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Sequencing applications in adoptive cell therapy development

14 Jul 2026

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Maryland Franklin, PhD, is the vice president and enterprise head of cell and gene therapy (CGT) at Labcorp. With over 25 years of experience in drug development across a range of modalities spanning small molecules, antibodies, and CGTs, Maryland has partnered on multidisciplinary teams to deliver therapeutic candidates, and she has played a key role in bringing four drugs into Phase I oncology clinical trials. She leads a matrixed team of CGT experts driving strategic vision, thought leadership, and cross-sector global collaborations.

Adoptive cell therapies are reshaping cancer care, driven by breakthroughs in gene editing, viral vector engineering, and next‑generation sequencing (NGS). Programs have expanded from hematologic cancers to solid tumors. However, the solid tumor microenvironment (TME) has emerged as a critical challenge to achieving therapeutic benefit, particularly when compared to hematologic cancers. Developers face demands for deeper product characterization, greater safety assurance, and more precise patient selection. Sequencing technologies provide insights to help overcome crucial obstacles and advance novel adoptive cell therapies with confidence.

How are adoptive cell therapies currently used in clinical oncology practice and which patients are most likely to benefit?

Chimeric antigen receptor (CAR) T-cell therapies are widely used, with seven FDA-approved therapeutics across hematologic malignancies as of May 2026. The field is also expanding into solid tumor indications with the first FDA approvals of a non-modified tumor‑Infiltrating lymphocyte (TIL) product and a genetically engineered T-cell receptor (TCR) T-cell therapy in 2024. Numerous adoptive cell therapies are being evaluated in the clinical trial setting across solid tumor indications and target antigens. Clinical benefit, however, has been primarily limited to a subset of patients in hematologic malignancies.

What barriers limit cell therapy adoption, and how can biomarker‑driven evaluation such as genomic profiling help mitigate these challenges?

Key barriers to cell therapy adoption include safety concerns, manufacturing complexity, and limitations related to clinical success in solid tumors. High-quality biomarker insights via measurements of cell persistence, potency, and on-target/off-tumor activity may help assess safety hurdles. Biomarker-driven evaluations like genomic profiling can provide a deeper understanding of the TME, tumor cell heterogeneity, and overall therapeutic response in patients. These insights can inform strategies to improve clinical success, for example, by modifying the TME to enhance CAR T-cell infiltration and cytotoxicity in solid tumors.

How are biomarkers being applied during the development of cell therapy products?

Biomarkers are foundational to adoptive cell therapy development. A multimodal biomarker strategy is essential, with platforms ranging from flow cytometry for real-time cellular tracking and phenotyping, functional (potency) assays to assess product quality, and genomic technologies (qPCR, dPCR, NGS) to evaluate vector copy number, persistence, off-target effects, and genomic safety. In earlier stages of development, strategies such as paired whole exome sequencing (WES) and whole transcriptome sequencing (WTS) yield deep insights into tumor biology and the TME. In clinical development, targeted assays may provide a cost-efficient method to track biomarkers of therapeutic response or resistance and cell persistence. For example, when we analyzed a cfDNA-derived genome instability number (GIN) in 12 relapsed B-cell lymphoma patients treated with autologous CAR T-cell therapy, we found correlations between the GIN levels and clinical and radiographic response, suggesting that cfDNA analysis may be useful in disease monitoring and relapse prediction.

How do sequencing platforms support product quality, consistency, and safety?

Adoptive cell therapy products are inherently variable due to factors including donor-to-donor differences and manufacturing complexities. Single-cell and bulk sequencing together with other multi-omics approaches are being implemented alongside traditional platforms to expand product characterization and enhance potency testing. Early application could improve donor or patient stratification, enable optimal candidate selection, and inform pre-conditioning strategies that would bolster T-cell fitness. Additionally, integrating omics approaches at the leukapheresis stage may meaningfully enhance manufacturing consistency and clinical efficacy.

Sequencing is also central to evaluating safety during the development and manufacturing of adoptive cell therapies. Traditionally, it has been used to quantify vector copy number and map integration sites, which are key measures for assessing genotoxicity risk. Increasingly, sequencing also enables TCR repertoire profiling and precise genomic assessment of gene-edited products, providing critical insights into efficacy and product quality.

What molecular data is being used to support regulatory approvals?

There is growing use of comprehensive genomic and transcriptomic data to support regulatory guidance for product characterization and safety and potency assessment. Continued implementation of these strategies should improve safety, identity, purity, and potency, as well as overall product consistency and clinical readiness.

Cell therapies are rapidly maturing treatment modalities, expanding beyond hematologic cancers into solid tumors.

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