PacBio and UC Davis Researchers Introduce CiFi, a New Long-Read 3C Method That Enables Chromosome-Scale Assemblies from a Single SMRT Cell

Rhea-AI Summary

PacBio (NASDAQ: PACB) and UC Davis researchers introduced CiFi, a community-developed method that combines multi-contact chromatin conformation capture (3C) with PacBio HiFi long-read sequencing to produce chromosome-scale, haplotype-resolved assemblies from a single Revio sequencing run.

CiFi generates long, concatemeric HiFi reads that capture multiple chromatin interactions per molecule, improving mapping in repetitive regions, enabling multi-contact resolution, and reducing input material, libraries, and sequencing runs. A Nature Communications publication and demonstration on prairie and meadow vole produced uncurated assemblies with scaffold N50 values exceeding 100 million base pairs and telomeric sequence at many scaffold ends.

Positive

• Uncurated assemblies with scaffold N50 >100 million bp
• Generates long, concatemeric HiFi reads capturing multiple chromatin contacts
• Enables chromosome-scale, haplotype-resolved assemblies from a single Revio run
• Reduces sample input, libraries, and sequencing runs required for assemblies

Negative

• None.

News Market Reaction – PACB

-4.23%

8 alerts

-4.23% News Effect

-2.9% Trough in 1 hr 19 min

-$27M Valuation Impact

$616M Market Cap

0.3x Rel. Volume

On the day this news was published, PACB declined 4.23%, reflecting a moderate negative market reaction. Argus tracked a trough of -2.9% from its starting point during tracking. Our momentum scanner triggered 8 alerts that day, indicating moderate trading interest and price volatility. This price movement removed approximately $27M from the company's valuation, bringing the market cap to $616M at that time.

Data tracked by StockTitan Argus on the day of publication.

Key Figures

Q3 2025 revenue: $38.4M Non-GAAP gross margin: 42% Non-GAAP operating expenses: $53.9M +5 more

8 metrics

Q3 2025 revenue $38.4M From Q3 2025 results; vs $40.0M a year ago

Non-GAAP gross margin 42% Q3 2025; improved from 33% a year earlier

Non-GAAP operating expenses $53.9M Q3 2025; vs $62.4M in Q3 2024

Non-GAAP net loss $36.8M Q3 2025 non-GAAP net loss (EPS $0.12)

Cash and investments $298.7M As of Sep 30, 2025 from Q3 2025 filings

Year-to-date net loss $506.0M Nine months ended Sep 30, 2025

Convertible notes $645.2M Net balance including 2029 and 2030 notes

Pathogenic variants detected 100% of 125 HiFi Solves study across 86 individuals, 11 complex regions

Market Reality Check

Price: $1.56 Vol: Volume 8,260,063 vs 20-da...

normal vol

$1.56 Last Close

Volume Volume 8,260,063 vs 20-day average 6,451,870 (relative volume 1.28x). normal

Technical Price $2.13 trades above the 200-day MA at $1.48.

Peers on Argus

PACB rose 2.4% while peers were mixed: DCTH and SENS up, RXST and CTKB down, SRD...

1 Up

PACB rose 2.4% while peers were mixed: DCTH and SENS up, RXST and CTKB down, SRDX slightly up. Only LAB appeared in momentum scanners, up 13.26% without news, suggesting stock-specific interest in PACB’s update rather than a broad sector move.

Historical Context

5 past events · Latest: Dec 30 (Neutral)

Pattern 5 events

Date	Event	Sentiment	Move	Catalyst
Dec 30	Conference appearance	Neutral	+1.2%	J.P. Morgan Healthcare Conference presentation and webcast details.
Nov 28	Conference participation	Neutral	-2.9%	Piper Sandler healthcare conference fireside chat and webcast information.
Nov 13	Multiple conferences	Neutral	-1.2%	Participation across three investor conferences with webcast access.
Nov 05	Earnings update	Negative	-4.3%	Q3 2025 revenue decline but margin improvement and narrowed non-GAAP loss.
Nov 05	Clinical data	Positive	-4.3%	HiFi Solves Consortium preprint showing strong pathogenic variant detection.

Pattern Detected

Past news flow shows generally aligned price reactions, with one notable divergence on positive clinical data.

Recent Company History

Over the last few months, PACB has mainly issued conference and results updates. Investor events on Nov 13, 2025 and Nov 28, 2025 saw modest moves around ±3%. The Q3 2025 earnings release on Nov 5 highlighted revenue of $38.4M, narrower losses, and improved non-GAAP gross margin of 42%, with a -4.25% price reaction. On the same day, strong HiFi clinical data also coincided with a -4.25% move, showing at least one case where positive technical news diverged from price action. Today’s technology-focused CiFi announcement fits the pattern of product and capability enhancements.

Market Pulse Summary

This announcement highlights CiFi as a community-developed 3C plus HiFi method enabling chromosome-s...

Analysis

This announcement highlights CiFi as a community-developed 3C plus HiFi method enabling chromosome-scale, haplotype-resolved assemblies from a single Revio sequencing run. It broadens use cases in genome biology and biodiversity studies while leveraging existing HiFi systems. In context with recent filings showing $38.4M in Q3 2025 revenue, improved 42% non-GAAP gross margin, and sizeable cash and debt balances, investors may track how such innovations translate into consumable demand and system adoption over time.

Key Terms

chromatin conformation capture (3C), HiFi sequencing, long-read sequencing, chromatin interactions, +3 more

7 terms

chromatin conformation capture (3C) medical

"By integrating chromatin conformation capture (3C) with PacBio HiFi..."

A laboratory method that maps which parts of the genome physically touch each other inside a cell, revealing how DNA folds in three dimensions. Think of it like noting which pages of a folded map are pressed together to find hidden connections; scientists use it to link regulatory regions with genes they control. For investors, results can point to new drug targets, biomarkers, or help de‑risk programs by clarifying biological mechanisms that affect a biotech's pipeline value.

HiFi sequencing technical

"By integrating chromatin conformation capture (3C) with PacBio HiFi long-read..."

HiFi sequencing is a DNA-reading technology that produces long stretches of genetic code with very high accuracy, like getting a clear, unbroken sentence rather than many short, noisy fragments. For investors, it matters because higher-quality genetic data can speed drug discovery, improve diagnostics, and reduce downstream costs and errors in genomics projects, making companies that use or sell the technology potentially more competitive and valuable.

long-read sequencing technical

"PacBio HiFi long-read sequencing, CiFi delivers multi-contact reads..."

Long-read sequencing is a laboratory method that reads much longer stretches of DNA at once than older approaches, giving a clearer, more continuous picture of a genome—like reading whole sentences instead of just chopped-up words. For investors, it matters because it can improve accuracy of genetic tests, speed up drug research, reduce costly follow-up testing, and create competitive advantages for companies that develop or use the technology in diagnostics and therapeutics.

chromatin interactions medical

"capture multiple chromatin interactions within a single molecule."

Chromatin interactions are the physical contacts and folding patterns that bring different parts of the genome and its associated proteins into close proximity, much like looping a long string so beads that are far apart touch. These contacts control which genes are turned on or off, so for investors they matter because evidence of specific chromatin interactions can validate drug targets, biomarkers or diagnostic approaches and reduce scientific or regulatory risk for therapies and diagnostics tied to gene regulation.

proximity ligation medical

"increase the information content of proximity ligation experiments..."

Proximity ligation is a laboratory method that detects when two specific molecules sit very close together by using pairs of tiny DNA tags attached to binding proteins; when those tags are brought into contact they are joined into one DNA strand that can be copied and measured. For investors, it matters because this approach creates highly specific and sensitive tests—like a two-key lock that only opens when both keys fit—enabling more accurate diagnostics, clearer biomarkers and potentially stronger clinical or commercial value for therapeutics and diagnostic products.

telomeric sequence medical

"with telomeric sequence detected at both ends of many scaffolds."

A telomeric sequence is a short, repeating stretch of DNA found at the ends of chromosomes that protects genetic material much like the plastic tip on a shoelace prevents fraying. It matters to investors because changes in these end caps are central to research and products in areas like aging, cancer diagnostics, and gene therapies, and developments can drive clinical value, regulatory scrutiny, and commercial opportunity for biotech companies.

scaffold N50 technical

"assemblies achieved scaffold N50 values exceeding one hundred million..."

Scaffold N50 is a single-number quality measure for a genome assembly that tells you how large the assembled pieces are: it is the length such that half of the total assembled genome sequence is contained in scaffolds at least that long. Think of it like saying half the puzzle is made from pieces of a certain minimum size — higher values mean fewer, larger pieces and a more complete, easier-to-interpret genome. For investors, a higher scaffold N50 indicates stronger sequencing or assembly technology and more reliable genetic data, which can reduce development risk and support regulatory or product claims.

AI-generated analysis. Not financial advice.

Community-developed approach combines multi-contact 3C with HiFi sequencing to deliver haplotype-resolved assemblies from minimal input material

MENLO PARK, Calif., Jan. 08, 2026 (GLOBE NEWSWIRE) -- PacBio (NASDAQ: PACB), developer of the world's most advanced sequencing technologies, today announced CiFi, a new community-developed method that enables chromosome-scale, haplotype-resolved genome assemblies from a single sequencing run, even when sample material is limited. By integrating chromatin conformation capture (3C) with PacBio HiFi long-read sequencing, CiFi delivers multi-contact reads and longer fragments that significantly increase the information content of proximity ligation experiments in a single Revio sequencing run.

A defining publication just released in Nature Communications by researchers in the Megan Dennis Laboratory at the University of California, Davis, shows how CiFi addresses long-standing limitations of short-read Hi-C by generating long, highly accurate reads that capture multiple chromatin interactions within a single molecule. The new method offers several advantages tailored to the needs of genome biology, biodiversity studies, and functional genomics.

These include improved mapping in repetitive regions, removing obstacles around low input performance, enabling multi-contact resolution, and saving project time and complexity through single platform simplicity.

“CiFi expands our multiomics capabilities, increasing what we can do on HiFi sequencing systems without new hardware and unlocking new customer use cases,” said David Miller, Vice President of Global Marketing at PacBio. “The work from the Megan Dennis Lab at UC Davis shows what becomes possible when innovative chromatin capture methods are paired with the accuracy of HiFi sequencing.”

When paired with Revio SPRQ chemistry, CiFi makes it possible to generate reference-quality assemblies using fewer cells, fewer libraries, and fewer sequencing runs. This lowers barriers for genome projects that have been limited by cost, complexity, or sample availability.

Traditional Hi-C approaches typically capture only two interacting genomic fragments per read pair and often struggle in repetitive or structurally complex regions. CiFi overcomes these limitations by producing long, concatemeric HiFi reads that can contain many interacting chromatin fragments, substantially increasing contact density while maintaining the accuracy of PacBio HiFi sequencing.

"We developed CiFi to make high-accuracy, multi-contact chromatin capture accessible to researchers working with limited or challenging samples,” said Megan Dennis, PhD, Associate Professor at UC Davis. “By combining 3C with HiFi sequencing, we can resolve chromatin architecture across complex genomic regions and generate chromosome-scale assemblies with greater confidence and far less input.”

In a demonstration of the method’s capabilities, UC Davis and PacBio applied the CiFi developed workflow to the prairie and meadow vole. The resulting uncurated assemblies achieved scaffold N50 values exceeding one hundred million base pairs, with telomeric sequence detected at both ends of many scaffolds. These results show that the UC Davis developed CiFi method, combined with HiFi sequencing, can routinely deliver chromosome scale, reference quality assemblies using only one sequencing run.

For more information about CiFi, visit the Application Note here.

About PacBio 

PacBio (NASDAQ: PACB) is a premier life science technology company that designs, develops, and manufactures advanced sequencing solutions to help scientists and clinical researchers resolve genetically complex problems. Our products and technologies, which include our HiFi long-read sequencing, address solutions across a broad set of research applications including human germline sequencing, plant and animal sciences, infectious disease and microbiology, oncology, and other emerging applications. For more information, please visit www.pacb.com and follow @PacBio.  

PacBio products are provided for Research Use Only. Not for use in diagnostic procedures.  

Forward Looking Statements 

This press release may contain “forward-looking statements” within the meaning of Section 21E of the Securities Exchange Act of 1934, as amended, and the U.S. Private Securities Litigation Reform Act of 1995. All statements other than statements of historical fact are forward-looking statements, including statements relating to: the uses, advantages, or quality or performance of, or benefits or expected benefits of using, PacBio products or technologies, such as in connection with genome biology, biodiversity studies, and functional genomics, improved mapping in repetitive regions, removing obstacles around low input performance, enabling multi-contact resolution, saving project time and complexity, expanding multiomics capabilities, generating reference-quality assemblies with fewer cells, libraries and sequencing runs, resolving chromatin architecture with less input, and other future events. You should not place undue reliance on forward-looking statements because they are subject to assumptions, risks, and uncertainties and could cause actual outcomes and results to differ materially from currently anticipated results, including, challenges inherent in using new sequencing methods, the difficulty of generating discoveries in new areas of research; potential product performance and quality issues; third-party claims alleging infringement of patents and proprietary rights or seeking to invalidate PacBio's patents or proprietary rights, among others. Additional factors that could materially affect actual results can be found in PacBio's most recent filings with the Securities and Exchange Commission, including PacBio's most recent reports on Forms 8-K, 10-K, and 10-Q, and include those listed under the caption "Risk Factors." These forward-looking statements are based on current expectations and speak only as of the date hereof; except as required by law, PacBio disclaims any obligation to revise or update these forward-looking statements to reflect events or circumstances in the future, even if new information becomes available.

Contacts 

Investors: 
Jim Gibson: jamesgibson@pacb.com or ir@pacificbiosciences.com 

Media: 
pr@pacificbiosciences.com 

FAQ

What is CiFi and how does it change genome assembly for PacBio (PACB)?

CiFi combines multi-contact 3C with HiFi long-read sequencing to produce long concatemeric reads that enable chromosome-scale, haplotype-resolved assemblies from a single Revio sequencing run.

How much sequencing input does CiFi require to generate chromosome-scale assemblies with PACB HiFi?

CiFi is reported to enable reference-quality assemblies using fewer cells, fewer libraries, and a single Revio sequencing run, lowering input requirements.

What assembly metrics did UC Davis and PacBio achieve using CiFi on vole genomes?

The uncurated assemblies achieved scaffold N50 values exceeding 100 million base pairs with telomeric sequence detected at many scaffold ends.

Does CiFi require new PacBio hardware to run on HiFi systems (PACB)?

No; CiFi is described as expanding multiomics capabilities on HiFi sequencing systems without requiring new hardware.

What advantages does CiFi provide over traditional short-read Hi-C for PACB users?

CiFi produces longer, highly accurate reads that capture multiple chromatin interactions per molecule, improving mapping in repetitive or structurally complex regions and increasing contact density.