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 .
Information Disclosure Statement
The information disclosure statements (IDSs) submitted on 05/31/2023, 06/19/2023, 04/03/2025 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Status of Claims
This office action is in response to Applicant's Response to Election / Restriction filed on July 14, 2025.
Claims 2-4, 6, 8, 10-13, 18-20 and 23-40 were previously pending. Applicant amended claims 3, 23, 26, 28, 30 and 32, in an amendment filed on July 14, 2025, responding to a requirement for restriction/election.
Claims 2-4, 6, 8, 10-13, 18-20 and 23-40 are currently pending, with claims 2-4, 6, 8, 10-13, 18-20, 23-28, 34 and 38 withdrawn.
Claims 29-33, 35-37 and 39-40 are under consideration. This is the first action on the merits.
Election/Restrictions
Applicant’s election with traverse of Group II (Claims 29-40) in the reply filed on July 14, 2025 is acknowledged.
Applicant's traversal presents the following arguments:
"Applicant respectfully disagrees that the claims of asserted Groups I and II are "unrelated". Claims 2, 27, and 29 can all be used together and have similar designs and modes of operation. Claim 29 provides a sequencing platform configured to implement a method similar to the methods of claims 2 and 27. Respectfully, the inclusion of "generate a plurality of sequencing reads" or "forward a plurality of data" as in claim 29 is not at all a significant departure from the requirements of claim 2. Nor are such elements excluded from claim 2 despite not being required. Indeed, the Office has not indicated why, specifically, the elements of claim 29 not required by claim 2 would mean that the subject matter of the two claims could not be used together.
Additionally, the Office has not provided any rationale as to why claims 27 and 29 should be restricted from one another. The system of claim 29 is configured to implement a method very similar to that of claim 27, with very little difference between the recited claim elements. These can clearly be used together and are not at all "unrelated".
As such, Applicant respectfully disagrees with the Office's conclusions that the claims of the two groups are "unrelated" and respectfully submits that there would be no serious search and/or examination burden were restriction not required. Withdrawal of the Election of Invention requirement is respectfully requested. Should the Office not grant withdrawal of the Election of Invention requirement as a whole, Applicant respectfully requests rejoinder of claims 27 and 29 into one group, given that these claims are very much related and their search and examination not requiring a serious burden on the Office. " (Remarks, page 8-9)
Therefore, applicant argues the invention groups I and II are related inventions, specifically, Applicant asserts that "claims 2, 27, and 29 can all be used together and have similar designs and modes of operation."
Applicant's arguments have been fully considered but are not found persuasive.
MPEP §818.01 states a traverse must include a written statement of the reasons for traverse, distinctly and specifically pointing out the supposed errors upon which the applicant relies for concluding that the requirement is in error.
MPEP§ 803 sets forth two criteria for a proper requirement for restriction between patentably distinct inventions:
• (A) The inventions must be independent (see MPEP § 802.01, § 806.06, § 808.01) or distinct as claimed (see MPEP § 806.05 - § 806.05(j)); and
• (B) There would be a serious search and/or examination burden on the examiner if restriction is not required (see MPEP § 803.02, § 808, and § 808.02).
Thus, Applicant's traversal must distinctly and specifically point out (A) basis supporting why the inventions as claimed are NOT patentably independent or distinct 1; and (B) basis supporting why there would Not be a serious search and/or examination burden on the examiner if restriction is not required.
Applicant's argument is unpersuasive for the following reasons:
First, the argument fails to specifically identify or point to any disclosed relationships in the claims between the inventions. While the Applicant appears to argue that the claims share some similar elements, this alone is insufficient to demonstrate a disclosed relationship or to show that the inventions are not independent, as required by the MPEP (see MPEP§ 806.06)
Second, Applicant asserts that "there would be no serious search and/or examination burden were restriction not required," but this is merely a conclusory statement without any supporting evidence or rationale to substantiate the assertion. As such, this argument is not found persuasive.
MPEP§ 806.06 provides guidance regarding independent (i.e., unrelated) inventions:
Inventions as claimed are independent if there is no disclosed relationship between the inventions, that is, they are unconnected in design, operation, and effect. If it can be shown that two or more inventions are independent, and if there would be a serious search and/or examination burden on the examiner if restriction is not required, applicant should be required to restrict the claims presented to one of such independent inventions.
In this instance case, Invention Group I (claims 2-4, 6, 8, 10-13, 18-20 and 23-28) is drawn to a bioinformatics data analysis method, classified in G16B30/00; whereas Invention Group II (29-40) drawn to a sequencing platform, classified in B01L2300/023. Therefore, the claim sets are directed to two different statutory categories (Process vs. Machine) with different modes of operation, different functions and different effects. These inventions are not disclosed as capable of use together, specifically the method claims in Group I do not require using the sequencing platform in Group II. While claim 27 recites a step of "generating, at a first location, a plurality of sequence reads from a plurality of tagmented nucleic acid fragments," it does not require using any specific systems or platforms to carry out this step.
Methods for generating sequencing reads were well-known in the art such as Roche/454 FLX Pyrosequencing, or Applied Biosystems SOLiD sequencing (See Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet. 2008;9:387-402. doi: 10.1146/annurev.genom.9.081307.164359. PMID: 18576944.)
Therefore, a person skilled in the art, while reading method claim 27, would understand that the step of generating sequencing reads could be achieved using sequencing technologies that were well-established and commercially available as of 2013.
As such, there is no objective evidence in the claims to support that the method of claim 27 and the sequencing platform of claim 29 are related.
This restriction is proper because these inventions are independent or distinct for the reasons given above and there would be a serious search and/or examination burden because Group I would require a search in at least G16B30/00 along with a unique text search. Group II would not be searched as above. Group II would require its own search in at least B01L2300/023 along with a unique text search. The claims in Group I necessitate a search focused on method steps, while the claims in Group II demands a search centered on system aspects.
Therefore, the restriction requirement between Group I and Group II as initially imposed is properly maintained. The requirement is still deemed proper and is therefore made FINAL 2.
Applicant's election with traverse of the following species in the reply filed July 14, 2025 is acknowledged:
Species of numerical outputs: I) numerical outputs comprises at least one of: cleavage sites associated with the insertional enzyme; sizes of the plurality of tagmented nucleic acid fragments; lengths of the plurality of tagmented nucleic acid fragments; positions of the plurality of sequence reads; or a sequence read abundance (claim 32) 3;
Species of molecular tag: L) molecular tag comprises at least one of a sequencing adaptor (claim 39, 40) 4.
Applicant's traversal is on the ground that the species identified by the Office are not mutually exclusive (Remarks, page 10). This is not found persuasive because MPEP §818.01 states a traverse must include a written statement of the reasons for traverse, distinctly and specifically pointing out the supposed errors upon which the applicant relies for concluding that the requirement is in error.
MPEP§ 803 sets forth two criteria for a proper requirement for restriction between patentably distinct inventions:
• (A) The inventions must be independent (see MPEP § 802.01, § 806.06, § 808.01) or distinct as claimed (see MPEP § 806.05 - § 806.05(j)); and
• (B) There would be a serious search and/or examination burden on the examiner if restriction is not required (see MPEP § 803.02, § 808, and § 808.02).
MPEP§ 803 further states: "An election of species requirement is a type of restriction requirement."
Applicant argues that the species are not mutually exclusive; however, this argument is unpersuasive. As noted in the above cited MPEP guidance, mutually exclusivity is not one of the two criteria for a proper restriction. Thus, the traversal by the applicant lacks argument that distinctly and specifically point out the reasons why this requirement for species election is improper. Therefore, the species election requirement for the species of method as initially imposed is properly maintained.
In this instant case, the requirement for species election is properly made. As stated in the restriction requirement (mail date 05/14/2025), and reiterated here:
The species are independent or distinct because the different species recite separate characteristics of such species, and there is no disclosure of relationship between species (see MPEP § 806.04(b)). In addition, these species are not obvious variants of each other based on the current record. The species necessitate separate searches, leading to serious search and/or examination burden (see MPEP § 808.01(a)) because the species of information about the plurality of tagmented nucleic acid fragments reflect different composition of required information, requiring separate searches; the species of molecular tag reflect different structures of the molecular tag, requiring separate searches; the species of method result in search requirements for different method steps with different mechanisms and materials; the species of numerical outputs reflect different composition of required output information, requiring separate searches.
There is a serious search and/or examination burden for the patentably distinct species as set forth above because at least the following reason(s) apply: The species require a different field of search (e.g., searching different classes/subclasses or electronic resources, or employing different search queries); and/or the prior art applicable to one species would not likely be applicable to another species; and/or the species are likely to raise different non-prior art issues under 35 U.S.C. 101 and/or 35 U.S.C. 112, first paragraph.
To further clarify, the species listed are presented as alternatives that do not depend from each other. According to the claims, each species is intended to be included independently rather than together. Each species requires a separate search. For example, a search for the molecular tag comprising fluorescent tag of claim 39 (species M) would not adequately cover the molecular tag of claim 40 (species L, further modifies sequencing adaptor as comprising a barcode label).
Therefore, these species in the species of method are directed to independent and patentably distinct inventions, and there would be a serious search and/or examination burden if species election is not required. The requirement is still deemed proper and is therefore made FINAL.
Claims 2-4, 6, 8, 10-13, 18-20, 23-28, 34 and 38 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention.
Claims 29-33, 35-37 and 39-40 are under consideration.
Priority
The priority date of the instant claims 29-33, 35-37 and 39-40 is March 07, 2025, the date on which the claims were first amended to include additional limitations reciting a sequencing platform configured to "generate a plurality of sequence reads from a plurality of tagmented nucleic acid fragment" and "forward a plurality of data from the plurality of sequence reads to a computer at a remote location relative to the sequencing platform for analysis", not disclosed by prior-filed applications and the specifications of the instant application.
If the applicant disagrees with the examiner's determination of the priority date, the burden shifts to the applicant to provide evidence demonstrating that the claims are supported by the disclosure in the earlier application. Such as providing specific references (e.g. paragraphs, figures, examples, etc.) in the prior application that correspond to the elements of each disputed claim. Additionally, the applicant should explain how these references are sufficient in complying with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112.
Claim Interpretation
In evaluating the patentability of the claims presented in this application, claim terms have been given their broadest reasonable interpretation (BRI) consistent with the specification, as understood by one of ordinary skill in the art, as outlined in MPEP§ 2111.
For the purpose of applying prior art, claim 29 recites:
A system comprising:
a sequencing platform configured to:
generate a plurality of sequence reads from a plurality of tagmented nucleic acid fragments,
wherein each tagmented nucleic acid fragment of the plurality of tagmented nucleic acid fragments comprises
(i) a nucleic acid fragment derived from a permeabilized nucleus of a cell and
(ii) at least one molecular tag generated by an insertional enzyme; and
forward a plurality of data from the plurality of sequence reads to a computer at a remote location relative to the sequencing platform for analysis,
wherein the computer at the remote location is configured to:
generate a plurality of numerical outputs based on the plurality of data; and
map the plurality of numerical outputs to a graphical representation of a region of a genome to generate an epigenetic map of the region.
Thus, claim 29 recites a sequencing platform using functional language only, thus it encompasses any sequencing platform capable of performing the steps of generate a plurality of sequence reads from tagmented nucleic acid fragments, and forward data to a computer at a remote location for analysis 5.
For the purpose of applying prior art, claim 29 includes a wherein clause reciting:
"wherein each tagmented nucleic acid fragment of the plurality of tagmented nucleic acid fragments comprises
(i) a nucleic acid fragment derived from a permeabilized nucleus of a cell and
(ii) at least one molecular tag generated by an insertional enzyme."
MPEP§ 2111.04 states:
"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."
Here, the claim recites a sequencing platform capable of generate a plurality of sequence reads from tagmented nucleic acid fragments. This wherein clause merely describes the tagmented nucleic acid fragments, which are intended input material for the sequencing platform.
There is no indication in the claim language or in the specification that the composition or sequence of the input nucleic acids imparts any structural features to the platform itself. Specifically, this wherein clause does not indicate any specific structural features of the claimed sequencing platform that can further distinguish it from any sequencing platform known in the art that is capable of generating sequence reads from tagmented nucleic acids (e.g., sequencers by Illumina). Additionally, a skilled artisan in the art would understand that the structure of a sequencing platform is not changed by the characteristics of its nucleic acids input, analogous to how the shape of ice does not modify the structure of a shaved ice machine.
As such, this wherein clause does not provide any structural limitation to the sequencing platform and is interpreted as descriptive language that does not further limit the claimed system.
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. In this instant case, claim 29 recites:
"wherein the computer at the remote location is configured to:
generate a plurality of numerical outputs based on the plurality of data; and
map the plurality of numerical outputs to a graphical representation of a region of a genome to generate an epigenetic map of the region."
The generic placeholder term "computer" is modified by computer-implemented functions only, and not modified by sufficient structure or algorithm to perform such functions.
MPEP §2181 provides guidance regarding Computer-Implemented Means-Plus-Function Limitations:
"To claim a means for performing a specific computer-implemented function and then to disclose only a general purpose computer as the structure designed to perform that function amounts to pure functional claiming. Aristocrat, 521 F.3d 1328 at 1333, 86 USPQ2d at 1239. … The corresponding structure is not simply a general purpose computer by itself but the special purpose computer as programmed to perform the disclosed algorithm. Aristocrat, 521 F.3d at 1333, 86 USPQ2d at 1239. Thus, the specification must sufficiently disclose an algorithm to transform a general purpose microprocessor to the special purpose computer. See Aristocrat, 521 F.3d at 1338, 86 USPQ2d at 1241."
"[a] microprocessor or general purpose computer lends sufficient structure only to basic functions of a microprocessor. All other computer-implemented functions require disclosure of an algorithm." Id., 114 USPQ2d at 1714"
Accordingly, in claim 29, the limitation that recite a computer "configured to generate a plurality of numerical outputs based on the plurality of data; and map the plurality of numerical outputs to a graphical representation of a region of a genome to generate an epigenetic map of the region" has been interpreted under 112(f) as a means plus function limitation because of the combination of generic placeholder "computer" and computer-implemented functional languages, without reciting sufficient structure or algorithm to achieve the functions (see pages 35-37 in section "Data Analysis" for disclosure of specific computer algorithms including BOWTIE, Picard, ZINBA, Danpos, Dantools, GEM, and CENTIPEDE ).
Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
Claim Rejections - 35 USC § 112(b)
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.
Claims 29-33, 35-37 and 39-40 are rejected under 35 U.S.C. 112(b), as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 29 recites:
A system comprising:
a sequencing platform configured to:
generate a plurality of sequence reads from a plurality of tagmented nucleic acid fragments,
wherein each tagmented nucleic acid fragment of the plurality of tagmented nucleic acid fragments comprises
(i) a nucleic acid fragment derived from a permeabilized nucleus of a cell and
(ii) at least one molecular tag generated by an insertional enzyme; and
forward a plurality of data from the plurality of sequence reads to a computer at a remote location relative to the sequencing platform for analysis,
wherein the computer at the remote location is configured to:
generate a plurality of numerical outputs based on the plurality of data; and
map the plurality of numerical outputs to a graphical representation of a region of a genome to generate an epigenetic map of the region.
Therefore, claim 29 recites a system comprising a sequencing platform configured to: (1) generate sequence reads; and (2) forward data to a computer at a remote location.
The claim then further describes the computer at the remote location using additional computer-implemented functional language.
However, the claim is indefinite because it is unclear whether the claimed system requires both the sequencing platform and the remote computer, or only the sequencing platform. While the remote computer is described, it is not clearly recited as part of the claimed system. As such, the metes and bounds of the claimed system are unclear.
For the purpose of compact prosecution and applying prior art under 35 USC§ 102 and 103, the claimed system is interpreted to comprise only the sequencing platform.
Claim 29 recites:
"a computer at a remote location relative to the sequencing platform for analysis" and
"wherein the computer at the remote location is configured to: generate a plurality of numerical outputs based on the plurality of data; and
map the plurality of numerical outputs to a graphical representation of a region of a genome to generate an epigenetic map of the region."
These claim languages are indefinite for the following reasons:
First, the term "remote location" is indefinite because it is unclear what qualifies as a remote location or how remoteness is determined. The claim and specification do not
define this term with any specific criteria or boundaries ꟷ such as spatial separation, distance, or network configuration (i.e., wired connection vs. wireless), that clarify whether a location within the same room, building, or wired network on campus would qualify as "remote."
Furthermore, it is unclear how far the location must be to qualify as "remote." For instance, it is unclear whether a distance at arm's length, 100 meters, or greater would qualify as a remote, leaving the claim scope uncertain.
For the purpose of compact prosecution and applying prior art under 35 USC§ 102 and 103, "remote location" is interpret to encompass any location that is not the location of the sequencing platform.
Second, as discussed in the claim interpretation section above, the recited computer and computer-implemented functions are interpreted under 112(f) as a means plus function limitations.
MPEP§ 2181 states:
"For a computer-implemented 35 U.S.C. 112(f) claim limitation, the specification must disclose an algorithm for performing the claimed specific computer function, or else the claim is indefinite under 35 U.S.C. 112(b). See Net MoneyIN, Inc. v. Verisign. Inc., 545 F.3d 1359, 1367, 88 USPQ2d 1751, 1757 (Fed. Cir. 2008). See also In re Aoyama, 656 F.3d 1293, 1297, 99 USPQ2d 1936, 1939 (Fed. Cir. 2011) ("[W]hen the disclosed structure is a computer programmed to carry out an algorithm, ‘the disclosed structure is not the general purpose computer, but rather that special purpose computer programmed to perform the disclosed algorithm.’") (quoting WMS Gaming, Inc. v. Int’l Game Tech., 184 F.3d 1339, 1349, 51 USPQ2d 1385, 1391 (Fed. Cir. 1999))."
In this instant case, although the specification lists various types of algorithms (e.g., see pages 35-37 in section "Data Analysis" for disclosure of specific computer algorithms including BOWTIE, Picard, ZINBA, Danpos, Dantools, GEM, and CENTIPEDE), it does not identify any specific algorithm for performing the recited, specific function.
Therefore, it is unclear which algorithms are required to perform the claimed specific computer functions; whether a subset of the disclosed algorithms is required; or if all of the disclosed algorithms are required. Therefore, it is unclear what structure is required for performing the claimed functions, rendering the limitation indefinite.
Claims 30-33, 35-37 and 39-40 are rejected for depending from claim 29 and not remedying the indefiniteness.
Claim Rejections - 35 USC § 112(a)
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.
Claims 29-33, 35-37 and 39-40 are rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement. The claims 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.
A) Claim 29 recites a sequencing platform configured to: (1) generate sequence reads; and (2) forward data to a computer at a remote location, but the applicant's disclosure lacks sufficient detail to demonstrate possession of the invention, as required under 35 U.S.C. 112(a).
Accordingly to MPEP 2163 (written description requirement), the specification must clearly demonstrate that the inventor was in possession of the claimed invention at the time of filling.
While the specification discloses generating sequence reads using conventional sequencing methods and platforms 6, it does not describe any sequencing platform as being capable of forwarding data to a remote computer. The specification also lacks any description of any process in which both functions ꟷ generating sequence reads and forwarding data to a computer at a remote location ꟷ are performed by a single sequencing platform.
Accordingly, the applicant's disclosure does not convey to those skilled in the art that the inventor had possession of the claimed "sequencing platform," capable of performing the recited functions at the time of filling, failing to meet the written description requirement of 35 U.S.C. 112(a).
B) Claim 29 recites "a computer at a remote location relative to the sequencing platform," but the applicant's disclosure lacks sufficient detail to demonstrate possession of the claimed subject matter, as required under 35 U.S.C. 112(a).
The closest relevant disclosure in the specification states that a lab may receive a blood sample from a remote location (e.g., a physician's office or hospital), and the lab may generate data and forward it to the remote location for analysis (page 29). However, this description makes no mention of a sequencing platform. The specification does not describe any computer located at a remote location relative to a sequencing platform, nor does it disclose any configuration involving a remote computer operating in accordance with the sequencing platform as claimed.
Accordingly, the claimed computer at a remote location relative to the sequencing platform lacks written description support.
Claims 30-33, 35-37 and 39-40 are rejected because they depend from claim 29 and inherit the deficiencies of the base claim.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 29-33, 35-37 and 39-40 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by SHENDURE (WO2012106546A2 - Massively parallel continguity mapping; Published on 2012-08-09; cited as Foreign Patent Document #11 in 9-page IDS filed 05/31/2023), as evidenced by
HiSeq 2000 (HiSeq 2000 System User Guide; Illumina; Initial Release Feb 2010; sections cited are not changed since initial release, see revision history);
Szopa-Comley ( Andrew Szopa-Comley; DNA Sequencing: Latest Developments In Next-Generation Sequencing; ddw-online.com; 4 April 2013), and
Cloud Computing (“Cloud Computing”; www.greenit-monaco.com; Archived on April 8 2013 on WaybackMachine).
SHENDURE teaches methods and compositions for applying transposase-based library construction for high-throughput whole-genome sequencing, useful for applications such as genome-wide chromatin interaction mapping (entire document; Figure 1, [0078] for example).
Regarding claim 29, SHENDURE teaches a system comprising a sequencing platform capable of:
generate a plurality of sequence reads from a plurality of tagmented nucleic acid fragments ([00210] Hiseq 2000 used to generate sequence reads from tagmented nucleic acid fragments; see also [0048] for Tagmentation-based DNA-seq library construction), and forward a plurality of data from the plurality of sequence reads to a computer at a remote location relative to the sequencing platform for analysis ([00210] HiSeq 2000, as evidenced by HiSeq 2000).
SHENDURE teaches a sequencing platform capable of forward data to a remote computer by teaching Illumina's HiSeq 2000 sequencing platform, which has cloud computing features, as evidenced by HiSeq 2000, Szopa-Comley, and Cloud Computing.
HiSeq 2000 teaches the HiSeq 2000 sequencer by Illumina is capable of forwarding sequencing reads data to BaseSpace genomics cloud solution (page 2, page 21, lines 17-18) for remote monitoring and data analysis. BaseSpace is Illumina’s cloud-based data analysis, storage and sharing platform (evidenced by Szopa-Comley, page 13, para 2), which qualifies as a “computer at a remote location” because cloud computing relies on remote servers for data processing (as evidenced by Cloud Computing, entire document, para 1-2 for definition). These servers are computers, aligning with the concept of “cloud computing.”
Regarding claims 30-31, they are anticipated by SHENDURE because they do not recite any structural features applicable to the claimed system.
The claims recite:
30. The system of claim 29, wherein the computer at the remote location is further configured to: generate the graphical representation of the region of the genome in the cell.
31. The system of claim 30, wherein the graphical representation comprises one or more regions of open chromatin, and wherein the epigenetic map graphically shows a profile of chromatin accessibility along the one or more regions of the open chromatin.
MPEP§ 2111.04 states: "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."
Claims 30-31 only use descriptive language to further describe the computer at the remote location. According to the claim interpretation applied in this Office Action (see section 35 USC § 112(b) for details ), the computer at the remote location is not a part of the claimed system.
Therefore, these claim languages are interpreted as descriptive statement without any associated structural relationship within the system and do not distinguish the claims from the prior art.
Regarding claims 32-33, they recite:
32. The system of claim 29, wherein the plurality of numerical outputs comprises at least one of: cleavage sites associated with the insertional enzyme; sizes of the plurality of tagmented nucleic acid fragments; positions of the plurality of sequence reads; or a sequence read abundance.
33. The system of claim 29, wherein generating the plurality of numerical outputs comprises identifying one or more ends of one or more tagmented nucleic acid fragments of the plurality of tagmented nucleic acid fragments.
Claims 32-33 are anticipated by SHENDURE because they do not recite any structural features applicable to the claimed system.
MPEP§ 2111.04 states: "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."
Claims 32-33 only use descriptive language to further describe the "generating a plurality of numerical outputs" function of the computer at the remote location, and the intended output of such function. According to the claim interpretation applied in this Office Action (see section 35 USC § 112(b) for details ), the computer at the remote location is not a part of the claimed system.
Therefore, these claim languages are interpreted as descriptive statement without any associated structural relationship within the system and do not distinguish the claims from the prior art.
Claim 35 is anticipated by SHENDURE because it does not recite any structural features applicable to the claimed system.
Claim 35 recites:
35. The system of claim 29, wherein the plurality of tagmented nucleic acid fragments are created from one or more regions of open chromatin such that the plurality of sequence reads correspond to the one or more regions of open chromatin.
Claim 35 recites a wherein clause that describes the process of making the plurality of tagmented nucleic acid fragments, but the claimed system is not required to comprise any tagmented nucleic acid fragments. Therefore, these claim languages do not distinguish the claimed system from the prior art.
Claim 36 is anticipated by SHENDURE because it does not recite any structural features applicable to the claimed system.
Claim 36 recites:
36. The system of claim 29, wherein the permeabilized nucleus is generated by permeabilizing the nucleus to allow access for the insertional enzyme such that the nucleus is minimally perturbed.
Claim 36 recites a wherein clause that describes a process of generating permeabilized nucleus, but the claimed system is not required to comprise any permeabilized nucleus.
Therefore, these claim languages do not distinguish the claimed system from the prior art.
Claim 37 is anticipated by SHENDURE because it does not recite any structural features applicable to the claimed system.
Regarding claim 37, it recites:
37. The system of claim 29, wherein the insertional enzyme is a transposase comprising a Tn5 transposase or an MuA transposase.
Claim 37 recites a wherein clause that describes insertional enzyme, but the claimed system is not required to comprise any insertional enzyme. Therefore, these claim languages do not distinguish the claimed system from the prior art.
Claims 39-40 are anticipated by SHENDURE because they do not recite any structural features applicable to the claimed system.
Regarding claims 39-40, they recite:
39. The system of claim 29, wherein the at least one molecular tag comprises at least one of a sequencing adaptor or a fluorescent tag.
40. The system of claim 39, wherein the sequencing adaptor comprises a barcode label.
MPEP§ 2111.04 states: "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."
Here, claims 39 and 40 do not further limit the claimed system, as they recite wherein clauses describing molecular tags in tagmented nucleic acid fragments, which the system is not required to include. Additionally, there is no evidence in the disclosure indicating that the structure of the molecular tag or tagmented nucleic acid fragments has any impact or effect on the structure of the sequencing platform.
Therefore, these claim languages do not distinguish the claimed system from the prior art.
Double Patenting- Obvious Type
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 29-33, 35-37 and 39-40 are rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 1 and 6 of U.S. Patent No. US12091660B2 (" '660 Patent") in view of Kumar (Kumar et al. A High-Throughput Method for Illumina RNA-Seq Library Preparation. Front Plant Sci. 2012 Aug 28;3:202. doi: 10.3389/fpls.2012.00202. PMID: 22973283; PMCID: PMC3428589).
Instant claim 29 recites a system comprising a sequencing platform configured to: (1) generate sequence reads; and (2) forward data to a computer at a remote location.
Claims 1 and 6 of the '660 Patent recite a high throughput sequencing platform capable of sequencing tagmented nucleic acid fragments, thereby generate sequence reads. While the '660 Patent does not explicitly claim its sequencing platform is capable of forwarding data to a remote computer, Kumar teaches a core laboratory platform that performs high-throughput sequencing and capable of transferring data to a remote could server for analysis (page 2, "SUMMARY OF LIBRARYPREPARATION AND SEQUENCING", lines 19-22; page 4, "BIOINFORMATICS," lines 1-3).
It would have been prima facie obvious to a person of ordinary skill in the art to combine the sequencing platform of the '660 Patent with the remote data transfer functionality taught by Kumar, in accordance with the KSR principle of applying known elements according to known methods to yield predictable results. A skilled artisan would have recognized that sequencing data generated by high-throughput platforms need to be transferred to a computer for downstream analysis, resulting in the predictable result of offloading sequencing data from the sequencer to a separate computer.
Therefore, instant claims 29-33, 35-37 and 39-40 are obvious over claims 1 and 6 of the '660 Patent, in view of Kumar.
Conclusion
No claims are allowed.
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/TIAN NMN YU/Examiner , Art Unit 1681 /AARON A PRIEST/Primary Examiner, Art Unit 1681
1 As stated in the restriction requirement (mail date 05/14/2025, page 3): "Should applicant traverse on the ground that the inventions are not patentably distinct, applicant should submit evidence or identify such evidence now of record showing the inventions to be obvious variants or clearly admit on the record that this is the case. "
2 Claims 2-4, 6, 8, 10-13, 18-20 and 23-28 are withdrawn as being drawn to non-elected group I.
3 Claim 34 is withdrawn as being drawn to non-elected species J.
4 Claim 38 is withdrawn as being drawn to non-elected species K.
5 "a sequencing platform configured to…" does not invoke claim interpretation under 35 U.S.C. 112(f), because the term "sequencing platform" indicates art-recognized structure to perform the claimed function of generating sequencing reads, such as an instrument comprising reaction chamber and detection unit, and sequencing reac