Overcoming Challenges To Effectively Leverage Genomic Biomarkers In Precision Oncology

The genomics landscape is constantly evolving as more genetic variants and epigenetic patterns are identified as biomarkers of disease progression, remission, or drug response. Precision medicine, a new, more personalized way to diagnose and treat patients based on genetic biomarkers, is driven by these emerging insights from advanced technology, analysis, and bioinformatics. In particular, there are many oncology indications with genomic variants that affect how the patient responds; these therapies can be designed specifically for these targets instead of a broader approach to cancer treatment like surgery, radiation, and chemotherapy. At Discovery, we have solutions that allow for tumor characterization as well as many other tissues/fluids across disease types to advance precision medicine with experts to design and validate clinical trial biomarkers every step of the way.

1. Integrating evolving and complex genomic technologies into development programs:

In the field of  genomics, the 21st century brought rapid discovery, transformative technological development and significantly decreased costs. The field has graduated from the human genome project, which involved international resources, took more than a decade to complete, and cost billions of dollars, to sequencing individual genomes quickly at a fraction of the cost. This explosion of technological advances creates a paradox for researchers leading precision oncology programs. On one hand, innovative technologies provide new, revolutionary ways to gain genomic insights that can create new paradigms in patient treatment. On the other hand, more information introduces myriad questions for developers to carefully navigate. Which technologies are best to solve complex, multi-faceted questions during drug and diagnostic development? How should the data from these technologies be interpreted and validated? Are there improved sample preparation, processing or workflow advances that can help save time, money, and unlock insights from samples previously thought impossible?

2. Embracing and Utilizing Multi-omics:

There is a substantial array of expanding requirements for multi-layered approaches across each individual for biomarker characterization in drug development and diagnostics. Use of genetics, transcriptomics, epigenomics, proteomics, metabolomics, and digital pathology to analyze tumors, adjacent tissues, peripheral blood, and other body fluids alongside patient history and clinical outcome data are needed for drug and diagnostic developers to construct a comprehensive profile of the patient’s condition and identify targets for treatment or stratification.

3. Leveraging Data to Stratify Patients in Context:

In addition, it’s challenging to accurately stratify patients to increase efficacy and safety of novel therapeutics. While larger panels and multi-omic testing can increase the likelihood of biomarker discovery, they also create unactionable noise. To interpret increasingly complex data sets, strategic analytical and bioinformatics approaches are required to ensure quality control, accurate data analysis, biomarker discovery, and validation. Compounding data issues is the need to ensure the data is produced in context, i.e. study cohorts must comprise a diverse range of samples from patients that mirror intended use populations prior to clinical trials, so developers can manage appropriate applications of genomic data and their impact on decision making during development.

To overcome these challenges, Discovery provides unmatched access to highly characterized samples, innovative, optimized services on cutting-edge multi-omic platforms, expert assay establishment and validation, and intricate data analysis / bioinformatics* to ensure accuracy, save time, and eliminate wasted resources.

EVALUATE, VALIDATE AND SCALE NOVEL SEQUENCING TECHNOLOGIES TO ACCELERATE PRECISION ONCOLOGY PROGRAMS

Discovery’s sequencing and bioinformatics service lab, HudsonAlpha Discovery^®, offers the latest genomic innovations delivered at speed and scale—proprietary workflows, advanced sequencing platforms, and the Discovery Life Sciences commitment to service. Our experts work with clients consultatively to better understand their needs and provide recommendations on experimental design, technology selection and application, custom workflow optimizations, etc.

Cancer tumors vary widely and are extremely diverse in their growth and mutation. Targeted therapies are the future of the genomics landscape. In Immuno-oncology, specific biomarkers such as Tumor Mutational Burden (TMB) and immune checkpoint protein target expression (e.g., PD-1 and PD-L1), provide broader biomarker signatures and opportunities for alternative means via combination and/or adjuvant therapies. But to realize and expand these advances, developers must have reliable data and methods to interpret data properly.

Don Skifter, PhD., MBA is Discovery’s SVP of Genomics whose expertise is focused on how clients can apply genomic technologies and bioinformatics analyses to advance researchers’ understanding of disease and development of diagnostics, drugs and therapies that improve patient care.

Correctly identify, develop and properly validate biomarker assays

In clinical trials, one challenge many pharma companies have is they’re unsure which biomarker to use when evaluating patient samples. However, based on the expression data, companies can design their own clinical studies with Discovery to get a better understanding of biomarker expression, especially in the cases of annotated samples and mutation status, etc. It’s important to have a variety of technologies and capabilities that can be applied, such as IHC, digital pathology, NGS, molecular and flow cytometry capabilities.

References

https://jamanetwork.com/journals/jamaoncology/article-abstract/2776756 utm_campaign=articlePDF&utm_medium=articlePDFlink&utm_source=articlePDF&utm_content=jamaoncol.2020.7988

https://www.ajmc.com/view/how-advances-in-precision-oncology-new-diagnostic-and-treatment-frontier

*For Research Use Only. Not Intended for use in Diagnostic Procedures.