The start of 2025 is proving to be an influential moment for long-read sequencing, with a surge of research showcasing the power of PacBio HiFi sequencing. This month, we’re featuring five standout studies—one more than usual—because the volume of impactful discoveries simply couldn’t be contained to four.
Join us for the January 2025 edition of our Powered by PacBio blog series where we explore how PacBio technology is unveiling genome-wide patterns of pathogenicity in tandem repeats to driving cost-effective trait mapping in plant genomics. January’s publications highlight how HiFi sequencing is providing clinical insights into rare diseases, enabling high-resolution microbial species identification, and even integrating multiomic profiling in a single run—a feat that is reshaping genomic research.
Join us as we see how HiFi sequencing is advancing research in the new year.
Jump to topic:
Tandem repeats | Low pass sequencing | Rare disease | Metagenomics technology comparison | Multiomics
Tandem repeats
In this preprint, researchers from All of Us, U Miami, Broad, Harvard, Stanford, U W Australia and PacBio create a “comprehensive database of 3.6 billion tandem repeat allele sequences from over one thousand individuals [all self-identified as Black or African-American] using HiFi long-read sequencing”.
Key findings:
- “Tandem repeats … are notoriously difficult to sequence using short-read techniques.”
- This study “revealed a strong enrichment of variation in LPS [longest pure segment] length in population controls among loci whose expansion causes rare disease”.
- Researchers introduced “a novel measure, ‘tandem repeat constraint’, that assists in distinguishing potentially pathogenic from benign loci”.
- The findings also provide evidence for two novel pathogenic repeat expansion candidates.
- Notably, “this analysis significantly clarifies the potential for short tandem repeat pathogenicity at over 1.7 million tandem repeat loci and will aid the identification of disease-causing repeat expansions.”
Conclusion:
Using HiFi sequencing, researchers developed innovative measures like tandem repeat (TR) constraint, enabling the prioritization of novel pathogenic loci and uncovering clinically significant patterns. These advancements pave the way for breakthroughs in neurological and movement disorder research, driving progress in diagnostics, treatments, and our understanding of complex diseases.
Low pass sequencing
Long-Read Low-Pass Sequencing for High-Resolution Trait Mapping
In this preprint, researchers from HAIB, U GA, USDA, Veil Genomics find “a more economical choice for high-resolution genomic analyses”.
Highlights:
- Researchers “developed a high-throughput methodology for DNA extraction and library preparation using new PacBio reagents and kits on the Revio sequencer”, and “a high-throughput, scalable approach for long-read low-pass (LRLP) sequencing and variant analysis with PacBio HiFi reads”.
- They found that “An increased number of variants are consistently called for LRLP data compared to short-read data”: at matched 1.6x coverage (tetraploid peanut), LRLP covered 55% of the genome and 58% of gene space, compared to 17% and 11% with short reads.”
- Noting that LRLP has “enhanced data retention … and an ∼8.5x decrease in cost per value” compared to short reads. For example, “LRLP sequences consistently have significantly higher locus similarity scores for important disease resistance loci for late leaf spot (LLS) and tomato spotted wilt virus (TSWV)”.
- These results position LRLP sequencing as “a scalable, cost-effective tool for high-resolution trait mapping, with transformative potential for plant breeding and broader genomic applications.”
Conclusion:
HiFi low-pass long-read sequencing (LRLP) is poised to revolutionize plant and animal genomics by delivering exceptional accuracy and insights. Unlike short-read sequencing, which is hindered by limited genomic resolution and alignment errors—often missing critical traits—LRLP offers precise, comprehensive data with 8x greater cost efficiency per insight. This transformative approach accelerates advancements in breeding programs, enhances trait mapping, and drives innovation across plant and animal breeding.
Rare disease
In this study, researchers from Germany and Pakistan utilize PacBio sequencing to find potential disease-causing variants in case of an infant with limb abnormalities.
Key findings:
- “Haplotype determination cannot be accurately done by short-read sequencing and traditionally requires extensive experiments. In comparison, it is straightforward with long-read sequencing to determine whether variants are in trans, supporting a recessive disease phenotype.”
- PacBio HiFi sequencing “revealed two WNT10B variants [one of them novel] … Phasing (based on genome-wide SNVs and indels) confirmed the variants were located on different alleles”.
- Researchers conclude that: “As sequencing costs decrease, long-read sequencing might become the preferred technology in clinical genetics, serving as a comprehensive diagnostic test.”
Conclusion:
This study on SHFM demonstrates how long-read sequencing surpasses the limitations of short-read technologies, delivering findings to support precise diagnostics in complex cases, such as compound-heterozygous inheritance or when parental samples are unavailable. By accurately resolving genetic variations, providing epigenetic insights, confirming inheritance patterns, and expanding the known mutational spectrum, long-read sequencing is emerging as the new standard and support for helping diagnose rare diseases and driving personalized treatments.
Metagenomics technology comparison
In this study, researchers from Ireland and Australia provide a detailed evaluation of full-length 16S-ITS-23S rRNA (RRN) sequencing (~4500 bp) on both PacBio and ONT.
Key findings:
- “Our results corroborated existing literature, suggesting v3-v4 16S rRNA sequencing was sufficient for genus-level analysis. However, mirroring previous studies, v3-v4 sequencing was shown to perform poorly at the species-level, whereas this study demonstrates sequencing using the RRN performs much better at this phylogenetic level.”
- “PacBio has achieved a commendable milestone in providing high-quality data, as evidenced in this study by its capability to generate OTUs with 99.9% similarity. PacBio’s higher sequencing quality has currently made it the more suitable choice for strain-level detection. ONT, on the other hand, requires additional advancements to produce data with sufficient accuracy to provide strain-level results, or even OTUs with 97% similarity which was another challenge identified in this study.”
Conclusion:
PacBio HiFi sequencing is the superior choice for strain-level detection and precise taxonomy, even in the most complex microbial community samples. In contrast, ONT requires additional improvements to meet these high standards, often struggling to achieve even 97% similarity without additional methods like UMIs to enhance data quality. PacBio continues to lead the field with its exceptional precision and reliability, making it the preferred solution for clinical microbiology and research applications.
Multiomics
In this study, researchers from the University of Washington and the Undiagnosed Diseases Network (UDN) leveraged PacBio sequencing to solve a rare Mendelian disorder. By integrating long-read genomic, transcriptomic, epigenomic, and methylomic data in a single analysis, researchers identified a balanced X;13 translocation that disrupted four key genes—each through a different molecular mechanism—providing answers where short-read sequencing had failed.
Highlights:
- A single sequencing run captured genome, methylome, epigenome, and transcriptome data simultaneously, streamlining analysis and reducing experimental redundancy.
- Long-read sequencing revealed diverse pathogenic mechanisms, including fusion transcripts, enhancer misregulation, transcriptional interference, and epigenetic alterations.
- The approach provided haplotype-resolved insights, essential for understanding the functional impact of rare variants in complex genomic regions.
Conclusion:
PacBio sequencing offers a high-resolution view of genetic and molecular disruptions in rare diseases. The study highlights the power of HiFi sequencing to replace multiple conventional assays with a single, comprehensive approach—reshaping the way scientists investigate complex conditions.”
Ready to make discoveries of your own?
From advancing rare disease research with the largest tandem repeat allele database to transforming plant genomics with cost-effective trait mapping, January’s publications show the power and versatility of PacBio HiFi sequencing. These studies showcase how long-read sequencing is not only overcoming the limitations of short-read technologies but also redefining the standards in clinical genetics, metagenomics, and multiomics research.
Stay tuned for next month’s edition as we continue to highlight the latest groundbreaking research made possible with HiFi sequencing.
Ready to make an impact of your own? Let’s get started.