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 .
Priority
This application filed 8/12/2021 is a divisional of application 14/854441 filed 9/15/2015, now Abandoned, which claim benefit to US Provisional application 62/052189 filed 9/18/2014.
Election/Restrictions
Examiner note: The claim for priority is as a divisional, and in review of prosecution of the parent, while there is a restriction requirement, it was between two methods and system/product claims were not presented nor considered for restriction.
The claim as a divisional is not improper, however based on the prosecution there does not appear to be a bar between methods and products created by a prior restriction requirement.
Claim Status
Original claims 1-20 filed 8/12/2021 are pending.
Information Disclosure Statement
The three information disclosure statements (IDS) submitted between 4/28/2022 and 9/30/2024 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
It is noted that several of the cited references are Office actions are from foreign offices, some translated and some providing a summary. It is noted that for review of these, the pending claims that were reviewed in these actions were not provided, but for completeness and clarity of the record the cited references when provided in this prosecution were not considered in light of the instant claims. The foreign statutes and comments of the reviewers were not clearly in context of the pending claims and were not considered for their logic nor factual accuracy of comments in actions from other foreign offices.
The listing of references in the specification is not a proper information disclosure statement. See for example listing in [0055]-[0057]. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Claim Rejections - 35 USC § 112
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 ‘sample analyzer’, a ‘first filter module’, an ‘aligner module’, a ‘second filter module’ in claim 1. More specifically at [0050] the specification teaches: “The above and the following detailed description of various embodiments will be better understood when read in conjunction with the appended drawings. To the extent that the figures illustrate diagrams of the functional blocks of the various embodiments, the functional blocks are not necessarily indicative of the division between hardware circuitry. Thus, for example, one or more of the functional blocks (e.g., modules, processors, or memories) may be implemented in a single piece of hardware (e.g., a general-purpose signal processor or a block of random access memory, hard disk, or the like) or multiple pieces of hardware. Similarly, the programs may be stand alone programs, may be incorporated as subroutines in an operating system, may be functions in an installed software package, and the like. It should be understood that the various embodiments are not limited to the arrangements and instrumentality shown in the drawings.” While one interpretation is that the embodiments are instructions, the embodiment for physical components is the specific issue and basis of this 112 6th. These are not terms of art, and more generally the specification appears to teach that these would be directed to general purpose computers/processors (note guidance at [0050] for the use of ‘hardware (e.g., a general purpose signal processor or a block of random access memory, hard disk, or the like)’ for hardware).
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. In this case, the modules and analyzer are being interpreted consistent with the use of generic purpose signal processor.
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.
Claims 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
Claim analysis
Claim 1 is generally directed to a ‘sample analyzer’ comprising a controller and user interface, where in the controller comprises a series of modules. In view of the specification, each of the ‘modules’ do not appear to be known or physical components, but rather instructions of a method for analyzing sequencing data where the user interface appears to be using a computer. The claims encompass and in dependent claims provide steps for associating regions of interest to loci and identifying potential alleles from sequence read data and whether the read represents a stutter product of an allele of interest. More specifically, the claims recite and require receiving sequence data, assigning the reads to a loci based on homology, and identifying a region of interest (suspected stutter product present in sequences) by analyzing a loci for potential alleles based on the presence of repeat motifs. As amended, the claim preamble recites ‘using a computer’ and the computer comprises ‘one or more programs, wherein the one or more programs include instructions for’ performing the steps as previously set forth. As amended, the claimed steps are performed by a ‘sample analyzer’, a ‘first filter module’, an ‘aligner module’, a ‘second filter module’, and a new final step for ‘calling’ where the analysis of the read data for a first and second allele are determined to be a stutter product or not. Claim 20 refers to claim 1, and indicates that the sample analyzer is comprised in a system.
For the required steps, it is noted that the data received of the ‘plurality of sample reads’ and no specific indication of how the reads are obtained. With respect to possible sources and preferred embodiments, in view of the guidance of [0065] which teaches: “In particular embodiments, the sample reads are directed toward predetermined genetic loci, such as those genetic loci having suspected STRs or suspected SNPs. The sample reads may be selected based on known primer sequences associated with the genetic loci- of-interest. For example, the sample reads may include PCR amplicons that are obtained using the primer sequences associated with the genetic loci-of-interest.” And the definition at [0098] which teaches “As used herein, the term "amplicon" refers to any suitable amplification product for which a sequence is obtained.” The read data can be specific for a loci of interest, and not necessarily represent a large nor complex set of reads/amplicon read data for analysis.
For step 1 of the 101 analysis, claims 1-20 are found to be directed to a statutory category of a product.
For step 2A of the 101 analysis, the judicial exception of the claims are the steps of accessing sequence data for sequences of interest that represent stutter/repeat sequences at a loci. The step of aligning and comparing sequence to arrive at the identification of repeat motif sequences are instructional steps. As amended, the claims require the use of a ‘sample analyzer’, a ‘first filter module’, an ‘aligner module’, a ‘second filter module’, and in review of the specification these can be interpreted as either physical devices or abstract instructions as stand-alone programs or subroutines of a program. Review of the specification at [0050] teaches: “The above and the following detailed description of various embodiments will be better understood when read in conjunction with the appended drawings. To the extent that the figures illustrate diagrams of the functional blocks of the various embodiments, the functional blocks are not necessarily indicative of the division between hardware circuitry. Thus, for example, one or more of the functional blocks (e.g., modules, processors, or memories) may be implemented in a single piece of hardware (e.g., a general purpose signal processor or a block of random access memory, hard disk, or the like) or multiple pieces of hardware. Similarly, the programs may be stand alone programs, may be incorporated as subroutines in an operating system, may be functions in an installed software package, and the like. It should be understood that the various embodiments are not limited to the arrangements and instrumentality shown in the drawings.” For purposes of 101, both embodiments will be examined. Here in prong 1, to the extent that the claims encompass instructions for the analysis of the sequence read data, the claim requires broadly and simply ‘analyzing’ for k repeat motifs within a sequence. The judicial exception is a set of instructions for analysis of sequence data. In view of the breadth of the claim and guidance of the specification, this is considered to be in the category of a mental processes, that is concepts performed in the human mind (including an observation, evaluation, judgment, opinion)
Recent guidance from the office requires that the judicial exception be evaluated under a second prong to determine whether the judicial exception is practically applied. In the instant case, the claims do not have an additional element to which the analysis is applied. The newly added step of ‘calling’ appears to be directed to outputting the information and a description of the outcome of the analysis as either an allele or a stutter product. This judicial exception requires steps recited at high level of generality for the analysis of sequence data, and is not found to be a practical application of the judicial exception as broadly set forth.
For step 2B of the 101 analysis, initially it is noted that he claims do not recite or require any details on implementation and are interpreted to no comprise any additional elements to evaluate under step 2B except that they are practiced with the use of a computer. As set forth above, one interpretation is that the modules are physical parts of a system, that are linked together to perform the method of analysis. In review of the specification and art of record, each of a ‘sample analyzer’, a ‘first filter module’, an ‘aligner module’, a ‘second filter module’ do not appear to be terms of art or defined modules, and are consistent with the disclosure at [0050] for the use of ‘hardware (e.g., a general purpose signal processor or a block of random access memory, hard disk, or the like)’ and so while the independent claim recites a possible additional element and they are found to be the steps of receiving/obtaining/analyzing sequence data with a computer, and appear to be separate steps for performing the analysis steps. In view of the guidance of the specification, it does not appear that how the data is received affects the analysis required of the claim, nor does there appear to be any importance to the physical nature of any of the modules or analyzer that is required. As such, the claims do not provide for any additional element to consider under step 2B, nor provide for significantly more when viewed in light of the guidance of the specification and limitations required of the claims as a whole.
As indicated in the summary of the judicial exception above and in view of the teachings of the specification, the steps are drawn to analysis of sequence read data. While the instruction can be stored on a medium and could be implemented on a computer, together the steps do not appear to result in significantly more than a means to compare and analyze read data of sequences. The judicial exception of the method as claimed can be performed by hand and in light of the teaching of the specification on a computer. In review of the instant specification the methods do not appear to require a special type of processor and can be performed on a general purpose computer.
Based upon an analysis with respect to the claim as a whole, the claims do not recite something significantly different than a judicial exception. Claims 1-20 are directed towards a method of receiving sequence data and comparing the data to identify ‘regions of interest’ wherein the sequences represent potential stutter sequences and alleles. Dependent claims set forth additional steps which are more specifically define the considerations and steps of calculating, and comparing, and do not add additional elements which result in significantly more to the claimed method for the analysis.
One way to overcome a rejection for non-patent-eligible subject matter is to persuasively argue that the claimed subject matter is not directed to a judicial exception. Another way for the applicants to overcome the rejection is to persuasively argue that the claims contain elements in addition to the judicial exception that either individually or as an ordered combination are not well understood, routine, or conventional. Another way for the applicants to overcome the rejection is to persuasively argue that the claims as a whole result in an improvement to a technology. Persuasive evidence for an improvement to a technology could be a comparison of results of the claimed subject matter with results of the prior art, or arguments based on scientific reasoning that the claimed subject matter inherently results an improvement over the prior art. The applicants should show why the claims require the improvement in all embodiments.
Conclusion
No claim is allowed.
The use of massive parallel sequencing in the analysis of amplification products was known at the time of filing. Further, issues related to the analysis of repeat sequences such as STRs in forensic analysis relative to amplification and sequencing relative to potential issues related to stutter were also known based on the art of record. While the art supports identifying and reviewing/analyzing multiple clones to confirm sequence information, the art of record fails to provide the steps set forth for the analysis ‘modules’ of any source of read data as required of the instant claims.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Joseph T Woitach whose telephone number is (571)272-0739. The examiner can normally be reached Mon-Fri; 8:00-4:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz R Skowronek can be reached at 571 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Joseph Woitach/Primary Examiner, Art Unit 1687
Prosecution Insights