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Run your analysis now →https://www.patsnap.com/resources/blog/rd-blog/combinatorial-indexing-library-preparation-patent-landscape/ · Patsnap · data cut-off 2026-07-31 · downloaded from the live page
Patent Landscape · Life Science ToolsCombinatorial Indexing Library Preparation Patents
- One assignee holds 78 of the tracked families, far ahead of a fifth-place holder at 7 — a genuine leader-and-long-tail structure, not a crowded field.
- Filings peaked in 2018 at 36 and had fallen to 7 by 2024, a documented -50% drop from 2021 to 2024 that predates any publication-lag distortion.
- C40B combinatorial-library claims sit under 8% of the 151 records, while C12Q enzyme/DNA assays cover nearly three-quarters — most of the claim activity is in assay mechanics, not library chemistry itself.
151
Published Records
-50%
Filing Growth 2021→2024
EP
Leading Jurisdiction
31
Active Filers Ranked
Filing growth compares 2021 (14 records) with 2024 (7) — a three-year span. 2024 is the most recent year we treat as complete: publication lags filing by roughly 18 months, so 2025 onwards are still filling in and any growth rate that ends there would understate the field.
Published byPatsnap Research··7 min readSourced from Patsnap Eureka
Overview
What this landscape covers
Combinatorial indexing and split-pool barcoding methods let a lab tag tens of thousands of single cells with unique DNA barcodes without physically isolating each one, replacing droplet- or well-based single-cell prep in some workflows. This landscape tracks 151 published patent families filed between 2015 and mid-2026 that combine that core method with claims on cell throughput, barcode collision rate, doublet identification, reagent compatibility, or uniformity of indexing. The scope deliberately excludes general single-cell sequencing filings that do not touch these specific technical control points.
Because the search string ties the method term to a named technical problem, the set is narrower than a generic 'single-cell sequencing' pull and skews toward filings that had to solve a measurable engineering issue rather than merely describe a workflow.
Filing activity and technical scope, 2015–2026
Source: Patsnap Eureka. Assignee ranking and totals. Derived from a Patsnap search on Combinatorial Indexing Library Preparation covering 2015–2026, data cut-off 2026-07-31. Counts reflect published records only and shift as new filings publish.Run this in Eureka MCP
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The Data
Filing trend and technology composition
Two views of the same 151-record set: how filing volume has moved year over year, and which IPC subclasses carry the claims.
Filing trend: a sharp rise, then a documented pullback
Filings ran from 17 in 2017 to a peak of 36 in 2018, then declined; the 2021-to-2024 span shows a -50% drop (14 to 7). 2025 and 2026 figures are still filling in under the usual ~18-month publication lag and should not be read as a continued fall.
IPC composition: assay mechanics dominate over library chemistry
C12Q (measuring/testing involving enzymes or DNA) appears in 72.8% of the 151 records and C12N (microorganisms and genetic engineering) in 43.0%, while C40B (combinatorial chemistry libraries proper) sits at just 7.9% and B81B (microfluidic/MEMS devices) at 4.0% — the claim pressure is concentrated on what you measure and manipulate, not on the barcoding library format itself.
Shares are the percentage of the 151 records in scope. A patent can carry several IPC classes, so the shares add up to more than 100%.
Source: Patsnap Eureka. Filing trend and technology composition. Derived from a Patsnap search on Combinatorial Indexing Library Preparation covering 2015–2026, data cut-off 2026-07-31. Counts reflect published records only and shift as new filings publish.
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The most-cited records in this set
Representative Recent Filing
Single cell co-sequencing of DNA methylation and RNA
THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
Methods, compositions and systems for co-sequencing DNA methylation and RNA from the same cell, using gel beads to compartmentalize single-cell nuclei and add DNA barcodes for combinatorial (including three-layer) indexing, enabling parallel high-throughput processing of tens of thousands or more cells in a single experiment.Filed by The Regents of the University of California, published 2025-10-02 as US20250305047A1.
Highest-citation documents
| # | Publication no. | Patent title | Citations |
|---|---|---|---|
| 1 | US20140248621A1 | Microfluidic devices and methods for cell sorting, cell culture and cells based diagnostics and therapeutics | 229 |
| 2 | US5994068A | Nucleic acid indexing | 135 |
| 3 | US20180312873A1 | Method and systems for high throughput single cell genetic manipulation | 114 |
| 4 | US20180023119A1 | Single cell whole genome libraries and combinatorial indexing methods of making thereof | 90 |
| 5 | US6280948B1 | Nucleic acid indexing | 69 |
| 6 | WO2018018008A1 | Single cell whole genome libraries and combinatorial indexing methods of making thereof | 59 |
| 7 | US20180355348A1 | Single cell whole genome libraries for methylation sequencing | 45 |
| 8 | WO2017070056A1 | Methods and systems for high throughput single cell genetic manipulation | 42 |
| 9 | US9149806B2 | Microfluidic devices and methods for cell sorting, cell culture and cells based diagnostics and therapeutics | 32 |
| 10 | WO1998040518A2 | Nucleic acid indexing | 28 |
Citation counts reflect influence within the searched corpus and skew toward older filings; treat them as a signal of prior-art density, not current commercial relevance.
Each row carries its publication number; clicking a row searches Eureka by that number.
Source: Patsnap Eureka. Citation counts and representative records. Derived from a Patsnap search on Combinatorial Indexing Library Preparation covering 2015–2026, data cut-off 2026-07-31. Counts reflect published records only and shift as new filings publish.Run this in Eureka MCP
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What the numbers signal
Reading the filing trend and citation pattern together points to a field where the founding IP is settled and recent activity is defensive or incremental.
Filing Momentum
-50%
2021 → 2024 filings (14 → 7)
Volume has pulled back from its 2018 peak
Filings peaked at 36 in 2018 and have declined since; the -50% move from 2021 to 2024 is the most recent complete-year comparison available. 2025-26 numbers are still incomplete under normal publication lag and should not be read as an acceleration of the decline.
Read against 2024 as the last complete year
Citation Age Skew
229 citations
top-cited record, filed pre-2018
The most-cited documents are the oldest ones
The five most-cited records include foundational 'nucleic acid indexing' patents from the late 1990s alongside a 2014 microfluidic cell-sorting filing. High citation counts here mark foundational prior art that later filings had to design around, not recent breakthroughs.
Citation counts favour older records by construction
Technology Split
72.8% vs 7.9%
C12Q share vs C40B share of 151 records
Assay claims outnumber library-format claims roughly 9 to 1
C12Q (enzyme/DNA measurement) covers 72.8% of the 151 records while C40B (combinatorial libraries) covers 7.9% — most patent activity addresses what happens after barcoding (detection, quantification) rather than the barcoding library architecture itself.
Shares overlap; records can carry multiple IPC classes
Eureka AI Agent
Looking for what nobody has claimed yet?
Eureka can read the same corpus for gaps instead of for coverage: under-claimed branches adjacent to combinatorial indexing library preparation, with the prior art for and against each one.
Source: Patsnap Eureka. Co-assignee relationships and derived observations. Derived from a Patsnap search on Combinatorial Indexing Library Preparation covering 2015–2026, data cut-off 2026-07-31. Counts reflect published records only and shift as new filings publish.Run this in Eureka MCP
Players
Who holds the ground
One organisation dominates the ranked assignee list by volume; behind it sits a long tail of universities and platform companies with single-digit family counts.
Scale Leader
78 families
leader vs. 7 at fifth place
A single leader, then a steep drop-off
The top-ranked assignee holds 78 of the tracked families against 7 at fifth place and 5 at tenth — this is a leader-and-long-tail structure rather than a competitive cluster, and freedom-to-operate work should start by mapping that leader's claim boundaries first.
31 companies appear in the ranked list overall
Co-filing Pattern
55 co-filings
strongest assignee pair, of 10 pairs total
The strongest tie is an industry-academic pair
Of 10 identified co-assignee pairs, the strongest links a commercial sequencing leader with a research university at 55 shared filings — evidence of a sustained licensing or joint-development relationship rather than one-off collaboration.
Second-strongest pair sits at just 10 shared filings
Recent Momentum
0 in latest year
across every assignee tracked for YoY momentum
No tracked assignee shows recent-year growth
Every assignee in the recent-momentum data shows zero filings in the latest year, with the two largest posting -100% YoY. This is consistent with the general 2024-26 publication-lag gap rather than a genuine stop in R&D activity.
Treat latest-year zeros as reporting lag, not exit
Recent-year filing momentum by assignee
| Assignee | Recent year | YoY |
|---|---|---|
| Illumina, Inc. | 0 | -100% |
| Oregon Health & Science University | 0 | -100% |
| The Regents of the University of California | 0 | — |
| Wisconsin Alumni Research Foundation | 0 | — |
| Chan Zuckerberg Biohub, Inc. | 0 | — |
| Fluent BioSciences, Inc. | 0 | — |
| Duke University | 0 | — |
| Takara Bio USA, Inc. | 0 | — |
Source: Patsnap Eureka. Assignee-level momentum. Derived from a Patsnap search on Combinatorial Indexing Library Preparation covering 2015–2026, data cut-off 2026-07-31. Counts reflect published records only and shift as new filings publish.Run this in Eureka MCP
What's Next
Where to take this
The dataset points to specific next steps depending on whether you are clearing freedom to operate or scouting where to file.
Map the leader's claim boundary
With one assignee holding 78 of 151 families, any new filing or product in this space should start with a claim-by-claim read of that portfolio before assuming open ground elsewhere.
Explore assignee portfolios in Eureka →Watch the 2025-26 filings as they resolve
Because publication lags filing by about 18 months, the apparent 2024 low is not the end of the story — track new publications as they land rather than reading the recent years as a slowdown.
Set up filing alerts in Eureka →Test the under-claimed branches
C40B and B81B classes carry a small share of the 151 records despite covering library format and device architecture — these are worth a deeper prior-art check before assuming they're occupied.
Run a white-space search in Eureka →Source: Patsnap Eureka. Forward-looking reading of the same dataset. Derived from a Patsnap search on Combinatorial Indexing Library Preparation covering 2015–2026, data cut-off 2026-07-31. Counts reflect published records only and shift as new filings publish.Run this in Eureka MCP
FAQ
Common questions
Combinatorial indexing, also called split-pool barcoding, is a method for tagging thousands to tens of thousands of individual cells with unique DNA barcode combinations without physically isolating each cell in a droplet or well. Cells or nuclei are pooled, split, and barcoded in repeated rounds, so each cell ends up with a distinctive combination of barcodes that lets sequencing data be traced back to its cell of origin. It is used as an alternative or complement to droplet-based single-cell platforms, particularly when very high cell throughput is needed at lower per-cell cost.
One assignee leads the ranked list with 78 of the 151 tracked patent families, well ahead of the fifth-ranked holder at 7 and tenth-ranked at 5. This is a concentrated-leader structure: a small number of universities and platform companies, including sequencing instrument makers and academic technology-transfer offices, hold the bulk of foundational claims, while 31 organisations appear in the ranking overall with most holding only a handful of families each.
Filings peaked at 36 in 2018 and the most recent complete comparison shows a -50% drop from 14 filings in 2021 to 7 in 2024. That said, patent publication typically lags the actual filing date by around 18 months, so 2025 and 2026 figures in any dataset are still incomplete and should not be read as evidence of a continuing decline. The honest read is that the field cooled after its initial land-grab phase around 2017-2018, with 2024 as the last year you can compare fairly.
The dominant classes are C12Q (measuring and testing involving enzymes or nucleic acids), present in 72.8% of the 151 records in this dataset, and C12N (microorganisms and genetic engineering), at 43.0%. Narrower classes include G01N (material analysis, 12.6%), C40B (combinatorial chemistry libraries specifically, 7.9%), and B01L and B81B (lab apparatus and MEMS devices, each around 4-7%). Because a single patent can carry multiple IPC classes, these shares add up to well over 100% and should not be summed.
The IPC composition shows claim density concentrated in assay-side classes like C12Q and C12N, while classes tied to the library format and device hardware itself, C40B and B81B, cover a much smaller share of the 151 records. That gap suggests under-claimed ground in areas like three-layer indexing scheme architecture, MEMS-based compartmentalisation hardware, and barcode collision-rate modelling, though any filing decision should be backed by a targeted prior-art search rather than the class-level share alone.
Answers are grounded in the same dataset. Derived from a Patsnap search on Combinatorial Indexing Library Preparation covering 2015–2026, data cut-off 2026-07-31. Counts reflect published records only and shift as new filings publish.Run this in Eureka MCP
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Disclaimer. This page is generated from Patsnap Eureka data drawn from a limited snapshot of global patent and scientific-literature records, and is provided for general information and reference only.
Patent data carries inherent limitations: recent filings (typically the most recent 18–24 months) are under-counted due to standard publication lag; counts may be reported at either a patent-family or a patent-record basis and are not always directly comparable; classification, applicant-name, and citation data may contain errors, duplicates, or omissions; and the underlying search query defines and constrains the scope shown. As a result, the analysis may be incomplete or inaccurate and may not reflect the full technology landscape.
Nothing on this page constitutes an exhaustive prior-art, novelty, freedom-to-operate, or validity search, nor does it constitute legal, financial, investment, or professional advice, and it should not be relied upon as such. Any patent, commercial, or strategic decision should be verified independently and reviewed with qualified patent, legal, and domain professionals. Patsnap makes no warranties, express or implied, as to the accuracy, completeness, or fitness for any particular purpose of the information presented.
Machine translation. Assignee and organisation names originally recorded in Chinese, Japanese or Korean have been rendered into English by an AI translation step so that the tables stay readable. These renderings are best-effort and may not match a company's registered English name; the original name is what the underlying patent record carries, and it is what any Eureka query launched from this page uses.