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 .
Priority
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d). The certified copy has been filed in parent Application No. TW111102676 filed Jan 21st, 2022.
The effective filing date is Jan 21st, 2022.
Election/Restrictions
Claims 5 and 6 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on December 27, 2022.
Status of Claims
Claims 1-4 and 7-14 are currently pending and examined on the merits.
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.
Claims 1-4 and 7-14 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.
Claims 1, 7, and 12 state: “… when the risk score sum is equal to or greater than a second threshold that is 1 or 2, the individual having the biological specimen is classified to a high risk group, wherein the high risk group is defined by less 25 months of an averaged survival time after surgery of the individual with 1 or 2 of the second threshold, or by less 10 months of an averaged survival time after surgery of the individual with 3 of the second threshold…”
One of ordinary skill in the art would not be clear as to what “3 of the second threshold” refers to considering the earlier portion of the claim (i.e., “the risk score sum is equal to or greater than a second threshold that is 1 or 2) and the specification, nor would one of ordinary skill in the art understand the average time of survival the post-surgery individual may have. One of ordinary skill in the art would further be unclear as to the act associated with the definition of such a high risk group, as the time of survival as denoted (25 months and 10 months on average) are not clearly associated with the act of the claim (defining a risk score group).
To further prosecution, the examiner interprets this as: “the individual having the biological specimen is classified to a high risk group, wherein the high risk group is defined by … a subject or biological sample containing a targeted gene and a measured survival time after surgery.”
Claims 1, 7, and 12 state: “the target gene combination is selected from the group consisting of at least two of the group consisting of PPT2, ARMH4, P4HB, SLC1A6 and ARID3A, a fragment, a homologue, a variant and a derivative thereof” One of ordinary skill in the art would not be clear as to the boundaries of the group referred to, and neither the specifications nor the claims provide further clarity.
To further prosecution, the examiner interprets this as: the inclusive group consisting of PPT2, ARMH4, P4HB, SLC1A6 and ARID3A, a fragment, a homologue, a variant and a derivative thereof.
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.
To further prosecution, the examiner interprets the corresponding portion of claims 1, 7, and 12 as:
“…the individual having the biological specimen is classified to a high risk group, wherein the high risk group is defined by … a subject or biological sample containing a targeted gene and a measured survival time after surgery…”,
And,
“…the inclusive group consisting of PPT2, ARMH4, P4HB, SLC1A6 and ARID3A, a fragment, a homologue, a variant and a derivative thereof”.
Claims 1-4 and 7-14 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of mental steps, mathematic concepts, organizing human activity, or a natural law without significantly more.
Step 2A, Prong 1
In accordance with MPEP § 2106, claims found to recite statutory subject matter (claims 1-4 and 7-14 are drawn to a method) (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 (reasonings in [brackets]):
Claim 1 states:
detecting expression levels of the target gene combination of the biological specimen…[which is a mental step, i.e. can be performed with pen and paper]
comparing one of the expression levels with a corresponding reference expression level of the target gene combination of a reference database respectively…[mental step]
obtaining a difference and a risk score, wherein a risk score of the one is given as 1 when an absolute value of the difference is equal to or more than a first threshold that is at least 5% of the reference expression level…[which is a mathematical concept of a mathematical calculation]
calculating or preparing input information for the pathogenicity determination…[which is a mathematical concept of a mathematical calculation]
the high risk group is defined by less 25 months of an averaged survival time after surgery of the individual with 1 or 2 of the second threshold…[mathematical calculation]
… or by less than 10 months of an averaged survival time after surgery…[mathematical calculation]
Claim 3 states:
…each of the reference expression levels is a normalized value…[mathematical calculation]
Claim 7 states:
establishing a reference data bank…[which is a mental step, i.e. can be performed with pen and paper]
detecting expression levels of the target gene combination of the biological specimen…[mental step]
comparing one of the expression levels with a corresponding reference expression level of the target gene combination of a reference database respectively…[mental step]
obtaining a difference and a risk score, wherein a risk score of the one is given as 1 when an absolute value of the difference is equal to or more than a first threshold that is at least 5% of the reference expression level…[mathematical calculation]
calculating a risk score sum of at least two of the target gene combination of the biological specimen…[mathematical calculation]
identifying the individual from the risk score sum, …[mental step]
when the risk score sum is equal to or greater than a second threshold that is 1 or 2…[mathematical calculation]
the individual having the biological specimen is classified to a high risk group …[mental step]
the high risk group is defined by less 25 months of an averaged survival time after surgery of the individual with 1 or 2 of the second threshold…[mathematical calculation]
the high risk group is defined by less 25 months of an averaged survival time after surgery of the individual with 1 or 2 of the second threshold…[mathematical calculation]
… or by less than 10 months of an averaged survival time after surgery…[mathematical calculation]
Claim 9 states:
each of the reference expression levels is a normalized value…[mathematical calculation]
Claim 12 states:
the detecting device detects the expression levels…[mental step]
comparing one of the expression levels with a corresponding reference expression level of the target gene combination of a reference database respectively…[mental step]
obtaining a difference and a risk score…[mathematical calculation]
calculating a risk score sum of at least two of the target gene combination of the biological specimen, wherein the risk score of the one is given as 1 when an absolute value of the difference is equal to or more than a first threshold that is more than at least 5% of the reference expression level…[mathematical calculation]
identifying the individual from the risk score sum, …[mental step]
when the risk score sum is equal to or greater than a second threshold that is 1 or 2…[mathematical calculation]
the individual having the biological specimen is classified to a high risk group …[mental step]
the high risk group is defined by less 25 months of an averaged survival time after surgery of the individual with 1 or 2 of the second threshold…[mathematical calculation]
the high risk group is defined by less 25 months of an averaged survival time after surgery of the individual with 1 or 2 of the second threshold…[mathematical calculation]
… or by less than 10 months of an averaged survival time after surgery…[mathematical calculation]
The claims recite an abstract idea of measuring gene expression in a biological sample (See MPEP 2106.07(a)).
These recitations are similar to the concepts of collecting information, analyzing it and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in 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 or mathematical relationships. Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas.
There are no additional limitations that indicate that these claims require anything other than carrying out the recited mental process or mathematical concept in a generic computer environment. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then if falls within the “Mental processes” grouping of abstract ideas. As such, claim(s) 1-18 recite(s) an abstract idea/law of nature/natural phenomenon (Step 2A, Prong 1: YES).
Step 2A, Prong 2
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 additional elements that reflects an improvement to technology or applies or uses the recited judicial exception to affect a particular treatment for a condition. Rather, the instant claims recite additional elements that amount to mere instructions to implement the abstract idea in a generic computing environment or mere instructions to apply the recited judicial exception via a generic treatment. Specifically, the claims recite the following additional elements:
Claim 1 states:
establishing a reference data bank, wherein the reference data bank comprises reference expression levels of a target gene combination originated from at least one in vitro normal bladder specimen, the target gene combination comprises at least two of PPT2, ARMH4, P4HB, SLC1A6 and ARID3A, a fragment, a homologue, a variant and a derivative thereof;
a biological specimen, wherein the biological specimen is originated from in vitro aggressive bladder cancer of the individual
obtaining a difference and a risk score
Claim 7 states:
storing a reference data bank comprising reference expression levels of a target gene combination originated from at least one in vitro normal bladder specimen in a system, wherein the target gene combination comprises at least two of PPT2, ARMH4, P4HB, SLC1A6 and ARID3A, a fragment, a homologue, a variant and a derivative thereof;
a program
Claim 12 states:
a detecting module comprising a detecting device,
a reaction solution,
nucleic acid probes and/or antibodies, wherein the nucleic acid probes and/or antibodies react with a target gene combination of a biological specimen and generate expression levels
a processing module coupled to the detecting module, for receiving the expression levels from the detecting module
an identifying module coupled to the processing module,
an identifying module coupled to the processing module
Claim 13 states:
a pretreating module coupling to the detecting module, for providing a nucleic acid sample and/or a protein sample of the biological specimen
There are no limitations that indicate that the claimed analysis engine or the formats of the provided data 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. As such, claims 1-18 is/are directed to an abstract idea/law of nature/natural phenomenon (Step 2A, Prong 2: NO).
Step 2B
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). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment. The instant claims recite the following additional elements:
Claim 1 states:
establishing a reference data bank, wherein the reference data bank comprises reference expression levels of a target gene combination …;
a biological specimen, wherein the biological specimen is originated from in vitro aggressive bladder cancer of the individual
obtaining a difference and a risk score
Claim 7 states:
storing a reference data bank comprising reference expression levels of a target gene combination originated from at least one in vitro normal bladder specimen in a system, …;
a program
Claim 12 states:
a detecting module comprising a detecting device,
a reaction solution,
nucleic acid probes and/or antibodies, wherein the nucleic acid probes and/or antibodies react with a target gene combination of a biological specimen and generate expression levels
a processing module coupled to the detecting module, for receiving the expression levels from the detecting module
an identifying module coupled to the processing module,
an identifying module coupled to the processing module
Claim 13 states:
a pretreating module coupling to the detecting module, for providing a nucleic acid sample and/or a protein sample of the biological specimen
Regarding claims 1-4 and 7-14, The steps of obtaining sequencing and/or training data and performing sample collection do not integrate the abstract idea into a practical application and constitutes an insignificant extra-solution activity (i.e., data gathering and presentation), which does not impose a meaningful limit on the abstract idea. As discussed above, there are no additional limitations to indicate that the claimed analysis engine requires anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. MPEP 2106.05(f) discloses that mere instructions to apply the judicial exception cannot provide an inventive concept to the claims.
Furthermore, the additional elements recited in the claims amount to well-understood, routine and conventional activity, as evidenced by Binsheng He et al. (Front. Bioeng. Biotechnol. 8:737.) who teaches a neural network (NN) framework using the expression of a 150-gene panel to infer the tumor tissue-of-origin for 15 common solid tumor cancer types, including lung, breast, liver, colorectal, gastroesophageal, ovarian, cervical, endometrial, pancreatic, bladder, head and neck, thyroid, prostate, kidney, and brain cancers.
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. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: NO). As such, claims 1-4 and 7-14 are not patent eligible.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
To further prosecution, the examiner interprets the corresponding portion of claims 1, 7, and 12 as: “the individual having the biological specimen is classified to a high risk group, wherein the high risk group is defined by … a subject or biological sample containing a targeted gene and a measured survival time after surgery…” ,and “the inclusive group consisting of PPT2, ARMH4, P4HB, SLC1A6 and ARID3A, a fragment, a homologue, a variant and a derivative thereof”.
Claim(s) 1-4 and 7-14 is/are rejected under 35 U.S.C. 103 as being unpatentable over Chung Chang et al. (Sci Rep 10, 3953 (2020) pg. 1-10) in view of Lei Lyu et al. (Front. Oncol. 10:1613 pg. 1-16. 2020. ) and further in view of Shahrokh Shariat et al. (CANCER. Vol. 112 No. 2. Jan. 2008 pg. 315-325).
Regarding claim 1, Shariat et al. teaches a method to predict bladder cancer recurrence and mortality in patients post-surgery (Title, Abstract, pg. 315, re: clm. 1, … method for predicting survival time of an individual with bladder cancer after surgery from an individual's biological sample, comprising…)
Shariat et al. further teaches comparing the expression levels of bladder cancer related genes using immunohistochemistry against a reference (positive and negative control sections, as disclosed on pg. 316, and mean scores with at least 10% nuclear reactivity disclosed on pg. 317), further teaches a bladder cancer recurrence score against biomarkers p21, p27, p53, pRB and Cyclin E using percent positive average (Figure 3, pg. 323) and multivariate recurrence analyses to measure predictive accuracy (as disclosed on pg. 318, “Addition of the number of altered…”, Table 2, and Table 3, “Cox Regression Models”; re: clm. 1, … comparing one of the expression levels with a corresponding reference expression level of the target gene combination of a reference database respectively, and obtaining a difference and a risk score, wherein a risk score of the one is given as 1 when an absolute value of the difference is equal to or more than a first threshold that is at least 5% of the reference expression level…)
Shariat et al. further teaches calculating a risk score sum (Abstract, “Addition of the number of altered biomarkers increased the predictive accuracy of nomograms based on the TNM staging system for disease recurrence and cancer-specific mortality by 10.9%”) and a high risk group with a measured survival as disclosed in Fig. 1, pg. 319 (Kaplan-Meier; re: clm. 1, … calculating a risk score sum of at least two of the target gene combination of the biological specimen, when the risk score sum is equal to or more than a second threshold that is 1 or 2, the individual having the biological specimen is classified to a high risk group, wherein the high risk group is defined by less 25 months of an averaged survival time after surgery of the individual with 1 or 2 of the second threshold, or by less 10 months of an averaged survival time after surgery of the individual with 3 of the second threshold…)
Shariat et al. does not teach establishing a reference data bank (re: clm. 1, … establishing a reference data bank, wherein the reference data bank comprises reference expression levels of a target gene combination originated from at least one in vitro normal bladder specimen, the target gene combination comprises at least two of PPT2, ARMH4, P4HB, SLC1A6 and ARID3A, a fragment, a homologue, a variant and a derivative thereof…).
Shariat et al. does not teach gene combinations (re: clm. 1, … at least two of PPT2, ARMH4, P4HB, SLC1A6 and ARID3A, a fragment, a homologue, a variant and a derivative thereof…)
Lyu et al. teaches a study of autophagy-related genes to determine their prognostic value in bladder urothelial carcinoma, in which the genes were collected from the Human Autophagy Database (Abstract, pg. 1). Lyu et al. further uses The Cancer Genome Atlas and bladder tissue samples in their study (Materials and Methods, pg. 2, re: clm. 1, … establishing a reference data bank, wherein the reference data bank comprises reference expression levels of a target gene combination originated from at least one in vitro normal bladder specimen, the target gene combination comprises at least two of PPT2, ARMH4, P4HB, SLC1A6 and ARID3A, a fragment, a homologue, a variant and a derivative thereof…)
Lyu et al. teaches a study of P4HB and alterations of it (pg. 3, “The frequency of P4HB and RGS19 alterations (amplification, deep deletion, and missense mutation) and copy number variations (CNVs) were obtained from Genomic Identification of Significant Targets in Cancer (CISTC).”, re: clm. 1, … the target gene combination comprises at least two of PPT2, ARMH4, P4HB, SLC1A6 and ARID3A, a fragment, a homologue, a variant and a derivative thereof…”)
Lyu et al. further teaches that “The transcription levels of P4HB and RGS19 were significantly higher in the tumor tissues than in the non-cancerous bladder tissues in subgroup analyses based on gender, age, cancer stage and nodal metastasis status…” on pg. 7, which reads on an in-vitro aggressive bladder cancer (due to metastasis).
Lyu et al. and Shariat et al. do not teach a method to predict survival time of an individual with bladder cancer explicitly post-surgery (re: clm. 1, … A method for predicting survival time of an individual with bladder cancer after surgery from an individual's biological sample…)
Chang et al. teaches HDMAC: A Web-Based Interactive Program for High-Dimensional Analysis of Molecular Alterations in Cancer (Title). Chang et al. further teaches mRNA expression level from bladder-cancer patients, including a study of SLC1A6 (Abstract, pg. 1; Table S2 “Genes selected for adapted Lasso”, re: clm. 1, … A method for predicting survival time of an individual with bladder cancer after surgery from an individual's biological sample, comprising… the target gene combination comprises at least two of PPT2, ARMH4, P4HB, SLC1A6 and ARID3A, a fragment, a homologue, a variant and a derivative thereof…)
Chang et al. does not teach providing a biological specimen explicitly originating from in vitro aggressive bladder cancer (re: clm. 1, … providing a biological specimen, wherein the biological specimen is originated from in vitro aggressive bladder cancer of the individual…)
In KSR Int 'l v. Teleflex, the Supreme Court, in rejecting the rigid application of the teaching, suggestion, and motivation test by the Federal Circuit, indicated that “The principles underlying [earlier] cases are instructive when the question is whether a patent claiming the combination of elements of prior art is obvious. When a work is available in one field of endeavor, design incentives and other market forces can prompt variations of it, either in the same field or a different one. If a person of ordinary skill can implement a predictable variation, § 103 likely bars its patentability.” KSR Int'l v. Teleflex lnc., 127 S. Ct. 1727, 1740 (2007).
Applying the KSR standard to Chang et al., Lyu et al. and Shariat et al., the examiner finds that the combination of HDMAC as taught by Chang et al. with the gene study as taught by Lyu et al. and the patient prognosis prediction method as taught by Shariat et al. represents some Teaching, suggestion or motivation in the prior art that would have lead one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention.
One of ordinary skill in genomics and cancer biology would have been motivated to combine the teachings to Chang et al., Lyu et al. and Shariat et al. as the combination would produce a stronger pathogenicity prediction method.
One of ordinary skill in genomics would have success in combining the teachings of Chang et al., Lyu et al. and Shariat et al., as all arts exist in the same field of invention (computational genomics, oncological studies). Therefore, the invention would have been prima facie obvious to one of skill in the art at the time of filing of the application, absent evidence to the contrary.
Regarding claim 7, Chang et al. teaches a software package in their analysis on pg. 4, Results (Introduction to HDMAC), and includes the storage of data, stating on the same page:
“On HDMAC, we provided a set of example data for users to get familiar with the platform. For analysis of their own data, users may choose to upload the data and run it through the statistical methods provided” (re: clm. 7, … A computer-implemented method for predicting survival time of an individual with bladder cancer after surgery from an individual's biological sample, comprising executing steps as follow…)
Therefore, the combination of Chang et al., Lyu et al. and Shariat et al. teach all explicit limitations of claim 7.
Regarding claims 2 and 8, Lyu et al. teaches a study of bladder tissue (Abstract, introduction, methods, pg. 1-4, re: clm. 2, 8, … wherein the biological specimen and the in vitro normal bladder specimen comprise ex vivo organs, tissues, cells, body fluid, lymphatic liquid, urine, whole bloods, serum and/or cell culture supernatant.). Lyu et al. teaches the limitations of claims 2 and 8.
Regarding claims 3 and 9, Chang et al. teaches Z-score normalized expression levels (Abstract, pg. 1, “The Z score data of mRNA expression were used to indicate the deviation from the mean of each gene’s expression level.”, re: clm. 3, 9… each of the reference expression levels is a normalized value.) Chang et al. teaches the limitations of claim 3.
Regarding claims 4 and 10, Chang et al. teaches mRNA expression levels in bladder-cancer patients (Abstract, pg. 1, re: clm. 4, 10 … the expression levels and the reference expression levels comprise nucleic acid expression levels and/or protein expression levels.). Chang et al. teaches the limitations of claims 4 and 10.
Regarding claim 11, Chang et al. includes instructions for implementation of their disclosed method on pg. 4, Results (Introduction to HDMAC; re: clm. 11, the program comprises instructions for implementing the method on the system…). Chang et al. teaches the limitations of claim 11.
Regarding claim 12, Shariat et al. discloses the application of immunohistochemistry to urothelial carcinoma of the bladder samples, and discloses an automated autostainer based on brightfield microscopy on pg. 324, which reads on a detection module receiving the expression levels from a biological specimen, a processing module (via imaging) and a controlling module (autostainer) (re: clm. a detecting module comprising a detecting device, a reaction solution, nucleic acid probes and/or antibodies, wherein the nucleic acid probes and/or antibodies react with a target gene combination of a biological specimen and generate expression levels, and the detecting device detects the expression levels, the biological specimen is originated from in vitro aggressive bladder cancer of an individual, the target gene combination is selected from the group consisting of at least two of the group consisting of PPT2, ARMH4, P4HB, SLC1A6 and ARID3A, a fragment, a homologue, a variant and a derivative thereof… a processing module coupled to the detecting module, for receiving the expression levels from the detecting module…a controlling module coupled to the detecting module, the processing module and the identifying module…)
As previously disclosed, Shariat et al. further teaches comparing the expression levels of bladder cancer related genes using immunohistochemistry against a reference (positive and negative control sections, as disclosed on pg. 316, and mean scores with at least 10% nuclear reactivity disclosed on pg. 317), further teaches a bladder cancer recurrence score against biomarkers p21, p27, p53, pRB and Cyclin E using percent positive average (Figure 3, pg. 323) and multivariate recurrence analyses to measure predictive accuracy (re: clm. 12, … comparing one of the expression levels with a corresponding reference expression level of the target gene combination of a reference database respectively, thereby obtaining a difference and a risk score; and for calculating a risk score sum of at least two of the target gene combination of the biological specimen, wherein the risk score of the one is given as 1 when an absolute value of the difference is equal to or more than a first threshold that is more than at least 5% of the reference expression level…)
Shariat et al. further teaches an assessment of the number of altered biomarkers, associating patients with their risk score (Materials and Methods, pg. 316 ,re: clm. 12, …an identifying module coupled to the processing module, for identifying the individual from the risk score sum, wherein when the risk score sum is equal to or greater than a second threshold that is 1 or 2, the individual having the biological specimen is classified to a high risk group, the high risk group is defined by less 25 months of an averaged survival time after surgery of the individual with 1 or 2 of the second threshold, or by less 10 months of an averaged survival time after surgery of the individual with 3 of the second threshold…)
Chang et al. teaches a program in the Methods section (re: clm. 12, … a program that includes instructions, thereby activating the detecting module, the processing module and the identifying module.) but does not explicitly disclose a module.
Applying the KSR standard to Chang et al., Lyu et al. and Shariat et al., the examiner finds that the combination of HDMAC as taught by Chang et al. with the gene study as taught by Lyu et al. and the patient prognosis prediction method as taught by Shariat et al. represents some Teaching, suggestion or motivation in the prior art that would have lead one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention.
One of ordinary skill in genomics and cancer biology would have been motivated to combine the teachings to Chang et al., Lyu et al. and Shariat et al. as the combination would produce a stronger pathogenicity prediction method.
One of ordinary skill in genomics would have success in combining the teachings of Chang et al., Lyu et al. and Shariat et al., as all arts exist in the same field of invention (computational genomics, oncological studies). In support of this motivation, it would have been reasonable for one of ordinary skill to adapt the database teachings of Lyu et al. to the immunohistochemistry, imaging, and predictive model of Shariat et al. in view of Chang et al.’s teaching of a computational method to analyze gene expression associated with bladder cancer. Therefore, the invention would have been prima facie obvious to one of skill in the art at the time of filing of the application, absent evidence to the contrary.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOHN T STUBBS whose telephone number is (571)272-0340. The examiner can normally be reached M-F 8-5 EST.
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/J.T.S./Examiner, Art Unit 1686
/LARRY D RIGGS II/ Supervisory Patent Examiner, Art Unit 1686
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