Personalised Medicine: Transforming lives one diagnosis at a time
Article Sep 27, 2017 | by Dr Sarah Holme
A rapid, definitive medical diagnosis is key to the most effective treatment and the best outcome for any patient. No longer confined to research projects and blue sky thinking, personalised medicine is having an impact in the real world, providing smarter diagnosis, guiding treatment decisions and producing better outcomes.
Lung cancer – getting the right treatment to the patient first time
A decade ago, treatment options for lung cancer were limited to blanket chemotherapy approaches. Since then there has been an explosion in our understanding of lung cancer biology, bringing it from the back of the pack to the front and improving the range and efficacy of new treatments. Numerous driver mutations have been identified and immunotherapies are now available to target them. Knowing which mutation is driving a person’s lung cancer is now fundamental to selecting an effective therapy.
Work published last year in JAMA Oncology by Geoffrey Oxnard, M.D., and colleagues at Dana Farber Cancer Institute on the use of digital polymerase chain reaction (dPCR) for liquid biopsy analysis in non-small cell lung cancer (NSCLC) triggered widespread adoption of this technology.
Hotspot analysis of patient blood samples (liquid biopsies) checks for commonly occurring cancer gene mutations in the patient’s gene sequence. Mutations in EGFR, ALK and KRAS are well characterised and their effects and role in cancer well understood. The presence or absence of these mutations in each lung cancer patient provides actionable information.
Dr Paul Walker is Chief of Haematology/Oncology at the Brody School of Medicine at East Carolina University. By identifying likely causative mutations and choosing therapies that selectively block the associated cell mechanisms, Dr Walker and his colleagues have improved treatment response in his patients.
“Nobody thought we’d be where we are today two years ago, liquid biopsy and immune checkpoint blockades have come on fast,” explains Dr Walker.
It was Dr Walker’s interventional thoracic pulmonary oncologist, Dr Bowling, who initially embraced the technology, taking blood samples at the time of the diagnostic bronchoscopy and sending it out to be analysed for hotspot mutations.
“At best, 30% of people treated with chemotherapy show a response. If you identify an actionable mutation, then this can increase to 70-80% of people who respond,” says Dr Walker.
Now Dr Walker and his team have treated over 150 lung cancer patients with a new immune checkpoint blockade therapy: “We talk about personalized oncology, precision oncology - liquid biopsies make that a reality. Liquid biopsies can be taken throughout a person’s treatment, monitoring resistance to treatment as it arises, allowing treatment to keep going forward in the right way.”
“Oncology has adopted this concept of an ‘exceptional responder’, i.e. when a patient receives one type of treatment and have an exceptional response. However, it’s not that they are an exceptional responder – it’s just people getting the right treatment! That level of response to treatment should be the goal for everybody. A huge part of that is identifying why a person has such a good response and that is the ultimate implementation of personalised oncology. Liquid biopsies are imperative to that, otherwise tissue will always be a limiting factor.”
For example, in lung cancer patients under the age of 40, the most common causative mutation occurs is ALK. Forty-six percent of these lung cancer patients have an ALK mutation, not EGFR. Getting this information quickly allows you to go forward with the right treatment as soon as possible. If there is an actionable mutation it is imperative that this is targeted, otherwise, the outcome will be compromised.
Dr Walker explains, “It has been easy to integrate liquid biopsy screening into a variety of routes lung cancer patients may come through, whether it is at bronchoscopy, surgery or even at the first consultation. The challenge is getting people onboard with how powerful it is! One of the biggest barriers to successful treatment remains early detection. There is still a widespread mindset of nihilism with lung cancer. So many patients that have a cough, or are coughing up blood know they could have a lung cancer but are slow to do anything about it because there is a stigma of shame and the belief that nothing good can happen with treatment. Now with the targeted therapies and immune therapies, it is radically different.”
Diagnosing rare genetic disorders – an end to the patient odyssey
For individuals with a rare genetic disease, getting an accurate diagnosis can be very difficult and take many years. Repeated visits to specialists with multiple, often invasive, tests can be damaging to the individual and their family. Thanks to recent seismic advances in DNA sequencing, sequencing of individual genomes is within the grasp of mainstream science, making it feasible to identify causative mutations.
The 100,000 genomes project continues to break new ground by combining genomic sequence data with medical records to investigate the best way to use genomics data to reveal the causes, diagnosis and treatment of disease.
A recent report to the UK government from the life sciences sector supports the critical role that genomics will play in future health and well-being in the UK. The report, written by Life Science’s Champion Professor Sir John Bell in collaboration with industry, academia, charity, and research organizations, provides recommendations to government to safeguard the long-term success of the life sciences sector; it bolsters personalised medicine approaches and the technologies and infrastructure that are being implemented to bring them into mainstream medicine. It states “The Genomics England project is an excellent example of how the NHS can work together with a commercial technology provider (Illumina) and Genomics England to create a whole new pathway of state-of-the-art genomic technologies to better diagnose patients with rare diseases and define genomic variants associated with cancer”.
Another commercial partner with Genomics England, Congenica, has been a technology provider for the 100,000 genomes project, providing annotation and clinical interpretation of samples with its software platform Sapientia.
Sapientia allows analysis of next-generation sequencing data for the identification of the genetic mutations that cause disease. It also provides a cloud-based IT platform in which experts can interpret that information to make a diagnosis.
Previous genetic testing allowed only sequencing and interrogation of one gene, or a handful of genes in a panel, at a time. This was very inefficient, resulting in the patients not getting an accurate diagnosis and a ‘patient odyssey’ with repeated single gene testing and visits to consultants. In the UK, the average time for obtaining a diagnosis of a genetic disease is five years, visiting as many as eight experts in a field, often because genetic testing is not performed until late in the process.
Careful sequencing analysis to identify significant sequence variants (mutations) within the large volume of sequence data is key to the diagnostic process. Equally important is the careful interpretation of the variants found. This involves the searching of databases of known clinically relevant mutations and interpretation considering the individual’s symptoms and other clinical information. Congenica’s software facilitates this entire process and allows the physicians to manage this in a simplified way.
“Sequencing the human genome took 13 years and 1 billion dollars and now you can sequence multiple patients, make a diagnosis and report back to the clinician and patients in less than a week. It’s amazing,” explains Congenica’s CEO Tom Weaver. There are over 7000 known genetic diseases, about 70% of which are paediatric. Dr Weaver continues, “It is very important that different organisations share this data so that everyone can take advantage of this. Each of the 7000 conditions is rare, but taken together they are not! Sharing that information and engaging with international projects is part of Congenica’s ethos.”
Next in line to benefit…antibiotic stewardship
Personalised medicine also extends to tailored treatment for infectious disease. Rapid diagnosis and treatment with the right antibiotics remain a major challenge. World sepsis day last month once again raised awareness of the devastating effects of systemic bacterial infections and the terrifying speed that it can escalate from even the most innocuous beginnings.
Distinguishing symptoms as a bacterial infection, as opposed to viral infection for example, and precisely identifying the bacterial agent and right antibiotics to use can be the difference between life and death or chronic debilitation. In addition, our one size fits all approach to antibiotic prescription has inexorably led to the current antibiotic resistance crisis. Precise identification of the infectious agent and tailored antibiotic prescription is part of the strategy to reverse this.
Rapid diagnosis is pivotal and new technologies are thankfully emerging that tackle the issue in our hospitals and surgeries. At the AACC meeting in August this year, Dr George Sakoulas and Dr Mike Broyles presented on the importance of antimicrobial stewardship and the role that more efficient diagnostics can play in this. For example, a PCT (procalcitonin) test identifies a common biomarker of bacterial infection and can help to identify patients suffering from sepsis and monitor their response to antibiotics. The hope is that tests such as this will help to reduce the one size fits all approach to antibiotic therapy, specifying the correct treatment and dosage regime plus monitoring for changes in patient response. “Companies such as Biomerieux have made great strides in helping doctors identify cases of sepsis and resistant infection as soon as possible,” comments Dr Colin Flatley speaking at AACR 2017.
The Longitude prize, set up by Nesta and supported by Innovate UK is a £10m prize fund to find a cheap, accurate, rapid and easy-to-use point of care test kit for bacterial infections. Longitude prize entrants MeMed have also used a biomarker approach to rapidly detect a bacterial infection, but have taken it one step further.
“There are a few protein biomarkers in the immune system that predominantly increase in response to bacteria, such as C-reactive proteins (CRP) and procalcitonin. Although each has merit, they also have blind spots.
We asked ourselves: What if we could discover novel protein biomarkers that increase in response to viral infections? Then maybe, we could identify a unique combination of viral-induced and bacterial-induced biomarkers, where participating proteins cover for one another’s blind spots.
We quantitatively screened over 600 proteins in patients with bacterial or viral infections (and as far as we know, it was the largest host-protein screening to date!). The best performing combination out of the numerous ones rigorously interrogated included three protein biomarkers called: TRAIL, IP-10, and CRP. Nicknamed the ‘TIC’ signature, this trilogy of proteins demonstrated robust performance, with sensitivity and specificity over 90% across different ages, pathogens, times from symptom onset - outperforming individual proteins and other routine laboratory parameters.
We developed a first-generation product based on the TIC signature called ImmunoXpert™ that is laboratory-based and takes two hours, just to launch and learn. Today ImmunoXpert™ (CE-IVD) has been used to diagnose infections in more than 10,000 children and adults as part of our early access program, which is steadily expanding.”
Whether it is lung cancer, rare genetic disease, or infection, early and precise diagnosis is the key to the best outcome. Thanks to advances in personalised medicine, physicians and the people they treat now have increasing access to the most effective treatments earlier, saving lives and ensuring our healthcare services are used in the most efficient way possible.