2021 – Precision Medicine linked with Genomic Medicine: A Work in Progress
2021 – A True Testimony that we Sit at The Intersection of Significant New Opportunities
The significant opportunities at the intersection of biology, technology, and big data and the advancements resulting from these opportunities are enormous and have allowed us to look at the bigger picture of population health, including the whole genome and exome. The resulting applications for genomic medicine are tremendous and include rare disease understanding, newborn screening, and precision medicine, as well as, new applications such as single cell genomics and spatial transcriptomics (read our AGBT conference blog with Spatial transcriptomics taking – yet again – center stage). The steady progress is reflected in national genomic data initiatives that focus on rare disease, cancer, infrastructure development, data integration, and population-based sequencing and includes existing initiatives such as the All of Us Research Program, the Genomics England Initiative, or the Qatar Genome Programme (QGP). In 2021 we also witnessed the $120M global iHope Genetic Health program launched by Illumina and Genetic Alliance with the aim to increase equity and improve outcomes for families impacted by genetic disease, the investment of $1.7 billion to improve the detection, monitoring, and mitigation of SARS-CoV-2 variants and to build infrastructure for future genomic sequencing needs by the Biden Administration, and the largest single release of whole genomes (200,000) by the UK Biobank (UKBB) for research purpose.
The developments the sector has brought us this year alone were of such significance and impact that it is not unreasonable to expect even more in 2022.
Companies have reached milestones: The Helix® Laboratory Platform was granted FDA authorization for a whole exome sequencing platform; Guardant360® CDx Liquid Biopsy was CE-marked for comprehensive tumor mutation profiling across all solid cancers; and DeepMind, in partnership with EMBL-EBI, announced the release of the predictive structure of all known proteins.
Many astounding acquisitions happened: Hologic acquired European molecular diagnostic company Diagenode, Agilent took over Resolution Bioscience, Roche bought GenMark Diagnostics, IDT acquired Swift Biosciences, One Medical acquired Iora Health, Immunai incorporated Nebion (read our interview with Nebion’s CEO Philip Zimmerman), Genome Medical announced the acquisition of GeneMatters, ProPhase Labs acquired whole genome sequencing company Nebula Genomics (read our interview with Nebula’s CEO Kamal Obbad), Hibercell took over Genuity Science, Bionano Genomics acquired BioDiscovery (read our interview with Sohail Shams, CEO of BioDiscovery), and 23andMe acquired Lemonaid Health.
While not an acquisition, it is worth mentioning, that Alphabet will be launching a new company that uses AI for drug discovery that builds on DeepMind’s work on protein folding.
IPOs were plentiful and included SOPHiA Genetics, Caribou Biosciences, and Oxford Nanopore. In addition, the digital health and genomics sector also witnessed a SPAC (Special Purpose Acquisition Company) boom as an approach to go public, which included companies such as 23andMe merging with Virgin Groups VG Acquisition Corp, Nautilus Biotechnology with Arya Sciences Acquisition Corp III, Sema4 with CM Life Sciences, Ginkgo Bioworks with Soaring Eagle Acquisition, and Roivant Sciences with Montes Archimedes Acquisition Corp. (MAAC).
Funding rounds were plentiful and included some significant investment numbers as shown here below:
- Color raised $167M (Series D) and another $100M (Series E)
- Liquid biopsy company Delfi Diagnostics raised $100M (Series A)
- Bluestart Genomics closed $70M (Series C)
- BioTheryX raised $92M (Series E)
- Cell and gene therapy company ElevatedBio raised $525M (Series C)
- Caribou Biosciences raised $115M (Series C)
- insitro raised $400M (Series C)
- EdiGene raised $62M (Series B)
- Inscripta closed $150M (Series E) Financing
- Helix raised $50M Series C
- Element Biosciences closed $276M (Series C)
- Deep Genomics raised $180M in Series C Financing
- Strata Oncology completed a $90M financing round (Series C)
- Mammoth Biosciences raised $195M
- ReCode Therapeutics raised $80M (Series B)
- DNA Script raised $165M (Series C)
- GenapSys closed $70M (Series D)
Omics platforms making (clinical) strides
On the omics platform front major developments have created new excitement with PacBio and Invitae entering a multi-year collaboration to develop a production-scale, high-throughput clinical whole genome sequencing platform, Illumina launching Illumina Connected Analytics (ICA), a cloud-based platform for multi-omics data exploration, Oxford Nanopore announcing the global distribution agreement with Avantor® for handheld MinION DNA/RNA sequencer, and Singular Genomics launching the G4 Sequencing Platform. And on a separate note: Illumina co-founder Mark Chee has moved from the genome to the proteome with his new startup Encodia.
Spatial transcriptomics goes mainstream
Last, but not least, there have been a number of platform, services, and assay releases in the spatial omics sector with Rebus Biosystems launching their spatial transcriptomics analysis platform, 10x Genomics their new Visium assay for whole transcriptome analysis in FFPE tissues, Resolve Biosciences their commercial Molecular Cartography Services, NanoString a Technology Access Program for their Spatial Molecular Imager (SMI) Platform, Vizgen a data release program and shares spatial genomics mouse brain map, while Akoya was announcing the rollout of a strategic clinical research program to advance adoption of spatial biology for clinical applications.
Select scientific genomics and precision medicine research publications and highlights
- An entire special Cell Genomics CellPress issue was dedicated to the work done by the Global Alliance for Genomics and Health (GA4GH)
- Exome sequencing and analysis of 454,787 UK Biobank participants
- An NYU study finds that ultrasound-analyzing AI improves breast cancer diagnoses by 37%
- Sequencing of 640,000 exomes resulted in the identification of mutations associated with protection from obesity.
- The Science and Art of Clinical Genetic Variant Classification and Its Impact on Test Accuracy
- ACMG has released an updated policy statement and gene list for the reporting of secondary findings (SF)
- Multi-Institutional Validation of a Mammography-Based Breast Cancer Risk Model
And the 2021 Nobel Prizes for Physiology or Medicine and Chemistry went to…
Surprisingly, we did not see a much anticipated award for the mRNA technology underlying some of the most prominent vaccines that have been instrumental in our fight against the COVID-19 pandemic. The Nobel Prize in Physiology or Medicine went to David Julius, UCSF and Ardem Patapoutian for their discoveries of receptors for temperature and touch, while the Nobel Prize in Chemistry was awarded to David W.C. MacMillan (Princeton University) and Benjamin List (Max Planck Institute) for the development of asymmetric organocatalysis.
Challenges and setbacks
As often the case in times of fast-paced developments, there are of course also challenges and set-backs that happened along the way and thus ought to be mentioned: the lack of representation of minority groups in genomic datasets that could affect cancer outcomes and therapy selection, uBiome co-founders being charged by the SEC with $60M fraud, Illumina being challenged by the EU antitrust regulators for the takeover of GRAIL after Illumina filed action for annulment of the European’s Commissions’ decision, or the challenges of creating effective drugs that fight diseases such as Alzheimer’s considering the marketing clearance of the much debated Alzheimer’s drug, Aduhelm, by the FDA which resulted in the resignation of three FDA advisers due to the fact that the approval was based on incomplete or unpublished data. And as an interesting recent development Biogen just dropped the price of Aduhelm by 50% (from $56K to $28K annual cost) to drive broader acceptance and uptake in the marketplace after disappointing sales so far.
And Last, but not least, COVID-19
No healthcare news blog is complete these days without a reference to the ongoing pandemic that dominates the public debate on health and disease:
Omicron a blessing in disguise?
2021 was in many ways a better year than 2020, but yes, we still need to turn the corner when it comes to COVID-19, especially now with Omicron becoming the dominant strain. But after all Omicron may be a “blessing in disguise”. Fingers crossed, that Omicron is truly not as dangerous in terms of disease outcome and will over time be displacing Delta, its predecessor which was first identified in India in late 2020 (see our Review on SARS-CoV-2 Variants).
A recent South Africa study highlighted that 90% of all Omicron infections are asymptomatic (up from 40%), come with a substantially lower risk of hospitalization (80% lower), and compared to the Delta variant, have 70% lower odds of severe disease. While it is too early to call out a specific death rate, the hope is that it will be substantially lower than the one related to Delta. The parallels to the Spanish flu are striking, possibly suggesting that we currently witness a pandemic virus mutating into a variant that causes milder infections, and thus transforming COVID-19 into an endemic disease that eventually manifests itself at lower, manageable levels.
Effective vaccines and novel COVID-19 oral antivirals
By now 8.81 billion doses of the anti-COVID-19 vaccines were administered globally, resulting in 48.3% of the entire world population being fully vaccinated (61.7% in the U.S.). This achievement is tremendous considering that the vaccines (Pfizer-BioNTech, Moderna) only received FDA EUA in December 2020. While the first experimental mRNA vaccines were being tested in the mid-1990s, key advances in both mRNA design and nanoparticle encapsulation underlying the vaccines developed by Moderna and by Pfizer-BioNTech didn’t arrive until the 2000s. Furthermore, the technology’s massive impact – enabling product development speeds not seen before – wasn’t apparent until early this year. Consult our COVID-19 vaccines blog post for more details.
Coinciding with the recent Omicron variant emergence, novel COVID-19 antiviral treatments have received FDA Emergency Use Authorization. Both Pfizer’s drug PAXLOVID and the Merck’s/Ridgeback’s MOLNUPIRAVIR have been authorized as additional treatment options and could very well represent game changers in areas and situations where vaccines are not (yet) widely available.
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