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 .
Claims 1-21 are currently pending and under examination. Any objection or rejection of record in the previous Office Action, which is not addressed in this action has been withdrawn in light of Applicant’s amendments and/or arguments. This action is Final.
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 1-21 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions (i.e., product of nature, a law of nature, a natural phenomenon, or an abstract idea) without significantly more. This rejection is maintained and modified as necessitated by amendments.
Every claimed invention must be examined to determine whether the claimed invention complies with 35 U.S.C. 101, particularly whether the claimed invention falls within a 35 U.S.C. 101 judicial exception of non-patentable subject matter (e.g., an abstract idea, law of nature, natural phenomenon, natural product etc.). Phenomena of nature, though just discovered, natural products, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work. See MPEP 2106. As per the “2019 Revised Subject Matter Eligibility Guidance” (Federal Register Vol. 84, No. 4, available 01-07-2019), claims drawn to a process, machine, manufacture or composition of matter are further analyzed according to a two-part process to determine if A) the claim(s) is/are “directed to” a judicial exception because the claims(s) recite(s) a judicial exception (i.e. prong one) that is not integrated into a practical application (i.e. prong two) and, if so, if B) the claim(s) provide(s) an inventive concept, i.e. recite(s) additional elements that amount to significantly more than the judicial exception.
Subject Matter Eligibility Test for Products and Processes
Step 1 - Is the Claim to a Process, Machine, Manufacture or Composition of Matter? YES
Claims 1-21 are directed to one of the statutory classes. Claims 1-15 and 20-21 are directed to a method for improving the reconstruction of a single cell genome and claims 16-19 are directed to a method for counting two DNA molecules (Processes).
Step 2A, Prong One — Does the Claim Recite an Abstract Idea, Law of Nature, or Natural Phenomenon? YES
Claims 1-21 recite the abstract ideas of receiving and processing data using mental steps. Claims directed to nothing more than abstract ideas, natural phenomena, and laws of nature are not eligible for patent protection (see MPEP 2106.04). Abstract ideas include certain methods of organizing human activity, and mental processes (including procedures for collecting, observing, determining, evaluating, and organizing information (See MPEP 2106.04(a)(2)). In particular, these abstract ideas include:
• Counting nucleic acids (mental process, human mind is capable of receiving data).
• Detecting shorter and longer extension products (mental process of observing, receiving and evaluating information).
• Disregarding the shorter extension products (mental process of observing, receiving and evaluating information).
•Identifying shorter extension products that are produced by defective transposition reactions, and then excluding them from genome reconstruction or the counting of DNA molecules (mental process of observing, receiving, evaluating and organizing information).
• Identifying appropriate connections (mental process of receiving and evaluating information).
• Determining the phase of each sequence (mental process of receiving and evaluating information as well as organizing information).
• Assigning the contiguous sequence to a first and second DNA molecule (mental process of receiving and evaluating information as well as organizing information).
Therefore, the claims recite elements that constitute one or more judicial exceptions.
Step 2A, Prong Two — Does the Claim Recite an Additional Elements that Integrate the Judicial Exception into a Practical Application? NO.
The Supreme Court has long distinguished between principles themselves, which are not patent eligible, and the integration of those principles into practical applications, which are patent eligible. However, absent are any additional elements recited in the claim beyond the judicial exceptions which integrate the exception into a practical application of the exception. The “integration into a practical application” requires an additional element or a combination of additional elements in the claim to apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception, such that it is more than a drafting effort designed to monopolize the exception.
The claim analysis continues with identifying additional elements beyond the judicial exceptions that might evidence integration of the judicial exceptions into a practical application. The steps or elements in addition to the judicial exceptions are: "obtaining a sample", "contacting and fragmenting the genomic DNA using a transposase loaded with two identical transposon ends", "extending a complementary strand of each fragment using a universal primer comprising a sequence complementary to the identical transposon end to generate one or more extension products", “the shorter extension product results from transposase cleavage of a first strand of the genomic DNA, and the longer extension product results from absence of transposase cleavage of a second strand of the genomic DNA”, which is not indicative of integration into practical application. These steps, recited at a high level of generality, comprise routine data gathering, which is considered an insignificant extra-solution activity. This data gathering is required for using the judicial exceptions. (See MPEP 2106.05(g)). There are no further/additional steps which applies either the identified judicial exception into practical application. Thus, a careful evaluation of the claim as a whole fails to reveal the practical application of the judicial exception to, e.g., effect an improvement to the functioning of a computer or other technology/technical field, effect a particular treatment or prophylaxis for a disease or medical treatment, implement a particular machine that is integral to the claim, or effect a transformation or reduction of a particular article to a different state or thing, or to apply the judicial exception in another meaningful way beyond generally linking its use to a particular technological environment. Accordingly, the claims do not integrate the judicial exception(s) into a practical application and is therefore directed to a judicial exception.
Step 2B - Does the Claim Recite Additional Elements that Amount to Significantly More than the Judicial Exception? NO.
The Supreme Court has identified a number of considerations for determining whether a claim with additional elements amounts to “significantly more” than the judicial exception(s) itself. The claims as a whole are analyzed to determine whether any additional element/step, or combination of additional elements/steps, in addition to the identified judicial exception(s) is sufficient to ensure that the claim amounts to “significantly more” than the exception(s).
The eligibility analysis proceeds with identifying any additional elements or limitations, separate from the judicial exceptions, that might potentially render the claims directed to a judicial exception patent eligible. To render the claims patent- eligible, these elements must comprise meaningful limitations that add to or transform the judicial exception to the effect that it amounts to significantly more than the natural correlation or abstract idea itself - i.e. provide an “inventive concept’. The elements that are in addition to the judicial exception comprise: obtaining a sample, contacting and fragmenting the genomic DNA using a transposase loaded with two identical transposon ends and extending a complementary strand of each fragment using a universal primer comprising a sequence complementary to the identical transposon end to generate one or more extension products as well as the shorter extension product results from transposase cleavage of a first strand of the genomic DNA, and the longer extension product results from absence of transposase cleavage of a second strand of the genomic DNA. When considered separately and in combination, these elements do not add significantly more to the judicial exception. These steps are well-understood, routine and conventional activities in the field. For example, Sternberg et al. (U.S. Patent No. US 10,947,534 B2, published March 16, 2021), discloses obtaining a sample, contacting and fragmenting the genomic DNA using a transposase loaded with two identical transposon ends and extending a complementary strand of each fragment using a universal primer comprising a sequence complementary to the identical transposon end to generate one or more extension products. The claims recite an abstract idea with additional elements. Because these elements are not inventive concepts, the claims do not integrate the abstract idea into a practical application. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). The claims therefore do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Accordingly, the claims do not qualify as patent-eligible subject matter.
For further information, please see the latest revision of MPEP 2104-2106 {Patent Subject Matter Eligibility Under 35 U.S.C. 101}, including MPEP 2106.04 {Eligibility Step 2A: Whether a Claim is Directed to a Judicial Exception} and 2106.05 {Eligibility Step 2B: Whether a Claim Amounts to Significantly More}, as well as the guidance on Subject Matter Eligibility, including the 2019 Guidance issued Jan. 7, 2019, and the October 2019 Update, provided on the USPTO website at https:/Awww.uspto.gov/patent/laws-and-regulations/examination-policy/subject-matter- eligibility.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-21 are rejected under 35 U.S.C. 103 as being unpatentable over Sternberg et al. (U.S. Patent No. US 10,947,534 B2, published March 16, 2021), previously cited in the November 17, 2025 Office Action, in view of Gunderson et al. (WIPO International Application Publication WO 2016/130704 A2, published August 18, 2016), previously cited in the November 17, 2025 Office Action. This rejection is maintained and modified as necessitated by amendments.
Regarding claim 1, Sternberg teaches a method for improving the reconstruction of a single cell genome (Column 2, Line 43-47, Column 9, Line 53-58, Column 10, Line 40-41 and Column 97, Lines 4-9). Sternberg teaches obtaining genomic DNA derived from a single fully disrupted cell (e.g., cell lysates, Column 79, Lines 9-11 and Column 107, Line 1). Sternberg teaches contacting and fragmenting the genomic DNA using a transposase loaded with two identical transposon ends to form a plurality of genomic DNA fragments each labeled with an identical transposon end at its 5' and 3' ends (Column 34, Lines 5-23, Column 172, Lines 25-26, Column 4, Lines18-22, Column 124, Lines 42-43 and Column 33, Lines 35-42). Sternberg teaches extending a complementary strand of each fragment using a universal primer comprising a sequence complementary to the identical transposon end to generate one or more extension products (Column 146, Line 60—Column 147, Line 9 and Column 90, Lines 13-14). Sternberg teaches determining the nucleotide sequence between transposon ends of the extension products (e.g., sequencing cargo in between transposon ends, Column 12, Line 1-20, column 123, Line 65—Column 124, Line 8 and Column 137, Line 64—Column 136, Line 12). Sternberg teaches detecting one or more shorter extension products and one longer extension product comprising one identical segment of genomic sequence (Column 107, Lines 14-27). Sternberg teaches the shorter extension product results from transposase cleavage of a first strand of the genomic DNA, and the longer extension product results from absence of transposase cleavage of a second strand of the genomic DNA (Column 22, Lines 27-35, Column 55, Lines 13-14, Column, 58, Lines 15-25, Column 107, Lines 16-31,Column 131, Lines 53-56, Column 142, Line 57—Column 132, Line 7). Sternberg teaches disregarding the one or more shorter extension products (Column 33, Lines 42-56, Column 106, Line 58—Column 107, Line 15, Column 108, lines 20-24, Column 117, Liens 30-53, Column 131, Lines 53-56). Sternberg teaches identifying appropriate connections that facilitate sequence chaining among the remaining extension products based on overlapping unique 8-10 nucleotide sequences immediately next to the transposon end (Column 21, Lines 11-40, Column 40, Line 63—Column 41, Line 15, Column 112, Lines 1-12, Column 124, Lines 1-8, Column 168, Lines 29-36 and Column 175, Lines 13-49).
Regarding claim 2, Sternberg teaches determining ploidy of a genomic region in the genome (Column 116, Lines 13-27).
Regarding claim 3, Sternberg teaches the extension products are linked together in 5' to 3' direction by concatenating contiguous fragments at transposon junctions (Colum 112, Lines 1-12, Column 168, Lines 29-36, Column 179, Lines 48-56 and Example 12).
Regarding claim 4, Sternberg teaches the sequenced extension products are linked according to their unique fragment identifiers (UFI) and each UFI comprises a start or an end nucleotide positions of each fragments (Column 34, Line 65—Column 34, Line 8, Column 78, Line 51—Column 79, Line 13, Column 146 and Line 60—Column 147, Line 22).
Regarding claim 5, Sternberg teaches the disregarded extension products from step (vi) comprise a sequence complementary to the 5' end of one or more retained extension products (Column 33, Lines 2-65).
Regarding claim 6, Sternberg teaches the disregarded extension products from step (vi) comprise a sequence complementary to the 3' end of one or more retained extension products (Column 69, Lines 23-35).
Regarding claim 7, Sternberg teaches the disregarded extension products from step (vi) comprise a sequence complementary to both the 5' and 3' ends of the one or more retained extension products (Column 33, Lines 2-65 and Column 69, Lines 23-35).
Regarding claim 8, Sternberg teaches the one or more retained extension products comprise a neighboring or adjacent in-phase extension product (Column 13, Lines 52-61).
Regarding claim 9, Sternberg teaches amplifying the extension products (Column 90, Lines 11-15).
Regarding claim 10, Sternberg teaches adding a barcode sequence to the amplified extension products (Column 146, Lines 60-67).
Regarding claim 11, Sternberg teaches the longer extension products are bioinformatically linked by concatenating the fragments at transposon junctions (Colum 112, Lines 1-12, Column 168, Lines 29-36, Column 179, Lines 48-56, Column 42, Lines 17-41and Example 12).
Regarding claim 12, Sternberg teaches the transposon end comprises a universal primer (Column 116, Lines 53-55, Column 142, Lines 25-61 and Column 146, Lines 23-36).
Regarding claim 13, Sternberg teaches the single cell genome comprises one or more alleles of at least one genetic locus (Column 2, Lines 8-18, Column 123, Lines 49-64 and Column 147, Lines 10-22).
Regarding claim 14, Sternberg teaches the single cell genome comprises two or more chromosomes (Column 77, Lines 19-26).
Regarding claim 15, Sternberg teaches the single fully disrupted cell is a monoploid cell, diploid cell, or a cancer cell (Column 15, Lines 13-15 and Column 156, Lines 26 and 39).
Regarding claim 16, Sternberg teaches a method for counting two DNA molecules, comprising obtaining genomic DNA derived from a single fully disrupted cell (e.g., cell lysates, Column 79, Lines 9-11, Column 107, Line 1, Column 164, Lines 31-36, Column 170, Lines 65-67 and Column 176, Lines 35-52). Sternberg teaches contacting and fragmenting the genomic DNA using a transposase loaded with two identical transposon ends to form a plurality of genomic DNA fragments each labeled with an identical transposon end at its 5' and 3' ends (Column 34, Lines 5-23, Column 172, Lines 25-26, Column 4, Lines18-22, Column 124, Lines 42-43 and Column 33, Lines 35-42). Sternberg teaches extending a complementary strand of each fragment using a universal primer comprising a sequence complementary to the identical transposon end to generate one or more extension products (Column 146, Line 60—Column 147, Line 9 and Column 90, Lines 13-14). Sternberg teaches determining the nucleotide sequence between transposon ends of the extension products (e.g., sequencing cargo in between transposon ends, Column 12, Line 1-20, column 123, Line 65—Column 124, Line 8 and Column 137, Line 64—Column 136, Line 12). Sternberg teaches detecting one or more shorter extension products and one longer extension product comprising one identical segment of genomic sequence (Column 107, Lines 14-27). Sternberg teaches the shorter extension product results from transposase cleavage of a first strand of the genomic DNA, and the longer extension product results from absence of transposase cleavage of a second strand of the genomic DNA (Column 22, Lines 27-35, Column 55, Lines 13-14, Column, 58, Lines 15-25, Column 107, Lines 16-31,Column 131, Lines 53-56, Column 142, Line 57—Column 132, Line 7). Sternberg teaches disregarding the one or more shorter extension products (column 33, Lines 42-56, Column 106, Line 58—Column 107, Line 15, Column 108, lines 20-24, Column 117, Liens 30-53, Column 131, Lines 53-56). Sternberg teaches identifying appropriate connections that facilitate sequence chaining among the longer extension products based on overlapping unique 8-10 nucleotide sequences immediately next to the transposon end (Column 21, Lines 11-40, Column 40, Line 63—Column 41, Line 15, Column 112, Lines 1-12, Column 124, Lines 1-8, Column 168, Lines 29-36 and Column 175, Lines 13-49).
Regarding claim 17, Sternberg teaches the two or more DNA molecules comprise the same or identical nucleic acid sequences (Column 58, Lines 53-56, Column 48, Lines 18-24 and Column 35, Lines 4-8).
Regarding claim 18, Sternberg teaches the assigning step occurs using the rules of exclusivity and greediness (Column 47, Lines 22-25, Column 48, Lines 47-50, Column 56, Lines 10-12, Column 133, Lines 7-9, Column 178, Line 63—Column 179, Line 1 and Column 80, Lines 22-32).
Regarding claim 19, Sternberg teaches counting the DNA molecules comprises counting digital DNA molecules (e.g., Python script, Column 176, Lines 35-52 and Column 139, Lines 13-62).
Regarding claim 20, Sternberg teaches a system for performing the method of claim 1 (Column 101, Line 48—Column 102, Line 27).
Regarding claim 21, Sternberg teaches the system or device is a computer system or computerized device (e.g., Python, Column 176, Lines 35-52 and Column 139, Lines 13-62).
Sternberg does not teach or suggest determining the phase of each sequence, thereby reconstructing the genome. Sternberg does not teach or suggest determining the phase of each sequence to create a contiguous sequence and assigning the contiguous sequence to a first or second DNA molecule.
Gunderson teaches single cell genome from genomic DNA and fully disrupting the cell (Page 2, Second Paragraph and Page 3, Last Paragraph). Gunderson teaches fragmenting the genomic DNA using a transposase loaded with two identical transposon ends (Page 24, Last Paragraph, Page 33, First Paragraph, and Page 22, Third Paragraph). Gunderson teaches using universal primers (Page 25, Second Paragraph). Gunderson teaches generating extension products (Page 24, Last Paragraph and Page 55, Last Paragraph). Gunderson teaches using digital DNA a computerized device to carry out the method as well as methods and compositions disclosed may be automated (Page 63, First Paragraph and Page 52, Third Paragraph). Gunderson teaches two or more chromosomes (Page 5, Third Paragraph). Gunderson teaches amplification and using barcodes (Page 13, Second Paragraph and Page 6, Last Paragraph—Page 7, Second Paragraph). Gunderson teaches short and long extension products (Page 33, Third Paragraph) Gunderson teaches determining the phase of each sequence (Page 5, First Paragraph and Page 32, First and Third Paragraph). Gunderson teaches determining the phase of each sequence to create a contiguous sequence and assigning the contiguous sequence to a first or second DNA molecule (Page 1, Last Paragraph—Page 2, First Paragraph, Page 5, First Paragraph). Gunderson teaches methods and compositions that use contiguous elements can be combined together with mutagenic assembly approaches to greatly improve assembly of DNA sequence information (Page 31, Last Paragraph). Gunderson teaches using the disclosed methods creates a larger diversity of sequencing reads which can improve read coverage and accuracy (Page 52, First Two Paragraphs).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the invention to modify the teachings of Sternberg with the teachings of Gunderson, to determine the phase of each sequence to create a contiguous sequence and assigning the contiguous sequence to a first or second DNA molecule. Using methods and compositions that use contiguous elements can be combined together with mutagenic assembly approaches to greatly improve assembly of DNA sequence information as well as the disclosed methods creates a larger diversity of sequencing reads which can improve read coverage and accuracy as taught by Gunderson (Page 31, Last Paragraph and Page 52, First Two Paragraphs).
Response to Arguments
Applicant’s arguments and amendments filed March 16, 2026, with respect to the rejections under U.S.C. § 112(b) have been fully considered and are persuasive. Therefore, these rejections have been withdrawn.
Applicant’s arguments and amendments filed January 31, 2024, with respect to the rejection under U.S.C. § 101 have been fully considered but are not deemed to be persuasive.
As discussed above adding the limitations of “the shorter extension product results from transposase cleavage of a first strand of the genomic DNA, and the longer extension product results from absence of transposase cleavage of a second strand of the genomic DNA" does not add something more to the judicial exception in that it does not describe how it solves the particular problem within the field of reconstructing the genome but merely describes limitations for the shorter and longer extension products. Additionally, applicant asserts “this solution is enabled by the method steps of identifying shorter extension products that are produced by defective transposition reactions, and then excluding/disregarding them from genome reconstruction or the counting of DNA molecules”, which can be mental processes, wherein the human mind is capable of receiving/collecting data, observing/evaluating/determining and organizing information/data as well as using mathematical concepts (identifying extension products, excluding/disregarding data, and counting), therefore this rejection is maintained..
Applicant’s arguments and amendments filed January 31, 2024, with respect to the rejection under U.S.C. § 103 have been fully considered but are not deemed to be persuasive.
Applicant asserts “Sternberg and Gunderson do not contemplate method steps for detecting and selectively disregarding shorter extension products before continuing with further method steps”.
As discussed above, Sternberg discloses disregarding or excluding shorter extension products, in that extension products without adapters (which are shorter), are excluded for further processing of PCR amplification (Column 33, Lines 45-52). Additionally, Sternberg discloses filtering reads based on length and excluding any reads that do not meet a certain required criteria or length (i.e., short sequences; Column 117, Lines 28-44 and Columns 131, Lines 46-56). Additionally, Sternberg teaches selectively detecting, amplifying and counting/quantifying sequences (Column, 22, Lines 4-5, Column 23, Lines 28-29 and Lines 54-64, Column 168, Lines 29-34). Therefore, Sternberg does in fact disclose disregarding or excluding shorter extension products.
.
Additionally, Sternberg teaches selectively detecting, amplifying and counting/quantifying sequences (Column, 22, Lines 4-5, Column 23, Lines 28-29 and Lines 54-64, Column 168, Lines 29-34).
Therefore, for all these reasons, Sternberg in view of Gunderson are deemed to render the instant invention obvious.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA DANIELLE PARISI whose telephone number is (571)272-8025. The examiner can normally be reached Mon - Friday 7:30-5:00 Eastern with alternate Fridays off.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached at 571-272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JESSICA D PARISI/Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684
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