personalized medicine – Lablogatory

There are often new buzzwords flying around that everyone uses, but few actually understand what they mean. Personalized and precision medicine are two of these terms that are often used interchangeably. Every lab wants to say they are performing personalized medicine. And to be fair we really do all provide personalized medicine in some form. Almost all lab results are used to customize the treatment for patients. However these buzzwords are used to refer to tests that describe linking genetic, lifestyle, or environmental information with predicted response to treatment. Precision medicine may be the more accurate term to describe identifying effective treatment for the right patient at the right time based on genetic, lifestyle, or environmental information. The term personalized medicine may give the false impression that therapies were developed specifically for the patient, when really they are developed to target a specific genotype or phenotype.

One example of precision medicine being used clinically today is in oncology. Many cancer drugs now require an associated test to determine the presence or absence of a specific biomarker to determine which patients are likely respond to the therapy. The biomarker tests that are linked to a specific therapy are called companion diagnostics. Biomarkers analyzed can be a specific protein or gene such as programmed death ligand-1 (PD-L1) or epidermal growth factor receptor (EGFR) or they can be much broader such as tumor mutational burden (TMB) or immune signatures. Identifying biomarkers that determine which patients are likely to respond to therapy and only giving patients with the biomarker the drug increases response rates to the therapy and may decrease side effects. More than half of the clinical trials for cancer drugs in 2018 were linked to a specific biomarker. Linking drug selection with specific laboratory tests is causing an increased need for multidisciplinary collaboration among pathology, oncology, and the laboratory.

In our lab we perform precision medicine using PCR or NGS assays to analyze patient’s tumor for specific genes. Although we still perform single gene testing when ordered, most of our cases are analyzed by a NGS panel. NGS panel testing allows us to look at numerous biomarkers with one test. This decreases the cost, time and tissue utilized to determine the patient’s biomarker status. Our NGS panel analyzes 52 genes to look for mutations that would indicate a patient is likely to respond to a targeted therapy. Most of our oncology testing is done on lung, colon, and melanoma specimens, although the panel is validated for most solid tumors. The report that we issue the oncologist provides clear information on which therapies the patient is likely to respond to or likely to be resistant to based on their tumor’s genetic profile. We also include information in the report to match patients to clinical trials. Precision medicine utilizing panel NGS testing for predicted response to treatment is becoming standard of care for many solid tumors.

-Tabetha Sundin, PhD, HCLD (ABB), MB (ASCP)^CM, has over 10 years of laboratory experience in clinical molecular diagnostics including oncology, genetics, and infectious diseases. She is the Scientific Director of Molecular Diagnostics and Serology at Sentara Healthcare. Dr. Sundin holds appointments as Adjunct Associate Professor at Old Dominion University and Assistant Professor at Eastern Virginia Medical School and is involved with numerous efforts to support the molecular diagnostics field.

I’m sure that everyone has heard about next generation sequencing (NGS). But why exactly is it a big deal? Even though I have spent a significant amount of time at the bench performing “wet lab” basic science research and was acquainted with the term, I did not have practical hands-on experience with NGS prior to residency. It was not a readily accessible technology during my biomedical research days prior to medical school and so I did not entirely grasp the full power of this then disruptive technology until I was a pathology resident, and even more so, as an applicant for molecular genetic pathology (MGP) fellowships.

All of us should have previously learned about the “gold standard,” Sanger sequencing. This method combined irreversible dideoxynucleotide chain termination with a detection method such as gel electrophoresis, or on a larger, automated level, capillary electrophoresis. It was powerful because it allowed us to read the genomic map that directs cellular life, albeit only one sequence at a time. It served as the mainstay for more than a quarter of a century and still is employed for smaller scale sequencing or for long (>500 bp) stretches of DNA.

In the 1990’s, initial methods of massively parallel signature sequencing (MPSS) and pyrosequencing began to appear which would lay the groundwork for today’s massively parallel sequencing (MPS), also known as second generation sequencing, or more popularly as NGS. The two most commonly utilized NGS platforms to date are based on semi-conductor technology for the Ion Torrent (now Life Technologies) and reversible dye-terminator, sequencing based synthesis (SBS) technology for the Illumina platforms.

The power of NGS comes from its ability to simultaneously sequence 1 million to 43 billion short reads (400-500 bp each). The Human Genome Project took over a decade to complete and cost nearly $3 billion whereas NGS can sequence the same genome for a cost on the order of $1000’s, a cost that is further decreasing as the technology is refined. When I was working in research (eons ago), we had nitrocellulose based dot arrays where each “dot” represented multiple copies of a specific cDNA sequence and which helped us to build expression profiles for our particular area of study. This would be analogous to analog technology and NGS would now be considered a digital version.

With conventional PCR, we could only amplify one target sequence per sample reaction. The results were also only qualitative. The results only measurable after multiple cycles of denaturation, annealing, and extension as amplified product of the expected size or no amplified product. Then came along real-time or quantitative PCR (qPCR) which some people refer to also as RT-PCR (although this is a confusing term for people like me who were around before qPCR and think of RT-PCR as meaning reverse transcription PCR). The power of qPCR was that within the linear range of detection, we could now quantitate the amount of product present in real time. NGS also provides the resolution of qPCR in terms of quantitation.

So, as a technology, NGS nicely combines and refines some (but not all) characteristics of multiple technologies with large scale profiling. But for a non-molecular person, what is the relevance? Obviously, it has taken us some time to get to this point, even though the Human Genome Project was completed in 2003 (it started in 1990). We needed time for biomedical and translational research to provide us with clinical significance to the mutations and genetic aberrations NGS could identify. We also needed to develop tools to distinguish true mutations with clinical significance from benign polymorphisms present in our population and to build our bioinformatics support.

But here we are, stepping into the new frontier of personalized genomic medicine. Sure, there is a lot of hype surrounding it and these promises will take time to keep. But these are exciting times for someone like me who fell in love with the molecular dance that plays out within our cells. One of the reasons that I want to complete an MGP fellowship is to get more hands-on practical knowledge of the nuances of NGS from a technical standpoint but also to collaborate with other physicians in directing patients to the correct clinical trials and targeted treatment – and therein, is where the power of NGS really lies. For someone who may never get to meet the patient, at least for me, there’s probably no greater satisfaction than knowing you had a pivotal part in helping a patient more effectively combat their disease. Personalized genomic medicine is another step in that direction.

[12/12/2014: edited to fix a few inaccuracies. We apologize for the error.]