biomarker and drug discovery, diagnosis, prediction of disease recurrence, classification of patients, determination of therapeutic drug efficacy, and drug therapy choices.

A few of the top areas in the field are the identification of new biomarkers for cancer and cardiovascular disease, the development of companion diagnostics for drug development, and the development of diagnostics tools for personalized medicine. A diagnostic test for personalized medicine can identify genetic variants in a patient that may render a particular treatment ineffective. Additionally, identification of patients whose tumors express a particular mutation may allow for the possibility of more targeted and personalized treatment.

CLP: What are some issues stopping more widespread adoption of molecular diagnostics in the clinical lab setting?

Gomez-Curet: Many challenges are associated with emerging molecular diagnostics. On the technical side, clinical laboratories will need to know how to work with new and complex platforms (eg, microarrays and next-generation sequencing); how to validate complex tests; and how to store, analyze, and integrate complex data. In addition, proteomic and gene-expression patterns used as biomarkers require special statistics as they can cause overfitting of the data. A related issue is the lack of scalable database systems and bioinformatics tools necessary to handle and integrate the data.

Other relevant issues are the identification of biomarkers of disease that show real clinical value and predict who will benefit from a targeted therapy and the lack of standardized procedures for proteomics- and metabolomics-based technologies.

Apart from technical issues, there are social, patent, ethical, regulatory, and legal implications associated with emerging molecular diagnostics. Such issues include the high cost of performing many of the new molecular tests, the lack of understanding of molecular tests and their clinical value by physicians and patients, as well a lack of laws preventing misuse of a patient’s genomic information.

CLP: What optimization do multiplex-, genomic-, and proteomic-based assays need before results can be interpreted correctly in a clinical setting?

Gomez-Curet: The sensitivity and specificity of new molecular tests need to increase and the rates of false positive and false negatives need to decrease before these tests can be transferred into the clinical lab. In many instances, the entire workflow—from sample preparation to assay run, data collection, and analysis—needs to be optimized, simplified, or automated to decrease assay variability. Similarly, standardization and automation of methodologies used in genomics, proteomics, and metabolomics will further increase the efficiency and reproducibility of high-throughput analysis.

Proteomics is a good example of the need for optimization. Incorporation of proteomic technologies into molecular diagnostics will depend on optimization of antibodies and aptamers to increase specificity and reproducibility of these techniques. The optimization of bioinformatics tools that allow efficient storage, normalization, analysis, and the integration of data from different sources is also a must.

Close attention to sample extraction and processing is essential to ensure that a high-quality starting material is used for downstream steps in the workflow. For instance, when performing nucleic acid-based assays, variations in the quantity, purity, and integrity of DNA or RNA samples can result in variable results and erroneous conclusions. To avoid this problem, it is important to optimize and standardized reagents for stabilization of specimens and gene-expression patterns. It is also vital to measure and assess purity of DNA and RNA samples before downstream steps in the diagnostic workflow are performed.

CLP: Is Thermo Fisher developing diagnostic tools alongside the development of drug therapies to heighten the usefulness and economic value of newly discovered drugs?

Gomez-Curet: As molecular biology techniques such as real-time PCR and microarray analysis continue to become standard methods for molecular diagnosis, quality control (QC) steps that minimize the loss of clinical samples are essential. Thermo Fisher has supporting instrumentation that can be invaluable in the QC process and validation of emerging molecular tests. One example is the Thermo Scientific NanoDrop 2000 series of spectrophotometers. These instruments remove traditional containment devices such as cuvettes and capillaries. The patented sample-retention system combines fiber optic technology and the natural liquid surface tension to capture and hold a 1- to 2-µL sample between two optical surfaces during measurement. By eliminating traditional containment devices, the volume of the required sample is greatly reduced, which conserves most of the sample for downstream analysis. To address the demands of higher-throughput environments, the Thermo Scientific NanoDrop 8000 spectrophotometer was design to perform up to eight 1- to 2-µL measurements simultaneously.

The reduction in the volume required for QC steps is the main reason why the Thermo Scientific NanoDrop microsample quantitation method is being adopted in several areas of molecular diagnostics. For example, the development of solid tumor testing is often extremely difficult due to the small amounts of available tumor cell mass. The samples are often difficult or impossible to reobtain, while the amount of genetic material extracted from a specific solid tumor may be so limited that microsample quantification is the only suitable way to measure concentration and assess the purity of the sample.

Thermo Scientific NanoDrop spectrophotometers have preconfigured methods for common applications including nucleic acid, microarray, proteins and labels, and protein quantification. They also measure DNA, RNA, and protein concentration and can determine sample purity (A260/A280 and A260/A230 ratios). These measurements, particularly during the validation of a new molecular diagnostic assay, can identify the need for improvements in sample processing or downstream steps in the diagnostic workflow, and will ultimately aid in the development of robust molecular diagnostic assays.

CLP: Please discuss emerging trends and potential future markets in molecular diagnostics.

Gomez-Curet: Some of the important trends are the development of collaborations between companies and diagnostics labs, the movement toward targeted therapies, and the collaborative efforts to standardized procedures and developed guidelines.

The field will continue with the development of genetic testing based on next-generation sequencing, nanotechnology, microRNA, and bead-based technologies. In addition, new or improved technologies will facilitate genome resequencing, methylation analysis, and transcriptome sequencing of clinically relevant areas of the genome. Progress should also be made in advancing microRNA-based assays from the bench to the clinic. For instance, several companies are developing miRNA-based assays for differential diagnosis of related, but different carcinomas, whereas other companies are pursuing siRNA-based therapies.

Some areas that will continue to grow are the use of personalized medicine, (primarily through the development and improvement of pharmacogenetic and epigenetic tests), the delivery of companion diagnostics for targeted cancer therapies, and the use of metabolomics to develop new therapies and biomarkers with prognostic and diagnostic value. The development of biosecurity testing to improve Homeland Security will also see growth over the next few years.

Lastly, efforts will continue to integrate data produced by genomic, proteomic, and metabolomic technologies. The integration of these data will facilitate drug discovery, targeted therapeutics, and will allow a better understanding of how genetic variation affect treatment outcomes.

Chris Gaerig is associate editor of CLP.