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 IDS filed 9/29/2023 and 1/18/2024 have been considered by the Examiner.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. Priority of US application KR10-2021-0180438 filed 12/16/2021 and KR10-2022-0055514 filed 5/42022 is acknowledged.
Status of Claims
Amendments to the claims are acknowledged.
Claims 18-20 are new.
Claims 1-20 are under examination.
Double Patenting
The rejection of claims 1-4, 6-11, 13, 14 and 16-17 on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 1, 5, 6, 8, 10-13 and 18-19 of US 11,869,632 is withdrawn in view of the Terminal Disclaimer filed 12/10/2025.
Claim Rejections - 35 USC § 101
The instant rejection is maintained from the previous Office Action of 9/10/2025 are modified in view of Amendments filed 12/10/2025.
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 1-10 and 12-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Step 1: Process, Machine, Manufacture or Composition
Claims 1-10 and 12-15 are drawn to a method, so a process.
Claim 16 and 18-20 are drawn to a non-transitory computer readable medium with instructions, so a manufacture.
Claim 17 is drawn to a system with a processor, so a machine.
Step 2A Prong One: Identification of an Abstract Idea
The claim(s) recite(s):
1. marking data is generated based on a sample of an organism, by a sequencer configured to identify nucleotides based on a genome of the sample in a plurality of cycles associated with a target length corresponding to a partial genome sequence.
The specification describes “marking data” as including one or more marking codes. For example, the marking data may be an image file (specification, page 12, lines 11-2). However under Broadest Reasonable Interpretation marking data as claimed reads on any data and the sequencer reads on a microprocessor attached to a sequencer. This step of generating marking data reads on a process of generating a sequence of nucleotides (i.e. ATT) based on analysis of fluorescence sequencing results. The step reads on a mental process and is therefore an abstract idea.
2. generate marking codes corresponding to the identified nucleotides and recording the marking codes in the marking data wherein the marking data comprises a first image data portion and second image data portion.
This step reads on a process that can be performed by the human mind or with the aid of paper/pen. The specification (page 12, lines 11-2) describes “marking data” as including one or more marking codes. Under Broadest Reasonable Interpretation, “image data portion” encompasses any data from an image. The step reads on marking identified nucleotides on an image file or adding marking codes to data describing an image (i.e. image data portion). The step can be performed by the human mind or with the aid of paper/pen and is therefore an abstract idea.
3. converting the marking data to sequence data
This step reads on a process that can be performed by the human mind by assembling the marked data on the image into a nucleotide sequence. The step can be performed by the human mind and is therefore an abstract idea.
4. aligning, based on reference sequence data associated with the organism, the sequence data, wherein the aligned sequence data comprises: a first aligned portion corresponding to the first read of paired end reads; and a second aligned portion corresponding to a partial portion of the second read of the paired end reads, wherein the second read is associated with the second length of the second polynucleotide chain.
Aligning sequence data to a reference sequence can be performed by the human mind and is therefore an abstract idea.
4. performing, based on the aligned sequence data, the partial genome sequence-based identification to identify at least one structural variant different from point mutations.
The step reads on analyzing the sequence to determine regions that vary from a reference sequence. Identifying variant information from a sequence can be performed by the human mind and is therefore an abstract idea.
Claims 2-15 and 18-20 further read on analysis steps that can be performed by the human mind and are therefore drawn to an abstract idea. New claims 18-20 are drawn to determining target data amount which falls into the mental processing grouping and is therefore an abstract idea.
Step 2A Prong Two: Consideration of Practical Application
The claimed process results in an alignment based partial genome sequence identification which is determination of information from an analysis of an abstract idea. The claims as a whole read on an abstract idea.
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than
a drafting effort designed to monopolize the exception.
Step 2B: Consideration of Additional Elements and Significantly More
The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea. The recited additional elements are drawn to:
1. receiving marking data from a sequencer, as in claims 1, 5 and 16.
This limitation reads on data transmission which is extra solution activity, as described in MPEP 2106.05(g).
2. a sequencer configured to identify nucleotides based on a genome of the sample, as in claims 1 and 16.
3. providing, as input to a sequencer, an amount of a determined sample, as in claim 18.
This limitation reads on data transmission of inputting data which is extra solution activity, as described in MPEP 2106.05(g).
This limitation is drawn to a generic sequencer configured with a generic computer for identifying nucleotides. Sequencers and their interfacing computers are well known, routine and conventional.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because transmitting data from a sequencer is well known, routine and conventional pre-solution and extra-solution activity. See MPEP 2106.05(g).
Other elements of the method include recitation of processors (claim 17) and memory (claim 17) which is a recitation of generic computer structures that serve to perform generic computer functions that are well-understood, routine, and conventional activities previously known to the pertinent industry. Viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself. Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
Response to Arguments
Applicant's arguments filed 12/10/2025 have been fully considered but they are not persuasive.
Applicants argue (Remarks, page 11) that the previous Action mistakes the hypothetical presence of an exception indicating that the claims are, as a whole, directed to an exception. Applicants argue that the claims involve steps performed by a computing device.
In response, examination is performed using the standard of Broadest Reasonable Interpretation. Furthermore, reciting a computer to perform steps that read on mental processes or math does not qualify as a practical application under Step A Prong Two or add “significantly more” under Step B. That is, other than reciting “performed by one or more processors,” nothing in the claimed element precludes the step from practically being performed in the mind. For example, but for the “performed by one or more processors” language, each of the steps in the context of this claim encompasses receiving, identifying and aligning nucleic acid sequence information, and recording image data portions with a marking code, can be performed as a mental process. If a claimed limitation, under its Broadest Reasonable Interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then it falls within the “mental process” grouping of abstract ideas. Accordingly, the claim recites abstract ideas.
Applicants argue (Remarks, pages 11-12) that the claims are rooted in a specific technological environment and involve a sequencer, and involve specific data including image data, a computer implementing the process, and performing specific processes based on the data. Applicants argue that the claims thereby recite a practical application of any alleged human process of “creating a file based on image data.”
In response, the claimed process does not recite any steps of creating a file based on image data. Even so, creating a file of image data would not be a practical application of the claimed process. The instant process is not drawn to, for example, an image pixel refinement process wherein outputting/creating an image data file would constitute a practical application. MPEP 2106.04(a)(2) provides an example:
• a claim to a method for rendering a halftone image of a digital image by comparing, pixel by pixel, the digital image against a blue noise mask, where the method required the manipulation of computer data structures (e.g., the pixels of a digital image and a two-dimensional array known as a mask) and the output of a modified computer data structure (a halftoned digital image), Research Corp. Techs., 627 F.3d at 868, 97 USPQ2d at 1280.
Here, the output of the halftone image data structure (i.e. an image file) would constitute a practical application of RCT’s claimed image pixel data analysis, even if abstract ideas were recited. In contrast, the instant claims are directed to marking image data with a marking code, identifying nucleic acids to identify a sequence, aligning the sequence data and identifying a structural variant different from point mutations. Instantly, creating a file based on image data is not a practical application of the recited abstract ideas but rather an extra solution activity as described in MPEP 2106.05(g).
Applicants argue that processing “making data” in real time, covering and aligning the data and using it to perform a partial genome sequence-based identification process to identify a structural variant enable the computers to perform these process steps. Applicants argue that their process is analogous to McRO where the claimed improvement was allowing computers to produce accurate and realistic lip synchronization.
In response, in McRO the claimed process included the setting or morph weights and transition through phonemes (as pointed out by instant Applicants, page 12, par. 2). In McRO the improvement to technology is reflected in the claims. McRO accomplished the automation/computerization of more realistic facial animation, which is not an abstract idea, by including the morph weights and phoneme transitions. In contrast, the instant claims merely invoke a computer for processing efficiency without any evident improvement to nucleic acid sequencing technology. While the instant claims do not currently recite processing robust amount of sequence data, for the record, it is important to note that analyzing a lot of data does not augment the steps being performed to analyze the data, which are abstract ideas. Computations on a lot of data performed mentally, or with paper and pencil, would take considerable time and effort, but that is, of course, the singular purpose of computers and computer networks, to perform large numbers of calculations, via algorithms, rapidly, and without error (assuming no error in user input). Although a general purpose computer can perform calculations at a rate and accuracy that can far outstrip the mental performance of a skilled artisan, the nature of the activity is essentially the same, and constitutes an abstract idea. See Bancorp Serves., L.L. C. v. Sun Life Assur. Co. of Canada (U.S.), 687 F.3d 1266,1278 (Fed. Cir. 2012) (holding that “the fact that the required calculations could be performed more efficiently via a computer does not materially alter the patent eligibility of the claimed subject matter”); see also See SiRF Tech., Inc. v. Int’l Trade Comm ’n, 601 F.3d 1319,1333 (Fed. Cir. 2010) (holding that: In order for the addition of a machine to impose a meaningful limit on the scope of a claim, it must play a significant part in permitting the claimed method to be performed, rather than function solely as an obvious mechanism for permitting a solution to be achieved more quickly, i.e., through the utilization of a computer for performing calculations).
Applicants argue (Remarks, page 13) that under Step 2B, the instant claims recite generic components that are able in combination to perform functions that are not merely generic.
In response, the only additional elements claimed are “receiving” marking data from a sequencer and “the sequencer” configured to identify nucleotides based on a genome of a sample. Sequencing genomic samples to generate data and receiving the data by a computer for further analysis is a combination of additional elements that is routine, conventional and well understood. Therefore under Step 2B these additional elements do not add “significantly more.” It is noted that marking data, image data portions, and sequence data are not additional elements because data is abstract and part of the abstract idea which is the analysis of said data. Furthermore, converting marking data, aligning sequence data, partial sequence-base identification to identify a structural variant are also not additional elements because they are steps that fall into the mental processes and math groupings of judicial exceptions (i.e. abstract ideas).
For the reasons set forth above, the 35 USC 101 rejection is maintained.
Claim Rejections - 35 USC § 112-2nd paragraph
The rejection of claims 1-17 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph is withdrawn in view of Applicant’s amendments filed 12/20/2025. The instant rejection is necessitated by Applicant’s amendments.
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 1-10 and 12-20 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.
Claims 1, 16 and 17 recite:
a. Receiving, from a sequencer, marking data, wherein the marking data is generated, based on a sample of an organism, by the sequencer, which is configured to identify nucleotides based on a genome of a sample in a plurality of cycles associated with a target length corresponding to a partial genome sequence,
b. Generate marking codes corresponding to the identified nucleotides, and
c. Recording the marking codes in the marking data.
It is unclear how the limitations (in a.) drawn to configuration of the sequencer (which is configured to identify nucleotides based on a genome of a sample in a plurality of cycles associated with a target length corresponding to a partial genome sequence) are intended to further limit the claim, in particular the step of receiving of marking data. The claimed method is drawn to a method performed by a processor. The same limitations are recited in claims 16 and 17 drawn to instructions and a system processor. The limitation describing the configuration of the sequencer does not further limit the recited instruction performed by the processor. This causes a lack of clarity with respect to how this limitation is intended to further limit the claim.
E-mail communication Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting the following statement via EFS Web (using PTO/SB/439) or Central Fax (571-273-8300):
Recognizing that Internet communications are not secure, I hereby authorize the USPTO to communicate with the undersigned and practitioners in accordance with 37 CFR 1.33 and 37 CFR 1.34 concerning any subject matter of this application by video conferencing, instant messaging, or electronic mail. I understand that a copy of these communications will be made of record in the application file.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.
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 extension fee 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 date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Anna Skibinsky whose telephone number is (571) 272-4373. The examiner can normally be reached on 12 pm - 8:30 pm.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Ram Shukla can be reached on (571) 272-7035. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Anna Skibinsky/
Primary Examiner, AU 1635