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 .
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 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.
Request for Continued Examination
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 03/05/2026 has been entered.
Claim Status
Claims 1-6, 8, 14, and 17-27, 29, 32, and 35 are pending.
Claims 7, 9-11, 12-13, 15-16, 28, 30-31, and 33-34 are canceled.
Claims 18-27, 29, and 32 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected species, as described in Non-Final Office Action dated 08/01/2025.
Claims 1-6, 8, 14, and 17 are rejected.
Priority
Applicant's claim for the benefit of as a 371 of PCT/KR2020/002921 filed 02/28/2020, is acknowledged.
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d) to App. No. Republic of Korea 10-2019-0024076, filed 02/28/2019. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Accordingly, each of claims 1-6, 8-9, 11, 14, and 17 are afforded the effective filing date of 02/28/2019.
Drawings
The replacement drawing sheets submitted 10/24/2025 are accepted.
Claim Rejections- 35 USC § 112
The outstanding 112(a) rejections to the claims are withdrawn in view of the amendments which deleted the new matter.
The outstanding 112(b) rejections to the claims are withdrawn in view of the amendments which deleted the indefinite limitation.
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.
For the following rejections, underlined text indicates newly recited portions necessitated by claim amendment.
Claims 1-6, 8, 14, and 17 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more. Any newly recited portions are necessitated by claim amendment.
MPEP 2106 organizes judicial exception analysis into Steps 1, 2A (Prongs One and Two) and 2B as follows below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Framework with which to Evaluate Subject Matter Eligibility:
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter;
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1
With respect to Step 1: yes, the claims are directed to method and process, i.e., a process, machine, or manufacture within the above 101 categories [Step 1: YES; See MPEP § 2106.03].
Step 2A, Prong One
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and mathematical concepts (in particular mathematical relationships and formulas) are as follows:
Independent claims 1 and 17:
selecting a start position from alignment positions of a plurality of target nucleic acid sequences; wherein the alignment positions comprise a conservative position and a non-conservative position of nucleotides of the plurality of target nucleic acid sequences that are aligned, the conservative position has one type of bases exhibiting conservativity, and the non-conservative position has two or more types of bases exhibiting non-conservativity;
selecting as an end position a position comprising a non-conservative position within a predetermined allowable number from the start position;
generating an oligonucleotide stick composed of a region from the start position to the end position; wherein the oligonucleotide stick comprises sequence information determined by a plurality of target nucleic acid sequences that are aligned in the region;
repeating the generation of an oligonucleotide stick by selecting at least one start position different from the start position in step (a); and performing steps (b) and (c);
determining as a designable region of oligonucleotides the regions in an alignment of the plurality of target nucleic acid sequences, which correspond to the regions of the oligonucleotide sticks.
providing the determined designable region; and wherein the oligonucleotide sticks generated in step (d) are generated or selected to satisfy at least one of the following criteria: (i) a predetermined minimum length of an oligonucleotide stick,(ii) a gap ratio; wherein when the alignment positions of the plurality of target nucleic acid sequences comprise a gap-containing position, the oligonucleotide sticks are generated by selecting as an end position a position before a gap- containing position having a gap ratio exceeding a predetermined gap ratio, and wherein the gap ratio represents a ratio between the number of gaps and the total number of bases at the gap-containing position and the total number of bases represents the sum of the numbers of existing bases and gaps,(iii) a base exist ratio (BER) at each position of an oligonucleotide stick; wherein the BER represents a ratio between the sum of the numbers of existing bases and gaps at an alignment position corresponding to each position of an oligonucleotide stick and the total number of sequences that are aligned, and wherein the oligonucleotide stick is selected according to the number of positions each having a BER of less than a predetermined value,(iv) a GC content; wherein a portion satisfying a predetermined GC content in an oligonucleotide stick is selected, and(v) amplicon region formation; wherein an amplicon region corresponding to a predetermined length in the 3' direction from the 5'-end or in the 5'-direction from the 3'-end of an oligonucleotide stick is set, and oligonucleotide sticks included in the amplicon region are selected considering criteria regarding a stick base sum (SBS) and/or respective lengths of the oligonucleotide sticks included in the amplicon region; and wherein the generated or selected oligonucleotide sticks are ranked according to at least one of the following priority items:(i) a ratio of the number of bases of an oligonucleotide stick to the number of non-conservative bases of the oligonucleotide stick; the larger the ratio, the higher the priority,(ii) an average base exist ratio (BER) of an oligonucleotide stick; the larger the average BER, the higher the priority, and(iii) the number of amplicon regions in which one oligonucleotide stick is included; the larger the number, the higher the priority.
Dependent claims2-6, 8 and 14 recite further steps that limit the judicial exceptions in independent claim 1 and, as such, also are directed to those abstract ideas. For example, claim 2 further limits the end position of claim 1, claim 3 further limits the oligonucleotide stick of claim 1, claims 4 and 5 further limits the start position of claim 1, claim 6 further limits the start and end position of claim 1, claim 8 further limits the predetermined allowable number of claim 1, and claim 14 further limits the designable region of claim.
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind and/or by mathematical operation because the method only requires a user to manually select, determine, prepare and generate. Without further detail as to the methodology involved in “selecting a start position”, “selecting as an end position”, and “providing “ under the BRI, one may simply, for example, use pen and paper to select end beginning and end positions. Some of these steps and those recited in the dependent claims require mathematical techniques: “generating an oligonucleotide stick“, and “determining as a designable region of oligonucleotides“.
Therefore, claims 1 and 17 and those claims dependent therefrom recite an abstract idea [Step 2A, Prong 1: YES; See MPEP § 2106.04].
Step 2A, Prong Two
Because the claims do recite judicial exceptions, direction under Step 2A, Prong Two, provides that the claims must be examined further to determine whether they integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d).III).
Additional elements, Step 2A, Prong Two
With respect to the instant recitations, the claims recite the following additional elements:
The claims also include non-abstract computing elements. For example, independent claim 17 includes a non-transitory computer readable storage medium and processor.
Considerations under Step 2A, Prong Two
With respect to Step 2A, Prong Two, the additional elements of the claims do not integrate the judicial exceptions into a practical application for the following reasons. Those steps directed to additional non-abstract elements of “a computer readable medium and processor” do not describe any specific computational steps by which the “computer parts” perform or carry out the judicial exceptions, nor do they provide any details of how specific structures of the computer, such as the computer-readable recording media, are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, and therefore the claim does not integrate that judicial exceptions into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc.… are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (MPEP 2106.05(f)).
Thus, none of the claims recite additional elements which would integrate a judicial exception into a practical application, and the claims are directed to one or more judicial exceptions [Step 2A, Prong 2: NO; See MPEP § 2106.04(d)].
Step 2B (MPEP 2106.05.A i-vi)
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to claim 17, the computer-related elements or the general purpose computer do not rise to the level of significantly more than the judicial exception. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, which the courts have found to not provide significantly more when recited in a claim with a judicial exception (see MPEP 2106.06(A)). The specification also notes that computer processors and systems, as example, are commercially available or widely used at [0165-0174]. The additional elements are set forth at such a high level of generality that they can be met by a general purpose computer. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the judicial exceptions (see MPEP 2106.05(b)I-III).
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself [Step 2B: NO; See MPEP § 2106.05].
Therefore, the instant claims are not drawn to eligible subject matter as they are directed to one or more judicial exceptions without significantly more. For additional guidance, applicant is directed generally to the MPEP § 2106.
Applicant submits claims 1 and 17 recite an additional element including: generating or selecting oligonucleotide sticks based on at least one of the following criteria [p. 14, par. 2 and p. 15, par. 1].
It is respectfully found not persuasive. The limitations of generating, selecting, and ranking are not additional elements. In the instant claims generating is discloses as producing a region using a machine learning model which is an abstract idea. Also selecting and ranking are a mental process not an additional element. It is important to keep in mind that an improvement in the abstract idea itself (e.g. a recited fundamental economic concept) is not an improvement in technology. Furthermore, it is important to note, the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements or by the additional element(s) in combination with the recited judicial exception. See MPEP 2106.05(a). The only additional element in the instant claims is a non-transitory computer readable storage medium and a processor in a generic format.
Applicant submits claims 1 and 17 recite additional elements that amount to significantly more than the judicial exception, by demonstrating real-world improvement (speed, coverage, and accuracy) over conventional methods [p. 16, par. 1].
It is respectfully found not persuasive. An inventive concept "cannot be furnished by the unpatentable law of nature (or natural phenomenon or abstract idea) itself. Instead, an "inventive concept" is furnished by an element or combination of elements that is recited in the claim in addition to (beyond) the judicial exception, and is sufficient to ensure that the claim as a whole amounts to significantly more than the judicial exception itself. Alice Corp., 573 U.S. at 27-18, 110 USPQ2d at 1981 (citing Mayo, 566 U.S. at 72-73, 101 USPQ2d at 1966). The only additional elements in the instant claims is a non-transitory computer readable storage medium and a processor in a generic format.
Conclusion
No claims are allowed.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Dawn Bickham whose telephone number (703)756-1817. The examiner can normally be reached on Monday - Friday 8-4.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia Wise can be reached on (571)272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see https://ppair-my.uspto.gov/pair/PrivatePair. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/Dawn Bickham/Examiner, Art Unit 1685
/Soren Harward/Primary Examiner, TC 1600
Prosecution Insights