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 .
Claims Status
Claims 1, 3-8, 10-13, & 16-19 filed on 07/31/2026 are pending. The cancellation of claims 2, 9, 14, 15, & 20 in the reply filed on 07/31/2026 is acknowledged. All the amendments and arguments have been thoroughly reviewed but are deemed insufficient to place this application in condition for allowance. The following rejections are either newly applied, as necessitated by amendment, or are reiterated. They constitute the complete set being presently applied to the instant application. Response to Applicant’s argument follow. This action is FINAL.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office Action.
Any rejection not reiterated is hereby withdrawn in view of the amendments to the claims.
Claim Rejections - 35 USC § 103
Claim(s) 1, 4, 7, 8, 10-13, & 16-19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kuznyetsov (Kuznyetsov et al.; PLOS One, Vol. 13, pages 1-15, May 2018), as cited on the IDS dated 10/25/2023, in view of ThermoFisher Scientific (ThermoFisher Scientific; Use of ExoSAP-IT PCR Product Cleanup Reagent in NGS, 2020), as evidenced by Illumina (Illumina SurePlex Summary Protocol, pages 1-13, September 2020).
Regarding amended claim 1, Kuznyetsov teaches a method for blastocyst stage non-invasive preimplantation genetic screening (NIPGS) for chromosomal aneuploidy comprising culturing fertilized oocytes from day 1 of fertilization, removing and washing off cumulus-corona radiata prior to intracytoplasmic sperm injection (ICSI) on day 1 to decrease likelihood of maternal contamination, culturing individually from day 1 to day 4 in Sage 1-Step medium (culture medium) with a serum protein supplement, conducting a laser-assisted biopsy on day 4 to release trophectoderm (TE) cells (embryonic cell free DNA), transferring washed fertilized oocytes on day 4 into fresh Global HP medium with HSA under oil until they reached a blastocyst stage on day 5 or 6 ( culturing until day 5 or day 6 to form an expanded blastocyst), performing a laser assisted trophectoderm biopsy on the expanded blastocyst performed in Global “total” w/HEPES and protein medium (exposing said expanded blastocyst to a laser pulse to extrude blastocoel fluid containing embryonic cfDNA in the fresh drop of culture medium to obtain day 5/6/7 cfDNA), and conducting whole genome amplification and next generation sequencing on the biopsied TE cells (cfDNA) (conducting genetic screening using whole genome amplification (WGA) prior to implantation of the embryo) (abstract objective lines 1-4; pg. 3 3rd full paragraph lines 1-4; pg. 3 4th full paragraph lines 1-7; pg. 3-4 paragraph bridging pg. 3 & 4 lines 1-13; pg. 4 1st full paragraph lines 1-9; pg. 4 3rd full paragraph lines 1-5; pg. 12 1st full paragraph lines 1-13; Fig. 1). Kuznyetsov also teaches a method for blastocyst stage non-invasive preimplantation genetic screening (NIPGS) for chromosomal aneuploidy comprising whole chromosome copy number (WCN) analysis as an indicator of aneuploidy (comprises aneuploidy testing using WGA to determine WCN) (abstract objective lines 1-4; pg. 4 4th full paragraph lines 8; Fig. 2). Kuznyetsov also teaches the samples were amplified using the SurePlex kit and use of NGS as the approach for preimplantation genetic screening (NIPGS) using the Illumina Veriseq PGS kit in which the SurePlex Kit protocol comprises 16 amplification cycles as evidenced by Illumina (pg. 10 Table 11 of Illumina) (preparation of cfDNA library using 16 amplification cycles) (pg. 4 3rd full paragraph lines 1-5; pg. 10 3rd full paragraph lines 2-3). Kuznyetsov also teaches data analysis and visualization of the WGA samples comprising copy number variation (CNV) analysis against a reference set from cell free embryonic DNA from euploid embryos (pg. 3 4th full paragraph lines 5-7; pg. 4 4th full paragraph lines 1-8; Fig. 2).
Kuznyetsov does not teach enzymatically treating the cfDNA with Exo nuclease I and Shrimp Alkaline phosphatase.
ThermoFisher Scientific teaches the use of ExoSAP-IT a PCR product cleanup reagent that is use in the library preparation for next generation sequencing (NGS) through removal of single-stranded DNA (cfDNA is enzymatically treated with Exo nuclease I and Shrimp Alkaline phosphatase (Exo-SAP-IT) to remove single stranded DNA prior to WGA) and that this product enables conservation of limited samples and improved workflow efficiency NGS for genotyping, targeted sequencing, etc. (pg. 1 column 1 1st full paragraph lines 1-15; pg. 1 column 1 2nd full paragraph lines 1-8; pg. 3 column 1 2nd full paragraph lines 1-4; Figure 1).
Kuznyetsov and ThermoFisher Scientific are considered to be analogous to the claimed invention because they are all in the same field of library preparation for NGS. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method preparing the samples for NGS in Kuznyetsov to incorporate the use of ExoSAP-IT as taught in ThermoFisher Scientific because ThermoFisher Scientific teaches that doing so would enable removal of single-stranded DNA and PCR product cleanup for library preparation prior to NGS while improving workflow efficiency.
Regarding claim 4, Kuznyetsov teaches culturing individually from day 1 to day 4 in Sage 1-Step medium (culture medium) with a serum protein supplement under oil in 25-μL droplets (under oil in a culture medium droplet of about 25 μL) (pg. 3 3rd full paragraph lines 1-4).
Regarding amended claim 7, Kuznyetsov teaches performing a laser assisted trophectoderm biopsy on the expanded blastocyst at day 5 or day 6 when a visible inner cell mass is illustrated (pg. 4 1st full paragraph lines 1-9; pg. 11 4th full paragraph lines 3-5; pg. 12 1st full paragraph lines 4-6; Fig. 1).
Regarding amended claim 8, Kuznyetsov teaches analysis of the samples with WGA in samples with combined blastocyst culture conditioned medium (BCCM) (spent culture media) and blastocoel fluid (BF) (genetic screening on the cfDNA is assessed in both the spent culture media and the blastocoel fluid) (pg. 4 2nd full paragraph lines 1-3).
Regarding amended claim 10, Kuznyetsov teaches the WGA is conducted on cfDNA from all samples amplified using SurePlexTM kit as quantified by Qubit 3.0TM fluorimeter (pg. 4 3rd full paragraph lines 1-5).
Regarding amended claim 11, Kuznyetsov teaches the WGA is conducted on cfDNA from all samples amplified using SurePlexTM kit in which the SurePlexTM kit teaches pre-amplification for a total of 14 cycles (employs 14 pre-amplification cycles for preparation of a library of sequences), as evidenced by Illumina (pg. 9 Table 9 of Illumina) (pg. 4 3rd full paragraph lines 1-5).
Regarding claims 12 & 13, Kuznyetsov teaches use of fluorescently labelled short tandem repeat (STR) marker for analysis of embryonic cfDNA (DNA resulting from WGA is subjected to PCR amplification followed by STR analysis wherein fluorescent markers are used) (pg. 4 3rd full paragraph lines 1-5; pg. 11 1st full paragraph lines 7-9).
Regarding claim 16, Kuznyetsov teaches the use of genetic screening through WGA for aneuploidy screening for use as a non-invasive preimplantation genetic screening (NIPGS) approach for human IVF before implantation into a human subject (step of implantation of the embryo if it satisfies the requirement of the genetic screening into a human subject (abstract conclusions lines 1-4).
Regarding claim 17, Kuznyetsov teaches the embryo may be frozen prior to implantation into a human subject from WGA for aneuploidy screening for use as a non-invasive preimplantation genetic screening (NIPGS) approach for human IVF (freezing the embryo that satisfies the requirement of the genetic screening prior to implanting in a human subject) (abstract conclusions lines 1-4; pg. 4 2nd full paragraph lines 1-3).
Regarding amended claim 18, Kuznyetsov teaches the use of genetic screening through WGA for aneuploidy screening for use as a non-invasive preimplantation genetic screening (NIPGS) approach for human IVF before implantation into a human subject (step of implantation of the embryo if aneuploidy is not indicated in the genetic screening into a human subject (abstract conclusions lines 1-4).
Regarding claim 19, Kuznyetsov teaches the embryo may be frozen prior to implantation into a human subject from WGA for aneuploidy screening for use as a non-invasive preimplantation genetic screening (NIPGS) approach for human IVF (freezing the embryo if aneuploidy is not indicated prior to implanting in a human subject) (abstract conclusions lines 1-4; pg. 4 2nd full paragraph lines 1-3).
Claim(s) 3, 5, & 6 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kuznyetsov (Kuznyetsov et al.; PLOS One, Vol. 13, pages 1-15, May 2018), as cited on the IDS dated 10/25/2023, and ThermoFisher Scientific (ThermoFisher Scientific; Use of ExoSAP-IT PCR Product Cleanup Reagent in NGS, 2020), as applied to claims 1, 4, 7, 8, 10-13, & 16-19 above, and further in view of Gynmed (GynMed; GM501 Hyaluronidase protocol, pages 1-2, March 2017).
The teachings of Kuznyetsov and ThermoFisher with respect to claim 1 are discussed above.
Regarding claim 3 & amended claim 5, Kuznyetsov teaches removing and washing off cumulus-corona radiata prior to intracytoplasmic sperm injection (ICSI) on day 1 to decrease likelihood of maternal contamination (see claim 3) and washing and replacing culture medium on day 4 to remove residual cumulus cells (see claim 5) (pg. 12 1st full paragraph lines 1-13).
Kuznyetsov does not teach that the washing comprises three washes to remove residual cumulus/corona cells.
Gynmed teaches a method of removing corona/cumulus cells with hyaluronidase comprising 3-5 washing steps (instructions for use lines 7, 8, & 13-16). Gynmed also teaches that this method enables washing steps to fully denude the oocyte for use in IVF (intended use lines 1-10; instructions for use lines 13-16).
Kuznyetsov and Gynmed are considered to be analogous to the claimed invention because they are all in the same field of removal of corona/cumulus cells from oocyte. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method washing off the cumulus-corona radiata at day 1 and at day 4 with fresh culture media to decrease likelihood of maternal contamination in Kuznyetsov to incorporate the use of three washing steps as taught in Gynmed because Gynmed teaches that doing so would enable full removal of the cumulus/corona cells from the oocyte of interest.
Regarding amended claim 6, Kuznyetsov teaches that each embryo was transferred on day 4 of culture, after washing and replacing to remove residual cumulus/corona cells, to Global HP medium with HSA in 24-μL droplets cultured under oil (fertilized oocyte is transferred to a fresh culture medium comprising Global HP medium with HSA under oil in a culture medium droplet of about 15 μL after washing to remove residual cumulus/corona cells) (pg. 3-4 paragraph bridging pg. 3 & 4 lines 1-3’ pg. 4 1st full paragraph lines 4-6).
Response to Arguments
The response traverses the rejection. The response asserts that given that all such features of previously pending claims 9, 14, & 15 are now combined in claim 1, that each obviousness objection raised to (a) claim 9, (b) claim 14, and (c) claim 15, would need to be taken together, e.g., as : (a) + (b) + (c), in order for claim 1 as amended to be considered obvious. Further, the response asserts that the method as now described in amended claim 1 provides the advantage of efficacy and accuracy while utilizing the small and most precious samples, by employing numerous specific steps in combination and that the various products inserts, prep kits, and other teachings may describe a specific use of a tool that is not new in and of itself, however that the combined steps and techniques utilized in claim 1 result in accurate and comprehensive pre-implantation genetic screening test that can advantageously make a significant different in the lives of individuals and families. Further, the response asserts that the accuracy and timing of conducting such a comprehensive genetic screening test as this according to amended claim 1 would not have been rendered obvious by knowing of individual steps of a technique as taught by a product or kit information. This argument has been thoroughly reviewed but was not found persuasive. First, the prior art of Bronner and Vossaert, as applied to previous claims 14 & 15, are no longer relied upon with the removal of the trademarked names. Further, the combination of Kuznyetsov and Thermofisher, as evidenced by Illumina, teaches all of the limitations of claim 1 as currently amended, as discussed further above. Specifically, Kuznyetsov teaches a method for blastocyst stage non-invasive preimplantation genetic screening (NIPGS) for chromosomal aneuploidy comprising whole chromosome copy number (WCN) analysis as an indicator of aneuploidy (comprises aneuploidy testing using WGA to determine WCN) (abstract objective lines 1-4; pg. 4 4th full paragraph lines 8; Fig. 2). Kuznyetsov also teaches the samples were amplified using the SurePlex kit in which the SurePlex Kit protocol comprises 16 amplification cycles as evidenced by Illumina (pg. 10 Table 11 of Illumina) (preparation of cfDNA library using 16 amplification cycles) (pg. 4 3rd full paragraph lines 1-5; pg. 10 3rd full paragraph lines 2-3). Further, Kuznyetsov also teaches data analysis and visualization of the WGA samples comprising copy number variation (CNV) analysis against a reference set from cell free embryonic DNA from euploid embryos (pg. 3 4th full paragraph lines 5-7; pg. 4 4th full paragraph lines 1-8; Fig. 2). Kuznyetsov does not teach enzymatically treating the cfDNA with Exo nuclease I and Shrimp Alkaline phosphatase. ThermoFisher Scientific teaches the use of ExoSAP-IT a PCR product cleanup reagent that is use in the library preparation for next generation sequencing (NGS) through removal of single-stranded DNA (cfDNA is enzymatically treated with Exo nuclease I and Shrimp Alkaline phosphatase (Exo-SAP-IT) to remove single stranded DNA prior to WGA) and that this product enables conservation of limited samples and improved workflow efficiency NGS for genotyping, targeted sequencing, etc. (pg. 1 column 1 1st full paragraph lines 1-15; pg. 1 column 1 2nd full paragraph lines 1-8; pg. 3 column 1 2nd full paragraph lines 1-4; Figure 1). Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method preparing the samples for NGS in Kuznyetsov to incorporate the use of ExoSAP-IT as taught in ThermoFisher Scientific because ThermoFisher Scientific teaches that doing so would enable removal of single-stranded DNA and PCR product cleanup for library preparation prior to NGS while improving workflow efficiency. Therefore, the combination of Kuznyetsov and Thermofisher, as evidenced by Illumina, teaches all of the limitations of claim 1 as currently amended.
The response also asserts that the feature of previous claim 9 (now found in claim 1), of treatment with Exo nuclease I and Shrimp Alkaline phosphatase is conducted to remove single stranded DNA prior to WGA and permits a more accurate reading on a more highly purified sample. Further, the response asserts that previous claim 14 (now found in claim 1) of employing 16 amplification cycles is now specified as part of the method and can improve the accuracy of the result of the genetic screen. Further, the response asserts that previous claim 15 in which CNV analysis is done allows for accurate testing against a reference for greater certainty. Further, the response asserts that by bringing the above limitations into the independent claim 1, it becomes clear that the specific direction of how to conduct the methos to its highest advantage is based on inventive step and that there are advantages of conducting this method in a clinical setting. This argument has been thoroughly reviewed but was not found persuasive for the reasons set forth above. Additionally, it is noted that ThermoFisher Scientific teaches the use of ExoSAP-IT and that this product enables conservation of limited samples and improved workflow efficiency NGS for genotyping, targeted sequencing, etc. (pg. 1 column 1 1st full paragraph lines 1-15; pg. 1 column 1 2nd full paragraph lines 1-8; pg. 3 column 1 2nd full paragraph lines 1-4; Figure 1).
For these reasons, and the reasons already made of record and modified to address the claims as currently amended, the rejections are maintained and applied to the newly amended claims.
Conclusion
Claims 1, 3-8, 10-13, & 16-19 are rejected.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BAILEY C BUCHANAN whose telephone number is (703)756-1315. The examiner can normally be reached Monday-Friday 8:00am-5:00pm ET.
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/BAILEY BUCHANAN/Examiner, Art Unit 1682
/JEHANNE S SITTON/Primary Examiner, Art Unit 1682
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