The Medical Futurist | October 20, 2018
By 2025, between 100 million and 2 billion human genomes will have been sequenced, researchers said. What do medical research, companies or governments do with such an incredible amount of data? How could genomics bring DNA-based targeted treatments, personalized drugs, and individualized clinical methods, in other words, precision medicine to healthcare?
Does disease categorize people?
In the previous centuries, healthcare systems focused mainly on working out generalized solutions for treating ill people in as high numbers as possible. If cough syrup was good for the majority of the coughing masses and only two people had a rash as an allergic reaction to it, there was no question about treating a sore throat with cough syrup. Experience and empirical evidence on a generalized basis was the working method of the medical community since Hippocrates until around the beginning of the 20th century.
Evidence-based medicine turned around the practice of relying on the wisdom of past doctors and traditions. As a consequence, nowadays physicians not only prescribe some pills because their ancestors used to do the same, but they proved the efficacy of treatments and diagnostic methods with the help of scientific tools, e.g., clinical studies. Research evidence and practical experience show why a sore throat is best treated with cough syrup, what are the side effects and how that could also be treated or avoided. Moreover, these pieces of evidence and experience are collected in clinical practice guidelines – for every condition and every clinician. These guidelines are regularly updated as the latest studies and/or the results of clinical trials get published.
So far, the working method has been viable, however, with the rise of personal genomics as well as other tools of precision medicine, a major flaw of the system came to light. Instead of putting individual patients in the center, generalized diseases take center-stage in healthcare. Conditions categorize people and not personal characteristics influence treatments. Patients usually receive care that is generally appropriate according to the guidelines. Existing technologies and the system enables this working method (which in many cases works just fine) – but personal genomics opens the door to another era by putting the patient and not the disease to the heart of healthcare.
The rise of genome sequencing
The completion of the Human Genome Project was a watershed in the development of medicine and healthcare. In the last fifteen years following the success of the quest to sequence all 3 billion letters or base pairs, in the human genome, the cost of sequencing started to free-fall, the access to testing has been multiplying day-by-day, the arsenal of sequencing technology widened spectacularly and new research fields appeared from thin air – such as pharmacogenomics or nutrigenomics.
While the Human Genome Project cost approximately $2.7 billion for the US government, currently, you can order currently you can order your whole genome sequence online for about $400-500! By now, there are more than 2,000 genetic tests for human conditions – and direct-to-consumer genetic testing companies make it even possible to order them online. These tests enable patients to learn their genetic risks for disease and also help healthcare professionals to diagnose illness. Consumer companies like 23andMe and Ancestry have so far created genetic profiles for more than 12 million people, according to recent industry estimates. Moreover, according to the latest research led by computational biologist Yaniv Erlich, published in October 2018 in Science Magazine, more than 60 percent of Americans with European ancestry can be identified through their DNA using open access genetic genealogy databases, regardless of whether they’ve ever sent in a spit kit.
Automated high-throughput sequencers appeared on the market, gradually decreasing in size while reducing the time necessary for sequencing. For example, in January 2017, DNA sequencing giant Illumina unveiled a new machine that the company says is “expected one day” to order up your whole genome for less than $100. It would mean that you might have a cheaper genetic test than a general blood test. The UK-based start-up, Oxford Nanopore Technologies offer real-time, out-of-the-lab DNA and RNA sequencing with their MinION device. It enabled researchers to carry out offline DNA sequencing of environmental samples on Antarctica using only a hand-held device.
What’s next on the frontier of genome sequencing research?
The Human Genome Project has already fueled the discovery of more than 1,800 disease genes, but scientists are doubling down on the efforts. The ambitious US-powered initiative, The Cancer Genome Atlas aims to identify all the genetic abnormalities seen in 50 major types of cancer, just as the EU-funded Cancer genome project supports cancer research. The Roadmap Epigenomics Projectis mapping DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in the human genome.
In the UK, GlaxoSmithKline, Roche, AstraZeneca, Biogen, AbbVie and others are reportedly working with Genomics England on their project to sequence 100,000 genomes from 70,000 NHS patients with rare diseases and cancer. Both Roche and Pfizer have agreed on deals with 23andMe to access their community of patients with Parkinson’s and Crohn’s respectively, to look for genetic clues to their causes.
In addition, in 2011 the Chinese research company, BGI, announced that it would sequence a million human genomes, a million plant and animal genomes and a million micro-ecosystems. Although it may take a few more years to reach the “million goals”, the list of current BGI’s collaborative sequencing projects looks impressive.
Where are industry players heading?
Start-ups, ventures, and innovative solutions spring up day by day with a new generation of targeted interventions based on genomic analysis for a wide variety of diseases – being more efficient and causing fewer side effects than some treatments available today. In 2014, eight of the 41 new drugs approved by the FDA were targeted therapies. These include cancer drugs as well as other treatments for rare diseases.
In the field of cancer research, you can send your biopsy sample from the primer tumor tissue to a company for analysis. They extract the DNA of cancer cells, sequence its code and try to find mutations for which there are available clinical trials and treatments. Genome sequencing giant, Illumina offers the examination of known mutations in cancer-related genes to reduce the costs of treatment and do complete studies more quickly.
The Swiss company Oncompass offers oncological biopsy analysis to provide better, personalized treatment plans for each cancer patient. Boston-based Veritas Genetics offers whole genome sequencing, interpretation and genetic counseling for $999 for anyone. They also have the $299 myBRCA HiRisk test on the market, which gauges 26 genes associated with a heightened predisposition for breast, ovarian and other associated cancers.
Governments at the forefront of genomics?
Not only the research field and the market is buzzing around genomics and genome sequencing, but certain states also recognized the potential of the technology.
In April 2018, news outlets surfaced that one of the biggest state in India, Andhra Pradesh, will secure the DNA base of 50 million citizens through the blockchain. On 20 March 2018, Estonia launched the first stage of a national state-sponsored genetic testing and information serviceproviding 100,000 of its 1.3 million residents with information on their genetic risk for certain diseases. Already in 2015, MIT Review reported that a genetics company in Iceland named DeCode Genetics collected full DNA sequences on 10,000 individuals. And since the population in Iceland totals around 320,000 citizens, and they are fairly closely related, DeCode said it could extrapolate to accurately guess the DNA makeup of nearly the whole population of the country, including those who never participated in its studies.
How to make use of personal genomics’ full potential?
It seems that from government initiatives through the activities of start-ups until the missions of groundbreaking research projects, the ultimate goal of genome sequencing is to help bring healthcare into the era of preventive, personalized and preemptive medicine. The supporters of genome sequencing are not alone in their undertaking to introduce tools of precision medicine in healthcare. Home sensors, portable diagnostic devices or digital biomarkers all aim to level up the process of care.
However, it is unimaginably difficult to bring the achievements of the latest studies or the innovative solutions of start-ups in the hospitals. Not to say how arduous it is to analyze such incredible amounts of data, how problematic it is to turn the results of genomic research into evidence – to be used as new guidelines for clinicians, and so forth. Moreover, the widening access to genome sequencing introduces the patient as a potential source who brings sequenced genomic data to healthcare facilities. Although that’s an excellent achievement in itself: the arrival of empowered, actively engaged patients, but as praiseworthy as it is, another problem arises with it: how will doctors know if the information brought about by the patient is reliable?
Short-term recommendations for bringing genomics-based precision medicine closer
These questions require careful consideration, and urgent response from healthcare professionals, medical facilities as well as regulators and policy-makers since genome sequencing and precision medicine are knocking on our doors louder than ever – especially due to the efforts of grass root actors, such as tech companies or patients. The Medical Futurist believes that the following steps could help ease the burden in the short-term and support the introduction of genomics-based precision medicine in the healthcare ecosystem.
1) Lowering the price of genome sequencing
Industry efforts coupled with political initiatives are attempting to bring down the cost of genome sequencing way below $1,000. If the price of whole-genome sequencing were somewhere around that of a blood test, that would be the most effective way to bring the new technology into the hospitals.
2) Using the power of artificial narrow intelligence
Tech giants, such as IBM, Google, and Microsoft, as well as a series of start-up, such as the Hungarian Turbine, already leverage on the power of artificial intelligence in cancer research. They are building artificial intelligence solutions to design personalized treatments for any cancer type or patient faster than any traditional healthcare service. In case of IBM, they launched Watson for Oncology; Google has its Deepmind Health project; while Microsoft’s research machine-learning project, dubbed Hanover, aims to ingest all the papers and help predict which drugs and which combinations are the most effective.
However, A.I. could also be used in genomics research for building databases, finding the appropriate studies for a specific case in seconds and recommending the best targeted treatment based on the given individual’s whole genome.
3) Creating inclusive guidelines
Medical associations should show some openness when creating and updating the latest guidelines – the most important recommendations for clinicians. They should, in fact, include genomic data – moreover, all OMICS-data such as proteomics, epigenomics or lipidomics – as the future points towards their increased utilization.
4) The GDPR of Genomics? – Regulation of DTC genetic testing
At the moment, there are hundreds of companies around the world offering their genetic testing kits online. Some are available in the US, others in the EU, but due to a globalized economy, shipping services and the wonder called the Internet, testing kits could arrive at every corner of the world within a reasonable amount of time. Thus, regulators should come up with a unified regulatory framework for DTC genetic testing – the GDPR of genomics, if you wish – to ensure the reliability of the products and companies alongside with clear genomic data protection policies. In such a way, patients could walk into the office of their doctor with a lighter heart saying that here’s my genomic data, suggest me a targeted treatment if such a therapy is available.