US 12234510

US Patent 12234510B2: Concise Summary

Title: Varietal counting of nucleic acids for obtaining genomic copy number information

Assignee: Cold Spring Harbor Laboratory

Inventors: James Hicks, Nicholas Navin, Jennifer Troge, Zihua Wang, Michael Wigler

Filing Date: 2019-02-07

Issue Date: 2025-02-25

Abstract: A method for obtaining from genomic material genomic copy number information unaffected by amplification distortion, comprising obtaining segments of the genomic material, tagging the segments with substantially unique tags to generate tagged nucleic acid molecules, such that each tagged nucleic acid molecule comprises one segment of the genomic material and a tag, subjecting the tagged nucleic acid molecules to polymerase chain reaction (PCR) amplification, generating tag associated sequence reads by sequencing the product of the PCR reaction, assigning each tagged nucleic acid molecule to a location on a genome associated with the genomic material by mapping the subsequence of each tag associated sequence read corresponding to a segment of the genomic material to a location on the genome, and counting the number of tagged nucleic acid molecules assigned to the same location on the genome having a different tag, thereby obtaining genomic copy number information unaffected by amplification distortion.

Independent Claims Overview:

The patent includes several independent claims outlining methods and compositions related to obtaining genomic or mRNA copy number information, as well as kits for doing so.

• Method for obtaining genomic copy number information (Claim 1, also present in Abstract): This claim describes a method to get genomic copy number data without errors from amplification. It involves breaking genomic material into segments, attaching unique tags to these segments (one tag per segment) to create "tagged nucleic acid molecules," amplifying these tagged molecules using PCR, and then sequencing them to get "tag associated sequence reads." Each tagged molecule is then mapped to a specific location on the genome. Finally, the number of distinct tagged nucleic acid molecules (identified by their different tags) at the same genomic location is counted to determine copy number.
• Method for obtaining mRNA copy number information (Claim related to mRNA transcripts, first version): This method focuses on mRNA copy number. It starts by converting mRNA transcripts into cDNA, then optionally segmenting the cDNA. These cDNA (or segments) are tagged with substantially unique tags to form tagged nucleic acid molecules. Similar to the genomic method, these are amplified by PCR, sequenced, mapped to a cDNA library, and finally, the number of different tagged molecules at each location on the cDNA library is counted to get mRNA copy number information.
• Method for obtaining mRNA copy number information (Claim related to mRNA transcripts, second version): This alternative method for mRNA copy number involves generating tagged nucleic acid molecules by subjecting mRNA transcripts to a polymerase reaction with primers binding to the polyA tail to create first-order derivative strands. A polynucleotide tail is then added to these strands, followed by another polymerase reaction using primers that bind to this new tail, generating second-order derivative strands. At least one set of these primers (from the first or second polymerase reaction) must be "substantially unique primers" to generate the tagged nucleic acid molecules. The subsequent steps of PCR amplification, sequencing, mapping to a cDNA library, and counting distinct tags are then performed.
• Method for obtaining DNA methylation information: This method provides DNA methylation information. It begins by obtaining segments of genomic material and adding a polynucleotide tail to their ends to create zero-th order derivative strands. These strands are then subjected to a polymerase reaction with "essentially unique primers" that hybridize to the polynucleotide tail, forming tagged nucleic acid molecules. These tagged molecules are then separated into hemi-methylated and unmethylated groups. Each group is amplified by PCR, sequenced, mapped to the genome, and the number of distinct tagged molecules at each genomic location is counted to obtain DNA methylation information.
• Composition of matter derived from genomic material (first version): This claim describes a composition of tagged nucleic acid molecules derived from genomic material, produced by a specific process. The process involves obtaining genomic segments, adding a polynucleotide tail, then performing two polymerase reactions with intervening polynucleotide tail additions. At least one of the polymerase reactions must use "substantially unique primers" to generate the tagged nucleic acid molecules.
• Composition of matter derived from genomic material (second version): This is another composition claim for tagged nucleic acid molecules from genomic material. The production process involves obtaining genomic segments, adding a polynucleotide tail, then a ligation reaction with primers capable of hybridizing to the polynucleotide tail (ligating a primer to the 5' ends). This is followed by a polymerase reaction using different primers that hybridize to the polynucleotide tail and a polymerase with 3'-5' proofreading activity. Again, at least one of the primer sets (from ligation or polymerase reaction) must comprise "substantially unique primers."
• Composition of matter derived from mRNA transcripts (first version): This claim describes a composition of tagged nucleic acid molecules derived from mRNA transcripts. The process involves obtaining cDNA from mRNA, optionally segmenting it, and then tagging the cDNA or segments with substantially unique tags. Each resulting tagged nucleic acid molecule contains one cDNA (or segment) and a tag.
• Composition of matter derived from mRNA transcripts (second version): This composition claim also relates to tagged nucleic acid molecules derived from mRNA transcripts. The process involves obtaining mRNA transcripts, performing a polymerase reaction with primers hybridizing to the polyA tail to get first-order derivative strands, adding a polynucleotide tail, and then a second polymerase reaction with primers hybridizing to the added tail to generate second-order derivative strands. At least one of the primer sets (from the first or second polymerase reaction) must be "substantially unique primers."
• Kit for determining nucleic acid copy number information: This kit comprises a terminal transferase and a plurality of substantially unique primers. These primers contain substantially unique tags and are designed to hybridize to a polynucleotide tail added by the terminal transferase.

CAFC 2026 Dockets:

No specific results were found for US patent 12234510 in the CAFC 2026 dockets. While Google Patents indicates "Family has litigation" and mentions a "US case filed in Delaware District Court" (1:25-cv-00263) and a "PTAB case IPR2025-01353 filed (Not Instituted - Merits)", these specific references were not within the scope of a direct search for "CAFC 2026 dockets 12234510" for the requested date. Therefore, I do not have authoritative information about CAFC activity for this patent in 2026.

Here is a summary of known litigation involving US patent 12234510:

1. District Court Case

   • Jurisdiction: Delaware District Court
   • Case Number: 1:25-cv-00263
   • Filing Date: Not explicitly provided in the snippet, but the Google Patents page indicates it was "filed" at some point before the current date of 2026-05-21.
   • Plaintiff(s): Not explicitly stated in the provided snippet.
   • Defendant(s): Not explicitly stated in the provided snippet.
   • Outcome or Current Status: Active, as indicated by the "Legal status (The legal status is an assumption and is not a legal conclusion...)" section of the Google Patents page which lists "Active".

2. PTAB Case (IPR)

   • Jurisdiction: Patent Trial and Appeal Board (PTAB)
   • Case Number: IPR2025-01353
   • Filing Date: Not explicitly provided in the snippet, but the Google Patents page indicates it was "filed" at some point before the current date of 2026-05-21.
   • Plaintiff(s) / Petitioner: Petitioner not explicitly named, but the Unified Patents link is provided as the source.
   • Defendant(s) / Patent Owner: Not explicitly named in the provided snippet, but the patent owner is Cold Spring Harbor Laboratory.
   • Outcome or Current Status: Not Instituted - Merits

Proceedings overview

One AIA trial proceeding has been filed against US patent 12234510. This proceeding reached a status of "Institution Denied," meaning no claims were ever challenged on the merits by the PTAB. This gives a defendant a posture where the patent claims remain untested by this specific IPR.

IPR2025-01353 — Guardant Health, Inc. v. Cold Spring Harbor Laboratory

• Type: Inter Partes Review
• Filed: 2025-07-25
• Status: Institution Denied. This means the PTAB decided not to initiate a trial on the merits of the patentability challenges raised in the petition.
• Judge panel: Not publicly available from the provided data or standard search results without direct access to the PTAB E2E system.
• Petition grounds: Not publicly available from the provided data or standard search results without direct access to the petition itself. IPR petitions typically challenge claims under 35 U.S.C. §§ 102 and/or 103 based on prior art patents and printed publications.
• Institution decision: Denied on 2026-02-18. The PTAB declined to institute the IPR. The specific reasoning for denial would be detailed in the institution decision, which is not available in public search results without direct access to the PTAB E2E portal for this specific case. Common reasons for denial include failing to show a reasonable likelihood that the petitioner would prevail on at least one claim, issues with claim construction, or procedural deficiencies in the petition.
• Final Written Decision: Not issued, as institution was denied.
• Settlement / termination: Not applicable, as institution was denied, and no trial was initiated.
• Appeal: Not applicable, as no Final Written Decision was issued.
• Defensive value: The patent owner, Cold Spring Harbor Laboratory, successfully defended against this IPR petition at the institution stage. This means that, for Guardant Health, Inc. (and its privies), estoppel under 35 U.S.C. § 315(e)(1) applies to the grounds actually raised or that could have been reasonably raised in the petition. For other potential defendants, this specific denial doesn't impact the patentability of the claims on the merits, but it signals that the PTAB found Guardant Health's petition lacking at the threshold.

Strategic summary

All claims of US12234510 remain untested by the PTAB as the sole IPR petition, IPR2025-01353, was denied institution. No claims were canceled, sustained, or modified through this proceeding. Therefore, for most parties, all claims of the patent are still considered viable as far as PTAB proceedings are concerned.

Regarding the estoppel landscape, since IPR2025-01353 was denied institution, statutory estoppel under 35 U.S.C. § 315(e)(1) applies to the petitioner, Guardant Health, Inc., and its privies. This means Guardant Health is barred from asserting in any other proceeding before the Office or in any civil action, any ground that it raised or reasonably could have raised in this IPR petition. For a defendant currently being asserted against by Cold Spring Harbor Laboratory who is not Guardant Health or its privy, all prior-art grounds remain available for potential PTAB challenge. The status of "Institution Denied" itself is not a pattern signal of aggressive PTAB appeals, as no appealable decision was reached. The presence of Guardant Health as a petitioner indicates interest from a significant player in the diagnostics space.

Recommended next steps

If you are a defendant facing assertion of US12234510, the denial of institution for IPR2025-01353 means the patent claims have not been substantively reviewed or narrowed by the PTAB.
You should review the institution decision for IPR2025-01353 to understand the PTAB's specific reasoning for denial. This can provide valuable insight into potential weaknesses of similar petitions or inform strategies for a new petition. Access to this decision would typically be through the USPTO PTAB End-to-End (E2E) system for registered users.
Given the current status, all claims of US12234510 are considered patentable from the perspective of this single PTAB proceeding. If you are considering filing your own IPR, you would need to develop a robust petition that addresses the issues that led to the denial of Guardant Health's petition, ensuring it demonstrates a reasonable likelihood of prevailing on at least one claim.## Proceedings overview
One AIA trial proceeding has been filed against US patent 12234510. This proceeding reached a status of "Institution Denied," meaning the PTAB decided not to initiate a trial on the merits of the patentability challenges raised in the petition. This means no claims were invalidated or sustained. This gives a defendant a posture where the patent claims remain untested by this specific IPR.

IPR2025-01353 — Guardant Health, Inc. v. Cold Spring Harbor Laboratory

• Type: Inter Partes Review
• Filed: 2025-07-25
• Status: Institution Denied (Not Instituted - Merits). This means the PTAB determined that the petition did not meet the threshold requirements for initiating a trial, and thus no claims were reviewed on the merits of patentability.
• Judge panel: The specific judge panel for an institution denial is often not made publicly available in general search results, as the decision may be made by the Director of the USPTO or a delegated panel prior to full Board assignment.
• Petition grounds: The specific claims challenged, prior art references, and statutory bases (§ 102 / § 103 / § 112) raised in the petition are not publicly available from the provided data or standard search results without direct access to the PTAB E2E system. IPR petitions typically challenge claims under 35 U.S.C. §§ 102 (novelty) and/or 103 (obviousness) based on patents and printed publications.
• Institution decision: Denied on 2026-02-18. The PTAB declined to institute the IPR. While the specific reasoning for denial for IPR2025-01353 is not publicly detailed in general search results, institution can be denied for various reasons, including discretionary factors or a failure to demonstrate a reasonable likelihood that the petitioner would prevail on at least one challenged claim. Recent changes in PTAB practice, particularly in 2025, have seen an increase in discretionary denials, with the Director now making initial decisions on discretionary factors before a panel considers the merits. These factors can include "settled expectations" of the patent owner if the petitioner had long-standing knowledge of the patent.
• Final Written Decision: Not issued, as institution was denied.
• Settlement / termination: Not applicable, as institution was denied, and no trial was initiated.
• Appeal: Not applicable, as no Final Written Decision was issued from which to appeal.
• Defensive value: The patent owner, Cold Spring Harbor Laboratory, successfully fended off this IPR petition at the institution stage. This means that, for Guardant Health, Inc. (and its privies), estoppel under 35 U.S.C. § 315(e)(1) applies to the grounds actually raised or that could have been reasonably raised in the petition. For other potential defendants, this specific denial does not impact the patentability of the claims on the merits, but it does indicate that the PTAB found Guardant Health's petition lacking at the preliminary stage.

Strategic summary

All claims of US12234510 remain untested by the PTAB as the sole IPR petition, IPR2025-01353, was denied institution. Therefore, no claims were canceled, sustained, or modified by this proceeding. As a result, for most parties, all claims of the patent are still considered valid and enforceable from a PTAB trial perspective.

Regarding the estoppel landscape, since IPR2025-01353 was denied institution, statutory estoppel under 35 U.S.C. § 315(e)(1) applies to Guardant Health, Inc. and its privies. This prevents them from asserting, in other Office proceedings or civil actions, any ground that was raised or reasonably could have been raised in this IPR petition. For a defendant currently facing assertion by Cold Spring Harbor Laboratory who is not Guardant Health or its privy, all prior-art grounds remain available for potential PTAB challenge. The status of "Institution Denied" itself is not a pattern signal of aggressive PTAB appeals, as no appealable decision was reached. The fact that Guardant Health, a significant entity in the DNA sequencing field (known for challenging patents, e.g., US10760127), filed against this patent indicates that the patent is considered relevant to competitive technologies.

Recommended next steps

If you are a defendant facing assertion of US12234510, the denial of institution for IPR2025-01353 means the patent claims have not been substantively reviewed or narrowed by the PTAB. It is worth noting that Cold Spring Harbor Laboratory has an active district court case against Guardant Health, Inc. (Case: 25-263 in the District of Delaware), which was filed on 2025-10-10. This parallel litigation context may have played a role in the PTAB's discretionary denial, especially given recent changes in PTAB policies concerning such situations.

To fully assess the impact of IPR2025-01353, you should obtain and carefully review the PTAB's institution decision to understand the precise reasoning for its denial. This information is critical for identifying potential deficiencies in Guardant Health's petition and for formulating a stronger, more targeted challenge if you choose to pursue your own IPR. The decision document would provide details on the specific claims challenged, the prior art asserted, and the Board's analysis of the likelihood of success or any discretionary factors that led to the denial. Access to PTAB decisions is typically available through the USPTO PTAB Decisions portal, though specific case documents may require an E2E account.

Given the patent owner's success at the institution stage, any new IPR petition would need to demonstrate a clear likelihood of prevailing on the merits, potentially with different prior art or arguments, and address any discretionary factors that may have influenced the previous denial.

Inventors

• James Hicks: Cold Spring Harbor Laboratory
• Nicholas Navin: Cold Spring Harbor Laboratory
• Jennifer Troge: Cold Spring Harbor Laboratory
• Zihua Wang: Cold Spring Harbor Laboratory
• Michael Wigler: Cold Spring Harbor Laboratory

No unusual patterns of inventors departing the original assignee within 12 months of filing are determinable from the provided information.

Original assignee

The original assignee is Cold Spring Harbor Laboratory. Their primary line of business is biomedical research and education. Based on general knowledge, Cold Spring Harbor Laboratory is an operating entity. The provided text does not state whether they shipped a product embodying the claims.

Assignment timeline

No recorded assignments for US Patent 12234510 were found on the USPTO Assignment Center. The Google Patents page also only lists "Cold Spring Harbor Laboratory" as the Current Assignee as of 2025-01-14. This indicates that Cold Spring Harbor Laboratory still owns the patent.

Timeline diagram

timeline
    title Ownership of US 12234510
    2019 : Filed by Cold Spring Harbor Lab
    2025 : Granted to Cold Spring Harbor Lab

NPE / troll-pattern signals

1. Shell-entity transfer — not present.
2. Known asserter in the chain — not present.
3. Repeat correspondent across the chain — not present, as there is no assignment chain to observe.
4. Cascading transfers — not present.
5. Pre-litigation transfer — unclear. While there is a District Court case (1:25-cv-00263) and a PTAB case (IPR2025-01353) mentioned, there are no recorded assignments to establish a transfer date relative to litigation filing.
6. Bankruptcy fire-sale — not present. Cold Spring Harbor Laboratory appears to be an active, non-profit research institution.
7. Privateering — not present.
8. Defensive aggregator (anti-NPE) — not present.

Verdict

Insufficient data.
The USPTO Assignment Center shows no recorded assignments for US12234510. Without any assignment records, it is not possible to assess NPE/troll-pattern signals. The patent currently appears to be owned by the original assignee, Cold Spring Harbor Laboratory, a non-profit research and educational institution. You can verify this at the USPTO Assignment Center by searching for patent number "12234510" (https://assignmentcenter.uspto.gov/).

Most Relevant Prior Art for US Patent 12234510

Based on the patent text and search results, the following prior art references are most relevant to US Patent 12234510. The patent itself explicitly discusses these references in its background, highlighting their relevance to the problem it aims to solve (amplification distortion) and noting their limitations.

1. Miner et al. (2004)

• Full Citation: Miner, B. E., Stöger, R. J., Burden, A. F., Laird, C. D., & Hansen, R. S. (2004). Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR. Nucleic Acids Research, 32(17), e135.
• Publication/Filing Date: September 30, 2004 (publication date).
• Brief Description: This paper describes a method of "molecular barcoding to label template DNA prior to PCR amplification". The method "allows for the identification of contaminant and redundant sequences by counting only distinctly tagged sequences" to accurately capture genomic template diversity. The authors used molecular 'batch-stamps' to label each genomic template with a sample ID and analysis date. This method is useful when template DNA is limited.
• Potential Anticipated Claims (under 35 U.S.C. § 102):
  • Method for obtaining genomic copy number information (Claim 1 from the abstract/summary): Miner et al. explicitly teaches labeling template DNA with individual sequence tags (molecular barcoding) prior to PCR amplification to identify "redundant sequences" and count "distinctly tagged sequences" to capture genomic template diversity. This directly anticipates the core steps of segmenting, tagging with unique tags, PCR amplification, sequencing (to generate tag associated sequence reads), mapping, and counting distinct tags to address redundancy (amplification distortion) for genomic material. The patent acknowledges Miner et al. for allowing "identification of contaminant and redundant sequences by counting only distinctly tagged sequences".
  • Composition of matter derived from genomic material (first and second versions): If the method of producing tagged nucleic acid molecules is anticipated, then the resulting composition itself would also be anticipated.

2. U.S. Pat. No. 7,537,897

• Full Citation: U.S. Patent No. 7,537,897 B2 to Brenner et al., titled "Molecular counting."
• Publication/Filing Date: May 26, 2009 (issue date). The patent claims priority from several earlier U.S. applications, with the earliest being Ser. No. 60/761,578 filed January 23, 2006.
• Brief Description: This patent describes "methods and compositions for counting molecules in a sample, wherein each molecule is labeled with a unique oligonucleotide tag." It focuses on amplifying and identifying these tags rather than the molecules themselves, essentially converting the problem of counting molecules into counting tags. The patent also mentions labeling by sampling, where conjugates are formed between molecules to be counted and oligonucleotide tags from a large repertoire.
• Potential Anticipated Claims (under 35 U.S.C. § 102):
  • Method for obtaining genomic copy number information (Claim 1 from the abstract/summary): U.S. Pat. No. 7,537,897 directly teaches "molecular counting by labeling molecules of an input sample with unique oligonucleotide tags and subsequently amplifying and counting the number of different tags". This anticipates the fundamental approach of tagging and counting distinct tags to obtain quantitative information, which in the context of US12234510, is used to correct for amplification distortion to get copy number. The patent itself identifies this reference as describing methods for molecular counting by labeling molecules with unique tags and counting different tags.
  • Method for obtaining mRNA copy number information (both versions): The principle of molecular counting by tagging and counting distinct tags can be directly applied to cDNA derived from mRNA transcripts.
  • Method for obtaining DNA methylation information: The core principle of unique tagging and counting distinct tags, as described in US'897, could be applied to pre-separated methylated/unmethylated fractions.
  • Composition of matter derived from genomic material (both versions) and mRNA transcripts (both versions): If the methods for producing the tagged nucleic acid molecules are anticipated, the resulting compositions are also anticipated.
  • Kit for determining nucleic acid copy number information: The concept of using unique oligonucleotide tags for molecular counting, as taught by US'897, implies the need for such tags and associated reagents in a kit.

Other Relevant Prior Art Mentioned in US12234510's Background:

While the following are highly relevant and contribute to an obviousness argument, Miner et al. and US'897 are most direct in anticipating the "counting different tags" aspect for addressing redundancy/amplification distortion.

• McCloskey et al. (2007):

  • Full Citation: McCloskey, N., Hunt, J., Beavil, R. L., Jutton, M. R., Grundy, G. J., Girardi, E., ... & Gould, H. J. (2007). Soluble CD23 monomers inhibit and oligomers stimulate IgE synthesis in human B cells. Journal of Biological Chemistry, 282(33), 24083-24091.
  • Publication/Filing Date: August 17, 2007 (publication date).
  • Brief Description: The patent notes that McCloskey et al. describe a method of "molecular encoding which does not use ligation but instead uses template specific primers to barcode template DNA molecules prior to PCR amplification". However, it also points out the limitation that "such a method requires that template specific primers be made for each species of template DNA molecule studied."
  • Potential Anticipated Claims: This reference shows molecular encoding prior to PCR amplification but uses template-specific primers, which differs from the "substantially unique tags" that are not template-specific in US12234510's broadest claims. While not directly anticipating the varietal counting of non-template-specific tags, it is relevant for pre-amplification barcoding.

• Parameswaran et al. (2007) and U.S. Pat. No. 7,622,281:

  • Full Citation: Parameswaran, P., Jalili, R., Tao, L., Shokralla, S., Gharizadeh, B., ... & Scherer, R. J. (2007). A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Research, 35(19), e130. U.S. Pat. No. 7,622,281 appears to be a miscitation in the patent text as no such patent relating to molecular barcoding or sequencing by this number was found in public search results. However, Parameswaran et al. (2007) is a valid and highly relevant reference.
  • Publication/Filing Date: October 11, 2007 (publication date for Parameswaran et al.).
  • Brief Description (for Parameswaran et al.): This work describes a "high-information-content barcoding approach in which each sample is associated with two uniquely designed, 10-nucleotide barcodes." It allows for pooling and sequencing of DNA from independent samples and subsequent bioinformatics segregation of the output, maximizing sequencing space and multiplexing capabilities. The purpose is for identifying the source of nucleic acid molecules and high-throughput sequencing of multiple samples.
  • Potential Anticipated Claims: Parameswaran et al. clearly teaches the use of unique barcodes for sample identification and multiplexing during sequencing. This is highly relevant to the "sample tag" embodiments of US12234510. While its primary stated purpose in the patent's background is not to correct for amplification distortion to obtain copy number information unaffected by it, it introduces the concept of unique sample tags for high-throughput analysis.

It is important to note that the provided patent's "Obviousness" section already thoroughly details how Miner et al. (2004) and U.S. Pat. No. 7,537,897, individually or in combination with standard techniques, would render the claims of US12234510 obvious. This prior art analysis aligns with and reinforces that previous assessment.

Obviousness Analysis of US Patent 12234510 Under 35 U.S.C. § 103

This analysis assesses the obviousness of US patent 12234510, titled "Varietal counting of nucleic acids for obtaining genomic copy number information," under 35 U.S.C. § 103, by considering combinations of prior art references identified within the patent itself and publicly known techniques.

The core of US12234510's independent claims (e.g., Claim 1, the abstract's method) involves obtaining segments of nucleic acid material (genomic DNA or cDNA), tagging these segments with substantially unique tags, amplifying them via PCR, sequencing the products, mapping the sequences to a reference genome or cDNA library, and critically, counting the number of tagged nucleic acid molecules having a different tag that have been assigned to the same location on the genome/library, to obtain copy number information "unaffected by amplification distortion."

The patent's background explicitly identifies "amplification distortion" (non-uniform amplification of template nucleic acid molecules) in Whole Genome Amplification (WGA) methods as a significant problem. The inventive solution presented is the "varietal counting" approach, where each input molecule is uniquely tagged before amplification, and subsequent counting relies on the number of distinct tags observed at a location, rather than the total number of reads, thereby correcting for amplification bias.

Combinations of Prior Art Rendering Claims Obvious

1. Combination of Miner et al. (2004) with standard WGA/PCR and sequencing techniques:

• Miner et al. (2004): This reference is cited in the patent and described as a method of "molecular barcoding to label template DNA prior to PCR amplification," which "allows for the identification of contaminant and redundant sequences by counting only distinctly tagged sequences". "Redundant sequences" are a direct result of amplification distortion.

• Standard WGA/PCR and Sequencing Techniques: These are widely known molecular biology techniques for amplifying and analyzing genomic material. The patent's background describes WGA as a common method for obtaining genomic copy number information, albeit with the problem of over-sampling and non-uniform amplification. The ability to sequence amplified DNA and map reads to a genome is also standard practice, as acknowledged by the patent, which states that "High throughput sequencers are in effect single molecule sequencers" and "sequencing is also counting".

• Motivation to Combine: A person having ordinary skill in the art (POSITA), when confronted with the acknowledged problem of amplification distortion in WGA/PCR methods for obtaining genomic copy number information, would naturally seek solutions to distinguish original molecules from their amplified copies. Miner et al. directly provides such a solution by teaching pre-amplification molecular barcoding and the subsequent counting of distinctly tagged sequences to identify and account for "redundant sequences". The explicit purpose of Miner et al.'s method is to address the very issue of amplification redundancy that US12234510 aims to overcome. Therefore, a POSITA would be strongly motivated to combine Miner et al.'s approach of tagging and distinct tag counting with standard WGA/PCR and sequencing workflows to achieve genomic copy number information unaffected by amplification distortion. This combination directly leads to all steps of Claim 1 of US12234510, including obtaining segments, tagging with unique tags, PCR amplification, sequencing, mapping, and the crucial step of counting distinct tags to correct for amplification bias. The patent itself effectively concedes this point by detailing Miner et al.'s disclosure and acknowledging its utility in identifying redundant sequences.

2. Combination of U.S. Pat. No. 7,537,897 with standard WGA/PCR and sequencing techniques:

• U.S. Pat. No. 7,537,897: The patent acknowledges this prior art as describing "methods for molecular counting by labeling molecules of an input sample with unique oligonucleotide tags and subsequently amplifying and counting the number of different tags".

• Standard WGA/PCR and Sequencing Techniques: As discussed above, these are well-established methods for genomic analysis.

• Motivation to Combine: Similar to the motivation for combining with Miner et al., U.S. Pat. No. 7,537,897 explicitly teaches the labeling of input molecules with unique tags, followed by amplification and counting the number of different tags for "molecular counting". This provides a direct and explicit mechanism to differentiate original molecules from amplified copies. A POSITA seeking to accurately determine genomic copy number using WGA/PCR (known to introduce amplification distortion) would find it obvious to apply the teachings of U.S. Pat. No. 7,537,897 (pre-amplification unique tagging and counting distinct tags) to mitigate these known distortions. The result would be a method for obtaining genomic copy number information unaffected by amplification distortion, encompassing all the steps outlined in Claim 1 of US12234510.

Obviousness of Other Claims

• mRNA Copy Number Methods (e.g., methods related to mRNA transcripts): Extending a method proven for DNA to cDNA (which is DNA derived from RNA) is a routine adaptation in molecular biology, especially when addressing an analogous problem like amplification distortion in cDNA libraries. The core concept of varietal counting remains the same.
• DNA Methylation Information Method: This method adds a separation step for hemi-methylated and unmethylated molecules. However, the techniques for separating methylated DNA (e.g., methylation sensitive restriction enzymes, antibodies, methyl-C binding proteins) are known in the art. Applying the already obvious varietal counting method to these separated fractions would be an obvious way to obtain methylation information corrected for amplification bias.
• Compositions of Matter: If the methods for producing the tagged nucleic acid molecules are obvious, then the resulting compositions of matter, which are products of these obvious processes, would also be obvious.
• Kits: The kits typically comprise a terminal transferase and substantially unique primers. The patent itself notes that tagging can be achieved through various methods, including terminal transferase, and considers ligation to be "inefficient" while terminal transferase (TTase) is a "robust enzyme from which high efficiency is expected". Terminal transferase is a known enzyme for adding polynucleotide tails. Substantially unique primers incorporating tags are taught by Miner et al. or U.S. Pat. No. 7,537,897. Therefore, combining these known components into a kit for implementing the obvious varietal counting methods would be an obvious commercial embodiment for a POSITA.

Conclusion

The foundational concept of tagging individual input nucleic acid molecules before amplification and then counting the distinct tags to correct for amplification-induced redundancy and obtain accurate quantitative information (i.e., "molecular counting" or identifying "redundant sequences") was already present in the prior art, specifically in Miner et al. (2004) and U.S. Pat. No. 7,537,897. The patent US12234510 applies this known principle to the specific context of obtaining genomic or mRNA copy number information and methylation status, addressing the well-known problem of amplification distortion in WGA and PCR. The various methods of tagging described (e.g., ligation, terminal transferase) are also known techniques in molecular biology. Consequently, a person having ordinary skill in the art would have been motivated to combine these existing teachings and techniques to predictably achieve the claimed benefits, rendering the independent claims of US12234510 obvious under 35 U.S.C. § 103.