Bioinformatics Variant Calling Patents: Leaders & Filing Trends 2026
- Five filers account for 92.3% of the 13 records in scope, with a sixth entrant closing the ranking to 100.0% — this is a tight field, not a crowded one.
- Filing peaked in 2022 at 4 records and has not exceeded that since, so the growth curve here is flat rather than accelerating.
- G16B bioinformatics classification covers all 13 records, while AI-model claims under G06N reach only 30.8% — machine learning integration is still a minority of filings.
What this patent set covers
This landscape tracks patent families addressing variant calling — the computational step that turns aligned sequencing reads into a list of germline or somatic variants — where the claims specifically touch sensitivity/precision benchmarking, structural variant detection, pangenome or reference-genome handling, per-genome compute cost, or clinical reporting standards. The scope is narrow by design: it sits at the intersection of bioinformatics classification (G16B) and molecular diagnostics (C12Q1), not general sequencing hardware or unrelated genomics software.
Thirteen records meet this definition across the 2015-2026 window, filed through the USPTO, WIPO's PCT route, the EPO and India. That is a small, specialist corpus: the assignee ranking behind it lists only six companies, and the filing trend has not shown sustained year-on-year growth since its 2022 peak.
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Filing trend and technology composition
Two views of the same 13-record corpus: how filings have moved year over year, and which IPC subclasses the claims actually sit in.
A flat curve since the 2022 peak
Filings rose from zero in 2017 to a peak of 4 in 2022, the corpus midpoint year. Nothing since has matched that peak, and the most recent year is a partial one, so the true 2025-2026 filing rate will only become visible after the usual 18-month publication lag closes.
Bioinformatics classification dominates; AI and clinical-informatics trail
Every one of the 13 records carries a G16B bioinformatics classification, confirming the search scope. Beyond that base layer, 30.8% also carry G06N (AI-based computing), 23.1% carry C12Q1 (enzyme/DNA measuring and testing), and another 23.1% carry G16H (healthcare informatics) — these shares overlap because a single record can carry more than one class.
Shares are the percentage of the 13 records in scope. A patent can carry several IPC classes, so the shares add up to more than 100%.
Go deeper on Bioinformatics Variant Calling Pipelines with Eureka
This page is one run against one query. Ask Eureka your own question about bioinformatics variant calling pipelines and every answer comes back with the patent numbers behind it.
Try EurekaThe most-cited records in this corpus
Structural variant alignment and variant calling by utilizing a structural-variant reference genome
This disclosure describes methods, non-transitory computer-readable media, and systems that identify reads aligning with alternative contiguous sequences representing structural-variant haplotypes within a structural-variant reference genome, generating alignment tags that guide identification of candidate structural-variant locations. The system also identifies read fragments overlapping alternate sequences representing insertions or other structural variants and masks such sequences during alignment.Filed by Illumina; published 2024-12-05 as US20240404624A1.
| # | Publication no. | Patent title | Citations |
|---|---|---|---|
| 1 | US20140143188A1 | Method of machine learning, employing bayesian latent class inference: combining multiple genomic feature det… | 69 |
| 2 | US20230064530A1 | Detection of Genetic Variants in Human Leukocyte Antigen Genes | 3 |
| 3 | WO2025217057A1 | Variant detection using improved sequence data alignments | 1 |
| 4 | US20240404624A1 | Structural variant alignment and variant calling by utilizing a structural-variant reference genome | 1 |
| 5 | WO2023009863A1 | Detection of genetic variants in human leukocyte antigen genes | 1 |
Citation counts are a signal of influence within this searched corpus, not a ranking of current commercial importance — older records accumulate citations simply by being available longer.
Publication numbers are shown where the record carries one (5 of 5 rows); clicking a row searches Eureka by that number.
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Browse MCP servers →What the numbers mean for filing strategy
Three read-outs from the concentration, trend and classification data above.
This is a tight field, not an open one
The top five assignees account for 92.3% of all 13 records in scope, and adding the sixth ranked filer closes the field to 100.0%. A new entrant is not choosing among dozens of established players to design around — the prior art is concentrated in a small number of portfolios.
Growth has flattened since 2022
Filings rose from zero in 2017 to a peak of 4 records in 2022, and no year since has exceeded that mark. Recent-year momentum by assignee shows most of the ranked leaders at zero in the latest year, with only one filer showing activity — read the most recent year as understated given publication lag, not as a real drop-off.
AI-integrated variant calling is still a minority claim
All 13 records sit in G16B bioinformatics, but only 30.8% also claim AI-based computing methods under G06N. Clinical reporting and healthcare informatics (G16H) sit at 23.1% — a similar minority — suggesting the bulk of claim language is still algorithmic-pipeline mechanics rather than downstream clinical or AI-model integration.
Eureka can read the same corpus for gaps instead of for coverage: under-claimed branches adjacent to bioinformatics variant calling pipelines, with the prior art for and against each one.
Who is filing, and where the gaps sit
Six assignees make up the entire ranked field for this corpus. The leader holds five records; the fifth-ranked filer holds one.
The leading filer sets the baseline claim scope
The top-ranked assignee holds 5 of the 13 records in this corpus, giving it the broadest coverage of the sensitivity/precision-benchmark and structural-variant claim space that defines this search. Recent-year momentum for this filer is at zero, consistent with the flat trend across the whole field.
The tail thins fast after the leader
Filing counts drop quickly outside the top position — the fifth-ranked assignee holds a single record. That gap between leader and tail is itself informative: it means most of the claim space outside the leader's portfolio has only been touched once.
Only one ranked filer shows latest-year activity
Of the six ranked assignees, only one shows a filing in the most recent year captured; the rest, including the leader, show zero latest-year activity or a -100% year-on-year change. Given the roughly 18-month lag between filing and publication, this understates true recent activity rather than confirming a slowdown.
| Assignee | Recent year | YoY |
|---|---|---|
| DR SUPRIYA SRIVASTAVA | 1 | — |
| Illumina, Inc. | 0 | -100% |
| TEMPUS LABS INC | 0 | — |
| TEMPUS AI INC | 0 | — |
| GENFORMATIC LLC | 0 | — |
| Broad Institute, Inc. | 0 | — |
Where to take this next
The dataset points to a small, concentrated field with specific under-claimed branches. These are the natural next steps for an IP or R&D team acting on it.
Map the leader's full claim boundaries
With one filer holding 5 of 13 records, understanding exactly what its granted claims cover — not just the abstracts — determines whether adjacent structural-variant or pangenome work is clear to file.
Explore claim scope in Patsnap EurekaTrack the single active recent filer
One assignee shows filing activity in the latest year while the rest of the ranked field is flat; watching that filer's follow-on applications is the cheapest early signal of where the field moves next.
Set up monitoring in Patsnap EurekaTest the under-claimed branches
Compute-cost benchmarking and clinical reporting interoperability sit outside the dense parts of this corpus. A freedom-to-operate check there is faster and cheaper than in the core variant-calling claim space.
Run a white-space search in Patsnap EurekaCommon questions on variant calling patents
This corpus of 13 records is led by a single assignee holding 5 of them, with the top five filers together accounting for 92.3% of all records in scope. The field closes out with a sixth assignee, bringing coverage to 100.0% of the corpus. That means the entire ranked landscape for this specific claim scope — sensitivity/precision benchmarking, structural variant detection, pangenome handling, compute cost and clinical reporting — is made up of just six companies, not dozens.
Not clearly. Filings rose from zero in 2017 to a peak of 4 records in 2022, and no year since has matched that peak, putting the trend's midpoint at 2022. The most recent year is a partial year and, because publication typically lags filing by around 18 months, the true current filing rate will not be visible in the data for some time. Treat the apparent flattening as inconclusive rather than as evidence of a declining field.
Every record in this corpus carries a G16B bioinformatics classification, which is the anchor class for the search. Beyond that, 30.8% of records also carry G06N for AI-based computing methods, 23.1% carry C12Q1 for enzyme and DNA measurement techniques, and another 23.1% carry G16H for healthcare informatics. Because a single patent can carry multiple classes, these percentages overlap rather than summing to 100%.
US20240404624A1, filed by Illumina and published 2024-12-05, covers methods and systems for aligning sequencing reads against a structural-variant reference genome — one built from alternative contiguous sequences representing known structural-variant haplotypes. The claims center on generating structural-variant-alignment tags during that process to flag candidate structural-variant locations, and on identifying and masking read fragments that overlap insertion-type alternate sequences. Anyone building a structural-variant caller that uses an augmented or graph-like reference genome should review this filing's claim boundaries directly rather than relying on the abstract alone.
Based on the classification data, AI-integrated variant calling (G06N, 30.8% of records) and clinical-reporting-standard integration (G16H, 23.1% of records) are minority claim areas relative to the 100% baseline coverage of core G16B bioinformatics methods. Sub-areas such as per-genome compute-cost benchmarking claims and pangenome-graph liftover show thin coverage in this corpus. A team filing in those specific branches faces less-dense prior art than one filing on core alignment or calling mechanics.
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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.