NTRK Fusion Testing for new therapies: Detecting & managing rare pediatric & adult cancers

Neurotrophic tyrosine receptor kinases (NTRK) can become abnormally fused to other genes resulting in growth signals that can lead to cancer in many organs of the human body. TRK gene fusion-based cancers are rare but present in pediatric and adult cancers such as lung, thyroid, colon, etc. (see, e.g., Figure 1). Anti-tumor drugs that target NTRK fusions have been shown to be largely effective across many tumor types regardless of patient age (adult or pediatric).

Figure 1: Estimated frequency of NTRK gene fusion in specific tumor types.[1]

New selective and targeted tyrosine kinase receptor inhibitor of the tropomyosin receptor kinases TrkA, TrkB, and TrkC are either in developmental stage (Entrectinib)[2] or recently approved Vitrakvi® (Larotrectinib)[3] for treatment of locally advanced or metastatic solid tumors with NTRK fusions without a known resistance mutation.[4] However, there is a dearth of NTRK fusion genes in many traditional solid tumor-based NGS targeted assays, which makes identifying patients that will benefit from these drugs by NGS testing a challenge. It also means that patient samples harboring NTRK fusions are extremely rare, thus hampering IVD development and compromising analytical validation according to CAP and CLIA guidelines.

NGS IVD vendors such as Illumina, Thermo Fisher, Archer, and others are expanding their NGS assays to incorporate RNA fusion analysis for NTRK genes. These new NGS assays will require analytical and clinical validation to support patient testing and eligibility for these anti-tropomyosin TKIs.  The use of highly multiplexed, patient-like reference samples containing NTRK fusion genes will be critical in the development, validation and clinical testing by NGS assays of solid tissue biopsies (FFPE) of metastatic solid tumor patients potentially harboring NTRK gene fusions in clinical trial stratification and targeted therapeutic treatments. The availability of designed NTRK quality control materials will immediately help overcome the lack of NTRK patient samples.

Today, the key need is designing and manufacturing solid tumor FFPE RNA NTRK fusion reference standards under ISO 13485 (cGMP) to support clinical testing laboratories looking to bring on board NTRK fusion testing assays as companion diagnostic or complementary tests for these classes of anti-tropomyosin TKIs.

SeraCare, in partnership with Bayer, has recently developed a panel of 15 RNA-based NTRK fusion genes in an FFPE format.[5] This reference standard contains NTRK1, NTRK2, and NTRK3 fusion genes with known actionable fusion partners in the TRK pathway.

Figure 2: List of NTRK fusions in the newly released Seraseq® FFPE NTRK RNA Fusion reference standard.5

In conclusion, anti-tropomyosin tyrosine kinase receptor drugs targeting NTRK genes have moved expeditiously from developmental stage all the way to the market. This has opened up new opportunities for cancer patients harboring these fusions to have access to therapeutic drugs that may ultimately address their diseases. To facilitate this, labs require highly-multiplexed FFPE NTRK RNA fusion reference standards for end-to-end evaluation of NGS assays from development to validation, and routine QC runs of patient samples. These reference standards provide readily available materials for rapid assay development and provide confidence to regulators and clinicians that an assay can detect the fusions pairs it claims to detect.

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Keys to Better Liquid Biopsy Assay Sensitivity

“So as everyone here is aware, I’m sure, detection of circulating tumor DNA is challenging. There’s very little of it, to start with.” Hardly a revolutionary statement by Tony Godfrey, PhD, (Associate Chair, Surgical Research and Associate Professor of Surgery, Boston University School of Medicine) but an important acknowledgement from a leading expert of the difficulty faced by laboratorians in unlocking the full promise of liquid biopsy assays. Both he and Bob Daber, PhD, (President and CTO of Genosity) detailed how they overcame common ctDNA challenges in their labs during SeraCare’s AMP Corporate Workshop in San Antonio, Texas. Watch the video to see the practical advice they gave in their presentations.

Bob Daber, with whom we collaborated on our NGS-based assay validation eBook, discussed the challenges that are unique or more pronounced in ctDNA assay validation. Chief among them being limited access to samples for the variety of studies needed to have true confidence in your assay. Drawing on his years of clinical genomics and bioinformatics expertise, including building the tumor sequencing lab at BioReference, Dr Daber talked about how ground-truth data from known-negative and known-positive materials are critical to determining your assay’s sensitivity and specificity; two attributes that take on even greater importance in liquid biopsy.

Tony Godfrey’s presentation highlighted how access to patient-like ctDNA reference standards allowed his team to refine their SiMSen-Seq technology by reducing background error rates, evaluating absolute copy numbers, and improving sensitivity. Dr Godfrey talked about how his team was able to confidently detect  0.1% mutant allele frequency, and how ground-truth reference materials help them improve performance. Something that wouldn’t have been possible with the inherent variability and scarcity of remnant specimens.

Both presentations are full of actionable information and instructive data from the speakers’ own labs. Watch the video for free today to learn how you can have more confidence in your liquid biopsy assay.

 

This blog post was originally published on the SeraCare blog.

Alzheimer’s disease diagnosis: the end of the guessing game?

There are currently around 850,000 people living with dementia in the UK, and the number of people affected is expected to reach 2 million by 2051. The costs associated with dementia, estimated now at £26 billion a year, are likely to treble.

Alzheimer’s disease is the most common type of dementia, affecting between 60 and 80 percent of those diagnosed. There is no known cure, with treatments limited to preserving cognitive function. Currently, there is no non-invasive method for diagnosing Alzheimer’s disease with GP’s relying on in depth cognitive tests, with clinical confidence in diagnosis typically at 70-80%.

Doctor Helping Elderly

If confident early diagnosis could be achieved through noninvasive techniques, treatment could be introduced earlier delaying the onset of memory impairment.

The solution

The development of plaques or tangles of certain proteins (β-amyloid and tau proteins) in the brain is a known feature in Alzheimer’s disease. It is also known that abnormal accumulation of metals underlies several neurodegenerative diseases. Iron, in particular, is associated with the formation of neurofibrillary tangles in the β-amyloid plaques. The recent advances in the use of Magnetic Resonance Imaging (MRI) for the earlier detection of neurological diseases require validation to ensure the integrity of the images obtained is adequate for diagnostic purposes.

Researchers at LGC, in collaboration with partners, have been working to establish a link between novel MRI scans and quantitative elemental mapping of soft tissues. A method of mapping the levels of iron in sections of the brain using laser ablation (LA) coupled to Inductively Coupled Plasma Mass Spectrometry (ICP-MS) has been developed, along with a novel calibration strategy and standard to support quantitative tissue imaging. Correlation of the metal content associated with β-amyloid protein and MRI images will help diagnosis of AD at an early stage, where preventative therapy will have greater impact.

LGC has developed a novel calibration strategy for LA-ICP-MS that produced quantitative images for iron in whole mouse brain sections (provided through collaboration with Kings College London and the University of Warwick) and compared them with results from micro x-ray fluorescence (μ-XRF) (provided through collaboration with Ghent University and the University of Warwick). The data showed good agreement in total iron concentrations for a selection of areas within the mouse brain sections. This finding supports the proposed method as a quantitative approach; the calibration strategy has been published in the Journal of Analytical Atomic Spectrometry¹.

Impact

The development of this method for quantitative imaging of iron in the brain has the potential to lead to techniques for earlier diagnosis of Alzheimer’s disease, enabling earlier intervention, therapies and treatment aimed at delaying the onset of symptoms.

Delaying the onset of neurodegenerative disorders, such as Alzheimer’s disease, by five years could halve the number of deaths from the condition, saving 30,000 lives a year and billions of pounds in treatment costs. Reducing severe cognitive impairment in the elderly by 1% pa would cancel all estimated increases in long-term care costs due to our ageing population.

The methodology will also provide deeper understanding of the early development of Alzheimer’s disease leading the way for new treatments aimed at preventing the disease.

Heidi Goenaga-Infante, Principal Scientist for inorganic analysis at LGC, commented: “This cutting-edge research is already proving to be of significant benefit to the validation of non-invasive diagnostic tools for Alzheimer’s disease. The potential for metal imaging mass spectrometry of other biological tissues to probe the reported links between metals and disease states is now a step closer.”

If you’d like to learn more about our work and read other case studies, visit our website.

¹ J O’Reilly, D Douglas, J Braybrook, P.-W. So, E Vergucht, J Garrevoet, B Vekemans, L Vinczec and H Goenaga-Infante, “A novel calibration strategy for the quantitative imaging of iron in biological tissues by LA-ICP-MS using matrix-matched standards and internal standardisation”, J Anal. At. Spectrom., 2014, 29, 1378-1384

World Immunization Week 2018: Why and how #VaccinesWork

This week is World Immunization Week, a global campaign to raise awareness of infectious diseases and to educate the public on the importance of vaccination.

Vaccines are a relatively modern tool, with the world’s first successful vaccine being developed in 1796 for smallpox.  Numbers show that when vaccinations steadily increase, rates of death from diseases like measles and polio were vastly reduced.

via WHOMeasles is a highly contagious disease and remains one of the leading causes of death for young children around the world. Before the first vaccine for measles was introduced in 1963, the disease caused 2.6 million deaths each year. However, between 2000 and 2016, the global death rate from measles was decreased by 84%, falling below 100,000 deaths annually for the first time.

Similarly, cases of polio have fallen 99% since the launch of the Global Polio Eradication Initiative in 1988, nearly achieving its goal of eradicating the disease entirely.

This illustrates that vaccinations aren’t just important to the people who take them: over time the use of vaccinations can protect entire populations from contagious disease with what’s known as herd immunity, or ‘community immunity’. Vaccines build immunity in individuals by mimicking an infection. The body’s immune system kicks in and learns to fight that particular infection, achieving immunity to that strain of disease.

In larger populations, the number of new infections decreases as individuals are vaccinated and go through this process. It’s more difficult for diseases to spread if more members of the population can’t be infected. This disrupts the wildfire-like spread of contagions and even protects more vulnerable members of the population who aren’t immune yet, like children, or cannot become immune due to medical reasons.  This only works if enough people get vaccinated though.

Making the world safer against viruses and bacteria is an important step for the future of our communities, which is why our scientists work so hard to help support immunization around the globe. We hope to play a part in the eradication of deadly illnesses by using our research capabilities to progress current research. 

Using mass spectrometry, genotyping technology, DNA/RNA extraction technology, and Next Generation Sequencing, our teams generate a broader understanding of the genetics of diseases, as well as how particular molecules behave and are characterised.

We develop biomaterials that enable researchers to develop vaccines for epidemic diseases such as the Zika and Ebola viruses. Our reference materials are used to prove the quality and purity of medicines, while our microbiology teams have a strong reputation in anti-infective research, as well as antimicrobial surveillance and drug development.

There’s still a long way to go, but in the meantime, visit the World Health Organisation’s website to learn about how vaccines work and how you can help.

Science for a safer world

In the twenty-first century, science has been brought to the forefront, informing all aspects of our lives. In order for it to make our world safer, it’s especially important for science to remain steadfast, reliable and responsible. Science should not have an agenda; science is the agenda. It should not be informed by policy or opinion, but should inform policy and opinion. And at LGC, we work to ensure that our science does just that.

From our origins testing tobacco, alcohol and food products for adulteration in the 19th century, LGC has built a commitment to using science for a safer world.

This commitment underpins all of what we do. From testing drinking water and the quality of food to researching medicines and diagnostics, we work to ensure both our customers and the public benefit from our knowledge. Our scientists develop accurate methods for detecting infectious and congenital diseases and we test more than 6,000 products and supplements for banned substances, certifying that they are safe for athletes at all levels to use.  In our role as UK designated National Measurement Institute for chemical and bio-measurement, we solve measurement challenges in diagnostics, food safety, cancer research and environmental testing. At the heart of everything we do is the question, How can we make the world safer?

LGC is also looking to the future, to advance research, technologies, solutions and medicines that will build a better, more secure future.

Now, through this blog, we hope to bring our science to you, shedding light on the vital work we do every day.

What does ‘Science for a safer world’ mean to you?