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 Status
Claims 1-16 are pending and under examination herein.
Claim 1 and 15 are objected to.
Claims 1-16 are rejected.
Priority
The instant application is a National Stage entry of PCT/GB2020/051753, International Filing Date: 07/22/2020, which claims foreign priority to GB1916002.7 filed 11/04/2019 and GB1910478.5 filed 07/22/2019. As such, the effective filing date assigned to each of claims 1-16 is 07/22/2019. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Drawings
The drawings filed 01/20/2022 are accepted by the examiner.
Claim Objections
Claims 1 and 15 are objected to because of the following informalities:
In claim 1, the sub-steps of are not properly indented (e.g. the sub-steps for “a computing arrangement….wherein the computing arrangement is configured to:” step). Where a claim sets forth a plurality of elements or steps, each element or step of the claim should be separated by a line indentation. There may be plural indentations to further segregate subcombinations or related steps
In claim 15, “comprising” should be “further comprising”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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.
Claim 12 is 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 12 is incomplete for omitting essential steps, such omission amounting to a gap between the steps. See MPEP § 2172.01. The omitted steps are: determining the CNV gain or loss and generating a confidence score.
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 1-16 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea/law of nature/natural phenomenon without significantly more. In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Claims 1, 13 and 16 recite compare the plurality of characteristic attributes in the interpretation request with the prestored metadata associated with each of the plurality of sample genomic DNA sequences in the database arrangement; - identify a set of sample genomic DNA sequences as a reference panel from the plurality of sample genomic DNA sequences, based on the comparison of the information in the interpretation request with the metadata of each sample genomic DNA sequence and a plurality of defined criteria; and - utilize the reference panel comprising the identified set of sample genomic DNA sequences for calling CNVs in the target genomic DNA sequence.
These recitations equate to steps of collecting information, analyzing data and making observations, evaluations and judgements that can be carried out in the human mind. Specifically, comparing attributes in a request to prestored metadata, identifying a set of sample genomic DNA sequences as a reference panel based on the comparison and defined criteria, and utilizing the reference panel for calling CNVs in a target DNA sequence can be practically performing the human mind as claimed, since the mind can read data and make comparisons, identify data that meets a set criteria based on the comparison, and then use this identified data to find matching data in a target DNA sequence as claimed, and are similar to the concepts of collecting and comparing known information in Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1067, 100 USPQ2d 1492, 1500 (Fed. Cir. 2011) and collecting information, analyzing it, and reporting certain results of the collection and analysis in Electric Power Group v. Alstom, S.A., 830 F.3d 1350, 1353-54, 119 USPQ2d 1739, 1741-42 (Fed. Cir. 2016) that the courts have identified as concepts that can be practically performed in the human mind. Therefore, each of the above recited limitations fall under the “Mental Processes” grouping of abstract ideas. Claims 2-13 and 14-15 further recite or qualify the judicial exceptions. As such, claims 1-16 recite an abstract idea (Step 2A, Prong 1: YES).
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, applies or uses the recited judicial exception to affect a particular treatment for a condition, implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, effects a transformation or reduction of a particular article to a different state or thing or applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception. Rather, the instant claims recite additional elements that amount to mere data gathering and outputting and mere instructions to implement the abstract idea in a generic computing environment. Specifically, the claims recite the following additional elements:
Claims 1, 13 and 16 recite a database arrangement that is configured to store a plurality of sample genomic DNA sequences and metadata that is associated with each of the plurality of sample genomic DNA sequences; and - a computing arrangement that is communicatively coupled to the database arrangement, wherein the computing arrangement is configured to: - render a user interface that is configured to receive a target genomic DNA sequence along with an interpretation request for calling CNVs in the target genomic DNA sequence, wherein the interpretation request comprises a plurality of characteristic attributes related to the target genomic DNA sequence; - compare the plurality of characteristic attributes in the interpretation request with the prestored metadata associated with each of the plurality of sample genomic DNA sequences in the database arrangement; wherein the user interface is configured to allow submission of target genomic DNA sequence separately at a timepoint that is different from a timepoint when the reference panel is identified and specified for use as the reference panel for the target genomic DNA sequence.
Claim 16 also recites a computer program product comprising a non- transitory computer-readable storage medium having computer-readable instructions stored thereon, the computer-readable instructions being executable by a computerized device comprising processing hardware.
Claims 2 and 14 recite wherein the computing arrangement is further configured to: - acquire the plurality of sample genomic DNA sequences from the database arrangement; - retrieve a plurality of characteristic attributes related to the sample genomic DNA sequences to generate metadata, wherein the plurality of characteristic attributes related to each of the sample genomic DNA sequence comprises: - at least one protocol applied to derive a genomic DNA sequence: a type of sequencing, an area-of-genomic-interest;- a type of sample used to derive the genomic DNA sequence; - a gender of an individual from which the sample is acquired for the derivation of the genomic DNA sequence; and - a familial record of the individual from which the sample is acquired for the derivation of the genomic DNA sequence; - store the plurality of sample genomic DNA sequences and the associated metadata with each of the plurality of sample genomic DNA sequences in the database arrangement.
Claim 5 recites store each group of identified sample genomic DNA sequences having the same metadata as one project of a plurality of projects
Claims 8 and 15 recites wherein the database arrangement is configured to store at least one CNV detection application
Claim 9 recites wherein the computing arrangement is further configured to execute the CNV detection application
Claim 12 recites wherein the computing arrangement is further configured to display patient information via the user interface, and wherein the patient information comprises at least patient overview information and variant information, and wherein - the patient overview information comprises: - a status of the interpretation request, wherein the status of the interpretation request is any one of: pending, complete, rejected; - a protocol applied to derive the target genomic DNA sequence of a patient; - a type of sample utilised to derive the target genomic DNA sequence of the patient.
Claims 3-4, 6-8 and 10-11 do not recite elements in addition to the recited judicial exceptions. Claims 1-2, 12-14 and 16 recites limitations for gathering and outputting data. These limitations equate to mere data gathering activity to obtain the data necessary for the mental evaluations and judgement and for outputting data, which the courts consider to be an insignificant extra-solution activity (see MPEP 2106.05(d) and MPEP 2106.05(g)). There is no indication that any of these additional elements provide a practical application of the recited judicial exception outside of the judicial exception itself. Claims 1-2, 5, 9, 12-16 also merely recites using a generic computing systems and computer program products to carry out instructions to implement an abstract idea on a computer. The computer system and computer program product as claimed fails to recite details of how a solution to a problem is accomplished and only recites the idea of a solution or outcome. There are no limitations that indicate that the claimed steps require anything other than generic computing systems. 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. Furthermore, the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit). As such, claims 1-16 are directed to an abstract idea (Step 2A, Prong 2: NO).
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). Further analyzing the additional elements under step 2B, the additional elements as described above do not rise to the level of significantly more than the judicial exception. As directed in the Berkheimer memorandum of 19 April 2018 and set forth in the MPEP, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims under the 2B analysis, the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not provide significantly more. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit). Therefore, 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, and the claims do not amount to significantly more than the judicial exception itself (Step 2B: NO). As such, claims 1-16 are not patent eligible under 35 U.S.C. 101.
Claim Rejections - 35 USC § 102
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 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.
Claims 1-16 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Reid et al. (US20160342733A1; hereafter referred to as Reid).
With respect to claims 1, 13 and 16, Reid discloses methods and systems for determining copy number variant by applying a sample grouping technique to select reference coverage data, normalizing sample coverage data comprising a plurality of genomic regions, and fitting a mixture model to the normalized sample coverage data based on the selected reference coverage data (abstract).
Reid discloses a computer with a database and a processor coupled to other remote computing devices via a network, and further that the database can be used to store the DNA sequence data and the metrics (i.e. metadata) of the samples (fig 7; para 0037; para 0111-0118).
Reid discloses sample coverage data comprising a plurality of genomic regions can be provided by a user, and indication of reference coverage data and plurality of metrics for the sample coverage data can also be received (para 0084-0085). Reid further discloses requesting identifying one or more CNV according to a HMM (fig 5).
Reid discloses “A reference panel of coverage data (e.g., reference coverage data comprising one or more genomic capture regions) can be selected for each sample (e.g., sample coverage data comprising one or more genomic capture regions) based on a plurality of metrics (e.g., sequencing Quality Control (QC) metrics) using a sample grouping technique. The sample grouping technique can comprise a technique (e.g., algorithm) for grouping samples by similarity. Examples of sample grouping techniques that can be used include, but are not limited to, a decision tree, a support-vector machine, a k-nearest neighbors (knn) algorithm, a Naïve Bayes algorithm, a CART (Classification and Regression Trees) algorithm, and/or the like. For example, a kNN algorithm can comprise generating a k-d tree data structure. The reference coverage data can be selected by inserting the sample coverage data (e.g., or metrics associated with the sample coverage data) into the k-d tree structure and identifying a predetermined number of nearest neighbors 10, 100, 1000, 10000, etc. . . . ). After selecting reference coverage data, samples can be processed in parallel. Sample-level analysis (right panel) includes normalizing coverage, fitting coverage distributions with a mixture model, and generating calls from an HMM”, and further discloses the reference panels are customizable and that the plurality of metrics can comprise, for example, sequencing quality control (QC) metrics, sample metadata, ancestry-based values, sequence-similarity scores, and/or any metric that captures sample-level variability (para 0036-para 0037; para 0044).
Reid discloses performing CNV calling for samples using the reference panel (0034). There is nothing to suggest that the target sequences cannot be separately submitted and Reid further discloses inputting normalized sample coverage data for each calling window into a HMM model, indicating sample data can be submitted at a separate timepoint than when the reference panel is identified (para 0093-0094; para 0119).
Reid further discloses the methods and systems may take the form of an entirely hardware embodiment, an entirely software embodiment, or an embodiment combining software and hardware aspects.
With respect to claims 2, 5 and 14, Reid discloses the computer contains the memory from which data is stored and retrieved, and that the databases can be centralized or distributed across many systems (para 0113-0118).
Reid further discloses a plurality of metrics of the reference coverage data can be used by the sample grouping technique and the metrics include sequencing quality control (QC) metrics, sample metadata, ancestry-based values, sequence-similarity scores, and/or any metric that captures sample-level variability, and that the sex of the sample can also be provided, which suggest the samples are tagged with the metadata (para 0037; para 0082).
With respect to claims 3 and 4, Redi discloses applying a sample grouping technique to select reference coverage data, normalizing sample coverage data comprising a plurality of genomic regions, and fitting a mixture model to the normalized sample coverage data based on the selected reference coverage data, and identifying one or more copy number variants (CNVs) according to a Hidden Markov Model (HMM) based on the normalized sample coverage data and the fitted mixture model, wherein a k-nearest neighbor algorithm that utilizes a k-d tree is used to illustrate the sample grouping technique and the k-d tree can comprise a multidimensional search tree for points in k dimensional space and the plurality of metrics of the reference coverage data can be used by the sample grouping technique to build the k-d tree, and further that each newly sequenced sample can be added to a k-d tree in this metric space. CNVs can be called using selected reference coverage data comprising the individual sample's k nearest neighbors, indicating the metadata attributes used are mutually common and use the plurality of metrics provided (abstract; para 0037-0039).
With respect to claim 4, Reid further discloses the sample grouping can be based on a classification algorithm such as a decision tree, which would be capable of facilitating comparison of the samples based on the defined criteria as defined in instant claim 4 (para 0036; para 0043).
With respect to claim 6, Reid discloses filtering and normalizing the data, including determining the minimum default binning resolution of the data to provide each bin with a sufficient sample size for estimation (para 0057-0061).
With respect to claim 7, Reid discloses basing the expected copy number (e.g., diploid or haploid) on sex explicitly can be more effective than normalizing the variance due to sex or comparing samples to highly-correlated samples because such approach accounts for the integer nature of copy number states, as a female with 0.5× the expected coverage for a region on chrX is likely to have a heterozygous deletion, while a male with the same level of coverage may not be likely to have a heterozygous deletion, because one cannot have a copy number of ½, suggesting that sex can be discloses as female based on the data even if the sex is not provided in the metadata (para 0082).
With respect to claims 8 and 15, Reid discloses the CNV calling software is stored in the system database, and are utilized to perform the CNV calls (fig 7; para 0045-0051; para 0115-0118).
With respect to claim 9, Reid discloses utilizing read depths within the CNV and also filtering based on sample coverage depth and using thresholds for filtering (para 0034; para 0039; para 0054-0058).
With respect to claim 10, Reid discloses filtering sample coverage data based on mappability scores of a genomic region, based on overlapping regions, and filtering the one or more calling windows based on a mappability score can comprise determining a mappability score for each genomic region of the plurality of genomic regions and excluding a calling window of the one or more calling windows that contains the genomic region of the plurality of genomic regions if the mappability score of the genomic region of the plurality of genomic regions is below a predetermined threshold, which also suggest ranking the samples based on the determined scores would be possible (para 0057).
With respect to claim 11, Reid discloses determining F-scores as the geometric mean of precision and recall for the CNV callers (para 0137;fig 10).
With respect to claim 12, Reid discloses any step and/or result of the methods can be output in any form to an output device. Such output can be any form of visual representation, including, but not limited to, textual, graphical, animation, audio, tactile, and the like, indicating the metrics, method, sample panel, CNV calling results and F-scores can be output to the user interface (para 0120).
Conclusion
No claims allowed.
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to NIDHI DHARITHREESAN whose telephone number is (571)272-5486. The examiner can normally be reached Monday - Friday 9:00 - 5:00.
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/N.D./Examiner, Art Unit 1686
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687