Fastest
Eureka on the web
When you want the answer in the next five minutes.
The agent works the prompt against patents and technical literature, citing every source.
Run your analysis now →https://eureka.patsnap.com/resources/blog/rd-blog/reference-guided-variant-calling-pipeline-algorithm-patent-landscape/ · Patsnap · data cut-off null · downloaded from the live page
Patent Landscape · Genomics & BioinformaticsReference-Guided Variant Calling Pipeline Patents: Who Holds the Claims
A patent landscape review of reference-guided variant calling pipeline algorithms: who holds the filings, how the IPC composition breaks down, and where claim
23
Published Records
US
Leading Jurisdiction
9
Filers Listed (max 100)
2013
Peak Filing Year
- One assignee holds 7 of the records in the ranking while the next four ranked entities hold 1 apiece, pointing to a concentrated core surrounded by a long tail of single-filing entrants.
- Every one of the 23 records in scope carries a G16B bioinformatics class and 43.5% pair it with G06F digital data processing, showing the field sits squarely at the software/bioinformatics boundary rather than in wet-lab chemistry.
- Filing activity shows no sustained recent peak with the tracked high point back in 2013 and a thin, still-lagging record count in the most recent years, a signal to check freshly published families before assuming the space is quiet.
Published byPatsnap Research··6 min readSourced from Patsnap Eureka
Overview
What this landscape covers
This landscape tracks patent families whose claims combine variant calling (or a variant caller) with a reference genome or reference-guided approach, executed as a pipeline. That combination narrows the field to computational and system claims for turning aligned sequencing reads into called variants against a reference, rather than the broader universe of sequencing chemistry or assay patents. The scope spans 2015 through the 2026-08-31 cut-off, with 23 total published records forming the base for every figure on this page.
Because publication lags filing by roughly 18 months, the most recent one or two years in the filing trend are understated by construction, recently filed families have not yet published. Readers should treat the 2013 peak as the clearest completed signal in the dataset and treat any apparent recent decline with that lag in mind rather than as proof of a cooling field.
Filing activity and technology composition, 2015–2026 cut-off
Ordered by volume only, not by importance or claim strength. Counted in published records, so one invention filed in several countries counts more than once. Names come from Patsnap's standardised assignee field as recorded on each document; subsidiaries and group companies are not merged. The icon before each name is read from the name itself (words such as University, Institute or Ltd); the data carries no organisation-type field, so treat it as a reading aid rather than a classification. 2 rows in this table share the name LIFE (LIFE TECHNOLOGIES CORP, VERILY LIFE SCIENCES LLC). They are left as separate rows, so the largest-filer figure above is per legal entity, not per group. Rows that look related still cannot be added together: one family can name several of them. Filings held by named individuals rather than organisations are removed where they can be identified; that identification is not exhaustive, so an individually held filing can still appear below. Either way those filings stay inside the totals above. This table shows the top 9 of the 9 filers returned for this search; the data endpoint returns at most 100 entities, so even that 9 is not the complete set of filers. A single record can name more than one filer, so these counts overlap and do not add up to the total.
Source: Patsnap Eureka. Assignee ranking and totals. Derived from one Patsnap search for Reference-Guided Variant Calling Pipeline Algorithm Patent Landscape, covering all matching records regardless of filing date (the search string sets no date limit). Counts cover published records only and move as new filings publish.Run this in Eureka MCP
The data
Filing trend and technology composition
Two views of the same 23-record set: how filings have moved year over year, and which IPC subclasses the claims sit in.
Filing trend
The tracked filing trend runs from 6 records in 2013 down to 0 in the partial, most-recent year. With fewer than four complete years available once the publication lag is accounted for, no growth rate can be stated, the honest reading is that 2013 remains the peak year so far, and later years need re-checking once more filings publish.
Counted in published records by earliest filing year, not de-duplicated into families. A filing is counted in the year it was filed, but it only becomes visible after it publishes: roughly 18 months for most routes, and up to 30 months where a PCT application enters national phase. 2022 onwards are therefore still filling in and are shaded; no growth figure on this page uses them. Because this series counts documents rather than inventions, a rise can mean more inventions or the same inventions filed in more countries; this dataset cannot separate the two.
IPC subclass composition
G16B (bioinformatics) appears in all 23 records in scope, unsurprising given the search terms, while G06F (electric digital data processing) appears in 43.5% of records, marking the software-implementation side of the claims. Smaller shares in C12Q, G01N, G06N, G16H, G06G and G06K (each 8.7% or below) show the pipeline claims occasionally reach into wet-lab measurement, AI-model computing, or healthcare informatics, but those are minority framings, not the core of the art.
Shares are the percentage of the 23 published records in scope. One published record can carry several IPC classes, so the shares add up to more than 100%.
Source: Patsnap Eureka. Filing trend and technology composition. Derived from one Patsnap search for Reference-Guided Variant Calling Pipeline Algorithm Patent Landscape, covering all matching records regardless of filing date (the search string sets no date limit). Counts cover published records only and move as new filings publish.
Go deeper on Reference-Guided Variant Calling Pipeline Algorithm Patent Landscape with Eureka
This page is one run against one query. Ask Eureka your own question about reference-guided variant calling pipeline algorithm patent landscape and every answer comes back with the patent numbers behind it.
Try EurekaRepresentative filing
A representative claim in this space
Representative record
Bioinformatics Systems, Apparatuses, and Methods Executed on an Integrated Circuit Processing Platform
ILLUMINA, INC.
A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One physical electrical interconnect forms an input to the integrated circuit connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each performing one or more steps in the sequence analysis pipeline on the reads of genomic data.Abstract excerpted from the published filing; full claim scope should be read from the granted claims, not this summary.
Selected as the first record the search returns under the database default order, then shown in full. It is not ranked by citations, claim breadth or commercial importance, and it is not a judgement about which filing in this space matters most.
Source: Patsnap Eureka. The first record the search returned, shown in full. Derived from one Patsnap search for Reference-Guided Variant Calling Pipeline Algorithm Patent Landscape, covering all matching records regardless of filing date (the search string sets no date limit). Counts cover published records only and move as new filings publish.Run this in Eureka MCP
Run it yourself
Put your own technology through the same analysis
Where to run it
For builders
MCP server & REST API
When it has to run inside your own pipeline.
Patent search, landscape analysis and assignee resolution as MCP tools. Drop them into any agent framework, or call REST directly.
Browse MCP servers →Reading the data
What the numbers mean for filing strategy
Four findings worth acting on before drafting or freedom-to-operate work in this space.
Concentration
7 vs. 1
leader vs. fifth-place record count
One filer ahead of a thin field
The leading assignee holds 7 of the records in the ranked list; the fifth-ranked entity holds only 1. With 9 companies in the ranking overall, that gap says the leader has built a substantial position while most other named filers have a single documented family, worth checking directly rather than assuming broad coverage.
Ranked assignees: 9
Technology core
100% G16B
share of the 23 records carrying a bioinformatics class
Every record sits in bioinformatics; software is the second axis
All 23 records in scope carry a G16B bioinformatics classification, confirming the search terms found the right art. G06F digital data processing follows at 43.5% of records, meaning close to half the claims are also framed as general-purpose computing implementations, a detail that matters for infringement analysis on software patents.
IPC shares sum above 100% because records carry multiple classes
Filing timing
Peak: 2013
highest tracked filing year in this set
No confirmed recent surge, check freshest filings directly
The tracked trend falls from 6 filings in 2013 to 0 in the current partial year. Because publication lag of roughly 18 months understates the newest years by construction, this is not evidence the field has gone quiet, it means the most recent filings have not surfaced yet in this data cut.
Coverage window: 2015-01-01 to 2026-08-31
Filing venues
US 10 · EPO 7
records by receiving office
Filing activity centres on the US and Europe
Of the tracked receiving offices, the United States accounts for 10 records and the European Patent Office for 7, with single-digit counts at AT, Germany, Hong Kong and India. Anyone assessing freedom to operate outside the US and Europe should check regional filings directly rather than assume equivalent coverage.
Receiving offices tracked: US, EPO, AT, DE, HK, IN
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 reference-guided variant calling pipeline algorithm patent landscape, with the prior art for and against each one.
Source: Patsnap Eureka. Derived observations on the same dataset. Derived from one Patsnap search for Reference-Guided Variant Calling Pipeline Algorithm Patent Landscape, covering all matching records regardless of filing date (the search string sets no date limit). Counts cover published records only and move as new filings publish.Run this in Eureka MCP
Next steps
Where to take this analysis
The dataset points to specific follow-up work rather than a single conclusion.
Map the leader's claim scope family by family
With 7 of the ranked records held by one assignee, the practical next step is reading each family's independent claims to see whether they cover the hardware-integration approach, the software pipeline logic, or both.
Explore assignee filings in EurekaTrack newly published filings against the lag
Because the most recent years are understated by publication lag, re-running this search periodically will surface filings that have not yet cleared publication, important before concluding the field has slowed.
Set up monitoring in EurekaCheck the minority IPC branches for open claim space
C12Q, G01N, G06N, G16H, G06G and G06K each cover a small minority of records; these are candidate areas where fewer claims currently sit and where a well-drafted filing may face less crowded prior art.
Run a white space search in EurekaSource: Patsnap Eureka. Suggested next steps. No new data: every figure named here is one of those above. Derived from one Patsnap search for Reference-Guided Variant Calling Pipeline Algorithm Patent Landscape, covering all matching records regardless of filing date (the search string sets no date limit). Counts cover published records only and move as new filings publish.Run this in Eureka MCP
FAQ
Frequently asked questions
The ranked list covers 9 companies, and one assignee leads with 7 of the records, ahead of the fifth-ranked entity, which holds just 1. That gap indicates a concentrated core position held by a single filer rather than an evenly split field. Anyone assessing competitive exposure should look directly at that leader's granted claims rather than relying on the count alone, since claim scope varies widely even within a single assignee's portfolio.
The tracked filing trend shows a peak of 6 filings in 2013 and falls toward 0 in the current partial year, but no growth rate can honestly be stated from this data because fewer than four complete years remain once the roughly 18-month publication lag is factored in. The apparent decline in the most recent years is most likely an artefact of that lag rather than a genuine slowdown. A reliable read on recent momentum requires re-checking the data after the lag window has cleared.
All 23 records in scope carry a G16B bioinformatics classification, which is expected given the search terms used to build this dataset. Beyond that universal class, 43.5% of records also carry G06F for electric digital data processing, reflecting the software-implementation side of these pipelines. Smaller shares sit in C12Q, G01N, G06N, G16H, G06G and G06K, each covering 8.7% or less of records, showing occasional overlap with wet-lab measurement, AI-model computing and healthcare informatics framings.
Based on receiving-office data in this set, the United States (10 records) and the European Patent Office (7 records) account for the bulk of tracked filings, with single-digit activity at AT, Germany, Hong Kong and India. That pattern suggests the US and Europe are the primary competitive arenas for this art, but it does not mean other jurisdictions are unclaimed, it may simply reflect where this particular dataset's filers chose to file. A freedom-to-operate check for any other jurisdiction should be run directly rather than inferred from this split.
The representative filing describes a hardwired integrated-circuit architecture for executing a sequence analysis pipeline, with dedicated processing engines built from hardwired digital logic circuits rather than general-purpose software execution. That framing means its claims are most directly relevant to anyone building custom silicon or FPGA-based variant calling acceleration, not necessarily to software-only implementations run on standard processors. Reading the granted independent claims in full is the only reliable way to determine whether a specific software or hardware design falls within its scope.
Answers are grounded in the same dataset. Derived from one Patsnap search for Reference-Guided Variant Calling Pipeline Algorithm Patent Landscape, covering all matching records regardless of filing date (the search string sets no date limit). Counts cover published records only and move as new filings publish.Run this in Eureka MCP
Research Reference-Guided Variant Calling Pipeline Algorithm Patent Landscape in depth with Eureka
Go past this page: query the whole reference-guided variant calling pipeline algorithm patent landscape corpus yourself, in your own scope.
Every answer comes back with patent numbers you can open.
How this page was built, and what the numbers do and do not mean
Search. Every figure on this page comes from one Patsnap search, run once and not edited afterwards. This is the exact search string:
TAC:(("variant calling" OR "variant caller") AND ("reference genome" OR "reference-guided") AND pipeline)Reading the field codes: TAC searches the title, abstract and claims of each record, not the full description. The search string sets no date limit, so the scope is every matching record in the database regardless of when it was filed. It is not restricted to recent years. How this string was built matters for how far the counts can be pushed. It was generated in batch from a topic list rather than hand-crafted for this page, and the result set is not manually screened. A keyword search over title, abstract and claims both over-captures (unrelated filings that happen to use the same words) and under-captures (the same invention written in different words). This page cannot measure either effect, so read every figure here as what this particular string returned, not as what exists in the field. One subclass (G16B) carries 100.0% of the published records, so this search returned a classification-tight set.
What is being counted. Two different units appear on this page and they are not interchangeable. The filer list and the technology split are counted in simple (DOCDB) patent families: one invention counts once however many countries it was filed in. The total, the jurisdiction split and the filing-year chart are counted in published records: the same invention counts once per publication. Record counts reward filing in many jurisdictions; family counts do not. Shares are only ever taken against a denominator in the same unit, and each one names it.
Who the filers are. Names come from Patsnap's standardised assignee field, as recorded on the documents themselves. They are not rolled up to corporate group: a parent and its subsidiaries appear as separate entries, and a portfolio acquired from another company stays under the name on the document unless the assignment is reflected there. This list is meant to carry organisations, not people. Filings held by a named individual are identified by matching the assignee against the inventors on the same search, and, for names written in Chinese, Japanese or Korean characters, by the name carrying no organisational suffix; those are removed from the list. Neither test is exhaustive: the inventor list it matches against is itself capped, and a personal name written in Latin script with no organisational wording in it cannot be told apart from a short company name by rule. So an individually held filing can still appear in the list. Those filings stay inside every total and share on this page either way, so the listed entries can add up to less than the total. A record shown in full further down still names its assignee exactly as the patent office records it, including where that is a person: that name is how the record is identified and checked. What is left out of the ranking is people as ranked entries, not people as cited sources. The table shows the top 9 of the 9 filers returned, ordered by count alone; the data endpoint returns at most 100 entities, so even that 9 is not every filer. One published record can name several filers and each is counted separately, so these rows are not slices of a divided whole: adding them together over-counts, and this page deliberately publishes no combined "top five" share for that reason. See every filer, individuals included
Dates. The year chart counts by earliest filing year, not publication year. A filing only becomes visible once it publishes: roughly 18 months for most routes, and up to 30 months where a PCT application enters national phase. Measured across these pages, the year four back from today still holds only about 89% of its eventual count. 2022 onwards are therefore shaded on the chart as still filling in. The data behind this page was retrieved shortly before the publication date shown above.
Legal status. Legal status was not available for this search, so no in-force figure is shown. Get the status breakdown in Eureka
Classification. The technology split uses IPC subclasses (four characters, for example H01M). A single record usually carries several, so the shares add up to more than 100% and a record can appear in more than one bar. Subclass is a coarse grouping; it describes the field a record was classified into, not what the claims cover. Break the classes down to subgroup level
Who wrote the words. The tables, charts, counts, shares and patent numbers on this page are produced directly from the search result by a program; none of them are written or estimated by a language model. The surrounding prose, headings, FAQ answers and the answers in the question panel are drafted by a language model that is given those same figures and is not permitted to introduce others. Prose can still mis-describe a correct figure, so where the two disagree, the tables and charts are the record.
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 limitations that apply to every figure above. Recent filings are under-counted, because an application is not public until roughly 18 months after filing and database loading adds further delay. The search string defines and constrains everything shown: records that use different terminology, or that sit outside the fields searched, are absent and cannot be counted. Applicant names, classification codes, legal-status codes and citation records are taken as recorded and may contain errors, duplicates, omissions or stale entries. Ordering by volume is not a measure of quality, scope, enforceability or commercial value, and a larger portfolio is not a stronger one. 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, validity or infringement search, nor does it constitute legal, financial, investment, or professional advice, and it should not be relied upon as such. No attorney-client relationship is created by it. Any patent, commercial, or strategic decision should be verified independently against the primary records 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.
The question panel. The answers behind the suggested questions on this page were written when the page was generated, not in response to your click. The progress steps that play before an answer appears are an animation of how that analysis was done; nothing is being searched or computed at that moment. Typing your own question instead opens Patsnap Eureka, which does run it live.