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 .
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.
Election/Restrictions
Applicant’s election of Group I of claims 1-14 in the reply filed 06/15/2026 is acknowledged. Because the applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Applicant cancelled claims 2 and 15-49.
Newly submitted claims 50-52 are directed to subject matter that was not discussed in the original claims nor in the disclosure of the instant application. Specifically, the combination of specific cell markers with specific fluorochromes was not discussed in the original disclosure. Thus, claims 50-52 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 06/15/2026.
Also, the Office action of 04/15/2026 required the Applicant to elect a single species from the list of mouse cell groups if Group I of claims is elected. Applicant’s election of “T cells, B cells, NK cells, dendritic cells, monocytes, macrophages, and granulocytes” with traverse in the reply filed 06/15/2026 is acknowledged. However, the Applicant cancelled claim 2 in which the species were to be elected, and the Applicant’s election is therefore moot.
Thus, claims 1 and 3-14 are under examination.
Priority
This is a U.S. application that claims priority to U.S. Provisional application No. 63/352,222 filed on 06/14/2022.
Claim Objections
Claim 14 is objected to because of the following informalities: the claim recites “dating traditionally defined PBMC populations”. A possible correction is “gating traditionally defined PBMC populations”. Appropriate correction is required.
Claim Rejections - 35 USC § 112(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.
Claims 1, 3-14 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 recites "pairing the eleven (11) optimal fluorochromes with two sets of the eleven (11) selected cell markers and one set of ten (10) cell markers " in lines 12-13 of claim 1. However, only one set of 11 cell markers was selected in line 3 of claim 1 “selecting eleven (11) cell markers for biological cells of interest;”. It is not clear from where the second set of eleven cell markers and the set of ten cell markers come from because they were not initially selected in the claim. Thus, there is insufficient antecedent basis for this limitation in the claim.
Claim 1 recites “staining the mouse cells of interest with the antibody conjugated fluorochromes”. It is not clear from where the mouse cells of interest come from because initially the claim only recites “selecting eleven (11) cell markers for biological cells of interest” without specifying the type of cell to use. Thus, there is insufficient antecedent basis for this limitation in the claim.
Claim 1 recites “staining the mouse cells of interest with the antibody conjugated fluorochromes, comprising … and the eleven (11) optimal fluorochromes and antibody specific to the one set of ten (10) cell markers to create a third multicolor mouse sample”. It is not clear how eleven optimal fluorochromes will be assigned to ten cell markers because there are more fluorochromes than cell markers. The specification does not provide an explanation for how to assign eleven optimal fluorochromes to ten cell markers. And a skilled artisan would not have been appraised of the scope of the claim from its language, and therefore claim 1 is deemed indefinite.
Claim Rejections - 35 USC § 102
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1 and 3-14 are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Jaimes et al. (US 12,487,167 B2).
Claim 1 recites:
“A method of building a color flow cytometry panel using a full spectrum laser
flow cytometer, the method comprising:
selecting eleven (11) cell markers for biological cells of interest;
identifying fluorochromes to be used in the flow cytometry panel;
analyzing spectrum of each fluorochrome across detectors in the full spectrum laser flow cytometer;
comparing spectra of combination of pairs of each of the commercially available fluorochromes by determining a similarity index for each pairing of fluorochromes;
selecting eleven (11) optimal fluorochromes using the similarity index for each of the fluorochromes and a complexity index;
calibrating the lasers and detectors in the flow cytometer;
pairing the eleven (11) optimal fluorochromes with two sets of the eleven (11) selected cell markers and one set of ten (10) cell markers, according to the brightness of the fluorochrome and the expression density of the cell marker;
staining the mouse cells of interest with the antibody conjugated fluorochromes, comprising the eleven (11) optimal fluorochromes and antibody specific to the two sets of eleven (11) cell markers to create two multicolor mouse samples, and the eleven (11) optimal
fluorochromes and antibody specific to the one set of ten (10) cell markers to create a third
multicolor mouse sample;
running each of the three multicolor mouse samples through the spectral flow cytometer;
receiving three sets of data from the detectors of the full spectrum flow cytometer for the three multicolor mouse samples; and
processing the three sets of received data using a computer processor to unmix spill over, identify different mouse cells, and count the number of identified different mouse cells in the three multicolor mouse samples”.
Regarding claim 1, Jaimes teaches a method of building a color flow cytometry panel using a full spectrum laser flow cytometer (Abstract). Jaimes further teaches that the number of fluorochromes and cell markers to use are based on the number needed to isolate and identify a specific cell type (Column 34, lines 23-28; column 39, lines 59-67; column 40, lines 1-5). Jaimes also teaches selecting cell markers for biological cells of interest (Column 1, lines 39-41; column 4, lines 44-46; column 20, lines 16-25). And Jaimes teaches identifying fluorochromes to be used in the flow cytometry panel (Column 20, lines 16-25). Jaimes further teaches analyzing the spectrum of each fluorochrome across detectors in the full spectrum laser flow cytometer (Sheet 30 of 66; “Block 4”; “Analyze full spectrum of each commercially available fluorochrome across detectors in flow cytometer”). Jaimes also teaches comparing spectra of combination of pairs of each of the commercially available fluorochromes by determining a similarity index for each pairing of fluorochromes (Sheet 30 of 66, “Block 5”, “Compare spectra of permutations of pairs of each of the commercially available fluorochromes by determining a similarity index for each pairing of fluorochromes”). And Jaimes teaches selecting optimal fluorochromes using the similarity index for each of the fluorochromes and a complexity index (Sheet 30 of 66, “Block 6”, “Select a group of 30 or more fluorochromes with similarity indexes less than a predetermined number {e.g., 0.98)”, “Block 7”, “Determine a complexity index for the group of 30 or more fluorochromes. Reject selected group if complexity is greater than a predetermined number”). Jaimes further teaches calibrating the lasers and detectors in the flow cytometer (Sheet 30 of 66, “Block 3”, “Calibrate the laser and detectors in the flow cytometer”). Jaimes also teaches pairing the optimal fluorochromes with selected cell markers according to the brightness of the fluorochrome and the expression density of the cell marker (Column 23, lines 4-9). And Jaimes teaches staining the cells of interest with the antibody conjugated fluorochromes, comprising optimal fluorochromes and antibody specific to cell markers to create multicolor samples (Sheet 31 of 66, Block 10, “Stain cells following best practice staining protocols with the following adjustments to create multicolor sample”; column 23, lines 21-31). Jaimes further teaches using more than one sample based on the results of matched fluorochromes and cell markers such as two reference samples and one tested sample (Column 6, lines 54-65). Jaimes also teaches running each of the multicolor samples through the spectral flow cytometer (column 40, lines 2-5). And Jaimes teaches receiving sets of data from the detectors of the full spectrum flow cytometer for the multicolor samples; and processing sets of received data using a computer processor to unmix spill over, identify different cells, and count the number of identified different cells in the multicolor samples (Column 38, lines 45-55).
Regarding claim 3, Jaimes teaches that selecting the optimal fluorochromes comprises, selecting the fluorochromes based on peak emission wavelength excited by three laser colors and spread across thirty-eight detectors of the spectral flow cytometer (Column 36, lines 31-34, “A flow cytometer can be configured with a combination of one, two three, four, five (5) or more lasers and fourteen, sixteen, twenty-two, thirty, thirty-eight, forty- eight, fifty-four, sixty-four (64) or more detectors”).
Regarding claim 4, Jaimes teaches selecting the optimal fluorochromes comprises, selecting the fluorochromes based on peak emission wavelength excited by three laser colors and spread across sixty-four detectors of the spectral flow cytometer (Column 36, lines 31-34, “A flow cytometer can be configured with a combination of one, two three, four, five (5) or more lasers and fourteen, sixteen, twenty-two, thirty, thirty-eight, forty- eight, fifty-four, sixty-four (64) or more detectors”).
Regarding claim 5, Jaimes teaches that selecting the optimal fluorochromes comprises, quantifying uniqueness of each of a group of sixty-five (65) fluorochromes (Column 5, lines 48-50; column 21, lines 27-31).
Regarding claim 6, Jaimes teaches selecting the optimal fluorochromes comprises, analyzing the spectra of each of the sixty-five (65) fluorochromes using the full spectrum flow cytometer (column 21, lines 27-31).
Regarding claim 7, Jaimes teaches that selecting the optimal fluorochromes comprises, comparing the spectra of each pairing of the sixty-five (65) fluorochromes; and assigning a similarity index to each pairing of fluorochromes (column 21, lines 27-31; column 22, lines 12-18).
Regarding claim 8, Jaimes teaches that selecting the optimal fluorochromes further comprises, determining a threshold similarity index value and not selecting at least one fluorochrome of the pair of fluorochromes with a similarity index value higher than the threshold similarity index value (Sheet 30 of 66, “Block 6”, “Select a group of 30 or more fluorochromes with similarity indexes less than a predetermined number {e.g., 0.98)”; column 29, lines 28-40).
Regarding claim 9, Jaimes teaches that selecting the optimal fluorochromes comprises, choosing the optimal fluorochromes with the lowest similarity index (Sheet 30 of 66, “Block 6”, “Minimizing fluorochrome pairs with very high similarity indices”).
Regarding claim 10, Jaimes teaches that the lowest similarity index value that will produce high resolution data is 0.98 (Sheet 30 of 66, “Block 6”, “Select a group of 30 or more fluorochromes with similarity indexes less than a predetermined number {e.g., 0.98)”).
Regarding claim 11, Jaimes teaches that identifying the optimal fluorochromes comprises determining a complexity index of the group of fluorochromes; and determining a threshold complexity index above which the group of fluorochromes are not considered optimal (Sheet 30 of 66, “Block 7”, “Determine a complexity index for the group of 30 or more fluorochromes. Reject selected group if complexity is greater than a predetermined number (e.g., 54) and repeat group selection to lower complexity index”).
Regarding claim 12, Jaimes teaches that the threshold complexity index is fifty-four (54) (Sheet 30 of 66, “Block 7”, “Determine a complexity index for the group of 30 or more fluorochromes. Reject selected group if complexity is greater than a predetermined number (e.g., 54) and repeat group selection to lower complexity index”).
Regarding claim 13, Jaimes teaches that pairing the optimal fluorochromes with the selected cell markers comprises: assigning the dimmest fluorochromes to the highest expressing antigens (Sheet 31 of 66, “Block 9”, “Dimmest fluorochromes were assigned to antigens expressed at high levels and with high level of coexpression with other cell markers in the panel to minimize spread”). Jaimes further teaches assigning tertiary markers to bright fluorochromes (Sheet 31 of 66, “Block 9”, “tertiary markers were assigned to bright fluorochromes to maximize resolution”). And Jaimes teaches avoiding placing highly expressed antigens adjacent to co-expressed antigens with lower expression for fluorochromes with a same primary excitation laser or similar emission wavelengths (Sheet 31 of 66, “Block 9”, “avoid highly expressed antigens being placed in cells adjacent to co-expressed antigens with lower expression”).
Regarding claim 14, Jaimes teaches that processing the received data comprises: manually gating to remove aggregates, dead cells, debris, and CD45 negative events; gating traditionally defined PBMC populations; sub-sample the data to include only the CD45+ live singlets; unmix data using software with an ordinary least squares algorithm.; performing opt-SNE analysis of the data; and assembling clusters into commonly recognized biological populations and generate a heatmap of the resulting populations (Sheet 31 of 66,“Block 12”)
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to OMAR RAMADAN whose telephone number is (571)270-0754. The examiner can normally be reached Monday-Friday 8:30 am - 5:00 pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gregory Emch can be reached at (571) 272-8149. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/OMAR RAMADAN/Examiner, Art Unit 1678
/GREGORY S EMCH/Supervisory Patent Examiner, Art Unit 1678
