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 .
Applicant’s amendment
Applicant’s amendment filed 7/15/2025 has been received and entered. Claims 1, 3, 8, 12, 16, 20, 24, 27 have been amended, claims 5-7, 13-14, 18, 21-22, 26 have been cancelled.
Claims 1-4, 8-12, 15-17, 19, 20, 23-25, 27 are pending.
Election/Restriction
Applicant's election with traverse of the species of DNA and methylation analysis, blood and over time in the reply filed on 1/28/2022 was acknowledged. Upon initial review and search, it was determined that it would not be an undue burden to examine all the inventions, and the restriction requirement was withdrawn.
The species election of DNA versus RNA was maintained. Claims 6-7 directed to non-elected RNA as a species have been cancelled.
Applicant is reminded that upon the cancellation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
Claims 1-4, 8-12, 15-17, 19, 20, 23-25, 27 are currently under examination.
Priority
This application filed 8/31/2021 is a continuation of 17/000010 filed 8/21/2020 (not docketed), which is a continuation of 15/431395 filed 2/13/2017 (final office action mailed 10/12/2021), which is a continuation of PCT/US2015/067717 filed 12/28/2015, which claims benefit to US Provisional applications 62/155763 filed 5/1/2015 and 62/098426 filed 12/31/2014.
No comment regarding the summary of priority is proved in Applicant’s response.
Information Disclosure Statement
The two information disclosure statements (IDS) submitted on 7/15/2025 and 10/1/2025 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 office actions are cited in the current IDS, however the pending claims, cited references for the applications are not provided for review.
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 27 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 is withdrawn.
Amendments to claim 27 to be dependent on claim 1 has addressed the basis of the rejection.
Claims 1-4, 8-12, 15-17, 19, 20, 23-25, 27 are 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. Specifically, the second step of the claim directed to partitioning is vague and unclear in the requirement of providing non-overlapping windows for a loci or more than one loci wherein the size is less than median spacing of origins of replication and whether the size is determined for the one or the more than one loci or for the whole genome. Further, it appears that a limitation is that one of the windows created overlaps a origin of replication locus and it is unclear if this is to limit the window size, a requirement of a window, for example if the partitioning requires only one window for partitioning must it require a ORI, can it comprise two if the two ORI are within the median spacing however that was determined. Additionally, in the first step a generic ‘population of nucleic acids’ are provided and it is unclear how they are related to the loci or windows that are generated in the partitioning step, and then for the step of quantification, how or what is performed to provide a measurement of CNV and what is done in making and adjusting based on ROCNV and how mutant allele frequency or methylation mutant frequency is derived and how or why it is related to a ‘quantifying’ step. The metes and bounds of the claims are not clear in what is required or performed the newly amended analysis claims. There is no clear requirement on the relationship of the generic sequence data provided and the analysis required using any generic reference and broad unclear analysis that requires quantification, mutant allele determination and methylation mutant allele determination and/or how this is related to quantification of the data first provided.
Dependent claims fail to provide further limitations or steps which clarify the issues of claim 1, and since they require claim 1 are included in the basis of the rejection.
More clearly setting forth steps which provide a clear indication of what the data represents and steps of analysis consistent and clear as to what is performed relative any reference data, and how the two are analyzed such that it provides the indicated values or general assessment set forth in the claim would address the basis of the rejection.
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-4, 8-12, 15-17, 19, 20, 23-25, 27 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. Specifically, a new step of partitioning is recited which requires that the partition windows are less than a median spacing between mammalian replication origins, and in review of the specification this median spacing and sized less than that do not appear to be supported by the specification. Initially, the search of the specification for support of a window sized ‘less than’ appears to be a range not specifically contemplated for partitioning. Further, there is no support for any mammalian ORI spacing and use or application to choosing window size for cfDNA from any subject or when the reference is a ‘reference human genome’. Additionally, there does not appear to be support for generic provision of cfDNA sequences and any nexus to providing the quantification and analysis required in the comparison of the nucleic acids from disease cells present in cfDNA and that of a partitioned reference data source of a human genome and providing information for all CNV, allele frequency and methylation mutant frequency as amended. Finally, if or once such information is provided in the quantification, there does not appear to be support for any database where information related to these analysis provides for retrieving any specific or ‘effective therapeutic intervention’ based on the steps required of the claim as a whole. The limitations and combinations of the limitations appear to be a new scope that is not specifically supported and is not contemplated given the guidance of the instant specification.
More clearly providing steps or limitations supported by the specification which are consistent with each other as a method of analysis would address the basis of this rejection.
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).
Response to Applicants arguments
Applicants acknowledge the rejections and indicate they are prepared to take appropriate action including the filing of a terminal disclaimer.
As noted previously, a rejection cannot be held in abeyance, and review of the claim amendments and other pending claims the rejections are maintained for the reasons of record.
The rejections are provided below for completeness of the record.
Claims 1-4, 8-12, 15-17, 19, 20, 23-25, 27 stand provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims of copending Application No. 17/000010 (FAOM mailed 7/11/2025).
As noted in the prior action, the instant claims comprise steps of analyzing biomolecules including cfDNA over time from a subject and as amended, the step of determining a therapeutic intervention for the subject based on the analysis has been deleted but therapy still appears in dependent claim 14 which also provides that the analysis and intervention uses a database containing relevant information to provide for an intervention. The claims of ‘010 provide for the use of a database for treatment without the steps of analysis (tough claims require that the data being used was obtained from subject and represents cfDNA. For implementation of ‘010 and use of a relevant database which provides biomolecule profiles and possible therapeutic interventions, it is implicit that the steps necessary to obtain information about the subject as provided in the instant claims are required for the use of the database and appear to make the claims obvious over each other. The relevant claims from ‘010 is provided below for comparison.
Claim 1 of Application No. 17/000010:
A method of treating a subject having cancer, the method comprising:
using a database to identify one or more effective therapeutic interventions for the subject having the cancer, which cancer comprises one or more somatic alterations detected by sequencing a plurality of tagged polynucleotides that comprise molecular barcodes to generate a set of sequencing reads, wherein the plurality of tagged polynucleotides is derived from cell-free nucleic acid (cfDNA) molecules from the subject and wherein the one or more somatic alterations are identified from the set of sequencing reads, and wherein the database comprises, for each of a plurality of subjects comprising at least 50 subjects having the cancer, tumor genomic testing data comprising
(i) one or more of the somatic alterations from cfDNA samples collected at two or more time intervals per subject,
(ii) one or more therapeutic interventions administered to each of the subjects at one or more times and
(iii) efficacy of the therapeutic interventions; and,
administering to the subject the one or more identified effective therapeutic interventions, thereby treating the subject having the cancer.
Claims 1-4, 8-12, 15-17, 19, 20, 23-25, 27 stand provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims of copending Application No. 15/431395 (parent of the instant application as a continuation, RCE filed 8/7/2025).
Specifically, the instant amended claims comprise steps of analyzing biomolecules including cfDNA over time from a subject and determining a therapeutic intervention for the subject based on the analysis, dependent claim 14 provides that the analysis and intervention uses a database containing relevant information to provide for an intervention. The claims of ‘395 provide for the creation and in dependent claims for the use of a database for treatment. In creating the database, information about a subject and disease state are required and use cfDNA. For implementation of claims 1 and more specifically claim 14 of the instant application, the use of a relevant database which provides biomolecule profiles and possible therapeutic interventions, it is implicit that the steps necessary to obtain information about the disease state were required prior to practicing the instantly claimed methodology as provided in the instant claims and appear to make the claims obvious over each other. The relevant claims from ‘395 are provided below for comparison.
Claim 43 of Application No. 15/431395 (as amended):
A method for generating a tumor response map indicating changes over time in genetic information from a tumor, comprising:
a) providing a plurality of tagged cell-free nucleic acid molecules, wherein the plurality of tagged cell-free nucleic acid molecules comprises molecular barcodes attached to [a] a heterogeneous population of original cell-free nucleic acid molecules obtained from bodily fluid samples from a subject collected at serial time points;
b) sequencing at least 1,000,000 set of sequencing reads comprises sequences of the molecular barcodes and sequences of corresponding to a plurality of genomic regions from each of at least 70 genes within a panel, sequences of the molecular barcodes;
c) determining, by a computer, a quantitative measure of each of a plurality of genetic variants among the panel
generating a tumor response map, comprising:
i) normalizing the quantitative measure of each of the plurality of genetic variants for rendering across serial time points; and -2-Attorney Ref.: 42534-714.301/GH0008US-CON Filed April 12, 2022 USSN: 15/431,395
ii) applying a scaling factor to the normalized quantitative measure of each of the plurality of genetic variants; wherein the tumor response map is a graphical representation of relative quantities of each of the plurality of genetic variants at each of the serial time points for somatic mutations present at a non-zero quantity and at least one of the serial time points.
Claims 1-4, 8-12, 15-17, 19, 20, 23-25, 27 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims of copending Application No. 17/699968 (FAOM mailed 5/12/2025).
Specifically, the instant amended claims comprise steps of analyzing biomolecules including cfDNA over time from a subject and determining a therapeutic intervention for the subject based on the analysis, dependent claim 14 provides that the analysis and intervention uses a database containing relevant information to provide for an intervention. The claims of ‘968 provide for the creation and in dependent claims for the use of a database for treatment. In creating the database, information about a subject and disease state are required and use cfDNA. The relevant claim from ‘968 is provided below for comparison.
Claim 1 of Application No. 17/699968 (as amended):
A method for treating a subject having cancer with an immunotherapy, the method comprising:
(a) determining a genetic profile of a tumor from the subject, the genetic profile providing an indication that the subject is likely to respond to the immunotherapy, by:
(i) obtaining or having obtained a biological sample from the subject, wherein the biological sample comprises cell-free deoxyribonucleic acid (cfDNA) molecules;
(ii) performing, having performed, or at least both, a diagnostic assay on the biological sample to determine the genetic profile of the tumor from the subject, wherein the diagnostic assay comprises:
A) obtaining a set of sequence reads from a plurality of polynucleotides derived from the cfDNA molecules,
B) analyzing the sequence reads to obtain a quantitative measure of somatic genetic variants in a portion of a genome of interest, wherein the somatic genetic variants include single nucleotide variations, insertions and/or deletions and the quantitative measure includes a number of somatic genetic variations in the portion of the genome,
and
(b) administering the immunotherapy to the subject based on the quantitative measure of somatic genetic variants exceeding a threshold.
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 USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The 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/process/file/efs/guidance/eTD-info-I.jsp.
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 1-4, 8-12, 15-17, 19, 20, 23-25, 27 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
Independent claim 1 has been amended and still is generally directed to providing cfDNA sequence data which is analyzed to reference, where the comparison requires partitioning the reference database into windows such that CNV, and different mutant allele frequency can be ascertained in a quantification step. As amended, claim 1 requires no physical steps and only providing sequence reads to be analyzed, and is generally drawn to steps of analyzing biomolecules including cfDNA to a reference database, where dependent claims provide that this is performed over time from a subject and determining a profile and in a final step using a database which provides a therapeutic intervention based on the data obtained from the analysis.
The claimed steps of analysis require a) obtaining sample with a population of cfDNA molecules, analyzing the biomolecules broadly and generically with appropriate known methodology to provide sequence reads of the cfDNA wherein one may be able to detect changes or variants that may be present, and based on the observation of the profile determined intervene with therapy. Dependent claims provide for specific samples sources which are analyzed, and specific methodology for analysis of epigenetic, genomic, cfDNA and protein that may be present in a sample, as well as for the use of a database where the profiles and disease state have been established, and provide possible correlative treatments for subject intervention. In broadening the claims, and in review of the guidance of the specification, none of the limitations appear to appear to affect the data per se and are consistent with known methods previously used to analyze a sample.
Response to Applicants arguments
Applicants provide an overview of analysis under 101 for patent eligibility citing Alice. For step 2A prong 1, guidance of MPEP 2106.04a is noted and argue that the analysis does not apply to the instant claims nor provide for limitation such as partitioning or the data obtained in the quantification step as amended. Applicants argue that the claims as amended could not be performed by the human mind and cite the fact pattern of ex parte Blundell and ex parte Zhou.
In response, the amendments to the claims have been analyzed above. With respect to the analysis provided in the previous action under prong 2A, step 1 it appears that the breadth of the claims and specific examples provided by the specification were discussed in support of finding the steps of the claims directed to a judicial exception. Applicants repeat the amendments to the claims, but it is not clear what cannot be performed in the human mind as each of the steps appears to be instructional and for any comparison of cfDNA to a reference appears to be observational, for example as to any difference which might represent a mutant or generally if the read data permits counting the number of reads in a window as an indication of quantity of the reads represented in a sample. While the claims could encompass a large amount of sequence read data, the steps required of the claims do not appear complicated or beyond tasks one could perform by observation using the human mind. It is unclear what the mind is not equipped to perform, or why it cannot practically perform any and all the steps of the amended claims. For example, it is argued specifically that the mind cannot partition a reference genome into a plurality of non-overlapping windows where the windows are less than the median distance of ORI, but while what the median distance of ORI might be questioned, once known it appears to be a simple task of making ‘windows’, counting a number of bases within a partition over a reference sequence and not allow the divisions to overlap, for example making 100 base windows as partitions over the reference sequence. Where a ORI might exist is inherent to a sequence, if it is even required of the claim in the analysis, and as such one or more of the 100bp windows would contain an ORI and meet the limitations required of the claims. Arguments that the complexity and quantity of the data is not practically analyzed does not appear consistent with the requirements of the claims. With respect to ex parte Blundell and ex parte Zhou, those decisions have not been provided but based on the claims in Applicants arguments do not appear consistent with the present claims as the type of data and analysis require are different. It is not clear how analysis of the position of atoms is to be assessed or supports the PTAB findings relative to comparing linear sequences which comprise only ATGC as required of the instant claims. As a whole, the claims are directed to steps of analysis and do not appear to provide a technical improvement consistent with 101 guidance to make the instant claims patent eligible. For dependent claims and using barcodes to label isolated nucleic acids were known and used. With respect to the claims, it is noted that the barcodes are not used in any of the steps to provide for any new structure or provide any use in the analysis that require the comparison of the various reads to determine CNV if present. The claims as a whole provide simply result in a profile and given the generic steps of analysis do not necessarily require that the information obtained is important or correlative to any cancer/condition, but rather that it was simply observed when the steps were performed. The embodiments for the use of ROCNV were previously set forth in dependent claims and given the generic nature of the claims to be applied to sequence read data, there does not appear to be any clear nexus with the analysis and the ability to access a database for any form of treatment for any possible correlative profile that may or may not exist. In review of the art of record, similar methods such as using HTS can obtain information that is useful however requires much more detail and design beyond obtaining the information from one individual and analyzing it as required of the instant claims.
As noted in prosecution, one interpretation of the claims does not require any physical step for adding the barcode but rather it was part of the initial data provided, and only that it is present on a read. However, if a physical step were required of the claims with respect to Step 2B, Applicants claim for the use of barcodes does not appear to materially change the analysis steps or provide any link to treatment. Further as noted before the process generally for the analysis of changes in the biomolecules of a cell during the progression of a disease or in comparing a normal state to disease state were known and an active area of research. As discussed below in greater detail, the Cancer Genome Atlas Research Network/Weinstein et al, provides a description of the Cancer Genome Atlas Pan-Cancer analysis project and a teaching and evidence that the Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, protein and epigenetic levels.
Previous rejection of record
For step 1 of the 101 analysis, the claims are found to be directed to a statutory category of a process.
For step 2A of the 101 analysis, the judicial exception of the claims are the steps of assessing the quantity of variants/variations seen in the analysis of genomic, epigenetic and proteomic information representing the sample from a subject to establish a profile. Further, the judicial exception of the claim requires that the profile be used to determine an appropriate intervention that is therapeutic if the profile is known or associated with a previously determined correlation. The judicial exception is a set of instructions for analysis of biopolymer data and falls into the category of a mental processes, that is concepts performed in the human mind (including an observation, evaluation, judgment, opinion). In this case, once the information is provided a conclusion and possible therapy is provided, and can be as simple as observing changes in the presence of a few genes as exemplified in Fig 7 or review of known genes associated with various forms of cancer such as BRCA1 as provided in CNV analysis (see for example [00214]). Given the general guidance of the specification, the plurality biomolecules can be of one target of interest (see claim 18 for limitation of CNV of a mutant allele), making the comparison simple and straightforward. In view of the guidance of the specification for CNV for example, it would target sequencing a limited number of specific genes (supported in the explanation and figure 10D for example). For other possible genomic, epigenetic or protein differences that may contribute to a subject profile, a similar simple comparison of an observed profile in a subject compared to a profile previously established and stored in a database (claim 14) or a table could easily be performed by eye and with one’s mind. Comparison and analysis of specific and relevant changes can be performed by observation in one’s mind or on paper.
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 have an additional element which is directed to obtaining the data about a sample related to epigenetic, genomic and protein information about the sample that is subsequently analyzed in the judicial exception and does not appear to be a practical application of the judicial exception, rather just a means to obtain information that is further analyzed. This judicial exception requires steps recited at high level of generality and are only stored on a non-transitory if the database is computerized (note the claims do not require method steps for the use of a computer and the ‘database’ as generically provided can be a table on a piece of paper), and is not found to be a practical application of the judicial exception as broadly set forth. Dependent claims set forth further indication of the sample source and means for analysis of genomic, epigenetic and protein information about the sample.
For step 2B of the 101 analysis, each of the independent claims recites additional elements and are found to be the steps of obtaining biomolecule data which were well known and conventional (see for example Zmetakova et al., Stephens et al. for epigenetic or Forshew et al 2012 and Ding et al 2012 for cfDNA). The data obtained from the steps considered the additional element are separate and appear to provide data for subsequent analysis and the judicial exception does not affect these steps, and as such, the claims do not provide for any additional element to consider under step 2B as a practical application or significantly more than analyzing possible changes within a sample as a whole. It view of the specification and possible forms of a database, or more general handling of the information about the sample, it is acknowledged that the analysis can use a computer, however in explaining the Alice framework, the Court wrote that "[i]n cases involving software innovations, [the step one] inquiry often turns on whether the claims focus on the specific asserted improvement in computer capabilities or, instead, on a process that qualifies as an abstract idea for which computers are invoked merely as a tool." The Court further noted that "[s]ince Alice, we have found software inventions to be patent-eligible where they have made non-abstract improvements to existing technological processes and computer technology." Moreover, these improvements must be specific -- "[a]n improved result, without more stated in the claim, is not enough to confer eligibility to an otherwise abstract idea . . . [t]o be patent-eligible, the claims must recite a specific means or method that solves a problem in an existing technological process." Here, in review of the evidence of record, there does not appear to be any new means of handling the data or creating new correlations based on observations of the data obtained.
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 biomoleucle data possibly present in sample. For implementing with a computer, 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 store data. The judicial exception of the method as claimed can be performed by hand and in light of the previous claims to a computer medium 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.
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.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
In the study of disease states Stephanie Watson (OCTOBER 2013) is noted to provide and demonstrate that even very focused research and analysis of biomarkers is not readily sufficient to provide a clear profile for conditions, such as cancer. Watson provides that cancers from different types of cells (breast vs. lung, for example) give off slightly different enzyme signatures, and that while results are encouraging that there are no overnight successes in treatment or medicine. ‘There is only meticulously conducted research, tested and retested in large groups of people until a positive result is achieved.’ Simlarly, Zhang and Chen (2013) provides further evidence and teaching that functional genomics studies using DNA Microarrays or tandem mass spectrometry have been shown effective in differentiating between breast cancer tissues and normal tissues, by measuring thousands of differentially expressed genes or proteins simultaneously. However, early detection of breast cancer in blood are both appealing clinically and challenging technically, partly because of 1) lack of routine blood test to screen early-stage breast cancers and 2) the fact that breast cancer is not a single homogeneous disease but consists of multiple disease subtypes, each arising from a distinct molecular mechanism and having a distinct clinical progression path. While generally acknowledging the analysis of markers for diagnosis useful research, the references highlight the details necessary to provide true and informative profiles of a disease state like cancer which fails to provide motivation to analyze cfDNA relative to ORI which then provides information about CNV and mutant allele frequency as broadly claimed.
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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/Joseph Woitach/Primary Examiner, Art Unit 1687