2024 was a true testimony to the fact that we are positioned at the intersection of significant AI opportunities and this in parallel to trends in declining costs of next-generation sequencing (NGS): healthcare, technology, AI, and big data. The technological advancements resulting from these opportunities are enormous and have allowed us to look at the bigger picture and complex biologic systems: multi-omics applications; protein structure prediction; efficient and accurate analysis of exponentially growing data, which has freed us from limiting ourselves with single data points.
The resulting applications are tremendous as we enter the era of rare disease understanding, newborn screening, protein structure prediction, advanced clinical trial development, and much more. The changes the sector has brought this year alone were of great significance and impact, and that we can expect even bigger developments in 2025. Companies have reached milestones that, until recently, seemed out of reach: Ultima Genomics launched high-end DNA sequencers that can read a genome for $100; Nucleus Genomics brought whole-genome sequencing to the public; the FDA approved Guardant Health’s Shield Blood test as a primary screening option for colorectal cancer, PacBio announced SPRQ Chemistry for Revio Sequencing Systems, a major advance in reducing the cost of a HiFi Human Genome to less than $500; Illumina introduced the MiSeq i100 Series: its simplest, fastest benchtop sequencers; Myriad Genetics and Ultima Genomics are jointly exploring the UG 100™ sequencing platform to advance clinical test offerings in oncology and reproductive genomics; and Illumina won its Grail battle in blow to EU merger power. Lastly, worth pointing out, Jill Biden announcing a $110M ARPA-H funding award, in support of women’s health.
In parallel, astounding mergers and acquisitions happened: Novartis acquired Kate Therapeutics for $1.1B, Tempus AI bought genetic testing company Ambry Genetics for $600M, Benchling acquired PipeBio to accelerate AI-powered antibody discovery, Danaher acquired Swiss Informatics Firm Genedata, Recursion bought smaller peer Exscientia for $688 million, and Thermo Fisher Scientific has completed its acquisition of Olink, a provider of next-generation proteomics solutions.
Major activity in the AI sector included the introduction of AlphaFold 3, a new AI model developed by Google DeepMind and Isomorphic Labs, accurately predicting the structure of proteins, DNA, RNA, ligands and more, and how they interact with each other. Clearly, AlphaFold 3 brings the biological world into high definition. It allows scientists to see cellular systems in all their complexity, across structures, interactions and modifications. This new window on the molecules of life reveals how they’re all connected and interact and helps understand how those connections affect biological functions — such as the actions of drugs, the production of hormones and the health-preserving process of DNA repair. Federal regulators are scrambling to keep up with AI in healthcare and are teaming up with industry players to set standards; Google launched AI-backed search-and-answer tool for doctors; and lastly, AlphaFold2’s Demis Hassabis and John Jumper received the much deserved Nobel Prize in chemistry for their AI model, predicting proteins’ complex structures.
While these exciting developments are offering many new opportunities, they will certainly also complicate matters, at least in the beginning phase of this new era. They will impact how studies have to been conducted and how data has to be collected, structured, and analyzed for standardized clinical applications and understanding, and at the same time these developments will also highlight the lack of regulatory guidelines.
As is often the case in times of fast-paced development, there are also challenges and set-backs that we need to be aware of: Invitae filed for Chapter 11 bankruptcy protection while pursuing its sale process; NanoString filed for Chapter 11 bankruptcy protection, while exploring a potential sale amid patent battle with 10x Genomics; All of Us Research Program received $357M, or 34%, less funding compared to the prior year which will result in several challenges, including a decrease in the rate of new enrollments, a delay in the launch of pediatric enrollment, and a slowing of new data collection; and 23andMe cut 40% of its workforce and discontinuing all therapy programs.
Exciting, noteworthy publications included
- A research study demonstrating that functions and risks of aging-related diseases change nonlinearly across the human lifespan, with substantial dysregulation occurring at two major periods at approximately 44 years and 60 years of chronological age.
- Brain clocks capturing diversity and disparities in aging and dementia across geographically diverse populations across 5,306 participants from 15 countries.
- Deciphering proteins in Alzheimer’s disease: A new Mendelian randomization method integrated with AlphaFold3 for 3D structure prediction
- Homozygosity for a stop-gain variant in CCDC201 causes primary ovarian insufficiency as shown with data analyzing over 174,000 women.
- Nature publishing a collection of research articles and content related to the Human Cell Atlas, with research supported by CZI.
- Human Cell Atlas consortium presents tools, data, and ideas towards the generation of their first draft atlas of cells in the human body.
- Genome Research publishing a special collection on long-read DNA and RNA sequencing, highlighting the advances in long-read sequencing applications in biology and medicine.
- Long-read DNA and RNA Sequencing, a Special Collection by Genome Research. This special issue (Volume 34, Number 11) highlights advances in long-read sequencing applications in biology and medicine.
- Deep generative AI models analyzing circulating orphan non-coding RNAs enable detection of early-stage lung cancer.
- Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections.
- Comprehensive genome analysis and variant detection at scale using DRAGEN Illumina’s DRAGEN outperforms current state-of-the-art methods (Google DeepVariant, Broad GATK) in speed and accuracy.
- The 1% gift to humanity: The Human Genome Project II Scientists are calling for human genomic research to be vastly expanded and widened to include many more people so it can fully deliver on its promise of becoming a tool for improved health care for all of humanity.
- Homozygosity for a stop-gain variant in CCDC201 causes primary ovarian insufficiency Scientists at deCODE genetics and collaborators, have identified a sequence variant in the CCDC201 gene that when inherited from both parents causes menopause homozygous women on average nine years earlier. By analyzing data from over 174,000 women across Iceland, Denmark, the UK, and Norway, the researchers discovered a stop gain variant leading to a change from and Arginine at position 162 to Termination in the CCDC201 gene, that dramatically impacts AOM.
- Genome-scale quantification and prediction of pathogenic stop codon readthrough by small molecules.
- Circular RNA in cancer New study published in Nature Reviews Cancer, predicts remarkable potential for circular RNAs to improve cancer treatment and patient outcomes within the next 5–10 years.
- Spatial molecular profiling of mixed invasive ductal and lobular breast cancers reveals heterogeneity in intrinsic molecular subtypes, oncogenic signatures, and mutations.
- Benefits for children with suspected cancer from routine whole-genome sequencing This study is the first time that the impact of using whole genome sequencing in current NHS practice has been assessed.
- Exome sequence analysis identifies rare coding variants associated with a machine learning-based marker for coronary artery disease.
Month by month news highlights
In the month of January, a study led by Genomics, NHS England, Queen Mary University of London, Guy’s and St Thomas’ NHS Foundation Trust and the University of Westminster provided valuable insights for precision oncology from the integration of genomic and clinical data of 13,880 tumors from the 100,000 Genomes Cancer Programme. The analyzed data, covering over 30 types of solid tumors collected from more than 13,000 participants with cancer in the 100,000 Genomes Project, were able to find specific genetic changes in the cancer associated with better or worse survival rates and improved patient outcomes.
During the month of February, the All of Us Research Program published their landmark paper demonstrating the most diverse biobank to date with half of the genomes from non-Europeans. Furthermore, the All of US Research Program identified more than 1 billion genetic variants, including more than 275 million previously unreported genetic variants, more than 3.9 million of which had coding consequences. Leveraging linkage between genomic data and the longitudinal electronic health record suggested that 3,724 genetic variants are associated with 117 diseases with high replication rates across both participants of European ancestry and participants of African ancestry.
In March, Thierry Bernard (CEO, QIAGEN) and Scott Whitaker (CEO, AdvaMed) published an important opinion piece: Putting Patients First: Why Congress Must Pass Diagnostic Test Reform. The article highlights the critical role of diagnostics in healthcare decisions, and the need for consistent standards and collaborations between private and public sectors to improve patient care. It touches on the impact of the COVID-19 pandemic, which brought the relevance of diagnostics in the healthcare value chain into focus. It also proves that patient care makes tremendous progress when private and public stakeholders come together and act as one. Today, hospitals are, on average, spending less than 4% of their budget on diagnostics, while – at the very least – over 70% of the medical decisions taken for a given patient are impacted by a diagnostic result.
During the month of April, the Office of Information and Regulatory Affairs (OIRA) at the White House, has cleared the long-awaited proposed rule by the FDA, approving a significant step towards the regulation of laboratory diagnostics tests (LDTs) under the agency’s oversight. This is a monumental milestone that will have far-reaching implications for clinical labs operating under CLIA and offering LTDs. The FDA is expected to publish the final rule anytime soon, with no major changes expected from the proposed version. The ruling will raise many questions and challenges for clinical labs.
In the month of May, the FDA has brought oversight to LTDs in a bid to improve accuracy and safety. The oversight will gradually be phased in and will apply to new tests developed by laboratories, a multibillion-dollar industry that regulators say poses growing risks to Americans. The goal is to ensure that new tests for genetic conditions, cancer, heart disease, COVID-19, and many other illnesses are safe, accurate and reliable. While the changes to the final rule lessen the burdens many laboratories were anticipating, laboratories still need to invest significant time, money, and other resources to understand the new regulations and comply.
During the month of July, we saw lots of activity in the funding sector, with Element Biosciences taking the lead, raising over $277M to develop and commercialize differentiated products and continue its rapid growth, Truvian Health raising $74M to bring blood testing to anyone anywhere, and Foresight Diagnostics raising $73.75M to advance the Forsight CLARITY™ MRD platform. Around the same time Agilent announced that they will acquire CDMO BioVectra for nearly $1B, Illumina will acquire Fluent BioSciences to accelerate single-cell analysis and discovery to broaden its customer base, and Thermo Fisher Scientific completed its Olink acquisition – the transaction values Olink at approximately $3.1B.
News worthy of mentioning for the month of August include the 23andMe board rejecting CEO Wojcicki’s take-private proposal, 23andMe cutting back on drug research and moving to weight loss, Danaher acquiring Swiss informatics company Genedata, Recursion buying peer company Exscientia for $688M, Roche considering selling cancer startup Flatiron Health, Walgreens landing $100M U.S. clinical trials partnership, and Genentech shutting down its cancer immunology research department.
One of the big headlines for the month of September included Illumina winning its battle against the European Union’s investigation of its $7.1billion purchase of cancer diagnostic test maker Grail. This annulment has important knock-on effects for Illumina: the EC’s record €432 million fine on Illumina for implementing the transaction without prior EC approval now falls away, and Illumina’s challenge to the EC’s prohibition of the deal is moot. With this, the ECJ’s (European Court of Justice) ruling is final.
October is the month of the Nobel Prize announcements. This year’s Nobel Prizes went to AI research as well as to the discovery of microRNA. Specifically, the Noble Prize in Physiology and Medicine recognized Victor Ambros and Gary Ruvkun for their discovery of microRNA, which helps determine how cells develop and function. AI was the big winner in both Physics and Chemistry. This year’s physics laureates – John J. Hopfield and Geoffrey E. Hinton- showed a completely new way for us to use computers to aid and to guide us in tackling many of the challenges our society face, while this year’s chemistry laureates – Demis Hassabis and John Jumper – have developed an AI model, AlphaFold2, to solve a 50-year-old problem: predicting proteins’ complex structures.
In the month of November, we saw some major acquisitions, including Novartis acquiring Kate Therapeutics for $1.1 billion for its gene therapy and Tempus AI acquiring genetic testing company Ambry Genetics for $600 million. Other news included, Oxford Nanopore and UK Biobank announcing the creation of the world’s first epigenetic dataset targeting the cause of cancer, dementia, and complex disease, 23andMe cutting 40% of its workforce and discontinuing all therapy programs, but while also notching a research partnership with Mirador Therapeutics to provide the biotech company with access to its trove of genetic data, the WHO releasing a handbook for digital transformation in primary care, and the new administration naming Dr. Mehmet Oz to head Centers for Medicare and Medicaid Services.
To sum it all up: 2024 was an eventful and exciting year setting the stage for what we may expect to hear in 2025.
We should expect to witness significant technological advancements, with AI/machine learning taking the lead and big data applications such as in drug discovery and clinical decision-making benefitting from these. The 2025 JP Morgan healthcare conference, January 13-16, will surely again live up to its reputation of providing a first comprehensive glimpse of what the new year has in store of us.
