DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Claim Status
Claims 1-16 are currently pending and under exam herein.
Priority
The instant Application is a continuation of U.S. Patent Application No. 15/894,283 filed on February 12, 2018, now US Patent 11,306,354, which is a continuation of U.S. Patent Application No. 13/782,857 filed on March 1, 2013, now U.S. Patent No. 9,920,361, which claims the benefit of U.S. Provisional Patent Application No. 61/740,368 filed on December 20, 2012 and U.S. Provisional Patent Application No. 61/649,841 filed on May 21, 2012. Priority is acknowledged to the Effective Filing Date (EFD) of 21 May 2012.
Information Disclosure Statements
The Information Disclosure Statements filed 24 May 2022; 29 November 2023; and 17 October 2024 are in-part in compliance with the provisions of 37 CFR 1.97 and have therefore been considered. Signed copies of the IDS documents are included with this Office Action. It is noted that certain references have not been considered and are lined-through, as they do not comply with the requirements set forth in 37 CFR 1.97, as said citations lack appropriate dates and/or page numbers.
Applicant is reminded that it is desirable to avoid the submission of long lists of documents if it can be avoided. As set forth in MPEP 2004, applicant is directed to eliminate clearly irrelevant and marginally pertinent cumulative information. If a long list is submitted, highlight those documents which have been specifically brought to applicant's attention and/or are known to be of most significance. See Penn Yah Boats, Inc. v. Sea Lark Boats, Inc., 359 F.Supp. 948, 175 USPQ 260 (S.D. Fla. 1972), aft'd, 479 F.2d 1338, 178 USPQ 577 (5th Cir. 1973), cert. denied, 414 U.S. 874 (1974). But cf. Molins PLC v. Textron Inc., 48 F.3d 1172, 33 USPQ2d1823 (Fed. Cir. 1995). Applicant has cited more than 1000 references, many of which are not clearly relevant to the claimed invention. Applicant is cautioned against burying material references and the appearance of inequitable conduct in this application.
Drawings
The Drawings filed 10 March 2022 have been accepted.
Specification
Note: All references to the Specification herein pertain to the PG publication: US20220205037.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. Please see, for example, paragraph [0345].
Claim Interpretation
Claim 1 includes a system with processors and a memory, of which the memory includes instructions executable by the processor(s) and wherein the memory comprises counts of thousands to millions of nucleotide sequence reads mapped to genomic portions of a reference genomes. The sequence reads are defined as those that are of circulating cell-free nucleic acids from a test sample from a pregnant female. The sequences are further defined as generated by a non-loci-specific massively parallel sequencing process. As such, claim 1 is interpreted as a system with information stored thereon. The information includes nucleotide sequence reads. Those reads are not actively sequenced in the claim, but rather the characteristic of said reads is hat they are from a sequencing process, as no active step of actual sequencing is performed. Therefore, the claim system houses information of said specific sequence data.
Claim 1, step (b) recites, “select counts for the thousands to millions of sequence reads from nucleic acid fragments that are shorter than about 150 bases to about 160 bases” wherein the claim is interpreted as fragment length that is less than a determined cutoff/threshold value, wherein the cutoff/threshold is about 150 bases to about 160 bases, as disclosed in the Specification at least at [0247].
Claim 14 recites, “wherein the sequencing process is performed at about 0.1- fold coverage, about 0.2-fold coverage, about 0.3-fold coverage, about 0.4-fold coverage, about 0.5-fold coverage, about 0.6-fold coverage, about 0.7-fold coverage, about 0.8-fold coverage, about 0.9-fold coverage, about 1-fold coverage, or greater than 1-fold coverage”. Because the claim is interpreted (see above with respect to claim 1) as not actively performing sequencing, the limitation herein is interpreted as directed to a characteristic of the housed data.
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 without significantly more.
The instant rejection reflects the framework as outlined in the MPEP at 2106.04:
Framework with which to Evaluate Subject Matter Eligibility:
(1) Are the claims directed to a process, machine, manufacture or composition of matter;
(2A) Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
(2B) If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1 Analysis: Are claims directed to process, machine, manufacture/composition of matter
With respect to step (1): yes, the claims are directed to a system.
Step 2A, Prong 1 Analysis: Do claims recite abstract idea
With respect to step (2A)(1), the claims recite abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
With respect to the instant claims, under the (2A)(1) evaluation, the claims are found herein to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and in conjunction with mathematical concepts (in particular mathematical relationships and formulas).
Note: The claims elements are italicized herein to highlight the judicial exceptions in the claim steps and underlined to represent the additional claim elements.
Claim 1:
A system comprising one or more processors and memory, which memory comprises instructions executable by the one or more processors and which memory comprises counts of thousands to millions of nucleotide sequence reads mapped to genomic portions of a reference genome, which sequence reads are reads of circulating cell-free nucleic acid from a test sample from a pregnant female bearing a fetus and which sequence reads are generated by a non-loci-specific massively parallel sequencing process, and which instructions executable by the one or more processors are configured to:
(a) measure the lengths of nucleic acid fragments from which the sequence reads are generated, wherein said operation is directed to mental processes whereby taking a measurement of the lengths of nucleic acid fragments can be performed using pen and paper or, alternatively, using a computer as a tool or in a computing environment to assess nucleic acid fragments from sequence reads;
(b) select counts for the thousands to millions of sequence reads from nucleic acid fragments that are shorter than about 150 bases to about 160 bases, thereby generating selected counts of the thousands to millions of sequence reads, wherein the selected counts are enriched for counts of reads from fetal nucleic acid, wherein said operation is a mental process of making a selection of given data to provide a desired outcome selection and can be performed using pen and paper or, alternatively, using a computer as a tool or in a computing environment to generate said counts; and
(c) normalize the selected counts of the thousands to millions of sequence reads for the test sample according to an experimental bias for the test sample and an experimental bias for each of multiple samples from multiple pregnant females, thereby generating normalized selected counts, wherein experimental bias in the normalized selected counts is reduced, wherein said operation is directed to mathematical concepts that include fitting calculations (see also claim 8) and see the Specification at [0391].
Claim 2:
The system of claim 1, wherein the instructions executable by the one or more processors are configured to select counts for the thousands to millions of sequence reads from nucleic acid fragments that are shorter than about 150 bases, wherein said operations further limit the step of selection in above claim 1 and are also directed to abstract ideas.
Claim 3:
The system of claim 1, wherein the instructions executable by the one or more processors are configured to select counts for the thousands to millions of sequence reads from nucleic acid fragments that are shorter than about 160 bases, wherein said operations further limit the step of selection in above claim 1 and are also directed to abstract ideas.
Claim 4:
The system of claim 1, wherein the lengths of the nucleic acid are measured according to positions of mapped sequence reads obtained from a paired-end sequencing process, wherein said operations further limit the step of measuring in above claim 1 and are also directed to abstract ideas.
Claim 7:
The system of claim 1, wherein the experimental bias for the test sample in (c) is a guanine and cytosine (GC) bias, and the experimental bias for each of multiple samples from multiple pregnant females in (c) is a guanine and cytosine (GC) bias, wherein said operations further limit the step of normalizing in above claim 1 and are also directed to abstract ideas.
Claim 8:
The system of claim 7, wherein the normalizing in (c) comprises 1) determining a guanine and cytosine (GC) bias coefficient for the test sample based on a fitted relation between (i) the counts of the sequence reads mapped to each of the genomic portions and (ii) GC content for each of the genomic portions, wherein the GC bias coefficient is a slope for a linear fitted relation or a curvature estimation for a non-linear fitted relation; and 2) determining a fitted relation, for each of the genomic portions, between (i) a GC bias coefficient for each of the multiple samples from multiple pregnant females and (ii) counts of sequence reads mapped to each of the genomic portions for the multiple samples, wherein said operations are further directed to limiting the normalization procedures in above claim 1 and include mathematical concepts further directed to linear fitting or curvature estimations, which are operations for modeling relationships among mathematical variables to best represent data.
Claim 9:
The system of claim 1, wherein the instructions executable by the one or more processors are further configured to map the sequence reads to the portions of the reference genome, and count the mapped sequence reads, thereby generating the counts of the sequence reads mapped to the portions of the reference genome, wherein said operations are further directed to limiting the abstract steps in above claim 1 and include mental operations of mapping and counting, in a computer environment or using a computer as a tool.
Claim 10:
The system of claim 1, wherein the sequence reads are mapped to multiple chromosome portions from multiple chromosomes of the reference genome, wherein said operations are further directed to limiting the abstract steps in above claim 1 and include mental operations of mapping and counting, in a computer environment or using a computer as a tool.
Claim 11:
The system of claim 1, wherein the sequence reads are mapped to portions of a complete human reference genome, wherein said operations are further directed to limiting the abstract steps in above claim 1 and include mental operations of mapping and counting, in a computer environment or using a computer as a tool.
Hence, the claims explicitly recite numerous elements that, individually and in combination, constitute abstract ideas.
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined herein to each cover performance either in the mind (calculations by hand or pen and paper or computer as a tool) and performance by mathematical operation (normalization; curve fitting; etc.). There are no specifics as to the methodology involved in “measureing” or in “selecting” and thus, under the BRI, one could simply, for example, perform said operation with pen and paper, or, alternatively with the aid of a generic computer as a tool to perform said operations. These recitations are similar to the concepts of collecting information, analyzing it and providing certain results from the collection and analysis (Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations (Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in (Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind with pen and paper, and can include mathematical concepts.
Further, see MPEP § 2106.04(a)(2), subsection III. The courts do not distinguish between mental processes that are performed entirely in the human mind and mental processes that require a human to use a physical aid (e.g., pen and paper or a slide rule) to perform the claim limitation (see, e.g., Benson, 409 U.S. at 67, 65, 175 USPQ at 674-75, 674: noting that the claimed "conversion of [binary-coded decimal] numerals to pure binary numerals can be done mentally," i.e., "as a person would do it by head and hand."); Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1139, 120 USPQ2d 1473, 1474 (Fed. Cir. 2016): holding that claims to a mental process of "translating a functional description of a logic circuit into a hardware component description of the logic circuit" are directed to an abstract idea, because the claims "read on an individual performing the claimed steps mentally or with pencil and paper"). Nor do the courts distinguish between claims that recite mental processes performed by humans and claims that recite mental processes performed on a computer. As the Federal Circuit has explained, "[c]ourts have examined claims that required the use of a computer and still found that the underlying, patent-ineligible invention could be performed via pen and paper or in a person’s mind" (see Versata Dev. Group v. SAP Am., Inc., 793 F.3d 1306, 1335, 115 USPQ2d 1681, 1702 (Fed. Cir. 2015); Mortgage Grader, Inc. v. First Choice Loan Servs. Inc., 811 F.3d 1314, 1324, 117 USPQ2d 1693, 1699 (Fed. Cir. 2016): holding that computer-implemented method for "anonymous loan shopping" was an abstract idea because it could be "performed by humans without a computer").
Step 2A, Prong 2 Analysis: Integration to a Practical Application
Because the claims do recite judicial exceptions, direction under (2A)(2) provides that the claims must be examined further to determine whether they integrate the abstract ideas into a practical application (MPEP 2106.04(d). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim is said to fail to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
With respect to the instant recitations, the claims recite the additional elements as underlined above. Specifically said steps are those that include a system and processor and memory with instructions executable by a processor. The computer memory stores the data of nucleotide sequence reads mapped to genomic portions and defined to be those that are circulating cell-free nucleic acids. Further steps directed to additional elements in the claim are those that further limit the data as in claim 1 and are those that include limitations on the data such as claims 5 and 12-16.
As the “system” includes the memory with stored data, said memory with stored data serves as the vehicle for data gathering in the claim. Additional elements in the instant claims directed to data gathering perform functions of collecting the data needed to carry out the abstract idea. Data gathering does not impose any meaningful limitation on the abstract idea, or on how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application. (MPEP 2106.05(g).
Further, the system, processor, memory and instructions are part of a general purpose computer system and there are no details herein wherein of how the specific computer structures are used to implement the judicial exceptions beyond generic computing operations, i.e., the computer elements of the claims do not provide improvements to the functioning of the computer itself (see: DDR Holdings, LLC v. Hotels.com LP); they do not provide improvements to any other technology or technical field (see: Diamond v. Diehr); nor do they utilize a particular machine (see: Eibel Process Co. v. Minn. & Ont. Paper Co.). Hence, these are mere instructions to apply the judicial exception using a computer, and therefore the claim does not provide integration into a practical application of any judicial exception.
Step 2B Analysis: Do Claims Provide an Inventive Concept
The claims are lastly evaluated using the (2B) analysis, wherein it is determined that because the claims recite abstract ideas, and do not integrate that abstract ideas into a practical application, the claims also lack a specific inventive concept. Applicant is reminded that the judicial exception alone cannot provide the inventive concept or the practical application and that the identification of whether the additional elements amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception. (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements of data gathering 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, the claim elements directed to a computer system with sequencing information are data gathering elements as in 2A, prong 2 and that under the assessment herein under 2B encompass steps that are routine, well-understood and conventional in the art. For example, the prior art to Fan et al. (2010/0138165-IDS reference) disclose sequencing protocols that include mapping to genomic regions that serve as the basis of the additional elements herein (see Fan at least at [0021]; [0032]; [0056]). It is noted that actual sequencing steps are not performed by the instant claims (see claim interpretation above). However if sequencing were to be performed, it is a routine and conventional practice in the art (as in Fan et al.) an would further not provide for an inventive concept under 2B.
Further, the instant Specification discloses that there are numerous sequencing methodologies that can be implemented for data acquisition, such as those at [0320]-[0336], citing numerous publications for protocols. The courts have recognized the following laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity (see MPEP 2106.05(d)II.): determining the level of a biomarker in blood by any means (Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017)); detecting DNA or enzymes in a sample (Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157); Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017)).
With respect to the claims to the system and processor, memory and instruction, the computer-related elements or the general purpose computer do not rise to the level of significantly more than the judicial exception. Further exemplified prior art to, for example, Fan teaches that computing elements are routine, well-understood and conventional in the art for implementing methods involving sequence read data [0031]. Further, the specification also discloses that computer processors and systems, as example, are generic computing systems [0581]. The additional elements are set forth at such a high level of generality that they can be met by a general purpose computer. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than an abstract idea (see MPEP 2106.05(b)I-III).
The dependent claims have been analyzed with respect to step 2B and none of these claims provide a specific inventive concept, as they all fail to rise to the level of significantly more than the identified judicial exception.
For these reasons, the claims, when the limitations are considered individually and as a whole, are rejected under 35 USC § 101 as being directed to non-statutory subject matter.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
1. Claims 1-16 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-15 of U.S. Patent No. 9,920,361. Although the claims at issue are not identical, they are not patentably distinct from each other because practicing the method claims of U.S. Patent No. 9,920,361 would necessarily anticipate the computer-implemented claims of the instant application. The patented claims are generic and the specification thereof openly contemplates the use of a generic computer to perform the claimed analysis. The claims of the instant application are broader in scope than the narrower claims as set forth in U.S. Patent No. 9,920,361 because the instant claims do not expressly recite the additional step of "performing a medical procedure" following the step of "determining the presence of a chromosome aneuploidy". The instant specification further openly contemplates additional steps wherein the claimed computer-implemented "detecting the presence or absence of a chromosomal aneuploidy" may be followed by medical procedural steps or operations.
2. Claims 1-16 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of U.S. Patent No. 11,306,354. Although the claims at issue are not identical, they are not patentably distinct from each other because practicing the method claims of U.S. Patent No. 11,306,354 would necessarily anticipate the processors and memory herein, as said operations in the ‘354 patent are directed to in silico operations. The patented claims are generic and the specification thereof openly contemplates the use of a generic computer to perform the claimed analysis.
Conclusion
No claims are allowed.
With respect to the prior art, the closest prior art to Fan et al. (Clinical Chemistry (2010) Vol. 56:1279-1286-IDS reference) does not teach or fairly suggest normalization of the selected counts of the thousands to millions of sequence reads for a test sample according to experimental bias for the test sample, an experimental bias for each of multiple samples from multiple pregnant females and counts of sequence reads mapped to each of the genomic portions for the multiple samples to generate normalized selected counts.
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/Lori A. Clow/Primary Examiner, Art Unit 1687