2018: Population Studies, Immunotherapy, CRISPR, Genomic Medicine,…2019

2018 was full of significant developments in the life sciences, precision medicine, genetics, and genomics sector. Highlights and notable news included various technological advancements, new clinical applications of next-generation sequencing, success in population studies, genetics moving into the clinic, artificial intelligence and machine learning investments and potentials, immunotherapy further establishing itself as the leading weapon to attack cancer, the CRISPR technology being under fire, and more.

The significance of these developments is further manifested by clinical omics taking shape, hospitals adopting new applications, and testing and treatments coming into play that are based on next-generation sequencing or omics data. The results speak a clear language: improved diagnostic tests, and more precise therapeutics.

Here a few highlights – not an all-inclusive summary – of what made 2018 so exciting. Find a more complete list of 2018 news on the enlightenbio Industry News site.

Population studies taking shape

Various population studies/initiatives took shape this year, as demonstrated with projects such as…

• Pioneering 100,000 Genomics England project reaches its goal and thanks all involved of sequencing 100K genomes in the NHS,

• Finland’s FinnGenproject which aims to match genome information with over 500,000 blood samples,
• Estonia is starting a program to recruit and genotype 100,000 new biobank participants as part of its National Personalized Medicine program,
• the GIANT Consortium is subscribing an additional 1 million research participants to its study on the genetics and biology of height and obesity with data from 23andMe and the UK Biobank,
• the Nightingale Health and UK Biobank announcing a major initiative to analyze half a million blood samples to facilitate global medical research,
• and in the US all eyes are on the All of Us Research Program (PMI), now officially inviting all Americans to contribute to its massive genetic library.

These are exciting developments and progress milestones, and along with the rapid advancement of precision medicine, questions are arising on how to keep up with educating the public which generally lacks sufficient understanding of personalized medicine as demonstrated in a recently released survey. Furthermore, doctors are stressing the need to prioritize actionability of unsolicited genomic results (UGRs) and the need for clear, evidence-based paths coupled with clinical decision support to deal with patients and providers receiving UGRs.

Other initiatives worthwhile mentioning are….

• the newly formed Drug Company Consortium that intends to sequence the genes of 500,000 Britons over the next two years, for which Regeneron will handle the sequencing, and AbbVie, Alnylam Pharmaceuticals, AstraZeneca, Biogen, and Pfizer will contribute $10 million each to create the genetic data. The pharmaceutical firms will have access to this data for a year before they will make it available for free to any researcher expressing interest.
• TCGA Completes Comprehensive Genomic Analysis of 33 Cancer Types: After a decade of analyzing over 11,000 tumors from 33 types of cancer, the collaboration between the National Cancer Institute and National Human Genome Research Institute has launched the Pan-Cancer Atlas, providing a comprehensive understanding of three focus areas: cell-of-origin patterns, oncogenic processes, and signaling pathways.
• Last but not least, 13 countries have committed to sharing 1 million genomes for research and to working together to ensure secure and authorized cross-border access to genomic and other health data. The countries that have pledged to share one million genomes for research purpose by 2022 include the UK, Sweden, Finland, Czech Republic, Estonia, Spain, Portugal, Slovenia, Malta, Luxembourg, Lithuania, Greece and Italy.

Genomic medicine with next-generation sequencing and genetic testing reached new milestones

The first month of 2018 already was rich in content and activities as it started out with a series of announcements emerging from the JP Morgan Healthcare Conference:

• Illumina announced their latest sequencer, the $20K  iSeq 100 desktop sequencer.
• Scientists mapped the most complete human genome using the Oxford Nanopores pocket MinION device.

Towards the end of the year, Veritas Genetics announced that it temporarily lowered its whole genome sequencing and interpretation service to just $199 for 1,000 people.

Other notable genomic medicine highlights included:

• The FDA authorization of 23andMe’s new reporting of three of the more than 1,000 BRCA1/BRCA2 mutations which initiated major debates: through this authorization 23andMe’s report is now not only classified as a medical device, but it also requires the company to address and reduce risks to customers. However, since it is argued that this test will only be helpful to a small subset of people, it has been considered by some a pitfall of consumer breast cancer testing.
• The FDA finalized guidance to accelerate the development of reliable, beneficial next generation sequencing-based tests. The guidance is meant to  provide a modern and flexible framework to generate data needed to support the FDA’s review of NGS-based tests, and give developers new tools to support the efficient development and validation of related technologies.
• The FDA approved the first NGS-based companion Dx – the Thermo Fisher Scientific’ Oncomine DX Target Test, which has the potential to detect multiple lung cancer mutations. This approval clearly signals adoption of NGS-based tests for clinical diagnostics.
• Geisinger will make DNA sequencing a part of routine clinical care as they launched its clinical DNA sequencing initiative with a 1,000-patient pilot program
• Invitae shared news they will expand their reproductive health offering with the launch of comprehensive genetic carrier screening.
• The National Health Service (NHS) in the United Kingdom announced that all new cancer patients will have their tumors screened for key mutations. This makes NHS the first health service in the world to routinely offer genomic medicine which is predicted to transform NHS patient care in the years to come.
  • Furthermore, in October, the NHS’ Health and Social Care Secretary, Matt Hancock, shared the organization’s ambitious goal to sequence 5 million genomes in the UK, within five years.
• Iceland faces a DNA dilemma, specifically whether to notify people that carry cancer genes, as Icelandic regulators have determined that without that explicit consent, neither the government nor private industry can notify people of these risks. The origin of this traces back to the late 1990s when tens of thousands of Icelanders agreed to contribute their DNA to public and private science projects but never signed an explicit consent of being notified of personal health risks that might be discovered in the process.
• Stanford researcher Michael Snyder and colleagues used an approach that draws on genetic data and patient health records to predict a person’s risk for an often fatal type of cardiovascular disease, called abdominal aortic aneurysm (AAA).

It is expected that by 2025, the total amount of genomics data alone will equal or exceed data totals from the three other major producers of large amounts of data: astronomy, YouTube, and Twitter. The generation of most biomedical data is highly distributed, and data exist in a wide variety of formats, which complicates the ability of researchers to find and use biomedical research data generated by others, and creates the need for extensive data “cleaning”. In this context, the NIH released a strategic plan for data science. In addition, the deluge of data means that genetic counselors – the specialized medical professionals trained to help patients interpret genetic test results – are in higher demand than ever which coincided with the introduction of the Genetic counseling Medicare bill.

Large moves by big players that are transforming healthcare

Interesting large developments demonstrated that the healthcare sector is undergoing transformational change:

• Amazon announced a partnership with Berkshire Hathaway and J.P. Morgan Chase to improve health care for employees via the formation of an independent healthcare company.
• Researchers turned to Facebook to survey rare disease patients for study participation, as described by Nara Sobreira who successfully used the social media platform to contact patients with two rare diseases she has been studying.
• Hospitals fed up with drug companies started their own not-for-profit generic drug company, Civica Rx, to gain some level of control over the drug supply chain.
• CVS and Aetna merged, while Walgreens and LabCorp entered into a partnership.

The therapeutics sector – pharma / drug discovery

Some of the biggest discussions in 2018 followed the announcement that 23andMe is sharing its 5 million clients’ genetic data with drug giant GlaxoSmithKline. During the four-year collaboration GSK will be investing $300 million in 23andMe, and will use 23andMe’s database to gather insights translatable to the discovery of novel drug targets driving disease progression and the subsequent development of novel therapies. Some of the discussions centered around the fact that initially some customers may have not been made aware of their information and data provided potentially being used for this type of work. As a result 23andMe underscored that privacy-loving customers need to opt out of its data deal with GlaxoSmithKline.

In other news in 2018 another major pharmaceutical – the Swiss-based Novartis – announced it is dropping out of the antibiotics game, following many of their competitors in the industry. This development is alarming, as interestingly, much like climate change, the growing emergence of antibiotic-resistant bacterial superbugs is a ticking time bomb that has the potential to threaten our very way of life. It is also a very expensive problem to tackle, and big pharma has struggled to find promising solutions which is part of the reason the attention has turned to other medical challenges with a clearer path to both scientific and commercial success.

Technological advancements

Some of the recurring technological themes of 2018 included artificial intelligence/machine learning, blockchain, and scientific innovations such as the CRISPR technology, liquid biopsy, and single cell genomics.

• AI/machine learning
  • As we recall 2017 ended with Google releasing its DeepVariant tool, an AI technology-based tool for the analysis of human genome data made available via the Google Cloud Platform. This set the stage perfectly for AI/machine learning taking the spotlight in 2018. However, while AI is on everybody’s mind, still only a few successful applications have been published or been announced in 2018. As per Eric Topol: “there have only been 14 peer-reviewed publications involving computer-vision software interpreting medical imagery.” AI clearly is not just hype, but admittedly it is just not progressing as fast as one would have hoped.
• Blockchain technology
  • The blockchain technology saw a surge in use in the life science sector with several companies developing capabilities to share / sell their genome information via blockchain-supported DNA marketplaces. These companies are all on a mission to protect your DNA while at the same time productizing it. The success of these products builds on a critical mass of content for their respective target audience, the pharma industry for example. Companies to watch in this sector include, but are not limited to:
    • Luna DNA – announced that they will offer company stock options in exchange for your sequence data
    • Nebula Genomics – announced that they will offer genome sequencing for free (read enlightenbio’s interview with CEO Kamal Obbad of Nebula Genomics),
    • EncrypGen,
    • Zenome,
    • Genomes.io, and
    • Coral Health.
• CRISPR technology
  • While positive advancements were demonstrated, the CRISPR technology came under fire in 2018 as the CRISPR news were not all as rosy as the scientific community would have wished for. Yes, CRISPR’d cells (“rehomed” cells) have been shown to attack cells in the original tumor, or as demonstrated by scientists using CRISPR, one can create faster, more precise of engineering cancer-fighting T cells. Another success story involved the use of CRISPR to correct mutations that cause Marfan syndrome.
  • On the critical side, it was also reported that CRISPR DNA editing may cause serious genetic damages and unwanted DNA deletions, hundreds of times more frequent than previously known.
  • On the legal and regulatory side new challenges emerged, when interestingly, the European Court of Justice ruled on a much disputed labeling of the output of the CRISPR gene editing tool as “Genetically Modified” (GM). In other words, CRISPR-based gene editing is seen as a form of genetic engineering and as such should be regulated. The reasoning behind it stems from the agricultural sector and states that gene-edited crops should be subject to the same strict regulations the continent uses for genetically modified (GM) organisms. This ruling represents a major setback for advocates of genetically engineered crops.
  • Finally, 2018 ended for CRISPR surely on not exactly a high note! He Jiankui of the Southern University of Science and Technology (SUST), in Shenzhen, China, was coming forward with his controversial announcement that his team has used CRISPR to modulate the human genome by creating twin girls whose genes were edited to make them resistant to HIV. He is now not only facing investigation over whether the experiment broke Chinese laws and regulations, but also experiencing strong push back from the scientific community largely condemning his work as unethical and premature given the unknown risks and questionable benefits in the particular case. 

Immunotherapy further establishing itself as a leader to successfully attack cancer

Immunotherapy, with several approved treatments for various cancer types and its various therapeutic forms including CAR T-cells, immune checkpoint inhibitors, tumor infiltrating lymphocytes which were reported to successfully clear all tumors from a metastatic breast cancer patient, is currently being expanded with over 2,500 immunotherapy trials registered. Given the significant impact of immunotherapy on cancer treatment leading to changes of standard care in some of the broadest cancer types, it is not surprising that two immunotherapy pioneers – Dr. James Allison (MD Anderson Cancer Center), together with Dr. Tasuku Honjo (Kyoto University) – won the 2018 Nobel Prize in Medicine. Moving forward, we can surely expect 2019 to bring us new exciting research findings and additional promising clinical applications in particular in the area of combination therapies.

With more and more clinical experience gained on both the mechanism of action as well as the predictive marker aspects, we are also seeing some adjustments on utilization of these powerful new weapons in the fight against cancer:

• the FDA recently altered the approved use (changed the label) of two checkpoint inhibitors for bladder cancer (for pembrolizumab (Keytruda) and atezolizumab (Tecentriq) suggesting that they should be used as an initial, or first-line, treatment in only those people with metastatic bladder cancer who can’t receive cisplatin-based chemotherapy and whose tumors have high levels of PD-L1. The assessment of PD-L1 levels must be made using an FDA-cleared test.

Last, but not least, Stanford researches eliminated all traces of cancer, including distant metastasis, by activating T-cells in mice using a cancer vaccine breathing new life into the hopes of mobilizing a patient’s immune system through a vaccination route involving neoantigens identified on a patient specific level.

The not so rosy side of 2018

As is often the case in times of fast-paced development, there are also challenges and setbacks that need to be mentioned. A few listed here below…:

• Theranos CEO Holmes and Balwani have been charged with massive fraud and the company is now officially dissolved, leaving not only investors but patients and providers shaken and in disbelieve about the scope and scale of deceit.
• Study finds inaccuracies in 40% percent of DTC genetic testing results.
• The Center for Medicare & Medicaid Services reduced its funds to $10 million for its navigator program resulting in far fewer individuals signing-up for Obamacare.
• The European Court of Justice ruled the CRISPR gene editing tool as “Genetically Modified”, complicating the legal and regulatory landscape for promising application in agrobiotechnology.
• A Chinese scientist used the CRISPR technology to create twin girls whose genes were edited to make them resistant to HIV causing an uproar in the scientific community regarding the lack of ethical considerations and oversight

Mergers & Acquisitions

Various major acquisitions took place (the list shown below is not meant to be comprehensive)

Large investments in technologies and companies shape the industry

Investments were bountiful, especially in the sector of AI and machine learning (Tempus, Verge Genomics, and HealthMine), CRISPR (Inscripta, Broad Institute by Editas Medicine), in the therapeutic sector (FogPharma, Viela Bio, uBiome, and PharmEasy), as well as in blockchain technology (Nebula Genomics). Again the list shown below is not comprehensive.

To sum it all up – 2018 was an eventful and exciting year creating a foundation for what is to come in 2019.

We should expect larger technological advancements, with AI/machine learning taking the lead and big data applications such as in drug discovery and clinical decision-making benefiting from these; population initiatives are expected to be increasing its diversity to help explain genomic differences across populations; whole genome sequencing slowly but steadily will increase its footprint the clinical sector; translating the potential of liquid biopsy tests into cheap and accurate simple diagnostic tests; defining the role of the microbiome in multiple sclerosis, inflammatory bowel disease and even cancer; clinical genomics further improving health diagnostics; and much more. All of which will help translate genetic discoveries and expedite clinical applications. The JP Morgan healthcare conference, scheduled for the first half of January, will surely provide a first glimpse of what 2019 may be all about.