Obviousness

Obviousness Analysis Under 35 U.S.C. § 103

This analysis evaluates whether the claimed invention in U.S. Patent 11,021,737 would have been obvious to a Person Having Ordinary Skill in the Art (PHOSITA) as of the priority date of December 22, 2011. An invention is considered obvious if the differences between the invention and the prior art are such that the invention as a whole would have been obvious to a PHOSITA at the time the invention was made.

Definition of a Person Having Ordinary Skill in the Art (PHOSITA)

As of late 2011, a PHOSITA in this field would possess a Ph.D. in molecular biology, biochemistry, or a related discipline, coupled with several years of experience in academic or industrial research. This individual would be well-versed in nucleic acid biochemistry, including hybridization, amplification, and sequencing technologies (both Sanger and next-generation methods). They would have practical knowledge of protein detection methods, such as immunohistochemistry and immunofluorescence, and would be familiar with standard bioconjugation techniques for linking nucleic acids to proteins like antibodies. The PHOSITA would also understand the scientific goal of highly multiplexed biomolecule analysis and the challenges of achieving it while preserving spatial context within a biological sample.

Obviousness Combination 1: Gunderson (US 2007/0231824) in view of Church (US 7,785,790)

A strong argument can be made that the independent claims of the '737 patent are rendered obvious by the combination of Gunderson and Church '790.

• Primary Reference: Gunderson (US 2007/0231824)
  Gunderson teaches the core detection methodology claimed in the '737 patent: a temporal code generated by the sequential application, detection, and removal of labeled "decoder probes" to identify unique nucleic acid tag sequences. This directly teaches the method of claims 1 and 12, including generating a "temporal order of the signal signatures" (claim 1) through repeated hybridization and removal steps (claim 12). However, Gunderson applies this method to decode a pre-fabricated, fixed microarray of beads before introducing a sample. It does not teach applying this method to soluble detection reagents bound to analytes within a biological sample.

• Secondary Reference: Church (US 7,785,790)
  Church '790 teaches the art of performing complex, multi-step, sequential nucleic acid analysis (specifically, sequencing) directly in situ within a fixed cell or tissue sample. This established the principle that the necessary enzymes, buffers, and oligonucleotides could successfully diffuse into and function within a complex biological matrix to provide spatially resolved nucleic acid information.

• Motivation to Combine and Reasonable Expectation of Success:
  By 2011, a primary goal in biology was to move from analyzing single molecules to analyzing many simultaneously (multiplexing) within their native context. Church '790 provided a breakthrough for in situ analysis of nucleic acids. A PHOSITA, aware of the need to apply similar high-plex spatial analysis to other molecules like proteins, would look for robust barcoding and decoding schemes.

  Gunderson provided just such a scheme—a powerful temporal decoding method capable of identifying thousands of tags. The motivation to combine these references would have been to take Gunderson's superior temporal decoding method "off the chip" and apply it to the in situ environment demonstrated to be viable by Church '790. Instead of decoding a static array of beads, the PHOSITA would be motivated to use Gunderson's method to decode probes that were freely binding to targets within a tissue sample. This combination would directly address the well-understood need for highly multiplexed in situ proteomics and transcriptomics.

  The PHOSITA would have had a reasonable expectation of success. Church '790 demonstrated that the microenvironment of a fixed cell was permeable to the reagents needed for sequential nucleic acid chemistry. Since Gunderson's method relies on basic hybridization, which is a less complex process than the enzymatic ligation or synthesis used by Church, it would be reasonably expected that Gunderson's decoder probes and buffers would also function effectively in an in situ setting.

• Conclusion for this Combination:

  • Claims 1 and 12 (Method Claims): The combination of Gunderson's temporal decoding method with the in situ application context taught by Church renders the method claims obvious. It would have been an obvious step to apply a known decoding technique (Gunderson) to a known environment for sequential analysis (Church) to achieve a desired and predictable result: highly multiplexed spatial analyte detection.
  • Claim 20 (Composition Claim): To practice the obvious method derived from this combination, one would need a suitable tool. This tool is a probe reagent (e.g., an antibody known to bind a protein of interest) conjugated to one of Gunderson's nucleic acid tags. The creation of such antibody-DNA conjugates was a routine technique known to the PHOSITA. Therefore, the detection reagent of claim 20 would have been obvious as the necessary and readily created composition for carrying out the obvious method.

Obviousness Combination 2: Church (US 7,785,790) in view of General Knowledge and Dimitrov (US 7,473,767)

An alternative argument starts with the problem Church '790 was trying to solve—multiplexed spatial analysis—and combines it with other known labeling technologies.

• Primary Reference: Church (US 7,785,790)
  Church establishes the goal and feasibility of high-plex in situ analysis but is limited to sequencing endogenous nucleic acids. A PHOSITA would immediately be motivated to extend this powerful technique to proteins.

• Secondary References: General Knowledge of Immunoassays and Dimitrov (US 7,473,767)
  The most common tool for specific protein detection is an antibody. The general knowledge in the art was to attach a label to an antibody to make it detectable. To adapt the sequencing-based detection of Church to proteins, the obvious label would be a synthetic nucleic acid barcode.

  Dimitrov teaches the use of such a "nanostring" probe: a probe reagent linked to a nucleic acid backbone that serves as a barcode. While Dimitrov's barcode is read spatially, it teaches the fundamental concept of using a nucleic acid molecule as a high-capacity information carrier to identify a probe.

• Motivation to Combine and Reasonable Expectation of Success:
  A PHOSITA seeking to adapt Church's in situ method for proteins would obviously arrive at using an antibody conjugated to a nucleic acid barcode, a concept explicitly taught by Dimitrov. The final step would be to decide how to "read" the barcode in situ. While one could use the sequencing-by-ligation method from Church, it would also be obvious to consider other known methods for reading nucleic acid tags. As discussed in the first combination, Gunderson's temporal decoding is a well-documented and efficient method for this purpose. Therefore, it would have been obvious to a PHOSITA to:

  1. Start with the goal of in situ protein detection (an extension of Church).
  2. Select a DNA-barcoded antibody as the tool (taught by Dimitrov and general knowledge).
  3. Choose an efficient, known method for reading the DNA barcode (such as the temporal decoding from Gunderson).

  This logical progression of design choices, each step being well-supported by the prior art, would lead directly to the claimed invention with a reasonable expectation of success.