Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Claims 1-18 are pending and will be examined.
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 1-9 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a method that includes an abstract step without significantly more. The claim(s) recite(s) a preamble which includes guidance to manage “patient treatment” and a conclusion step “wherein the patient is determined to be suitable for the treatment if the level is at or above a predetermined level”. This judicial exception is not integrated into a practical application because while the claimed method includes the detection of a patient, the condition is not specified and the application into a method of treatment is recited at a high level of generality and not a specific application. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because
This judicial exception is not integrated into a practical application because while the claims include a method of treatment which could include a practical application of the abstract step, the application is recited at a high level of generality and without specific guidance regarding the need for or the manner of treatment. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the application into a method of treatment is recited at a high level of generality.
According to the 2019 Revised Patent Subject Matter Eligibility Guidance, an initial two step analysis is required for determining statutory eligibility.
According to the Manual of Patent Examination Procedure (MPEP) sections 2103 through 2106.07(c), which now incorporates the 2019 Revised Patent Subject Matter Eligibility Guidance (2019 PEG), October 2019 Patent Eligibility Guidance Update (October 2019 Update),
and the Berkheimer Memo, an initial two step analysis is required for determining statutory
eligibility.
Step 1 requires a determination of whether the claims are directed to a process, machine,
manufacture, or a composition of matter. In the instant case, the Step 1 requirement is satisfied as
the claims are directed towards a process.
Step 2
The Step 2 analysis is a two-part analysis, Step 2A and Step 2B.
Step 2A. prong 1
Step 2A, prong 1 requires a determination of whether the claims are directed towards a
judicial exception, i.e. a law of nature, natural phenomenon, or an abstract idea, while step 2A, prong 2 requires an analysis of whether the judicial exception integrated into a practical
application if the claim recites a judicial exception under Prong 1.
Step 2A. prong 2
Step 2A, prong 2 requires an analysis of whether the judicial exception integrated into a
practical application if the claim recites a judicial exception under Prong 1.
Step 2B
The second part, Step 2B of the two-step analysis is drawn to determining whether any
element or combination of elements, in the instant claims is/are sufficient to ensure that the
claims as a whole amount to significantly more than the judicial exception.
Following the analysis below the claims are not patent eligible under 35 U.S.C. 101.
Concerning Step 1: YES. Claims 1-9 are directed to methods, therefore the claims are directed to a process, which is a statutory category.
Concerning Step 2A: YES. Claims 1-9 recite methods of treatment of patients following a determination of the level of a gene encoding a polypeptide of SEQ ID NO:1. Claims 1-9 rely on an abstract step to determine a patient is suitable for treatment based on a predetermined value that is not provided. In other words, claims 1-9 rely on a judicially excluded abstract idea associated with a method of treatment, without significantly more.
Concerning Step 2A, prong 1, claims 1-9 are directed towards a judicial
exception, i.e. a law of nature, as noted above. Claims 1-9 recite abstract ideas of comparing and parsing data, as these claims recite step(s) of calculating a level/quantity in a manner that could be achieved as a mental step.
The step of determining the expression of SEQ ID NO:1 (claim 1), falls within the grouping of abstract ideas and as they merely instruct a user to analyze various target sequence(s) (analyze natural law/natural sequences) and to draw a conclusion (i.e. treating a patient/person) is suitable for treatment.
Concerning Step 2A, prong 2, the judicial exception of the abstract step of claims 1-9 are
not integrated into a practical application because of the following.
A claim that integrates a judicial exception into a practical application will apply, rely on,
or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception, such that the claim is more than a drafting effort designed to monopolize the judicial
exception. When the exception is so integrated, then the claim is not directed to a judicial
exception.
Claims 1-9 do not recite steps beyond the recited steps of determining expression level within specific targets and determine a patient is suitable for treatment.
Claims 1-9 do not recite steps/elements that are construed to be a practical application that apply, rely on, or use the judicial exceptions. The steps of detecting the level of SEQ ID NO:1 target sequence is not a practical application as this step must be applied to realize the judicial exception(s).
They are also recited with a high level of generality and therefore do not add any meaningful limitation to practicing the natural law and/or abstract idea.
Concerning Step 2B, claims 1-9 do not recite any additional elements
that ensure that the claims as a whole amount to significantly more than the judicial exception(s).
The steps of analyzing methylation levels at specific sites as associated with treatment
response constitute well understood, routine, conventional activity.
There is no inventive concept in claims 1-8, and thus they are rejected as
being ineligible under 35 U.S.C. 101.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of pre-AIA 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a) the invention was known or used by others in this country, or patented or described in a printed publication in this or a foreign country, before the invention thereof by the applicant for a patent.
(b) the invention was patented or described in a printed publication in this or a foreign country or in public use or on sale in this country, more than one year prior to the date of application for patent in the United States.
(e) the invention was described in (1) an application for patent, published under section 122(b), by another filed in the United States before the invention by the applicant for patent or (2) a patent granted on an application for patent by another filed in the United States before the invention by the applicant for patent, except that an international application filed under the treaty defined in section 351(a) shall have the effects for purposes of this subsection of an application filed in the United States only if the international application designated the United States and was published under Article 21(2) of such treaty in the English language.
Claim(s) 1-7 is/are rejected under pre-AIA 35 U.S.C. 102(b) as being anticipated by Mintz et al. (US Patent 7745391; June 2010).
With regard to claim 1, Mintz teaches a method for managing patient treatment comprising identifying a patient under, or in need of, a treatment for a condition (col. 24-25, where oligonucleotides are useful in managing treatment),
obtaining a biological sample from the patient, and determining the expression level of a gene encoding a polypeptide containing SEQ ID NO: 1 in the sample,
wherein the patient is determined to be suitable for the treatment if the level is at or above a predetermined value (See alignment below where SEQ ID NO:750604 corresponds to SEQ ID NO:1).
SEQ ID NO:1
Qy 1 MRLSSSPPRGPQQLSSFGSVDWLSQSSCSGPTHTPRPADFSLGSLPGPGQTSGAREPPQA 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4 MRLSSSPPRGPQQLSSFGSVDWLSQSSCSGPTHTPRPADFSLGSLPGPGQTSGAREPPQA 63
Qy 61 VSIKEAAGSSNLPAPERTMAGLSKEPNTLRAPRVRTAFTMEQVRTLEGVFQHHQYLSPLE 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 64 VSIKEAAGSSNLPAPERTMAGLSKEPNTLRAPRVRTAFTMEQVRTLEGVFQHHQYLSPLE 123
Qy 121 RKRLAREMQLSEVQIKTWFQNRRMKHKRQMQDPQLHSPFSGSLHAPPAFYSTSSGLANGL 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 124 RKRLAREMQLSEVQIKTWFQNRRMKHKRQMQDPQLHSPFSGSLHAPPAFYSTSSGLANGL 183
Qy 181 QLLCPWAPLSGPQALMLPPGSFWGLCQVAQEALASAGASCCGQPLASHPPTPGRPSLGPA 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 184 QLLCPWAPLSGPQALMLPPGSFWGLCQVAQEALASAGASCCGQPLASHPPTPGRPSLGPA 243
Qy 241 LSTGPRGLCAMPQTGDAF 258
||||||||||||||||||
Db 244 LSTGPRGLCAMPQTGDAF 261
With regard to claim 2, Mintz teaches a method of claim 1, wherein the method further comprises communicating the expression level to the patient or to a physician or a caretaker of the patient (col. 24-25, where oligonucleotides are useful in managing treatment).
With regard to claim 3, Mintz teaches a method of claim 1, wherein the condition is a cellular proliferative disorder (col. 69, where the method is useful for predicting risk for disorders or disease).
With regard to claim 4, Mintz teaches a method of claim 1, wherein the condition is an inflammatory or autoimmune disorder (col. 69, where the method is useful for predicting risk for disorders or disease).
With regard to claim 5, Mintz teaches a method of diagnosing an immune disorder in a subject, the method comprising obtaining a biological sample from the subject; and determining the expression level of a gene encoding a polypeptide containing SEQ ID NO:1 in the sample (Fig 11-14, where an example is given of measuring expression levels; see also col. 1-2 and 4, for example where expression is discussed).
With regard to claim 6, Mintz teaches a method of claim 5, wherein the disorder is a cellular proliferative disorder and the subject is determined to have or be prone to develop the cellular proliferative disorder if the expression level is below a first predetermined level or absent (col. 69, where the method is useful for predicting risk for disorders or disease).
With regard to claim 7, Mintz teaches a method of claim 5, wherein the disorder is an inflammatory or autoimmune disorder and the subject is determined to have or be prone to develop the disorder if the expression level is above a second predetermined level (col. 69, where the method is useful for predicting risk for disorders or disease).
Claim(s) 10-17 is/are rejected under pre-AIA 35 U.S.C. 102(b) as being anticipated by Trinklein et al. (US PgPub 20070161031; July 2007).
With regard to claim 10, Trinklein teaches a method of detecting expression of a gene encoding a Hom-1 polypeptide in a sample, the method comprising:
(i) performing a nucleic acid hybridization assay on a sample, RNA isolated from the sample, or cDNA prepared from the RNA with an oligonucleotide probe that, under a stringent condition, hybridizes to a reference nucleic acid or the compliment thereof, or
(ii) performing a nucleic acid amplification assay on the sample, the RNA, or the cDNA with a pair of primers for amplifying a fragment of the reference nucleic acid or the compliment thereof, whereby expression of the gene is detected, and wherein the reference nucleic acid consists of the sequence of SEQ ID NO:3 (paragraph 146-152, where functional probe arrays hybridize to the sequences identified by the PPA v1.1 or 1.2 algorithm; see Figure 15, which “summarizes the output of PPA v1.1 and PPA v1.2. PPA v 1.1 predicts 64,526 promoters and PPA v1.2 predicts 45,096 promoters (the sequences of which are designated SEQ ID NOs:1-45096, where SEQ ID NO:6269 corresponds to the sequence upstream of Hom-1, as recited below at SEQ ID NO:3).
SEQ ID NO:3
Qy 1 CGAATGCAGAGGCTCCTGCGATGGCCCCGGAGTGAGTCCCCCAGAGGAGCCGGATTAGGG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1401 CGAATGCAGAGGCTCCTGCGATGGCCCCGGAGTGAGTCCCCCAGAGGAGCCGGATTAGGG 1460
Qy 61 CTGGAGGCGGCCGAGTCCCCCGAGAGGCCCCTCCCGACATTCCCGCCCCCGCGCGCCGCT 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1461 CTGGAGGCGGCCGAGTCCCCCGAGAGGCCCCTCCCGACATTCCCGCCCCCGCGCGCCGCT 1520
Qy 121 CCCCGGGTCCTCCGCGTCTCTTTCCCGGGAAAGCCTCCCTCGGTTCCTGCGCGGCCGCAC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1521 CCCCGGGTCCTCCGCGTCTCTTTCCCGGGAAAGCCTCCCTCGGTTCCTGCGCGGCCGCAC 1580
Qy 181 AGCCTGGACGCAGCGCACGCGGGCACCGGCCTGACTCTCCCACCCCGAAGCCTGCTCCCA 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1581 AGCCTGGACGCAGCGCACGCGGGCACCGGCCTGACTCTCCCACCCCGAAGCCTGCTCCCA 1640
Qy 241 ACCTAAGTCCGCCCTGACTCTCCCAGCCTGAAGCCTGCTCGCCCTCGGGTGTCCGGGCTG 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1641 ACCTAAGTCCGCCCTGACTCTCCCAGCCTGAAGCCTGCTCGCCCTCGGGTGTCCGGGCTG 1700
Qy 301 GGCACAGGCGCCAGCGTCCCCCTGGAGAGGAGAGGTCGCCCGGCACCTCCCAGGACAGGC 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1701 GGCACAGGCGCCAGCGTCCCCCTGGAGAGGAGAGGTCGCCCGGCACCTCCCAGGACAGGC 1760
Qy 361 CCAAGTGGGAGTGGGACCCTCCTACCTTCCTGCAGCCTCGGCCCGCGGGGTGGGGGGTTG 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1761 CCAAGTGGGAGTGGGACCCTCCTACCTTCCTGCAGCCTCGGCCCGCGGGGTGGGGGGTTG 1820
Qy 421 GGAGAGATGAAAGGAGGTGACCGATCCCGAACCATCGCCTCTCCATTAACCAGGGCCCGC 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1821 GGAGAGATGAAAGGAGGTGACCGATCCCGAACCATCGCCTCTCCATTAACCAGGGCCCGC 1880
Qy 481 AGCCCCGCCCCTCCCCCAGACATCGAGGAGCCGGGGAGGTGTGAACGGCCTCCTTTGTGC 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1881 AGCCCCGCCCCTCCCCCAGACATCGAGGAGCCGGGGAGGTGTGAACGGCCTCCTTTGTGC 1940
Qy 541 CTCTGAATCGAAGGCAATTAGGCGCTGCTTATCTGGGCATTAGCCGTGTATGCAAACCGG 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1941 CTCTGAATCGAAGGCAATTAGGCGCTGCTTATCTGGGCATTAGCCGTGTATGCAAACCGG 2000
Qy 601 GCTCCCGCCCCCTCCTCCTGGGCTTATAAACGCCGCCGCCTGGCGAGGCCCGAGGTGGAT 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2001 GCTCCCGCCCCCTCCTCCTGGGCTTATAAACGCCGCCGCCTGGCGAGGCCCGAGGTGGAT 2060
Qy 661 CCTGCGCCTGGCCAGCCCCGCCTGGCCTTCCCTCCGGCCCACCTGGCCGCC 711
|||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2061 CCTGCGCCTGGCCAGCCCCGCCTGGCCTTCCCTCCGGCCCACCTGGCCGCC 2111
With regard to claim 11, Trinklein teaches a method of claim 10, wherein the sample is a bodily fluid, tissue, or cell sample (p 9, paragraph 86).
With regard to claim 12, Trinklein teaches a method of claim 10, wherein the hybridization assay is a Southern blot, Northern blot, or in situ hybridization (p 2, paragraph 12, where hybridization occurs; see also p 24, paragraph 225, where real time PCR occurs).
With regard to claim 13, Trinklein teaches a method of claim 10, wherein the amplification assay is polymerase chain reaction (PCR), reverse transcription PCR, quantitative PCR, or in situ PCR (p 24, paragraph 225, where real time PCR is carried out).
With regard to claim 14, Trinklein teaches a method of claim 13, wherein reverse transcription PCR is performed and the pair of primers are for amplifying a fragment of the reference nucleic acid (p 24, paragraph 225, where real time PCR is carried out).
With regard to claim 15, Trinklein teaches a method of claim 13, wherein quantitative PCR is performed and the pair of primers are for amplifying a fragment of the reference nucleic acid (p 24, paragraph 225, where real time PCR is carried out).
With regard to claim 16, Trinklein teaches a method of claim 10, wherein the sample is from a subject having or suspected of having a cellular proliferative disorder (p 19, paragraph 190).
With regard to claim 17, Trinklein teaches a method of claim 10, wherein the sample is from a subject having or suspected of having an immune disorder (p 10, paragraph 91; p 19, paragraph 190).
Claim Rejections - 35 USC § 103
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claim 8-9 and 18 is/are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Mintz et al. (US Patent 7745391; June 2010) as applied over claims 1-7 above and further in view of Trinklein et al. (US PgPub 20070161031; July 2007).
With regard to claim 18, Mintz teaches a method of claim 10, wherein the Hom-1 polypeptide contains the sequence of SEQ ID NO:1.
With regard to claim 8, Trinklein teaches a method of claim 5, wherein the determining step is carried out with a pair of PCR primers for amplifying a fragment of SEQ ID NO:2 or 3 (p 24, paragraph 225, where real time PCR is carried out).
With regard to claim 9, Trinklein teaches a method of claim 5, wherein the determining step is carried out with an oligonucleotide that, under a stringent condition, hybridizes to the compliment of a reference nucleic acid, wherein the reference nucleic acid is the sequence of SEQ ID NO:2 or 3 (see Figure 15, where SEQ ID NO:6269, which corresponds to SEQ ID NO:3 as recited below; further, see paragraph 267, where Trinklein specifically discusses primer design to amplify the promoter regions and where “for each promoter fragment, the PPA requires that the PCR primers include the TSS in each amplified fragment and that primers avoid repetitive DNA).
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have adjusted the teachings of Mintz to include the sequences as taught by Trinklein to arrive at the claimed invention with a reasonable expectation for success. Trinklein teaches “technologies currently exist to study the functional regions of the human genome” and that “solutions to problems in functional characterization of regulatory elements and uses of the information generated in the functional studies for research, diagnosis, prevention and treatment of diseases or conditions (p 1, paragraph 5). Therefore, one of ordinary skill in the art at the time the invention was made would have adjusted the teachings of Mintz to include the sequences as taught by Trinklein to arrive at the claimed invention with a reasonable expectation for success.
Conclusion
No claims are allowed. All claims stand rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEPHANIE KANE MUMMERT whose telephone number is (571)272-8503. The examiner can normally be reached M-F 9:00-5:30.
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/STEPHANIE K MUMMERT/Primary Examiner, Art Unit 1681