In biopharmaceutical research and development, the path from discovery to approved therapy can be long and complex, requiring innovation at every step. Success depends on understanding biology at its most precise level, whether the goal is to reveal new therapeutic targets, ensure the safety of a novel therapy, or validate the integrity of a production process.
HiFi sequencing delivers highly accurate, long-read data that enables scientists to see every detail across entire molecules, identifying rare variants, and resolving difficult-to-sequence regions with confidence. This level of clarity not only improves confidence in the findings but also helps shorten timelines by reducing the need for rework, using multiple orthogonal methods, replication, or iterative troubleshooting.
To see this in action, join us on August 26 for a webinar showcasing how industry-leading scientists are using HiFi sequencing to advance their research and development. They will share real-world examples spanning the discovery of novel genetic biomarkers, the precise engineering promoting advanced gene therapies, and the optimization of complex biologics. These case studies highlight how HiFi data drives faster breakthroughs.
Register now and discover what’s possible when accuracy meets innovation.
A more complete view for biomarker discovery
The search for new therapeutic targets and biomarkers lays the foundation for future treatments, but incomplete or inaccurate molecular information can lead to setbacks later in development. HiFi sequencing offers a more complete, more confident view from the start.
Many drug development projects fail in later stages because initial data missed key details hidden in the genome, transcriptome, or epigenome. HiFi sequencing overcomes these roadblocks by enabling researchers to see the full picture from the outset, integrating whole genome sequencing (WGS), full-length RNA sequencing with Kinnex kits, and 5mC and 6mA methylation detection in every run.
HiFi WGS allows you to comprehensively phase and characterize challenging regions with complete identification of disease-associated variants, including single nucleotide variants (SNVs), indels, and structural variants across the entire genome. For example, HiFi sequencing has been used in recent research to characterize a repeat expansion in the C9orf72 gene, the leading known genetic cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). The ability to size and phase this repeat expansion, and to detect any changes after gene editing, is critical for both understanding disease progression and developing novel targeted therapies.
Figure 2 from Salomonsson, Maltos, et al. (2024). PacBio sequencing traces of the C9orf72 repeat region for patient and control cell lines showing the number of reads per repeat count. The WT line (A) has a bimodal repeat length distribution, while the patient lines show an expanded allele size (B).
Kinnex full-length RNA sequencing powered by the Iso-Seq method delivers complete isoform structures, allowing the identification of novel transcripts, fusion genes, and alternative splicing patterns. This is essential for understanding gene expression changes in health and disease, and for ensuring that a candidate biomarker truly reflects the relevant molecular processes. Having the full isoform context can also reveal disease-associated transcripts that may be invisible to short-read assembly methods, which can influence drug target selection and inform diagnostic development.
In Alzheimer’s disease research, Iso-Seq analysis identified region-specific isoforms of the APOER2 gene that are altered in patients. These isoforms impact cell surface expression and receptor processing, offering important clues into disease mechanisms and potentially revealing new therapeutic targets.
HiFi sequencing also simultaneously integrates methylation detection into every dataset, capturing 5mC and 6mA methylation and chromatin accessibility information without the need for bisulfite conversion or additional workflows. This allows researchers to assess epigenetic features that influence gene expression, adding another critical dimension to biomarker discovery. By combining genomic, transcriptomic, and epigenomic data in one coherent view, HiFi sequencing enables a richer and more confident understanding of disease biology.
How HiFi sequencing accelerates innovation in cell and gene therapy
Cell and gene therapy research unites multiple sequencing applications, from designing precise viral vectors to characterizing accurate genome edits to ensuring the stability of therapeutic cell lines. These approaches demand exceedingly precise sequencing data, as even small inaccuracies can have potential downstream effects on safety, efficacy, and manufacturability.
Complete and accurate sequences are key for all stages of Adeno-associated virus (AAV) vector development, from novel AAV vector discovery to implementing and evaluating vector design. HiFi sequencing spans entire AAV molecules, including inverted terminal repeats (ITRs), in a single read of up to 25 kb. This enables high-confidence profiling of impurities such as plasmid backbone or host genomic DNA, as well as quantification of size distributions and detection of truncation hotspots that can affect therapeutic performance. Researchers can also evaluate ITR integrity and identify rearrangements, which are closely linked to genome heterogeneity. Because HiFi reads cover the full cap gene, variant discovery and screening for novel capsids with tissue-specific tropism becomes faster and more comprehensive, accelerating the process of optimizing delivery vehicles.
Gene editing workflows benefit equally from HiFi sequencing’s ability to capture the entire edited region and its genomic context. For CRISPR-Cas9-mediated editing, this means detecting single nucleotide edits, small and large indels, and complex rearrangements in both on-target and off-target locations. Allele-specific resolution allows researchers to measure editing efficiency across different haplotypes, providing insights into how natural variation may influence outcomes. HiFi sequencing can also facilitate insertion site analysis by characterization of integration events from homology-directed repair or other insertion strategies, revealing concatenations, inversions, and other structural changes that might compromise the therapeutic goal or raise safety concerns.
For cell therapy quality control, highly accurate HiFi sequencing confirms the genomic integrity of master cell banks and production cell lines by detecting SNVs, structural variants, and methylation patterns across the genome. This ensures that any genetic drift, contamination, or instability is identified before it can impact product safety or performance. The ability to perform this comprehensive analysis at high throughput means quality checks can be embedded more effectively into the development pipeline.
How HiFi sequencing advances biologics research and development
The development of biologics, from therapeutic antibodies and RNA-targeted therapies to mRNA vaccines, relies on precise molecular design and rigorous validation. HiFi sequencing provides the accuracy and completeness needed to improve these processes while helping teams make faster, more confident decisions.
In antibody discovery and optimization, scFv and Fab constructs pose challenges for other sequencing technologies, which don’t have the read lengths or accuracy to fully capture the whole molecule. HiFi sequencing can capture these regions in a single read, including regions with repetitive motifs or high GC content that often cause dropouts in short-read sequencing, enabling accurate detection of sequence variation across the whole molecule. In phage display workflows, the ability to sequence more clones and detect multiple mutations per molecule increases the probability of identifying antibodies with the desired specificity, stability, and manufacturability. Full-length coverage also ensures that mutations are interpreted in the correct structural and functional context, avoiding misleading partial data.
RNA-targeted therapies benefit from the ability of the Iso-Seq method to reveal the complete isoform landscape for a gene of interest. By identifying the most abundant and disease-relevant isoforms, researchers can design antisense oligonucleotides (ASOs) that target the majority of pathogenic transcripts, improving therapeutic reach and efficiency. This approach was the focus of our recent webinar with Dr. Mina Ryten, which highlighted how isoform-level data from HiFi sequencing can inform ASO design in neurological disease research, ensuring that therapeutic oligonucleotides target the transcripts most likely to influence disease progression. This approach supports a wide range of disease areas, from rare inherited disorders to neurodegenerative conditions, evidenced recently in Parkinson’s disease research.
For mRNA vaccines, HiFi sequencing spans the full length of the molecule, including the complete poly(A) tail, allowing developers to confirm sequence identity and measure poly(A) tail length with precision. This is especially important because tail length influences both stability and translational efficiency, and homopolymer regions are notoriously challenging for other sequencing technologies. By providing this level of detail, HiFi sequencing helps optimize constructs and ensures product consistency, even under demanding development and production timelines.
What’s next for biopharma innovation
HiFi sequencing is helping researchers obtain richer molecular insights so that they can translate their learnings into faster, more confident decision-making. As therapeutic modalities become increasingly complex, the ability to generate Sanger-quality, full-length DNA and RNA data integrated with epigenetic information will continue to accelerate discovery, development, and quality assurance.
Don’t miss your chance to see how this technology is changing the game – Register now for our upcoming biopharma webinar and be part of what’s next.