Prior art

As a senior US patent analyst, my examination of the prior art cited during the prosecution of U.S. Patent 11,566,276 reveals several key references that the USPTO examiner considered before granting the patent. The following analysis details the most relevant of these references and assesses their potential impact on the patent's claims, particularly under 35 U.S.C. § 102 (anticipation).

Anticipation under § 102 requires that a single prior art reference discloses, either expressly or inherently, each and every element of a patent claim.

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Analysis of Most Relevant Prior Art

1. U.S. Patent Application Publication No. US 2011/0086776 A1 ("Drmanac et al.")

• Full Citation: US 2011/0086776 A1
• Publication Date: April 14, 2011
• Filing Date: October 6, 2010
• Brief Description: Drmanac discloses methods for in situ sequencing of nucleic acids within fixed cells or tissues. The method involves hybridizing probes, including "activator probes," to target nucleic acids within a sample. These probes can then be identified to determine the sequence of the target. A key aspect is the ability to analyze nucleic acids in their original spatial context within a biological sample.
• Potential Anticipation Analysis:
  • This reference is highly relevant as it teaches the core concept of identifying nucleic acids in situ. It describes fixing a sample, introducing nucleic acid probes, and analyzing them to gain information about the sample's contents in a spatially resolved manner.
  • Claim 1: Drmanac discloses a method for detecting nucleic acid analytes, fixing them in a sample, and using nucleic acid probes for detection. However, the claims of '276 are broader, applying to any type of analyte (not just nucleic acids) through the use of a probe (e.g., an antibody) conjugated to a nucleic acid label. Drmanac's focus is on directly probing and sequencing existing nucleic acids in the sample. It does not appear to disclose the use of non-nucleic acid probes (like antibodies or aptamers) attached to pre-determined, unique nucleic acid labels for the purpose of identifying non-nucleic acid analytes, followed by amplification and sequencing of those labels. Therefore, Drmanac likely does not anticipate claim 1.
  • Claims 19 & 28: For the same reasons, Drmanac does not appear to disclose the claimed composition or kit, which require detection reagents for a plurality of different analyte types where the probe portion can be non-nucleic acid and is conjugated to a unique nucleic acid label for subsequent identification.

2. Larsson et al., Nature Methods, 2004 ("Larsson")

• Full Citation: Larsson, C. et al. "In situ genotyping individual DNA molecules by target-primed rolling-circle amplification of padlock probes." Nature Methods 1.3 (2004): 227-232.
• Publication Date: December 2004
• Brief Description: Larsson describes a method for detecting and genotyping specific DNA sequences within fixed cells. The method uses "padlock probes," which are circularizable oligonucleotide probes. When a padlock probe hybridizes to its target sequence, its ends are brought together and can be ligated to form a closed circle. This circularized probe then serves as a template for rolling-circle amplification (RCA), creating a long concatemer of the probe's sequence that is easily detectable as a discrete point of light in situ.
• Potential Anticipation Analysis:
  • Larsson is a seminal paper in the field of in situ nucleic acid analysis and is highly relevant. It teaches fixing a sample, using nucleic acid probes (padlock probes), and performing in situ amplification (RCA) to generate a detectable signal at the location of the target molecule.
  • Claim 1: Larsson's method is for detecting nucleic acid targets (DNA), not a general class of analytes. The claims of '276 cover detection reagents where the probe can be an antibody, aptamer, or other molecule to detect proteins, small molecules, etc., which is a key distinction. Larsson amplifies the probe itself after it has been circularized by the target; it does not describe sequencing an attached, pre-determined label to identify the analyte. While RCA is a form of amplification, the '276 patent specifically claims sequencing the amplified products as the readout method. Larsson's readout is primarily fluorescence-based detection of the amplified product. Therefore, Larsson does not appear to anticipate the full scope of claim 1.
  • Claims 19 & 28: Larsson does not describe a composition or kit with a plurality of detection reagents for different types of analytes (e.g., protein and RNA) using unique nucleic acid labels.

3. Mitra & Church, Nucleic Acids Research, 1999 ("Mitra")

• Full Citation: Mitra, R. D., & Church, G. M. "In situ localized amplification and contact replication of many individual DNA molecules." Nucleic Acids Research 27.24 (1999): e34.
• Publication Date: December 15, 1999
• Brief Description: This paper, co-authored by one of the inventors of the '276 patent, describes a method for amplifying single DNA molecules within a polyacrylamide gel matrix. The amplification products remain localized near the original template molecule, creating distinct colonies of amplified DNA ("polonies"). This allows for the simultaneous analysis of many individual molecules in a multiplexed fashion. The method is a foundational technique for in situ amplification.
• Potential Anticipation Analysis:
  • Mitra is a foundational reference for the in situ amplification element of the claims. It clearly teaches immobilizing nucleic acids in a matrix and amplifying them in a way that the products remain spatially localized.
  • Claim 1: Mitra's method is focused on amplifying DNA that is already present or has been introduced into the gel. It does not describe the central concept of the '276 patent: a detection reagent composed of a probe for a specific analyte (which could be a protein) conjugated to a distinct nucleic acid label. In Mitra's work, the DNA being amplified is the analyte of interest. The '276 patent uses the nucleic acid label as a barcode to be sequenced for identifying a potentially non-nucleic acid analyte. Therefore, Mitra does not anticipate claim 1.
  • Claims 19 & 28: Mitra does not disclose the claimed composition of detection reagents or a kit for detecting a plurality of different analyte types via nucleic acid labels.

4. U.S. Patent No. 9,598,731 B2 ("Church et al.")

• Full Citation: US 9,598,731 B2
• Issue Date: March 21, 2017
• Filing Date: August 15, 2013
• Brief Description: This patent, from the same inventor group and assignee, is part of the same patent family as the '276 patent. It describes methods for in situ analysis of nucleic acids in a biological sample. The method involves amplifying target nucleic acids within the sample and then sequencing the amplification products in situ. This is often referred to as in situ sequencing.
• Potential Anticipation Analysis:
  • As a related patent, this document shares significant portions of its specification with the '276 patent. It establishes the technical feasibility of in situ amplification and sequencing.
  • However, the claims of '731 are focused on analyzing the sequence of the target nucleic acids themselves within the sample. The '276 patent claims a different method where a pre-determined label or barcode is sequenced to identify the analyte, and that analyte is not limited to being a nucleic acid. The novelty in the '276 patent lies in the use of these artificial nucleic acid labels conjugated to a diverse set of probes (e.g., antibodies) to create a map of various molecules (proteins, RNA, etc.) in a sample. This reference would not anticipate the '276 claims because it describes a different, albeit related, process. It is used for context and to support the underlying technology but does not disclose the specific combination of elements in the '276 claims.

Summary of Prior Art Impact

The prior art cited by the examiner establishes the state of the art for in situ analysis prior to the invention of the '276 patent. Key techniques like fixing biological samples, introducing probes, performing localized amplification (e.g., RCA or polony amplification), and even in situ sequencing of native nucleic acids were known.

However, none of the cited references appear to explicitly disclose the core concept that unites the independent claims of US 11,566,276: a multiplexed method for detecting a plurality of different analyte types (including non-nucleic acids) by using detection reagents that pair a specific probe (e.g., antibody) with a unique, pre-determined, non-naturally occurring nucleic acid label, followed by the amplification and sequencing of those labels to identify and locate the original analytes.

The examiner likely concluded that combining these known in situ techniques with the concept of nucleic acid-barcoded affinity probes (like antibody-oligonucleotide conjugates) for highly multiplexed spatial analysis was non-obvious and not anticipated by any single reference.