October 16, 2023  |  General

Powered by PacBio: Selected publications for September 2023

PacBio HiFi sequencing technology continues to play an increasingly pivotal role in advancing critical research across the life sciences. In this blog series, we explore some of the latest and most exciting scientific papers and preprints that demonstrate the power of PacBio sequencing in unraveling new insights in areas as diverse as immune response, genetic disease detection, agrigenomics, and Alzheimer’s research.

Immune response and RNA sequencing

Article: Multi-omic profiling of pathogen-stimulated primary immune cells

Researchers at Radboud University in the Netherlands exposed blood cells to four different pathogen stimuli, employing PacBio full-length RNA sequencing technology –Iso-Seq method– to observe the outcome. Their findings shed light on the intricate and important immune response processes:

Key takeaways:

  • “Long-read transcriptome profiling reveals the expression of novel sequences and isoform switching induced upon pathogen stimulation, including transcripts that are difficult to detect using traditional short-read sequencing.”
  • The study observed widespread loss of intron retention and identified “novel transcripts of NFKB1 and CASP1 that may indicate novel immunological mechanisms.”
  • The conclusion highlights that “Isoform-aware long-read sequencing of pathogen-stimulated immune cells highlights the potential of these methods to identify novel transcripts, revealing a more complex transcriptome landscape than previously appreciated.”


Genetic disease detection and SVs

Article: Identification of a novel 91.5kb-deletion (αα)FJ in the α-globin gene cluster using single-molecule real-time (SMRT) sequencing

A biomedical research team in China found that a routine genetic screening assay yielded inconclusive results in a suspected case of hereditary disease. The team leveraged PacBio HiFi sequencing (referred to as SMRT sequencing in the paper) to uncover a previously hidden 91.5 kb deletion that was associated with the disease phenotype.

Key takeaway:

  • This research underscores how “SMRT can undertake comprehensive and accurate gene detection”, which can enable scientists to explain disease phenotypes that would have otherwise remained a mystery using conventional assays.



Article: The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Nestle and 40 global research institutions joined forces to extensively analyze the genome of Coffea arabica using PacBio HiFi sequencing. C. arabica is the source of nearly 60% of global coffee products –making scientifically informed breeding critical for a stable and sustainable supply.

Key takeaway:

  • Researchers leveraged HiFi-based, chromosome-level assemblies to unravel the genome structure, evolution, and “loci that may contribute to …superior pathogen resistance and lay the groundwork for future genomics-based breeding [of C. arabica].”


Alzheimer’s research and RNA sequencing

Article: Long-read transcript sequencing identifies differential isoform expression in the entorhinal cortex in a transgenic model of tau pathology

This research paper was the result of a collaborative effort between the University of Exeter in the UK, Harvard University, and Eli Lilly UK. The international team employed long-read RNA sequencing of transcripts in an Alzheimer’s mouse model to make exciting new findings.

Key takeaways:

  • The study revealed that “previously reported gene-level expression differences between wild-type and transgenic mice reflect changes in the abundance of specific transcripts.”
  • The use of ultra-deep targeted long-read cDNA sequencing identified hundreds of novel isoforms and specific transcripts associated with the development of tau pathology.
  • The results emphasize the importance of differential transcript usage in understanding gene regulation in the development of neuropathology.


Ready to kickstart breakthroughs of your own?

These recent publications showcase the versatility and power of PacBio sequencing technology to enable scientists around the world to advance research across multiple domains. From transcriptome profiling in immune response to genetic disease detection, agrigenomics, and Alzheimer’s research, PacBio long-read sequencing continues to facilitate innovative discoveries and insights that shape our understanding of complex biological processes.

Be it through a purchase, financing, or a certified service provider, PacBio sequencing is now more accessible than ever for research teams great and small. To find out how to get PacBio data for your project:

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