DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Location of Application
The location of the subject application has changed. The subject application is now located in Workgroup 1680, Art Unit 1682, and has been docketed to Primary Examiner Bradley L. Sisson.
Drawings
New corrected drawings in compliance with 37 CFR 1.121(d) are required in this application because:
The lettering is not of proper size, uniform density, and well-defined in Figure(s) 1-5. See 37 CFR 1.84(p)(1) – (5). (“Numbers, letters, and reference characters must measure at least .32 cm (1/8 inch) in height.”)
In Figure(s) 1 - 5 the reference characters, sheet numbers, and view numbers are not all oriented in the same direction so as to avoid having to rotate the sheet. See 37 CFR 1.84(p)(1).
Applicant is advised to employ the services of a competent patent draftsperson outside the Office, as the U.S. Patent and Trademark Office no longer prepares new drawings. The corrected drawings are required in reply to the Office action to avoid abandonment of the application. The requirement for corrected drawings will not be held in abeyance.
INFORMATION ON HOW TO EFFECT DRAWING CHANGES
Replacement Drawing Sheets
Drawing changes must be made by presenting replacement sheets which incorporate the desired changes and which comply with 37 CFR 1.84. An explanation of the changes made must be presented either in the drawing amendments section, or remarks, section of the amendment paper. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). A replacement sheet must include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of the amended drawing(s) must not be labeled as “amended.” If the changes to the drawing figure(s) are not accepted by the examiner, applicant will be notified of any required corrective action in the next Office action. No further drawing submission will be required, unless applicant is notified.
Identifying indicia, if provided, should include the title of the invention, inventor’s name, and application number, or docket number (if any) if an application number has not been assigned to the application. If this information is provided, it must be placed on the front of each sheet and within the top margin.
Annotated Drawing Sheets
A marked-up copy of any amended drawing figure, including annotations indicating the changes made, are required by the examiner. The annotated drawing sheet(s) must be clearly labeled as “Annotated Sheet” and must be presented in the amendment or remarks section that explains the change(s) to the drawings.
Timing of Corrections
Applicant is required to submit acceptable corrected drawings within the time period set in the Office action. See 37 CFR 1.85(a). Failure to take corrective action within the set period will result in ABANDONMENT of the application.
If corrected drawings are required in a Notice of Allowability (PTOL-37), the new drawings MUST be filed within the THREE MONTH shortened statutory period set for reply in the “Notice of Allowability.” Extensions of time may NOT be obtained under the provisions of 37 CFR 1.136 for filing the corrected drawings after the mailing of a Notice of Allowability.
Claim Interpretation
Attention is directed to MPEP 904.01 [R-08.2012].
The breadth of the claims in the application should always be carefully noted; that is, the examiner should be fully aware of what the claims do not call for, as well as what they do require. During patent examination, the claims are given the broadest reasonable interpretation consistent with the specification. See In re Morris, 127 F.3d 1048, 44 USPQ2d 1023 (Fed. Cir. 1997). See MPEP § 2111 - § 2116.01 for case law pertinent to claim analysis.
It is noted with particularity that narrowing limitations found in the specification cannot be inferred in the claims where the elements not set forth in the claims are linchpin of patentability. In re Philips Industries v. State Stove & Mfg. Co, Inc., 186 USPQ 458 (CA6 1975). While the claims are to be interpreted in light of the specification, it does not follow that limitations from the specification may be read into the claims. On the contrary, claims must be interpreted as broadly as their terms reasonably allow. See Ex parte Oetiker, 23 USPQ2d 1641 (BPAI, 1992). In added support of this position, attention is directed to MPEP 2111 [R-11.2013], where, citing In re Prater, 415 F.2d 1393, 1404-05, 162 USPQ 541, 550-51 (CCPA 1969), is stated:
The court explained that “reading a claim in light of the specification, to thereby interpret limitations explicitly recited in the claim, is a quite different thing from ‘reading limitations of the specification into a claim,’ to thereby narrow the scope of the claim by implicitly adding disclosed limitations which have no express basis in the claim.” The court found that applicant was advocating the latter, i.e., the impermissible importation of subject matter from the specification into the claim.
Additionally, attention is directed to MPEP 2111.01 [R-01.2024], wherein is stated:
II. IT IS IMPROPER TO IMPORT CLAIM LIMITATIONS FROM THE SPECIFICATION
“Though understanding the claim language may be aided by explanations contained in the written description, it is important not to import into a claim limitations that are not part of the claim. For example, a particular embodiment appearing in the written description may not be read into a claim when the claim language is broader than the embodiment.” Superguide Corp. v. DirecTV Enterprises, Inc., 358 F.3d 870, 875, 69 USPQ2d 1865, 1868 (Fed. Cir. 2004).
Attention is also directed to MPEP 2111.02 II [R-07.2022]. As stated herein:
II. PREAMBLE STATEMENTS RECITING PURPOSE OR INTENDED USE
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The claim preamble must be read in the context of the entire claim. The determination of whether preamble recitations are structural limitations or mere statements of purpose or use "can be resolved only on review of the entirety of the [record] to gain an understanding of what the inventors actually invented and intended to encompass by the claim" as drafted without importing "'extraneous' limitations from the specification." Corning Glass Works, 868 F.2d at 1257, 9 USPQ2d at 1966. If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction. Shoes by Firebug LLC v. Stride Rite Children’s Grp., LLC, 962 F.3d 1362, 2020 USPQ2d 10701 (Fed. Cir. 2020) (The court found that the preamble in one patent’s claim is limiting but is not in a related patent); Pitney Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1305, 51 USPQ2d 1161, 1165 (Fed. Cir. 1999). See also Rowe v. Dror, 112 F.3d 473, 478, 42 USPQ2d 1550, 1553 (Fed. Cir. 1997) ("where a patentee defines a structurally complete invention in the claim body and uses the preamble only to state a purpose or intended use for the invention, the preamble is not a claim limitation")… (Emphasis added)
Attention is directed to MPEP 2111 [R-10.2019]. As stated therein:
During patent examination, the pending claims must be "given their broadest reasonable interpretation consistent with the specification." The Federal Circuit’s en banc decision in Phillips v. AWH Corp., 415 F.3d 1303, 1316, 75 USPQ2d 1321, 1329 (Fed. Cir. 2005) expressly recognized that the USPTO employs the "broadest reasonable interpretation" standard:
The Patent and Trademark Office ("PTO") determines the scope of claims in patent applications not solely on the basis of the claim language, but upon giving claims their broadest reasonable construction "in light of the specification as it would be interpreted by one of ordinary skill in the art." In re Am. Acad. of Sci. Tech. Ctr., 367 F.3d 1359, 1364[, 70 USPQ2d 1827, 1830] (Fed. Cir. 2004). Indeed, the rules of the PTO require that application claims must "conform to the invention as set forth in the remainder of the specification and the terms and phrases used in the claims must find clear support or antecedent basis in the description so that the meaning of the terms in the claims may be ascertainable by reference to the description." 37 CFR 1.75(d)(1). (Emphasis added).
Attention is directed to MPEP 2173.04 [R-10.2019]. As stated therein:
Breadth of a claim is not to be equated with indefiniteness. In re Miller, 441 F.2d 689, 169 USPQ 597 (CCPA 1971); In re Gardner, 427 F.2d 786, 788, 166 USPQ 138, 140 (CCPA 1970) ("Breadth is not indefiniteness."). A broad claim is not indefinite merely because it encompasses a wide scope of subject matter provided the scope is clearly defined. But a claim is indefinite when the boundaries of the protected subject matter are not clearly delineated and the scope is unclear. For example, a genus claim that covers multiple species is broad, but is not indefinite because of its breadth, which is otherwise clear. But a genus claim that could be interpreted in such a way that it is not clear which species are covered would be indefinite (e.g., because there is more than one reasonable interpretation of what species are included in the claim). (Emphasis added)
Claim Rejections - 35 USC § 112, second paragraph / (b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Standard for Definiteness.
Attention is directed to MPEP 2171 [R-11.2013]:
Two separate requirements are set forth in 35 U.S.C. 112(b) and pre-AIA 35 U.S.C. 112, second paragraph, namely that:
(A) the claims must set forth the subject matter that the inventor or a joint inventor regards as the invention; and
(B) the claims must particularly point out and distinctly define the metes and bounds of the subject matter to be protected by the patent grant.
The first requirement is a subjective one because it is dependent on what the inventor or a joint inventor for a patent regards as his or her invention. Note that although pre-AIA 35 U.S.C. 112, second paragraph, uses the phrase "which applicant regards as his invention," pre-AIA 37 CFR 1.41(a) provides that a patent is applied for in the name or names of the actual inventor or inventors.
The second requirement is an objective one because it is not dependent on the views of the inventor or any particular individual, but is evaluated in the context of whether the claim is definite — i.e., whether the scope of the claim is clear to a hypothetical person possessing the ordinary level of skill in the pertinent art.
Attention is directed to MPEP 2173.02 I [R-01.2024]:
During prosecution, applicant has an opportunity and a duty to amend ambiguous claims to clearly and precisely define the metes and bounds of the claimed invention. The claim places the public on notice of the scope of the patentee’s right to exclude. See, e.g., Johnson & Johnston Assoc. Inc. v. R.E. Serv. Co., 285 F.3d 1046, 1052, 62 USPQ2d 1225, 1228 (Fed. Cir. 2002) (en banc). As the Federal Circuit stated in Halliburton Energy Servs., Inc. v. M-I LLC, 514 F.3d 1244, 1255, 85 USPQ2d 1654, 1663 (Fed. Cir. 2008):
“We note that the patent drafter is in the best position to resolve the ambiguity in the patent claims, and it is highly desirable that patent examiners demand that applicants do so in appropriate circumstances so that the patent can be amended during prosecution rather than attempting to resolve the ambiguity in litigation.”
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During examination, after applying the broadest reasonable interpretation to the claim, if the metes and bounds of the claimed invention are not clear, the claim is indefinite and should be rejected. Packard, 751 F.3d at 1310 (“[W]hen the USPTO has initially issued a well-grounded rejection that identifies ways in which language in a claim is ambiguous, vague, incoherent, opaque, or otherwise unclear in describing and defining the claimed invention, and thereafter the applicant fails to provide a satisfactory response, the USPTO can properly reject the claim as failing to meet the statutory requirements of § 112(b).”); Zletz, 893 F.2d at 322, 13 USPQ2d at 1322.
Attention is also directed to MPEP 2173.02 III B [R-01-2024], which states in part:
To comply with 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph, applicants are required to make the terms that are used to define the invention clear and precise, so that the metes and bounds of the subject matter that will be protected by the patent grant can be ascertained. See MPEP § 2173.05(a), subsection I. It is important that a person of ordinary skill in the art be able to interpret the metes and bounds of the claims so as to understand how to avoid infringement of the patent that ultimately issues from the application being examined. See MPEP § 2173.02, subsection II (citing Morton Int ’l, Inc. v. Cardinal Chem. Co., 5 F.3d 1464, 1470 (Fed. Cir. 1993)); see also Halliburton Energy Servs., 514 F.3d at 1249, 85 USPQ2d at 1658 (“Otherwise, competitors cannot avoid infringement, defeating the public notice function of patent claims.”). Examiners should bear in mind that “[a]n essential purpose of patent examination is to fashion claims that are precise, clear, correct, and unambiguous. Only in this way can uncertainties of claim scope be removed, as much as possible, during the administrative process.” Zletz, 893 F.2d at 322, 13 USPQ2d at 1322 [Fed. Cir. 1989]. (Emphasis added)
Attention is also directed to MPEP 2173.04 [R-10-2019], which states in part:
A broad claim is not indefinite merely because it encompasses a wide scope of subject matter provided the scope is clearly defined. But a claim is indefinite when the boundaries of the protected subject matter are not clearly delineated and the scope is unclear. For example, a genus claim that covers multiple species is broad, but is not indefinite because of its breadth, which is otherwise clear. But a genus claim that could be interpreted in such a way that it is not clear which species are covered would be indefinite (e.g., because there is more than one reasonable interpretation of what species are included in the claim).
Holding and Rationale
Claims 1, 5, 7-8, 12, 15-16, 18-20, 25, 30, 33, 36, 37, 39-45, 48, 53-57, and 89 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 is indefinite with respect to what constitutes the metes and bounds of “a biological sample”, “a cell or tissue sample”, “a first analyte”, “a second analyte”, “a first probe and a second probe”. Claims 5, 7-8, 12, 15-16, 18-20, 25, 30, 33, 36, 37, 39-45, 48, 53-57, and 89, which depend from claim 1, fail to overcome these issues and are similarly rejected.
Claim 1 is confusing where in line 17 is stated “wherein one or more of the sequential cycles”. Perhaps applicant had intended to refer to “sequencing”.
The term “more” in claim 1 is a relative term which renders the claim indefinite. The term “more” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Claims 5, 7-8, 12, 15-16, 18-20, 25, 30, 33, 36, 37, 39-45, 48, 53-57, and 89, which depend from claim 1, fail to overcome these issues and are similarly rejected.
The term “more” in claims 7, 15, 18-20, 30, 36, 37, 40, 43, 48, 55, and 89 is a relative term which renders the claims indefinite. The term “more” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
Claim 7 is indefinite with respect to what constitutes the metes and bounds of “a decision rule”.
Claim 8 is confusing as to what constitutes the metes and bounds of “expression data”.
The term “reduce” in claim 15 is a relative term which renders the claim indefinite. The term “reduce” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Claim 15 depends from claims 7, 5, and 1. Given such, claims 1, 5, and 7 must encompass such an embodiment and are thusly similarly rejected.
Claim Rejections - 35 USC § 112, Enablement
The following is a quotation of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), first paragraph:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Standard for Enablement
It is well settled that in order to satisfy the enablement requirement, “the specification of a patent must teach those skilled in the art how to make and use the full scope of the claimed invention without ‘undue experimentation.’” Genentech, Inc. v. Novo Nordisk, A/S, 108 F.3d 1361, 1365 [42 USPQ2d 1001] (Fed. Cir. 1997). (Emphasis added)
For purposes of examination, the aspect of just what constitutes the “full scope” of the claims is that which is consistent with the broadest reasonable interpretation. See MPEP 904.01 and In re Morris, 127 F.3d 1048, 44 USPQ2d 1023 (Fed. Cir. 1997). See MPEP § 2111 - § 2116.01 for case law pertinent to claim analysis.
As set forth in the unanimous U.S. Supreme Court decision in Amgen Inc., et al. v. Sanofi et al. 598 U.S. ___ (2023):
Our decisions in Morse, Incandescent Lamp, and Holland Furniture reinforce the simple
statutory command. If a patent claims an entire class of processes, machines,
manufactures, or compositions of matter, the patent’s specification must enable a person skilled in the art to make and use the entire class. In other words, the specification must enable the full scope of the invention as defined by its claims. The more one claims, the more one must enable. See §112(a); see also Continental Paper Bag Co. v. Eastern Paper Bag Co., 210 U. S. 405, 419 (1908) (“[T]he claims measure the invention.”). (Emphasis added)
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To be fair, Amgen does not dispute this much. It freely admits that it seeks to claim for
itself an entire universe of antibodies. Still, it says, its broad claims are enabled because scientists can make and use every undisclosed but functional antibody if they simply follow the company’s “roadmap” or its proposal for “conservative substitution.” We cannot agree. These two approaches amount to little more than two research assignments… Whether methods like a “roadmap” or “conservative substitution” might suffice to enable other claims in other patents—perhaps because, as this Court suggested in Incandescent Lamp, the inventor identifies a quality common to every functional embodiment, supra, at 13—they do not here. They leave a scientist about where Sawyer and Man left Edison: forced to engage in “painstaking experimentation” to see what works. 159 U. S., at 475. That is not enablement. More nearly, it is “a hunting license.” Brenner v. Manson, 383 U. S. 519, 536 (1966). (Emphasis added)
It is further noted that “routine experimentation is ‘not without bounds.’” Wyeth v. Abbott Laboratories 107 USPQ2d 1273, 1275, 1276 (Fed. Cir. June 2013), citing Cephalon, Inc. v. Watson Pharm., Inc., 707 F.3d 1330, 1339 [105 USPQ2d 1817] (Fed. Cir. 2013), and that what constitutes "undue experimentation" can be evaluated from the perspective of the amount of time required to enable the full scope of the invention. In support of this position, attention is directed to Cephalon at 1823, citing White Consol. Indus., Inc. v. Vega Servo-Control, Inc., 218 USPQ 961 (Fed. Cir. 1983), that work that would require 18 months to 2 years so to enable the full scope of an invention, even if routine, would constitute undue experimentation. As stated therein:
Permissible experimentation is, nevertheless, not without bounds. This court has held that experimentation was unreasonable, for example, where it was found that eighteen months to two years’ work was required to practice the patented invention. See, e.g., White Consol. Indus., Inc. v. Vega Servo-Control, Inc., 713 F.2d 788, 791 [218 USPQ 961] Fed. Cir.1983). (Emphasis added)
Holding and Rationale
Claims 1, 5, 7, 8, 12, 15, 16, 18-20, 25, 30, 33, 36, 37, 39-45, 48, 53-57, and 89 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for analyzing a biological sample that comprises nucleic acid and wherein one uses nucleic acid probes that comprise a barcode, does not reasonably provide enablement for analyzing any and all types of analytes present in any cell in any biological sample wherein the analysis encompasses the use of any and all manner of binding moiety. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
As set forth in Cephalon Inc. v. Watson Pharmaceuticals Inc. 105 USPQ2d 1817, 1821 (CAFC, 2013):
To satisfy section 112 of the 1952 Patent Act, the specification must enable a person of ordinary skill in the art to make and use the invention. 35 U.S.C. § 112, ¶1. This requirement is met when at the time of filing the application one skilled in the art, having read the specification, could practice the invention without “undue experimentation.” In re Wands, 858 F.2d 731, 736-37 [8 USPQ2d 1400] (Fed. Cir. 1988). Whether undue experimentation is required “is not a single, simple factual determination, but rather is a conclusion reached by weighing many factual considerations.” ALZA Corp. v. Andrx Pharms., LLC, 603 F.3d 935, 940 [94 USPQ2d 1823] (Fed. Cir. 2010) (citing Wands, 858 F.2d at 737).
The following factors may be considered when determining if a disclosure requires undue experimentation:
(1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims.
Wands, 858 F.2d at 737 (“Wands factors”); Enzo Biochem, Inc. v. Calgene, Inc., 188 F.3d 1362, 1372 [52 USPQ2d 1129] (Fed. Cir. 1999) (“The Wands factors, when applied from the proper temporal perspective … are a useful methodology for determining enablement….”). These factors while illustrative are not mandatory. Enzo Biochem, Inc., 188 F.3d at 1371. What is relevant depends on the facts, and although experimentation must not be undue, a reasonable amount of routine experimentation required to practice a claimed invention does not violate the enablement requirement. Id. The burden of proof here is on Watson to show that the Khankari patents are invalid for lack of enablement by clear and convincing evidence. See Auto. Tech. Int'l, Inc. v. BMW of N. Am., Inc., 501 F.3d 1274, 1281 [84 USPQ2d 1109] (Fed. Cir. 2007).
The breadth of the claims; The nature of the invention; and The state of the prior art
Claim 1 is the only independent claim pending. For convenience, claim 1 and dependent claims 41-43, 53, 56, and 57 are reproduced below.
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Applicant, at page 37, paragraph [0106], provides the following definition for “analyte”. As stated therein:
Analytes may include, but are not limited to, a protein, a receptor, an antigen, a surface protein, a transmembrane protein, a cluster of differentiation protein, a protein channel, a protein pump, a carrier protein, a phospholipid, a glycoprotein, a glycolipid, a cell-cell interaction protein complex, an antigen-presenting complex, a major histocompatibility complex, an engineered T-cell receptor, a T-cell receptor, a B-cell receptor, a chimeric antigen receptor, a gap junction, an adherens junction, or any combination thereof. In some instances, cell features may include intracellular analytes, such as proteins, protein modifications (e.g., phosphorylation status or other post-translational modifications), nuclear proteins, nuclear membrane proteins, or any combination thereof. In some
embodiments, the method comprises one or more post-fixing (also referred to as post-fixation) steps after contacting the sample with one or more labeling agents. (Emphasis added)
As seen in claim 1, “the first probe and the second probe directly or indirectly bind to the first analyte and the second analyte”. Applicant, at page 37, paragraph [0107], provides the following definition for analyte binding moiety.
A binding moiety may include, but is not limited to, a protein, a peptide, an antibody ( or an epitope binding fragment thereof), a lipophilic moiety (such as cholesterol), a cell surface receptor binding molecule, a receptor ligand, a small molecule, a bi-specific antibody, a bi-specific T-cell engager, a T-cell receptor engager, a B-cell receptor engager, a pro-body, an aptamer, a monobody, an affimer, a darpin, and a protein scaffold, or any combination thereof. The binding moiety can be directly or indirectly attached to a reporter oligonucleotide that is indicative of the analyte or feature to which
the binding moiety binds. (Emphasis added)
As evidenced above, the binding moiety can be an antibody of any type as well as “an epitope binding fragment thereof”, as well as an aptamer.
Applicant, at page 38, paragraph [0108], teaches:
[0108] In some embodiments, an analyte binding moiety comprises one or more nucleic acid moieties. The one or more nucleic acid moieties can specifically bind to a target analyte, e.g., a target nucleic acid via nucleic acid hybridization. In some embodiments, an analyte binding moiety comprises one or more antibodies or epitope-binding fragments thereof. The antibodies or epitope-binding fragments including the analyte binding moiety can specifically bind to a target analyte. In some embodiments, the analyte is a protein ( e.g., a protein on a surface of the biological sample (e.g., a cell) or an intracellular protein). (Emphasis added)
Applicant, at page 94, paragraph [0235], asserts:
A biological sample can also be obtained from a eukaryote, such as a tissue sample, a patient derived organoid (PDQ) or patient derived xenograft (PDX). A biological sample from an organism may comprise one or more other organisms or components therefrom. For example, a mammalian tissue section may comprise a prion, a viroid, a virus, a bacterium, a fungus, or components from other organisms, in addition to mammalian cells and non-cellular tissue components. (Emphasis added)
Applicant, at pages 95-96, paragraphs [0239] - [0242], asserts:
[0239] The biological sample can include any number of macromolecules, for example, cellular macromolecules and organelles (e.g., mitochondria and nuclei). The biological sample can be obtained as a tissue sample, such as a tissue section, biopsy, a core biopsy, needle aspirate, or fine needle aspirate. The sample can be a fluid sample, such as a blood sample, urine sample, or saliva sample. The sample can be a skin sample, a colon sample, a cheek swab, a histology sample, a histopathology sample, a plasma or serum sample, a tumor sample, living cells, cultured cells, a clinical sample such as, for example, whole blood or blood-derived products, blood cells, or cultured tissues or cells, including cell suspensions. In some embodiments, the biological sample may comprise cells which are deposited on a surface. In some embodiments, the biological sample may comprises transcripts of antigen receptor molecules. (Emphasis added)
[0240] Biological samples can be derived from a homogeneous culture or population of the subjects or organisms mentioned herein or alternatively from a collection of several different organisms, for example, in a community or ecosystem. (Emphasis added)
[0241] Biological samples can include one or more diseased cells. A diseased cell can have altered metabolic properties, gene expression, protein expression, and/or morphologic features. Examples of diseases include inflammatory disorders, metabolic disorders, nervous system disorders, and cancer. Cancer cells can be derived from solid tumors, hematological malignancies, cell lines, or obtained as circulating tumor cells. Biological samples can also include fetal cells and immune cells.
[0242] Biological samples can include analytes ( e.g., protein, RNA, and/or DNA)
embedded in a 3D matrix. In some embodiments, amplicons ( e.g., rolling circle amplification products) derived from or associated with analytes (e.g., protein, RNA, and/or DNA) can be embedded in a 3D matrix. In some embodiments, a 3D matrix may comprise a network of natural molecules and/or synthetic molecules that are chemically and/or enzymatically linked, e.g., by crosslinking. In some embodiments, a 3D matrix may comprise a synthetic polymer. In some embodiments, a 3D matrix comprises a hydrogel.
As evidenced above, the “biological sample” can be virtually biological sample, including that which is found in any ecosystem.
Attention is directed to the following publications which teach of the enormity of the subphylum Vertebrata as well as the enormity of the genera of virus, plants, insects, bacteria, mammals, and species encompassed by the subfamily Murinae as the detection of any and all genes from all members of the various genera are encompassed by the instant claims.
“Vertebrate” (Wikipedia.com, accessed 04 September 2025) teaches:
Vertebrates (j'v3:rtabrit, - ~~.!!D, also called Craniates, are animals with a vertebral column and a cranium. The vertebral column surrounds and protects the spinal cord, while the cranium protects the brain.
The vertebrates make up the sub hylum Vertebrata ({ V3:rta'bre,ta/ VUR-ta-BRAY-ta) with some 65,000 species, by far the largest ranked grouping in the phylum Chordata. The vertebrates include mammals, birds, amphibians, and various classes of fish and reptiles. (Emphasis added)
“Viruses” (Wikipedia.com, accessed 08 September 2023), teaches:
An enormous variety of genomic structures can be seen among viral species; as a group, they contain more structural genomic diversity than plants, animals, archaea, or bacteria. There are millions of different types of viruses, although fewer than 7,000 types have been described in detail. (Emphasis added)
“How many species of bacteria are there” (wisegeek.com; accessed 21 January 2014) teaches:
Currently, estimates of the total number of species of bacteria range from about 10 million to a billion, but these estimates are tentative, and may be off by many orders of magnitude. By comparison, there are probably between 10 and 30 million species of animals, the vast majority of them insects. The number of scientifically recognized species of animals is about 1,250,000. There are almost 300,000 recognized species of plants.
“Fungi,” (Wikipedia.com; accessed 08 September 2023), teaches:
As of 2020, around 148,000 species of fungi have been described by taxonomists,[6] but the global biodiversity of the fungus kingdom is not fully understood.[48] A 2017 estimate suggests there may be between 2.2 and 3.8 million species.[5]
“Insect”, (Wikipedia.com; accessed 09/10/2020) teaches:
Insects are the most diverse group of animals; they include more than a million described species and represent more than half of all known living organisms. The total number of extant species is estimated at between six and ten million; potentially over 90% of the animal life forms on Earth are insects.
“Plant,” (Wikipedia.com; accessed 08 September 2023) teaches:
There are about 380,000 known species of plants, of which the majority, some 260,000, produce seeds.
“Mammal,” (Wikipedia.com; accessed 08 September 2023) teaches:
According to Mammal Species of the World, which is updated through periodic editions, 5,416 species were identified in 2006. These were grouped into 1,229 genera, 153 families and 29 orders.[5]
“Murinae,” (Wikipedia.com, accessed 10 June 2024) teaches:
The Old World rats and mice, part of the subfamily Murinae in the family Muridae, comprise at least 519 species. Members of this subfamily are called murines. In terms of species richness, this subfamily is larger than all mammal families except the Cricetidae and Muridae, and is larger than all mammal orders except the bats and the remainder of the rodents.
“Fish,” (Wikipedia.com, accessed 08 September 2023) teaches:
Fish are abundant in most bodies of water. They can be found in nearly all aquatic environments, from high mountain streams (e.g., char and gudgeon) to the abyssal and even hadal depths of the deepest oceans (e.g., cush-eels and snailfish), although no species has yet been documented in the deepest 25% of the ocean.[4] At 34,300 described species, fish exhibit greater species diversity than any other group of vertebrates.[5]
“Archaea,” Wikipedia.com (accessed 08 September 2023), teaches:
The classification of archaea into species is also controversial. Ernst Mayr defined a species as a group of interbreeding organisms which are reproductively isolated, but this is of no help since archaea only reproduce asexually.[37]
Archaea show high levels of horizontal gene transfer between lineages. Some researchers suggest that individuals can be grouped into species-like populations given highly similar genomes and infrequent gene transfer to/from cells with less-related genomes, as in the genus Ferroplasma.[38] On the other hand, studies in Halorubrum found significant genetic transfer to/from less-related populations, limiting the criterion's applicability. Some researchers question whether such species designations have practical meaning.[40]
Current knowledge on genetic diversity is fragmentary, so the total number of species cannot be estimated with any accuracy.[22] (Emphasis added)
“Algae,” Wikipedia.com (accessed 03-04-2016) teaches:
The most recent estimate suggests 72,500 algal species worldwide.
“Protozoa,” Wikipedia.com (accessed 05-11-2016), teaches:
The classification of protozoa has been and remains a problematic area of taxonomy. Where they are available, DNA sequences are used as the basis for classification; however, for the majority of described protozoa, such material is not available. (Emphasis added)
Attention is directed to “Eukaryotic Genome Complexity” (Pray, Nature Education, 1(1):36, 2008, pages 1-4.). As seen therein, a table of estimated protein encoding genes in different genomes is provided.
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The quantity of experimentation necessary
The quantity of experimentation necessary is great, on the order of many man-years, and then with little if any reasonable expectation of successfully enabling the full scope of the claims. In support of this position, it is noted that the art suggests that there are millions of species of viruses and fungi that are yet to be identified and characterized. Assuming, arguendo, that one were to identify a new virus or fungus every day, 365 days a year, and to also determine in the same day the nucleotide sequence of the genome of said organism, and additionally, identify probes and primers that would be useful in the identification of a target sequence found in said new organism wherein said target sequence has utility under 35 USC 101, it would take approximately 2739 years to sequence even 1 million viruses or fungi. Clearly, such an effort to enable the full scope of that claimed would constitute undue experimentation. In support of this position attention is directed to Cephalon, 1823:
Permissible experimentation is, nevertheless, not without bounds. This court has held that experimentation was unreasonable, for example, where it was found that eighteen months to two years’ work was required to practice the patented invention. See, e.g., White Consol. Indus., Inc. v. Vega Servo-Control, Inc., 713 F.2d 788, 791 [218 USPQ 961] (Fed. Cir. 1983). Likewise, we have held that the amount of experimentation would be undue where: (1) the specification lacks guidance by teaching away from the subject matter that was eventually claimed; and (2) there is evidence of the patentee's own failures to make and use the later claimed invention at the time of the application. See, e.g., AK Steel Corp. v. Sollac, 344 F.3d 1234, 1244 [68 USPQ2d 1280] (Fed. Cir. 2003)
Alternatively, even if the claimed method was limited to the detection of known organisms, the selection of probes and primers would also constitute undue experimentation. In support of this position, it is noted that if one were to utilize a probe or primer that was but 20 nucleotides long, and to then substitute each of the positions with the four common dNTPs, there are some 420, or 1.099 x 1012 different sequences to screen/evaluate. In support of the position that to screen such a number of candidate molecules would constitute undue experimentation, attention is directed to Wyeth v. Abbott Laboratories 107 USPQ2d 1273, 1276 (Fed. Cir. June 2013):
The remaining question is whether having to synthesize and screen each of at least tens of thousands of candidate compounds constitutes undue experimentation. We hold that it does. Undue experimentation is a matter of degree. Chiron Corp. v. Genentech, Inc., 363 F.3d 1247, 1253 [70 USPQ2d 1321] (Fed. Cir. 2004) (internal quotation omitted). Even “a considerable amount of experimentation is permissible,” as long as it is “merely routine” or the specification “provides a reasonable amount of guidance” regarding the direction of experimentation. Johns Hopkins Univ. v. CellPro, Inc., 152 F.3d 1342, 1360-61 [47 USPQ2d 1705] (Fed. Cir. 1998) (internal quotation omitted). Yet, routine experimentation is “not without bounds.” Cephalon, Inc. v. Watson Pharm., Inc., 707 F.3d 1330, 1339 [105 USPQ2d 1817] (Fed. Cir. 2013). (Emphasis added)
Our cases have described limits on permissible experimentation in the context of enablement. For example, in ALZA Corp. v. Andrx Pharmaceuticals, LLC, we affirmed a judgment of nonenablement where the specification provided “only a starting point, a direction for further research.” 603 F.3d 935, 941 [94 USPQ2d 1823] (Fed. Cir. 2010) (internal quotation omitted). We concluded that one of ordinary skill “would have been required to engage in an iterative, trial-and-error process to practice the claimed invention even with the help of the … specification.” Id. at 943. In Cephalon, although we ultimately reversed a finding of nonenablement, we noted that the defendant had not established that required experimentation “would be excessive, e.g., that it would involve testing for an unreasonable length of time.” 707 F.3d at 1339 (citing White Consol. Indus., Inc. v. Vega Servo-Control, Inc., 713 F.2d 788, 791 [218 USPQ 961] (Fed. Cir. 1983)). Finally, in In re Vaeck, we affirmed the PTO's nonenablement rejection of claims reciting heterologous gene expression in as many as 150 genera of cyanobacteria. 947 F.2d 488, 495-96 [20 USPQ2d 1438] (Fed. Cir. 1991). The specification disclosed only nine genera, despite cyanobacteria being a “diverse and relatively poorly understood group of microorganisms,” with unpredictable heterologous gene expression. Id. at 496. (Emphasis added)
Here, the specification similarly discloses only a starting point for further iterative research in an unpredictable and poorly understood field. Synthesizing candidate compounds derived from sirolimus could, itself, require a complicated and lengthy series of experiments in synthetic organic chemistry. Even putting the challenges of synthesis aside, one of ordinary skill would need to assay each of at least tens of thousands of candidates. Wyeth's expert conceded that it would take technicians weeks to complete each of these assays. The specification offers no guidance or predictions about particular substitutions that might preserve the immunosuppressive and antirestenotic effects observed in sirolimus. The resulting need to engage in a systematic screening process for each of the many rapamycin candidate compounds is excessive experimentation. We thus hold that there is no genuine dispute that practicing the full scope of the claims, measured at the filing date, required undue experimentation. (Emphasis added)
As evidenced above, the analyte can be a “non-nucleic acid analyte” (claim 53). As seen in paragraph [0108], the “analyte binding moiety comprises one or more antibodies or epitope-binding fragments thereof” as well as an aptamer. The claimed method does not limit the type and source of antibody or fragment thereof that may be used. Attention is directed to US 6,300,093 B1 (Kindsvogel et al.), which teaches at column 22, last paragraph:
Antibodies of the present invention may be produced by immunizing an animal, a wide variety of warm-blooded animals such as horses, cows, goats, sheep, dogs, chickens, rabbits, mice, and rats can be used, with a recombinant or synthetic islet cell antigen polypeptide or a selected portion thereof (e.g., a peptide).
Attention is also directed to US 2003/0092624 A1 (Wang et al.). As disclosed at paragraph [0194]:
[0194] According to yet an additional aspect of the present invention there is provided an antibody, either polyclonal or monoclonal antibody, recognizing at least one epitope of the polypeptide described herein. The present invention can utilize serum immunoglobulins, polyclonal antibodies or fragments thereof, (i.e., immunoreactive derivative of an antibody), or monoclonal antibodies or fragments thereof. Monoclonal antibodies or purified fragments of the monoclonal antibodies having at least a portion of an antigen binding region, including, such as, Fv, F(ab1)2, Fab fragments (Harlow and Lane, 1988 Antibody, Cold Spring Harbor), single chain antibodies (U.S. Pat. No. 4,946,778), chimeric or humanized antibodies and complementarily determining regions (CDR)… Antibodies of the IgG class are made up of four polypeptide chains linked together by disulfide bonds. The four chains of intact IgG molecules are two identical heavy chains referred to as H-chains and two identical light chains referred to as L-chains. Additional classes includes IgD, IgE, IgA, IgM and related proteins. (Emphasis added)
Attention is also directed to US 2013/0338038 A1 (DuBridge et al.), which teaches the following at paragraph [0061]:
[0061] Examples of suitable sources for immunoglobulin genes include, but are not limited to, humans, primates, rodents (e.g., rat, mouse, hamster, guinea pig, etc.), non-rodents such as sheep, donkey, goat, horse, cow, pig, chicken, llama, camel, dog, cat, rabbit, fish, and birds. In addition to immunoglobulins obtained from various organisms, variant forms of known antibodies can be used, including humanized, chimeric, and monoclonal antibodies. Further, the immunoglobulin molecules or antibodies of the invention can be of any type (e.g., IgG, IgE, IgM, IgD, IgA, and IgY), class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2), or subclass of immunoglobulin molecule. (Emphasis added)
The claimed method has been construed as encompassing antibodies to any target, and which can be of any type and produced via any source.
As can be seen in “Custom Antibody Services” from Precision Antibody (2014), monoclonal antibody can be obtained in “40 to 60 days”. As evidenced above, it has been held that 18 months to 2 years of experimentation to enable the full scope of the claimed invention was held to be an unreasonable amount of time and effort. In using the 18 months as a standard, and converting 18 months to days, using 30 days/month, such would convert to 540 days. Using 40 days to obtain a single monoclonal antibody, one would obtain 13.5 monoclonal antibodies in 540 days. As evidenced above, there are many millions of organisms, each of which comprises numerous different “analytes”. Given such, it stands to reason that one would not enable the invention for all analytes found in just one organism encompassed by applicant’s “biological sample”, much less enable all types of antibodies (e.g., IgG, IgE, IgM, IgD, IgA, and IgY), and class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2), and antibody fragments (Fv, F(ab1)2, Fab) produced in all known sources/organisms, for each of the analytes. As seen in claim 1, one is to detect “a first analyte and a second analyte”. Such effectively compounds the amount of time and effort needed to enable the full scope of the claimed invention.
The amount of direction or guidance presented,
The amount of guidance provided is limited, generally prophetic, and not commensurate with the scope of the claims.
The presence or absence of working examples
The disclosure has been found to comprise the following 4 examples:
“Example 1: Dark bases”, page 127;
“Example 2: Use of different nucleotide mixtures during cycles of decoding”, page 130;
“Example 3: Method of using a common sequencing primer to decode a given block of different analytes”, page 132; and
“Example 4: Method of using multiple sequencing primers to decode the same analyte”, page 134.
The predictability or unpredictability of the art
The sequences of nucleic acid targets and the epitopes of proteins, much less the epitopes of non-nucleic acid targets and non-amino acid targets is highly unpredictable.
While the aspect of hybridization between complementary nucleic acid sequences is understood, the sequences of the nucleic acids, be it DNA or RNA, as found in any organism, is highly unpredictable
As noted in In re Fisher 166 USPQ 18 (CCPA, 1970):
In cases involving predictable factors, such as that, once imagined, other embodiments can be made without difficulty and their performance characteristics predicted by resort to known scientific laws. In cases involving unpredictable factors, such as most chemical reactions and physiological activity, the scope of enablement obviously varies inversely with the degree of unpredictability of the factors involved.
Attention is also directed to Wyeth v. Abbott Laboratories 107 USPQ2d 1273 (Fed. Cir. June 2013):
The remaining question is whether having to synthesize and screen each of at least tens of thousands of candidate compounds constitutes undue experimentation. We hold that it does. Undue experimentation is a matter of degree. Chiron Corp. v. Genentech, Inc., 363 F.3d 1247, 1253 [70 USPQ2d 1321] (Fed. Cir. 2004) (internal quotation omitted). Even “a considerable amount of experimentation is permissible,” as long as it is “merely routine” or the specification “provides a reasonable amount of guidance” regarding the direction of experimentation. Johns Hopkins Univ. v. CellPro, Inc., 152 F.3d 1342, 1360-61 [47 USPQ2d 1705] (Fed. Cir. 1998) (internal quotation omitted). Yet, routine experimentation is “not without bounds.” Cephalon, Inc. v. Watson Pharm., Inc., 707 F.3d 1330, 1339 [105 USPQ2d 1817] (Fed. Cir. 2013).
Our cases have described limits on permissible experimentation in the context of enablement. For example, in ALZA Corp. v. Andrx Pharmaceuticals, LLC, we affirmed a judgment of nonenablement where the specification provided “only a starting point, a direction for further research.” 603 F.3d 935, 941 [94 USPQ2d 1823] (Fed. Cir. 2010) (internal quotation omitted). We concluded that one of ordinary skill “would have been required to engage in an iterative, trial-and-error process to practice the claimed invention even with the help of the … specification.” Id. at 943. In Cephalon, although we ultimately reversed a finding of nonenablement, we noted that the defendant had not established that required experimentation “would be excessive, e.g., that it would involve testing for an unreasonable length of time.” 707 F.3d at 1339 (citing White Consol. Indus., Inc. v. Vega Servo-Control, Inc., 713 F.2d 788, 791 [218 USPQ 961] (Fed. Cir. 1983)). Finally, in In re Vaeck, we affirmed the PTO's nonenablement rejection of claims reciting heterologous gene expression in as many as 150 genera of cyanobacteria. 947 F.2d 488, 495-96 [20 USPQ2d 1438] (Fed. Cir. 1991). The specification disclosed only nine genera, despite cyanobacteria being a “diverse and relatively poorly understood group of microorganisms,” with unpredictable heterologous gene expression. Id. at 496.
Here, the specification similarly discloses only a starting point for further iterative research in an unpredictable and poorly understood field. Synthesizing candidate compounds derived from sirolimus could, itself, require a complicated and lengthy series of experiments in synthetic organic chemistry. Even putting the challenges of synthesis aside, one of ordinary skill would need to assay each of at least tens of thousands of candidates. Wyeth's expert conceded that it would take technicians weeks to complete each of these assays. The specification offers no guidance or predictions about particular substitutions that might preserve the immunosuppressive and antirestenotic effects observed in sirolimus. The resulting need to engage in a systematic screening process for each of the many rapamycin candidate compounds is excessive experimentation. We thus hold that there is no genuine dispute that practicing the full scope of the claims, measured at the filing date, required undue experimentation.
In view of the breadth of scope clamed, the limited guidance provided, the unpredictable nature of the art to which the claimed invention is directed, and in the absence of convincing evidence to the contrary, the claims are deemed to be non-enabled by the disclosure.
In view of the above analysis and in the absence of convincing evidence to the contrary, claims 1, 5, 7, 8, 12, 15, 16, 18-20, 25, 30, 33, 36, 37, 39-45, 48, 53-57, and 89 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement.
Claim Rejections - 35 USC § 112, Written Description
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Standard for Written Description.
Attention is directed to MPEP 2163.02 Standard for Determining Compliance With the Written Description Requirement [R-07-2022]:
An objective standard for determining compliance with the written description requirement is, "does the description clearly allow persons of ordinary skill in the art to recognize that he or she invented what is claimed." In re Gosteli, 872 F.2d 1008, 1012, 10 USPQ2d 1614, 1618 (Fed. Cir. 1989). Under Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Fed. Cir. 1991), to satisfy the written description requirement, an applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention, and that the invention, in that context, is whatever is now claimed. (Emphasis added)
Attention is also set directed to MPEP 2161.01 I [R-07-2022], wherein is stated:
For instance, generic claim language in the original disclosure does not satisfy the written description requirement if it fails to support the scope of the genus claimed. Ariad, 598 F.3d at 1349-50, 94 USPQ2d at 1171 ("[A]n adequate written description of a claimed genus requires more than a generic statement of an invention’s boundaries.") (citing Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1405-06); Enzo Biochem, Inc. v. Gen-Probe, Inc., 323 F.3d 956, 968, 63 USPQ2d 1609, 1616 (Fed. Cir. 2002) (holding that generic claim language appearing in ipsis verbis in the original specification did not satisfy the written description requirement because it failed to support the scope of the genus claimed); Fiers v. Revel, 984 F.2d 1164, 1170, 25 USPQ2d 1601, 1606 (Fed. Cir. 1993) (rejecting the argument that "only similar language in the specification or original claims is necessary to satisfy the written description requirement").
As set forth in Fiers v. Revel 25 USPQ2d 1601, 1604-5 (CAFC, January 1993):
We thus determined that, irrespective of the complexity or simplicity of the method of isolation employed, conception of a DNA, like conception of any chemical substance, requires a definition of that substance other than by its functional utility.
Fiers' attempt to distinguish Amgen therefore is incorrect. We also reject Fiers' argument that the existence of a workable method for preparing a DNA establishes conception of that material. (Emphasis added)
Conception of a substance claimed per se without reference to a process requires conception of its structure, name, formula, or definitive chemical or physical properties...
The difficulty that would arise if we were to hold that a conception occurs when one has only an idea of a compound, defining it by its hoped-for function, is that would-be inventors would file patent applications before they had made their inventions and before they could describe them. That is not consistent with the statute or the policy behind the statute, which is to promote disclosure of inventions.
Attention is also directed to MPEP 2163 Guidelines for the Examination of Patent Applications Under the 35 U.S.C. 112(a) or Pre-AIA 35 U.S.C. 112, first paragraph, “Written Description” Requirement [R-01-2024], at part II ii):
The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice (see i)(A) above), reduction to drawings (see i)(B) above), or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the inventor was in possession of the claimed genus (see i)(C) above). See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. See Juno Therapeutics, Inc. v. Kite Pharma, Inc., 10 F.4th 1330, 1337, 2021 USPQ2d 893 (Fed. Cir. 2021) ( "[T]he written description must lead a person of ordinary skill in the art to understand that the inventor possessed the entire scope of the claimed invention. Ariad, 598 F.3d at 1353–54 ('[T]he purpose of the written description requirement is to ensure that the scope of the right to exclude, as set forth in the claims, does not overreach the scope of the inventor's contribution to the field of art as described in the patent specification.' (internal quotation marks omitted).") (Emphasis added)
Attention is also directed to the decision of University of California v. Eli Lilly and Co. (CA FC, July 1997) 43 USPQ2d 1398 wherein is stated:
In claims involving chemical materials, generic formulas usually indicate with specificity what the generic claims encompass. One skilled in the art can distinguish such a formula from others and can identify many of the species that the claims encompass. Accordingly, such a formula is normally an adequate written description of the claimed genus. In claims to genetic material, however, a generic statement such as “vertebrate insulin cDNA” or “mammalian cDNA,” without more, is not an adequate written description of the genus because it does not distinguish the claimed genus from others, except by function. It does not specifically define any of the genes that fall within its definition. It does not define any structural features commonly possessed by members of the genus that distinguish them from others. One skilled in the art therefore cannot, as one can do with a fully described genus, visualize or recognize the identity of the members of the genus. A definition by function, as we have previously indicated, does not suffice to define the genus because it is only an indication of what the gene does, rather than what it is See Fiers, 984 F.2d at 1169-71, 25 USPQ2d at 1605-06 (discussing Amgen). It is only a definition of a useful result rather than a definition of what it achieves as a result. Many such genes may achieve that result. The description requirement of the patent statute requires a description of an invention, not an indication of a result that one might achieve if one made that invention. See In re Wilder, 736 F.2d 1516, 222 USPQ 369, 372-373 (Fed. Cir. 1984) (affirming rejection because the specification does “little more than outlin[e] goals appellants hope the claimed invention achieves and the problems the invention will hopefully ameliorate.”). Accordingly, naming a type of material generally known to exist, in the absence of knowledge as to what that material consists of, is not a description of that material.
Thus, as we have previously held, a cDNA is not defined or described by the mere name cDNA,” even if accompanied by the name of the protein that it encodes, but requires a kind of specificity usually achieved by means of the recitation of the sequence of nucleotides that make up the cDNA. See Fiers, 984 F.2d at 1171, 25 USPQ2d at 1606.
Acknowledgement is made of the fact that the claims are to a method and not to a product. However, it is well settled that in order to satisfy the written description for a method, one must also disclose the molecules required to perform the method. In support of this position attention is directed to University of Rochester v. G.D. Searle & Co. 68 USPQ2D 1424 (W.D.N.Y. 2003) at 1433 (affirmed; University of Rochester v. G.D. Searle & Co. 69 USPQ2d 1886 (Fed. Cir. 2004)):
Plaintiff also argues that the requirements for written descriptions of claims to chemical compounds are irrelevant to this case because the '850 patent does not claim a compound, but a method of treatment by targeting PGHS-2 activity over PGHS-1 activity. Virtually any compound claim could be transformed into a method claim, however, simply by means of wording the claim in terms of a method of using the compound. With respect to the issue before the Court, then, this is little more than a semantic distinction without a difference. The claimed method depends upon finding a compound that selectively inhibits PGHS-2 activity. Without such a compound, it is impossible to practice the claimed method of treatment. It means little to “invent” a method if one does not have possession of a substance that is essential to practicing that method. Without that substance, the claimed invention is more theoretical than real; it is, as defendants argue, akin to “inventing” a cure for cancer by utilizing a substance that attacks and destroys cancer cells while leaving healthy cells alone. Without possession of such a substance, such a “cure” is illusory, and there is no meaningful possession of the method.
***
What the inventors did not do, however, is succeed in taking the last, critical step of actually isolating such a compound, or at least of developing a process through which one skilled in the art would be directly led to such a compound. Absent that step, their discoveries, valuable though they might have been, did not blossom into a full-fledged, complete invention. Scientific discoveries, and theories based on those discoveries, frequently lay the groundwork for later inventions, but that does not make the discoverer the inventor as well.
Attention is also directed to the decision in Ariad Pharmaceuticals Inc. v. Eli Lilly & Co.
(Fed. Cir. 2010) 94 USPQ2d 1161, 1175, which teaches:
In accordance with Rochester, the ?516 patent must adequately describe the claimed methods for reducing NF-?B activity, including adequate description of the molecules that Ariad admits are necessary to perform the methods. (Emphasis added)
Holding and Rationale
Claims 1, 5, 7, 8, 12, 15-16, 18-20, 25, 30, 33, 36, 37, 39-45, 48, 53-57, and 89 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 1 is the only independent claim pending. For convenience, claim 1 and dependent claims 41-43, 53, 56, and 57 are reproduced below.
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Applicant, at page 37, paragraph [0106], provides the following definition for “analyte”. As stated therein:
Analytes may include, but are not limited to, a protein, a receptor, an antigen, a surface protein, a transmembrane protein, a cluster of differentiation protein, a protein channel, a protein pump, a carrier protein, a phospholipid, a glycoprotein, a glycolipid, a cell-cell interaction protein complex, an antigen-presenting complex, a major histocompatibility complex, an engineered T-cell receptor, a T-cell receptor, a B-cell receptor, a chimeric antigen receptor, a gap junction, an adherens junction, or any combination thereof. In some instances, cell features may include intracellular analytes, such as proteins, protein modifications (e.g., phosphorylation status or other post-translational modifications), nuclear proteins, nuclear membrane proteins, or any combination thereof. In some
embodiments, the method comprises one or more post-fixing (also referred to as post-fixation) steps after contacting the sample with one or more labeling agents. (Emphasis added)
As can be seen above, the analyte can be virtually any chemical found in or on any organism, including those found in any ecosystem.
As seen in claim 1, “the first probe and the second probe directly or indirectly bind to the first analyte and the second analyte”. Applicant, at page 37, paragraph [0107], provides the following definition for analyte binding moiety.
A binding moiety may include, but is not limited to, a protein, a peptide, an antibody ( or an epitope binding fragment thereof), a lipophilic moiety (such as cholesterol), a cell surface receptor binding molecule, a receptor ligand, a small molecule, a bi-specific antibody, a bi-specific T-cell engager, a T-cell receptor engager, a B-cell receptor engager, a pro-body, an aptamer, a monobody, an affimer, a darpin, and a protein scaffold, or any combination thereof. The binding moiety can be directly or indirectly attached to a reporter oligonucleotide that is indicative of the analyte or feature to which
the binding moiety binds. (Emphasis added)
Applicant, at page 38, paragraph [0108], teaches:
[0108] In some embodiments, an analyte binding moiety comprises one or more nucleic acid moieties. The one or more nucleic acid moieties can specifically bind to a target analyte, e.g., a target nucleic acid via nucleic acid hybridization. In some embodiments, an analyte binding moiety comprises one or more antibodies or epitope-binding fragments thereof. The antibodies or epitope-binding fragments including the analyte binding moiety can specifically bind to a target analyte. In some embodiments, the analyte is a protein ( e.g., a protein on a surface of the biological sample (e.g., a cell) or an intracellular protein). (Emphasis added)
Applicant, at page 94, paragraph [0235], asserts:
A biological sample can also be obtained from a eukaryote, such as a tissue sample, a patient derived organoid (PDQ) or patient derived xenograft (PDX). A biological sample from an organism may comprise one or more other organisms or components therefrom. For example, a mammalian tissue section may comprise a prion, a viroid, a virus, a bacterium, a fungus, or components from other organisms, in addition to mammalian cells and non-cellular tissue components. (Emphasis added)
Applicant, at pages 95-96, paragraphs [0239] - [0242], asserts:
[0239] The biological sample can include any number of macromolecules, for example, cellular macromolecules and organelles (e.g., mitochondria and nuclei). The biological sample can be obtained as a tissue sample, such as a tissue section, biopsy, a core biopsy, needle aspirate, or fine needle aspirate. The sample can be a fluid sample, such as a blood sample, urine sample, or saliva sample. The sample can be a skin sample, a colon sample, a cheek swab, a histology sample, a histopathology sample, a plasma or serum sample, a tumor sample, living cells, cultured cells, a clinical sample such as, for example, whole blood or blood-derived products, blood cells, or cultured tissues or cells, including cell suspensions. In some embodiments, the biological sample may comprise cells which are deposited on a surface. In some embodiments, the biological sample may comprises transcripts of antigen receptor molecules. (Emphasis added)
[0240] Biological samples can be derived from a homogeneous culture or population of the subjects or organisms mentioned herein or alternatively from a collection of several different organisms, for example, in a community or ecosystem. (Emphasis added)
[0241] Biological samples can include one or more diseased cells. A diseased cell can have altered metabolic properties, gene expression, protein expression, and/or morphologic features. Examples of diseases include inflammatory disorders, metabolic disorders, nervous system disorders, and cancer. Cancer cells can be derived from solid tumors, hematological malignancies, cell lines, or obtained as circulating tumor cells. Biological samples can also include fetal cells and immune cells.
[0242] Biological samples can include analytes ( e.g., protein, RNA, and/or DNA) embedded in a 3D matrix. In some embodiments, amplicons ( e.g., rolling circle amplification products) derived from or associated with analytes (e.g., protein, RNA, and/or DNA) can be embedded in a 3D matrix. In some embodiments, a 3D matrix may comprise a network of natural molecules and/or synthetic molecules that are chemically and/or enzymatically linked, e.g., by crosslinking. In some embodiments, a 3D matrix may comprise a synthetic polymer. In some embodiments, a 3D matrix comprises a hydrogel.
As evidenced above, the “biological sample” can be virtually biological sample, including that which is found in any ecosystem.
As evidenced above, the binding moiety can be an antibody of any type as well as “an epitope binding fragment thereof”, as well as an aptamer.
Attention is directed to the following publications which teach of the enormity of the subphylum Vertebrata as well as the enormity of the genera of virus, plants, insects, bacteria, mammals, and species encompassed by the subfamily Murinae as the detection of any and all genes from all members of the various genera are encompassed by the instant claims.
“Vertebrate” (Wikipedia.com, accessed 04 September 2025) teaches:
Vertebrates (j'v3:rtabrit, - ~~.!!D, also called Craniates, are animals with a vertebral column and a cranium. The vertebral column surrounds and protects the spinal cord, while the cranium protects the brain.
The vertebrates make up the sub hylum Vertebrata ({ V3:rta'bre,ta/ VUR-ta-BRAY-ta) with some 65,000 species, by far the largest ranked grouping in the phylum Chordata. The vertebrates include mammals, birds, amphibians, and various classes of fish and reptiles. (Emphasis added)
“Viruses” (Wikipedia.com, accessed 08 September 2023), teaches:
An enormous variety of genomic structures can be seen among viral species; as a group, they contain more structural genomic diversity than plants, animals, archaea, or bacteria. There are millions of different types of viruses, although fewer than 7,000 types have been described in detail. (Emphasis added)
“How many species of bacteria are there” (wisegeek.com; accessed 21 January 2014) teaches:
Currently, estimates of the total number of species of bacteria range from about 10 million to a billion, but these estimates are tentative, and may be off by many orders of magnitude. By comparison, there are probably between 10 and 30 million species of animals, the vast majority of them insects. The number of scientifically recognized species of animals is about 1,250,000. There are almost 300,000 recognized species of plants.
“Fungi,” (Wikipedia.com; accessed 08 September 2023), teaches:
As of 2020, around 148,000 species of fungi have been described by taxonomists,[6] but the global biodiversity of the fungus kingdom is not fully understood.[48] A 2017 estimate suggests there may be between 2.2 and 3.8 million species.[5]
“Insect”, (Wikipedia.com; accessed 09/10/2020) teaches:
Insects are the most diverse group of animals; they include more than a million described species and represent more than half of all known living organisms. The total number of extant species is estimated at between six and ten million; potentially over 90% of the animal life forms on Earth are insects.
“Plant,” (Wikipedia.com; accessed 08 September 2023) teaches:
There are about 380,000 known species of plants, of which the majority, some 260,000, produce seeds.
“Mammal,” (Wikipedia.com; accessed 08 September 2023) teaches:
According to Mammal Species of the World, which is updated through periodic editions, 5,416 species were identified in 2006. These were grouped into 1,229 genera, 153 families and 29 orders.[5]
“Murinae,” (Wikipedia.com, accessed 10 June 2024) teaches:
The Old World rats and mice, part of the subfamily Murinae in the family Muridae, comprise at least 519 species. Members of this subfamily are called murines. In terms of species richness, this subfamily is larger than all mammal families except the Cricetidae and Muridae, and is larger than all mammal orders except the bats and the remainder of the rodents.
“Fish,” (Wikipedia.com, accessed 08 September 2023) teaches:
Fish are abundant in most bodies of water. They can be found in nearly all aquatic environments, from high mountain streams (e.g., char and gudgeon) to the abyssal and even hadal depths of the deepest oceans (e.g., cush-eels and snailfish), although no species has yet been documented in the deepest 25% of the ocean.[4] At 34,300 described species, fish exhibit greater species diversity than any other group of vertebrates.[5]
“Archaea,” Wikipedia.com (accessed 08 September 2023), teaches:
The classification of archaea into species is also controversial. Ernst Mayr defined a species as a group of interbreeding organisms which are reproductively isolated, but this is of no help since archaea only reproduce asexually.[37]
Archaea show high levels of horizontal gene transfer between lineages. Some researchers suggest that individuals can be grouped into species-like populations given highly similar genomes and infrequent gene transfer to/from cells with less-related genomes, as in the genus Ferroplasma.[38] On the other hand, studies in Halorubrum found significant genetic transfer to/from less-related populations, limiting the criterion's applicability. Some researchers question whether such species designations have practical meaning.[40]
Current knowledge on genetic diversity is fragmentary, so the total number of species cannot be estimated with any accuracy.[22] (Emphasis added)
“Algae,” Wikipedia.com (accessed 03-04-2016) teaches:
The most recent estimate suggests 72,500 algal species worldwide.
“Protozoa,” Wikipedia.com (accessed 05-11-2016), teaches:
The classification of protozoa has been and remains a problematic area of taxonomy. Where they are available, DNA sequences are used as the basis for classification; however, for the majority of described protozoa, such material is not available. (Emphasis added)
Attention is directed to “Eukaryotic Genome Complexity” (Pray, Nature Education, 1(1):36, 2008, pages 1-4.). As seen therein, a table of estimated protein encoding genes in different genomes is provided.
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A review of the disclosure does locate a Sequence Listing. Said Sequence Listing is found to comprise a total of 3 sequences, each of which is identified as being both DNA and an “Artificial Sequence”.
The disclosure has not been found to disclose the amino acid sequence for any protein, much less the amino acid sequence for any epitopes found in any protein, much less polypeptide sequence of antibodies, antibody fragments, or small molecules. Likewise, the disclosure has not been found to disclose the nucleotide sequence for aptamers that would bind to such epitopes and the disclosure has not been found to disclose the nucleotide sequence for any nucleic acid target in any organism, much less those targets that have utility under 35 USC 101.
Such nondisclosure by applicant of such essential material1 has not been found to satisfy the written description requirement, and thusly does not reasonably suggest that applicant was in possession of the full range of essential material required to practice the claimed method.
In view of the above analysis and in the absence of convincing evidence to the contrary, claims 1, 5, 7, 8, 12, 15-16, 18-20, 25, 30, 33, 36, 37, 39-45, 48, 53-57, and 89 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim 1 is rejected under 35 U.S.C. 103 as being unpatentable over US 2021/0340618 A1 (Kuhnemund et al.) in view of US 2021/0207192 A1 (Kim).
Claim 1 is reproduced below.
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The aspect of “analyzing a biological sample” has been construed as encompassing sequencing nucleic acid probes that may comprise a barcode sequence.
Kuhnemund et al., disclose methods of analyzing a biological sample that comprises nucleic acid and wherein one uses probes that comprise a barcode.
Kuhnemund et al., at paragraph [0237], teach:
[0237] Padlock probes can be provided with a barcode sequences with single base barcode subunits flanked by common spacer sequences in order to prove the principle. In this example a padlock probe against Actb was produced, with a single base difference in the middle of a common barcode sequence, RCA products were generated in vitro or in situ, inside fixed mouse brain tissue sections and were then interrogated with a set of probes targeting that single base barcode position. The barcodes were effectively decoded by a sequencing by hybridisation reaction using the detection probes. (Emphasis added)
Kuhnemund et al., at paragraph [0137], teach:
[0005] The barcode sequence may be provided directly within a target molecule, for example it may be linked directly to a target nucleic acid molecule, for example by ligation, or it may be incorporated, for example into an amplification product, e.g. by the use of a primer containing the barcode sequence, or it, or its complement, may simply be provided as part of a target molecule, e.g. where the target molecule is a probe or some other synthetic molecule
Kuhnemund et al., at paragraph [0212], teach:
[0212] The method may be for detecting multiple different nucleic acid molecules present in a sample, wherein each different nucleic acid molecule is assigned a different signal code sequence and is detected using a specific padlock probe with a different nucleotide barcode sequence. In some embodiments, a different set of subsequent detection probes is provided for each different nucleic acid molecule, each different set of detection probes yielding a different signal code sequence. (Emphasis added)
Kuhnemund et al., at paragraph [0137], teach:
A signal code sequence may be provided instead by repeatedly interrogating the same two barcode positions in turn, one to the other and back again, using detection probes provided with different reporters, which yield distinguishable signals (including absence of signal, or alternatively termed a blank or “dark” reporter). In such a method rather than detection probes which sequentially displace themselves in one direction, the detection probes are sequentially displaced in both a forward and reverse direction. (Emphasis added)
Kuhnemund et al., at paragraph [0181], teach:
[T]he target sequence may be a sequence which occurs naturally in the molecule to be detected (i.e. it can be a native sequence). Thus, a specific sequence which occurs in a target nucleic acid molecule, or in its complement, may be selected as the target nucleotide sequence. One may thus select adjacent target sequences, which have an overlapping region, and which are designated as first and second domains according to the method set out above. Each domain has two (first and second) subunits. The overlapping region may be designated as one subunit of the first and second domains, and the non-overlapping regions of the first and second domains represent the other subunit of the respective domains. Accordingly, the target nucleotide sequence may be a specific target sequence which is present in a native genomic DNA or in a naturally occurring RNA molecule, or in a cDNA or amplification product generated therefrom. In a particular embodiment, the nucleic acid molecule may be detected in situ in a cell or tissue sample.
The above showing is deemed to fairly suggest that the cell or tissue is part of a “biological sample”.
While Kuhnemund et al., has been found to teach sequencing-by-hybridization, they have not been found to teach performing base-by-base sequencing.
Kim, at paragraph [0160], teaches:
The barcode sequence generally includes certain features that make the sequence useful, e.g., in sequencing reactions. For example, the barcode sequences are designed to have minimal or no homopolymer regions, e.g., 2 or more of the same base in a row such as AA or CCC, within the barcode sequence. In some embodiments, the barcode sequences are also designed so that they are at least one edit distance away from the base addition order when performing a manipulation or molecular biological process, such as base-by-base sequencing, ensuring that the first and last bases do not match the expected bases of the sequence. (Emphasis added)
In view of the above presentation, it would have been obvious to one of ordinary skill in the art at the time of the invention to have not only designed multiple probes that not only bind to their intended targets (e.g., nucleic acid) but have designed probes so to have a barcode sequence therein allowing for the distinction of different probes by way of their code. It would have also been obvious to said ordinary artisan to have incorporated the act of sequencing base-by-base versus sequencing by hybridization as such would allow for greater accuracy in identify just what is the code for different probes, and with it, the identification of just which sequences are present in the biological sample.
In view of the above presentation and in the absence of convincing evidence to the contrary, claim 1 is rejected under 35 U.S.C. 103 as being unpatentable over US 2021/0340618 A1 (Kuhnemund et al.) in view of US 2021/0207192 A1 (Kim).
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Chen et al. (2020) (Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer's Disease, Cell, 2020 Aug 20;182(4):976-991.e19. doi: 10.1016/j.cell.2020.06.038. Epub 2020 Jul 22.
Chen et al. (2020) teaches in the abstract that
“Although complex inflammatory-like alterations are observed around the amyloid plaques of Alzheimer’s disease (AD), little is known about the molecular changes and cellular interactions that characterize this response. We investigate here, in an AD mouse model, the transcriptional changes occurring in tissue domains in a 100-mmdiameter around amyloid plaques using spatial transcriptomics. We demonstrate early alterations in a gene co-expression network enriched for myelin and oligodendrocyte genes (OLIGs), whereas a multicellular gene co-expression network of plaque-induced genes (PIGs) involving the complement system, oxidative stress, lysosomes, and inflammation is prominent in the later phase of the disease. We confirm the majority of the observed alterations at the cellular level using in situ sequencing on mouse and human brain sections. Genome-wide spatial transcriptomics analysis provides an unprecedented approach to untangle the dysregulated cellular network in the vicinity of pathogenic hallmarks of AD and other brain diseases
See “Graphical Abstract”, below.
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Chen et al. (2020) teach more detailed methodology under “EXPERIMENTAL MODEL AND SUBJECT DETAILS”
Tissue collection for Spatial Transcriptomics
OCT-embedded hemispheres were cryosectioned coronally to a thickness of 10 mm (bregma: _2.0 to _2.2) using a CryoStar NX70 cryostat (ThermoFisher). We layered tissue sections onto a spatially barcoded array to collect in situ 2D-RNaseq of Spatial Transcriptomics (Lot#10001, Spatial Transcriptomics, Stockholm, Sweden) or to a regular glass slide for immunohistochemistry. Each spatially barcoded array has 1007 TDs, with a diameter of 100 mm and a center-to-center distance of 200 mm, over an area of 6.2 mm by 6.6 mm. One coronal section normally covers the area of 500 to 600 spots on the array, each spot defining one TD. Each spot contains approximately 200 million barcoded reverse-transcription oligo(dT) primers allowing to get a global transcriptomic profile of a TD with a volume of 0.00008mm3(pr2h with r = 50 mmand h = 10 mm). After cryosection, all sections were stored at _80_C before proceeding with experiments (See page e3).
In situ sequencing and immunostaining of mouse samples
OCT-embedded hemispheres of mice at 18-month of age were cryosectioned coronally into 14 mm (bregma _2.0 to _2.2) and layered onto SuperFrost Plus glass slides (ThermoFisher) and further stored at _80_C before experiments. Samples were shipped on dry ice to CARTANA (Solna, Sweden) for tissue fixation, reverse transcription, probe ligation, rolling cycle amplification with reagents and according to the procedures supplied in the Neurokit (1010-01, CARTANA, Sweden), followed by fluorescence labeling, and sequencing by sequential images at 20X objective (Ke et al., 2013). Five probes were designed for each gene, except Itgam, which has 10 customized probes to increase the detection sensitivity. We included probes for 7 additional genes that do not belong to the PIG module but significantly react to the presence of amyloid plaques at 18-months of age in the ST analysis: Cst7, Cd68, Ccl6, Prox1, Hcrt, Pmch, and C1ql2 (LFC: 1.91, 1.70, 1.69, _1.42, _1.72, _1.83, and _2.01, respectively). Probes with design issues (H2- D1, Cd63-ps and RP23-269H21.1) are removed and probes cross-reacted with their related genes are renamed (C4a, C4b as C4, Serpina3n as Serpina3, Lyz2 as Lyz). To reduce lipofuscin autofluorescence, 1X TrueBlack (Biotium, Fremont, CA) was applied for 30 s before fluorescence labeling. The result table of the spatial coordinates of each molecule of 84 targets together with the reference DAPI image per sample were provided by CARTANA (See page e4).
As evidenced above, Chen et al., fairly teaches the methods of claim 1.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
Marx, Method of the Year: spatially resolved transcriptomics, Nat Methods, 2021 Jan;18(1):9-14. doi: 10.1038/s41592-020-01033-y.
Salas et al. Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps, BMC Bioinformatics, 2021 Jul 31;22(1):391.doi: 10.1186/s12859-021-04302-5.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Bradley L. Sisson whose telephone number is (571)272-0751. The examiner can normally be reached Monday to Thursday, from 6:30 AM to 5 PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Shen can be reached at 571-272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Bradley L. Sisson/Primary Examiner, Art Unit 1682
1 Attention is directed to 37 CFR 1.57(d), which sates in part:
(d) "Essential material" may be incorporated by reference, but only by way of an incorporation by reference to a U.S. patent or U.S. patent application publication, which patent or patent application publication does not itself incorporate such essential material by reference. "Essential material" is material that is necessary to:
(1) Provide a written description of the claimed invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and set forth the best mode contemplated by the inventor of carrying out the invention as required by 35 U.S.C. 112(a);
(2) Describe the claimed invention in terms that particularly point out and distinctly claim the invention as required by 35 U.S.C. 112(b); or
(3) Describe the structure, material, or acts that correspond to a claimed means or step for performing a specified function as required by 35 U.S.C. 112(f). (Emphasis added)
(e) Other material ("Nonessential material") may be incorporated by reference to U.S. patents, U.S. patent application publications, foreign patents, foreign published applications, prior and concurrently filed commonly owned U.S. applications, or non-patent publications. An incorporation by reference by hyperlink or other form of browser executable code is not permitted.
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