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 .
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitation(s) is/are: “a signal acquisition unit”, “a signal detection unit”, and “a correction unit” in claim 26, “a first determination subunit” in claim 27, “a phase correction subunit” in claim 28, “an identification unit” in claim 29, “a fourth determining subunit”, “a normalization subunit”, and “an identification subunit” in claim 30, and “a second determining subunit” and “a third determining subunit” in claim 31.
The specification describes “a signal acquisition unit” 601, “a signal detection unit” 602, and “a correction unit” 603, “a first determination subunit” 603, “a phase correction subunit” 603, “an identification unit”, “a fourth determining subunit”, “a normalization subunit”, “an identification subunit”, “a second determining subunit”, and “a third determining subunit” as being hardware or software executed by a processor. As such, sufficient structure is shown in the specification to avoid a 35 USC 112(b) rejection.
Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
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.
The broadest reasonable interpretation of a claim drawn to a computer readable medium covers forms of non-transitory tangible media and transitory propagating signals per se in view of the ordinary and customary meaning of computer readable media. See MPEP 2111.01. When the broadest reasonable interpretation of a claim covers a signal per se, the claim must be rejected under 35 U.S.C. § 101 as covering non-statutory subject matter. See In re Nuijten, 500 F.3d 1346, 1356-57 (Fed. Cir. 2007) (transitory embodiments are not directed to statutory subject matter) and Interim Examination Instructions for Evaluating Subject Matter Eligibility Under 35 U.S.C. § 101, Aug. 24, 2009; p. 2.
Claim 34 is drawn to such a computer readable medium that covers both transitory and non-transitory embodiments but may be amended to narrow the claim to cover only statutory embodiments by adding the limitation "non-transitory" to the claim.
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.
Claims 18-34 are rejected under 35 U.S.C. 103(a) as being unpatentable over Langlois et al. (US 2020/0080142), cited in the IDS dated 6/6/25, in view of Vicceli et al. (US 2023/0410944), cited in the IDS dated 3/5/26.
Regarding claims 18 and 26, Langlois discloses an apparatus for determining inter-channel crosstalk correction strength and a method for determining inter-channel crosstalk correction strength, comprising:
detecting multiple cycles of sequencing by synthesis based on a multi-channel microscopic imaging system, such that a first channel signal and a second channel signal are generated in each cycle, wherein the first channel signal is indicative of a signal of incorporation of a first nucleotide into a plurality of identical polynucleotide molecules in the cycle, the second channel signal is indicative of a signal of incorporation of a second nucleotide into the plurality of identical polynucleotide molecules in the cycle, the first nucleotide and the second nucleotide are nucleotides comprising different types of bases, and a part of the first channel signal is noise related to second channel crosstalk (see paras 15, 40, 45, 50, 76, and 94, multiple cycles of sequencing is performed, first and second channel signals are generated, the channel signals being indicative of polynucleotide molecules);
detecting the first channel signal and the second channel signal in each cycle, wherein the first channel signal and the second channel signal both have intensity (see paras 40 and 76-78, channel signal intensities are detected); and
performing inter-channel crosstalk correction on the first channel signal intensity by using a predetermined coefficient and the second channel signal intensity to determine the crosstalk-corrected first channel signal intensity (see paras 76-79 and 81, crosstalk correction is performed using coefficients).
Langlois does not disclose expressly wherein the predetermined coefficient is a fixed coefficient associated with the multi-channel microscopic imaging system.
Vicceli discloses performing inter-channel crosstalk correction on the first channel signal intensity by using a predetermined coefficient and the second channel signal intensity to determine the crosstalk-corrected first channel signal intensity, wherein the predetermined coefficient is a fixed coefficient associated with the multi-channel microscopic imaging system (see para 88, a phasing coefficient is applied to one or more of the intensity values 240 as part of a correction, e.g., signal correction function).
Before the effective filing date of the claimed invention, it would have been obvious to a person of ordinary skill in the art to combine the predetermine coefficient, as described by Vicceli, with the system of Langlois.
The suggestion/motivation for doing so would have been to avoid errors (Vicceli paras 2-4).
Therefore, it would have been obvious to combine Vicceli with Langlois to obtain the invention as specified in claims 18 and 26.
Regarding claims 19 and 27, Vicceli further discloses wherein performing the inter-channel crosstalk correction on the first channel signal intensity by using the predetermined coefficient and the second channel signal intensity to determine the crosstalk-corrected first channel signal intensity comprises: determining the crosstalk-corrected first channel signal intensity by I1' = I1 – K × I2, wherein I1' is the crosstalk-corrected first channel signal intensity, I1 is the detected first channel signal intensity, I2 is the detected second channel signal intensity, and K is the predetermined coefficient (see para 88, a phasing coefficient is applied to one or more of the intensity values 240 as part of a correction, e.g., signal correction function).
Regarding claims 20 and 28, Langlois further discloses after performing the inter-channel crosstalk correction on the first channel signal intensity by using the predetermined coefficient and the second channel signal intensity: performing phase correction on the first channel signal intensity after the inter-channel crosstalk correction by using the detected first channel signal intensity in the previous cycle and/or the next cycle to obtain the phase-corrected first channel signal intensity (see Fig. 5 and para 81, phase correction is performed).
Regarding claims 21 and 29, Langlois further discloses identifying the first nucleotide incorporated into the plurality of identical polynucleotide molecules in the cycle according to the phase-corrected first channel signal intensity (see Fig. 5 and paras 40 and 81-83, the bases of nucleotides incorporated into clusters of the poly nucleotides can be determined by the base caller 226).
Regarding claims 22 and 30, Langlois further discloses wherein identifying the first nucleotide incorporated into the plurality of identical polynucleotide molecules in the cycle according to the phase-corrected first channel signal intensity comprises: determining a normalization parameter based on the signal intensity of each channel; normalizing the phase-corrected first channel signal intensity based on the normalization parameter to obtain the normalized first channel signal intensity; and identifying the first nucleotide incorporated into the plurality of identical polynucleotide molecules in the cycle according to the normalized first channel signal intensity (see para 86, normalizing of the corrected intensities is performed).
Regarding claims 23 and 31, Langlois further discloses wherein the first channel signal and the second channel signal are both fluorescence signals, and determining the predetermined coefficient comprises: determining a range of possible values for the predetermined coefficient based on a spectral overlap region of a first channel and a second channel; and determining a value that can meet a preset correction requirement as the predetermined coefficient within the range of possible values (see paras 76-78, a two-channel color matrix can be a 2×2 matrix that is used to correct for the cross-talk between two channels capturing, for example a first channel and a second channel, the first channel can capture the first fluorescent images and the second fluorescent images at sequencing cycles).
Regarding claims 24 and 32, Langlois further discloses wherein the determining the value that can meet the preset correction requirement as the predetermined coefficient within the range of possible values comprises: determining the preset correction requirement based on configuration information of the multi-channel microscopic imaging system; and traversing corresponding values within the range of possible values according to traversal parameters, and determining the value that can meet the preset correction requirement as the predetermined coefficient, wherein the traversal parameters comprise at least a step size parameter, and the step size parameter characterizes an interval parameter of two values in the traversal process (see paras 76-78, a two-channel color matrix can be a 2×2 matrix that is used to correct for the cross-talk between two channels capturing, for example a first channel and a second channel, the first channel can capture the first fluorescent images and the second fluorescent images at sequencing cycles).
Regarding claims 25 and 33, Langlois further discloses wherein the preset correction requirement comprises an alignment rate and/or an error rate, wherein the alignment rate characterizes a ratio of the number of reads aligned to a reference genome to the total number of reads; the error rate characterizes a proportion of the number of bases that do not match the reference genome when reads generated by sequencing are aligned with the reference genome (see para 90, correcting intensities can decrease error rates).
Regarding claim 34, Langlois further discloses a computer-readable storage medium having a program stored thereon, wherein the program can be executed by a processor to implement the method for determining the inter-channel crosstalk correction strength according to claim 18 (see paras 36-37).
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. To further show the state of the art please refer to the attached Notice of References Cited.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARK R MILIA whose telephone number is (571) 272-7408. The examiner can normally be reached Monday-Friday, 8am-5pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Akwasi Sarpong can be reached at 571-270-3438. The fax number for the organization where this application or proceeding is assigned is 571-273-8300.
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/MARK R MILIA/ Primary Examiner, Art Unit 2681
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