Patent landscape: native-fragmentomic contrived plasma matrices and ultra-low-VAF spike-in characterization methods

1. Summary

Two granted US patents held by Natera, both titled "Cell free DNA diagnostic testing standards" (priority 2013-09-27), claim proficiency-testing standard compositions built from nucleosomal nucleic acid preparations derived from two cell sources mixed in unequal quantity, including a cancer (circulating tumor DNA) variant of that composition [1][2]. A granted Covaris patent claims a method of generating cfDNA (cell-free DNA) reference material from formaldehyde-fixed, acoustically sheared chromatin digested to 147–195 bp nucleosome material [3]. SeraCare/LGC hold one granted EP patent on liposome-encapsulated nucleic acid controls and two pending US applications on cfDNA controls [4][5][6]. Twist, Bio-Rad and Sensid have pending applications, published 2022–2025, on cfDNA-background variant libraries and on cell-line-derived cfDNA-like fragments [7][8][9]. No record located in this pass claims spiking variant-bearing DNA at sub-0.01% allele fraction with digital-PCR value assignment; the search results behind that absence are listed in section 5.

2. What Changed

_Baseline (v1). No prior version; this establishes the starting point for future diffs._

3. Details

(a) Native fragment-size / nucleosomal profile in reference material

US10577655B2 claim 1, verbatim: "A prenatal nucleic acid proficiency testing standard composition, comprising a first nucleosomal nucleic acid preparation derived from a first cell source and a second nucleosomal nucleic acid preparation from a second cell source, wherein the quantity of the first nucleic acid preparation is greater than the quantity of the second nucleic acid preparation." [2] [single-source]

US11215622B2 claim 1 recites, verbatim in part, "treating the chromatin with formaldehyde to generate fixed chromatin … exposing the fixed chromatin to acoustic energy to shear the fixed chromatin into sheared, fixed chromatin fragments each having a size of 1 kbp to 5 kbp; treating the sheared, fixed chromatin fragments with an enzyme to digest chromatin in linker regions … and generate nucleosome material having a size of 147 to 195 bp" [3] [single-source]. Dependent claims name micrococcal endonuclease, the GM24385 cell line, a 165–180 bp average size, and incorporation of known mutations [3] [single-source].

(b) Matrix and encapsulation

EP3292221B1 (LGC Clinical Diagnostics; priority 2015-05-06; granted 2021-06-23; Google Patents anticipated expiry 2036-05-06) claims "Use of liposomes for reducing aggregation of the nucleic acids of a control for in vitro use in identifying a plurality of genotypes … the first mixture of nucleic acids is incorporated into the liposomes." [6] [single-source]. Its US counterpart US20220178939A1 (SeraCare; filed 2021-12-16) is shown as pending; claim 1 text was not retrieved [5] [single-source].

(c) Low-VAF variant spiking and digital-PCR characterization

US20220356463A1 (Twist Bioscience; priority 2021-04-09; pending) describes libraries of variant-bearing polynucleotides in a background set comprising cell-free DNA, with the specification describing variant frequencies of 0.01–5%, a predominantly 125–200 base mono/dinucleosomal background, and ddPCR measurement [7] [single-source]. The numbered claims were not retrieved, so whether any of this is claimed is open (section 5).

Bio-Rad's WO2025151472A1 specification describes dPCR (digital polymerase chain reaction) or qPCR on the cfDNA-like fragments to obtain relative chromosome abundance, not variant allele fraction [8] [single-source].

4. Sources

[1] US9499870B2 — Cell free DNA diagnostic testing standards — Natera, Inc. (granted 2016-11-22; accessed 2026-09-25). US9499870B2; bibliographic data cross-read via EPO OPS epodoc US9499870 — https://patents.google.com/patent/US9499870B2/en [federal-registry] [2] US10577655B2 — Cell free DNA diagnostic testing standards — Natera, Inc. (granted 2020-03-03; accessed 2026-09-25). US10577655B2; EPO OPS epodoc US10577655 — https://patents.google.com/patent/US10577655B2/en [federal-registry] [3] US11215622B2 — Generation of cfDNA reference material — Covaris (granted 2022-01-04; accessed 2026-09-25). US11215622B2; EPO OPS epodoc US11215622 — https://patents.google.com/patent/US11215622B2/en [federal-registry] [4] US20230407400A1 — Methods for preparing DNA reference materials and controls — SeraCare Life Sciences, Inc. (published 2023-12-21; accessed 2026-09-25). US20230407400A1, application US 18/210,452; EPO OPS epodoc US2023407400 — https://patents.google.com/patent/US20230407400A1/en [federal-registry] [5] US20220178939A1 — Liposomal preparations for non-invasive-prenatal or cancer screening — SeraCare Life Sciences, Inc. (published 2022-06-09; accessed 2026-09-25). US20220178939A1; EPO OPS epodoc US2022178939 — https://patents.google.com/patent/US20220178939A1/en [federal-registry] [6] EP3292221B1 — Liposomal preparations for non-invasive-prenatal or cancer screening — LGC Clinical Diagnostics, Inc. (granted 2021-06-23; accessed 2026-09-25). EP3292221B1 — https://patents.google.com/patent/EP3292221B1/en [other] [7] US20220356463A1 — Libraries for mutational analysis — Twist Bioscience Corporation (published 2022-11-10; accessed 2026-09-25). US20220356463A1; EPO OPS epodoc US2022356463; family member CA3214947A1 — https://patents.google.com/patent/US20220356463A1/en [federal-registry] [8] WO2025151472A1 — Methods for generating cfDNA-like DNA fragments — Bio-Rad Laboratories, Inc. (published 2025-07-17; accessed 2026-09-25). WO2025151472A1; EPO OPS epodoc WO2025151472 — https://patents.google.com/patent/WO2025151472A1/en [other] [9] WO2024246014A1 — Reference material comprising nucleic acids having a fragmentation and nucleosome profile and diagnostic method — Sensid GmbH (published 2024-12-05; accessed 2026-09-25). WO2024246014A1; EPO OPS epodoc WO2024246014 — https://patents.google.com/patent/WO2024246014A1/en [other]

5. Sourcing & Gaps

Well established: Applicant, filing date and priority chain for [1]–[5] and [7]–[9] were read from two mirrors of the same office data, Google Patents and EPO OPS, and they agree. Those two are not independent of each other, so no line in section 3 is stated without a marker.

Thin: Every claim-gist and status line is [single-source] (one Google Patents page each). Claim text was read through WebFetch, which returns a model summary of the page rather than raw HTML. Quotes marked verbatim should be re-read against the USPTO/EPO publication before counsel relies on them. Claim 1 of US9499870B2 [1] came back truncated, so its gist is taken from the page's independent-claim summary and matches claim 1 of [2]. Claim text was not retrieved for US20220178939A1 [5] or US20220356463A1 [7]. "Active" and anticipated expiry dates are Google Patents' displayed estimates. The connector's naive 20-year terms differ from them: 2034-09-26 for [1], 2036-01-14 for [2], 2038-01-23 for [3]. Neither source is an INPADOC legal-status record, and maintenance-fee payment was not checked.

Rescoped from class 3: Claim 56 asks whether this candidate could file into unclaimed scope, which is partly a question about what an examiner or a competitor would do. It was rescoped to the record question "which published claims recite the mechanism's elements". No patentability or FTO conclusion is drawn.

Out of scope: CPC-class browse, including C12Q1/6806 and C12N15/10, which carry [1][2]. Also out of scope: USPTO Patent Center file wrappers, assignment records and continuation status; the SeraCare parent applications US 15/816,263 (filed 2017-11-17) and US 15/571,689, whose fate was not retrieved; EP3875606B1, a divisional in the family of [6], which was not opened; CA2985135C and CA3006464C, which were not opened; and non-English family members such as CN109055487A (Suzhou Ankeji, "circulating tumor dissociative DNA standard items").

Not searched vs. not found:

• Not found, meaning a search returned zero records: Horizon Discovery plus "cell-free DNA"; Revvity plus "cell-free DNA" plus reference material/standard; "value assignment"/"assigned value" plus digital PCR plus ctDNA plus reference.
• Not found, meaning a search returned records but none on reference-material preparation or low-VAF (variant allele frequency) value assignment on title triage: Guardant (20 results, including the "fragmentome profiling" family AU2017292854B2/US12590326B2, which by title concerns analysing patient samples; claims not read); Illumina (7); Grail (5); Roche (3); Natera beyond [1][2]; Revvity (2, amplification and barcoding); Horizon Discovery (15 results with "reference standard", none on cfDNA).
• Not searched: LGC Clinical Diagnostics' US20250207200A1 / CA3006464C, "Multiplex cellular reference materials", surfaced but was not opened. Two follow-up queries returned HTTP 503 and were not retrieved: "contrived plasma" plus fragment size, and Bio-Rad reference/control material.

[inference] Among the records retrieved, the granted claims on reference-material preparation ([1][2][3]) recite nucleosomal fragmentation of cell-line or primary-cell chromatin. None recites a VAF below 0.01% or dPCR value assignment. Twist's pending spec [7] reaches a 0.01% lower bound in its description. A search of this depth cannot support the statement in claim 54 that no live patent reads on the mechanism. That needs counsel's claim-by-claim reading against the candidate's actual process.

[inference] The Natera and Covaris claims are composition-of-nucleosomal-preparation and fixed-chromatin-digestion claims. Whether a contrived matrix preserving a "native" profile from donor plasma, rather than cell-line chromatin, falls outside them is a legal question this report does not answer.

6. Claim Candidates