Today’s cancer drug development has evolved far beyond traditional chemotherapies. Curre oncology pipeline includes precision small molecules, monoclonal antibodies, antibody-drug conjugates (ADCs), CAR-T therapies, TCR-engineered cells, and personalized cancer vaccines.
What unites these diverse modalities is a shared requirement: a complete and accurate understanding of genomic, transcriptomic, and epigenetic variation — both in tumors and in engineered therapeutic cells.
Cancer is driven not only by mutations, but also by structural rearrangements, altered RNA isoforms, and epigenetic dysregulation such as abnormal DNA methylation (Stratton et al. 2009; Hanahan 2022). Capturing this full molecular landscape is essential for identifying therapeutic targets, validating biomarkers, and ensuring the safety of engineered cell products.
HiFi sequencing, combining long read lengths (10–25+ kb) with >99.9% per-base accuracy, provides more comprehensive genomic resolution. When paired with full-length RNA isoform sequencing and native DNA methylation detection, it delivers an integrated view of tumor biology that directly supports next-generation drug development.
Learn more about our SMRT Grant program open today supporting multiomic strategies for clinical cancer research and drug discovery and apply to win free sequencing.
How long reads enable actionable variant detection
Many cancer-driving events are structurally complex. Large insertions, inversions, tandem duplications, gene amplifications, and multi-breakpoint rearrangements can activate oncogenes or disable tumor suppressors (Keskus et al. 2024).
Structural variation is a major driver of oncogenesis, yet is historically under-detected with short-read approaches. HiFi long-read sequencing enables more complete detection of:
- Single nucleotide variants
- Structural variants
- Copy number alterations
- Gene fusions
- Phased haplotypes
This comprehensive blueprint strengthens target identification and prioritization (Ishino, Watanabe, et al. 2026).
Adding functional insight with RNA isoform sequencing
DNA reveals what alterations are present, while RNA reveals what is functionally expressed.
Gene fusions are powerful oncogenic drivers. Full-length RNA isoform sequencing with Kinnex enables comprehensive profiling of these events through:
- Exact fusion breakpoint identification
- Confirmation of in-frame, functional transcripts
- Detection of complex multi-partner fusions
Transcript-level validation strengthens development of kinase inhibitors and biologics targeting fusion proteins.
Improving neoantigen discovery
Tumor-specific splice variants and fusion transcripts can generate novel peptides as potential neoantigens for immunotherapy and biomarkers to predict response to therapy (Tzaban et al 2025).
Resolving full-length transcripts and phased mutations improves neoantigen prediction for:
- Personalized cancer vaccines
- TCR-engineered therapies
- CAR-T strategies
Accurate transcript reconstruction is critical for understanding which mutations are actually expressed and presented as neoantigens, directly informing the design of targeted immunotherapies.
HiFi sequencing powers epigenetics toward cancer drug development
Cancer progression is often driven by epigenetic dysregulation. Aberrant DNA methylation can silence tumor suppressor genes or activate oncogenic pathways.
Direct detection of native DNA methylation patterns provides:
- Base-resolution methylation profiling
- Long-range regulatory context
- Allele-specific methylation analysis
Epigenetic alterations are clinically actionable and are already targeted by approved therapies in hematologic malignancies. Integrating sequence and methylation data enables more refined tumor classification and biomarker development. HiFi sequencing enables this integration directly, capturing both sequence and methylation information in a single run without additional library preparation. With SPRQ-Nx chemistry, methylation detection will expand beyond 5mC and 6mA to include 5hmC, alongside Fiber-seq for chromatin architecture, providing a more comprehensive view of epigenetic regulation.
Long-read sequencing enables antibody discovery and development
Antibody-based therapies remain central to oncology. Gene amplifications and structural rearrangements can drive aberrant surface protein expression. Accurate structural resolution is necessary for biomarker-driven antibody and ADC development.
At the same time, phage display has become a foundational technology for therapeutic antibody discovery (Frei & Reddy 2025; Ferrara et al 2024). Accurate full-length sequencing of antibody variable regions with HiFi technology supports:
- Complete VH/VL characterization for scFv and Fab antibodies
- Correct heavy/light chain pairing
- Precise resolution of CDR regions
- Comprehensive immune repertoire analysis
High-fidelity sequencing improves lead identification and reduces artifact-driven errors during library screening, increasing confidence in selecting developable antibody candidates.
How HiFi sequencing can strengthen CAR-T and engineered cell therapy development
CAR-T therapies have transformed treatment of certain hematologic malignancies. However, safety and durability require precise molecular characterization.
- Selecting robust antigen targets – Structural variants and fusion-derived proteins may serve as tumor-specific antigens. Transcript validation ensures that targets are expressed.
- Insertion site analysis – Vector integration site mapping is critical for assessing insertional mutagenesis risk. HiFi long-read sequencing enables precise mapping of integration loci and structural characterization of inserted constructs.
- Gene editing characterization – CRISPR-based gene editing requires careful evaluation of on-target and off-target effects (Kosicki et al. 2018). Comprehensive detection of large deletions and rearrangements strengthens quality control and regulatory confidence.
- Design of novel CAR constructs – HiFi sequencing supports the development of novel CAR constructs that target a desired antigen (Liu et al. 2025).
Advancing precision small molecules and biomarkers
For potential companion diagnostics, integrating genomic, transcriptomic, and epigenetic data supports more precise patient stratification—an increasingly central component of oncology drug approval pathways.
HiFi sequencing as a more complete molecular foundation for oncology innovation
Highly accurate HiFi reads provide a unified framework for translating molecular complexity into potentially actionable therapeutic strategies. From fusion-driven oncogenes to CAR-T integration site analysis, modern cancer drug development depends on comprehensive molecular insight.
HiFi sequencing delivers this comprehensive framework for oncology innovation by combining:
- Complete structural variant detection
- Full-length RNA isoform characterization
- Native DNA methylation profiling
- Precise gene editing and insertion analysis
- Phased genomic context
As oncology becomes increasingly personalized and mechanistically driven, technologies capable of resolving genomic, transcriptomic, and epigenetic complexity in an integrated workflow will shape the next era of drug development.
Want to try out HiFi for your drug development work? Apply for free sequencing with our SMRT Grant supporting Cancer long-read multi-omics for clinical research and drug discovery
Learn more about HiFi sequencing for antibody development and watch our webinar to learn about immunogenic profiling in cancer with HiFi sequencing.
References
- Ferrara, F., et al. (2024). A next-generation Fab library platform directly yielding drug-like antibodies with high affinity, diversity, and developability. mAbs, 16(1), 2394230. https://doi.org/10.1080/19420862.2024.2394230
- Frei, L. & Reddy, S. T. (2025). A yeast mating-based platform enables the generation and screening of ultra large antibody libraries. bioRxiv, 2025.10.06.680701. https://doi.org/10.1101/2025.10.06.680701
- Hanahan, D. (2022). Hallmarks of cancer: New dimensions. Cancer Discovery, 12, 31–46. https://doi.org/10.1158/2159-8290.CD-21-1059
- Ishino, T., Watanabe, T., et al. (2026). Immunopeptidomics combined with full-length transcriptomics uncovers diverse neoantigens. Cell Reports, 45(1), 116781. https://doi.org/10.1016/j.celrep.2025.116781
- Kosicki, M. Tomberg, K., & Bradley, A. (2018). Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements. Nature Biotechnology, 36, 765–771. https://doi.org/10.1038/nbt.4192
- Keskus, A. et al. (2024). Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads. medRxiv. https://doi.org/10.1101/2024.03.22.24304756
- Kjer-Hansen, P., Phan, T. G. & Weatheritt, R. J. (2024). Protein isoform-centric therapeutics: expanding targets and increasing specificity. Nature Reviews Drug Discovery, 1–21. https://doi.org/10.1038/s41573-024-01025-z
- Liu, Y., et al. (2025). Integrated scFv identification and CAR T cell generation for AML targeting in vivo. International Journal of Cancer. https://doi.org/10.1002/ijc.70146
- Stratton, M.R., Campbell, P.J., & Futreal, P.A. (2009). The cancer genome. Nature, 458, 719–724. https://doi.org/10.1038/nature07943
- Tzaban, S., et al. (2025). RNA splicing dynamics in CD8 T cells uncovers isoforms that impact T cell-mediated cancer immunotherapy. bioRxiv, 2025-09. https://doi.org/10.1101/2025.09.07.674706