The potential of
low cost sequencing beyond Oncology

January 3, 2023

Sequencing gets cheaper and faster:

In 2003, the Human Genome Project sequenced the first human genome which cost $3B and took 13 years to complete. Since then, the cost to sequence human genomes and exomes has declined exponentially even as speed has increased, allowing genomic data to become accessible for researchers and clinicians across disease areas. With the recent launch of Illumina’s NovaSeqX, the cost of sequencing could soon drop further and the NovaSeqX will be capable of generating more than 20,000 whole genomes a year. Increasing competition from genomic sequencing companies like Oxford Nanopore, 10X Genomics, Thermo Fisher, Pacific Biosciences and Singular Genomics will only reduce costs and further expand the use of genomics and emerging omics like single cell and proteomics in research and clinical care.

What does this mean for drug development?

The ubiquity of genomic data that has resulted from this availability of sequencing technology is unparalleled to anything we’ve seen before and is starting to bring to life the vision that President Obama laid out in 2016’s Precision Medicine Initiative. Sequencing more patient genomes across a wide range of disease areas and patient demographics allows researchers to better stratify populations for therapeutic development based on patients’ unique genomic signatures. This means that we can better take into account genetic variations in addition to clinical variations that impact whether a patient responds to treatment and how safe that treatment is to take. Although we’ve made significant progress in genome sequencing, we are only at the beginning of characterizing the diverse cohorts of genomes needed by researchers and practicing clinicians alike to understand the nuances of complex disease.

What can we learn from oncology and apply to autoimmune diseases?

In 2005, two years after the Human Genome Project sequenced the full genome, the National Cancer Institute and the National Human Genome Research Institute launched The Cancer Genome Atlas Project which aimed to develop a comprehensive understanding of the genomes of three cancers – lung, ovarian, and glioblastoma. In the years since, targeted therapies have become increasingly common in oncology. Cheaper sequencing and availability of next generation sequencing testing (NGS) in clinical care has allowed researchers to gain a deeper understanding of genetic drivers of tumors, molecular signatures and the mutational landscape of cancers which has led to these innovations in cancer treatment. Now many mutations in genes like EGFR, PD-L1, ALK, BRAF and others, are instrumental in patient diagnosis and treatment strategies used in the oncology community by drug developers and clinicians in the standard care of patients. Many other less well known biomarkers are the subject of clinical research to expand eligible populations and test new therapies in sub populations to develop treatment strategies where none existed previously.

Outside of Oncology however, genomic diagnostic tests and genomic data in drug development are less common. Autoimmune diseases with great unmet need such as MS, RA, IBD, Crohn’s disease and others, make up 3-5% of all human diseases and are heterogeneous in their clinical presentations. Studies that use sequencing data to screen relevant patient populations, validate findings in patient cohorts, identify novel targets or assess molecular signatures associated with outcomes are just starting to take off for autoimmune conditions. Although several genome-wide association studies (GWAS) for autoimmune are known, deeper genomic analysis will be required to identify prognostic and therapy predictive genomic biomarkers at more precise detail allowed by whole genome sequencing (WGS).

In IBD, for example, we have seen GWAS and proteomics studies that assess mechanism(s) of action, genomic causal factors and susceptibility to disease in patients. RNA seq, has been used to assess transcriptomic differences in mucosa of Crohn’s patients compared to healthy tissue. We also see large pharma companies like Pfizer, J&J and Merck investing in companies like Nucleome Therapeutics which aim to mine the genome for precision medicines to treat autoimmune disease. Although progress has been made in some areas we have yet to see this translate into standard clinical care or personalized therapies.

Looking to the future:

In order to maximize efficacy and minimize toxicity for patients, we need to incorporate patient stratification with greater levels of granularity, including genomic variations, into research as standard practice, which will lead to better and more targeted therapies coming to market in the future. As the cost benefit increases given lower costs of sequencing in disease areas like IBD, and other autoimmune disorders, we hope to see more interest from drug manufacturers in targeting biomarker driven therapies to patients in these chronic disease areas with unmet need.

Learn more about how Ovation is helping researchers access genomic data in IBD.

 

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