If you had the chance, how would you elevate your human genomics research using highly-accurate full-length isoform-level sequencing? We posed that question to researchers in January with the chance to win sequencing for their ideas, and we were blown away by the responses. Nearly 200 applicants shared with us how they would utilize the Kinnex kits with scalable RNA sequencing and massively increased throughput. Researchers proposed a wide range of topics including rare disease, disease or developmental biology, early drug development or biomarker discovery, and cancer research.
We are pleased to announce and congratulate the finalists and winning proposals for both the Kinnex full-length and Kinnex single-cell prizes of the 2024 human RNA SMRT Grant.
Kinnex Full-Length
Winner: Christopher Vollmers
Associate Professor, Biomolecular Engineering Department, University of California Santa Cruz
Proposal Title: Generating a tissue-level annotation of the human genome
Summary: A detailed, easy-to-access tissue-level annotation of the human genome does not currently exist. While Encode and GTEx have generated full-length cDNA sequencing data, their efforts are hampered by choice of tissues, methodology, and analysis tools as well as data use restrictions.
I propose a project using 4 SMRT Cells worth of PacBio Kinnex data as a foundation for creating this easy-to-access tissue-level annotation. We will combine the Kinnex data with other datasets and analyze it using our Mandalorion tool and host the resulting annotations on the UCSC Genome Browser as we have done previously for the mouse genome.
Finalist: Hanneke van Deutekom
PhD, Head of Bioinformatics, Department of Genetics, University Medical Center Utrecht, Netherlands
Proposal Title: Joining forces: applying long-read RNAseq on muscle biopsies for the diagnosis of neuromuscular disorders
Summary: Identification of aberrant transcriptomic events can support a genetic diagnosis in Mendelian disorders. Given the differences in transcription programs across tissues, selecting the right tissue for the right disorder is key for optimal diagnostic yield. Short-read RNAseq (shRNAseq) approaches on muscle biopsies have been reported to uplift diagnostic yield for neuromuscular disorder (NMD) by 30%. Long-read sequencing promises to enhance sensitivity for the detection of aberrant splicing events. I propose applying PacBio bulk RNAseq to 24 muscle biopsies of undiagnosed NMD cases, to evaluate the added value of PacBio sequencing over shRNAseq.
Finalist: Se Song Jang, Research Professor, Seoul National University Hospital, South Korea
Proposal Title: Dissecting transcriptomes of undiagnosed muscle disorder patients using long-read RNA sequencing
Summary: Despite extensive genomic investigations on our cohort of 8,000 rare disease patients, approximately 50% remain undiagnosed, including those with rare muscle disorders. To uncover the genetic factors causing their conditions, we propose utilizing long-read RNA sequencing on muscle specimens. This innovative approach will provide full-length transcript reads, enabling the detection of rare alternative splicing events, exon-skipping, intron-inclusion, and novel isoforms potentially missed by short-read RNA sequencing methods. By also facilitating the analysis of non-coding RNAs, we aim to uncover previously overlooked regulatory elements implicated in these muscle disorders. Through this comprehensive view of the whole transcriptome, we anticipate improving diagnoses.
Kinnex Single-Cell
Winner: Douglas Brownfield
Assistant Professor
Division of Pulmonary and Critical Care Medicine
Department of Physiology and Biomedical Engineering
Department of Biochemistry and Molecular Biology
Mayo Clinic College of Medicine and Science
Proposal Title: Differential FGFR2-isoform expression underlies pulmonary emphysema pathogenesis
Summary: In emphysema, FGF signaling is disrupted in the airway and alveolar epithelia. Both populations express isoform FGFR2IIIb, and FGFR2IIIc is restrictively expressed in lung myofibroblasts. We hypothesize that cell-specific expression of FGFR2 isoforms contributes to proliferation and differentiation differences between airway and alveolar epithelial stem cells. Current sequencing cannot thoroughly map FGFR2 isoforms at the single-cell level and other isoform datasets are absent in the lung field. We propose using PacBio single-cell Kinnex sequencing to characterize the FGFR2 isoforms in human lung airway and alveolar epithelial cells from healthy and pulmonary emphysema patients to investigate isoforms’ contribution to disease development.
Finalist: Watip Tangjittipokin
Ph.D., SFHEA, Associate Professor
Siriraj Center of Research Excellence for Diabetes and Obesity (SiCORE-DO)
Department of Immunology
Faculty of Medicine Siriraj Hospital
Mahidol University
Proposal Title: Single‐cell atlas of peripheral blood mononuclear cells from gestational diabetes mellitus (GDM)
Summary: During pregnancy, mother-child interactions trigger a variety of subtle changes, which may be reflected in the status of peripheral blood mononuclear cells (PBMCs). Also, PBMC atlas for GDM has not yet been constructed. We will apply single‐cell RNA sequencing (scRNA‐seq) to profile PBMCs derived from pregnant women and establish a transcriptomic clock, reconfiguration of the immune cell phenotype during pregnancy, including interferon‐stimulated gene upregulation, activation of RNA splicing‐related pathways, and immune activity. A cell‐type‐specific model will be developed to predict the gestational age and diabetes status, which should help improve understanding of PBMC composition turnover in gestational diabetes mellitus.
How to apply for PacBio grants
Interested in how you could win free PacBio sequencing for an upcoming project?
The PacBio Grant Program invites researchers globally to apply for complimentary PacBio sequencing services for a diverse array of genomics research projects.
To participate, choose an active grant program that aligns with your research area, follow the guidelines, complete the application, and explain how PacBio sequencing will enhance your work. Applications are reviewed, and selected winners will be notified by PacBio to arrange for free consumables, library preparation, sequencing, and preliminary bioinformatic analyses, all provided by an authorized sequencing service provider. For support of this 2024 Human RNA grant, we acknowledge and thank our service provider Eremid.
These grants encompass all life sciences disciplines. Whether you are exploring intricate microbiomes, complex cancer tumors, rare and endangered species, or the uncharted regions of the human genome, there’s a grant that fits your research needs!