Uploaded March 2026 | Updated September 2026, 1 hour ago
When barcode calling precision drops from 99% to 97%, PacBio data detects dramatically more spatially variable isoforms than ONT at equivalent read depth — a difference researchers hypothesize is driven by that small accuracy gap. In this webinar, two researchers show how pairing PacBio HiFi long-read sequencing with near-single-cell spatial platforms (Visium HD and Stereo-seq) uncovers biology that short-read and lower-resolution approaches miss entirely.
Patrick Truong (KTH Royal Institute of Technology) maps immune receptor clonotypes across human lymph node and tonsil tissue at 2 µm resolution using spatial VDJ enrichment with Visium HD. He finds evidence of localized immune diversification, with phylogenetic sub-clades mapping to separate germinal centers and heavy-light chain pairs co-localizing at nearly the exact same spatial position. Lieke Michielsen (Weill Cornell Medicine) introduces spl-IsoQuant 2, a universal barcode calling tool supporting five spatial platforms (including Visium, Visium HD, Stereo-seq, and Slide-seqV2) for spatial isoform sequencing, and demonstrates that PacBio data detects dramatically more spatially variable isoforms than ONT at equivalent read depth — including 319 spatially variable isoforms in colon cancer tissue.
*What you'll learn*
- Identify localized immune diversification patterns at 2 µm resolution using Visium HD that are invisible at 55 µm with standard Visium
- Apply a long molecule selection + exome enrichment strategy that yields more informative reads
- Detect cell-type-specific and region-specific spatially variable isoforms in brain and cancer tissue using dedicated bioinformatics software
*Featured speakers*
- Patrick Truong, Postdoctoral Associate (KTH Royal Institute of Technology / SciLifeLab, Sweden)
- Lieke Michielsen, Postdoctoral Associate (Weill Cornell Medicine, Brain and Mind Research Institute)
- Elizabeth Tseng, PhD, Associate Director of Product Marketing (PacBio) — Host
*Chapters*
00:00 Welcome and introduction to HiFi sequencing
03:04 Spatial VDJ with Visium HD — Patrick Truong
09:51 Germinal center heterogeneity at 2 µm resolution
14:40 BCR/TCR clonality across resolutions
18:22 Phylogenetic tracking of immune clone evolution
21:10 Heavy-light chain pairing at near-single-cell resolution
24:09 Spatial isoform sequencing — Lieke Michielsen
30:50 spl-IsoQuant 2: universal barcode calling tool
34:21 Detecting spatially variable isoforms
37:07 PacBio vs. ONT: why barcode precision matters
41:00 Cancer isoforms and enrichment recommendations
43:35 Live Q&A
*Resources*
- Kinnex single-cell RNA kit for Visium HD 3' (app note): pacb.com/wp-content/uploads/Application-note-Kinnex-single-cell-RNA-kit-for-10x-Visium-HD-3-Spatial-Gene-Expression.pdf
- Kinnex technology overview: pacb.com/technology/kinnex
- Single-cell RNA sequencing with PacBio: pacb.com/products-and-services/applications/rna-sequencing/single-cell-rna-sequencing
- HiFi sequencing delivers a cutting-edge view of RNA isoforms in cancer: pacb.com/blog/rna-isoforms-in-cancer
What spatial biology has your current sequencing approach been missing? *Comment below.*
*Subscribe for more PacBio genomics content:*
youtube.com/@PacificBiosciences?sub_confirmation=1
Learn more about PacBio at pacb.com
Legal & Trademarks: pacb.com/legal-and-trademarks
#SpatialTranscriptomics #LongReadSequencing #HiFiSequencing
When barcode calling precision drops from 99% to 97%, PacBio data detects dramatically more spatially variable isoforms than ONT at equivalent read depth — a difference researchers hypothesize is driven by that small accuracy gap. In this webinar, two researchers show how pairing PacBio HiFi long-read sequencing with near-single-cell spatial platforms (Visium HD and Stereo-seq) uncovers biology that short-read and lower-resolution approaches miss entirely.
Patrick Truong (KTH Royal Institute of Technology) maps immune receptor clonotypes across human lymph node and tonsil tissue at 2 µm resolution using spatial VDJ enrichment with Visium HD. He finds evidence of localized immune diversification, with phylogenetic sub-clades mapping to separate germinal centers and heavy-light chain pairs co-localizing at nearly the exact same spatial position. Lieke Michielsen (Weill Cornell Medicine) introduces spl-IsoQuant 2, a universal barcode calling tool supporting five spatial platforms (including Visium, Visium HD, Stereo-seq, and Slide-seqV2) for spatial isoform sequencing, and demonstrates that PacBio data detects dramatically more spatially variable isoforms than ONT at equivalent read depth — including 319 spatially variable isoforms in colon cancer tissue.
*What you'll learn*
- Identify localized immune diversification patterns at 2 µm resolution using Visium HD that are invisible at 55 µm with standard Visium
- Apply a long molecule selection + exome enrichment strategy that yields more informative reads
- Detect cell-type-specific and region-specific spatially variable isoforms in brain and cancer tissue using dedicated bioinformatics software
*Featured speakers*
- Patrick Truong, Postdoctoral Associate (KTH Royal Institute of Technology / SciLifeLab, Sweden)
- Lieke Michielsen, Postdoctoral Associate (Weill Cornell Medicine, Brain and Mind Research Institute)
- Elizabeth Tseng, PhD, Associate Director of Product Marketing (PacBio) — Host
*Chapters*
00:00 Welcome and introduction to HiFi sequencing
03:04 Spatial VDJ with Visium HD — Patrick Truong
09:51 Germinal center heterogeneity at 2 µm resolution
14:40 BCR/TCR clonality across resolutions
18:22 Phylogenetic tracking of immune clone evolution
21:10 Heavy-light chain pairing at near-single-cell resolution
24:09 Spatial isoform sequencing — Lieke Michielsen
30:50 spl-IsoQuant 2: universal barcode calling tool
34:21 Detecting spatially variable isoforms
37:07 PacBio vs. ONT: why barcode precision matters
41:00 Cancer isoforms and enrichment recommendations
43:35 Live Q&A
*Resources*
- Kinnex single-cell RNA kit for Visium HD 3' (app note): pacb.com/wp-content/uploads/Application-note-Kinnex-single-cell-RNA-kit-for-10x-Visium-HD-3-Spatial-Gene-Expression.pdf
- Kinnex technology overview: pacb.com/technology/kinnex
- Single-cell RNA sequencing with PacBio: pacb.com/products-and-services/applications/rna-sequencing/single-cell-rna-sequencing
- HiFi sequencing delivers a cutting-edge view of RNA isoforms in cancer: pacb.com/blog/rna-isoforms-in-cancer
What spatial biology has your current sequencing approach been missing? *Comment below.*
*Subscribe for more PacBio genomics content:*
youtube.com/@PacificBiosciences?sub_confirmation=1
Learn more about PacBio at pacb.com
Legal & Trademarks: pacb.com/legal-and-trademarks
#SpatialTranscriptomics #LongReadSequencing #HiFiSequencing
