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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 5/4/2026 has been entered.
Applicant’s arguments and amendments have been thoroughly reviewed and considered. Claim 21 has been added. Claim 6 has been canceled. Claims 1-2, 4-5, 7, and 9-21 are pending and are examined on the merits herein.
Response to Applicant’s Amendments
Claim Objections
Claims 1, 7, and 9 were objected to due to minor informalities. In light of Applicant’s amendments to the claims submitted 5/4/2026, these objections have been withdrawn, but see new grounds of objection below.
35 USC 112(b) Rejections
Claims 6 and 11 were rejected due to indefiniteness issues. Claim 6 has been canceled, and so this rejection has been rendered moot. In light of Applicant’s amendments to the claims submitted 5/4/2026, the rejection of claim 11 has been withdrawn.
35 USC 112(d) Rejections
Claims 14 and 18 were rejected due to failing to further limit the subject matter upon which they depend. In light of Applicant’s amendments to the claims submitted 5/4/2026, these rejections have been withdrawn.
35 USC 101 Rejections
Claims 1-2, 4-7, and 9-20 were rejected for reciting abstract ideas without significantly more. Applicant’s arguments have been thoroughly reviewed and considered. These rejections have been maintained for all currently pending claims, and see new grounds of rejection below for newly added claim 21. Claim 6 has been canceled, and so this rejection has been rendered moot.
35 USC 103 Rejections
Claims 1-2, 4, 7, and 13-14 were rejected under 35 U.S.C. 103 as being unpatentable over Reischl et al. (EP 2985350 A1; cited in Applicant’s IDS) in view of Harness et al. (US 2022/0002781 A1).
Claims 6, 10-12, and 15 were rejected under 35 U.S.C. 103 as being unpatentable over Reischl et al. (EP 2985350 A1; cited in Applicant’s IDS), in view of Harness et al. (US 2022/0002781 A1), and further in view of Chiu et al. (WO 2017/053446 A2; cited in Applicant’s IDS).
Claims 5, 16-18, and 20 were rejected under 35 U.S.C. 103 as being unpatentable over Reischl et al. (EP 2985350 A1; cited in Applicant’s IDS) in view of Harness et al. (US 2022/0002781 A1), as evidenced by Kotra et al. (Microbes and Infection, 2000).
Claim 19 was rejected under 35 U.S.C. 103 as being unpatentable over Reischl et al. (EP 2985350 A1; cited in Applicant’s IDS), in view of Harness et al. (US 2022/0002781 A1), and further in view of Chiu et al. (WO 2017/053446 A2; cited in Applicant’s IDS), as evidenced by Kotra et al. (Microbes and Infection, 2000).
Claims 1-2, 4, 9, and 13-14 were rejected under 35 U.S.C. 103 as being unpatentable over Reischl et al. (EP 2985350 A1; cited in Applicant’s IDS) in view of Mercer (US 2021/0317518 A1).
Applicant’s arguments have been thoroughly reviewed and considered. These rejections have been maintained for all currently pending claims, and see new grounds of rejection below for newly added claim 21. Claim 6 has been canceled, and so this rejection has been rendered moot.
Double Patenting
Claims 1 and 7 were provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 8-10 and 20 of copending Application No. 17/629,055 (reference application) in view of Harness et al. (US 2022/0002781 A1). Applicant’s arguments have been thoroughly reviewed and considered. These rejections have been maintained. See “Response to Applicant’s Arguments” below.
Response to Applicant’s Arguments
Regarding the 35 USC 103 Rejections, Applicant argues that Reischl, the primary reference, does not teach the newly amended portions of instant claim 1 (Remarks, page 8). Regarding Reischl in view of Harness, Applicant argues that Harness does not provide a reasonable predictability of using the genome size criteria in a sample with a target and a calibrator (Remarks, page 8). Regarding Reischl in view of Mercer, Applicant argues that Mercer similarly does not provide any reasonable predictability (Remarks, pages 9-10).
Regarding newly amended claim 1, the substantive amendments to the claims are in steps (a) and (b). In (a), extraction of nucleic acids from various biological species must now occur, which equate to an extracted population. In (b), sequencing of “an inventory of” nucleotide sequences from the population is recited. The term “inventory” is not defined in the instant specification, but in paras. 6 and 32, appears to naturally result from sequencing multiple species in a sample with high-throughput methods. However, these contexts are not limiting, and so “inventory” will be interpreted to be a collection of sequences resulting from the sequencing of multiple species.
In the portions of Reischl cited in the Final Rejection, specifically the examples recited in para. 53 of the Final Rejection, multiple bacterial species are already examined and sequenced (see Figure 8 in particular for support). Additionally, the reference repeatedly references the use of next-generation sequencing technologies (paras. 7-9 and 49). Thus, Reischl is considered to meet the limitations of the newly amended limitations of claim 1. These teachings are incorporated into the 35 USC 103 Rejections below.
Regarding the combination of Reischl and Harness, this combination amounts to performing a mathematical calculation as taught by Harness using the information that would already be available to the ordinary artisan in the method of Reischl. This combination is explained in para. 56 of the Final Rejection, and a motivation (“Harness provides an easy way to determine estimated sample concentration with concrete measurements using values the ordinary artisan would already have when performing the method of Reischl (i.e. spike bacteria concentration, genome size, and number of sequence reads). This method does not add any steps to the hands-on procedures of Reischl, and simply involves algebraic calculations. This would prevent the need to do intensive spectrometric methods to determine concentrations, which would require more equipment and resources.”) and reasonable expectation of success (“There would be a reasonable expectation of success as the calculations required could easily be performed by the ordinary artisan.”) were provided. Applicant does not directly address this rationale in their arguments.
Regarding the combination of Reischl and Mercer, Mercer provides an illustration of the positive relationship between sequence coverage and DNA concentration, and as the methods of Reischl are directed in part to determining concentration of a specific target in a sample, the ordinary artisan would recognize sequence coverage as a useful metric to measure. Such coverage would also already be possible to gather in the sequencing data of Reischl by comparing the sequence reads to the known genomic sequences for each bacteria. In the specific combination of these references presented in para. 81 of the Final Rejection, a motivation (“Measuring sequence coverage generally would also aid in determining the accuracy of taxa determinations for particular sequences. For example, if certain taxa have very low coverage, their results may be less accurate compared to others.”) as well as a reasonable expectation of success (“There would be a reasonable expectation of success as measuring sequence coverage is already well-known in the art, as evidenced by Mercer, and the subsequent calculations would require techniques and knowledge available to the ordinary artisan.”) were provided. Applicant does not directly address this rationale in their arguments.
Thus, Applicant’s arguments against these rejections are not persuasive, and these rejections have been maintained for all currently pending claims.
Regarding newly added claim 21, the term “substantially” is not specifically defined by the instant specification. Thus, “substantially all” will be considered to encompass sequencing a vast majority of the extracted nucleic acids. In Reischl, the entirety of the isolated sample DNA and spike-in bacteria in para. 48 is amplified, and paras. 49-50 describe the sequencing of this amplification product. No sequences are described to be removed or filtered out before sequencing occurs. In discussing the specifics of the examples, Reischl describes that stool samples were used, bacterial lysis buffer was applied, and DNA was isolated from lysate (paras. 52-53). Thus, the extracted nucleic acids are composed of bacterial nucleic acids, and these are all sequenced and further categorized/analyzed in the method of Reischl. Thus, this reference is considered to meet the limitations of newly added claim 21. See the new grounds of rejection below.
Regarding the 35 USC 101 Rejections, Applicant argues that the amendments to claim 1, along with the addition of a calibrator, practically manipulates the samples, and so presents an ordered combination of manipulating a modified sample and amount to the improvement of a technological process with non-conventional aspects (Remarks, pages 3-6).
In considering the overall rationale behind the 35 USC 101 Rejections, the following is concluded:
With respect to Step 1: the claim is directed to a statutory category (i.e. a process).
With respect to Step 2A: the claim is direct to a judicial exception, namely abstract ideas.
With respect to Step 2B: the claims do not recite additional elements that are not well-understood, routine, and conventional. Namely, the use of spike-in sequences is well-known in the art (see Reischl, Harness, and Mercer for example). Applicant states that the combination of claimed limitations to manipulate the sample is unconventional, but the actual claimed manipulations are simply extracting nucleic acids, adding a spike-in calibrator, and sequencing said nucleic acids (which are all taught by at least Reischl, see the prior art rejections below). The rest of the steps of the method are analysis steps that do not involve nucleic acid manipulation. In considering whether the claims are directed to an improvement in technology, Applicant points to para. 127 of the instant specification, which states that using control species allowed for improvements to specificity without a loss of sensitivity. This improvement appears to be compared to analyses that do not involve the use of a control species. Thus, the alleged improvement shown by Applicant is not due to an element that is unconventional in the art, and rather, is a well-known element. Thus, the claimed methods do not amount to new and improved ways of analyzing nucleic acids. The claims therefore do not amount to significantly more than the judicial exception.
Thus, Applicant’s arguments are not considered persuasive, and the 35 USC 101 Rejections are maintained for all currently pending claims. See also new grounds of rejection below for added claim 21.
Regarding the double patenting rejections, as noted above, the amendments to claim 1 amount to the requirement of extracting and sequencing nucleic acids from multiple species. Claim 1 of the ‘055 application requires that the sample contain nucleic acids from multiple species, and so the new limitations of instant claim 1 are still encompassed by claim 1 of the ‘055 application. Therefore, these rejections are maintained.
Claim Objections
Claim 1 is objected to because of the following informality: under the first option for estimating the concentration of the biological species in (d), the word “analysis” appears to have been erroneously removed from the phrase “taking into account the concentration of the calibrator added to the
Claim 9 is objected to because of the following informality: in the final line, “the sample” should read “the analysis sample.” Appropriate correction is required.
Claim 21 is objected to because of the following informality: in line 1, “wherein the sequencing b) is a sequencing of” should read “wherein the sequencing of b) is a sequencing of.” Applicant may also choose to amend this phrase to be “wherein the sequencing is a sequencing of,” or “wherein b) is a sequencing of.” Appropriate correction is required.
Claim Interpretation
It is noted that the term “concentration” does not have a specific definition in the instant specification. Therefore, any estimate of concentration will be considered to be encompassed by the method of claim 1 – this may include relative concentrations or percent concentrations.
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 1-2, 4-5, 7, and 9-21 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more. The claims recite abstract ideas.
Claim 1 is directed to a method for detecting a biological species of interest in a sample containing various biological species via the use of extracting and sequencing methods, as well as the use of a calibrator sequence of known concentration. The abstract ideas recited are the determinations of the number of sequence reads for the calibrator and species of interest, as well as the determination of the concentration of the species of interest, as these are mathematical concepts and/or determinations. Also, the limitations in the final wherein clause of the claim specify particular mathematical relationships and calculations to perform to determine the concentration of the biological species of interest, adding further abstract ideas to the claim. Finally, the assigning of (i) can be considered a mental process, as this can amount to comparing sequence reads to a list of known sequence reads, and so could be done in the human mind with or without an aid. These judicial exceptions are not integrated into a practical application because there is no required active treatment step or other step that integrates the judicial exception into a practical application. See MPEP 2106.04(d). The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because they do not amount to more than well-understood, routine, and conventional activity in view of Reischl et al. (EP 2985350 A1).
Reischl teaches methods for microbiome analysis using a quantifiable standard (Abstract and para. 1). These methods can comprise sampling, DNA isolation, sequencing, sequence analysis, and a quantification step (paras. 22-23), and the goal is to find an absolute quantity of the bacteria in a sample (para. 16). A spike bacteria can be added to the sample as the quantifiable sample, where said spike bacteria comprises at least one bacterial species (paras. 19-20). The spike bacteria can be added to the DNA sample in a quantifiable number and all of the nucleic acids present can then be isolated (para. 24). The original DNA (i.e. the non-spiked sample) can also be quantified (para. 25). Sequencing can be done after isolation and amplification, and the number of reads of the spike bacteria can provide normalization for the bacteria in the sample (para. 38). Reischl teaches that the spike bacteria were added in known concentrations (para. 45) and the percentage of the sample that each spike-in comprises can be determined (para. 50). In Reischl, multiple bacterial species are examined and sequenced, particularly in their working examples (see paras. 46-65, and Figure 8 in particular for support). Additionally, the reference repeatedly references the use of next-generation sequencing technologies (paras. 7-9 and 49). Thus, claim 1 is directed to a judicial exception without significantly more.
Claim 2 requires the use of a reference quantity to normalize the species of interest and calibrator. The judicial exception is not integrated into a practical application because there is no required active treatment step or other step that integrates the judicial exception into a practical application. See MPEP 2106.04(d). The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because it does not amount to more than well-understood, routine, and conventional activity in view of Reischl, which teaches an external quantification standard can also be used in addition to the spike bacteria. This additional standard can be used to determine amounts of the original DNA and spiked bacteria in a sample (para. 26). Para. 31 also teaches normalization of sequence reads based on a standard, and para. 62 teaches normalization with spike bacterium as well. Thus, claim 2 is directed to a judicial exception without significantly more.
Claim 4 specifies the type of genomes the calibrator and sequence of interest must be, and so simply serves to further the abstract ideas presented in claim 1. The judicial exception is not integrated into a practical application because there is no required active treatment step or other step that integrates the judicial exception into a practical application. See MPEP 2106.04(d). The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because it does not amount to more than well-understood, routine, and conventional activity. Thus, claim 4 is directed to a judicial exception without significantly more.
Claim 5 specifies the genome size and concentration of the calibrator to be used. This limitation simply serve to further the abstract ideas presented in claim 1. The judicial exception is not integrated into a practical application because there is no required active treatment step or other step that integrates the judicial exception into a practical application. See MPEP 2106.04(d). The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because they do not amount to more than well-understood, routine, and conventional activity. Thus, claim 5 is directed to a judicial exception without significantly more.
Claims 7 and 9 specify particular options for use in the method of claim 1, where each option includes mathematical relationships and calculations to perform to determine the concentration of the biological species of interest. Thus, these claims recite the same abstract ideas presented in claim 1. The judicial exception is not integrated into a practical application because there is no required active treatment step or other step that integrates the judicial exception into a practical application. See MPEP 2106.04(d). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because they do not amount to more than well-understood, routine, and conventional activity. Thus, claims 7 and 9 are directed to a judicial exception without significantly more.
Claims 10 recites use of a decision threshold. The judicial exception is not integrated into a practical application because there is no required active treatment step or other step that integrates the judicial exception into a practical application. See MPEP 2106.04(d). The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because it does not amount to more than well-understood, routine, and conventional activity in view of Chiu et al. (WO 2017/053446 A2). Chiu teaches methods of sequencing and analyzing genetic material (Abstract). This reference also teaches the use of spike in control samples that can be used with target samples (paras. 147-148), and these spike ins can be added at specific concentrations (para. 150). Chiu teaches that during analysis of sequencing, ratios of sequence reads and controls can be compared to a threshold value to determine if pathogens are present in a test sample (paras. 11 and 112). For example, if the ratio of the test sample reads to negative control reads exceeds a set threshold, then this may indicate pathogenicity or clinical significance (paras. 11 and 153). Thus, claim 10 is directed to judicial exceptions without significantly more.
Claim 11 specifies a particular concentration of the calibrator, and so simply serves to further the abstract ideas presented in claim 1. The judicial exception is not integrated into a practical application because there is no required active treatment step or other step that integrates the judicial exception into a practical application. See MPEP 2106.04(d). The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because it does not amount to more than well-understood, routine, and conventional activity. Thus, claim 11 is directed to a judicial exception without significantly more.
Claim 12 specifies the use of a decision threshold, similar to claim 10. The judicial exception is not integrated into a practical application because there is no required active treatment step or other step that integrates the judicial exception into a practical application. See MPEP 2106.04(d). The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because it does not amount to more than well-understood, routine, and conventional activity in view of Chiu et al. (WO 2017/053446 A2). Chiu teaches methods of sequencing and analyzing genetic material (Abstract). This reference also teaches the use of spike in control samples that can be used with target samples (paras. 147-148), and these spike ins can be added at specific concentrations (para. 150). Chiu teaches that during analysis of sequencing, ratios of sequence reads and controls can be compared to a threshold value to determine if pathogens are present in a test sample (paras. 11 and 112). For example, if the ratio of the test sample reads to negative control reads exceeds a set threshold, then this may indicate pathogenicity or clinical significance (paras. 11 and 153). Thus, claim 12 is directed to judicial exceptions without significantly more.
Claims 13-15 specify the types of organisms and/or genomes that the sample and calibrator may be from. These limitations simply serve to further the abstract ideas presented in claim 1. The judicial exception is not integrated into a practical application because there is no required active treatment step or other step that integrates the judicial exception into a practical application. See MPEP 2106.04(d). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because they do not amount to more than well-understood, routine, and conventional activity. Thus, claims 13-15 are directed to a judicial exception without significantly more.
Claims 16-20 specify particular genome sizes for the calibrator. These limitations simply serve to further the abstract ideas presented in claim 1. The judicial exception is not integrated into a practical application because there is no required active treatment step or other step that integrates the judicial exception into a practical application. See MPEP 2106.04(d). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because they do not amount to more than well-understood, routine, and conventional activity. Thus, claims 16-20 are directed to a judicial exception without significantly more.
Claim 21 requires that the sequencing encompass all the extracted nucleic acids of claim 1. The claim does not require any additional or more narrow type of sequencing method. The judicial exception is not integrated into a practical application because there is no required active treatment step or other step that integrates the judicial exception into a practical application. See MPEP 2106.04(d). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because they do not amount to more than well-understood, routine, and conventional activity in view of Reischl, as this reference teaches that the entirety of the isolated sample DNA and spike-in bacteria in para. 48 is amplified, and paras. 49-50 describe the sequencing of this amplification product. No sequences are described to be removed or filtered out before sequencing occurs. In discussing the specifics of the examples, Reischl describes that stool samples were used, bacterial lysis buffer was applied, and DNA was isolated from lysate (paras. 52-53). Therefore, the extracted nucleic acids are composed of bacterial nucleic acids, and these are all sequenced and further categorized/analyzed in the method of Reischl. Thus, claim 21 is directed to a judicial exception without significantly more.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-2, 4, 7, 13-14, and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Reischl et al. (EP 2985350 A1; cited in Applicant’s IDS) in view of Harness et al. (US 2022/0002781 A1).
It is noted that all paragraph numbers for the Reischl reference cited in the prior art rejections refer to those used in the English machine translation provided by Applicant.
Reischl teaches methods for microbiome analysis using a quantifiable standard (Abstract and para. 1). These methods can comprise sampling, DNA isolation, sequencing, sequence analysis, and a quantification step (paras. 22-23), and the goal is to find an absolute quantity of the bacteria in a sample (para. 16). A quantifiable spike bacteria can be added to the sample, where said spike bacteria comprises at least one bacterial species (paras. 19-20). The spike bacteria can be added to the DNA sample in a quantifiable number and all of the nucleic acids present can then be isolated (para. 24). The original DNA (i.e. the non-spiked sample) can also be quantified (para. 25). Sequencing can be done after isolation and amplification, and the number of reads of the spike bacteria can provide normalization for the bacteria in the sample (paras. 31 and 38).
In their examples, Reischl teaches that the spike bacteria were added in known concentrations (para. 45) and the percentage of the sample that each spike-in comprises can be determined (para. 50). Then, DNA concentrations from isolated DNA from the sample can be determined (para. 51). These concentrations are shown in Table 2 (view the German Language version for a clearer image of the table, where the table clearly lists the ng/ul for each sample). Reischl then goes on to specifically discuss sequence analysis, and notes that with their barcoding methods, they are able to determine the specific taxa related to each read (para. 57 and Table 3). These reads are then normalized relative to the amount of spike-in sequences. Figure 8 then shows the relative frequency of each taxonomic group in the sample, with counts for each (para. 58). This table provides percentages for each taxonomic unit relative to the composition of the entire sample. Thus, Reischl’s methods can be used to find the relative percent concentration of particular bacterial species in a sample. It is noted that in these examples of Reischl, multiple bacterial species are already examined and sequenced (see Figure 8 in particular for support). Additionally, the reference repeatedly references the use of next-generation sequencing technologies (paras. 7-9 and 49). Thus, Reischl is considered to meet the limitations of the newly amended limitations of claim 1, as noted above in the “Response to Applicant’s Arguments” section.
Reischl also teaches the normalization of the sequence reads for the bacterial species of interest in the sample via the spike bacteria, which would involve creating a ratio of the quantities of sequence reads (para. 38). Reischl also notes the concentration of the spike bacteria when added to the overall sample. However, Reischl does not teach any analysis concerning genome sizes (para. 45).
Harness teaches methods for quantifying target nucleic acids using next generation sequencing (Abstract). This can involve the use of a normalization control (NC; para. 36). The NC is composed of DNA or RNA and can be used to determine the relative or absolute amounts of different nucleic acids in a sample (paras. 1002 and 1004-1005). Harness explains how this can be done using sequence length and genome size (paras. 1005-1006). In para. 1006, the reference explains the relationship between the known concentration of the NC, genome lengths for the NC and sample, and number of sequence reads for the NC and sample, in order to determine sample concentration. These calculations are equivalent to the calculations provided in instant claims 1 and 7.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the teachings of Harness in the method of Reischl. Specifically, Harness provides an easy way to determine estimated sample concentration with concrete measurements using values the ordinary artisan would already have when performing the method of Reischl (i.e. spike bacteria concentration, genome size, and number of sequence reads). This method does not add any steps to the hands-on procedures of Reischl, and simply involves algebraic calculations. This would prevent the need to do intensive spectrometric methods to determine concentrations, which would require more equipment and resources. There would be a reasonable expectation of success as the calculations required could easily be performed by the ordinary artisan.
Thus, claims 1 and 7 are prima facie obvious over Reischl in view of Harness.
Regarding claim 2, an external quantification standard can also be used in addition to the spike bacteria. This additional standard can be used to determine amounts of the original DNA and spiked bacteria in a sample (para. 26). Para. 31 also teaches normalization of sequence reads based on a standard (though this standard likely refers to the spiked bacteria), and para. 62 teaches normalization with spike bacteria as well. It would thus be prima facie obvious to the ordinary artisan that the external quantification standard could also be used for normalization of sequence reads in the method of Reischl in view of Harness. As this standard is not involved in the same reaction chamber as the target and spike bacteria, comparing the quantities of the external standard to the target and spike bacteria would aid in determining if the analyses are functioning as expected, and would provide a more standardized means of comparison across multiple samples, multiple types of target bacteria, and multiple types of spiked bacteria. These comparisons could then be used to determine bacterial expression over time in individuals or compare groups of individuals, both of which would be useful in clinical settings. Giving that this normalization simply involves manipulation of numbers already provided in the methods of Reischl in view of Harness, there would be a reasonable expectation of success.
Regarding claims 4 and 13-14, the spike bacteria of Reischl is specifically noted to be preferably exogenous (para. 24) and the spike bacteria should preferably have various different properties compared to the target bacteria in the sample (para. 27).
Regarding claim 21, in Reischl, the entirety of the isolated sample DNA and spike-in bacteria in para. 48 is amplified, and paras. 49-50 describe the sequencing of this amplification product. No sequences are described to be removed or filtered out before sequencing occurs. In discussing the specifics of the examples, Reischl describes that stool samples were used, bacterial lysis buffer was applied, and DNA was isolated from lysate (paras. 52-53). Thus, the extracted nucleic acids are composed of bacterial nucleic acids, and these are all sequenced and further categorized/analyzed in the method of Reischl.
Claims 10-12, and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Reischl et al. (EP 2985350 A1; cited in Applicant’s IDS), in view of Harness et al. (US 2022/0002781 A1), and further in view of Chiu et al. (WO 2017/053446 A2; cited in Applicant’s IDS).
Reischl in view of Harness teaches the methods of claim 1-2, 4, 7, and 13-14, as described above. However, these references do not teach the use of a decision threshold.
Chiu teaches methods of sequencing and analyzing genetic material (Abstract). This reference also teaches the use of spike in control samples that can be used with target samples (paras. 147-148), and these spike ins can be added at specific concentrations (para. 150). Chiu teaches that during analysis of sequencing, ratios of sequence reads and controls can be compared to a threshold value to determine if pathogens are present in a test sample (paras. 11 and 112). For example, if the ratio of the test sample reads to negative control reads exceeds a set threshold, then this may indicate pathogenicity or clinical significance (paras. 11 and 153).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the threshold teachings of Chiu in the method of Reischl in view of Harness. Chiu teaches similar methods to those of Reischl, particularly with regard to sample and spike in sequences, and both methods can be used with bacteria (see Chiu para. 29). By utilizing a threshold in the method of Reischl in view of Harness taught above, it can be determined what concentrations of the target DNA cause disease, which would be relevant for diagnostic and treatment purposes, as well as preventing the spread of disease, and would therefore be valuable to clinicians. There would be a reasonable expectation of success because adding a threshold to the analysis would not add any materials or steps to the isolation, amplification, and/or sequencing aspects of the method of Reischl in view of Harness, and would only require additional mathematical analysis steps that would be possible for the ordinary artisan, as evidenced by Chiu.
Therefore, the methods of claims 10 and 12 are prima facie obvious over Reischl, in view of Harness, and further in view of Chiu.
Regarding claim 11, Chiu teaches a typical decision threshold of 10 RPM (e.g. para. 153). The reference also notes that the purpose of their internal control is at least partially to ensure that a particular concentration of sequence can be successfully detected (para. 150). Chiu then teaches that to ensure quality control of samples, internal control spike ins that exceed the decision threshold (i.e. are greater than 10 RPM) should be included (para. 155). Thus, Chiu teaches providing spike ins greater than 1 times the decision threshold, overlapping with the range provided in instant claim 11. It would therefore be prima facie obvious to include spike ins in this range in the method of Reischl, in view of Harness, and further in view of Chiu.
Regarding claim 15, Reischl, in view of Harness, and further in view of Chiu teaches the method of claims 10-12, as described above. Reischl also teaches that the spike bacteria is specifically noted to be preferably exogenous (para. 24) and the spike bacteria should preferably have various different properties compared to the target bacteria in the sample (para. 27).
Claims 5, 16-18, and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Reischl et al. (EP 2985350 A1; cited in Applicant’s IDS) in view of Harness et al. (US 2022/0002781 A1), as evidenced by Kotra et al. (Microbes and Infection, 2000).
Reischl in view of Harness renders obvious the methods of claims 1-2, 4, 7 and 13-14, as described above. In this combination, Reischl teaches that the target DNA and the spike DNA are from bacteria.
Kotra teaches that bacterial genomes vary between 0.6 and 6 Mb (page 651, column 2, para. 2), and so even if the target bacteria and spike bacteria in Reischl had genomes at the ends of this size range, the difference would not be more than 10x, the maximum difference allowed by instant claims 5, 16-18, and 20.
Thus, claims 5, 16-18, and 20 are prima facie obvious over Reischl, in view of Harness, as evidenced by Kotra.
Claim 19 is rejected under 35 U.S.C. 103 as being unpatentable over Reischl et al. (EP 2985350 A1; cited in Applicant’s IDS), in view of Harness et al. (US 2022/0002781 A1), and further in view of Chiu et al. (WO 2017/053446 A2; cited in Applicant’s IDS), as evidenced by Kotra et al. (Microbes and Infection, 2000).
Reischl, in view of Harness, and further in view of Chiu teaches the methods of claim 10-12 and 15, as described above. Reischl also makes clear that the target DNA and the spike DNA are from bacteria.
Kotra teaches that bacterial genomes vary between 0.6 and 6 Mb (page 651, column 2, para. 2), and so even if the target bacteria and spike bacteria in Reischl in view of Chiu had genomes at the ends of this size range, the difference would not be more than 10x, the maximum difference allowed by instant claim 19.
Thus, claim 19 is prima facie obvious over Reischl, in view of Harness, and further in view of Chiu, as evidenced by Kotra.
Claims 1-2, 4, 9, 13-14, and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Reischl et al. (EP 2985350 A1; cited in Applicant’s IDS) in view of Mercer (US 2021/0317518 A1).
It is noted that all paragraph numbers for the Reischl reference cited in the prior art rejections refer to those used in the English machine translation provided by Applicant.
Reischl teaches methods for microbiome analysis using a quantifiable standard (Abstract and para. 1). These methods can comprise sampling, DNA isolation, sequencing, sequence analysis, and a quantification step (paras. 22-23), and the goal is to find an absolute quantity of the bacteria in a sample (para. 16). A quantifiable spike bacteria can be added to the sample, where said spike bacteria comprises at least one bacterial species (paras. 19-20). The spike bacteria can be added to the DNA sample in a quantifiable number and all of the nucleic acids present can then be isolated (para. 24). The original DNA (i.e. the non-spiked sample) can also be quantified (para. 25). Sequencing can be done after isolation and amplification, and the number of reads of the spike bacteria can provide normalization for the bacteria in the sample (paras. 31 and 38).
In their examples, Reischl teaches that the spike bacteria were added in known concentrations (para. 45) and the percentage of the sample that each spike-in comprises can be determined (para. 50). Then, DNA concentrations from isolated DNA from the sample can be determined (para. 51). These concentrations are shown in Table 2 (view the German Language version for a clearer image of the table, where the table clearly lists the ng/ul for each sample). Reischl then goes on to specifically discuss sequence analysis, and notes that with their barcoding methods, they are able to determine the specific taxa related to each read (para. 57 and Table 3). These reads are then normalized relative to the amount of spike-in sequences. Figure 8 then shows the relative frequency of each taxonomic group in the sample, with counts for each (para. 58). This table provides percentages for each taxonomic unit relative to the composition of the entire sample. Thus, Reischl’s methods can be used to find the relative percent concentration of particular bacterial species in a sample. It is noted that in these examples of Reischl, multiple bacterial species are already examined and sequenced (see Figure 8 in particular for support). Additionally, the reference repeatedly references the use of next-generation sequencing technologies (paras. 7-9 and 49). Thus, Reischl is considered to meet the limitations of the newly amended limitations of claim 1, as noted above in the “Response to Applicant’s Arguments” section.
However, Reischl does not teach the use of sequence coverage values in making concentration calculations.
Mercer teaches artificial controls for calibrating genetic sequencing and quantitation methods (Abstract). Figure 35 shows the observed abundance relative to the expected concentration of DNA standards (para. 102). The abundance is shown in reads per million per kilobase (para. 490). The concentration of DNA standard was shown to be related to sequence coverage (para. 491), where high concentrations were associated with high sequence coverage, and low concentrations were associated with low coverage. Mercer teaches that abundance is tightly correlated with concentration (para. 490). Mercer also shows examples where DNA standards were added to genomic DNA and sequenced (para. 543). The coverage and expected abundance of each standard was measured (Figure 42E).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the teachings of Mercer with Reischl to arrive at the invention of instant claims 1 and 9. Specifically, Mercer teaches a tight relationship between sequencing read coverage and concentration, and so the ordinary artisan would be motivated to measure coverage for the sample and spike bacteria in Reischl. Measuring sequence coverage generally would also aid in determining the accuracy of taxa determinations for particular sequences. For example, if certain taxa have very low coverage, their results may be less accurate compared to others. Then, with the relationship shown by the standards of Mercer, the ordinary artisan would recognize that an equation could be made where the spike in concentration divided by the sequence coverage is equal to the sample concentration divided by sequence coverage. In solving for sample concentration, the calculations described in instant claim 9 would be performed. There would be a reasonable expectation of success as measuring sequence coverage is already well-known in the art, as evidenced by Mercer, and the subsequent calculations would require techniques and knowledge available to the ordinary artisan.
Thus, claims 1 and 9 are prima facie obvious over Reischl in view of Mercer.
Regarding claim 2, an external quantification standard can also be used in addition to the spike bacteria. This additional standard can be used to determine amounts of the original DNA and spiked bacteria in a sample (para. 26). Para. 31 also teaches normalization of sequence reads based on a standard (though this standard likely refers to the spiked bacteria), and para. 62 teaches normalization with spike bacteria as well. It would thus be prima facie obvious to the ordinary artisan that the external quantification standard could also be used for normalization of sequence reads in the method of Reischl in view of Mercer. As this standard is not involved in the same reaction chamber as the target and spike bacteria, comparing the quantities of the external standard to the target and spike bacteria would aid in determining if the analyses are functioning as expected, and would provide a more standardized means of comparison across multiple samples, multiple types of target bacteria, and multiple types of spiked bacteria. These comparisons could then be used to determine bacterial expression over time in individuals or compare groups of individuals, both of which would be useful in clinical settings. Giving that this normalization simply involves manipulation of numbers already provided in the methods of Reischl in view of Mercer, there would be a reasonable expectation of success.
Regarding claims 4 and 13-14, the spike bacteria of Reischl is specifically noted to be preferably exogenous (para. 24) and the spike bacteria should preferably have various different properties compared to the target bacteria in the sample (para. 27).
Regarding claim 21, in Reischl, the entirety of the isolated sample DNA and spike-in bacteria in para. 48 is amplified, and paras. 49-50 describe the sequencing of this amplification product. No sequences are described to be removed or filtered out before sequencing occurs. In discussing the specifics of the examples, Reischl describes that stool samples were used, bacterial lysis buffer was applied, and DNA was isolated from lysate (paras. 52-53). Thus, the extracted nucleic acids are composed of bacterial nucleic acids, and these are all sequenced and further categorized/analyzed in the method of Reischl.
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.
Claims 1 and 7 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 8-10 and 20 of copending Application No. 17/629,055 (reference application) in view of Harness et al. (US 2022/0002781 A1).
Claim 8 of the ‘055 application contains all of the listed limitations of instant claims 1 and 7, with the primary exception being the fact that the ‘055 application does not teach the specific multiplication presented in the genome size mathematical calculations of instant claims 1 and 7. It is noted that though claim 8 of the ‘055 application contains additional limitations not described in instant claims 1 and 7 (e.g. the described detection thresholds or the use of a control and calibrator), these are not prohibited by the instant claims, as the claims comprise the listed steps.
Additionally, regarding the newly amended portions of instant claim 1, as stated above in the “Response to Applicant’s Arguments” section, these amendments amount to the requirement of extracting and sequencing nucleic acids from multiple species. Claim 1 of the ‘055 application (from which claim 8 depends) requires that the sample contain nucleic acids from multiple species, and so the new limitations of instant claim 1 are still encompassed by claim 1 (and subsequently, claim 1) of the ‘055 application.
Regarding the calculations presented in instant claims 1 and 7, Harness teaches methods for quantifying target nucleic acids using next generation sequencing (Abstract). This can involve the use of a normalization control (NC; para. 36). The NC is composed of DNA or RNA and can be used to determine the relative or absolute amounts of different nucleic acids in a sample (paras. 1002 and 1004-1005). Harness explains how this can be done using sequence length and genome size (paras. 1005-1006). In para. 1006, the reference explains the relationship between the known concentration of the NC, genome lengths for the NC and sample, and number of sequence reads for the NC and sample, in order to determine sample concentration. These calculations are equivalent to the calculations provided in instant claims 1 and 7. Harness provides an easy way to determine estimated sample concentration with concrete measurements using values the ordinary artisan would already have when performing the method of claim 8 of the ‘055 application (i.e. calibrator concentration, genome size, and number of sequence reads). This would prevent the need to do intensive spectrometric methods to determine concentrations, which would require more equipment and resources. Thus, it would be obvious to the ordinary artisan that mathematical calculations such as those taught by Harness could be used in claim 8 of the ‘055 application, arriving at the methods of instant claims 1 and 7.
Claim 9 of the ‘055 application recites the same limitations regarding calculating the concentration of the species of interest as instant claims 1 and 7 (i.e. the claim includes the multiplication described in instant claims 1 and 7 that was missing from claim 8 of the ‘055 application), and so reads on these claims. It is noted that claim 9 of the ‘055 application has both a control and a calibrator, but the use of both is not precluded by the instant claims.
Claim 10 of the ‘055 application depends on claim 8, and requires that the control and calibrator are the same. Thus, this also meets the limitations of instant claims 1 and 7.
Claim 20 of the ‘055 application depends on claim 9, and requires that the control and calibrator are the same. Thus, this also meets the limitations of instant claims 1 and 7.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims are currently allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FRANCESCA F GIAMMONA whose telephone number is (571)270-0595. The examiner can normally be reached M-Th, 7-5pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gary Benzion can be reached at (571) 272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/FRANCESCA FILIPPA GIAMMONA/Examiner, Art Unit 1681
Prosecution Insights