DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim status
2. Claims 4-5 and 7-18 are currently pending and under exam herein.
Claims 1-3, 6, and 19-20 are cancelled.
Claims 4-5 and 7-18 are rejected.
Claim 14 is objected to.
Priority
3. Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d). Application is a United States national phase under 35 USC 371 of International Patent Application No. PCT/KR2020/010853 filed August 19, 2020, which in turn claims priority under 35 USC 119 of each of Korean Patent Application No. 10-2019-0101246 filed August 19, 2019, Korean Patent Application No. 10-2019-0160407 filed December 5, 2019, and Korean Patent Application No. 10-2020-0103240 filed August 18, 2020.
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
In this action, all claims are examined as though they had an effective filing date of 08/19/2019. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further analysis of the disclosures of the priority applications.
Drawings
4. The objection to the drawings is withdrawn in view of the amendment to the drawings filed 02 July 2026.
Specification
5. The objection to the specification is withdrawn in view of the amendment to the abstract filed 02 July 2026.
Claim Objections
6. Claim 14 is objected to because of the following informalities: Claim 14(E-i) recites determining a representative FD for an entire chromosomal region or for specific region of a chromosome. This is grammatically incorrect. A possible solution is to correct it to claim “a specific region of a chromosome”. Appropriate correction is required.
Claim Rejections - 35 USC § 112
7. The rejection of claims 19-20 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement has been withdrawn in view of the amendment to the claims filed 02 July 2026. Claims 19 and 20 are cancelled.
The rejection of claim 3 and dependent claims 4-18 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, is withdrawn in view of the amendment to the claims filed 02 July 2026. Claim 3 is cancelled.
The rejection of claim 7 (and dependent claims 8-9 and 12-13) under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, is withdrawn in view of the amendment to the claims filed 02 July 2026.
The rejection of claim 12 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, is withdrawn in view of the amendment to the claims filed 02 July 2026.
The rejection of claim 14 (and dependent claims 15-18) under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, is withdrawn in view of the amendment to the claims filed 02 July 2026.
The rejection of claims 19 and 20 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, is withdrawn in view of the amendment to the claims filed 02 July 2026. Claims 19-20 are cancelled.
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.
The rejection of claims 1-3, 6 and 19-20 under 35 U.S.C. 101 as being not patent eligible is withdrawn in view of the claim amendments filed 2 July 2026. Claims 1-3, 6 and 19-20 are canceled.
8. Claims 4-5 and 7-18 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. This rejection is maintained and any newly recited portions herein are necessitated by claim amendment.
Step 2A, Prong 1
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Claim 4C recites: grouping the sequence information (reads) into whole sequences group, forward sequences group, and reverse sequences group based on an alignment direction, wherein whole sequences group consists of forward sequences group and reverse sequences group
Claim 4D recites: defining Representative Positions of the respective nucleic acid fragments using the grouped sequence information
Claim 4D recites: measuring the distance between the Representative Positions to calculate a fragment distance (FD) for each group
Claim 4E recites: calculating a fragment distance index (FDI) for the entire chromosomal region or specific region of a chromosome based on the FD for each group calculated in step (D)
Claim 4E recites: determining that there is a chromosomal abnormality when all group-specific FDI values fall below or exceed the reference value
Claim 4E recites: wherein the FD of each group in step (D) is calculated as a distance between the Representative Position of an ith nucleic acid fragment and the Representative Position of at least one nucleic acid fragment selected from i+1th to nth nucleic acid fragments among obtained n nucleic acid fragments in each group.
Claim 7 recites: wherein the Representative Position of the nucleic acid fragment is obtained by adding an arbitrary value to a median of the nucleic acid fragment or subtracting the arbitrary value therefrom
Claim 7 recites: wherein the median of the nucleic acid fragment is a center position value of the nucleic acid fragment
Claim 8 recites: wherein, in paired-end sequencing, the Representative Position of the nucleic acid fragment is derived based on position values of forward and reverse reads
Claim 9 recites: excluding nucleic acid fragments having a mapping quality score of reads below a cutoff value from calculation
Claim 10 recites: the method according to claim 4, wherein in single-end sequencing, the Representative Position of the nucleic acid fragment is one type of position value of forward or reverse read
Claim 11 recites wherein an arbitrary value is added when a position value is sequence information aligned in the forward direction and the arbitrary value is subtracted when a position value is on sequence information aligned in the reverse direction
Claim 12 recites: the method according to claim 7, wherein the arbitrary value is 30 to 70% of a mean length of the nucleic acid fragments
Claim 13 recites: the method according to claim 7, wherein the arbitrary value is 0 to 5 kbp or 0 to 300% of a length of the nucleic acid fragment
Claim 14E-i recites determining a representative FD (RepFD) for an entire chromosomal region or for specific region of a chromosome
Claim 14E-ii recites calculating one or more selected from the group consisting of a sum, difference, product, mean, log of product, log of sum, median, quantile, minimum, maximum, variance, standard deviation, median absolute deviation and coefficient of variance of RepFD, reciprocals thereof and a combination thereof in a certain region in the sample, rather than the entire chromosomal region or the specific genomic region of the chromosome, to derive a normalized factor
Claim 14E-iii recites calculating a representative FD ratio (RepFD ratio) based on Equation 1 below; and Equation 1 recites RepFD ratio = RepFD Target genomic region / Normalized Factor
Claim 14E-iv recites comparing the RepFD ratio of a normal reference group with that of the sample to calculate a fragment distance index (FDI)
Claim 15 recites wherein the representative FD (RepFD) of step (E-i) is at least one selected from the group consisting of a sum, difference, product, mean, log of product, log of sum, median, quantile, minimum, maximum, variance, standard deviation, median absolute deviation and coefficient of variance of FDs, and/or a reciprocal thereof
Claim 16 recites wherein the representative FD (RepFD) of step (E-i) is a median, mean, or reciprocal of FD
Claim 17a recites: wherein the certain region in the sample other than the entire chromosomal region or the specific region of the chromosome in step (E-ii) is selected using a method comprising: randomly selecting a region other than an entire chromosomal region or a specific genomic region to be analyzed
Claim 17b recites: determining a representative RepFD of the genomic region selected in step a) with a pre-normalized factor (PNF)
Claim 17c recites: calculating a representative FD ratio (RepFD ratio) based on Equation 2. Equation 2: RepFD ratio = RepFD Target genomic region / PNF
Claim 17d recites: calculating a coefficient of variance (SD/mean) of the RepFD ratio of a normal reference group
Claim 17e recites: determining a genomic region having a smallest value among obtained coefficients of variance obtained by repeatedly performing steps a) to d) as the certain region in the sample, other than the entire chromosomal region or the specific genomic region
Claim 18 recites: comparing the RepFD ratio of the normal reference group with the RepFD ratio of the sample
The limitations regarding: ‘measuring the distance between the Representative Positions’, ‘calculating a distance between representative positions’, ‘calculating a fragment distance index (FDI) for the chromosomal region’, ‘adding or subtracting an arbitrary value to/from a median’, ‘calculating a normalization factor’, and ‘calculating a representative FD’, ‘calculating an FD ratio’, ‘comparing ratios’ to get an FDI’, calculating a fragment distance index (FDI), calculating a representative FD ratio, ‘calculating one or more selected from the group consisting of a sum, difference, product, mean, log of product, log of sum, median, quantile, minimum, maximum, variance, standard deviation, median absolute deviation and coefficient of variance of RepFD and reciprocals thereof’ and ‘calculating a coefficient of variance’ are verbal equivalents that describe mathematical calculations that are performed as the limitation and are so simple that they could be performed with a pen and paper. Therefore, these limitations fall under the “Mathematical concepts” and “Mental process” grouping of abstract ideas.
The limitations for ‘identifying positions of the nucleic acid fragments in a reference genome database’, ‘defining Representative Positions of nucleic acid fragments’, ‘determining a representative FD (RepFD) for a chromosomal region’, ‘grouping the sequence information (reads)’, ‘determining that there is a chromosomal abnormality’, comparing the RepFD ratio, ‘randomly selecting a region’, ‘determining a representative RepFD of the genomic region’, ‘excluding nucleic acid fragments based on mapping quality score’, and determining a genomic region’ are generically recited data analysis steps that can be practically performed in the human mind because the human mind is capable of identifying relevant information, defining values, determining representative values, grouping data, comparing data, excluding data. Therefore, these limitations fall into the “Mental process” grouping of abstract ideas.
Limitations that further limit which nucleic acid fragments are analyzed, the types of sequencing reads used, the chromosomal region being compared, the threshold of arbitrary values that can be added or subtracted to fragment positions, how the fragment distance of each group is calculated, how the ‘median of the nucleic acid fragment’ is defined and the composition of the ‘whole sequence group’ merely further limit the judicial exceptions but do not change the limitations from being “Mathematical concepts” and/or “Mental processes”.
As such, claims 4-5 and 7-18 recite an abstract idea (Step 2A, Prong 1: YES).
Step 2A, Prong 2
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). This judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology or applies or uses the recited judicial exception in some other meaningful way. Rather, the instant claims recite additional elements that amount to mere instructions to implement the abstract idea in a generic computing environment, or insignificant extra-solution activity with generic laboratory tools. Specifically, the claims recite the following additional elements:
Claim 4A recites: a method of detecting a chromosomal abnormality, the method comprising: extracting nucleic acids from a biological sample and obtaining nucleic acid fragments to obtain sequence information therefrom
Claim 4B recites: identifying positions of the nucleic acid fragments in a reference genome database based on the obtained sequence information (reads)
Claim 4B recites: wherein the length of the sequence information (reads) in step (B) is 5 to 5000 bp
Claim 4B recites: wherein the number of sequence information (reads) in step (B) is at least 5000
Claim 5A-i recites: obtaining nucleic acids from blood, semen, vaginal cells, hair, saliva, urine, oral cells, amniotic fluid containing placental cells or fetal cells, tissue cells, and a mixture thereof
Claim 5A-ii recites: removing proteins, fats, and other residues from the collected nucleic acids using a salting-out method, a column chromatography method, or a bead method to obtain purified nucleic acids
Claim 5A-iii recites: producing a single-end sequencing or pair-end sequencing library for the purified nucleic acids or nucleic acids randomly fragmented by an enzymatic digestion, pulverization, or hydroshear method
Claim 5A-iv recites: reacting the produced library with a next- generation sequencer
Claim 5A-v recites: obtaining sequence information (reads) of the nucleic acids in the next-generation sequencer
The limitations for extracting nucleic acids from a biological sample, obtaining nucleic acids from samples, removing proteins, fats, and other residues from the collected nucleic acids, producing a single-end sequencing or pair-end sequencing library for the purified nucleic acids or fragments, reacting the produced library with a next- generation sequencer, obtaining or decoding sequence information (reads) and aligning nucleic acid fragments (or identifying positions of nucleic acid fragments or aligning decoded sequences) merely serve to gather data that is used as an input for the judicial exception. The use of generic laboratory devices for DNA extraction and sequencing and the use of generic tools for sequence alignment do not add a practical application. Supporting the generality of these steps of the claimed method, it is disclosed in the specification that in the present invention, various known devices for sequencing and various known algorithms for sequence alignment may be used (para. 0104 – 0114; para. 0057, 0079). Therefore, these limitations are mere data gathering activities. As set forth in MPEP 2106.05(g), mere data gathering activity has been identified by the courts as insignificant extra-solution activity that does not provide a practical application.
The limitation son claim 4 that further limit the length or the number of reads in the sequencing information, merely further limits the sequencing information gathered, but does not change its position as data gathering activity.
The above recited additional elements do not provide a practical application of the recited judicial exception. As such, claims 4-5 and 7-18 are directed to an abstract idea (Step 2A, Prong 2: NO).
Step 2B
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that equate to mere instructions to apply the recited exception in a generic computing environment or well-understood, routine and conventional activity.
The additional elements recited in the claims amount to well-understood, routine and conventional activity, including:
1) procurement and purification of nucleic acids from biological samples, as described in standard biobanking protocols (Yong, Springer protocols, Methods in Molecular Biology, 2018, p. 1-445, chapters 9-14, 30)
2) preparation of nucleic acid samples for next generation sequencing and conducting next generation sequencing (Yong, Springer protocols, Methods in Molecular Biology, 2018, p. 1-445, Chapter 31)
3) generation of single-end and paired-end sequencing libraries and obtaining sequence information by next-generation sequencing (Head et al. BioTechniques, Vol 52, No. 2, 2014, p. 61-77)
4) alignment of nucleic acid fragments to a genomic sequence (Yong, Springer protocols, Methods in Molecular Biology, 2018, p. 1-445, Chapter 29 and 31) and
5) storing and retrieving information in memory, Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93.
Furthermore, it is stated in the specification of the instant application that the present invention uses Next-generation sequencing known in the art that is commercially available (para. 0057, 0079). As such, the combination of additional elements recited in the claims is well-understood, routine and conventional.
The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: No). As such, claims 4-5 and 7-18 are not patent eligible.
Response to Arguments
Regarding claims 4-5 and 7-18, applicants arguments filed 02 July 2026 have been fully considered but they are not persuasive.
Argument 1: the claims integrate the judicial exception into a practical application (at Step 2a, Prong 2)
The applicant asserts that the amendments to claims 4-5 and 7-18 adds the technical improvement to NGS-based detection of a chromosomal abnormality by reducing false positives and enhancing accuracy and thus integrating the abstract idea into a practical application because it is an improvement to technology.
Response to argument: As set forth in the MPEP 2106.05(a)(II), while the assessment of improvement to technology considers the claims as a whole, an improvement in the abstract idea itself is not an improvement in technology. Instead, the improvement must be in the additional elements. In the instant application, the asserted improvement to technology is in the data analysis steps (i.e. the abstract idea), whereas there is no asserted improvement to the additional elements, which include standard nucleic acid extraction, sequencing and alignment of nucleic acid fragments.
Claim Rejections - 35 USC § 102
The rejection of claims 1-3 and 19-20 under 35 U.S.C. 102(a)(1) and 102(a)(2) as being unpatentable over Talkowski et al. (US 2015/0286773 A1; 4/11/2023 IDS Document, previously cited) is withdrawn in view of the claim amendments filed 2 July 2026. Claims 1-3 and 19-20 are canceled.
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.
The rejection of claim 6 under 35 U.S.C. 103 as being unpatentable over Talkowski et al. (US 2015/0286773 A1; 04/11/2023 IDS document, previously cited), as applied to claims 1-3 above, as evidenced by Kappal (Compilation 1.0, Vol. 19, Iss. 4, p. 39-44, previously cited) is withdrawn in view of the claim amendments filed 2 July 2026. Claim 6 is canceled.
9. Claims 4-5 and 14-18 are rejected under 35 U.S.C. 103 as being unpatentable over Talkowski et al. (US 2015/0286773 A1; 04/11/2023 IDS document, previously cited), as evidenced by Kappal (Compilation 1.0, Vol. 19, p. 39-44, previously cited). The italicized text corresponds to the instant claim limitations. This rejection is maintained and any newly recited portions herein are necessitated by claim amendment.
Regarding claim 4, Talkowski et al. teaches a method of detecting a chromosomal abnormality (abstract; para. 0011; a method of detecting a chromosomal abnormality).
Regarding claim 4A, Talkowski et al. discloses extracting genomic DNA from cells in an amniotic fluid sample and obtaining nucleic acid fragments from the genomic DNA. Talkowski et al. further discloses using paired-end sequencing, de novo sequencing, next generation sequencing or another technology to sequence the fragmented large-insert jumping library (para. 0007, 0041-0043, 0060; (A) extracting nucleic acids from a biological sample and obtaining nucleic acid fragments to obtain sequence information therefrom).
Regarding claim 4B, Talkowski et al. disclose that paired-end sequence reads obtained from the whole-genome sequence analysis are aligned against sequence of at least one or more chromosomes. Talkowski et al. further discloses that the mapping positions of aligned fragments are used for structural variant identification (para. 0011, 0064; (B) identifying positions of the nucleic acid fragments in a reference genome database based on the obtained sequence information (reads)).
Regarding claim 4B, Talkowski et al. discloses that in an execution of the method, each aligned pair allowed assessment of a chromosomal region corresponding to the original fragment size (median, 1914 bp; standard deviation, 369 bp) (para. 0209; wherein the length of the sequence information (reads) in step (B) is 5 to 5000 bp).
Regarding claim 4B, Talkowski et al. discloses that the method was executed using large-insert, paired-end sequencing of DNA from cells in the amniotic fluid generated 282,294,280 individual reads (141 million pairs) (para. 0209; wherein the number of the sequence information (reads) in step (B) is at least 5000).
Pertaining to claim 4C, Talkowski et al. discloses that all read-pairs with both ends mapped are categorized by variant types (i.e. groups), which can include (but are not limited to): 1) inversion pairs, which are read-pairs where the same DNA strand orientation on both sides indicating pairs that span a putative inversion . These read pairs are in forward-forward (FF) or reverse-reverse (RR) orientation; 2) deletion pairs, which are read-pairs where the two sides represent the breakpoint of a deletion. These read pairs are in forward-reverse (FR) relative orientation; 3) tandem-duplication pairs, which are read-pairs where the two sides represent one breakpoint of a tandem duplication. These read pairs are in reverse-forward (RF) orientation. Talkowski et al. further disclose that all of the categorized read-pairs with both ends mapped in each of the variant types can then be clustered (for example by hierarchical clustering based on insert size distribution) and each cluster is processed to separate distinct orientation pairs (e.g. FF, RR, FR, RF) into separate clusters (groups) to categorize multiple derivative breakpoints of a putative structural variant event (para. 0301 - 0314; (C) grouping the sequence information (reads) into whole sequences group, forward sequences group, and reverse sequences group based on an alignment direction, wherein whole sequences group consists of forward sequences group and reverse sequences group).
With respect to claim 4D, Talkowski et al. discloses that the categorized clusters (i.e. FF, RR, FR and RF) are further analyzed to determine the validity of the clusters (groups) of read-pairs representing a true structural variant using a Random forest classifier. Talkowski et al. further discloses using features for each cluster for classification and that features can include “span” which is the distance between the maximum and minimum mapping positions on both ends of a cluster. In this example, mapping position are equivalent to representative positions and “span” is equivalent to fragment distance (FD) (para. 315 – 329; (D) defining Representative Positions of the respective nucleic acid fragments using the grouped sequence information, and measuring the distance between the Representative Positions to calculate a fragment distance (FD) for each group).
Pertaining to claim 4E, fragment distance index (FDI) is interpreted to be a metric based on fragment distance (FD) to make a determination about the entire chromosomal region or a specific genomic region as to whether there is a chromosomal abnormality or not, wherein there is an abnormality when FDI does not fall within a cutoff value range (see para. 0015 of specification). Furthermore, as indicated in para. 0044 of the specification, FDI can be based on a comparison of values between of the sample with normal subjects.
Regarding claim 4E, Talkowski et al. disclose that each feature (including span which is equivalent to fragment distance) that was calculated for all clusters (i.e. all groups) is input into a pre-trained Random Forest classifier which outputs a probability for each cluster representing validity or invalidity of a cluster in describing a true structural variant in the underlying DNA. In this teaching by Talkowski et al. the classifier score teaches the FDI, which can indicate presence or absence of an abnormality based on exceeding or falling below a reference value (established by pretraining the classifier with case and control samples/inter sample comparisons) (para. 315-328; 0331; Table 4; (E) calculating a fragment distance index (FDI) for the entire chromosomal region or specific region of a chromosome based on the FD for each group calculated in step (D).
The threshold of determining that there is a chromosomal abnormality when all group-specific FDI values fall below or exceed the reference value, was not specifically disclosed by Talkowski et al., but this would be obvious to try because Talkowski et al. discloses that there is a need to rapidly localize breakpoints of cytogenetically balanced chromosomal rearrangements to individual genes, which can improve prediction of phenotypic outcomes and inform postnatal medical care (para. 0005). In addition, there was a finite number of identified, predictable potential solutions to the need; that is, the threshold of calling a chromosomal abnormality could be to 1) call a valid abnormality if one or more cluster-specific classifier scores exceeded/fell below the threshold or 2) call a valid chromosomal abnormality if all of the group-specific classifier scores exceeded/fell below the threshold. A person having ordinary sill in the art could have pursued the known potential solutions with a reasonable expectation of success as all aspects of identifying the chromosome anomaly have been taught by Talkowski et al. except for selecting which of the two or three optional thresholds would be used (see MPEP 2143(I)(E)). The invention is therefore prima facie obvious.
Regarding claim 4, Talkowski et al. discloses clustering read pairs categorized as anomalous at a putative structural variant break point and calculating the distance between the maximum and minimum mapping positions on both ends of the cluster, and using these data to determine presence of a valid structural rearrangement. Clustering multiple reads together and calculating the distance between the maximum and minimum position (i.e. the span) is a method measuring distance between Representative Positions between different nucleic acid fragments (para. 0315-0328; 0010-0011 and 0094c; wherein the FD of each group in step (D) is calculated as a distance between the Representative Position of an ith nucleic acid fragment and the Representative position of at least one nucleic acid fragment selected from I + 1th to nth nucleic acid fragments among obtained n nucleic acid fragments in each group).
Regarding claim 5, Talkowski et al. discloses examples of tissue that can be used for extraction of genomic DNA can include, but are not limited to, blood, lung, heart, liver, skin, pancreas, or tissue of any organs (A-i). Talkowski et al. discloses that after PCR amplification, DNA libraries are purified using a magnetic stand to separate post-PCR solution from the beads using a purification kit (such as Qiagen PCR purification column), and further purifying by gel extraction using a Qiagen gel purification reagents (A-ii). Talkowski et al. further discloses that the large-insert jumping library can be generated by paired-end sequencing and that the library can be produced by shearing genomic DNA or by partial or complete digestion with endonucleases or restriction endonucleases (A-iii). Talkowski et al., discloses that the library can be sequenced using a next-generation sequencer (A-iv) and that raw sequencing reads are collected (A-v) (para. 0043, 0060, 0074, 0268-0269, 0280, wherein the step (A) comprises:(A-i) obtaining nucleic acids from blood, semen, vaginal cells, hair, saliva, urine, oral cells, amniotic fluid containing placental cells or fetal cells, tissue cells, and a mixture thereof, (A-ii) removing proteins, fats, and other residues from the collected nucleic acids using a salting-out method, a column chromatography method, or a bead method to obtain purified nucleic acids; (A-iii) producing a single-end sequencing or pair-end sequencing library for the purified nucleic acids or nucleic acids randomly fragmented by an enzymatic digestion, pulverization, or hydroshear method; (A-iv) reacting the produced library with a next-generation sequencer; and (A-v) obtaining sequence information (reads) of the nucleic acids in the next-generation sequencer).
Regarding claim 14, according to para. 0044 of the specification, RepFD is interpreted to comprise the fragment distance (FD) of a group, where groups are based on direction of reads of the read pairs (which can be forward groups, reverse groups or whole groups with forward and reverse) and RepFD ratio is a normalized version of RepFD.
Regarding claim 14 limitation E(i), Talkowski et al. discloses mapping read-pairs of the sequence data against a reference genome and categorizing the read-pairs into clusters based on at least one common feature and measuring at least two or more features of the remaining read-pair clusters, wherein said features can include the distance between the maximum and minimum mapping positions on both ends of the cluster (span) (para. 0010-0011; 0315-0328; (E-i) determining a representative FD (RepFD) for an entire chromosomal region or for specific region of a chromosome).
Regarding claims 14 limitations E (ii-iv) and claim 18, FDI interpretation is indicated above in section pertaining to claim 4E. Talkowski et al. discloses a computational pipeline with various modules for identifying structural variants from the aligned sequence data by comparing fragment distances of potentially anomalous groups to those of normal reference groups. Talkowski et al. discloses identifying and categorizing as ‘anomalous’, read pairs that align to genomic sequences separated by significantly greater than or less than the size of the DNA fragments selected for library creation and grouping anomalous read pairs into clusters of fragments representing putative structural variant breakpoints. Two analyses are disclosed to characterize these clusters that embody calculating an FDI. First, Talkowski et al. discloses analyzing a clusters by determining a normalized distance between the maximum and minimum mapping positions on both ends of cluster calibrated to the library size (i.e. average fragment size) and analyzing these data using a random forest classifier to determine if the putative anomaly is valid or invalid (with probability assignments). Second, Fragments representing a putative chromosomal abnormality (with abnormal distances) are grouped separately from fragments in the same chromosomal position representing a normal (or ‘proper’) chromosome (with the expected distances). The ratio of the number fragments with abnormal distances to the number of proper fragments (both locally and globally) is calculated. Talkowski et al. further discloses that these distances and ratios are used to classify the presence or absence of a structural variant in a region of DNA (with probability assignments). This can be done using a random forest classification program including inter-sample comparisons to control samples. In both embodiments, the probability of a valid variant assigned by the classifier is equivalent to an FDI (para. 0010-0011, 0064, 0208-0209, and 0279-0331; (E-ii) calculating one or more selected from the group consisting of a sum, difference, product, mean, log of product, log of sum, median, quantile, minimum, maximum, variance, standard deviation, median absolute deviation and coefficient of variance of RepFD, reciprocals thereof and a combination thereof in a certain region in the sample, rather than the entire chromosomal region or specific region if the chromosome, to derive a normalized factor), (E-iii) calculating a representative FD ratio (RepFD ratio) based on Equation 1 below: Equation 1: RepFD ratio = RepFD Target genomic region / Normalized Factor); (E-iv) comparing the RepFD ratio of a normal reference group with that of the sample to calculate a fragment distance index (FDI)); claim 18, wherein step (E-iv) comprises comparing the RepFD ratio of the normal reference group with the RepFD ratio of the sample).
Talkowski et al. is silent to the specific RepFD normalization step disclosed to derive a normalization factor from a ‘certain region of the sample’ and specifically divide RepFD by this factor to get the RepFD ratio. In the first embodiment of FDI disclosed by Talkowski et al., the distance between the maximum and minimum mapping positions on both ends of cluster is normalized to the library size (i.e. the average fragment size of the library) to get the value corresponding to RepFD ratio. As evidenced by Kappal, normalization indicates division by the normalization factor (p. 39, sect. I, para. 1 ). However, the claimed method indicates that the normalization must be to one of the listed characteristics of RepFD in a certain region of the sample. The RepFD ratio calculated by Talkowski et al. can simply be substituted for the RepFD ratio of the instant application because it would yield effectively the same value. This is because it is disclosed in the specification that the certain region can be selected randomly (para. 00163 and 0239) and the ‘average fragment size of the library’ used by Talkowski et al. is effectively the same as a mean or median representative fragment distance in a randomly selected region of the alignment. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the invention to substitute the RepFD ratio of the instant application with those of Talkowski et al. to measure length variation in a structural variant sample to identify structural variants. Furthermore, one of ordinary skill in the art would predict that the RepFD ratio taught by Talkowski et al. could be readily be substituted in the system of the present invention with a reasonable expectation of success because both inventions pertain to structural variant calling in diploid organisms by fragmenting, sequencing and genome alignment, followed by analysis of grouped aligned reads. The invention is therefore prima facie obvious.
Regarding claim 15, Talkowski et al., discloses that the representative fragment distance of a cluster of read-pairs representing a putative ‘breakpoint’ can be calculated as the maximum FD of the cluster. This is calculated by calculating the Span, which is the distance between the maximum and minimum mapping positions on both ends of a cluster of reads, which corresponds to the maximum FD of the cluster in the instant application (para. 0011, 0317, 0322; wherein the representative FD (RepFD) of step (E-i) is at least one selected from the group consisting of a sum, difference, product, mean, log of product, log of sum, median, quantile, minimum, maximum, variance, standard deviation, median absolute deviation and coefficient of variance of FDs, and/or a reciprocal thereof).
With respect to claim 16, Talkowski et al. discloses that in some embodiments, a variant call is made by using a categorizing analysis program (e.g., BamStat) and clustering analysis program (e.g. readPairCluster) to generate output clusters where each output cluster generally represents a putative structural variant breakpoint. In some embodiments these clusters are further analyzed to determine validity of the variants using machine learning machine learning. The data input into these algorithms includes insert size measurements such as mean and median insert sizes for FR and RF read-pairs, as well as standard deviation and median absolute deviation, respectively, of all proper-pairs found in the file (para. 0279-0315; wherein the representative FD (RepFD) of step (E-i) is a median, mean, or reciprocal of FDs).
Concerning claim 17 limitations a-c, Talkowski et al., discloses an example bioinformatic pipeline for whole-genome analysis that identifies structural variations in any region without pre-selecting a specific region. Talkowski et al. further discloses categorizing anomalous read pairs into the same cluster if both sides of the read pairs align within a selected distance of each other; wherein each output cluster represents a putative structural variant breakpoint. Talkowski et al. further discloses calculating a distance and a normalized distance between the maximum and minimum mapping positions on both ends of the cluster (corresponding to RepFD and RepFD ratio). The normalization can be done to calibrate the distance (or span) measurement to the current library size (para. 0010-0011, 0279-0315, and 0323; the method according to claim 14, wherein the certain region in the sample other than the entire chromosomal region or the specific region of the chromosome in step (E-ii) is selected using a method comprising: a) randomly selecting a region other than an entire chromosomal region or a specific genomic region to be analyzed; b) determining a representative RepFD of the genomic region selected in step a) with a pre-normalized factor (PNF); c) calculating a representative FD ratio (RepFD ratio) based on Equation 2: Equation 2: RepFD ratio = RepFD Target genomic region / PNF.
Regarding claim 17 limitations d-e, Talkowski et al. teaches for (forward-reverse) and (reverse-forward) read-pairs, calculating mean and median insert sizes, as well as standard deviation and median absolute deviation, respectively, of all proper-pairs (which correspond to normal references) (para. 300; d) calculating a coefficient of variance (SD/mean) of the RepFD ratio of a normal reference group; and e) determining a genomic region having a smallest value among obtained coefficients of variance obtained by repeatedly performing steps a) to d) as the certain region in the sample, other than the entire chromosomal region or the specific genomic region).
Talkowski et al. discloses using a variety of statistical tests in identification of structural variants, but is silent to specifically calculating coefficient of variance and determining a genomic region having a smallest value to determine a certain region of the sample. However, these steps are directed to identifying a genomic region to use as a normal reference for comparing to those with putative structural variants and Talkowski et al. proposes an alternative method that could be simply substituted. Talkowski et al. discloses that within one genomic region of an alignment of a sample with a reference genome, fragments representing a putative chromosomal abnormality (with abnormal distances) are grouped separately from a group of fragments in the same chromosomal position representing a normal (or ‘proper’) chromosome (with the expected distances). Therefore, in comparing the putative anomalous reads to proper normal reads, identifying a region of low variance of the normal reference is not necessary because the same region is used for both proper and anomalous reads. (para 0011, 0316-0328; d) calculating a coefficient of variance (SD/mean) of the RepFD ratio of a normal reference group; and e) determining a genomic region having a smallest value among obtained coefficients of variance obtained by repeatedly performing steps a) to d) as the certain region in the sample, other than the entire chromosomal region or the specific genomic region).
The method of Talkowski et al. for identifying a genomic region to use as a normal reference region is different from that in the instant application, but both methods effectively identify a normal region to use as a control for comparison to putative variants. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the invention to substitute the components of the instant application with those of Talkowski et al. to identify normal reference regions. Furthermore, one of ordinary skill in the art would predict that the normal regions used by Talkowski et al. could be readily be substituted in the system of the present invention with a reasonable expectation of success because both inventions pertain to structural variant calling in diploid organisms by fragmenting, sequencing and genome alignment, followed by analysis of grouped aligned reads. The invention is therefore prima facie obvious.
10. Claims 7-13 are rejected under 35 U.S.C. 103 as being unpatentable over Talkowski et al. (US 2015/0286773 A1; 04/11/2023 IDS document, previously cited), as applied to claims 4-5 and 14-18 above, as evidenced by Kappal (Compilation 1.0, Vol. 19, p. 39-44, previously cited) and further in view of Zhang et al. (Genome biology, 2008, vol. 9 issue 9, R137.1-R137.9, previously cited). The italicized text corresponds to the instant claim limitations. This rejection is maintained and any newly recited portions herein are necessitated by claim amendment.
The limitations of claims 4-5 and 14-18 have been taught by Talkowski et a. as indicated above.
Claims 7 and 10-13 are directed to estimating the center position of a nucleic acid fragment in an alignment based on mean or median fragment length of the library (for example in single-end (SE) sequencing). Talkowski et al. is silent to estimating the center position of a fragment based adding or subtracting a value to the either the forward or reverse read positions based on the mean or median fragment length in claims 7 and 11-13 . However, these limitations were known in the art at the time of the effective filing date of the invention, as taught by Zhang et al.
[AltContent: textbox (Figure 1. Estimating fragment position from Watson or Crick strand tags. Zhang et al.)]
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Regarding claims 7 and 11-13, Zhang et al. teaches a method of estimating fragment position in an alignment using the binding position of either a Watson strand tag or a Crick strand tag (forward or reverse primers) in MACS software for analyzing ChIP-Seq data. For high-quality peaks (fragment clusters), MACS separates their Watson and Crick tags, and aligns them by the midpoint between their Watson and Crick tag centers (if the Watson tag center is to the left of the Crick tag center). The distance between the modes of the Watson and Crick peaks in the alignment is defined as 'd', and MACS shifts all the tags by d/2 toward the 3' ends to the most likely protein-DNA interaction sites. In this example, the value added or subtracted is 63 bp, which is 31.5% of the mean fragment length of 200 bp (R137.2, para. 4-5, Fig. 1a, Fig. 1 of this office action; claim 7: wherein the Representative Position of the nucleic acid fragment is obtained by adding an arbitrary value to a median of the nucleic acid fragment or subtracting the arbitrary value therefrom; claim 11: wherein an arbitrary value is added when a position value is derived based on sequence information aligned in the forward direction and the arbitrary value is subtracted when a position value is derived based on sequence information aligned in the reverse direction; claim 12: wherein the arbitrary value is 30 to 70% of a mean length of the nucleic acid to be analyzed; claim 13: wherein the arbitrary value is 0 to 5 kbp or 0 to 300% of a length of the nucleic acid fragment).
An invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the invention if some motivation in the prior art would have led that person to combine the prior art teachings to arrive at the claimed invention. Zhang et al. taught that empirically modeling the distance d and shifting tags by d/2, improved the spatial resolution of the predicted sites over previous algorithms (p. R137.8, para. 1). Therefore, one of ordinary skill in the art would have been motivated to utilize the method of Zhang et al. to the method of detecting chromosomal abnormalities taught by Talkowski et al. in order to improve spatial resolution of the predicted positions of the fragments in the alignment and thus improve mapping of structural variants. Furthermore, one of ordinary skill in the art would predict that the alignment method taught by Zhang et al. could be readily added to the system of Talkowski et al. with a reasonable expectation of success because they both pertain to mapping position of fragments to a reference genome. The invention is therefore prima facie obvious.
Pertaining to claim 8,Talkowski et al. discloses that read-pairs of the sequence data are mapped against a reference genome and categorizing as anomalous, those read pairs that align to genomic sequences separated by significantly greater than or less than the size of the DNA fragments selected for library creation. This method requires calculating the positions of both forward and reverse reads for the sequenced fragment (para. 0010; wherein, in paired-end sequencing, the Representative Position of the nucleic acid fragment is derived based on position values of forward and reverse reads).
Regarding claim 9, Talkowski et al. discloses an example analysis pipeline of cluster identification and filtering wherein reads were filtered to remove those with mapping quality lower than a minimum of Q20 (para. 0015 and 0205; comprising excluding nucleic acid fragments having a mapping quality score of reads below a cutoff value from calculation).
Regarding claim 10, Talkowski et al. teaches that their method of variant detection is compatible with SE sequencing platforms including massively parallel signature sequencing (MPSS), pyrosequencing and microfluidic Sanger sequencing, and thus in these cases, position would be based on one type of position value (forward or reverse). Talkowski et al. also discloses calculating mean and median insert sizes and that in calculating the distance between aligned read pairs, the distance can be determined based on the median and variance of the original size selected fragments (para. 0060, 0066 and 0300; claim 10: wherein in single-end sequencing, the Representative Position of the nucleic acid fragment is derived based on one type of position value of forward or reverse read).
Response to Arguments
Applicant’s argument filed 2 July 2026 have been fully considered but they are not persuasive.
Response to argument that none of the references teach calculating fragment distance as in the claimed invention (claim 4D)
Applicant argues that based on para. 0064 and claim 3 of Taklowski et al., that the prior art does not teach calculating the distance between read pairs (i.e. inter-pair comparisons), rather they only teach calculating distance between the reads inside the read pair (i.e. intra-pair comparisons). Applicant further asserts that the method disclosed by Tallkowski et al. uses a size selected library in generating sequences; therefore, they cannot be using inter-pair comparisons in their method (see response to OA, p. 14, para. 1-5).
Response: This argument is not persuasive because, while Talkowski et al. teaches intra-pair comparisons in para. 0064, they also teach inter-pair comparisons in many other locations in the disclosure, where they describe distances between the maximum and minimum mapping positions on both ends of the cluster (for example, para. 0011). The argument pertaining to use of a size selected library is not persuasive as restrictions on use of such library was not a limitation of the claimed invention and does not preclude using inter-pair comparisons. New grounds of rejection of claim 4 and dependent claims is made in in view of the claim amendments.
Response to argument that Talkowski et al. does not teach dividing reads into three groups based on their direction (i.e. forward, reverse, or forward and reverse) (claim 4C-D)
Applicant argues that none of the 3 references alone or in combination, teach dividing reads into three groups based on direction (i.e. forward, reverse, or forward and reverse), and calculating the FD and FDI for each group and using this information to predict a chromosomal abnormality based on a specific threshold. Applicant further asserts that the method of the instant application has very high sensitivity and specificity for detecting chromosomal abnormalities (see response to OA, p. 15, para. 1-6).
Response: This argument is not persuasive because the limitation is taught by Talkowski et al. as indicated in the rejection of amended claim 4 above. The argument pertaining to the performance of the detection of chromosomal abnormalities is a moot point as a performance threshold was not a limitation of the claimed invention. New grounds of rejection of claim 4 and dependent claims is made in in view of the claim amendments.
Double Patenting
11. The provisional rejection of claims 1 and 3 on the ground of nonstatutory double patenting as being unpatentable over claims 4 and 8 of copending Application No. 17/780,813 is withdrawn in view of the claim amendments filed 2 July 2026. Claims 1 and 3 have been cancelled.
Conclusion
12. No claims are allowed.
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.
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/J.J.S./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
