DETAILED ACTION
Applicant’s response, filed 16 July 2025 has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114 was filed in this application after a decision by the Patent Trial and Appeal Board, but before the filing of a Notice of Appeal to the Court of Appeals for the Federal Circuit or the commencement of a civil action. Since this application is eligible for continued examination under 37 CFR 1.114 and the fee set forth in 37 CFR 1.17(e) has been timely paid, the appeal has been withdrawn pursuant to 37 CFR 1.114 and prosecution in this application has been reopened pursuant to 37 CFR 1.114. Applicant’s submission filed on 17 July 2025 has been entered.
Status of Claims
Claims 5, 14-15, 17-22, and 25-26 are cancelled
Claims 1-4, 6-13, 16, 23-24, and 27-28 are pending.
Claims 1-4, 6-13, 16, 23-24, and 27-28 are rejected.
Priority
The instant application claims the benefit of priority to U.S. Provisional Application No. 62/466,807 filed 3 March 2017. Claims 1 and 10, and those claims dependent therefrom, recite “controlling incubation of the cells in the bioprocessing reactor by changing an incubation parameter of the bioprocessing reactor wherein the change in the incubation parameter occurs when the concentration of unproductive cells has been determined to have risen above a threshold value”. However, U.S. Provisional Application No. 62/466,807 does not provide any support for these limitations as there is no mention of a bioprocessing reactor or using the concentration of unproductive cells to change an incubation parameter of a bioprocessing reactor. Therefore, the claims 1 and 10, and those claims dependent therefrom, are not granted the claim to the benefit of priority to U.S. Provisional 62/466,807 filed 03 March 2017.
Accordingly, the effective filing date of the claimed invention is 25 July 2017.
Claim Interpretation
Claims 1 and 10 recite “controlling incubation of the cells in the bioprocessing reactor by changing an incubation parameter of the bioprocessing reactor wherein the change in the incubation parameter occurs when the concentration of unproductive cells has been determined to have risen above a threshold value”. This limitation makes the controlling incubation by changing on the incubation parameter contingent upon the concentration of unproductive cells being above a threshold value. However, the method claims, as currently recited, may be practiced without this condition happening, i.e. the concentration of unproductive cells could be equal to or below the threshold value. If a claimed invention can be practiced without the condition happening, then the step that is contingent upon that condition is not required to be performed and that step is not required by the broadest reasonable interpretation of the claim (see MPEP 2111.04). Therefore, under the broadest reasonable interpretation of claims 1 and 10, and those claims dependent therefrom, the step of controlling incubation by changing the incubation parameter is not required.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-4, 6-13, 16, 23-24, and 27-28 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. This rejection is previously recited.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355). Applicant is also directed to MPEP 2106.
Step 1: The instantly claimed invention (claims 1 and 10 being representative) is directed a method. Therefore, the instantly claimed invention falls into one of the four statutory categories. [Step 1: YES]
Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in in Prong Two if the recited judicial exception is integrated into a practical application of that exception.
Step 2A, Prong 1: In accordance with MPEP § 2106, claims found to recite statutory subject matter are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon.
In the instant application, the claims recite the following limitations that equate to one or more categories of judicial exception:
Claim 1 recites generating an expression matrix of the two or more biological samples, the expression matrix being derived from the signal intensity values of the expression data of each individual biological sample and having dimensions representative of the two or more genes and the two or more of biological samples; generating a joint expression matrix from the expression matrix, the joint expression matrix having a co-expression probability element between every two genes of the two or more genes for the two or more biological samples; normalizing rows of the joint expression matrix to generate a conditional expression matrix; determining a concentration of unproductive cells within the bioreactor by identifying a distinguishing row of the conditional expression matrix based on a highest magnitude of a row vector in the distinguishing row; and comparing the concentration of the unproductive cells to a threshold value.
Claim 3 recites the expression matrix is spiked by a constant.
Claim 4 recites the expression distinguisher has a normalized signal intensity of one in the conditional expression matrix.
Claim 6 recites re-centering the conditional expression matrix based on the distinguishing row to generate a re-centered conditional expression matrix.
Claim 7 recites identifying a second distinguishing row based on a highest magnitude of a row vector from the re-centered conditional expression matrix.
Claim 8 recites where additional distinguishing rows are identified based on having a highest magnitude of orthogonal projection with another row of the re-centered conditional expression matrix and is determined via:
u
⃑
-
u
⃑
∙
v
⃑
v
⃑
∙
v
⃑
∙
v
⃑
wherein
u
⃑
is a potential expression distinguisher and
v
⃑
is a previous potential expression distinguisher.
Claim 9 recites ranking all distinguishing rows based upon their distances from each other distinguishing row.
Claim 10 recites generating an expression matrix from the signal intensities of the expression data and having dimensions representative of each gene and each individual biological sample, eliminating a subset of the two or more genes in the intensity matrix, wherein the subset comprises individual genes having an outlier signal intensity in the respective expression data of an individual biological sample, the outlier signal intensity deviating from signal intensities relative to other biological samples in the two or more biological samples, to generate an adjusted expression matrix; generating a conditional expression matrix,
Q
-
, of size g x g from the expression matrix, wherein an element,
Q
-
i
,
j
, of the gene-gene conditional expression matrix is:
Q
-
i
,
j
=
P
r
f
2
=
i
f
1
=
j
wherein i and j denote genes of two fragments f1 and f2; normalizing rows of the joint expression matrix to generate a conditional expression matrix; determining a first gene expression distinguisher based on the highest magnitude row of the conditional expression matrix; re-centering the conditional expression matrix to generate a re-centered conditional expression matrix; determining a second gene expression distinguisher based on the highest magnitude row of the re-centered conditional expression matrix; determining two or more subsequent gene expression distinguishers based on respective highest magnitude orthogonal projections of each rows of the re-centered conditional expression matrix with another row of the re-centered conditional expression matrix; generating an output that the genes associated with highest magnitude rows are the gene expression distinguishers; determining a concentration of unproductive cells within the bioreactor based on the gene expression distinguishers; and comparing the concentration of the unproductive cells to a threshold value.
Claim 12 recites identifying a preset number of gene expression distinguishers.
Claim 16 recites that the gene expression distinguishers distinguish between cells of the mix of cell types.
Claims 23 and 27 recite assessing a characteristic expression difference between cells at different stages in differentiation.
Claims 24 and 28 recite tracking stem cell growth for the presence of undesired differentiated cells.
These recitations are similar to the concepts of collecting information, analyzing it and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind or mathematical relationships. Specifically, the steps for generating the matrices, manipulating the data in these matrices either by removing rows, re-centering the rows or performing mathematical calculations on the data contained in the matrix, identifying rows in the matrices based on comparisons of data obtained via mathematical calculations on the information in these rows, and determining ratios can be performed by writing out these matrices on paper and carrying out the various manipulations, identifications or calculations with a pen and paper. Therefore, these limitations fall under the “Mental process” grouping of abstract ideas. Furthermore, the steps of determining a concentration of unproductive cells, comparing the concentration to a threshold value, or assessing or tracking information are so generically recited that they encompass generic analyses that can be done in the mind. While claims 1 and 10 recite that the methods are computer implemented methods, there are no additional limitations that indicate that this computer requires anything other than a generic computer environment. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then if falls within the “Mental processes” grouping of abstract ideas. Furthermore, the limitations for the mathematical manipulations that are performed require carrying out mathematical calculations or determining mathematical relationships between data that also fall under the “Mathematical concepts” grouping of abstract ideas. As such, claims 1-4, 6-13, 16, 23-24, and 27-28 recite an abstract idea [Step 2A, Prong 1: YES]
Step 2A: Prong 2: Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). This judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology or applies or uses the recited judicial exception to affect a particular treatment for a condition. Rather, the instant claims recite additional elements that amount to insignificant extra-solution activity, mere instructions to implement the recited judicial exception in a generic computer or mere instructions to apply the judicial exception in a generic way.
Specifically, the claims recite the following additional elements:
Claims 1 and 10 recite implementing the recited method in a computer, acquiring respective expression data of two or more biological samples of cells within the bioprocessing reactor, the expression data comprising signal intensity values corresponding to a respective two or more genes, and controlling incubation of the cells in the bioprocessing reactor by changing an incubation parameter of the bioprocessing reactor wherein the change in the incubation parameter occurs when the concentration of unproductive cells has been determined to have risen above a threshold value.
Claims 2 and 11 recite receiving a user input defining a threshold value of a deviation of the outlier signal intensity.
Claim 13 recites acquiring expression data from additional biological samples using signal generators specific for the genes associated with highest magnitude rows and not signal generators specific for the subset of the two or more genes.
Claim 16 recites that the biological samples comprise a mix of cell types.
There are no limitations that indicate that the claimed computer requires anything other than a generic computing system. As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984.
The limitations for acquiring data, or receiving user input equate to limitations of receiving or transmitting information or performing clinical tests to obtain information that the courts have found to be insignificant extra-solution activity in In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989), IP Technologies, 788 F.3d at 1363, 115 USPQ2d at 1092-93 and CyberSource v. Retail Decisions, Inc., 654 F.3d 1366, 1375, 99 USPQ2d 1690, 1694 (Fed. Cir. 2011).
As an initial matter, the step of controlling incubation by changing an incubation parameter when the concentration of unproductive cells has risen above a threshold value is not a required step under the broadest reasonable interpretation of the claimed method, as discussed in the Claim Interpretation section above. However, even in consideration of the step being performed, the step of controlling incubation by changing the incubation parameter based on the concentration of unproductive cells equates more to an idea of a solution or outcome because the claims do not provide any details as to how the parameters might be changed or how they are affected by the judicial exception itself. In Intellectual Ventures I v. Capital One Fin. Corp., 850 F.3d 1332, 121 USPQ2d 1940 (Fed. Cir. 2017), there was no indication in the claims of what specific steps were undertaken to make modifications in the dynamic document and therefore effectively cover any solution to the identified problem. This is similar to the instant claims because there is no indication of what specific steps were undertaken to change the incubation parameters of the bioreactor and therefore effectively covers any solution to the identified problem. Furthermore, the claims seem to merely link the claims to a field of use for bioreactors since there is no direct link of how the information from the abstract idea is used to change the incubation parameters.
Because the claims only recite additional elements that equate to insignificant extra-solution activity or mere instructions to implement the abstract idea on a generic computer or in a generic way, the claims do not integrate the recited judicial exception into a practical application. As such, claims 1-4, 6-13, 16, 23-24, and 27-28 are directed to an abstract idea. [Step 2A, Prong 2: NO]
Step 2B: Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that equate to insignificant extra-solution activity or well-understood, routine and conventional activity.
The instant claims recite the following additional elements:
Claims 1 and 10 recite implementing the recited method in a computer, acquiring respective expression data of two or more biological samples of cells within the bioprocessing reactor, the expression data comprising signal intensity values corresponding to a respective two or more genes and controlling incubation of the cells in the bioprocessing reactor by changing an incubation parameter of the bioprocessing reactor wherein the change in the incubation parameter occurs when the concentration of unproductive cells has been determined to have risen above a threshold value.
Claims 2 and 11 recite receiving a user input defining a threshold value of a deviation of the outlier signal intensity.
Claim 13 recites acquiring expression data from additional biological samples using signal generators specific for the genes associated with highest magnitude rows and not signal generators specific for the subset of the two or more genes.
Claim 16 recites that the biological samples comprise a mix of cell types.
As discussed above, there are no additional limitations to indicate that the claimed computer requires anything other than a generic computer to carry out the recited abstract idea in the claims. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984.
As also discussed above, limitations for receiving and transmitting information or performing clinical tests to obtain information that the courts have found to be insignificant extra-solution activity in In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989), IP Technologies, 788 F.3d at 1363, 115 USPQ2d at 1092-93 and CyberSource v. Retail Decisions, Inc., 654 F.3d 1366, 1375, 99 USPQ2d 1690, 1694 (Fed. Cir. 2011). Furthermore, the courts have found that acquiring data, receiving data and transmitting data are well-understood, routine and conventional functions in Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information); TLI Communications LLC v. AV Auto. LLC, 823 F.3d 607, 610, 118 USPQ2d 1744, 1745 (Fed. Cir. 2016) (using a telephone for image transmission); OIP Techs., Inc., v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1093 (Fed. Cir. 2015) (sending messages over a network); buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network).
Furthermore, the use of signal generators to measure gene expression values is well-understood, routine and conventional in the art, as evidenced by Parmigiani et al. (The analysis of gene expression data: an overview of methods and software. The analysis of gene expression data, 2003, pgs. 1-45; previously cited). Parmigiani et al. discloses a review of microarray technologies for analysis of gene expression data (pg. 2, para. 2). Parmigiani et al. discloses that there are several commercially available microarray technologies that detect signal intensities to determine gene expression (pg. 2, para. 2 to pg. 4, para. 2; Table 1.1; pg. 12, para. 3). Parmigiani et al. also discloses that there are several available database servers available for storing such microarray generated gene expression data (pg. 9, para. 3 to pg. 10, para. 2). Therefore, the use of micro array technologies coupled with accessible data storage technology is well-understood, routine and conventional.
In addition, the concept of automated cell culture bioreactors that can change incubation parameters is well-understood, routine and conventional, as evidenced by Kempner et al. (JALA 2002, vol. 7, no. 2, pgs. 56-62; previously cited). Kempner et al. discloses that there are a number of automated cell culture systems that can operate unattended over a period of days or weeks and allow for evaluation of pH, nutrient or waste concentration, and cell concentration and viability (pg. 56, col. 1, para. 3 to pg. 57, col. 2, para. 3).
The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself. [Step 2B: NO]
As such, claims 1-4, 6-13, 16, 23-24, and 27-28 are not patent eligible.
Response to Arguments
Applicant's arguments filed 16 July 2025 regarding 35 U.S.C. 101 have been fully considered but they are not persuasive.
Applicant remarks the claims have been amended to add “controlling incubation of the cells in the bioprocessing reactor by changing an incubation parameter…when the concentration of unproductive cells has been determined to have risen above a threshold value”, which removes the question of whether the term previously existing only in the preamble is limiting, and thus the claims recite controlling incubation in a way that is limiting and provides eligibility (Applicant’s remarks at pg. 7, para. 3 to pg. 8, para. 3). Applicant further points to the Board Decision, which suggested “[i]f prosecution continues, we leave….how to best amend the claims to unambiguously make clear that no condition step is included” (Applicant’s remarks at pg. 8, para. 3).
This argument is not persuasive. Claims 1 and 10 each recite “controlling incubation of the cells in the bioprocessing reactor by changing an incubation parameter of the bioprocessing reactor wherein the change in the incubation parameter occurs when the concentration of unproductive cells has been determined to have risen above a threshold value”.
While Applicant has amended the claims to recite “controlling incubation of the cells”, this is still only performed by the act of “changing an incubation parameter”, which is still contingent on the concentration of unproductive cells having risen above a threshold value. However, as currently recited, the claims do not require that the concentration of unproductive cells was determined to be above the recited threshold value. As a result, the step of “controlling incubation of the cells in the bioprocessing reactor by changing an incubation parameter” is still not required under the broadest reasonable interpretation of the claims.
While it is noted that the preamble does recite “A…method for controlling incubation….”, MPEP 2111.01 II. states 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. In the instant case, the body of the claims set forth all of the limitations of the claimed invention, and the preamble stating “for controlling” is merely reciting an intended use of the claimed method of controlling incubation of the cells. The intended use of “controlling” is claimed as only occurring “when the concentration of unproductive cells has been determined to have risen above a threshold value”. As discussed above, nothing in the claims requires that the concentration of unproductive cells is above the threshold.
Regarding the Board Decision received 16 May 2025, it is further noted that the Board also agreed with the Examiner’s position that “any recited ‘changing’ of a parameter is no more than a vague instruction to apply a result of the earlier-recited mental process in some unspecified way” (see pg. 13, para. 2 of the decision).
In order to require a step of controlling incubation, Applicant could amend the claims to recite, after the step of “determining a concentration of unproductive cells…”, to recite a step of “determining the concentration of unproductive cells is above a threshold value”, and then reciting the final step of “controlling incubation…has been determined to have risen above the threshold value”. Although as discussed above, the limitation would still not be sufficient to integrate the recited judicial exception into a practical application.
Applicant remarks the claimed methods allow for automation of culturing processes in bioreactors containing heterogenous cell cultures based on measured expression distinguishers, and utilize these methods for “changing an incubation parameter”, and further remarks that while the claims are not limited to specific incubation parameters, the specification gives concrete examples of parameters that may be changed including “incubation temperature” and the “media” (Applicant’s remarks at pg. 8, para. 4 to pg. 9, para. 1).
This argument is not persuasive. First, the step of “changing an incubation parameter” is not required under the broadest reasonable interpretation of the claims, as discussed above. Therefore, any arguments relating to a practical application of automating culturing processes are not commensurate with the scope of the claims.
Second, even in consideration of the step being performed, the step of controlling incubation by changing the incubation parameter based on the concentration of unproductive cells equates more to an idea of a solution or outcome because the claims do not provide any details as to how the parameters might be changed or how they are affected by the judicial exception itself. While Applicant points out that the specification provides examples of certain parameters, such as temperature or the media, it is improper to import claim limitations from the specification. See MPEP 2111.01. Currently, the claims do not require any specific type of “incubation parameters”. Regardless, even if the incubation parameters included temperature or media, the claims still would not provide any details of how the temperature or media of the bioreactor are supposed to be changed in response to the identified problem of a presence of a threshold number of unproductive cells. As stated in MPEP 2106.05(f), the recitation of claim limitations that attempt to cover any solution to an identified problem with no restriction on how the result is accomplished and no description of the mechanism for accomplishing the result, does not integrate a judicial exception into a practical application or provide significantly more because this type of recitation is equivalent to the words "apply it". See also Intellectual Ventures I v. Capital One Fin. Corp., 850 F.3d 1332, 121 USPQ2d 1940 (Fed. Cir. 2017), discussed in the above rejection.
Applicant remarks because the claims require “controlling incubation…”, they recite significantly more than the judicial exception, and the present claims are much like those of Diamond v. Diehr and that eligibility should be found for similar reasons (Applicant’s remarks at pg. 9, para. 2).
This argument is not persuasive. As discussed above, the step of controlling incubation is not required by the claims, and furthermore, even if the step was required, the recitation is equivalent to the words “apply it” and does not integrate a judicial exception into a practical application or provide significantly more because the claim attempts to cover any solution to an identified problem with no restriction on how the result is accomplished and no description of the mechanism for accomplishing the result.
This is dissimilar from the claims of Diehr, which recited additional elements such as installing rubber in a press, closing the mold, constantly measuring the temperature in the mold and automatically opening the press at the proper time. The claims in Diehr, necessarily resulted in the production of an improved rubber product by automatically opening the press door at the specified time.
Conclusion
No claims are allowed.
All claims are identical to or patentably indistinct from, or have unity of invention with claims in the application prior to the entry of the submission under 37 CFR 1.114 (that is, restriction (including a lack of unity of invention) would not be proper) and all claims could have been finally rejected on the grounds and art of record in the next Office action if they had been entered in the application prior to entry under 37 CFR 1.114. Accordingly, THIS ACTION IS MADE FINAL even though it is a first action after the filing of a request for continued examination and the submission under 37 CFR 1.114. See MPEP § 706.07(b). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAITLYN L MINCHELLA whose telephone number is (571)272-6485. The examiner can normally be reached 7:00 - 4:00 M-Th.
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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685