Uploaded March 2026 | Updated September 2026, 6 hours ago
Short-read sequencing captures only 20–40% of the cancer transcriptome. In one study, HiFi long-read sequencing found 2.5x more isoforms — here's how.
In this first episode of Cancer Sequencing 101, Samantha Kalla walks through how HiFi long-read RNA sequencing with the Kinnex workflow reads complete transcripts from 5' cap to poly-A tail, with no assembly and no guesswork. The results are striking: in HER2-positive breast cancer, researchers using Iso-Seq discovered nearly 100,000 novel isoforms — 2.5x more than short reads found in the same samples. For gene fusions, long reads resolved a fusion between IGF2BP2 and TESPA1 in ovarian cancer that short reads had completely misclassified as simple overexpression.
*What you'll learn*
- See why short reads capture less than half the cancer transcriptome
- See how the Kinnex workflow generates thousands of full-length reads per run
- Discover how Iso-Seq found nearly 100,000 novel isoforms in HER2-positive breast cancer
- Learn how pbfusion detects gene fusions that short reads misclassify
*Featured speakers*
- Samantha Kalla, Field Application Scientist (PacBio)
*Chapters*
00:00 Why do short reads miss cancer isoforms?
00:48 The BCL-X example: one gene, opposite effects
01:27 HiFi long-read RNA sequencing with Kinnex
02:04 100,000 novel isoforms in HER2-positive breast cancer
02:36 Gene fusions: what short reads misclassify
04:11 Explore the cancer body map
*Resources*
- Interactive cancer body map: programs.pacb.com/l/1652/2026-03-10/45fw1y
- PacBio RNA Sequencing: pacb.com/products-and-services/applications/rna-sequencing
Are you still using short reads for cancer transcriptomics? Why or why not? *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
#CancerSequencing #HiFiSequencing #PacBio
Short-read sequencing captures only 20–40% of the cancer transcriptome. In one study, HiFi long-read sequencing found 2.5x more isoforms — here's how.
In this first episode of Cancer Sequencing 101, Samantha Kalla walks through how HiFi long-read RNA sequencing with the Kinnex workflow reads complete transcripts from 5' cap to poly-A tail, with no assembly and no guesswork. The results are striking: in HER2-positive breast cancer, researchers using Iso-Seq discovered nearly 100,000 novel isoforms — 2.5x more than short reads found in the same samples. For gene fusions, long reads resolved a fusion between IGF2BP2 and TESPA1 in ovarian cancer that short reads had completely misclassified as simple overexpression.
*What you'll learn*
- See why short reads capture less than half the cancer transcriptome
- See how the Kinnex workflow generates thousands of full-length reads per run
- Discover how Iso-Seq found nearly 100,000 novel isoforms in HER2-positive breast cancer
- Learn how pbfusion detects gene fusions that short reads misclassify
*Featured speakers*
- Samantha Kalla, Field Application Scientist (PacBio)
*Chapters*
00:00 Why do short reads miss cancer isoforms?
00:48 The BCL-X example: one gene, opposite effects
01:27 HiFi long-read RNA sequencing with Kinnex
02:04 100,000 novel isoforms in HER2-positive breast cancer
02:36 Gene fusions: what short reads misclassify
04:11 Explore the cancer body map
*Resources*
- Interactive cancer body map: programs.pacb.com/l/1652/2026-03-10/45fw1y
- PacBio RNA Sequencing: pacb.com/products-and-services/applications/rna-sequencing
Are you still using short reads for cancer transcriptomics? Why or why not? *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
#CancerSequencing #HiFiSequencing #PacBio
