DETAILED ACTION
Applicant’s response, filed 07/24/2026, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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.
Claim Status
Claims 1-5, 14, and 17-27, 29, 32, and 35 are pending.
Claims 6-13, 15-16, 28, 30-31, and 33-34 are canceled.
Claims 18-27, 29, 32, and 35 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected species, as described in Non-Final Office Action dated 08/01/2025.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drawing sheets submitted 10/24/2025 are accepted and the outstanding objections from the previous Office Action are withdrawn.
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, the non-conservative position has two or more types of bases exhibiting non-conservativity, and the start position is a conservative position;
selecting as an end position a position comprising a non-conservative position within a predetermined allowable number from the start position wherein the end position is a conservative position and the predetermined allowable number is 1, 2, 3, 4, or 5;
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.
Dependent claims 2-5 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, and claim 14 further limits the designable region of claim.
Under the BRI, the instant claims recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mental process”, such as procedures for evaluating, analyzing or organizing information, and forming judgement or an opinion. The instant claims further recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mathematical concept”, such as mathematical relationships and mathematical equations.
The claim recites selecting. The human mind is capable of selecting a start position from alignment positions of a plurality of target nucleic acid sequences and selecting as an end position a position. The claims recite a mathematical concepts of generating an oligonucleotide stick, 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:
Independent claims 1 and 17:
providing the determined designable region for designing an oligonucleotide for amplification or detection of the plurality of target nucleic acid sequences; 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.
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 data outputting, such as “providing”, perform functions of collecting the data needed to carry out the judicial exceptions. Data outputting does not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. Data outputting steps are not sufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
Further 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 the instant claims, the courts have found that receiving and outputting data are well-understood, routine, and conventional functions of a computer when claimed in a merely generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, as discussed in MPEP 2106.05(d)(II)(i)).
As such, the claims simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception (MPEP2106.05(d)). The data outputting steps as recited in the instant claims constitute a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
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.
Response to Remarks
1. Applicant submits amended claims 1 and 17 are not directed to a mental process or mere information analysis. When considered as a whole, the claims are directed to a specific technological process for identifying biologically functional regions used in oligonucleotide design for amplification and detection of target nucleic acid sequences, rather than a mental process or mere information analysis [p. 12, par. 8].
It is respectfully found not persuasive. The human mind is capable of selecting a start position from alignment positions of a plurality of target nucleic acid sequences and selecting as an end position a position further the claims also recite a mathematical concepts of generating an oligonucleotide stick, determining as a designable region of oligonucleotides.
2. Applicant submits accordingly, when considered as a whole, claims 1 and 17 are directed to a technological process for identifying biologically functional regions used in oligonucleotide design rather than to a mental process or abstract information analysis [p. 13, par. 3].
It is respectfully found not persuasive. The human mind is capable of selecting a start position from alignment positions of a plurality of target nucleic acid sequences and selecting as an end position a position further the claims also recite a mathematical concepts of generating an oligonucleotide stick, determining as a designable region of oligonucleotides. Additionally as stated in the remarks “generating a designable region that is specifically selected and used as an input for designing primers and/or probes that function in nucleic-acid amplification and detection workflows” [p. 13, par. 1] which describes an abstract idea that is to be used for designing primers and probes, however the designing and synthesizing of those primers or probes are not required in the claims.
3. Applicant submits amended claims 1 and 17 recite additional elements that integrate the alleged judicial exception into a practical application [p. 13, par. 4].
It is respectfully found not persuasive. The claims recite the additional element of data outputting, such as “providing”, which perform functions of outputting the data needed to carry out the judicial exceptions. Data output does not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. 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 practical application must be found among the additional elements of the claims; ie elements that are not judicial exceptions (MPEP 2106.04(d)). Mathematical calculations are judicial exceptions, so no matter how useful or beneficial those calculations are, they are not a practical application.
4. Applicant submits the recited output has a direct functional relationship to downstream molecular diagnostic processes and is integrated into a practical application [p. 15, par. 2].
It is respectfully found not persuasive. As stated in the remarks “it is an intermediate biological input used in the physical design of primers and probes that are subsequently employed in amplification and detection reactions involving biological samples” [p. 15, par. 2] which describes an abstract idea or data output that is to be used as input for designing primers and probes, however the designing and synthesizing of those primers or probes are not required in the claims.
5. Applicant submits the claims are directed to improving the technological process of designing oligonucleotides used for amplification and detection in molecular diagnostic assays, not merely to generating or displaying information. Accordingly, claims 1 and 17 integrate any alleged judicial exception into a practical application [p. 15, par. 3].
It is respectfully found not persuasive. The claims recite the additional element of data outputting, such as “providing”, which perform functions of outputting the data needed to carry out the judicial exceptions. Data output does not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. 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 practical application must be found among the additional elements of the claims, ie elements that are not judicial exceptions (MPEP 2106.04(d)). Mathematical calculations are judicial exceptions, so no matter how useful or beneficial those calculations are, they are not a practical application.
6. Applicant submits therefore, the recited technological improvement arises from the specific ordered combination recited in the claims rather than from generic automation [p. 17, par. 2].
It is respectfully found not persuasive. The examiner acknowledges Applicant’s arguments which set forth that the claims lead to an improvement in oligonucleotide design by reducing the likelihood of selecting regions that are conserved yet unsuitable for amplification or detection. According to the guidance set forth in MPEP 2106, this is an improvement to the judicial exception itself and is not reflected back into a specific technological environment or practically applied process.
7. Applicant submits Office has not identified evidence demonstrating that the recited ordered combination is well-understood, routine, or conventional, thereby supporting the conclusion that the recited arrangement represents more than well-understood, routine, and conventional activity [p. 17, par. 4].
It is respectfully found not persuasive. With respect to Applicant's arguments regarding step 2B, and whether the examiner met the burden demonstrating that the recited ordered combination is well-understood, routine, or conventional, this argument is not persuasive. In step 2B we evaluate whether any additional element or combination of elements are other than what is well-understood, routine, conventional activity in the field, or simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, per MPEP § 2106.05(d). The claims recite the additional element of data outputting, such as “providing”, which perform functions of outputting the data needed to carry out the judicial exceptions. Data output does not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. 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 courts have found that receiving and outputting data are well-understood, routine, and conventional functions of a computer when claimed in a merely generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, as discussed in MPEP 2106.05(d)(II)(i)). Further the computer components described in the specification also notes that computer processors and systems, as example, are commercially available or widely used at [0165-0174]. 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.
7. Applicant submits when viewed as a whole, claims 1 and 17 recite a specific technological solution to a technological problem: identifying regions suitable for designing amplification and detection oligonucleotides across genetically diverse nucleic acid sequences [p. 17, par. 5].
It is respectfully found not persuasive. The examiner acknowledges Applicant’s arguments which set forth that the claims lead to an improvement in oligonucleotide design by reducing the likelihood of selecting regions that are conserved yet unsuitable for amplification or detection. According to the guidance set forth in MPEP 2106, this is an improvement to the judicial exception itself and is not reflected back into a specific technological environment or practically applied process.
Response to Declaration
The declaration under 37 CFR 1.132 filed 07/24/2026 is insufficient to overcome the rejection of claims 1 and 17 based upon the 35 USC § 101 rejection as set forth in the last Office action because:
1. Applicant submits the recited designable regions are not merely informational outputs, but are specifically used as inputs for designing oligonucleotides, such as primers and probes [11].
It is respectfully found not persuasive. The limitation of providing an input is an intended use and is not required to be done with the scope of the claims. Therefore it can not integrate the judicial exception into a practical application.
2. Applicant submits claims 1 and 17 apply biologically grounded constraints to produce regions suitable for actual laboratory use [15].
It is respectfully found not persuasive. The limitation of providing an input is an intended use and is not required to be done with the scope of the claims. Therefore it can not integrate the judicial exception into a practical application.
3. Applicant submits the output of the methods of claims 1 and 17 is not merely informational data, but a designable region that is used for designing primers and probes [16].
It is respectfully found not persuasive. As stated in the remarks “it is an intermediate biological input used in the physical design of primers and probes that are subsequently employed in amplification and detection reactions involving biological samples” [p. 15, par. 2] which describes an abstract idea or data output that is to be used as input for designing primers and probes, however the designing and synthesizing of those primers or probes are not required in the claims.
4. Applicant submits determining a designable region for designing oligonucleotides based on alignment results of such a large number of sequences cannot practically be performed in the human mind [17].
It is respectfully found not persuasive. The human mind is capable of selecting a start position from alignment positions of a plurality of target nucleic acid sequences and selecting as an end position a position further the claims also recite a mathematical concepts of generating an oligonucleotide stick, determining as a designable region of oligonucleotides.
5. Applicant submits the specific technical improvements of claims 1 and 17 are described in the Specification and highlighted in the responses to Office Actions dated 1 August 2025 and 9 December 2025 [21].
It is respectfully found not persuasive. The examiner acknowledges Applicant’s arguments which set forth that the claims lead to an improvement in oligonucleotide design by reducing the likelihood of selecting regions that are conserved yet unsuitable for amplification or detection. According to the guidance set forth in MPEP 2106, this is an improvement to the judicial exception itself and is not reflected back into a specific technological environment or practically applied process.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. 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.
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.
/D.M.B./Examiner, Art Unit 1685
/Soren Harward/Primary Examiner, TC 1600
