Those of you who follow The Genetic Link know that our top 10 list is an annual article we have published since 2010. Each year, we highlight the key scientific advancements from DNA Genotek’s perspective. In the 10 plus years we have written this annual article, never did we imagine a year like 2020. Despite a year unlike any other, researchers and clinicians rose to all manner of challenges and kept the scientific field moving forward. Here is our top 10 list for this unforgettable year.
It is impossible to write a top 10 list for the year without acknowledging the overwhelming impact of COVID-19. The deadly virus that swept the world dominated headlines as it killed over a million people, sickened tens of millions more and prompted profound social and economic dislocation. The pandemic burst into the collective consciousness in March, infusing conversations and news reports alike. Lockdowns, closed businesses, laboratories and research facilities, social distancing, shortages of critical PPE and testing supplies, hospitals over capacity and exhausted frontline workers all became part of our daily vernacular. This was, quite simply, the story of the year.
The past year was significant for those involved in the microbiome clinical trials. There was significant growth in the publication of clinical data for microbiome projects and in September, the first microbiome-based drug cleared phase III in clinical trial. The role of the microbiome in healthcare is coming of age. Diversigen, our microbiome services sister company, began building its microbiome data pipeline this year by signing a collaboration agreement for a research study on patients with Acute Severe Ulcerative Colitis (ASUC) with Alimentiv. The data will be co-published upon completion of the study. Diversigen expanded their customer base with organizations like Nom Nom and Pure Culture Beauty joining the growing list of microbiome companies turning to Diversigen for services. We know that microbiome sequencing, bioinformatics, and statistical analysis is needed to facilitate the study of the microbiome and we look forward to the possibilities of deriving new data insights that could lead to improvements in treatments.
The shift toward analytes beyond DNA is occurring rapidly as life science researchers are increasingly adopting a multiomic approach. The use of multiomics techniques (i.e., genomics, microbiome, transcriptomics, proteomics, and metabolomics) is becoming increasingly popular in all facets of life science. Multiomics approaches integrate data from multiple omes and provide a more holistic approach compared to traditional approaches. This year, we continued to evolve our multiomic offerings by deploying our technology to create and capture value from multiple sample types and multiple analytes beyond nucleic acids. First, we created a new product for metabolites, which are the products of metabolic activity within people’s bodies, which help scientists understand the influences of genes, microbiome, diet, life style and drug treatment on the state of health and progression of disease. In June, we launched a new collection device and the stabilization chemistry necessary to protect the sensitive nature of metabolites in feces and ensure sample integrity. We were proud to collaborate with Metabolon, Inc., the metabolomics market leader, to validate the performance of the OMNImet™·GUT collection device. Second, we launched the OMNIgene®·SKIN microbiome collection kit (OMR-140) for research use, expanding the list of sample types supported by our product family. OMNIgene·SKIN offers a standard method for collecting skin microbiome samples from sebaceous, dry and wet skin sites which will aid researchers in obtaining reproducible high quality samples. This also marked the first time that DNA Genotek and our Diversigen microbiome services sister company collaborated to develop sample processing, sequencing and analysis approaches optimized for OMNIgene·SKIN that solve many of the common challenges facing skin microbiome researchers. This is a key milestone in the evolution of our multiomics vision for the company.
This year, there were many research projects focused on studying the virus as we tried to understand the novel RNA virus. Here are just a few of the many studies that addressed human genomics and COVID-19 susceptibility and severity:
Continued research to understand variations in the SARS-CoV-2 genome will provide critical insight for the developmental history of the pandemic and disease management.
When the global pandemic was declared in March and there was a worldwide shortage of testing supplies, we immediately began looking for ways to help. We started with our collection kits that detected RNA and began collaborating with customers to validate use to detect the SARS-CoV-2 virus. It was quickly apparent that both OMNIgene·ORAL (OM/E-505) and ORAcollect·RNA (OR/E-100) were able to detect the virus when combined with a PCR-based SARS-CoV-2 assay. Over the course of the year, we worked with 7 customers to obtain EUAs from the FDA for our devices in conjunction with the customers’ COVID-19 laboratory test. We were also granted device EUAs from the FDA for both the OMNIgene·ORAL (OM/E-505) and ORAcollect·RNA (OR/E-100). I am so proud of the DNA Genotek team for their rapid response to support our customers and bring non-invasive COVID-19 collection devices to address this pandemic.
[4] Over the years, urine has shown great potential as a sample type in areas including infectious disease and oncology. Urine is being evaluated as part of research studies and we are learning more every day. One field where urine has gained acceptance is in cervical cancer screening. As we know, cervical cancer can be prevented through vaccination and screening; however, it remains the fourth most common cancer type in women. While regular cytology-based screening via a Pap smear has directly shown to improve incidence and mortality rates, screening up-take varies from region to region. Many women are often reluctant to undergo a Pap smear because it is invasive and associated with physical discomfort. Consequently, self-collection techniques, including urine sampling has been recommended to improve screening coverage, as it is easy, non-invasive and can be performed independently at home. Interestingly, urine fractions are not the same. First-void urine (initial urine flow) contains higher concentrations of Human Papillomavirus (HPV) DNA, the primary cause of cervical cancer, than midstream urine. First-void urine has also shown to contain higher concentrations of other sexually transmitted infections (STIs) related DNA and cancer biomarkers, such as prostate cancer.[5] Colli-Pee®, an innovative urine self-collection solution from our sister company Novosanis, allows standardized, and volumetric collection of first-void urine. The device architecture also enables immediate mixing of the sample with a urine preservative, improving the stability of the sample. As the move to non-invasive self-sampling continues, we are excited to see the role of urine in various fields.
The human genomics community in the bio-pharmaceutical industry is growing rapidly, however the healthcare provider’s genomic experts (such as genetic counselors and more) is not growing at the same rate. Industries are trying to educate and advocate the benefits of human genetics to people everywhere, so they can unite the diagnostic/bio-pharmaceutical companies and healthcare providers to conduct biomedical research and translate actionable information to patients. This would increase the number of genetic experts in healthcare institutions as pharmacogenomics becomes more common.[6] An example of this relationship between diagnostic companies and healthcare providers happened this year with Helix and Renown Institute for Health Innovation (Renown IHI) in Nevada in January [Learn more about the partnership between Helix and Renown IHI here]. Companies like Invitae acquired ArcherDx to accelerate the utilization of genetic information throughout a cancer patients' journey. [For more information you can read Invitae’s press release].
We define multiomics as the approach where the insights from two or more “omics” data sets (genomic, transcriptomic, proteomic, metabolomics, lipidomics, immunomics, etc.) are combined during the analysis to derive biological correlation or association. In 2020, it’s clear that the focus is no longer merely on human genomics, but how our genome links and interacts to other “–omes”, such as the proteome, transcriptome, epigenome, and microbiome. This year, we saw more multiomic research, more funding to multiomics projects, more start-up companies developing multiomic platforms for precision diagnostics and more work to take complex multiomics data and combine it with patient-friendly visualizations. I can’t wait to see watch this expand further in 2021.
In recent years, the increase in microbiome sequencing data output during the few years has not been matched with additional data processing or data integration. This hinders the ability to mine the data for other applications and prevents meta-analysis of the data using new strategies and tools that have the potential to increase the power of individual studies and generate valuable insights. As I look to 2021, I see the beginnings of a change in approach – one that maximizes the sequencing data generated in current research studies while transforming the deluge of data from a problem to a solution. This includes a long-term strategy that will support the anticipated data growth, and that will ensure that the data revolution efficiently addresses fundamental biological questions critical to human health, biotechnology, energy, food, and more. This will be a very exciting field to watch in the next 5 years.
The field of genomics has surpassed expectations over the past three decades, due to massive changes in technology that allowed researchers to interrogate larger pieces of the human genome. Workflow simplification, continued cost reductions, and enhanced bioinformatics capabilities, will facilitate NGS adoption for research studies. We are also seeing a broader adoption of NGS-based testing in clinical markets in the areas of oncology, reproductive health, and genetics. We are only at the beginning of the genomics revolution and there’s so much more to come.
I have no resolutions for 2021, only hope. The world was rocked by the COVID-19 pandemic this year but researchers and clinicians rose to all manner of challenges. The scientific community proved it is resilient in the face of lockdowns and restrictions by continuing to deliver astounding accomplishments in the development of diagnostics, research and vaccines. This is a testament to the creativity and dedication of the scientific community. COVID-19 cast a light on our society and its divides but also showed us how we can unite for the common good. That is the hope I carry with me. Welcome 2021. We’ve been waiting for you.
[1] Kosmicki, J. et al. Abstract: Trans-ancestry imputation and exome sequencing of 868,021 individuals identifies 4 loci and 3 genes associated with COVID-19 susceptibility and hospitalization. Presented at the American Society of Human Genetics 2020 Virtual Meeting.
[2] Ganna, A. et al. Abstract: The COVID-19 host genetics initiative identifies genetic factors associated with COVID-19 susceptibility, severity, and outcomes. Presented at the American Society of Human Genetics 2020 Virtual Meeting.
[3] Banday, A.R. et al. Abstract: The discovery of a novel primate-specific and inducible truncated isoform of ACE2 and its implications for SARS-Cov-2 infection. Presented at the American Society of Human Genetics 2020 Virtual Meeting.
[4] For research use only in the Unites States.
[5] https://www.sciencedirect.com/science/article/pii/S016609341830329X?via%3Dihub, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6500257/,
https://pubmed.ncbi.nlm.nih.gov/19759844/
[6] Presidential Symposium. The Big Tent of Genetics and Genomics: Research, Translation, and Advocacy. ASHG 2020