Expanding Access to Genomic Testing for Cancer Patients

Genomic testing has revolutionized cancer diagnostics and treatment, offering personalized insights that enable more effective therapies. However, the high cost of genomic testing often makes it inaccessible to patients in resource-constrained settings.

Why is it important to reduce the cost of genomic testing?

Cancer prevention, diagnosis, and treatment strategies should target the basis of disease without bias for or against any group. Therefore, successfully implementing genomic testing for cancer patients means ensuring they enjoy equal, affordable, and efficient access to genomic medicine.

Incorporating genomics more widely into oncological care promotes health equity and could reduce morbidity and mortality for millions of people.

Strategies to make genomic testing more accessible to cancer patients

Targeted genomic panels

Whole-genome sequencing (WGS) is a comprehensive method for analyzing entire genomes. WGS can be used to detect cancer susceptibility variants, characterize the mutations that drive cancer progression, and monitor tumors in the clinic. However, due to its high cost and complexity, WGS is mainly carried out in high-income countries.

A cost-effective alternative that provides valuable genomic information without the need for complete genome sequencing is the use of targeted genomic panels. “Targeted panels focus on specific genes or genomic regions associated with cancer, reducing the cost of sequencing and analysis while still obtaining critical insights into a patient’s cancer profile,” says Ágatha Cristhina Faria, PhD, a geneticist specializing in molecular diagnostics.

“Targeted panels also allow for deeper coverage of the selected genes, which can be beneficial for detecting rare and common variations with high accuracy,” says Faria. “Moreover, this technique improves the interpreting steps and reduces the turnaround time for the patient.”

Targeted sequencing has many advantages, but clinical labs considering integrating it into routine clinical practice should be aware of the challenges they may face. “A challenge associated with targeted panels is the lack of a gold standard for identifying cancer-associated mutations,” says Faria. “Each clinical lab has its own pipelines with varying parameters, leading to inconsistent results. […] To improve patient outcomes, clinical labs must aim for reliable and standard approaches to data processing and analysis.”

Sample multiplexing

Multiplexing is a technique that enables multiple samples to be combined and analyzed in a single run. When the run is finished, a demultiplexing algorithm deciphers pooled data and ensures the accurate extraction of individual patient information.

By using multiplexing technology, clinical labs can significantly increase their output while reducing labor and reagent expenses. Another advantage of multiplexing is the reduction in sample handling errors. Handling individual samples can introduce variability and potential errors in the testing process. By combining and processing multiple samples together, clinical labs minimize the risk of errors. This enhances the quality of genomic testing, reduces the need for costly retesting, and ensures that patients receive accurate diagnostic information.

Currently, multiplexing technology is primarily advantageous for mid- to high-volume laboratories. But in the next few years, even smaller to mid-size laboratories will be able to justify the purchase of multiplex systems.

Open-source bioinformatics tools

Bioinformatics plays a crucial role in the analysis and interpretation of genomic data. However, proprietary bioinformatics software can be expensive, posing a significant barrier to resource-constrained settings. Open-source bioinformatics tools offer a cost-effective solution to this challenge.

Platforms like Galaxy, Bioconductor, and Burrows-Wheeler Aligner provide a wide range of bioinformatics capabilities, from alignment and variant calling to functional annotation. By embracing open-source solutions, resource-constrained settings can build their genomics expertise and infrastructure at reduced cost, ultimately making genomic testing more accessible to patients.

“Bioinformatics tools will be increasingly used to optimize analyses and reduce costs,” says Glorister Altê, MSc, a biomedical scientist exploring bioinformatics applications. “When clinical labs consider using open-source bioinformatic tools for genomic analysis, they must prioritize regulatory compliance and data security. Rigorous validation, quality control, and documentation processes are also essential to ensure the accuracy and reliability of results.”

Altê also highlights the importance of training and education for lab personnel. “As bioinformatics evolves and helps expand genomic knowledge, the need for staff members that understand bioinformatics concepts will rise.” 

“Clinical labs must ensure that their team is proficient in using appropriate open-source tools and understands their limitations.”

Collaborative initiatives between clinical labs

Pooling resources and sharing expertise provide great opportunities for cost reductions in genomic testing.

For example, Mayo Clinic Laboratories and Helix have formed a strategic partnership to optimize resources and provide comprehensive laboratory support to biopharma companies. This collaboration merges Helix’s advanced next-generation sequencing capabilities with Mayo Clinic Laboratories’s wide-ranging portfolio of tests and pathology services, with a particular focus on critical fields like hematology, cardiology, and oncology.

Similarly, four clinical laboratories—Ambry Genetics, GeneDx, Partners HealthCare Laboratory for Molecular Medicine, and University of Chicago Genetic Services Laboratories— joined forces to address disparities in variant interpretations submitted to ClinVar, a public archive that aggregates information about genomic variation and its relationship to human health. Participating laboratories increased their overall concordance from 88.3 percent to 91.7 percent, indicating that sharing expertise not only reduces costs but also improves consistency in data interpretation.

“Establishing consensus methodologies for data analysis and interpretation enhances the accuracy and comparability of results across different laboratories, ultimately fostering confidence in the clinical utility of genomic testing,” says Faria.

Public–private partnerships to conduct genomic profiling

Public–private partnerships usually involve a health authority, public hospitals or research centers, and private companies, such as pharmaceutical companies. The purpose is commonly to advance cancer understanding and develop personalized treatments.

For example, Roche France, Foundation Medicine, Inc., and the Institute Gustave Roussy, a leading European cancer center, have embarked on a pioneering public–private partnership to expand access to genomic testing in cancer. This collaboration leverages cutting-edge technology transfer from Foundation Medicine’s FoundationOne®Liquid CDx, a genomic profiling blood-based test, to establish in-house liquid biopsy testing at the Institute Gustave Roussy’s facilities in France.

New forms of public–private partnerships involve information technology companies, which provide computing infrastructure and services to store, analyze, and share the massive amounts of data that genomic-related projects produce.

Since multiple partners combine their economic funds, infrastructure, expertise, and information, they can allocate resources more efficiently and extend their services to more patients. Moreover, public–private partnerships can serve regions with poor socioeconomic conditions that are usually passed over by pharmaceutical companies.

Genomics as a global resource

By combining the above strategies, clinical labs can help reduce the financial barriers that prevent many individuals from benefiting from personalized cancer care. As health authorities, research centers, and private companies continue to innovate and collaborate, using genomics as a global tool and resource for cancer diagnosis and treatment may soon become a reality, ensuring more patients have access to quality