DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
The claims filed 12/2/2025 are under consideration.
The amendments and arguments presented in the papers filed 12/2/2025 ("Remarks”) have been thoroughly considered. The issues raised in the Office action dated 6/3/2025 listed below have been reconsidered as indicated.
a) The rejections of claims 7, 8, 13, 14-17, 21, 24-25, 28, 39, 41, 45-46, 52, 53, 59, 72 and 79 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, are withdrawn in view of the amendments to the claims.
The Examiner’s responses to the Remarks regarding issues not listed above are detailed below in this Office action.
New and modified grounds of rejection necessitated by amendment are detailed below and this action is made FINAL.
Priority
The present application is a continuation-in-part of PCT/US2020/063786, which claims benefit of us provisional application 62/945,850.
The ‘786 PCT application and the ‘850 provisional application do not provide support for the present claims.
The present claims recite “contacting a pair of single-stranded sister chromatids with two or more pools of single-stranded oligonucleotides”. The ‘786 PCT application describes such probes a being within a “directional genomic hybridization”, which is defined in para. 165 stating:
As used herein, “directional genomic hybridization” or “dGH” refers to a method of sample preparation combined with a method of probe hybridization whereby (1) a DNA analog (BrdU) is provided to an actively dividing cell for one-replication cycle and is incorporated At selectively into the newly synthesized daughter strand; (2) a metaphase spread is prepared; (3) the incorporated analog is targeted photolytically to achieve DNA nicks which are used selectively to enzymatically digest and degrade the newly synthesized strand; (4) the single stranded metaphase spread is hybridized in situ with uni-directional probes that are designed against unique sequences of a reference genome such that only one single-stranded sister chromatid of the metaphase chromosome is labeled at the unique target site or sites.
The present application defines a “directional genomic hybridization” in para. 33 stating:
As used herein, “directional genomic hybridization” or “dGH” refers to a method of sample preparation, such that the sister chromatids of a metaphase spread become single-stranded, combined with a method of hybridization with a dGH probe made up of a pool of single-stranded oligonucleotides before chromosome visualization using fluorescent microscopy. Further details regarding dGH and a dGH reaction are provided herein.
Thus, the ‘786 PCT application does not support the full scope of the present claims because the present claims are broader than those in the ‘786 PCT application.
The present application does not provide a limiting definition for the term “single-stranded sister chromatids”. The ‘786 PCT application defines “single stranded chromatids” in para. 171 stating:
As used herein, “single stranded chromatid” refers to the product of the process in which a DNA analog (e.g BrdU) is provided to an actively dividing cell for a single replication cycle, which is then incorporated selectively into the newly synthesized daughter strand ,a metaphase spread is prepared, the incorporated analog is targeted photolytically to achieve DNA nicks which are used to selectively to enzymatically digest and degrade the newly At synthesized strand, resulting in a single-stranded product. If we use the terms Watson and Crick to describe the 5’ to 3’ strand and 3’ to 5’ strand of a double-stranded DNA complex, an untreated metaphase chromosome will have one sister chromatid with a parental Watson/ daughter Crick, one sister chromatid with a daughter Watson/parental Crick. In the chromosomes prepared according to the method above, one sister chromatid will consist of the Parental Watson strand only, and the other sister chromatid will consist of the parental Crick strand only.
Thus, the ‘786 PCT application does not support the full scope of the present claims because the present claims encompass a broader scope of “single-stranded sister chromatids” than those defined in the ‘786 PCT application.
The present claims recite “each pool comprises a same fluorescent label of a set of fluorescent labels”. This language is not recited in the ‘786 PCT application.
The present claims recite “each single stranded oligonucleotide of a pool binds a different complementary DNA sequence within a same target DNA sequence found on one of the single-stranded sister chromatids, wherein at least two of the two or more pools each binds to a different target DNA sequence on one of the single-stranded sister chromatids and each comprises a fluorescent label of a different color”. This language is not recited in the ‘786 PCT application.
The present claims recite “generating a fluorescence pattern from one or both single-stranded sister chromatids using fluorescence detection, wherein the fluorescence pattern is based on a hybridization pattern of the two or more pools to one or both single-stranded sister chromatids of the pair”. This language is not recited in the ‘786 PCT application.
The ’850 provisional also does not provide support for the full scope of the present claims for the same reasons described above.
Drawings
The petition for color drawings was granted on 12/16/2022.
Claim Objections
Claim 13 is objected to because of the following informalities: as amended claim 13 states “which each pool a same fluorescent baled of a set of fluorescent labels”. As annotated the word “pool” is both underlined and struck-through, so it unclear based on the annotations whether term is being added or deleted. Based on the prior claim set, it appears the term is intended to be added. Also, it appears the word “comprises” is missing from the phrase
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 7, 8, 4, 15, 16, 17, 21, 24, 25, 28, 39, 41, 46, 52, 53, 59, 72 and 79 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
The following are new rejections necessitated by the amendments to the claims.
Regarding claim 7, the amended claim recites “wherein the method is capable of detecting de novo structural variants and differentiating a true inversion event from a sister chromatid exchange event”. The clause sets forth a property and/or result of the claimed method. It is unclear what additional elements, if any are required, in order to confer the method with this property and/or to yield the recited result.
Claims 8, 4, 15, 16, 17, 21, 24, 25, 28, 39, 41, 46, 52, 53, 59, 72 and 79 depend from claim 7 and are rejected for the same reason.
Response to the traversal of the 112(b) rejections
The Remarks argue the amendments address the prior rejections (p. 11).
The prior 112(b) rejections have been withdrawn. However, the claims remain rejected for the reasons provided above in view of the amendments to the claims. The arguments do not address above rejections.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 7, 14, 15, 16, 24, 25, 28, 39, 41, 45, 46, 52, 53 and 59 is/are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Ray (WO 2014/008425 A1; cited on the 10/24/2024 IDS).
The following are new rejections necessitated by amendment. While the Ray reference was previously applied, a different analysis of the reference is applied in view of the amendments.
Regarding claim 7, Ray teaches directional genomic hybridization reactions (See entire document).
Ray teaches contacting a pair of single-stranded sister chromatids in a metaphase spread from a cell with pools directional hybridization probes (Fig. 5D; and para. 50). See also Fig. 1; and Fig. 2.
The probes pools have the same fluorescent label (e.g., “red” or “green”), where fluorescent labels are different between probe pools (Fig. 5D; and para. 50). See also Fig. 2.
The probes of the pools are complementary to a portion of a larger genomic target region within a single-stranded chromatid, and are “tiled” along the target in order to “paint” the target (Fig. 5D). See also, Fig. 2.
The probes of the pools a complementary to different target regions and are labeled with different labels (Fig. 5D; and para. 50). See also, Fig. 2.
Ray teaches generating a fluorescence pattern based on a hybridization pattern of the probes to one or both the single-stranded sister chromatids (Fig. 5D). See also, Fig. 2; and Fig. 3.
Ray teaches detecting the presence of a structural variation in the chromosome of the cell based on the fluorescence pattern (Fig. 5D). See also, Fig. 2; and Fig. 3.
Ray teaches all the active method steps and structures required by the method of claim 7, and thus, is deemed to have the property recited in the final amended “wherein” clause and/or is deemed sufficient to produce the result recited in the final amended “wherein” clause.
It is also noted in para. 50, Ray teaches the following:
However, it has surprisingly been determined that much smaller inversions can be detected. We designed a mock "mini-inversion" within a 10 Mb region of the large contig of chromosome 3q. Probe sets covering the region were tagged with fluorescein (green); excluded from coverage was a contiguous 6kb segment nested within the region. For this nested segment, oligos were intentionally designed in the reverse orientation, synthesized and tagged with Cy3 (red). The result (FIG. 5D) is a "simulated" 6kb inversion, which serves to further validate the methodology, provides a useful reference marker, and demonstrates that even quite small inversions are cytogenetically detectable, provided that probe coverage is sufficiently dense. In fact, the only limitation with respect to how small an inversion can be detected by the presently disclosed methods and kits is any lower limit on the detection equipment's ability to visualize a signal from the probes hybridized to the chromatid within the inverted region.
This demonstrates that Ray had possession of probe pools that are capable of detecting de novo structural variants and differentiating a true inversion event from a sister chromatid exchange event. For example, Fig. 5D demonstrates staining of a sister chromatid exchange event. However, if the cell had contained a “true inversion event”, the “red probes” would hybridize between the “green” regions as the region targeted by the “red probes” would be present in both chromatids. Because the probe pool, which is a collection of individual probes, spans a region, de novo “true inversions” within this region may be identified. Alternatively, inversions may be detected within the “green” regions, based on the presence of gaps in staining without a corresponding staining pattern in the sister chromatid.
Regarding claims 14-16, Ray teaches the labeled probe pools as described above. The probes are capable producing the results recited in the claims for the reasons provided above.
Regarding claim 24, Ray teaches measuring fluorescent intensities (para. 50; and Fig. 5D), which would be measuring intensities at the wavelength of the fluorescent label. See also, para. 52; and Fig. 6A-B.
Regarding claim 25, Ray teaches measuring the intensities of “red” and “green” along a single-stranded chromatid (Fig. 2, 3 and 5), forming a “spectral fingerprint” for the chromatid.
Regarding claim 28, Ray teaches detecting as noted above the location or “density” of probes along the single-stranded chromatid to detect the structural variation.
Regarding claims 39 and 41, Ray teaches the target regions bound by the probes are consecutive target regions as noted above (para. 75), including a 65 kb. These regions include regions as small as 1,000 nucleotides.
Ray teaches all the steps and structures required by the steps, and as a consequence is able to achieve the property of claim 39 as recited.
Regarding claims 45 and 46, Ray teaches detecting a structural variation as described above.
Ray teaches all the steps and structures required by the steps, and as a consequence is able to achieve the property of claims 45 and 46 as recited.
Regarding claim 52, Ray teaches detecting an inversion as a structural variation (Fig. 2, 3 and 5).
Regarding claims 53 and 59, Ray teaches probes of the pools have length of 20 bases and has 10, 50, 100, 150 or more oligonucleotides (para. 39).
Response to the traversal of the 102 rejections
The Remarks argue claim 7 has been amended to recite that the "method is capable of detecting de novo structural variants and differentiating a true inversion event from a sister chromatid exchange event" and the methods taught by Ray are insufficient for detection of de novo structural events and differentiation of true inversion events versus sister chromatid exchange events. The Remarks further argue Ray describes targeted dGH and monochrome dGH and the present specification clearly enumerates the distinctions between the presently claimed method and the monochrome dGH method as taught by Ray. See p. 7.
The arguments have been fully considered but are not persuasive. As noted above, in para. 50, Ray teaches the following:
However, it has surprisingly been determined that much smaller inversions can be detected. We designed a mock "mini-inversion" within a 10 Mb region of the large contig of chromosome 3q. Probe sets covering the region were tagged with fluorescein (green); excluded from coverage was a contiguous 6kb segment nested within the region. For this nested segment, oligos were intentionally designed in the reverse orientation, synthesized and tagged with Cy3 (red). The result (FIG. 5D) is a "simulated" 6kb inversion, which serves to further validate the methodology, provides a useful reference marker, and demonstrates that even quite small inversions are cytogenetically detectable, provided that probe coverage is sufficiently dense. In fact, the only limitation with respect to how small an inversion can be detected by the presently disclosed methods and kits is any lower limit on the detection equipment's ability to visualize a signal from the probes hybridized to the chromatid within the inverted region.
This demonstrates that Ray had possession of probe pools that are capable of detecting de novo structural variants and differentiating a true inversion event from a sister chromatid exchange event. For example, Fig. 5D demonstrates staining of a sister chromatid exchange event. However, if the cell had contained a “true inversion event”, the “red probes” would hybridize within “green region” as the region targeted by the “red probes” would be present in both chromatids. Because the plurality of fluorescent probes in the pool spans a region, de novo “true inversions” within this region may be identified. Alternatively, inversions may be detected within the “green” regions, based on the presence of gaps in staining without a corresponding staining pattern in the sister chromatid.
The Remarks argue as described in paragraphs [0016]-[0019] and [0055]-[0058] of the specification and the figures, the specification illustrates examples of intrachromosomal (Fig. 1) and interchromosomal (Figs. 2 and 3) rearrangements that are detectable by the presently-claimed method but not by the monochrome dGH described by Ray (p. 7-8).
The arguments have been fully considered but are not persuasive. The arguments are not commensurate in scope with the claims and arguments that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., 19 differently stained “bands”) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
The Remarks argue targeted probes designed to bind a specific known site are not sufficient to detect structural variations occurring at other sites (de novo structural variants) (p. 8).
The arguments have been fully considered but are not persuasive. First, to some extent all probes of the present application and the prior art are “targeted” as they are designed to hybridize to particular regions within chromatid, whether a particular strand or chromatid. Second, the arguments rely on elements not recited in the claim. The claim does not require specific genomic coordinates. Third, Ray teaches all the active method steps and structural features recited in claim 7 as detailed above, and thus is sufficient to confer and/or achieve the property/result recited in the amended “wherein” clause.
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.
Claim(s) 8 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ray (WO 2014/008425 A1; cited on the 10/24/2024 IDS).
Regarding claim 8, Ray teaches directional genomic hybridization reactions (See entire document).
Ray teaches contacting a pair of single-stranded sister chromatids in a metaphase spread from a cell with pools directional hybridization probes (Fig. 5D; and para. 50). See also Fig. 1; and Fig. 2.
The probes pools have the same fluorescent label (e.g., “red” or “green”), where fluorescent labels are different between probe pools (Fig. 5D; and para. 50). See also Fig. 2.
The probes of the pools are complementary to a portion of a larger genomic target region within a single-stranded chromatid, and are “tiled” along the target in order to “paint” the target (Fig. 5D). See also, Fig. 2.
The probes of the pools a complementary to different target regions and are labeled with different labels (Fig. 5D; and para. 50). See also, Fig. 2.
Ray teaches generating a fluorescence pattern based on a hybridization pattern of the probes to one or both the single-stranded sister chromatids (Fig. 5D). See also, Fig. 2; and Fig. 3.
Ray teaches detecting the presence of a structural variation in the chromosome of the cell based on the fluorescence pattern (Fig. 5D). See also, Fig. 2; and Fig. 3.
Ray teaches all the active method steps and structures required by the method of claim 7, and thus, is deemed to have the property recited in the final amended “wherein” clause and/or is deemed sufficient to produce the result recited in the final amended “wherein” clause.
It is also noted in para. 50, Ray teaches the following:
However, it has surprisingly been determined that much smaller inversions can be detected. We designed a mock "mini-inversion" within a 10 Mb region of the large contig of chromosome 3q. Probe sets covering the region were tagged with fluorescein (green); excluded from coverage was a contiguous 6kb segment nested within the region. For this nested segment, oligos were intentionally designed in the reverse orientation, synthesized and tagged with Cy3 (red). The result (FIG. 5D) is a "simulated" 6kb inversion, which serves to further validate the methodology, provides a useful reference marker, and demonstrates that even quite small inversions are cytogenetically detectable, provided that probe coverage is sufficiently dense. In fact, the only limitation with respect to how small an inversion can be detected by the presently disclosed methods and kits is any lower limit on the detection equipment's ability to visualize a signal from the probes hybridized to the chromatid within the inverted region.
This demonstrates that Ray had possession of probe pools that are capable of detecting de novo structural variants and differentiating a true inversion event from a sister chromatid exchange event. For example, Fig. 5D demonstrates staining of a sister chromatid exchange event. However, if the cell had contained a “true inversion event”, the “red probes” would hybridize between the “green” regions as the region targeted by the “red probes” would be present in both chromatids. Because the probe pool, which is a collection of individual probes, spans a region, de novo “true inversions” within this region may be identified. Alternatively, inversions may be detected within the “green” regions, based on the presence of gaps in staining without a corresponding staining pattern in the sister chromatid.
Ray further compares the differences between a reference or normal chromosome and a sample having a rearrangement of chromosomal material (Fig. 2; Fig. 5).
It would have been prima facie obvious at the time of filing the present application to have utilized Figs. 2 and 5 of Ray in order to compare references and samples for the purpose of identifying when a fluorescence pattern is similar to or different from a known fluorescence pattern associated with specific chromosomal structure.
Claim(s) 17 and 21 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ray (WO 2014/008425 A1; cited on the 10/24/2024 IDS) in view of Macville (Histochem Cell Biol. 1997. 108:299-305; previously cited).
Regarding claims 17 and 21, Ray teaches directional genomic hybridization reactions (See entire document).
Ray teaches contacting a pair of single-stranded sister chromatids in a metaphase spread from a cell with pools directional hybridization probes (Fig. 5D; and para. 50). See also Fig. 1; and Fig. 2.
The probes pools have the same fluorescent label (e.g., “red” or “green”), where fluorescent labels are different between probe pools (Fig. 5D; and para. 50). See also Fig. 2.
The probes of the pools are complementary to a portion of a larger genomic target region within a single-stranded chromatid, and are “tiled” along the target in order to “paint” the target (Fig. 5D). See also, Fig. 2.
The probes of the pools a complementary to different target regions and are labeled with different labels (Fig. 5D; and para. 50). See also, Fig. 2.
Ray teaches generating a fluorescence pattern based on a hybridization pattern of the probes to one or both the single-stranded sister chromatids (Fig. 5D). See also, Fig. 2; and Fig. 3.
Ray teaches detecting the presence of a structural variation in the chromosome of the cell based on the fluorescence pattern (Fig. 5D). See also, Fig. 2; and Fig. 3.
Ray teaches all the active method steps and structures required by the method of claim 7, and thus, is deemed to have the property recited in the final amended “wherein” clause and/or is deemed sufficient to produce the result recited in the final amended “wherein” clause.
It is also noted in para. 50, Ray teaches the following:
However, it has surprisingly been determined that much smaller inversions can be detected. We designed a mock "mini-inversion" within a 10 Mb region of the large contig of chromosome 3q. Probe sets covering the region were tagged with fluorescein (green); excluded from coverage was a contiguous 6kb segment nested within the region. For this nested segment, oligos were intentionally designed in the reverse orientation, synthesized and tagged with Cy3 (red). The result (FIG. 5D) is a "simulated" 6kb inversion, which serves to further validate the methodology, provides a useful reference marker, and demonstrates that even quite small inversions are cytogenetically detectable, provided that probe coverage is sufficiently dense. In fact, the only limitation with respect to how small an inversion can be detected by the presently disclosed methods and kits is any lower limit on the detection equipment's ability to visualize a signal from the probes hybridized to the chromatid within the inverted region.
This demonstrates that Ray had possession of probe pools that are capable of detecting de novo structural variants and differentiating a true inversion event from a sister chromatid exchange event. For example, Fig. 5D demonstrates staining of a sister chromatid exchange event. However, if the cell had contained a “true inversion event”, the “red probes” would hybridize between the “green” regions as the region targeted by the “red probes” would be present in both chromatids. Because the probe pool, which is a collection of individual probes, spans a region, de novo “true inversions” within this region may be identified. Alternatively, inversions may be detected within the “green” regions, based on the presence of gaps in staining without a corresponding staining pattern in the sister chromatid.
Ray does not specifically teach between 20 and 23 human chromosomes are stained as encompassed by claim 17 or a staining combination of claim 21.
However, Macville demonstrates an ability to design probes for staining up to all chromosomes in a human cell. Macville also teaches using 3 different stains for pools to identify multiple different chromosomes (Table 1).
It would have been prima facie obvious to the ordinary artisan to have modified the method of Ray by incorporating the staining combinations of Macville such that one can screen for inversions in some to all of the chromosomes in a human cell using the different combination of stains taught by Macville.
Claim(s) 72 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ray (WO 2014/008425 A1) in view of Ray 2014 (Radiat Environ Biophys. 2014. 53:255-263).
Regarding claim 72, Ray teaches directional genomic hybridization reactions (See entire document).
Ray teaches contacting a pair of single-stranded sister chromatids in a metaphase spread from a cell with pools directional hybridization probes (Fig. 5D; and para. 50). See also Fig. 1; and Fig. 2.
The probes pools have the same fluorescent label (e.g., “red” or “green”), where fluorescent labels are different between probe pools (Fig. 5D; and para. 50). See also Fig. 2.
The probes of the pools are complementary to a portion of a larger genomic target region within a single-stranded chromatid, and are “tiled” along the target in order to “paint” the target (Fig. 5D). See also, Fig. 2.
The probes of the pools a complementary to different target regions and are labeled with different labels (Fig. 5D; and para. 50). See also, Fig. 2.
Ray teaches generating a fluorescence pattern based on a hybridization pattern of the probes to one or both the single-stranded sister chromatids (Fig. 5D). See also, Fig. 2; and Fig. 3.
Ray teaches detecting the presence of a structural variation in the chromosome of the cell based on the fluorescence pattern (Fig. 5D). See also, Fig. 2; and Fig. 3.
Ray teaches all the active method steps and structures required by the method of claim 7, and thus, is deemed to have the property recited in the final amended “wherein” clause and/or is deemed sufficient to produce the result recited in the final amended “wherein” clause.
It is also noted in para. 50, Ray teaches the following:
However, it has surprisingly been determined that much smaller inversions can be detected. We designed a mock "mini-inversion" within a 10 Mb region of the large contig of chromosome 3q. Probe sets covering the region were tagged with fluorescein (green); excluded from coverage was a contiguous 6kb segment nested within the region. For this nested segment, oligos were intentionally designed in the reverse orientation, synthesized and tagged with Cy3 (red). The result (FIG. 5D) is a "simulated" 6kb inversion, which serves to further validate the methodology, provides a useful reference marker, and demonstrates that even quite small inversions are cytogenetically detectable, provided that probe coverage is sufficiently dense. In fact, the only limitation with respect to how small an inversion can be detected by the presently disclosed methods and kits is any lower limit on the detection equipment's ability to visualize a signal from the probes hybridized to the chromatid within the inverted region.
This demonstrates that Ray had possession of probe pools that are capable of detecting de novo structural variants and differentiating a true inversion event from a sister chromatid exchange event. For example, Fig. 5D demonstrates staining of a sister chromatid exchange event. However, if the cell had contained a “true inversion event”, the “red probes” would hybridize between the “green” regions as the region targeted by the “red probes” would be present in both chromatids. Because the probe pool, which is a collection of individual probes, spans a region, de novo “true inversions” within this region may be identified. Alternatively, inversions may be detected within the “green” regions, based on the presence of gaps in staining without a corresponding staining pattern in the sister chromatid.
Ray does not specifically teach the additional steps of claim 72.
However, Ray 2014 teaches staining with DAPI, detecting a staining pattern and determining a structural variation based on the DAPI staining pattern (p. 257, Chromatid painting and Scoring).
It would have been prima facie obvious to the ordinary artisan at the time of filing to have modified the method of Ray by including the analysis of DAPI staining of Ray 2014 to aid in detecting inversions. The modification has a reasonable expectation of success as Ray already includes a DAPI stain (para. 78 and 85) and the modification is simply based on the analysis of data. Furthermore, Ray compares the differences between a reference or normal chromosome and a sample having a rearrangement of chromosomal material (Fig. 2).
It would have been prima facie obvious at the time of filing the present application to have utilized Figs. 2 and 5 of Ray in order to compare references and samples for the purpose of identifying when a fluorescence pattern is similar to or different from a known fluorescence pattern associated with specific chromosomal structure.
Claim(s) 79 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ray (WO 2014/008425 A1; cited on the 10/24/2024 IDS) in view of Ray 2013 (Chromosome Res. 2013. 21:165-174; cited on the 5/23/2024 IDS).
Regarding claim 79, Ray teaches directional genomic hybridization reactions (See entire document).
Ray teaches contacting a pair of single-stranded sister chromatids in a metaphase spread from a cell with pools directional hybridization probes (Fig. 5D; and para. 50). See also Fig. 1; and Fig. 2.
The probes pools have the same fluorescent label (e.g., “red” or “green”), where fluorescent labels are different between probe pools (Fig. 5D; and para. 50). See also Fig. 2.
The probes of the pools are complementary to a portion of a larger genomic target region within a single-stranded chromatid, and are “tiled” along the target in order to “paint” the target (Fig. 5D). See also, Fig. 2.
The probes of the pools a complementary to different target regions and are labeled with different labels (Fig. 5D; and para. 50). See also, Fig. 2.
Ray teaches generating a fluorescence pattern based on a hybridization pattern of the probes to one or both the single-stranded sister chromatids (Fig. 5D). See also, Fig. 2; and Fig. 3.
Ray teaches detecting the presence of a structural variation in the chromosome of the cell based on the fluorescence pattern (Fig. 5D). See also, Fig. 2; and Fig. 3.
Ray teaches all the active method steps and structures required by the method of claim 7, and thus, is deemed to have the property recited in the final amended “wherein” clause and/or is deemed sufficient to produce the result recited in the final amended “wherein” clause.
It is also noted in para. 50, Ray teaches the following:
However, it has surprisingly been determined that much smaller inversions can be detected. We designed a mock "mini-inversion" within a 10 Mb region of the large contig of chromosome 3q. Probe sets covering the region were tagged with fluorescein (green); excluded from coverage was a contiguous 6kb segment nested within the region. For this nested segment, oligos were intentionally designed in the reverse orientation, synthesized and tagged with Cy3 (red). The result (FIG. 5D) is a "simulated" 6kb inversion, which serves to further validate the methodology, provides a useful reference marker, and demonstrates that even quite small inversions are cytogenetically detectable, provided that probe coverage is sufficiently dense. In fact, the only limitation with respect to how small an inversion can be detected by the presently disclosed methods and kits is any lower limit on the detection equipment's ability to visualize a signal from the probes hybridized to the chromatid within the inverted region.
This demonstrates that Ray had possession of probe pools that are capable of detecting de novo structural variants and differentiating a true inversion event from a sister chromatid exchange event. For example, Fig. 5D demonstrates staining of a sister chromatid exchange event. However, if the cell had contained a “true inversion event”, the “red probes” would hybridize between the “green” regions as the region targeted by the “red probes” would be present in both chromatids. Because the probe pool, which is a collection of individual probes, spans a region, de novo “true inversions” within this region may be identified. Alternatively, inversions may be detected within the “green” regions, based on the presence of gaps in staining without a corresponding staining pattern in the sister chromatid.
Ray does not take into account the level of condensation.
However, Ray 2013 demonstrates that chromosome level of condensation or compaction is of interest and may be analyzed using directional genomic hybridization.
It would have been prima facie obvious at the time of filing to the ordinary artisan to have included measuring the level of condensation and using the information to detect the level of condensation as described by Ray 2013.
Claim(s) 13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bodvarsdottir (Mutation Research. 2012. 729:90-99) in view Ray (WO 2014/008425 A1).
Regarding claim 13, Bodvarsdottir teaches detecting extrachromosomal telomeric repeat DNA in metaphase chromosomes using CO-FISH using probes for leading and lagging strand. See entire document.
Bodvarsdottir does not teach the use of pools of single-stranded oligonucleotides.
However, Ray teaches directional genomic hybridization reactions (See entire document).
Ray teaches contacting a pair of single-stranded sister chromatids in a metaphase spread from a cell with pools directional hybridization probes (Fig. 5D; and para. 50). See also Fig. 1; and Fig. 2.
The probes pools having the same fluorescent label (e.g., “red” or “green”), where fluorescent labels are different between probe pools (Fig. 5D; and para. 50). See also Fig. 2.
The probes of the pools are complementary to a portion of a larger genomic target region within a single-stranded chromatid, and are “tiled” along the target in order to “paint” the target (Fig. 5D). See also, Fig. 2.
The probes of the pools a complementary to different target regions and are labeled with different labels (Fig. 5D; and para. 50). See also, Fig. 2.
Ray teaches generating a fluorescence pattern based on a hybridization pattern of the probes to one or both the single-stranded sister chromatids (Fig. 5D). See also, Fig. 2; and Fig. 3.
Ray teaches detecting the presence of a structural variation in the chromosome of the cell based on the fluorescence pattern (Fig. 5D). See also, Fig. 2; and Fig. 3.
Ray further teaches detecting inversions, dicentrics and translocation (para. 2 and 42). For example, Ray detects dicentric chromosomes and can identify the source of the extrachromosomal DNA in the dicentric chromosome (para. 53; and Fig. 7).
It would have been prima facie obvious to the ordinary artisan to have modified the method of Bodvarsdottir by using the single-stranded oligonucleotide dGH probe approach of Ray. The modification has a reasonable expectation of success as the method of Ray relies CO-FISH techniques to generate single-stranded chromatid. One would have been motivated to make such a modification as dGH offers higher resolution. The modification allows one to detect not only the telomere issues of Bodvarsdottir but also dicentric chromosomes also of interest to Bodvarsdottir (p. 92 and 94).
Response to the traversal of the 103 rejections
The Remarks argue Ray does not render obvious claim 8, because Ray is insufficient to detect de novo structural variations (p. 8-9).
The arguments have been fully considered but are not persuasive. Ray teaches all the active method steps and structural features recited in claim 7, and thus is sufficient to confer and/or achieve the property/result recited in the amended “wherein” clause.
The Remarks argue Macville fails to cure the deficiencies of Ray (p. 9).
The arguments have been fully considered but are not persuasive. Ray teaches all the active method steps and structural features recited in claim 7, and thus is sufficient to confer and/or achieve the property/result recited in the amended “wherein” clause.
The Remarks argue Ray 2014 fails to cure the deficiencies of Ray (p. 9-10).
The arguments have been fully considered but are not persuasive. Ray teaches all the active method steps and structural features recited in claim 7, and thus is sufficient to confer and/or achieve the property/result recited in the amended “wherein” clause.
The Remarks argue Ray 2013 fails to cure the deficiencies of Ray (p. 9).
The arguments have been fully considered but are not persuasive. Ray teaches all the active method steps and structural features recited in claim 7, and thus is sufficient to confer and/or achieve the property/result recited in the amended “wherein” clause.
The Remarks summarize the rejection of claim 13 over Bodvarsdottir in view Ray (p. 10).
The Examiner’s position is detailed in the above rejections.
The Remarks argue Bodvarsdottir utilizes targeted probes that detect telomere repeat DNA and such a method would be wholly insufficient for identifying the "at least one chromosome that is the chromosomal source of the ECDNA", as recited in claim 13 (p. 10-11).
The argument has been considered but is not persuasive because they amount to a general allegation that the claims define a patentable invention without specifically pointing out how the language of the claims patentably distinguishes them from the references.
Ray teaches detecting dicentric chromosomes, which have extrachromosomal DNA from chromosome 3. Bodvarsdottir teaches detecting mixtures of probes, which demonstrates the ability to detect sources of different genomic sequences.
Conclusion
No claims allowed.
It is noted the instant specification states that mBAND is a well-known technique for band-specific multicolor labeling strategies (para. 138) and that “oligopainting” (US 2010/0304994) provides advantages over mBAND in that allows for precise identification of genomic coordinates (para. 139).
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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/JOSEPH G. DAUNER/Primary Examiner, Art Unit 1682