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 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)(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.
Claim(s) 1-4, 6, 8, 9-11, 15, 21, 22, 30, 32, 33, 41, 43 and 53 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Reed et al (US PGPub 2020/0209257) .
The applied reference has a common inventor ( Reed) and assignee ( Quantum-Si Incorporated) with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2). This rejection under 35 U.S.C. 102(a)(2) might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C. 102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B) if the same invention is not being claimed; or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed in the reference and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement.
Regarding Claim 1, Reed et al teaches a method for determining chemical characteristics of a polypeptide (see abstract), [0008] and [0064]), comprising:
contacting a polypeptide with one or more amino acid recognizers, wherein the one or more amino acid recognizers, which comprise a first set of one or more amino acid recognizers that bind to the polypeptide (such as a set of labeled aptamers 150 comprising four DNA aptamer types, each type recognizing a different N-terminal amino acid) (see [0133] and [0137]);
detecting a first series of signal pulses (i.e. a signal output 300) indicative of a first series of binding events between the first set of one or more amino acid recognizers and the polypeptide (see [0007], [0145] and [0150]) ; and determining at least one chemical characteristic (i.e. characteristic signatures) of a first set of at least two amino acids of the polypeptide based on at least one characteristic of the first series of signal pulses (see [0064], [0097] and [0275]). Regarding Claim 2, Reed et al teaches that the first series of binding events is between the first set of one or more amino acid recognizers (i.e. a first set of labels) and a first amino acid of the polypeptide (see [0094] and [0133]).
Regarding Claim 3, Reed et al teaches that the first amino acid is a terminal amino acid of the polypeptide (see [0007], [0079]-[0080] and [0133]).
Regarding Claim 4, Reed et al teaches that the first amino acid is an internal amino acid of the polypeptide (see [0079], [0092] and [0164]).
Regarding Claim 6, Reed et al teaches that the first set of at least two amino acids of the polypeptide comprises the first amino acid of the polypeptide ([0011], [0081], [0086] and [0133]).
Regarding Claim 8, Reed et al teaches that the first set of at least two amino acids comprises a second amino acid, and wherein the first amino acid and the second amino acid are separated by at least one other amino acid (of a plurality of nucleotides) in the polypeptide (see [0202] and [0218]).
Regarding Claim 9, Reed et al teaches that the first set of at least two amino acids comprises at least three amino acids (see [0202]).
Regarding Claim 10, Reed et al teaches that the first set of at least two amino acids does not consist of a terminal amino acid and a penultimate amino acid of the polypeptide (see [0332] and [0341]).
Regarding Claim 11, Reed et al teaches that at least one amino acid recognizer of the first set of one or more amino acid recognizers comprises a detectable label (see [0021], [0131] and [0133]).
Regarding Claim 15, Reed et al teaches that the at least one characteristic of the first series of signal pulses comprises a first pulse duration, a first interpulse duration, and/or a first recognition segment duration (see [0005], [0074] and [0146]).
Regarding Claim 21, Reed et al teaches detecting a second series of signal pulses indicative of a second series of binding events between a second set of one or more amino acid recognizers that bind to the polypeptide; and determining at least one chemical characteristic of a second set of at least two amino acids of the polypeptide based on at least one characteristic of the second series of signal pulses (see [0069], [0094]-[0095] and [0262]).
Regarding Claim 22, Reed et al teaches the second set (wherein each set is a set of a panel of multiple sets) of at least two amino acids of the polypeptide comprises at least one amino acid of the first set of at least two amino acids (see [0069]).
Regarding Claims 30 and 32, Reed et al teaches determining at least one chemical characteristic of the first set of at least two amino acids comprises identifying a modification of at least one amino acid of the first set of at least two amino acids (such as methylation, citrullation, phosphorylation) (see [0081]-[0082] and [0093]).
Regarding Claim 33, Reed et al teaches that the modification comprises methylation or citrullination (see [0082]), and wherein at least one amino acid comprises an arginine (see [0080] or [0083]).
Regarding Claim 41, Reed et al teaches that wherein the modification affects the at least one characteristic (such as pulse duration or rate) of the first series of signal pulses (see [0164]).
Regarding Claim 43, Reed et al teaches identifying the polypeptide based on the determined at least one chemical characteristic of the first set of at least two amino acids (see [0012] and [0097]).
Regarding Claim 53, Reed et al teaches loading a sample onto a device (such as loading onto an array of sample wells), wherein the sample comprises a mixture of the polypeptide and a second polypeptide (see [0079] and [0138]); detecting a second series of signal pulses indicative of a second series of binding events between a second set of one or more amino acid recognizers and the second polypeptide (wherein each binding event forms a set in a panel)(see [0067]-[0070]), wherein the first series of signal pulses and the second series of signal pulses are detected while the polypeptide and the second polypeptide are disposed in different chambers of the device (wherein a plurality of polypeptides are attached to a plurality of sample wells (e.g., with one polypeptide attached to a surface, for example a bottom surface, of each sample well), for example in an array of sample wells on a substrate) (see [0138] and [0268]-[0269]) ; and determining at least one chemical characteristic of at least two amino acids of the second polypeptide based on at least one characteristic of the second series of signal pulses (see [0275]).
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) 1-4, 6, 9, 11, 21, 22, 30, 32 and 43 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Van Roosmalen et al (US PGPub 2017/0356921).
Regarding Claim 1, Van Roosmalen et al teaches a method for determining chemical characteristics of a polypeptide (such as a recombinantly produced polypeptide, comprising an amino acid sequence corresponding to amino acid 83through 154 of HNL)(see [0014] and [0033] ), comprising:
contacting a polypeptide with one or more amino acid recognizers (specifically a binding agent specifically recognizing HNL), wherein the one or more amino acid recognizers (i.e. a binding agent specifically recognizing HNL), which comprise a first set of one or more amino acid recognizers that bind to the polypeptide (see [0014], [0111] and [0199]);
detecting a first series of signal pulses (i.e. a measurable signal) indicative of a first series of binding events between the first set of one or more amino acid recognizers and the polypeptide (see [0092]); and determining at least one chemical characteristic (i.e. the interaction between the binding agent (recognizer) and the amino acid) of a first set of at least two amino acids of the polypeptide based on at least one characteristic of the first series of signal pulses (see [0092]-[0093] and [0412]). Regarding Claim 2, Van Roosmalen et al teaches that the first series of binding events is between the first set of one or more amino acid recognizers (i.e. binding agents, antibodies) and a first amino acid of the polypeptide (see [0014], [0095], [0111] and [0145]).
Regarding Claim 3, Van Roosmalen et al teaches that the first amino acid is a terminal amino acid of the polypeptide (see [0118] and [0165]).
Regarding Claim 4, Van Roosmalen et al teaches that the first amino acid is an internal amino acid of the polypeptide (see [0165]).
Regarding Claim 6, Van Roosmalen et al teaches that the first set of at least two amino acids of the polypeptide comprises the first amino acid of the polypeptide (one of amino acids 82 to 102) (see [0014] and [0111]).
Regarding Claim 9, Van Roosmalen et al teaches that the first set of at least two amino acids comprises at least three amino acids (of amino acids 82 to 102) (see [0014] and [0111]).
Regarding Claim 11, Van Roosmalen et al that at least one amino acid recognizer of the first set of one or more amino acid recognizers comprises a detectable label ([0126] and [0195]).
Regarding Claim 21, Van Roosmalen et al teaches detecting a second series of signal pulses indicative of a second series of binding events between a second set of one or more amino acid recognizers (i.e. binding agents that react to different amino acids, such as amino acids 82-102) that bind to the polypeptide; and determining at least one chemical characteristic of a second set of at least two amino acids of the polypeptide based on at least one characteristic of the second series of signal pulses ([0092], [0111] and [0402]).
Regarding Claim 22, Van Roosmalen et al teaches the second set (i.e. one of the sets of amino acids, i.e. either 51 to 76 and/or 82 to 102 and/or 113 to 132 and/or 141 to 156 of HNL( of at least two amino acids of the polypeptide comprises at least one amino acid of the first set of at least two amino acids (see [0015] and [0111]).
Regarding Claims 30 and 32, Van Roosmalen et al teaches determining at least one chemical characteristic of the first set of at least two amino acids comprises identifying a modification of at least one amino acid of the first set of at least two amino acids (such as methylation) (see [0116] and [0194]).
Regarding Claim 43, Van Roosmalen et al teaches identifying the polypeptide based on the determined at least one chemical characteristic (i.e. interaction) of the first set of at least two amino acids (see [0092]-[0093] and [0412]).
Claim Rejections - 35 USC § 103
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.
Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over Van Roosmalen et al as applied to claim 1 above, and further in view of Goix et al (US PGPub 2010/0255518).
Regarding Claim 15, Van Roosmalen et al does not teach that the at least one characteristic of the first series of signal pulses comprises a first pulse duration, a first interpulse duration, and/or a first recognition segment duration.
However, in the analogous art of amino acid analysis and detection, Goix et al teaches a detector 309 (FIG. 1A), or detectors (364, 365, FIG. 1B), which are capable of capturing the amplitude and duration of photon bursts from a fluorescent label-moiety complex, and further converting the amplitude and duration of the photon burst to electrical signals. Detection devices such as CCD cameras, video input module cameras, and Streak cameras can be used to produce images with contiguous signals (see [0179]). It would have been obvious to one of ordinary skill in the art to modify the method of Van Roosmalen et al by detecting photon bursts (as taught by Goix et al) in amino acid analysis/detection for the benefit of enabling one to determine a characteristic (or diagnosis of cardiac troponin) of the biological sample (which comprises amino acids).
Conclusion
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/JENNIFER WECKER/ Primary Examiner, Art Unit 1797