US 10036012

A concise summary of US patent 10036012 is provided below:

US Patent 10036012 Summary

• Title: Compositions and methods for targeted nucleic acid sequence enrichment and high efficiency library generation
• Assignee: Tecan Genomics Inc (originally Nugen Technologies Inc)
• Inventors: Doug Amorese, Chris Armour, Nurith Kurn
• Filing Date: March 28, 2017
• Issue Date: July 31, 2018
• Abstract: The patent describes compositions and methods for enriching specific target nucleic acid sequences from a sample containing nucleic acids, as well as methods for high-efficiency generation of nucleic acid libraries. The enrichment methods involve fragmenting nucleic acids, appending a first adaptor, annealing one or more oligonucleotides with a 3′ portion complementary to a target sequence and a 5′ portion with a second adaptor sequence, extending these oligonucleotides with a polymerase, and then amplifying the resulting products.

Plain-Language Overview of Independent Claims:

The patent includes four independent claims, each outlining a method for either enriching target nucleic acid sequences or generating a library of nucleic acid sequences:

• Independent Claim 1: This claim describes a method for enriching target nucleic acid sequences. It involves:

  1. Fragmenting nucleic acids in a sample.
  2. Attaching a first adaptor to the 5′ end of each fragment.
  3. Annealing specific oligonucleotides to these fragments. Each oligonucleotide has a 3′ end that matches a target sequence and a 5′ end with a second adaptor sequence.
  4. Extending these oligonucleotides using a polymerase, creating products with the first adaptor at one end and the second adaptor at the other.
  5. Amplifying these extended products to enrich the target sequences.

• Independent Claim 13: This claim describes another method for enriching target nucleic acid sequences, introducing a specific type of first adaptor. It involves:

  1. Fragmenting nucleic acids in a sample.
  2. Attaching a first adaptor to the nucleic acid fragments. This first adaptor is a partial duplex with a short and a long strand. The short strand's 3′ end has a blocking group, and the long strand's 5′ end has a restriction or cleavage site for a nucleic acid modifying enzyme.
  3. Denaturing the fragments to create single-stranded nucleic acid fragments.
  4. Annealing one or more oligonucleotides to these single-stranded fragments. These oligonucleotides have a sequence complementary to a target nucleic acid.
  5. Extending these oligonucleotides with a polymerase, generating products with the long strand of the first adaptor at one end and a sequence complementary to the long strand of the first adaptor at the other.
  6. Modifying the restriction or cleavage site with a nucleic acid modifying enzyme to create a site for a second adaptor.
  7. Ligating a second adaptor to this modified site.
  8. Amplifying the resulting products using a first primer for the second adaptor and a second primer for the short strand of the first adaptor.

• Independent Claim 22: This claim focuses on generating a library of nucleic acid sequences using random priming. It involves:

  1. Fragmenting nucleic acids in a sample.
  2. Attaching a first adaptor to each fragment.
  3. Denaturing the fragments to create a library of single-stranded nucleic acid fragments.
  4. Annealing one or more oligonucleotides to these single-stranded fragments. Each oligonucleotide has a 3′ portion with a random sequence and a 5′ portion with a second adaptor sequence.
  5. Extending these oligonucleotides with a polymerase, generating products with the first adaptor at one end and the second adaptor sequence at the other.
  6. Amplifying these products to create the library.

• Independent Claim 35: This claim describes a method for enriching target nucleic acid sequences from an existing library. It involves:

  1. Denaturing nucleic acid inserts from a library (which already have a first adaptor on one end and a second adaptor on the other) to create single-stranded inserts.
  2. Annealing one or more oligonucleotides to these single-stranded inserts. Each oligonucleotide has a 3′ portion complementary to a target sequence and a 5′ portion with a third adaptor sequence.
  3. Extending these oligonucleotides with a polymerase, generating products with either the first or second adaptor at one end and the third adaptor sequence at the other.
  4. Amplifying these products to enrich the target sequences.

CAFC 2026 Dockets:

As of April 26, 2026, a search of the CAFC 2026 dockets for patent 10036012 did not yield any specific cases directly referencing this patent number. The search results provided general information about scheduled cases and case law for 2026 at the Federal Circuit, but no direct mention of US10036012 was found.

Known litigation involving US patent 10036012 includes:

1. PTAB Case

   • Case Number: IPR2025-00015 [cite: Unified Patents portal link on US10036012 Google Patents page]
   • Plaintiff(s): Unified Patents (as Petitioner) [cite: Unified Patents portal link on US10036012 Google Patents page]
   • Defendant(s): Tecan Genomics Inc. (as Patent Owner, inferred from current assignee) [cite: US10036012 Google Patents page]
   • Jurisdiction: Patent Trial and Appeal Board (PTAB) [cite: Unified Patents portal link on US10036012 Google Patents page]
   • Filing Date: 2025 (inferred from IPR number) [cite: Unified Patents portal link on US10036012 Google Patents page]
   • Outcome/Current Status: Final Written Decision [cite: Unified Patents portal link on US10036012 Google Patents page]

2. PTAB Case

   • Case Number: IPR2025-00028 [cite: Unified Patents portal link on US10036012 Google Patents page]
   • Plaintiff(s): Unified Patents (as Petitioner) [cite: Unified Patents portal link on US10036012 Google Patents page]
   • Defendant(s): Tecan Genomics Inc. (as Patent Owner, inferred from current assignee) [cite: US10036012 Google Patents page]
   • Jurisdiction: Patent Trial and Appeal Board (PTAB) [cite: Unified Patents portal link on US10036012 Google Patents page]
   • Filing Date: 2025 (inferred from IPR number) [cite: Unified Patents portal link on US10036012 Google Patents page]
   • Outcome/Current Status: Pending - Instituted [cite: Unified Patents portal link on US10036012 Google Patents page]

3. US District Court Case

   • Case Number: 1:23-cv-01115 [cite: Delaware District Court link on US10036012 Google Patents page]
   • Plaintiff(s): Not specified in the provided information.
   • Defendant(s): Not specified in the provided information.
   • Jurisdiction: Delaware District Court [cite: Delaware District Court link on US10036012 Google Patents page]
   • Filing Date: 2023 (inferred from case number) [cite: Delaware District Court link on US10036012 Google Patents page]
   • Outcome/Current Status: Not specified in the provided information.

4. US District Court Case

   • Case Number: 1:23-cv-01114 [cite: Delaware District Court link on US10036012 Google Patents page]
   • Plaintiff(s): Not specified in the provided information.
   • Defendant(s): Not specified in the provided information.
   • Jurisdiction: Delaware District Court [cite: Delaware District Court link on US10036012 Google Patents page]
   • Filing Date: 2023 (inferred from case number) [cite: Delaware District Court link on US10036012 Google Patents page]
   • Outcome/Current Status: Not specified in the provided information.

5. Worldwide Family Litigation

   • Case Number: Not explicitly provided for US10036012 itself. [cite: Darts-ip link on US10036012 Google Patents page]
   • Plaintiff(s): Not specified in the provided information.
   • Defendant(s): Not specified in the provided information.
   • Jurisdiction: Not explicitly provided for US10036012 itself. [cite: Darts-ip link on US10036012 Google Patents page]
   • Filing Date: Not explicitly provided for US10036012 itself. [cite: Darts-ip link on US10036012 Google Patents page]
   • Outcome/Current Status: "First worldwide family litigation filed" [cite: Darts-ip link on US10036012 Google Patents page]

Proceedings overview

Two Inter Partes Review (IPR) proceedings have been filed against US Patent 10036012, both of which have reached a Final Written Decision (FWD) as of May 2026. The bottom-line defensive posture for a defendant is highly dependent on the claim-level outcomes of these FWDs. If claims were invalidated, the patent's scope has been narrowed, potentially weakening any assertion built on those claims. If claims were largely sustained, the patent has been "hardened" against these specific prior art challenges, making future IPRs on similar grounds more difficult.

IPR2025-00028 — QIAGEN Sciences, LLC v. Tecan Group AG

• Type: Inter Partes Review
• Filed: 2024-10-10
• Status: Final Written Decision (last modified 2026-05-13)
• Judge panel: Information not found in the provided context or readily available from general search results without direct access to the PTAB E2E system.
• Petition grounds: Information not found in the provided context or readily available from general search results without direct access to the PTAB E2E system.
• Institution decision: Information not found in the provided context or readily available from general search results without direct access to the PTAB E2E system.
• Final Written Decision (if issued): Information regarding specific claim-level outcomes and reasoning is not publicly available through general search at this time. Direct access to the USPTO PTAB E2E system would be required to retrieve the full Final Written Decision document.
• Settlement / termination: Information not found.
• Appeal: Information not found.
• Defensive value: Without the claim-level outcomes of the Final Written Decision, the defensive value cannot be fully assessed. If claims were invalidated, it could significantly weaken assertions. If claims were sustained, it strengthens the patent against similar challenges.

IPR2025-00015 — Integrated DNA Technologies, Inc. et al. v. Tecan Group AG

• Type: Inter Partes Review
• Filed: 2024-10-04
• Status: Final Written Decision (last modified 2026-04-06)
• Judge panel: Information not found in the provided context or readily available from general search results without direct access to the PTAB E2E system.
• Petition grounds: Information not found in the provided context or readily available from general search results without direct access to the PTAB E2E system.
• Institution decision: Information not found in the provided context or readily available from general search results without direct access to the PTAB E2E system.
• Final Written Decision (if issued): Information regarding specific claim-level outcomes and reasoning is not publicly available through general search at this time. Direct access to the USPTO PTAB E2E system would be required to retrieve the full Final Written Decision document.
• Settlement / termination: Information not found.
• Appeal: Information not found.
• Defensive value: Similar to IPR2025-00028, without the claim-level outcomes of the Final Written Decision, the defensive value cannot be fully assessed. The result (invalidation or sustenance of claims) would dictate the strength of the patent against new assertions.

Strategic summary

As of the current date, US Patent 10036012 has been subjected to two Inter Partes Review proceedings, IPR2025-00028 and IPR2025-00015, both of which have culminated in a Final Written Decision. However, critical details regarding the claim-level outcomes – specifically, which claims were canceled, sustained, or left untested – are not publicly available through general search results and would require direct access to the USPTO PTAB E2E (End-to-End) system to retrieve the full FWD documents. Therefore, a comprehensive assessment of the patent's current scope and robustness cannot be provided at this time.

Regarding estoppel, under 35 U.S.C. § 315(e)(2), a petitioner (and any privy of the petitioner) in an IPR that results in a final written decision is estopped from asserting in a civil action or another USPTO proceeding that a claim is invalid on any ground that the petitioner raised or reasonably could have raised during the IPR. Without knowing the specific prior art grounds and claims challenged in IPR2025-00028 (by QIAGEN Sciences, LLC) and IPR2025-00015 (by Integrated DNA Technologies, Inc. et al.), it is impossible to precisely define the estoppel landscape for a defendant. The current information does indicate that both petitioners are active in the genomics/life sciences space.

A pattern signal is that both IPRs have been filed by different entities (QIAGEN and Integrated DNA Technologies) and have proceeded to a Final Written Decision, suggesting that the patent is considered a relevant asset in the industry. The involvement of two distinct petitioners may indicate a broader interest in challenging this patent.

Recommended next steps

Given that Final Written Decisions have been issued for both IPR2025-00028 and IPR2025-00015, the immediate and most crucial next step is to obtain and thoroughly review these decisions from the USPTO PTAB E2E system. These documents will explicitly state which claims, if any, were found unpatentable and which were confirmed as patentable.

If you are a defendant facing assertion of this patent, access to these FWDs is paramount. They will directly inform your defensive strategy by:

• Identifying any claims that have been cancelled, rendering them unusable for infringement allegations. If a demand letter or complaint relies on invalidated claims, that portion of the assertion is baseless.
• Revealing the prior art that was considered and either succeeded or failed in invalidating claims, which guides further prior art searches and invalidity contentions.
• Clarifying the estoppel implications for the specific petitioners and their privies.

Without these FWDs, it is difficult to give specific, actionable advice beyond noting that two challenges have concluded.

Inventors

• Doug Amorese (Employer at time of filing: Nugen Technologies Inc.)
• Chris Armour (Employer at time of filing: Nugen Technologies Inc.)
• Nurith Kurn (Employer at time of filing: Nugen Technologies Inc.)

All inventors were employed by the original assignee, Nugen Technologies Inc., at the time of filing.

Original assignee

The original assignee named on the issued patent is Nugen Technologies Inc. Nugen Technologies Inc. was a company focused on genomics tools, specifically developing and shipping products for nucleic acid sample preparation for next-generation sequencing, such as the "Encore™ Ultra Low Input NGS Library System I" mentioned in the patent. Nugen Technologies Inc. was acquired by Tecan Group in 2019 and subsequently underwent a name change, becoming Tecan Genomics Inc. Thus, Nugen Technologies Inc. is no longer an independently operating entity under that name.

Assignment timeline

• 2017-12-07 (executed) / recorded 2017-12-07 — Reel 041876/0130

  • Conveyance: Assignment
  • Assignor: ARMOUR, CHRIS; AMORESE, DOUG; KURN, NURITH
  • Assignee: NUGEN TECHNOLOGIES, INC.
  • Correspondent: Michael J. Bell, ESQ., NIXON PEABODY LLP, 1100 CLINTON SQUARE, ROCHESTER, NY, 14604-1792.
  • Context: Transfer of invention rights from inventors to original operating company.

• 2023-08-28 (executed) / recorded 2023-08-29 — Reel 065563/0180

  • Conveyance: Change of Name
  • Assignor: NUGEN TECHNOLOGIES, INC.
  • Assignee: TECAN GENOMICS, INC.
  • Correspondent: Joseph P. Hamilton, Esq., Dorsey & Whitney LLP, 1400 Wewatta Street, Suite 400, Denver, CO, 80202-5561.
  • Context: Name change following acquisition, indicating an internal corporate re-organization or renaming of the subsidiary.

Timeline diagram

timeline
    title Ownership of US 10036012
    2017 : Inventors assign to Nugen Technologies
    2018 : Patent granted
    2023 : Nugen changes name to Tecan Genomics

NPE / troll-pattern signals

1. Shell-entity transfer — Not present. The transfers involve an operating company (Nugen Technologies Inc.) and its successor after acquisition (Tecan Genomics Inc.). There is no evidence of a transfer to a licensing-only LLC, and Tecan Genomics Inc. is a subsidiary of an active, product-shipping public company.
2. Known asserter in the chain — Not present. Neither Nugen Technologies Inc. nor Tecan Genomics Inc. (or its parent Tecan Group) are listed as known NPEs. Tecan Genomics Inc. is an operating company.
3. Repeat correspondent across the chain — Not present. Michael J. Bell (Nixon Peabody LLP) handled the inventor assignment (Reel 041876/0130), and Joseph P. Hamilton (Dorsey & Whitney LLP) handled the change of name (Reel 065563/0180). These are different correspondents.
4. Cascading transfers — Not present. There are only two recorded events: the initial assignment from inventors and a change of name. These are not multiple consecutive assignments through chained LLCs.
5. Pre-litigation transfer — Unclear. While there are US District Court litigation cases and PTAB IPRs filed in 2023 and 2025 respectively, the change of name (recorded 2023-08-29, executed 2023-08-28) from Nugen Technologies Inc. to Tecan Genomics Inc. occurred before the reported litigation filings. It's a change of name, not a transfer to an asserting entity, so it's not a clear signal of pre-litigation transfer for assertion purposes.
6. Bankruptcy fire-sale — Not present. Nugen Technologies Inc. was acquired by Tecan Group, not dissolved in bankruptcy.
7. Privateering — Not present. The current owner, Tecan Genomics Inc., is an operating company, not an NPE asserting on behalf of another.
8. Defensive aggregator (anti-NPE) — Not present. The patent is currently owned by Tecan Genomics Inc., an operating company, not a defensive aggregator.

Verdict

Operating-company assertion

The patent is currently assigned to Tecan Genomics Inc. (via a change of name from Nugen Technologies Inc.), which is a subsidiary of the Tecan Group, an active operating company that develops and sells products in the genomics field. The recorded assignments show a standard transfer from inventors to the original operating company (Nugen Technologies Inc. on 2017-12-07, Reel 041876/0130) followed by a name change to Tecan Genomics Inc. (on 2023-08-28, Reel 065563/0180). The presence of ongoing litigation (PTAB and District Court cases filed in 2023 and 2025) suggests assertion by the operating company, likely against competitors.

USPTO Assignment Center record: https://assignmentcenter.uspto.gov/

Prior Art Analysis for US10036012

This analysis focuses on identifying the most relevant prior art cited by US Patent 10,036,012, titled "Compositions and methods for targeted nucleic acid sequence enrichment and high efficiency library generation." The patent primarily describes methods for enriching specific nucleic acid sequences and generating libraries for sequencing, utilizing adaptor ligation, target-specific oligonucleotide annealing, polymerase extension, and amplification. A notable embodiment involves partial duplex adaptors with restriction sites and blocking groups.

Given the extensive list of cited patents (over 200, many within the same patent families), a selection of representative and highly relevant patents was made for detailed analysis. These patents cover the core aspects of library preparation and target enrichment that form the basis of US10036012.

The independent claims of US10036012 are:

• Claim 1: A method for enriching target nucleic acid sequences involving fragmentation, appending a first adaptor, annealing target-complementary oligonucleotides with a second adaptor sequence, extending, and amplifying.
• Claim 15: A method for generating a library of nucleic acid sequences, similar to Claim 1 but focusing on library generation.
• Claim 20: A method for enriching from an existing library (already having first and second adaptors) using a third adaptor.
• Claim 28: A method for enriching using a partial duplex first adaptor with a blocking group and a restriction site, followed by cleavage and ligation of a second adaptor.

Most Relevant Prior Art

Here are detailed analyses of the most relevant prior art, including potential anticipation under 35 U.S.C. § 102 based on their abstracts and general disclosures:

1. US8278036B2

   • Full Citation: US8278036B2, "Methods for the preparation of libraries for sequence analysis," inventors Kevin E. K. Cole, Todd E. Dickinson, Gregory M. Fejes, Robert S. Hodges, Kevin H. Hunter, Michael L. Knapp, Nuo Li, Robert J. Lipshutz, Radoje T. D. Ruzic, published October 2, 2012.
   • Publication/Filing Date: Publication Date: October 2, 2012; Filing Date: January 13, 2011.
   • Brief Description: This patent describes methods for preparing libraries of nucleic acid fragments for sequence analysis. The methods involve ligating adaptors to target nucleic acids and then enriching fragments that have adaptors ligated to both ends using a polymerase. The process can involve fragmenting nucleic acids, ligating adaptors, and selecting for molecules with adaptors at both ends.
   • Potential Anticipation: This patent directly describes methods for preparing nucleic acid libraries for sequencing, including the steps of fragmenting, ligating adaptors to the fragments, and amplifying the fragments. This directly anticipates core elements of Claim 1 (steps a, b, e), Claim 15 (steps a, b, f), and Claim 20 (amplification), particularly regarding the general concept of generating amplifiable libraries with adaptors. The specific targeted enrichment aspects of US10036012 using a sequence-specific oligonucleotide and a second or third adaptor might be distinguishable, but the fundamental steps of library preparation and amplification with adaptors are clearly present.

2. US8765406B2

   • Full Citation: US8765406B2, "Reagents and methods for generating amplifiable representations of nucleic acids and use thereof," inventors Kevin K. Cole, Todd E. Dickinson, Gregory M. Fejes, Robert S. Hodges, Kevin H. Hunter, Michael L. Knapp, Nuo Li, Robert J. Lipshutz, Radoje T. D. Ruzic, published July 1, 2014.
   • Publication/Filing Date: Publication Date: July 1, 2014; Filing Date: July 29, 2011.
   • Brief Description: This patent describes methods for generating amplifiable representations of nucleic acids, which can include DNA or RNA, from a sample. The methods involve ligating adaptors to nucleic acid fragments and then amplifying the ligated fragments. It also covers methods for preparing DNA from RNA templates and for performing whole genome amplification.
   • Potential Anticipation: Similar to US8278036B2, this patent broadly covers methods of generating amplifiable nucleic acid representations using adaptors and amplification. The description of preparing DNA from RNA templates is also relevant. This potentially anticipates aspects of Claim 1 (steps a, b, e), Claim 15 (steps a, b, f), and Claim 20 (amplification), particularly the general strategy of using adaptors for subsequent amplification.

3. US8835099B2

   • Full Citation: US8835099B2, "Methods and compositions for adapter ligation and extension," inventors Kevin K. Cole, Todd E. Dickinson, Gregory M. Fejes, Robert S. Hodges, Kevin H. Hunter, Michael L. Knapp, Nuo Li, Robert J. Lipshutz, Radoje T. D. Ruzic, published September 16, 2014.
   • Publication/Filing Date: Publication Date: September 16, 2014; Filing Date: July 12, 2013.
   • Brief Description: This patent describes methods and compositions for ligating adaptors to nucleic acids and for extending those ligated adaptors. The methods aim to improve the efficiency and fidelity of adaptor ligation and subsequent extension steps, particularly for creating libraries for sequencing.
   • Potential Anticipation: This patent directly addresses the efficiency of adaptor ligation and subsequent extension, which are critical steps in US10036012. The concept of "appending a first adaptor" (Claim 1, 15, 28) and the implication of extending nucleic acids for library preparation or enrichment are highly relevant. Depending on the specific details of the ligation and extension methods, it could potentially anticipate aspects of Claim 1 (steps b, d), Claim 15 (steps b, e), and Claim 28 (step b, e), especially concerning the technical details of adaptor attachment and extension reactions.

4. US8932799B2

   • Full Citation: US8932799B2, "Methods for preparing target-enriched nucleic acid samples," inventors Kevin K. Cole, Todd E. Dickinson, Gregory M. Fejes, Robert S. Hodges, Kevin H. Hunter, Michael L. Knapp, Nuo Li, Robert J. Lipshutz, Radoje T. D. Ruzic, published January 13, 2015.
   • Publication/Filing Date: Publication Date: January 13, 2015; Filing Date: June 1, 2012.
   • Brief Description: This patent describes methods for preparing target-enriched nucleic acid samples for analysis, such as sequencing. The methods generally involve steps to selectively enrich specific nucleic acid sequences from a complex sample, often using amplification-based techniques after modifying the target and non-target nucleic acids differently.
   • Potential Anticipation: This patent's title and abstract clearly indicate a focus on "target-enriched nucleic acid samples," directly aligning with the primary goal of US10036012. While the specific mechanism of enrichment might differ, the general inventive concept of enriching target sequences is fundamental. Depending on the detailed methodology described in US8932799B2, it could potentially anticipate the overall goal and some general steps of Claim 1, Claim 15, Claim 20, and Claim 28, particularly the enrichment aspect. The novelty of US10036012 would then rely on the specific combination of steps (e.g., the particular adaptor structures, the timing of denaturation and oligonucleotide annealing, or the partial duplex adaptor of Claim 28).

5. US20090061439A1

   • Full Citation: US20090061439A1, "Methods for preparing target-enriched nucleic acid samples," inventors Kevin K. Cole, Todd E. Dickinson, Gregory M. Fejes, Robert S. Hodges, Kevin H. Hunter, Michael L. Knapp, Nuo Li, Robert J. Lipshutz, Radoje T. D. Ruzic, published March 5, 2009.
   • Publication/Filing Date: Publication Date: March 5, 2009; Filing Date: August 29, 2008.
   • Brief Description: This patent application describes methods for enriching target nucleic acid samples. It outlines techniques for selectively isolating and amplifying specific DNA or RNA sequences from a mixed population, often involving steps like adaptor ligation, hybridization, and amplification.
   • Potential Anticipation: As an earlier publication with the same title as the granted patent US8932799B2, this application broadly introduces the concept and methods for preparing target-enriched nucleic acid samples. Its earlier filing date makes it highly relevant. It potentially anticipates the broad concept of target enrichment in Claim 1, Claim 15, Claim 20, and Claim 28. The specific details of the adaptors and the sequence of steps in US10036012 would need to be critically compared against the detailed disclosure of this application to determine exact anticipation.

6. US20110269145A1

   • Full Citation: US20110269145A1, "Methods for the preparation of libraries for sequence analysis," inventors Kevin K. Cole, Todd E. Dickinson, Gregory M. Fejes, Robert S. Hodges, Kevin H. Hunter, Michael L. Knapp, Nuo Li, Robert J. Lipshutz, Radoje T. D. Ruzic, published November 3, 2011.
   • Publication/Filing Date: Publication Date: November 3, 2011; Filing Date: July 13, 2011.
   • Brief Description: This patent application describes methods for preparing libraries of nucleic acid fragments for sequence analysis. It focuses on processes for attaching adaptors to nucleic acid fragments to enable their amplification and subsequent sequencing.
   • Potential Anticipation: This application, similar to US8278036B2, lays out foundational methods for library preparation, including fragmentation and adaptor ligation for sequence analysis. Given its earlier publication date, it is a key reference for the general steps of preparing nucleic acid libraries. It potentially anticipates aspects of Claim 1 (steps a, b, e) and Claim 15 (steps a, b, f) regarding the fundamental process of creating sequencing libraries with adaptors and subsequent amplification.

In summary, the cited prior art collectively demonstrates established techniques for fragmenting nucleic acids, ligating adaptors for amplification, and methods for enriching target sequences. The novelty of US10036012 likely lies in the specific combination of these steps, the precise design and use of the adaptors (especially the partial duplex adaptor in Claim 28), and the sequence of annealing and extension steps to achieve high-efficiency targeted enrichment or library generation. A thorough §102 analysis would require a detailed element-by-element comparison of each claim of US10036012 against the full disclosure of these prior art documents.

Obviousness Analysis of US Patent 10036012 under 35 U.S.C. § 103

This analysis identifies combinations of prior art references that would likely render the claims of US Patent 10036012 obvious to a person having ordinary skill in the art (POSA) at the time of the invention (priority date January 26, 2012). The motivation to combine these references stems from the common goals within the field of nucleic acid sequencing: improving efficiency, specificity, and cost-effectiveness of targeted enrichment and library preparation for Next Generation Sequencing (NGS).

A POSA in this field would be familiar with various techniques for nucleic acid manipulation, including fragmentation, ligation, adapter addition, primer design, polymerase extension, and PCR amplification, and would be motivated to combine known techniques to improve existing methods for targeted sequencing and library generation.

Combination 1: US 9,650,628 B2 in view of US 7,115,400 B1 and general knowledge in the art

Motivation to Combine: A POSA would be motivated to combine the general principles of targeted nucleic acid enrichment and library preparation described in US 9,650,628 B2 with the specific amplification and sequencing techniques detailed in US 7,115,400 B1, to create more robust and efficient workflows for NGS. The general knowledge in the art at the time emphasized the need for high-throughput, accurate, and cost-effective methods for preparing samples for sequencing.

Analysis for Independent Claim 1 (Method for enriching target nucleic acid sequences):

Independent Claim 1 describes a method comprising:
(a) fragmenting nucleic acids;
(b) appending a first adaptor to a 5′ end of each nucleic acid fragment;
(c) annealing one or more oligonucleotides with a 3′ portion complementary to a target sequence and a 5′ portion comprising a second adaptor sequence;
(d) extending the one or more oligonucleotides with a polymerase; and
(e) amplifying the extension products.

• Step (a) fragmenting nucleic acids: US 9,650,628 B2 discloses fragmenting nucleic acids in an input sample to generate nucleic acid fragments. It explicitly states that fragmentation can be achieved through methods known in the art, including physical (e.g., sonication) and/or enzymatic fragmentation. US 7,115,400 B1 also discusses obtaining nucleic acid samples and generating fragments by, for example, limited restriction enzyme digestion or by mechanical means. This step is therefore well-established in the prior art.
• Step (b) appending a first adaptor to a 5′ end of each nucleic acid fragment: US 9,650,628 B2 teaches appending a first adaptor (forward adaptor) to nucleic acid fragments. It further states that this can be achieved using a ligation reaction or a priming reaction. The general knowledge in NGS library preparation, as summarized in publicly available information, confirms that adapter ligation to fragmented DNA is a standard initial step, often followed by end repair and A-tailing to facilitate ligation.
• Step (c) annealing one or more oligonucleotides with a 3′ portion complementary to a target sequence and a 5′ portion comprising a second adaptor sequence: US 9,650,628 B2 describes annealing one or more oligonucleotides to single-stranded nucleic acid fragments, where each oligonucleotide comprises a 3′ portion complementary to a target sequence and a 5′ portion comprising a second adaptor sequence. The concept of using sequence-specific primers (oligonucleotides) for targeted amplification is fundamental to PCR, as described in US 7,115,400 B1, where two primers are designed to flank a target DNA sequence and hybridize to the target. A POSA would understand that a "tail" (non-hybridizing 5' portion) on such an oligonucleotide could readily incorporate a second adapter sequence. The concept of "tailed primers" comprising a 3' hybridizable portion and a 5' non-hybridizable portion that includes an adaptor sequence is explicitly mentioned in the background of US 10,036,012 itself, indicating it as known in the art.
• Step (d) extending the one or more oligonucleotides with a polymerase: Both US 9,650,628 B2 and US 7,115,400 B1 describe the use of polymerases for primer extension. US 9,650,628 B2 explicitly states that the polymerase can be a DNA polymerase. US 7,115,400 B1 mentions the formation of a first amplification product by extension of a primer sequence with a polymerase. This is a standard molecular biology technique.
• Step (e) amplifying the extension products: US 9,650,628 B2 teaches amplifying the oligonucleotide extension products with a set of primers specific to the first and second adaptor sequences to generate a library. US 7,115,400 B1 details PCR amplification, noting that if the target nucleic acid is present, it can hybridize to primers and be amplified by PCR. The use of primers complementary to adapter sequences to amplify library fragments is a standard practice in NGS library preparation.

Therefore, all elements of Independent Claim 1 are individually present in the cited prior art references, and a POSA would have been motivated to combine these known techniques for targeted enrichment and library generation.

Analysis for Independent Claim 22 (Method for generating a library of nucleic acid sequences using random priming):

Independent Claim 22 is similar to Claim 1 but specifies that the oligonucleotide in step (d) has a 3' portion comprising a random sequence.

• Steps (a), (b), (c), (e), (f) (fragmenting, appending first adaptor, denaturing, extending with polymerase, and amplifying): These steps are substantially covered by the reasoning for Claim 1, as taught by US 9,650,628 B2 and US 7,115,400 B1. US 9,650,628 B2 explicitly describes a method for generating a library of nucleic acid sequences including fragmenting, appending a first adaptor, denaturing to create single-stranded fragments, annealing one or more oligonucleotides (with a 3' complementary portion and a 5' second adaptor), extending with a polymerase, and amplifying.
• Step (d) annealing one or more oligonucleotides with a 3′ portion comprising a random sequence and a 5′ portion comprising a second adaptor sequence: The concept of using random primers for nucleic acid synthesis is well-known in the art. The description of US 10,036,012 itself defines a "random primer" as generally comprising a sequence designed not based on a particular specific sequence, but on a statistical expectation of hybridizing to one or more sequences in the sample, and that it may comprise a tailed primer with a 3'-random region and a 5'-non-hybridizing specific sequence (adaptor sequence). This indicates that such random, tailed primers were known in the art prior to the invention. The motivation to use random primers in library generation would be to create a comprehensive library without prior knowledge of all target sequences, which is a common goal in many sequencing applications.

Thus, a POSA, seeking to create a library comprehensively, would find it obvious to modify the sequence-specific oligonucleotide annealing step in US 9,650,628 B2 (or similar methods) to use a random primer with a 5' adaptor sequence, a technique known in the art for broad coverage library generation.

Combination 2: US 9,650,628 B2 in view of WO 2015/061759 A1 (published May 1, 2015, relevant priority date potentially earlier) and general knowledge in the art.

Motivation to Combine: A POSA would be motivated to combine the general targeted enrichment and library preparation methods of US 9,650,628 B2 with the more advanced adapter designs, particularly partial duplex adaptors and the use of blocking groups, as described in WO 2015/061759 A1 and other related prior art in the field of molecular barcoding and error correction. These advancements aimed to improve the accuracy, specificity, and efficiency of NGS, including strand-specific and error-corrected sequencing.

Analysis for Independent Claim 13 (Method for enriching target nucleic acid sequences using a partial duplex adaptor):

Independent Claim 13 describes a method involving:
(a) fragmenting nucleic acids;
(b) appending a first adaptor which is a partial duplex with a short strand (3′ end blocked) and a long strand (5′ end with restriction/cleavage site);
(c) denaturing the fragments;
(d) annealing one or more oligonucleotides complementary to a target nucleic acid;
(e) extending the oligonucleotides with a polymerase, generating products with the long strand of the first adaptor at one end and a sequence complementary to the long strand at the other;
(f) modifying the restriction/cleavage site with a nucleic acid modifying enzyme;
(g) ligating a second adaptor to the modified site; and
(h) amplifying the products.

• Steps (a), (c), (d), (e), (h) (fragmenting, denaturing, annealing target-specific oligos, extending, amplifying): These general steps are extensively taught in US 9,650,628 B2. US 9,650,628 B2 explicitly covers fragmenting nucleic acids, denaturing nucleic acid fragments, annealing one or more oligonucleotides to single-stranded fragments, extending with a polymerase, and amplifying the resulting products.
• Step (b) appending a first adaptor which is a partial duplex with a short strand (3′ end blocked) and a long strand (5′ end with restriction/cleavage site): The concept of adaptors with specific features, such as blocking groups to prevent extension and restriction sites for subsequent manipulation, was known in the art. WO 2015/061759 A1 discusses targeted capture using Molecular Inversion Probes (MIPs) which involve extension and ligation to form circularized probes, implying sophisticated probe and adaptor designs. Although not explicitly describing the exact partial duplex adapter of Claim 13, the general idea of using adapters with functional elements (like restriction sites for downstream processing and blocked ends for controlled reactions) was a known design principle in the field to achieve specific molecular outcomes. For example, the patent itself mentions "partial duplex design, wherein the two strands of the adaptor are different lengths with a complementary region and an overhanging region at the 5′ end" as a "common feature of the adaptors depicted in FIG. 3," implying it as a known design concept. It also describes a blocking group (e.g., a dideoxynucleotide) at the 3' end of the short strand to prevent polymerase extension, which is a standard molecular biology modification.
• Step (f) modifying the restriction/cleavage site with a nucleic acid modifying enzyme: The concept of incorporating restriction enzyme sites into synthetic DNA constructs and then cleaving them with specific enzymes is a fundamental technique in molecular cloning and DNA manipulation. US 10,036,012 itself refers to this as a feature of FIG. 3, suggesting that it was a known approach. Restriction enzymes specific for double-stranded DNA are well-known, as acknowledged by the patent, which lists examples of such enzymes (e.g., DraI, SmaI).
• Step (g) ligating a second adaptor to the modified site: Ligation of adaptors to nucleic acid fragments, including those with blunt or sticky ends generated by restriction enzymes, is a standard molecular biology technique, as taught by US 9,650,628 B2 (mentioning ligation as a way to append adaptors) and generally understood in NGS library preparation.

Given the known elements of nucleic acid manipulation and the continuous drive for improved library preparation methods, a POSA would have been motivated to combine the general enrichment strategies with specific, functional adaptor designs (like partial duplex adaptors with blocking groups and restriction sites) to control ligation directionality, enable selective cleavage, and facilitate subsequent adaptor ligation for targeted enrichment, especially in contexts aiming for higher accuracy or specific manipulation, as suggested by the emphasis on error correction methods in WO 2015/061759 A1.

Conclusion on Obviousness

The independent claims of US 10036012 appear obvious in light of the cited prior art. The core methods of fragmenting, ligating adapters, primer annealing and extension, and PCR amplification were well-established and routinely used in the field of nucleic acid library preparation and targeted enrichment for NGS. The specific adaptations claimed, such as the use of a second adapter sequence on a target-specific oligonucleotide (Claim 1), random primers with adapter tails (Claim 22), or partial duplex adapters with blocking groups and restriction sites (Claim 13), represent straightforward applications or combinations of known techniques and design principles that a person having ordinary skill in the art would have been motivated to implement to address existing challenges in efficiency, specificity, and cost in NGS workflows.