As we close out 2024, the power of PacBio technology has never been more evident. December brought an inspiring array of research that highlights how HiFi sequencing is driving discovery across diverse areas of genomics. From unlocking the epigenetic mysteries of the human brain to creating a pangenome for the Emirati population and resolving complex rearrangements in rare genetic syndromes, these studies demonstrate the growing versatility and impact of PacBio solutions.
Join us for the December 2024 edition of our Powered by PacBio blog series where we explore how PacBio technology is enabling breakthroughs that inspire, from the foundational knowledge gained in December to the limitless possibilities that await in the new year.
Ready to see how PacBio technology can elevate your research? Let’s make 2025 the year of discovery.
Jump to topic:
Neurology | Pangenomes | Rare disease | Technology comparison
Neurology
Single chromatin fiber profiling and nucleosome position mapping in the human brain
In this study, researchers from Mt. Sinai, VA Med Ctr NY, UCLA, and UW worked together to “demonstrate the application of Fiber-seq to sorted intact adult human brain nuclei, amplification free, and on a genome-wide scale”.
Highlights:
- “To date, no brain-related genome-scale maps exist for nucleosome positioning and occupancy”, “conventional chromatin accessibility mappings face major limitations”, DNase-seq & ATAC-seq “offer only a crude approximation of the regulatory architecture of chromatin fibers”, and “short-read sequencing is suboptimal at low-complexity repetitive loci, duplicated regions, tandem arrays, and complex structural variants. As these types of sequences constitute far more than 50% of the human genome, the epigenomic composition of the majority of the nuclear genome is left unexplored.”
- Fiber-Seq enables “chromatin accessibility maps at superior resolution”:
- “initial reference maps for nucleosomal positioning specific to neuronal and non-neuronal nuclei”
- demarcates “nucleosome-depleted regulatory sequences with sharper resolution compared to conventional nucleolytic short-read chromatin assays”
- uncovers “tens of thousands of nucleosome-depleted regions (NDRs) and actively regulated genomic “dark matter”, including repetitive sequences that hitherto had remained epigenomically unmappable”
- uncovers “haplotype-specific nucleosome positioning and occupancy, and co-regulation of cis-bound promoter and enhancer elements at single-fiber levels”
- Simultaneous “detection of methylated CpGs together with nucleosome position mapping (Figures 2H and 3H) could capture 89% of structural variation that had been missed by short-read sequencing and inform about epigenetic regulation”.
Conclusion:
HiFi-powered Fiber-seq unveils new insights into the human brain’s epigenome, unlocking regions previously inaccessible with short-read methods. On-instrument 6mA calling (and improved 5mC calling) with SPRQ on Revio offers more powerful, high-throughput HiFi epigenomics research. By streamlining multiomic workflows and delivering highly accurate data, Fiber-seq accelerates neuroscience research, paving the way for transformative breakthroughs in understanding brain function and neurodegenerative diseases.
Pangenomes
An Emirati pangenome incorporating a diploid telomere-to-telomere reference
In this preprint, researchers from UAE, Germany, and Australia create “a comprehensive representation of the genomic diversity within the UAE population”.
Highlights:
- “The genetic diversity of the Emirati population, which, while small, is highly heterogeneous due to its unique history of migration and admixture”.
- Researchers used one multi-tech T2T reference genome, and 52 diploid HiFi assemblies to build the pangenome.
- The new pangenome “adds approximately 159.63 Mb of novel sequence, offering valuable insights into the region’s genetic landscape”.
- Comprehensive variant calling from the pangenome “fills an important gap by focusing on the genetic variation of a population of the Middle Eastern and North African (MENA) region”.
Conclusion:
Scalable and cost-effective WGS and high-quality assemblies with Revio & SPRQ are the tools needed to create human pangenomes. As of now, all pangenome projects to date have used PacBio HiFi data to build the pangenomes, highlighting millions of bases unique to certain populations, and uncovering the true extent of human genetic variation across the globe.
Rare disease
Long-read genome sequencing resolves complex genomic rearrangements in rare genetic syndromes
In this study, researchers from Nationwide Childrens and OH State use PacBio technology to resolve “novel complex chromosomal rearrangements in two rare genetic syndromes”.
Highlights:
- PacBio “not only confirmed these CNVs [from microarray analysis] but also revealed their genomic structures”.
- In the first case, “we resolved a novel recombinant chromosome 8 (Rec8)-like rearrangement with a 3.43 Mb chr8q terminal duplication that was linked to a 7.25–8.21 Mb chr8p terminal deletion.”
- In the second case, “we uncovered a novel complex rearrangement involving a 1.17 Mb rearranged segment and four interstitial deletions ranging from 9 bp to 12.39 Mb.”
- Researchers note that “Our results underscore the diversity of clinically relevant structural rearrangements and the power of long-read sequencing in unraveling their nuanced architectures.”
- Also finding that “Considering the limitations of microarray and short-read sequencing in resolving complex chromosomal rearrangements along with the decreasing cost of long-read genome sequencing, a compelling case can be made for more mainstream use of long-read technologies to improve the diagnostic yield in patients with rare genetic disorders. This approach may also serve to test for carrier alterations in parents and thereby better define the risk of recurrence of these complex rearrangements in future pregnancies.”
Conclusion:
HiFi sequencing empowers researchers with longer, more accurate reads that uncover structural variants and chromosomal structures missed by traditional microarray and short-read technologies. Comprehensive and accurate WGS is now scalable, easier, and more affordable with automated HiFi prep kit 96 and SPRQ workflows on Revio. By resolving both coding and non-coding regions, HiFi enhances diagnostic accuracy, making it an invaluable tool for identifying complex genetic anomalies and advancing our understanding of genetic disorders.
Technology comparison
Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
In this study, researchers from Spain, U FL, and Germany show that “Incorporating PacBio transcripts into our annotation pipeline significantly outperformed traditional methods”.
Highlights:
- In this detailed comparison of ab initio, Illumina, ONT and PacBio for annotation using well-annotated human cell line WTC11. PacBio outperformed all other methods: “the best performance was achieved using the transcriptome inferred from PacBio data as experimental evidence”.
- “PacBio Sequel II sequencing data yielded better results than ONT v9.4.1 chemistry data or a combination of both. This result is in agreement with conclusions of the LRGASP project, that revealed that the longer read distribution and sequence accuracy of the long reads were more important for accurate transcript model prediction than the number of reads.”
- Applied to Florida manatee (non-model species), the Iso-Seq method identified 4,906 novel loci, represented by 5,707 isoforms.
Conclusion:
Iso-Seq provides the most accurate data for genome annotations of model and non-model organisms. For best-in-class RNA sequencing, researchers can scale to high throughput when using Kinnex kits and the Revio system.
Ready to start the new year with breakthroughs of your own?
These studies from December 2024 demonstrate the profound potential of PacBio technology to reshape our understanding of the genome. From mapping chromatin fiber in the human brain to constructing a pangenome that captures the unique diversity of the Emirati population, and from resolving complex genetic rearrangements in rare diseases to refining genome annotation methods, researchers are breaking new ground with HiFi sequencing.
As we look ahead to 2025, the possibilities are even greater. With tools like Revio and platforms like Vega making high-quality sequencing more accessible than ever, the opportunities for discovery are boundless. Whether you’re unraveling the complexities of epigenetics, exploring population genomics, or solving the puzzles of rare genetic disorders, PacBio empowers you to tackle challenges with confidence.
Let these achievements inspire your next breakthrough. Together, we can unlock the full potential of genomics and chart a path toward discoveries that will shape the future.
Ready to make an impact? Let’s get started.