DETAILED CORRESPONDENCE
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 .
Claim Status
Claims 1, 3, 4, 6-11, 14-32 are pending.
Response to Amendments
Regarding applicants claim amendments and remarks received on 12/8/25, the previous 101 rejection remains with modifications to address the claim amendments (see below).
With respect to the claim amendments and remarks, the previous 112a and 112b rejections are withdrawn. However, new rejections have been entered to address the claim amendments.
As to the amended claims and remarks, the prior art rejection is modified to address the claim amendments (see below).
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, 3, 4, 6-11, 14-32 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The instant rejection reflects the Guidance published in the Federal Register notice titled 2019 Revised Patent Subject Matter Eligibility Guidelines (Vol. 84, No. 4, Monday January 7, 2019 at 50) and the October 2019 Updated Subject Matter Eligibility Guidance (hereinafter both referred to as the “Guidance”).
Framework with which to Evaluate Subject Matter Eligibility:
(1) Are the claims directed to a process, machine, manufacture or composition of matter;
(2A) Are the claims directed to a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea (Prong One); If the claims are directed to a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
(2B) If the claims are directed to a judicial exception and do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
With regard to Step 1, the instant claims recite a “method implemented on one or more computers” (claim 1), a “biological specimen pooling system” (claim 27), and a “non-transitory computer-readable storage medium” (claim 30), and therefore the answer is "yes".
With regard to Step 2A, Prong One, under the broadest reasonable interpretation (BRI), the instant claims recite claim steps directed to the judicial exception that is an abstract idea of the type that is in the grouping of “mental process” and/or “mathematical concept” (See MPEP 2106.04(a)(2) subsections (I) and (III)) because said operations could be performed in the mind or are done via mathematical relationships, but for the recitation of a plurality of flow cells each having a lane and computers having processors to perform the method. Mental operations in the instant claims are recited as: identifying flow cell characteristics; generating a group of flow cells based on flow cell characteristics and first specimen characteristics; generating eligible an eligible lane arrangement of each flow cell by applying a mass or priority algorithm to the second plurality of specimen characteristics and at least one lane characteristic, or placing specimens sharing barcodes in different lanes before evaluating others of the second plurality of specimen characteristics and the at least one lane characteristic; and generating for each lane a plurality of pools based on evaluating a total cost of sequencing the specimens and a likelihood of obtaining valid results; and outputting the generated pools, where the generating steps are associated with, and adjustable to balance computational costs and qualitative metrics. In summary, the claim(s) recite(s) a method for determining the organization or grouping of samples in flow cells (and their corresponding lane). Identifying and generating groupings are processes that can be performed as mental steps and/or math. The use of an algorithm to generate lane arrangements is explicitly math, and evaluating cost may also be math as described in [75] of the instant specification. Further, [102] discusses using “heuristics’ to generate eligible flow cells, [104-105] discusses using “heuristics” to generate eligible lanes, and [111] discusses using “heuristics” to generate pools, where [112-118] also describe the pool generation as a search tree, which is an algorithm. Thus, the generating lane arrangements and generating pools of the claims requires the use of heuristics/search tree/algorithm, which is math. Further, balancing costs and metrics during the generating steps is either just a mental process or a mathematical concept. Therefore, each of the identified abstract ideas may also be considered an algorithm and/or mathematical process because a user could perform the recited steps as mental steps, or with the assistance of pencil and paper or a computer.
The claims recite the judicial exceptions all being performed by a computer(s) having a processor(s), which is just a generic and general-purpose computer. A claim, under its BRI, which covers performance of the limitation in the mind as a mental process and/or math, but for the recitation of generic computer elements, falls within the “mental processes” grouping of abstract ideas (see MPEP 2106.04(a)(2)(III)(C)). MPEP 2106.04(a)(2)III is clear that using a computer/controller, or pencil and paper, to perform the abstract idea does not preclude the steps from being considered an abstract idea.
Because the claims are directed to abstract ideas, they must further be analyzed under Step 2A, Prong Two to determine if said judicial exceptions are integrated into a practical application as determined by further assessment of the “additional steps” recited in the claims. With respect to Prong Two, the additional elements and the rationale pertaining to why the additional elements are not integrated, are as follows:
(a) The claims recite mental steps (judicial exception) which are not integrated into a practical application because the method amounts to mental processes/data organization (generating groups/pools based on heuristics) as a general mental concept/process, but the method does not describe a resultant action/step that is taken by applying generated pool in a physical flow cell or sequencing device, and therefore the method does not add a meaningful limitation to the abstract idea. The “output” of the generated pools does not integrate the exception into a practical application because “outputting” or “displaying” is insignificant post-solution activity, similar to the alarm in Parker v. Flook. See MPEP 2106.04(d) and 2106.05(g).;
(b) Although the claims recite a computer/processor/memory that performs the abstract idea, a general-purpose computer is not a particular machine and performing the abstract ideas on a computer does not integrate the exception into a particular practical application. See MPEP 2106.05(b), I. Further, the claims do not apply the exception, as the claim does not transform the flow cell to a different state or thing beyond its ordinary purpose (See MPEP 2106.05(f) and MPEP 2106.05(c)). The only recited structure in the claims is a processor, which is just a general-purpose computer and not a particular machine. Further, even if the flow cells were required (which they are currently not required in the claims), then the examiner further points to evidence of this in [79, 135, 142] of applicants’ instant specification where the flow cells used are stated as conventional flow cells, such as flow cells from Illumina.
Because the claims fail under step 2A, the claims are further evaluated under Step 2B. The claims herein do not include additional elements that are sufficient to amount to significantly more than the judicial exception under (2B) because, as discussed above with regard to integration of the recited abstract idea into a practical application, the additional elements herein amount to no more than flow cells that include generic computer elements (processor/memory), which do not provide an inventive concept as generic flow cells with a computer is well-understood, routine and conventional. The only recited structure in the claims is a processor, which is just a general-purpose computer and not a particular machine and would be routine and conventional. Even if the claims were deemed to require a flow cell, then the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because (1) the computer/processors/memory and flow cells are being used in their ordinary capacity and are merely tools to execute the abstract idea (See MPEP 2106.05(d)), (2) the additional claim elements of identifying, and generating/determining information based on heuristics, whether considered individually or as a whole, do not meaningfully limit the judicial exception (See MPEP 2106.05(e)). Further, the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because using lanes of flow cells to arrange/pooling specimens is well understood, routine and conventional (see MPEP 2106.05) when claimed in a generic manner as evidenced by Smith et al (US 20200202977; hereinafter “Smith”; already of record), where Smith teaches arranging/pooling/grouping in to specific lanes of flow cells; [125-135]. See also, Figures 1, 3, 5, 7, 9, 11. Therefore, Smith shows that the additional elements of the flow cells are not significantly more. Additionally, the additional element of a flow cell being well-understood, routine and conventional is further evidenced by applicants’ instant specification, which states that the abstract idea/judicial exception can be performed on conventionally known flow cells, such as flow cells from Illumina (see [79, 135, 142] of applicants’ instant specification).
The claims 1, 3, 4, 6-11, 14-32 do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the features represent an abstract idea.
Dependent claims 3, 4, 6-11, 14-26, 28-29, 31-32 amount to no more than determining information (abstract idea under Step 2A, Prong One, or outputting (which is insignificant extra solution activity under Step 2A, Prong Two), or performing well-understood and conventional sample preparation techniques for flow cells (routine and conventional under Step 2B). Thus, these claims similarly are directed towards the judicial exception itself, do not integrate the exception into a practical application, or include additional elements that amount to significantly more.
Thus, in light of the above considerations the claims remain non-statutory, and are thus not patent eligible under 35 U.S.C. 101.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1, 3, 4, 6-11, 14-32 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 1, 27, 30 have been amended to recite that the various generating steps are “associated with respective processor computational cost” and “the generated pools are associated with qualitative metrics” and that the various generating steps are “adjustable to balance…costs with the associated qualitative metrics” (see last 5 lines of the claims), which is new matter. Support for the newly added limitation of the instant claims was not found by the examiner in the original disclosure, as no mention of a the various generating steps are “associated with respective processor computational cost” or of “qualitative metrics” or “the generated pools are associated with qualitative metrics” and that the various generating steps are “adjustable to balance…costs with the associated qualitative metrics” exists in the disclosure. Although the specification discusses costs (see figure 9 of the instant specification), this cost is an actual monetary cost and not a computational cost. Also, there is no discussion of processor computational costs in relation to the generating steps or adjusting/”balancing” the computational costs with qualitative metrics. Further, there is no discussion of the term “qualitative metric” anywhere in the disclosure. Thus, the limitations in the last five lines of the claims are considered new matter. Claims 3, 4, 6-11, 14-26, 31-32 are rejected based on further claim dependency.
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, 3, 4, 6-11, 14-32 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention.
As to “the generated pools are associated with qualitative metrics” in the fourth to last line of claim 1 (and also in the last clause of claim 1), it is unclear what a qualitative metric is defined by the pools are associated with these metrics. In what manner are the pools associated with metrics and what are the qualitative metrics? Claims 27 and 30 recite similar limitations and are therefore similarly rejected.
Claims 3, 4, 6-11, 14-26, 28-29, 31-32 are rejected based on further claim dependency.
Appropriate clarification and/or correction is required.
Claim Rejections - 35 USC § 103
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.
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 set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied 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.
Claims 1, 3, 4, 6-11, 14-32 are rejected under 35 U.S.C. 103 as being unpatentable over Smith et al (US 20200202977; hereinafter “Smith”; already of record) in view of Dean et al (US 20180127804; hereinafter “Dean”; already of record) and in view of Hannon et al (US 20120185177; hereinafter “Hannon”; already of record).
As to claims 1, 27 and 30, Smith teaches a method implemented on a pooling system with one or more computers having one or more processors for pooling a plurality of biological specimens comprising genetic material in a for short read next generation sequencing, each specimen included in the plurality of specimens associated with a first plurality of specimen characteristics and a second plurality of specimen characteristics (Smith teaches samples as tumor tissue; [71, 88]), the method comprising: instructing the one or more processors to identify a plurality of flow cell characteristics for each flow cell included in a plurality of flow cells, each flow cell including one or more lanes for receiving specimens, wherein one flow cell characteristic in the plurality of flow cell characteristics is an availability of a flow cell in the plurality of flow cells (Smith teaches the flow cell characteristic of being available in that if the flow cell can be used for sequencing then it is available; [48, 60, 66, 75, 119, 232, 382]. See also, Figures 1, 3, 5, 7, 9, 11, 13); generating, by the one or more processors, one or more groups of eligible, available flow cell configurations from among a plurality of possible flow cell configurations based in part on the plurality of flow cell characteristics and the first plurality of specimen characteristics, wherein the first plurality of specimen characteristics; generating, by the one or more processors, one or more eligible lane arrangements comprising which specimens to put in each lane of each of the one or more groups of eligible flow cell configurations, based at least in part on either applying a priority optimization heuristic to the second plurality of specimen characteristics and at least one lane constraint or first placing specimens sharing barcodes into different lanes before evaluating others of the second plurality of specimen characteristics and the at least one lane constraint; generating, by the one or more processors a plurality of pools of specimens, and where the pools are associated with qualitative metrics and where the steps of generating the one or more lane arrangements, and generating a plurality of pools of specimens are adjustable based the associated qualitative metrics/heuristics; and outputting, by the one or more processors, the generated pools (As best understood, Smith teaches pooling/grouping in to specific lanes based on sample type; [125-135] and [48, 60, 66, 75, 119, 232, 382]. See also, Figures 1, 3, 5, 7, 9, 11, 13. Smith teaches groups of flow cells; [125-135, 498], Figures 1, 3, 5, 7, 9, 11. Smith teaches outputting a plurality of pools (Smith; Figures 1, 3, 5, 7, 9, 11); arranging the at least one specimen in an associated pool in an associated lane of a flow cell of the group of flow cells according to the output of the at least one pool (Smith; [71, 88, 239, 495, 498]). Smith teaches priority heuristics; [303, 339, 367-383]. Smith teaches that flow cells and lanes are available/eligible if they are able to receive samples. Smith teaches that there are many specimen characteristics and flow cell characteristics including sample type or how sample types are organized in each lane/pool [126], sample identifiers or barcodes [66, 75], various thresholds and constraints or metrics that can be defined by a user [175, 178, 187, 191-192], and also requeuing specific samples to match lanes [383], and weight or byproducts or labels [484]. Smith also teaches more efficient data processing; [35, 86]).
Although Smith teaches weight as a known characteristic (Smith; [484]), Smith does not specifically teach that the specimens are grouped based on mass, such as applying a mass heuristic/algorithm. However, Dean teaches the analogous art of sequencing, where samples are pooled based on mass concentration (Dean; [110]). It would have been obvious to one of ordinary skill in the art to have arranged the pooled groups in the flow cell lanes of Smith to have been based on a mass concentration as in Dean because Dean teaches that this enables pooling to be achieved without determining the distribution of fragment sizes, which improves efficiency and throughput (Dean; [110]).
Although modified Smith teaches generating available flow cells, generating one or more lane arrangements, and generating a plurality of pools of specimens is based on heuristics/evaluation decisions, modified Smith does not specifically teach the heuristics are associated with a respective processor computational cost with respect to the plurality of specimens, or is adjustable to balance respective processor computational costs with the associated qualitative metrics. However, Hannon teaches the analogous art of sequencing specimens (Hannon; Title) where multiple flow cell groups are determined based on heuristics which include cost of sequencing (Hannon; [214], and Figs. 3A, 4, 18 [49-51, 53, 64, 66, 111, 124, 210, 213, 293], and table 2. Hannon teaches evaluating costs associated with pool analysis [53] which is the computational process, and costs associated with pool preparation, which would be the computational process of creating the pools and not the sequencing itself; [ 64]. Similarly, Hannon teaches balancing various metrics with the cost in time [66], where time cost is interpreted as a computational cost since the less time that computational resources are used means that there are less computational costs). It would have been obvious to one of ordinary skill in the art to have included in the made the generating available flow cells, generating one or more lane arrangements, and generating a plurality of pools of specimens evaluation decision of modified Smith to have included a cost heuristic as in Hannon because Hannon teaches that accounting for cost when pooling specimens helps to decrease cost and time, thereby providing a more efficient method of pooling (Hannon; [53, 64, 66]).
As to claim 3, modified Smith teaches the method of claim 1, wherein the outputting the generated pools comprises: outputting the generated pools to a flow cell allocation system (As best understood, Smith teaches the pools being mapped and allocated in the computer program; Figures 1, 3, 5, 7, 9, 11. Smith also teaches the flow cells used for sequencing; see claim 1 above and [71, 88, 495, 498]).
As to claim 4, modified Smith teaches the method of claim 1, wherein the outputting the generated pools comprises: outputting the generated pools to a display for viewing by a lab technician (As best understood, Smith teaches the pools being mapped and allocated in the computer program; Figures 1, 3, 5, 7, 9, 11, [78, 99]).
As to claim 6, modified Smith teaches the method of claim 1 further comprising: sequencing the at least one specimen in each outputted pool to generate sequencing information (Smith; [71, 88, 239, 495, 498]).
As to claim 7, modified Smith teaches the method of claim 1 (see above).
Modified Smith does not specifically teach wherein when a flow cell is unavailable, the method further comprises: delaying sequencing the unavailable flow cell until the unavailable flow cell becomes available. However, it would have been obvious to one of ordinary skill in the art that the flow cell would be unavailable for sequencing when in use, and that the sequencing would need to wait until the flow cell was available and no longer being sequenced since one of ordinary skill in the art would understand that sequencing would need to be delayed if it could not be performed (where when the flow cell is unavailable then sequencing cannot be performed). Additionally, one of ordinary skill in the art would understand that an unavailable flow cell would not be available for use.
Note: “When” a flow cell is unavailable does not necessarily have to occur since it is a conditional statement, thereby being functional and not further defining the apparatus structure beyond that of a capability (MPEP 2114 and 2111.04). Claim scope is not limited by claim language that suggests or makes optional but does not require steps to be performed, or by claim language that does not limit a claim to a particular structure. Thus, the broadest reasonable interpretation of a method (or process) claim having contingent limitations requires only those steps that must be performed and does not include steps that are not required to be performed because the condition(s) precedent are not met. (See § MPEP 2111.04). The PTAB has determined that analysis of the claimed method as a whole requires giving the claim its broadest reasonable interpretation, where “if the condition for performing a contingent step is not satisfied, the performance recited by the step need not be carried out in order for the claimed method to be performed”. Therefore, evidence of the obviousness of all contingent method steps is not required to be performed under a broadest reasonable interpretation of the claim; however, in the case of system claims, the prior art must teach the structure that performs the function of the contingent step along with the other recited claim limitations to render the claimed system obvious. See Ex parte Schulhauser, PTAB Appeal No. 2013-007847 (April 28, 2016) (precedential) for an analysis of contingent claim limitations in the context of both method claims and system claims.
As to claim 8, modified Smith teaches the method of claim 1, wherein the plurality of specimens comprises blood sample specimens, and the at least one pool of the plurality of pools in a selected lane comprises at least a portion of the blood specimens (Smith; [71]).
As to claim 9, modified Smith teaches the method of claim 1, wherein the plurality of specimens comprises liquid sample specimens, and the at least one pool of the plurality of pools in a selected lane comprises at least a portion of the liquid specimens (Smith; [71], and see claim 1 above).
As to claim 10, modified Smith teaches the method of claim 9, wherein the selected lane including the pool comprising at least a portion of the liquid specimens has a second pool comprising solid samples (Smith teaches multiple pools and lanes; see claim 1 above. Smith teaches solids [444, 466]).
As to claim 11, modified Smith teaches the method of claim 1, wherein the outputting the generated pools comprises: outputting the generated pools to a whole genome processing system (As best understood, Smith teaches the pools being mapped and allocated in the computer program; Figures 1, 3, 5, 7, 9, 11. Smith also teaches the flow cells used for sequencing; see claim 1 above and [71, 88, 495, 498]).
As to claim 14, modified Smith teaches the method of claim 1, wherein the step of selecting one or more of the flow cells includes evaluating a number of specimens included in the plurality of specimens in addition to evaluating the plurality of flow cell characteristics and the first plurality of specimen characteristics, and selecting which specimen to put in each lane of each selected flow cell by: determining a flow cell specimen configuration based on the specimen data and the flow cell data, the flow cell specimen configuration comprising a flow cell group included in the set of flow cell groups and configured to house each specimen included in the plurality of specimens; and determining the flow cell specimen configuration based on the specimen data, the flow cell data, and at least one other constraint, each flow cell specimen configuration included in the flow cell specimen configurations comprising a flow cell specimen configuration included in the flow cell specimen configuration (As best understood, Smith teaches pooling/grouping into groups with various configurations; Figures 1, 3, 5, 7, 9, 11 and see claim 1 above. In Smith, the pooling of 105A-105N means that specimen 105A is pooled, and similarly specimen 105C is pooled. Further, Smith teaches multiple different biosamples/specimens can be used; [48, 60, 66, 75, 119, 232, 382]).
Modified Smith does not specifically teach determining multiple flow cell grouping configurations. However, Hannon teaches the analogous art of sequencing specimens (Hannon; Title) where multiple flow cell groups are determined based on characteristics of the specimens and flow cells (Hannon; Figs. 3A, 4, 18 [49-51, 53, 64, 66, 111, 124, 210, 213, 293]). It would have been obvious to one of ordinary skill in the art to have modified the pooling and grouping of modified Smith to have included multiple groupings as in Hannon because Hannon teaches that the grouping method enables only one flow cell to be used instead of multiple (Hannon; [111]) and that using the multiple groupings enables the capacity of the entire system to be utilized (Hannon; [210]). Additionally, Hannon teaches the advantages of decreasing costs and time, thereby providing a more efficient method of pooling (Hannon; [53, 64, 66]).
As to claim 15, modified Smith teaches the method of claim 14, wherein the plurality of flow cell characteristics comprises a turnaround time, the step of selecting which specimens to put in each lane of each selected one or more of the flow cells comprises: generating, a plurality of hold costs based on the turnaround time associated with each specimen included in the plurality of specimens, each specimen included in the plurality of specimens being associated with a hold cost included in the plurality of hold costs, and the second plurality of flow cell specimen configurations being determined based on the plurality of hold costs; and allocating specimens included in a specific flow cell specimen configuration included in the second plurality of flow cell specimen configurations to the at least one flow cell associated with the specific flow cell specimen configuration (The modification of Smith to determine groupings based on characteristics as in Hannon has already been taught in claim 14 above. Hannon teaches determining groupings to reduce cost; Figs. 3A, 4, 18 [49-51, 53, 64, 66, 111, 124, 210, 213, 293]).
As to claim 16, modified Smith teaches the method of claim 14, wherein the first plurality of specimen characteristics further comprise a unique identifier, a source tissue type, an age, and a turn- around-time (Modified Smith teaches identifiers and tissue types; see claim 1 above. Modified Smith also teaches turn around time; see claim 14 above).
As to claim 17, modified Smith teaches the method of claim 14, wherein the plurality of flow cell characteristics comprises a maximum capacity, a minimum capacity, and a number of lanes, the [[set]] first plurality of specimen characteristics comprises a barcode, and the step of selecting one or more of the flow cells comprises: generating a preliminary set of flow cell groups comprising unique combinations of one or more flow cells included in the plurality of flow cells; determining a secondary set of flow cell groups based on a number of specimens included in the plurality of specimens comprising at least a portion of the preliminary set of flow cell groups by, for each flow cell group included in the secondary set of flow cell groups: determining that the maximum capacity of each flow cell included in the flow cell group is not exceeded by the number of specimens; and determining that the minimum capacity of each flow cell included in the flow cell group is satisfied by the number of specimens; determining a maximum number of repeated barcodes based on the barcode associated with each specimen in the plurality of specimens; and determining a tertiary set of flow cell groups by determining, for each flow cell group included in the secondary set of flow cell groups, that a sum of the number of lanes associated with each flow cell in the flow cell group is at least as great as the maximum number of repeated barcodes, the set of flow cell groups comprising the tertiary set of flow cell groups (Smith teaches plural flow cells; see claim 1 above. Smith teaches a barcode; [61, 75]. The modification of Smith to determine groupings based on characteristics as in Hannon has already been taught in claim 14 above. Hannon teaches groupings can be based on capacities; [210]).
As to claim 18, modified Smith teaches the method of claim 14, wherein the plurality of flow cell characteristics comprises a maximum capacity, a minimum capacity, and a number of lanes, the second plurality of specimen characteristics comprises a barcode, and the determining the first plurality of flow cell specimen configurations comprises: determining, for a specific flow cell specimen configuration included in the first plurality of flow cell specimen configurations, that the maximum capacity and the minimum capacity of each flow cell included in the specific flow cell specimen configuration can be satisfied while keeping specimens associated with equal barcodes in different lanes included in the specific flow cell specimen configuration based on the number of lanes associated with each flow cell in the target flow cell specimen configuration and the barcode associated with each specimen included in the plurality of specimens (Smith teaches a barcode; [61, 75]. The modification of Smith to determine groupings based on characteristics as in Hannon has already been taught in claim 14 above. Hannon teaches groupings can be based on capacities; [210]).
As to claim 19, modified Smith teaches the method of claim 14, wherein the second plurality of specimen characteristics comprises the specimen type, wherein the specimen type is selected from a tumor, a normal match, and a control, and the determining the first plurality of flow cell specimen configurations comprises: determining, for each flow cell specimen configuration included in the first plurality of flow cell specimen configurations, a processing cost based on the specimen type associated with the flow cell specimen configuration and the flow cell data; and ranking each flow cell specimen configuration included in the first plurality of flow cell specimen configurations based on the processing cost associated with the flow cell specimen configuration (Smith teaches specimen types; [71]. The modification of Smith to determine groupings based on characteristics as in Hannon has already been taught in claim 14 above. Hannon teaches determining groupings to reduce cost; Figs. 3A, 4, 18 [49-51, 53, 64, 66, 111, 124, 210, 213, 293]).
As to claim 20, modified Smith teaches the method of claim 14, wherein the plurality of flow cell characteristics comprises a turnaround time and the determining the second plurality of flow cell specimen configurations comprises: generating, from the second plurality of flow cell specimens, unique pairs of specimens; generating a plurality of compatibility scores based on the specimen data, each unique pair of specimens being associated with a compatibility score included in the plurality of compatibility scores; generating a plurality of hold costs based on the turnaround time associated with each specimen included in the plurality of specimens, each hold cost included in the plurality of hold costs being associated with a specimen included in the plurality of specimens; and wherein the step of generating at least one pool of specimens comprises generating a plurality of pools based on the plurality of compatibility scores and the plurality of hold costs, each pool included in the plurality of pools comprising at least one specimen (The modification of Smith to determine groupings based on characteristics as in Hannon has already been taught in claim 14 above. Hannon teaches determining groupings to reduce cost; Figs. 3A, 4, 18 [49-51, 53, 64, 66, 111, 124, 210, 213, 293]).
As to claim 21, modified Smith teaches the method of claim 20, wherein the step of selecting one or more of the flow cells further comprises: generating a plurality of preliminary flow cell specimen configurations based on at least a portion of the plurality of pools and the at least one constraint, the second plurality of flow cell specimen configurations comprising at least a portion of the plurality of preliminary flow cell specimen configurations (Smith teaches the generation of multiple sets of pools; Figures 1, 3, 5, 7, 9, 11. Additionally, the modification of Smith to determine groupings based on characteristics as in Hannon has already been taught in claim 14 above. Hannon teaches multiple pools; Figs. 3A, 4, 18).
As to claim 22, modified Smith teaches the method of claim 14, wherein the step of generating at least one pool of specimens comprises: generating a first set of pools based on the second plurality of specimen characteristics, the at least one lane characteristic, and a first constraint included in the at least one other constraint, each pool included in the first set of pools comprising at least one specimen included in the plurality of specimens; and generating a second set of pools comprising a subset of the first set of pools based on the second plurality of specimen characteristics, the at least one lane characteristic, and a second constraint included in the at least one other constraint (Smith teaches the generation of multiple sets of pools; Figures 1, 3, 5, 7, 9, 11. Additionally, the modification of Smith to determine groupings based on characteristics as in Hannon has already been taught in claim 14 above. Hannon teaches multiple pools; Figs. 3A, 4, 18).
As to claim 23, modified Smith teaches the method of claim 22, wherein the step of generating at least one pool of specimens further comprises: determining a group of one or more pools included in the second set of pools that satisfies the second constraint, and further comprising the allocating the at least a portion of the specimens included in the plurality of specimens to one or more flow cells included in the plurality of flow cells comprises; and placing each pool included in the group of one or more pools into one or more lanes included in the one or more flow cells (Smith teaches the generation of multiple sets of pools; Figures 1, 3, 5, 7, 9, 11. Additionally, the modification of Smith to determine groupings based on characteristics as in Hannon has already been taught in claim 14 above. Hannon teaches multiple pools; Figs. 3A, 4, 18).
As to claim 24, modified Smith teaches the method of claim 14, wherein the at least one other constraint comprises at least one of a maximum pool mass, a maximum flow cell mass, a minimum pool mass, a minimum flow cell mass, a mass balancing threshold, a turnaround time constraint, a prioritization level, or a flow cell cost (The modification of the pooling of Smith to include mass as in Dean has already been discussed in claim 1 above. Additionally, the modification of Smith to determine groupings based on characteristics as in Hannon has already been taught in claim 14 above. Hannon teaches determining groupings to reduce cost; Figs. 3A, 4, 18 [49-51, 53, 64, 66, 111, 124, 210, 213, 293]).
As to claim 25, modified Smith teaches the method of claim 14, wherein the at least one other constraint comprises a hard constraint (The modification of Smith to determine groupings based on characteristics as in Hannon has already been taught in claim 14 above. Hannon teaches capacity limits as hard constraints; [210]. Hannon also teaches controlling the lane number groupings as a hard constraint which cannot be violated).
As to claim 26, modified Smith teaches the method of claim 14, wherein the at least one other constraint comprises a soft constraint (The modification of Smith to determine groupings based on characteristics as in Hannon has already been taught in claim 14 above. Hannon teaches that weightings can be applied as constraints to each grouping where the weightings can vary, and that some constraints can be violated; [99, 193, 229-230]).
As to claim 28, modified Smith teaches the system of claim 27, wherein the step of selecting one or more of the flow cells includes evaluating a number of specimens included in the plurality of specimens in addition to evaluating the plurality of flow cell characteristics and the first plurality of specimen characteristics, and selecting which specimen to put in each lane of each selected flow cell by: determining a flow cell specimen configuration based on the specimen data and the flow cell data, the flow cell specimen configuration comprising a flow cell group included in the set of flow cell groups and configured to house each specimen included in the plurality of specimens; and determining the flow cell specimen configuration based on the specimen data, the flow cell data, and at least one constraint, each flow cell specimen configuration included in the flow cell specimen configurations comprising a flow cell specimen configuration included in the flow cell specimen configuration (As best understood, Smith teaches pooling/grouping into groups with various configurations; Figures 1, 3, 5, 7, 9, 11 and see claim 1 above. In Smith, the pooling of 105A-105N means that specimen 105A is pooled, and similarly specimen 105C is pooled. Further, Smith teaches multiple different biosamples/specimens can be used; [48, 60, 66, 75, 119, 232, 382]).
Modified Smith does not specifically teach determining multiple flow cell grouping configurations. However, Hannon teaches the analogous art of sequencing specimens (Hannon; Title) where multiple flow cell groups are determined based on characteristics of the specimens and flow cells (Hannon; Figs. 3A, 4, 18 [49-51, 53, 64, 66, 111, 124, 210, 213, 293]). It would have been obvious to one of ordinary skill in the art to have modified the pooling and grouping of modified Smith to have included multiple groupings as in Hannon because Hannon teaches that the grouping method enables only one flow cell to be used instead of multiple (Hannon; [111]) and that using the multiple groupings enables the capacity of the entire system to be utilized (Hannon; [210]). Additionally, Hannon teaches the advantages of decreasing costs and time, thereby providing a more efficient method of pooling (Hannon; [53, 64, 66]).
As to claim 29, modified Smith teaches the system of claim 27, wherein the memory further comprises instructions to: output the at least one pool to a flow cell allocation system (As best understood, Smith teaches the pools being mapped and allocated in the computer program; Figures 1, 3, 5, 7, 9, 11. Smith also teaches the flow cells used for sequencing; see claim 1 above and [71, 88, 495, 498]).
As to claim 31, modified Smith teaches the method of claim 3, further comprising: arranging, by the flow cell allocation system the plurality of specimens in associated pools (As best understood, Smith teaches the pools being mapped and allocated in the computer program, which would be part of the flow cell allocation system; Figures 1, 3, 5, 7, 9, 11. Smith also teaches the flow cells used for sequencing; see claim 1 above and [71, 88, 239, 495, 498]).
As to claim 32, modified Smith teaches the method of claim 4, further comprising: arranging, by the lab technician, the plurality of specimens in associated pools (Smith teaches the pools being mapped and allocated in the computer program which is interacted with and controlled by a user/technician; Figures 1, 3, 5, 7, 9, 11, [78, 99, 142]. Smith also teaches the flow cells used for sequencing, where the flow cells would have the samples placed into the system, and would be turned on/off and controlled by a user; see claim 1 above and [71, 88, 239, 495, 498]).
Response to Arguments
Applicant's arguments, filed 12/8/25, towards the claim amendments have been fully considered. The arguments that are not considered persuasive are addressed below.
Applicants on pages 12-15 of their remarks that the claims were amended to overcome the 101 rejections.
On pages 15-17 of their remarks, applicants argue that the claims do not recite a mental process. Specifically, applicants argue that a human cannot reasonably “evaluate” 65,536 combinations in their head. Applicants also state that the claims do not recite an algorithm or math. The examiner respectfully disagrees that the claims do not recite an abstract idea. With regard to Step 2A, Prong One, under the broadest reasonable interpretation (BRI), the instant claims recite claim steps directed to the judicial exception that is an abstract idea of the type that is in the grouping of “mental process” and/or “mathematical concept” (See MPEP 2106.04(a)(2) subsections (I) and (III)) because said operations could be performed in the mind or are done via mathematical relationships, but for the recitation of a plurality of flow cells each having a lane and computers having processors to perform the method. Mental operations in the instant claims are recited as: identifying flow cell characteristics; generating a group of flow cells based on flow cell characteristics and first specimen characteristics; generating eligible an eligible lane arrangement of each flow cell by applying a mass or priority algorithm to the second plurality of specimen characteristics and at least one lane characteristic, or placing specimens sharing barcodes in different lanes before evaluating others of the second plurality of specimen characteristics and the at least one lane characteristic; and generating for each lane a plurality of pools based on evaluating a total cost of sequencing the specimens and a likelihood of obtaining valid results; and outputting the generated pools, where the generating steps are associated with, and adjustable to balance computational costs and qualitative metrics. In summary, the claim(s) recite(s) a method for determining the organization or grouping of samples in flow cells (and their corresponding lane). Identifying and generating groupings are processes that can be performed as mental steps and/or math. The use of an algorithm to generate lane arrangements is explicitly math, and evaluating cost may also be math as described in [75] of the instant specification. Further, [102] discusses using “heuristics’ to generate eligible flow cells, [104-105] discusses using “heuristics” to generate eligible lanes, and [111] discusses using “heuristics” to generate pools, where [112-118] also describe the pool generation as a search tree, which is an algorithm. Thus, the generating lane arrangements and generating pools of the claims requires the use of heuristics/search tree/algorithm, which is math. Further, balancing costs and metrics during the generating steps is either just a mental process or a mathematical concept. Therefore, each of the identified abstract ideas may also be considered an algorithm and/or mathematical process because a user could perform the recited steps as mental steps, or with the assistance of pencil and paper or a computer. The claims recite the judicial exceptions all being performed by a computer(s) having a processor(s), which is just a generic and general-purpose computer. A claim, under its BRI, which covers performance of the limitation in the mind as a mental process and/or math, but for the recitation of generic computer elements, falls within the “mental processes” grouping of abstract ideas (see MPEP 2106.04(a)(2)(III)(C)). MPEP 2106.04(a)(2)III is clear that using a computer/controller, or pencil and paper, to perform the abstract idea does not preclude the steps from being considered an abstract idea.
On pages 17-19 of their remarks, applicants argue that the claims do integrate the exception into a particular practical application because the claims improve the functioning of a computer and also the technical field of genetic sequencing. As to applicants arguments that a computer is improved, these arguments are directed towards the fact that a computer performs more mathematical processing and/or determination steps in a complex manner, which isn’t improving a computer itself but is rather just using the computer as a tool to perform the method. Further, the specification at [133] states that as throughout is increased that the processing and optimization logic becomes more complex, thereby requiring computing systems. This statement further affirms that the “logic” as abstract ideas are what are attempting to be improved. This argument is not persuasive because in order to overcome the 101 rejection, the improvement cannot be the abstract idea but must be in a particular technology (See p