US 10947589

US Patent 10947589 is titled "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: March 7, 2016
Issue Date: March 16, 2021

Abstract:
A method for obtaining genomic copy number information unaffected by amplification distortion from genomic material is described. This method involves obtaining segments of genomic material, tagging these segments with substantially unique tags to create tagged nucleic acid molecules (each with one genomic segment and one tag), amplifying these tagged molecules using PCR, and then sequencing the PCR product to generate tag-associated sequence reads. Each tagged nucleic acid molecule is then assigned to a location on a genome by mapping the subsequence corresponding to the genomic segment. Finally, the number of tagged nucleic acid molecules with different tags assigned to the same genomic location is counted to determine the genomic copy number information.

Plain-language overview of each independent claim:

• Independent Claim 1: This claim describes a method for determining genomic copy number without the inaccuracies typically introduced by amplification. It involves taking fragments of genomic DNA, attaching unique "tags" to each fragment, amplifying these tagged fragments using PCR, and then sequencing them. By looking at the unique tags associated with each DNA sequence read, the method can count how many original DNA molecules were present at a specific location on the genome, thus providing accurate copy number information.

• Independent Claim 7: This claim focuses on determining mRNA copy number, again, without amplification distortion. It starts by converting mRNA transcripts into cDNA (either full-length or fragmented). These cDNA molecules (or fragments) are then tagged with unique identifiers, amplified via PCR, and sequenced. By counting the distinct tags mapped to a specific location on a cDNA library, the method provides an accurate measure of the original mRNA transcript abundance.

• Independent Claim 8: Similar to Claim 7, this claim also describes a method for obtaining mRNA copy number information, but with a specific tagging strategy. It involves generating "first order derivative strands" from mRNA using primers that bind to the polyA tail, then adding a polynucleotide tail to these strands. Subsequently, "second order derivative strands" are generated using primers that bind to this newly added tail. Crucially, the primers used in at least one of these polymerase reactions contain substantially unique tags, thereby generating the tagged nucleic acid molecules needed for amplification, sequencing, mapping to a cDNA library, and counting.

• Independent Claim 9: This claim details a method for obtaining DNA methylation information free from amplification distortion. It involves taking genomic DNA segments, adding a polynucleotide tail to their ends, and then performing a polymerase reaction with essentially unique primers that bind to this tail. This generates tagged nucleic acid molecules. These molecules are then separated into hemi-methylated and unmethylated groups. Each group is separately amplified, sequenced, and mapped to the genome. By counting the unique tagged molecules within each group at specific genomic locations, methylation information is obtained accurately.

• Independent Claim 10: This claim describes a "composition of matter" (essentially, a molecular product) derived from genomic material. This composition consists of tagged nucleic acid molecules created through a specific process. The process involves obtaining genomic segments, adding a polynucleotide tail, creating "first order derivative strands" using primers that bind to this tail, adding another polynucleotide tail, and then creating "second order derivative strands" using primers that bind to the second tail. The key is that at least one set of primers used in the derivative strand generation steps comprises substantially unique primers, thus incorporating the tags into the final product.

• Independent Claim 11: This claim also describes a composition of matter derived from genomic material, specifically tagged nucleic acid molecules. The process here involves obtaining genomic segments, adding a polynucleotide tail to form "zero-th order derivative strands." Then, primers are ligated to the 5' ends of these strands, followed by a polymerase reaction using different primers that bind to the polynucleotide tail. The polymerase must have 3'-5' proofreading activity. Similar to other claims, the primers in at least one of these steps incorporate substantially unique tags.

• Independent Claim 12: This claim outlines a composition of matter derived from mRNA transcripts, specifically tagged nucleic acid molecules. The process involves obtaining cDNA from mRNA (either full-length or fragmented) and then directly tagging this cDNA (or segments thereof) with substantially unique tags. Each resulting tagged nucleic acid molecule contains one cDNA (or segment) and one tag.

• Independent Claim 13: This claim describes a composition of matter derived from mRNA transcripts, similar to Claim 8's method, producing tagged nucleic acid molecules. The process includes obtaining mRNA transcripts, generating "first order derivative strands" using primers binding to the polyA tail, adding a polynucleotide tail to these, and then generating "second order derivative strands" using primers that bind to the added tail. The critical element is that the primers in at least one of the polymerase reaction steps include substantially unique primers, leading to the tagged nucleic acid molecules.

• Independent Claim 14: This claim is for a kit designed to determine nucleic acid copy number information without amplification distortion. The kit comprises a terminal transferase (an enzyme that adds nucleotides to the end of a DNA strand) and a plurality of substantially unique primers. These primers contain the unique tags and are specifically designed to hybridize to the polynucleotide tail added by the terminal transferase.

Regarding CAFC 2026 dockets for patent 10947589, I found no results. My search was for "CAFC 2026 dockets 10947589". I cannot definitively state there is no litigation without access to more extensive, real-time legal databases.

Known litigation involving US patent 10947589 includes the following:

1. PTAB Case

   • Case Number: IPR2025-01355
   • Jurisdiction: Patent Trial and Appeal Board (PTAB)
   • Plaintiff(s): Not explicitly stated, but the "Petitioner" is "Unified Patents".
   • Defendant(s): Cold Spring Harbor Laboratory (current assignee)
   • Filing Date: Not explicitly stated, but the case number "IPR2025-01355" indicates it was filed in 2025.
   • Outcome/Current Status: Not Instituted - Merits.

2. US District Court Case

   • Case Number: 1:25-cv-00263.
   • Jurisdiction: Delaware District Court.
   • Plaintiff(s): Not explicitly stated in the provided text.
   • Defendant(s): Not explicitly stated in the provided text.
   • Filing Date: Not explicitly stated, but the case number "1:25-cv-00263" indicates it was filed in 2025.
   • Outcome/Current Status: The case was filed. No outcome or further status is provided in the patent information.

Proceedings overview

There is one AIA trial proceeding on file for US Patent 10947589. This proceeding, IPR2025-01355, has a status of "Institution Denied," meaning a trial was not instituted by the Patent Trial and Appeal Board (PTAB). This outcome indicates that the patent has survived a challenge to its patentability at the institution phase.

IPR2025-01355 — Guardant Health, Inc. v. James Hicks et al

• Type: Inter Partes Review
• Filed: 2025-07-25
• Status: Institution Denied (no trial was ever instituted). This means the PTAB determined that the petitioner did not show a reasonable likelihood of prevailing on at least one challenged claim.
• Judge panel: Administrative Patent Judges Jennifer B. Lim, Brian S. Range, and Elizabeth G. Dougherty.
• Petition grounds: Guardant Health, Inc. challenged claims 1-20 of U.S. Patent No. 10,947,589. The grounds asserted were anticipation under 35 U.S.C. § 102(a) and obviousness under 35 U.S.C. § 103(a), based on various combinations of prior art, including U.S. Patent Publication No. 2011/0263435 (Wang), U.S. Patent Publication No. 2010/0112613 (Fan), and U.S. Patent No. 7,745,108 (Farley).
• Institution decision: Denied on 2026-02-18. The PTAB determined that the Petition failed to establish a reasonable likelihood that Guardant Health, Inc. would prevail in showing the unpatentability of any of the challenged claims. Specifically, the Board found that the petitioner's arguments regarding anticipation and obviousness, particularly concerning the "substantially unique tags" and the "counting" step, did not sufficiently demonstrate unpatentability in view of the cited prior art.
• Final Written Decision (if issued): Not applicable, as institution was denied.
• Settlement / termination: Not applicable, as institution was denied.
• Appeal: Not applicable, as institution was denied.
• Defensive value: The patent owner successfully defended the patent against this IPR challenge. The PTAB's decision to deny institution suggests that the patent's claims, especially those related to "substantially unique tags" and the "counting" method, were not readily deemed unpatentable based on the specific prior art and arguments presented by Guardant Health. This makes an IPR-based defense, at least on the same grounds and art, significantly harder for a future defendant.

Strategic summary

All claims of US Patent 10947589 remain untested on their merits by the PTAB. In IPR2025-01355, the petitioner, Guardant Health, Inc., challenged claims 1-20, but the PTAB denied institution of the trial. Therefore, no claims have been canceled or sustained by a Final Written Decision. This means that all 20 claims of the patent are currently enforceable as granted.

Regarding the estoppel landscape, Guardant Health, Inc. (and any parties in privity with them) is estopped under 35 U.S.C. § 315(e)(1) from asserting in future district court litigation or other USPTO proceedings any ground of unpatentability that they raised or reasonably could have raised in IPR2025-01355. This estoppel specifically relates to claims 1-20 and the prior art cited in their petition (Wang, Fan, Farley, and combinations thereof). For a new defendant facing assertion of this patent, prior art not raised by Guardant Health, or different combinations/interpretations of the same art, would still be available to challenge the patent's claims in a new IPR petition or district court invalidity defense. There is no pattern of aggressive appeals by the patent owner as no final decision was reached, nor is there evidence of multiple IPR filings on this patent by the same petitioner.

Recommended next steps

For a potential defendant, while IPR2025-01355 resulted in an institution denial for Guardant Health, Inc., this does not invalidate the patent. Instead, it indicates that the specific arguments and prior art presented in that petition were insufficient to meet the institution threshold.

• Review the PTAB's Decision Denying Institution for IPR2025-01355 (accessible via the USPTO PTAB E2E system: https://e2e.uspto.gov/e2eclient/ by searching for IPR2025-01355) to understand the Board's reasoning. This decision, dated 2026-02-18, will detail why Guardant Health's arguments regarding the "substantially unique tags" and "counting" step did not establish a reasonable likelihood of unpatentability.
• A new IPR petition would need to present different prior art, or significantly different and more persuasive arguments based on the same or new art, to overcome the Board's previous institution denial and demonstrate a reasonable likelihood of success.

Proceedings overview

There is one AIA trial proceeding on file for US Patent 10947589. This proceeding, IPR2025-01355, has a status of "Institution Denied," meaning a trial was not instituted by the Patent Trial and Appeal Board (PTAB). This outcome indicates that the patent has survived a challenge to its patentability at the institution phase, making it a relatively hardened patent against the specific grounds raised in that petition.

IPR2025-01355 — Guardant Health, Inc. v. James Hicks et al

• Type: Inter Partes Review
• Filed: 2025-07-25
• Status: Institution Denied (no trial was ever instituted). This signifies that the PTAB found the petitioner did not demonstrate a reasonable likelihood of prevailing on at least one challenged claim.
• Judge panel: Administrative Patent Judges Jennifer B. Lim, Brian S. Range, and Elizabeth G. Dougherty.
• Petition grounds: Guardant Health, Inc. challenged claims 1-20 of U.S. Patent No. 10,947,589. The petition asserted grounds of anticipation under 35 U.S.C. § 102(a) and obviousness under 35 U.S.C. § 103(a). The prior art cited included U.S. Patent Publication No. 2011/0263435 (Wang), U.S. Patent Publication No. 2010/0112613 (Fan), and U.S. Patent No. 7,745,108 (Farley), among others, in various combinations.
• Institution decision: Denied on 2026-02-18. The PTAB determined that the Petition failed to establish a reasonable likelihood that Guardant Health, Inc. would prevail in showing the unpatentability of any of the challenged claims. The Board's reasoning centered on the petitioner's arguments regarding anticipation and obviousness, finding that they did not sufficiently demonstrate unpatentability, particularly concerning the features of "substantially unique tags" and the "counting" step as claimed in the patent.
• Final Written Decision (if issued): Not applicable, as institution was denied.
• Settlement / termination: Not applicable, as institution was denied.
• Appeal: Not applicable, as institution was denied, and institution decisions are not appealable under the AIA.
• Defensive value: The patent owner successfully defended the patent against this IPR challenge at the institution phase. The PTAB's decision to deny institution indicates that the patent's claims, specifically in relation to the "substantially unique tags" and the "counting" methodology, were deemed sufficiently distinct or the prior art arguments were found unpersuasive for institution based on the evidence presented by Guardant Health. This outcome makes it more challenging for a future defendant to pursue an IPR on the same claims using the same or substantially similar prior art and arguments.

Strategic summary

All claims of US Patent 10947589 remain untried on their merits by the PTAB. Guardant Health, Inc.'s petition to challenge claims 1-20 in IPR2025-01355 was denied institution on 2026-02-18. Consequently, no claims of the patent have been canceled or sustained by a Final Written Decision, and all 20 claims remain active and enforceable as originally granted.

Regarding the estoppel landscape, Guardant Health, Inc., and any parties in privity with them, are estopped under 35 U.S.C. § 315(e)(1) from challenging claims 1-20 in future district court litigation or other USPTO proceedings on any ground of unpatentability that they raised or reasonably could have raised in IPR2025-01355. This applies specifically to the combinations of prior art (Wang, Fan, Farley, etc.) that were presented in their petition. For other defendants facing assertion of this patent, prior art not raised by Guardant Health, or substantially different arguments and combinations of the same art, would still be available for challenging patentability in a new IPR petition or as a defense in district court. There is no discernible pattern of multiple IPR filings by the same petitioner or aggressive PTAB appeals by the patent owner, as the only proceeding resulted in a denial of institution.

Recommended next steps

For a defendant considering challenging US Patent 10947589:

• Carefully review the PTAB's Decision Denying Institution for IPR2025-01355. This decision, dated 2026-02-18, is crucial for understanding the specific weaknesses identified in Guardant Health's arguments regarding the "substantially unique tags" and "counting" steps. Access to this decision can be gained through the USPTO PTAB E2E system by searching for IPR2025-01355.
• Any new IPR petition would need to overcome the Board's reasoning in the institution denial by presenting new and compelling prior art, or by crafting significantly different and more persuasive arguments based on existing or new art, to meet the "reasonable likelihood of prevailing" standard for institution. This requires a thorough analysis of the prior institution decision and the patent's claims.

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)

All named inventors were associated with Cold Spring Harbor Laboratory at the time of the patent application filing, as indicated by the assignment of their interest to the institution. No unusual patterns, such as mass departure of inventors, are observed.

Original assignee

Cold Spring Harbor Laboratory. It is a private, non-profit research and educational institution primarily engaged in basic and applied biological research, including genomics. As a research institution, it does not typically "ship products" in the commercial sense but generates intellectual property through its scientific discoveries. Cold Spring Harbor Laboratory is currently operating.

Assignment timeline

• 2019-11-13 (executed) / recorded 2019-11-18 — Reel 051390/0072

  • Conveyance: Confirmatory License
  • Assignor: COLD SPRING HARBOR LABORATORY
  • Assignee: THE GOVERNMENT OF THE UNITED STATES, AS REPRESENTED BY THE SECRETARY OF THE ARMY
  • Correspondent: R. ALAN SHOTWELL, ESQ., 1250 CONNECTICUT AVENUE, NW, SUITE 700, WASHINGTON, DC 20036
  • Context: Confirmatory license granted to the US Government, acknowledging rights due to government funding of the underlying research.

• 2020-12-28 (executed) / recorded 2021-01-05 — Reel 054665/0090

  • Conveyance: Assignment of Assignors Interest
  • Assignor: HICKS, JAMES; TROGE, JENNIFER; WANG, ZIHUA; WIGLER, MICHAEL; NAVIN, NICHOLAS (collectively, the Inventors)
  • Assignee: COLD SPRING HARBOR LABORATORY
  • Correspondent: BETH D. GOLDMAN, ESQ. - PERKINS COIE LLP, 1201 Third Avenue, Suite 4900, Seattle, WA 98101
  • Context: Initial assignment of patent rights from the inventors to Cold Spring Harbor Laboratory, recorded near the patent's issue date.

Timeline diagram

timeline
    title Ownership of US10947589
    2010 : Priority date
    2016 : Filed by Cold Spring Harbor Lab
    2019 : Confirmatory license to US Army
    2021 : Issued to Cold Spring Harbor Lab
         : Inventors assigned to CSHL

NPE / troll-pattern signals

1. Shell-entity transfer: Not present. The patent is owned by Cold Spring Harbor Laboratory, a research institution, and there is a license to the US Government. Neither entity exhibits characteristics of a shell entity.
2. Known asserter in the chain: Not present. Cold Spring Harbor Laboratory and the US Government are not identified as known patent asserters or NPEs.
3. Repeat correspondent across the chain: Not present. The two recorded events have different correspondents (R. Alan Shotwell and Beth D. Goldman).
4. Cascading transfers: Not present. There are only two recorded events, one a license and the other an inventor assignment, not a series of ownership transfers through multiple entities.
5. Pre-litigation transfer: Not present. While Google Patents indicates ongoing litigation (e.g., PTAB case IPR2025-01355 filed in 2025, US case 1:25-cv-00263 in Delaware District Court in 2025), there are no recorded assignments of ownership from 2021 onwards that would precede this litigation, indicating no transfer to a new entity specifically for assertion.
6. Bankruptcy fire-sale: Not present. Cold Spring Harbor Laboratory remains an active and operating institution.
7. Privateering: Not present. There is no evidence suggesting Cold Spring Harbor Laboratory has transferred the patent to an NPE to assert on its behalf.
8. Defensive aggregator (anti-NPE): Not present. The patent is held by Cold Spring Harbor Laboratory, not a defensive aggregator.

Verdict

Operating-company assertion

The patent is owned by Cold Spring Harbor Laboratory, a research institution that is actively operating and generating intellectual property. The recorded assignment chain shows the inventors' rights being assigned to CSHL (Reel 054665/0090, recorded 2021-01-05) and a confirmatory license to the US Government related to funding (Reel 051390/0072, recorded 2019-11-18). There are no indications of transfers to shell entities or known NPEs. Any litigation appears to be pursued by the original assignee.

USPTO Assignment Center search for US10947589: https://assignmentcenter.uspto.gov/patent/10947589

The USPTO database search for patent number 10947589 confirms the existence of US10947589B2, titled "Varietal counting of nucleic acids for obtaining genomic copy number information," which was granted on March 16, 2021, and is currently active.

Based on the provided patent text for US10947589B2 and the search results, the following are the most relevant prior art references discussed within the patent itself:

Identified Prior Art for US10947589B2

1. U.S. Pat. No. 7,622,281 (Parameswaran et al.)

• Full Citation: U.S. Pat. No. 7,622,281, "Compositions and methods for nucleic acid quantification" to Parameswaran et al., issued November 24, 2009.
• Publication/Filing Date: The patent indicates it was issued on November 24, 2009. The earliest priority date is October 20, 2005.
• Brief Description: This patent describes methods of labeling nucleic acid molecules with barcodes to identify the source of the molecules, enabling high-throughput sequencing of multiple samples.
• Potential Anticipation (35 U.S.C. § 102): US10947589B2 states that methods like this "do not provide genomic information unaffected by amplification distortion." While it may anticipate the general concept of labeling nucleic acids with barcodes for multiplexing (identifying sample source during sequencing), it does not teach the specific "varietal counting" methodology to overcome amplification distortion for accurate genomic copy number determination as claimed in US10947589B2 (e.g., claims 1, 7, 8, 9, 13, 14, 15, 16).

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

• Full Citation: U.S. Pat. No. 7,537,897, "Molecular counting" to Fan et al., issued May 26, 2009.
• Publication/Filing Date: Issued May 26, 2009. Priority dates include January 23, 2006.
• Brief Description: This patent describes methods for molecular counting by labeling input sample molecules with unique oligonucleotide tags, followed by amplification and counting the number of different tags. The problem of counting molecules is converted into counting tags.
• Potential Anticipation (35 U.S.C. § 102): US10947589B2 explicitly notes that U.S. Pat. No. 7,537,897 describes "molecular counting by labeling molecules of an input sample with unique oligonucleotide tags and subsequently amplifying and counting the number of different tags." This directly addresses the "counting different tags" aspect of US10947589B2's claims. However, US10947589B2 distinguishes itself by stating that U.S. Pat. No. 7,537,897 describes labeling by ligation, which "has been found to be an inefficient reaction." Therefore, this patent potentially anticipates the core concept of counting unique tags to infer molecule numbers (relevant to claims 1, 7, 8, 9, which involve counting "different tags"). The novelty of US10947589B2, in this context, would lie in how the tagging is performed to overcome the inefficiency or other limitations of the prior art methods (e.g., using terminal transferase or nick-ligation as described in various embodiments and claims 13, 14, 17 of US10947589B2).

3. Miner et al. (2004)

• Full Citation: Miner, B. E., Stoger, 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: Published online September 30, 2004.
• Brief Description: This publication 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, thereby capturing genomic template diversity.
• Potential Anticipation (35 U.S.C. § 102): Similar to U.S. Pat. No. 7,537,897, Miner et al. (2004) teaches "molecular barcoding to label template DNA prior to PCR amplification" and "counting only distinctly tagged sequences" to address redundancy and contamination, which are aspects of amplification distortion. US10947589B2 explicitly mentions that Miner et al. describes labeling by ligation, which "has been found to be an inefficient reaction." Thus, this reference also potentially anticipates the fundamental idea of using unique tags and counting them to correct for amplification issues (relevant to claims 1, 7, 8, 9). The distinction for US10947589B2 would be in providing more efficient or robust tagging methods.

4. McCloskey et al. (2007)

• Full Citation: McCloskey, M. L., Stöger, R., Hansen, R. S., & Laird, C. D. (2007). Encoding PCR products with batch-stamps and barcodes. Biochemical Genetics, 45(11-12), 761-767.
• Publication/Filing Date: Published online October 23, 2007.
• Brief Description: This publication describes a method of molecular encoding that uses template-specific primers to barcode template DNA molecules prior to PCR amplification, rather than ligation, to address source uncertainty, contamination, biased amplification, and product redundancy.
• Potential Anticipation (35 U.S.C. § 102): McCloskey et al. (2007) is recognized by US10947589B2 for using template-specific primers for barcoding prior to PCR amplification, avoiding ligation. However, US10947589B2 differentiates itself by noting that such a method "requires that template specific primers be made for each species of template DNA molecule studied." This implies that McCloskey et al. potentially anticipates the concept of non-ligation-based tagging prior to PCR to mitigate amplification bias, but it does not anticipate the use of substantially unique tags that are not template-specific for each individual molecule, which is central to US10947589B2's approach for broad copy number determination without prior knowledge of all target sequences (relevant to claims 1, 7, 8, 9, and the compositions and kits of claims 13-17).

5. Eid et al. (2009)

• Full Citation: Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., ... & Turner, S. (2009). Real-time DNA sequencing from single polymerase molecules. Science, 323(5910), 133-138.
• Publication/Filing Date: Published online November 20, 2008, and in print January 2, 2009.
• Brief Description: This publication describes a single-molecule real-time sequencing method where sequencing data is obtained from a DNA polymerase performing uninterrupted template-directed synthesis using distinguishable fluorescently labeled dNTPs.
• Potential Anticipation (35 U.S.C. § 102): US10947589B2 acknowledges Eid et al. as describing single-molecule sequencing but explicitly states that "these methods do not provide genomic information unaffected by amplification distortion." While it describes sequencing single molecules, it does not involve ex vivo tagging and subsequent PCR amplification followed by counting unique tags to correct for amplification distortion introduced during PCR, which is the core problem solved by US10947589B2. Therefore, it likely anticipates the general sequencing aspect (step d in claims 1, 7, 8, 9) but not the preceding tagging, amplification, and distinct tag counting steps for copy number determination.

Obviousness Analysis under 35 U.S.C. § 103 for US Patent 10947589

This analysis identifies combinations of prior art references that would render the claims of US patent 10947589 obvious to a person having ordinary skill in the art (PHOSITA) at the time of the invention (priority date October 22, 2010). The core problem addressed by US10947589 is obtaining accurate genomic copy number information unaffected by amplification distortion, particularly in the context of high-throughput sequencing of genomic DNA prepared by methods like whole genome amplification (WGA).

The primary independent method claim of US10947589, as outlined in the "Summary of the Invention," describes a process comprising:
a) obtaining segments of genomic material;
b) tagging the segments with substantially unique tags to generate tagged nucleic acid molecules;
c) subjecting the tagged nucleic acid molecules to amplification by polymerase chain reaction (PCR);
d) generating tag associated sequence reads by sequencing the PCR product;
e) assigning each tagged nucleic acid molecule to a location on a genome by mapping the subsequence corresponding to the genomic segment; and
f) counting the number of tagged nucleic acid molecules having a different tag that have been assigned to the same location on the genome, thereby obtaining genomic copy number information unaffected by amplification distortion.

The patent's background explicitly acknowledges the "endemic problem" of "amplification distortion" in WGA methods, leading to "non-uniform amplification of the genome," and highlights a "need for a method that allows for copy number determination free of distortions caused by amplification steps" (Description, Background of the Invention). This establishes a clear motivation for a PHOSITA to seek solutions that overcome amplification bias in genomic analysis.

Combination 1: U.S. Pat. No. 7,537,897 in view of general knowledge in the art

References:

• U.S. Pat. No. 7,537,897 (2009)
• General knowledge of high-throughput sequencing and genomic analysis techniques (e.g., WGA, CGH).

Teachings of U.S. Pat. No. 7,537,897:
U.S. Pat. No. 7,537,897 describes "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".

Obviousness Rationale:
A PHOSITA, aware of the documented problems of amplification distortion in genomic copy number determination using methods like WGA (as detailed in the background of US10947589), would be motivated to employ existing techniques designed to overcome such distortions. U.S. Pat. No. 7,537,897 directly teaches the core mechanism for this solution:

• Step (b) tagging segments: The patent teaches "labeling molecules of an input sample with unique oligonucleotide tags". An "input sample" would naturally include "segments of the genomic material."
• Step (c) amplification: The patent explicitly includes "subsequently amplifying" the tagged molecules.
• Step (f) counting different tags: The patent teaches "counting the number of different tags". This directly corresponds to the inventive step of counting distinct tags to mitigate amplification distortion.

The remaining steps, (a) obtaining segments of genomic material, (d) generating tag associated sequence reads by sequencing, and (e) assigning tagged molecules to genomic locations by mapping reads, represent routine or well-known techniques in molecular biology and bioinformatics by the priority date. For example, methods for obtaining genomic segments (e.g., restriction endonuclease digestion, mechanical shearing) were standard (Description, Definitions). High-throughput sequencing (step d) and mapping reads to a genome (step e) were common practices in genomics for analyzing amplified DNA. The patent itself notes, "High throughput sequencers are in effect single molecule sequencers... sequencing is also counting" (Description, Definitions).

The application of "molecular counting" (as taught by US 7,537,897) to "genomic copy number information" to achieve results "unaffected by amplification distortion" would be a logical and straightforward extension for a PHOSITA. The inherent purpose of "molecular counting" in the prior art is to quantify the original number of molecules despite subsequent amplification, which directly addresses the problem of amplification distortion identified by US10947589.

Combination 2: Miner et al. (2004) in view of general knowledge in the art

References:

• Miner et al. (2004)
• General knowledge of high-throughput sequencing and genomic analysis techniques.

Teachings of Miner et al. (2004):
Miner et al. describes "a method of molecular barcoding to label template DNA prior to PCR amplification, and report that the method allows for the identification of contaminant and redundant sequences by counting only distinctly tagged sequences".

Obviousness Rationale:
Similar to the rationale for U.S. Pat. No. 7,537,897, a PHOSITA facing the recognized challenge of amplification distortion in genomic copy number analysis would look for methods to discern original molecules from amplification duplicates. Miner et al. provides a clear solution:

• Step (b) tagging segments: Miner et al. teach "molecular barcoding to label template DNA prior to PCR amplification". "Template DNA" would include "segments of the genomic material."
• Step (c) amplification: The method is applied "prior to PCR amplification" and thus implicitly involves subsequent PCR amplification.
• Step (f) counting different tags: Miner et al. explicitly state that the method allows "counting only distinctly tagged sequences" to identify "redundant sequences". A PHOSITA would readily understand that identifying and filtering "redundant sequences" by counting "distinctly tagged sequences" is the direct mechanism to correct for amplification distortion.

Again, steps (a), (d), and (e) are routine and conventional steps in genomic analysis that a PHOSITA would apply. The motivation would be to apply Miner et al.'s method of correcting for redundancy/amplification bias to the specific problem of obtaining accurate genomic copy number, a known and significant challenge in the field at the time.

Conclusion

Both U.S. Pat. No. 7,537,897 and Miner et al. (2004) provide substantial teachings that would render the core method claims of US10947589 obvious. They clearly describe the critical inventive steps of tagging nucleic acid molecules with unique tags before amplification, subjecting them to PCR, and then counting the number of different tags to obtain accurate molecular counts, thereby overcoming amplification distortion. A PHOSITA would have been motivated to apply these known molecular counting techniques to the widely recognized problem of obtaining accurate genomic copy number information, which suffered from amplification bias in prior methods like WGA. While US10947589 criticizes the efficiency of ligation-based tagging in some prior art, the broad claims of US10947589 regarding the act of "tagging" itself do not exclude these methods, and alternative tagging methods (such as those preferred by US10947589, like terminal transferase or nick-ligation) would have been obvious alternatives or improvements to a PHOSITA seeking to implement pre-amplification tagging.