DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application is being examined under the pre-AIA first to invent provisions.
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 prior art rejections set forth below will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejections, would be the same under either status.
Status of the Application
2. Applicant’s response filed on September 9, 2025 been entered.
Claims 1-16 are pending and under examination.
Response to Arguments
3. Applicant’s arguments filed on September 9, 2025 have been fully considered.
Objection to the Drawings
Applicant argues that the objection should be withdrawn in view of the amendments to the specification filed with the response (Remarks, page 8).
This argument was persuasive. The objection has been withdrawn.
Rejection of claims 1-8 and 10-15 under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Dhallan in view of Shoemaker and Varley & Mitra
Argument:
Applicant first argues that the cited portions of Dhallan, and especially Example 13, fail to meet the requirement for “the amplification products may be derived from cell-free DNA of fetal origin and cell-free DNA of maternal origin” as recited in step (b) of independent claims 1 and 10 (Remarks, pages 8-10).
Response:
This argument was not persuasive because Dhallan does, in fact, teach amplification of fetal cell-free DNA as well as cell-free DNA of maternal origin in Example 13. In particular, Dhallan teaches isolating plasma from whole blood and ultimately amplifying and analyzing SNPs in fetal DNA (see, e.g., paras. 1789-1792, 1799-1800, 1947-1957, and 2128-2144 of Example 13). It is also noted that Dhallan expressly states, “Blood from a pregnant female was collected…The blood sample was used to demonstrate that fetal DNA can be detected in the maternal plasma” (para. 1788 in Example 13). Further, Dhallan reports results obtained from analyzing fetal and maternal DNA amplified from the plasma sample in Example 13 (see, e.g., paras. 2135-2137, 2141-2145, and 2147), thus clearly indicating that fetal and maternal DNA from plasma (i.e., cell-free fetal DNA and cell-free maternal DNA) was analyzed using the method disclosed in Example 13.
Further, as to Applicant’s argument on page 10 of the Remarks, which alleges that the multiplex PCR disclosed in Example 13 of Dhallan cannot be used to amplify cell-free fetal DNA because its primers are designed to amplify DNA with a length greater than that of cell-free fetal DNA, it is noted that the portions of the reference cited in the rejection and/or above indicate that such amplification was done. Therefore, attorney arguments cannot substitute for evidence when evidence is necessary (see MPEP 2144.05). In this case, evidence is necessary to show that the plain statements and results reported in Dhallan are somehow inaccurate or untrue.
As well, it is not clear that Applicant’s interpretation of the spacing of Dhallan’s primers set forth on page 10 of the Remarks is correct. Since Example 13 of Dhallan is directed to the analysis of SNP loci (i.e., point mutations), it is reasonable to consider that “primers located about 130-150 bases upstream and downstream of each locus of interest” means primers spaced about 130-150 bases upstream and downstream of a single nucleotide of interest (i.e., to generate relatively short amplification products that are less than 200 bp in length). Such amplification primers would be reasonably expected to be capable of amplifying cell-free DNA fragments of about 140-160 bp.
Argument:
Applicant also argues that Shoemaker does not remedy the deficiencies in Dhallan with respect to the claimed degree of multiplexing because that reference only describes how to amplify cellular DNA (i.e., not cell-free DNA) (Remarks, page 11).
Response:
This argument was not persuasive. Shoemaker does discuss amplifying cellular DNA rather than cell-free DNA, but the teachings in the reference concerning the advantages of combining multiplex PCR and next-generation sequencing would not appear to be limited to methods performed with cellular DNA. That is, the ordinary artisan would have recognized that combining multiplex PCR and next-generation sequencing would offer the same benefit of allowing for efficient analysis of large numbers of polymorphic loci to methods directed to analysis of cell-free DNA. The ordinary artisan also would have reasonably expected the guidance provided by Shoemaker concerning multiplex PCR to apply to the methods of Dhallan.
Argument:
Applicant also argues that the ordinary artisan would have lacked a reasonable expectation of success in combining the preparation methods of Dhallan with next-generation sequencing as described in Shoemaker because the second PCR in the method of Dhallan is specifically designed to generate overhangs to be used in the subsequent fill-in reaction that provides sequence information (Remarks, pages 11-12). In other words, Applicant argues that the combination proposed in the rejection alters the principle of operation of Dhallan, which is improper per MPEP 2143.01 VI.
Response:
This argument was not persuasive because the method proposed in the rejection would still result in obtaining sequence information, which is the goal of the method of Dhallan. As discussed in the rejection, the second PCR and subsequent fill-in reaction used by Dhallan to obtain sequence information would be replaced by the more efficient and high-throughput next-generation sequencing methods described in Shoemaker to result in a faster method capable of analyzing more loci at once and requiring less user intervention. Thus, the principle of operation of the method of Dhallan—obtaining sequence information for loci of interest—is not changed in the rejection. Argument:
Applicant further argues that Varley & Mitra do not teach or suggest using the disclosed methods with cell-free DNA (Remarks, page 12). Here, Applicant additionally argues that the authors of the cited non-patent literature article also filed a patent application concerning the same subject matter, which was published as US 2010/0129874, and that this published application states that the disclosed methods are not suitable for capturing DNA fragments or cell-free DNA. Therefore, Applicant argues, the ordinary artisan would have lacked motivation and reasonable expectation of success in combining Shoemaker or Varley & Mitra with Quake to arrive at the claimed methods.
Response:
These arguments were not persuasive. More specifically, the cited portions of the related pre-grant publication discussed on page 12 of the Remarks do not indicate that a separate barcoding step cannot be performed on amplified cell-free DNA as argued in the rejection. Instead, the teachings against cell-free DNA and DNA fragments apparently relate to the initial amplification step in Varley & Mitra and do not apply to the subsequent barcoding step disclosed in Figure 2 of the cited non-patent literature reference. The cited portion of the related pre-grant publication discusses the need for known end sequences, but the barcoding PCR in Varley & Mitra targets known adapter/common sequences added during the initial amplification. In other words, although the ordinary artisan may have concluded that the initial amplification step in Varley & Mitra may not be suitable for use with cell-free DNA, which is typically highly fragmented, said artisan would not have extended this conclusion to the downstream barcoding step, which is used with DNA that has already been amplified to add a sample index that allows for pooling of samples. In other words, the negative teachings in Varley & Mitra concerning cell-free DNA do not apply to the teachings in the reference cited in the rejection.
Since Applicant’s arguments were not persuasive, the rejection has been maintained.
Rejection of claims 9 and 16 under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Dhallan in view of Shoemaker and Varley & Mitra and further in view of Craig
Applicant argues that the rejection should be withdrawn because the additional secondary reference cited in the rejection (Craig) does not remedy the deficiencies in the primary combination of references (Remarks, page 13).
This argument was not persuasive because the primary combination of references is not deficient for the reasons set forth above. Accordingly, the rejection has been maintained.
Double Patenting
Applicant argues that a terminal disclaimer has been submitted to address the provisional non-statutory double patenting rejection citing co-pending Application Serial No. 17/868,238 (Remarks, page 13).
This argument was not persuasive because a terminal disclaimer is not present in the electronic application file. The rejection has been converted to a non-provisional rejection since the ‘238 application has since issued as US Patent No. 12,410,476.
Information Disclosure Statement
4. The Information Disclosure Statement (IDS) filed on October 21, 2025 has been considered.
Priority
5. As noted in the last Office action, the instant claims have an effective filing date of May 18, 2011.
Claim Rejections - 35 USC § 103
6. The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
7. This application currently names joint inventors. In considering patentability of the claims under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
8. Claims 1-8 and 10-15 and are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Dhallan (US 2004/0137470 A1) in view of Shoemaker et al. (US 2008/0090239 A1) and Varley & Mitra (Genome Research 2008; 18: 1844-1850).1
These claims are drawn to a method for preparing amplified DNA from a biological sample comprising cell-free DNA of maternal origin and cell-free DNA of fetal origin. The method comprises the following steps: (a) extracting cell-free DNA of maternal and cell-free DNA of fetal origin from the sample, (b) performing multiplexed PCR on the cell-free DNA to amplify a plurality of SNP loci in a single reaction mixture, and (c) performing universal PCR to further amplify the resulting products and to also add a sequencing adaptor to the amplification products of step (b). Dependent claims require the use of sequencing to obtain quantitative allele measurements (claims 2 and 11) and also determining a ploidy state using the quantitative allele measurements (claims 7 and 14).
Dhallan teaches a method for detecting trisomy of at least one chromosome of interest (see, e.g., Example 14 on pages 117-122, esp. paras. 2152-2158 for a general description; see also Example 13 on pages 109-117, esp. paras. 1783-1787 for a general description). In Example 13, the method is conducted using DNA present in the plasma portion of a maternal blood sample (see, e.g., paras. 1783 and 1788), and Dhallan also teaches that the method of Example 14 can be practiced using cell-free fetal DNA from a sample of maternal plasma, serum, or blood sample (para. 169; see also paras. 2152-2158).
And more specifically regarding claims 1, 3, 6, and 10, the method disclosed in Example 13 of Dhallan comprises the following steps: (a) extracting cell-free DNA of maternal origin and cell-free DNA of fetal origin from the plasma portion of a maternal blood sample (paras. 1788-1792); and (b) using multiplex PCR and target-specific primers to amplify 29 SNP loci in the same reaction mixture (paras. 1799-1957).
Regarding claims 2 and 11, Dhallan teaches obtaining quantitative allele measurements at the amplified loci and using the quantitative allele measurements obtained from a fill-in reaction to estimate the fetal fraction of cell-free DNA in the sample (see, e.g., paras. 1783-1787, 2120-2129, 2145, and 2147-2150).
Further regarding claim 3, Dhallan also teaches applying the method to maternal blood or serum samples (para. 2146).
Further regarding claim 6, Dhallan also teaches that the method may be practiced using variant loci other than SNP loci (see, e.g., paras. 41 and 136).
Regarding claims 7 and 14, the SNP loci amplified by Dhallan are on chromosome 13 (paras. 1800 and 2145). Dhallan also teaches applying the method to loci on chromosome 18 and/or 21 (paras. 1786-1787 and 2145). Dhallan further teaches using the quantitative allele measurements to determine the ploidy state of a chromosome of interest (see, e.g., paras. 1783-1787 and 2145-2150).
Regarding claims 8 and 15, Dhallan additionally teaches that the method can include analysis of loci on a chromosome expected to be disomic (see, e.g., para. 2148).
Dhallan does not teach all of the elements of the rejected claims. As to independent claims 1 and 10, Dhallan fails to teach the recited universal PCR and sequencing adaptor addition step. Dhallan also fails to teach adding an index as recited in claim 10. Further, Dhallan amplifies a smaller number of SNP loci compared to the ranges recited in claims 1, 4, 5, 10, 12, and 13. Dhallan additionally fails to teach next-generation sequencing as recited in claims 2 and 11 since only conventional Sanger sequencing is disclosed (see, e.g., paras. 43 and 208).
Like Dhallan, Shoemaker also discloses methods for non-invasive detection of nucleic acids of interest in samples of mixed origin. The methods disclosed by Shoemaker include amplification, which may be multiplexed PCR, followed by high-throughput sequencing (see, e.g., paras. 14-15 and paras. 226-234). The high-throughput sequencing methods disclosed in Shoemaker include next-generation methods as required by the instant claims 2 and 11 (see, e.g., paras. 229 and 232-234). Quantitative analysis of large numbers of polymorphic markers (e.g., SNPs) is also disclosed (see, e.g., paras. 15 and 159).
Further regarding claims 1, 4, 5, 10, 12, and 13, Shoemaker discloses multiplex PCR amplification of as many as 100 SNPs (see, e.g., para. 147). This range for the number of SNPs analyzed overlaps with the claimed ranges.
Shoemaker does not disclose a separate barcoding PCR (i.e., a universal PCR as recited in the instant claims 1 and 10) since the analogous “locater tag” is added during multiplex PCR (see, e.g., paras. 115-118), but Varley & Mitra disclose a method that comprises the following steps: (i) multiplex PCR; (ii) barcoding PCR; and (iii) next-generation sequencing of the barcoded PCR products (see, e.g., the abstract, Figs. 1-2, and p. 1845). As noted in Figure 2 of Varley & Mitra, the barcoding PCR adds a sample-specific barcode (i.e., an index) as well the sequencing tag recited in claims 1 and 10. Varley & Mitra teach that barcoding allows for pooling of a plurality of different samples and subsequently sequencing the pooled samples together since the barcode will allow sample identification (see, e.g., p. 1845).
It would have been prima facie obvious for one of ordinary skill in the art at the time of the invention to substitute next-generation sequencing as disclosed in each of Shoemaker and Varley & Mitra for the quantitative fill-in reaction disclosed in Dhallan. The ordinary artisan would have been motivated to do so to obtain a method for obtaining quantitative allele measurements that requires less user manipulation and has greater throughput. The ordinary artisan would have had a reasonable expectation of success in view of the guidance provided throughout Shoemaker and Varley & Mitra as to the use of next-generation sequencing to analyze amplification products.
It also would have been prima facie obvious to practice the method suggested by Dhallan in view of Shoemaker and further in view of Varley & Mitra using any desired number of SNP loci in the multiplex PCR step. As noted above, the multiplex PCR of Dhallan amplifies a number of loci (29 loci) that lies close to the lower limit of the claimed ranges (50 loci) and further suggests analysis of large numbers of loci to improve the accuracy of the method (para. 2149). As well, Shoemaker discloses a range for the number of SNP loci to be amplified by multiplex PCR that overlaps with the claimed ranges (para. 147), and no evidence of unexpected results has been presented with respect to the claimed numbers of loci. This is sufficient to establish a prima facie case of obviousness for the ranges recited in claims 1, 4, 5, 10, 12, and 13 per MPEP 2144.05 I.
It also would have been prima facie obvious to further include a barcoding PCR to add a sample index and a sequencing tag when practicing the method suggested by Dhallan in view of Shoemaker. As noted above, Shoemaker discloses barcoding, but not in a separate PCR. The teachings of Varely & Mitra, though, indicate that barcoding may be performed in a separate universal PCR that also adds a sequencing tag (see, e.g., Fig. 2 and p. 1845). The ordinary artisan would have recognized from these teachings in the art that a barcoding/sequencing tag addition step could be performed either during a multiplex PCR suggested by Dhallan in view of Shoemaker or in a separate step conducted between the multiplex PCR and the sequencing step, and accordingly, would have been motivated to select either method of barcode/sequencing tag addition with a reasonable expectation of success. The ordinary artisan would have been particularly motivated to include barcoding since each of Shoemaker and Varley & Mitra taught that sample barcoding allowed for pooling different samples and sequencing them together (see, e.g., Shoemaker at para. 228; see Varley & Mitra at p. 1845).
Thus, the methods of claims 1-8 and 10-15 are prima facie obvious.
9. Claims 9 and 16 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Dhallan (US 2004/0137470 A1) in view of Shoemaker et al. (US 2008/0090239 A1) and Varley & Mitra (Genome Research 2008; 18: 1844-1850) and further in view of Craig et al. (Nature Methods 2008; 5: 887-893).2
As discussed above, the teachings of Dhallan in view of Shoemaker and further in view of Varley & Mitra render obvious the methods of claims 1-8 and 10-15.
Regarding claims 9 and 16, each of Shoemaker and Varley & Mitra teaches pooling amplified DNA from multiple samples and sequencing said pooled DNA in parallel (Shoemaker at, e.g., paras. 118 and 121-122; Varley & Mitra at, e.g., page 1845, col. 2 and page 1847, col. 2).
Neither Shoemaker nor Varley & Mitra teaches sequencing in a single sequencing lane as required by claims 9 and 16, but this would have been prima facie obvious in view of the teachings of Craig, which state that indexed samples derived from multiple individuals can be pool into a single sample, further amplified, and sequenced in a single lane of a next-generation/high-throughput sequencing device (page 887, col. 2). The ordinary artisan would have recognized from the teachings of that pooled amplified DNA to be sequenced in parallel could be sequenced in a single lane, and accordingly, would have been motivated to select this known option for parallel sequencing with a reasonable expectation of success. Thus, the methods of claims 9 and 16 are prima facie obvious.
Double Patenting
10. The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
11. Claims 1-6, 8-13, 15, and 16 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 5-19, and 21-30 of U.S. Patent No. 12,410,476 B2.3
Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of the ‘476 patent overlap in scope with the instant claims and recite or suggest all of their limitations.
More specifically, the claims in both applications are drawn to a method comprising multiplex amplification of a plurality of loci in a cell-free DNA sample followed by sequencing to determine the amount of alleles at the different loci.
The limitations of the instant claims 1 and 10, which are independent claims, are recited in claims 1, 3, and 15 as well as claims 18, 19, and 28 of the ‘476 patent.
The limitations of the instant claims 2 and 11 are recited in/suggested by claims 1, 15, and 17 of the ‘476 patent as well as claims 18, 28, and 30 of the ‘476 patent.
The limitations of the instant claim 3 are recited in claims 2 and 18 of the ‘476 patent.
The limitations of the instant claims 4, 5, 12, and 13 are suggested by claims 1 and 8-11 of the ‘476 patent as well as claims 18 and 24-27 of the ‘476 patent, which recite overlapping ranges for the number of SNP loci.
The limitations of the instant claims 6, 8, and 15 are recited in, e.g., claims 1 and 18 of the ‘476 patent.
The limitations of the instant claims 9 and 16 are recited in claims 15 and 28 of the ‘476 patent.
Conclusion
12. No claims are currently allowable.
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 Angela Bertagna whose telephone number is (571)272-8291. The examiner can normally be reached 8-5, M-F.
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/ANGELA M. BERTAGNA/Primary Examiner, Art Unit 1681
1 Each of these references was cited in the last Office action.
2 Each of these references was cited in the last Office action.
3 It is noted that the previously cited copending Application (i.e., Application Serial No. 17/868,238) has now issued as U.S. Patent No. 12,410,476 B2.
Prosecution Insights