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 2, 4, 7, 8, 10, 13, 14, 16-19, 23, 27-31, & 34 filed on 10/07/2025 are pending. Claims 30 & 31 are currently under examination directed to the elected species of over 200 in claim 30 and of nucleotide repeat expansion disorder in claim 31 (see response dated 02/27/2025). The cancellation of claims 1 & 22 without prejudice or disclaimer of its subject matter in the reply filed on 10/07/2025 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Any rejection not reiterated is hereby withdrawn in view of the amendments to the claims.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 § 112
Claims 2, 4, 7, 8, 10, 13, 14, 16-19, 23, 27-31, & 34 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.
Regarding amended claim 34, the recitation of “wherein identifying uses the UMI sequence to identify a separate sequence for the target nucleic acid product” in lines 17-18 of the claim is unclear. It is unclear what is required by the recitation of “uses the UMI to identify a separate sequence for the target nucleic acid product”. Does the UMI in the first and second adapters identify the original target nucleic acid sequence? What separate sequence is being identified and how is it related to the target nucleic acid product?
Claims 2, 4, 7, 8, 10, 13, 14, 16-19, 23, & 27-31 are rejected due to their dependence on claim 34.
Claim Rejections - 35 USC § 101
Claims 2, 4, 7, 8, 10, 13, 14, 16-19, 23, 27-31, & 34 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural correlation/law of nature and an abstract idea without significantly more. This judicial exception is not integrated into a practical application and the claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception for the reasons set forth below.
35 U.S.C. § 101 requires that to be patent-eligible, an invention (1) must be directed to one of the four statutory categories, and (2) must not be wholly directed to subject matter encompassing a judicially recognized exception. M.P.E.P. § 2106. Regarding judicial exceptions, “[p]henomena of nature, though just discovered, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.” Gottschalk v. Benson, 409 U.S. 63, 67 (1972); see also M.P.E.P. § 2106. The unpatentability of abstract ideas was confirmed by the U.S. Supreme court in Bilski v. Kappos, 561 U.S. 593, 601 (June 28, 2010) and Alice Corp. Pty. Ltd. v. CLS Bank Int’l, 134 S. Ct. 2347, 2354 (2014). See also Myriad v Ambry, CAFC 2014-1361, -1366, December 17, 2014. The unpatentability of laws of nature was confirmed by the U.S. Supreme Court in Mayo Collaborative Services v. Prometheus Laboratories, Inc., 566 U.S. 66, 71 (2012). “[L]aws of nature, natural phenomena, and abstract ideas” are not patentable. Dia-mond v. Diehr, 450 U. S. 175, 185 (1981); see also Bilski v. Kappos, 561 U. S. at 601 (2010).
Claims Analysis:
As set forth in MPEP 2106, the claims have been analyzed to determine whether they are directed to one of the four statutory categories (STEP 1).
The instant claims are directed to methods and therefore are directed to one of the four statutory categories of invention.
The claims are then analyzed to determine if they recite a judicial exception (JE) (STEP 2A, prong 1) [Mayo Collaborative Services v. Prometheus Labs., Inc., 132 S. Ct. 1289, 1293 (2012), Alice Corp. Pry. Ltd. v. CLS Bank Int'l, 134 S. Ct. 2347 (2014)].
The claimed invention recites a method for genotyping a target nucleic acid sequence to identify a number of repeats in the repeat sequence of the target nucleic acid and a genotype of the target nucleic acids based on the sequenced target nucleic acid product and also to identify whether the subject has a genetic disorder based on the number of repeats (see claim 31). This recitation is a natural correlation between the number of repeats in the repeat sequence of a target nucleic acid and classification of a nucleotide repeat expansion disorder or having a genetic disorder. With regard to the natural correlation, as in Mayo, the relationship is itself a natural process that exists apart from any human action. The claimed invention also recites “identifying a number of repeats” which is a recitation of an abstract idea because it encompasses conclusions and determinations which can occur entirely within the mind. It is therefore determined that the claims are directed to judicial exceptions.
The claims are then analyzed to determine whether they recite an element or step that integrates the JE into a practical application (STEP 2A, prong 2) [Vanda Pharmaceuticals Inc., v. West-Ward Pharmaceuticals, 887 F.3d 1117 (Fed. Cir. 2018)].
The claims recite steps of providing a target nucleic acid comprising a target nucleic acid sequence with a first and second flanking region from a subject, cleaving the first and second flanking region to produce cleaved target nucleic acid, connecting adapters to the first and second end of the cleaved target nucleic acids to produce target nucleic acid product, sequencing the target nucleic acid product, and identifying a number of repeats based on the sequenced target nucleic acid product, however, this does not integrate the JE into a practical application because it is a mere data gathering steps to use the correlation and does not add a meaningful limitation to the method.
In the absence of steps or elements that integrate the JE into a practical application, the additional elements/steps are considered to determine whether they add significantly more to the JE either individually or as an ordered combination, to “’transform the nature of the claim’ into a patent eligible application” [Mayo Collaborative Services v. Prometheus Labs., Inc., 132 S. Ct. 1289, 1293 (2012), Alice Corp. Pry. Ltd. v. CLS Bank Int'l, 134 S. Ct. 2347 (2014)] (STEP 2B).
The steps of classifying multiple aspects of a nucleotide repeat expansion disorder and identifying a number of repeats in the repeat sequence of the sequenced target nucleic acid products are generally recited and do not provide any particular reagents that might be considered elements that transform the nature of the claims into a patent eligible application because no specific elements/steps are recited. This step is not only a mere data gathering step, but the general recitation of detection of known nucleic acids is well understood, routine, and conventional activity (See MPEP 2106.05(d)(II)). Applicant is reminded that in Mayo, the Court found that “[i]f a law of nature is not patentable, then neither is a process reciting a law of nature, unless that process has additional features that provide practical assurance that the process is more than a drafting effort designed to monopolize the law of nature itself." Further "conventional or obvious" "[pre]solution activity" is normally not sufficient to transform an unpatentable law of nature into a patent-eligible application of such a law”. Flook, 437 U. S., at 590; see also Bilski, 561 U. S., at ___ (slip op., at 14) (“[T]he prohibition against patenting abstract ideas ‘cannot be circumvented by’ . . . adding ‘insignificant post-solution activity’” (quoting Diehr, supra, at 191–192)). The Court also summarized their holding by stating “[t]o put the matter more succinctly, the claims inform a relevant audience about certain laws of nature; any additional steps consist of well understood, routine, conventional activity already engaged in by the scientific community; and those steps, when viewed as a whole, add nothing significant beyond the sum of their parts taken separately.” Therefore these limitations/steps do not “‘transform the nature of the claim’ into a patent-eligible application.’” Alice, 134 S. Ct. at 2355 (quoting Mayo, 132 S. Ct. at 1297).
When viewed as an ordered combination, the claimed limitations are directed to nothing more than the determination that a natural correlation/phenomena exists. Any additional element consists of using well understood, routine and conventional activity, and those steps, when viewed as a whole, add nothing significant beyond the sum of their parts taken separately.
Accordingly, it is determined that the instant claims are not directed to patent eligible subject matter.
Response to Arguments
The response traverses the rejection. The response asserts that applicant has cancelled claim 1 and amended claims 2, 4, 7, 8, 10, 13, 14, 16-19, 23, & 27-31 to depend, directly or indirectly, from claim 34 in which claim 34 was not rejected for being directed to patent ineligible subject matter and, therefore, claims 2, 4, 7, 8, 10, 13, 14, 16-19, 23, & 27-31 are not directed to patent ineligible subject matter at least because they depend from claim 34 and recite additional elements of particular advantage and utility. This argument has been thoroughly reviewed but was not found persuasive as claim 34 was an independent claim that did not recite a natural correlation between the number of repeats in the repeat sequence of a target nucleic acid and classification of a nucleotide repeat expansion disorder or having a genetic disorder. However, claim 34 as currently amended does recite this natural correlation as claim 34, as currently amended, recites identifying a number of repeats in the repeat sequence of the target nucleic acids and claim 31, which as currently amended now depends from claim 34, recites identifying whether the subject has a genetic disorder based on the number of repeats in the repeat sequence of the target nucleic acid and wherein the genetic disorder is a nucleotide repeat expansion disorder. Therefore, claim 34 and the claims directly or indirectly dependent from claim 34, as currently amended, recite a natural correlation between the number of repeats in the repeat sequence of a target nucleic acid and classification of a nucleotide repeat expansion disorder or having a genetic disorder and are not directed to patent eligible subject matter, as discussed further above.
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.
Claim Rejections - 35 USC § 102
Claim(s) 2, 7, 8, 10, 13, 14, 16, 19, 23, 27-31, & 34 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Tsai (WO 2016/028887 A1).
Regarding amended claim 2, Tsai teaches the nucleic acid sample can be from any source including genomic DNA, RNA, or cDNA (paragraph [0025] lines 1-4 & 10-11; paragraph [0026] lines 1-2).
Regarding amended claim 7, Tsai teaches cleaving with a Cas9 endonuclease (paragraph [0007] lines 6-12).
Regarding amended claim 8 & claim 10, Tsai teaches providing two guide RNAs that form a complex with Cas9 (enzyme) and target the Cas9 (enzyme) to the first location (first flanking region) and second location (second flanking region) to cleave at the first and second location specifically (targets the enzyme to a separate target site of the first and second flanking region) (paragraph [0007] lines 3-8).
Regarding amended claim 13, Tsai teaches the adapters are stem-loop adapters (hairpin adapters) (paragraph [0007] lines 12-13; paragraph [0077] lines 5-8).
Regarding amended claim 14, Tsai teaches the adapter-linked fragments (target nucleic acid products) can be repeatedly sequenced to provide redundant sequencing information (multipass sequencing) (paragraph [0023] lines 12-18; paragraph [0041] lines 1-7).
Regarding amended claim 16, Tsai teaches ligating the stem-loop adapters to both ends of the cleaved nucleic acid sample (cleaved target nucleic acids) (ligating the first adapter nucleic acid to the first end and ligating the second adapter nucleic acid to the second end) (paragraph [0007] lines 12-13; paragraph [0041] lines 1-7).
Regarding amended claim 19, Tsai teaches the adapter sequences (first and second adapter nucleic acid) comprises a primer binding site (primer initiation site) (paragraph [0040] lines 14-23).
Regarding amended claim 23, Tsai teaches that exonuclease enzymes degrade non-target fragments that do not comprise the stem-loop adapters (nucleic acids not comprising the target nucleic acid products) (paragraph [0077] lines 5-11).
Regarding amended claim 27, Tsai teaches the method can be used to enrich the repeat sequence within the Fragile X (FRM1) gene sequence (paragraph [00100] lines 1-10; paragraph [00128] lines 1-3).
Regarding amended claim 28 & claim 29, Tsai teaches the method can be used to enrich the trinucleotide repeat sequence of CGG (paragraph [0024] lines 1-8; paragraph [00128] lines 1-3).
Regarding amended claim 30, Tsai teaches the target repeat region to be enriched can have 100 or more (over 200) repeats (paragraph [0024] lines 1-8).
Regarding amended claim 31, Tsai teaches using this method to determine an individual’s risk of developing a genetic disorder wherein the genetic disorder is repeat expansion disorders (paragraph [00100] lines 1-10).
Regarding amended claim 34, it is noted as discussed above, the recitation of “wherein identifying uses the UMI sequence to identify a separate sequence for the target nucleic acid product” in lines 17-18 of the claim is unclear what is required by the recitation of “uses the UMI to identify a separate sequence for the target nucleic acid product”. Therefore, for the purposes of this rejection, the claim is given its broadest reasonable interpretation to encompass the UMI in the first and second adapters to identify the original target nucleic acid sequence (separate sequence from the target nucleic acid product) from which the target nucleic acid product is enriched from.
Tsai teaches a method for enriching a target region in a nucleic acid sample comprising providing the nucleic acid sample (target nucleic acid) comprising the target region, providing guide RNAs wherein the first guide comprises a sequence complementary to the first location within the nucleic acid sample (target nucleic acid) that is 3’-adjacent to the target region (first flanking region upstream of the target sequence) and the second guide RNA comprises a sequence complementary to a second location within the nucleic acid sample (target nucleic acid) that is 5’-adjacent to the target region (second flanking region downstream of the target sequence), exposing the guide RNAs to Cas9 endonucleases to form a sgRNA-Cas9 complex, then combining the sgRNA-Cas9 complex with the nucleic acid sample (target nucleic acid) to promote binding and cleavage of the nucleic acid sample (target nucleic acid) at the first location (first flanking region) and the second location (second flaking region), then linking stem-loop adapters to the at the cleaved ends of the nucleic acid sample (cleaved target nucleic acids) to form adapter-ligated fragments (target nucleic acid product) wherein the adapter sequences (first and second adapter nucleic acids) can contain barcodes (unique molecule index (UMI)) to provide information about the sample from which the adapter-ligated fragments (target nucleic acid products) were enriched (using the UMI sequence to identify a separate sequence for the target nucleic acid product), sequencing the adapter-linked fragments (target nucleic acid product), thereby enriching the target region (paragraph [0007] lines 1-23; paragraph [0008] lines 1-5; paragraph [0040] lines 1-3 & 16-18; paragraph [0077] lines 5-8). Tsai also teaches that the target region to be enriched include repeat sequences linked to repeat expansion disorders (identifying number of repeats in target nucleic acid products) (paragraph [00100] lines 1-10; paragraph [00108] lines 12-26). Tsai also teaches that this method can be used for genetic screening (genotyping) and for assessing risk of genetic disorders (paragraph [0023] lines 5-12; paragraph [00100] lines 1-10).
Response to Arguments
The response traverses the rejection. The response asserts that claim 34 is novel over Tsai because Tsai does not teach or disclose all of the elements in this claim and that specifically, Tsai does not use barcoded adapter sequence to identify a separate sequence for the target nucleic acid product, thereby identifying a number of repeats in the repeat sequence of the target nucleic acid, as recited in claim 34. Further, the response asserts that, in contrast, Tsai uses barcoded adapter sequence to provide information about the sample from which the fragment was enriched or to link the data from the two strands [of the original nucleic acid] during data analysis. This argument has been thoroughly reviewed but was not found persuasive. First, it is noted as discussed above, the recitation of “wherein identifying uses the UMI sequence to identify a separate sequence for the target nucleic acid product” in lines 17-18 of the claim is unclear what is required by the recitation of “uses the UMI to identify a separate sequence for the target nucleic acid product”. Therefore, for the purposes of this rejection, the claim is given its broadest reasonable interpretation to encompass the UMI in the first and second adapters to identify the original target nucleic acid sequence (separate sequence from the target nucleic acid product) from which the target nucleic acid product is enriched from. Tsai teaches linking stem-loop adapters to the at the cleaved ends of the nucleic acid sample (cleaved target nucleic acids) to form adapter-ligated fragments (target nucleic acid product) wherein the adapter sequences (first and second adapter nucleic acids) can contain barcodes (unique molecule index (UMI)) to provide information about the sample from which the adapter-ligated fragments (target nucleic acid products) were enriched (using the UMI sequence to identify a separate sequence for the target nucleic acid product). Second, the response asserts that Tsai also teaches using the barcoded adapter sequence to link the data from the two strands [of the original nucleic acid] during data analysis in which the original nucleic acid is a separate sequence that the target nucleic acid product (using the UMI sequence to identify a separate sequence for the target nucleic acid product). Therefore, Tsai does teach using the UMI sequence to identify a separate sequence for the target nucleic acid product as claim 34, as currently amended, recites.
The response also asserts that claims 2, 7, 8, 10, 13, 14, 16, 19, 23, & 27-31 depend, directly or indirectly, from claim 34 and recite additional elements of particular utility and advantage and that Tsai does not teach or disclose all of the elements of claim 34, much less the combination of elements of the dependent claims. This argument has been thoroughly reviewed but was not found persuasive for the reasons set forth above.
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.
Claim Rejections - 35 USC § 103
Claim(s) 4 is/are rejected under 35 U.S.C. 103 as being unpatentable over Tsai (WO 2016/028887 A1) in view of Lo (U.S. Patent Application Publication No. US 2015/0011403 A1).
The teachings of Tsai with respect to claim 34 are discussed above and incorporated herein.
Regarding amended claim 4, Tsai teaches epigenetic modifications, such as methylation, can be analyzed with this method of enriching target regions in a nucleic acid sample in methods such as bisulfite sequencing (paragraph [0028] lines 1-16; paragraph [0029] lines 1-4 & 9-13; paragraph [0094] lines 1-6; paragraph [00103] lines 1-9). Tsai does not teach converting a non-methylated cytosine to uracils.
Lo teaches a method of determining the DNA methylation levels of plasma DNA in repeat and non-repeat regions through bisulfite treatment prior to sequencing wherein the bisulfite treatment converts the unmethylated cytosines to uracils (paragraph [0027] lines 1-4; paragraph [0112] lines 1-4; paragraph [0123] lines 7-10; paragraph [0291] lines 7-13; paragraph [0292] lines 3-7). Lo also teaches this method can provide information on methylation densities of the repeat and non-repeat regions between diseased and healthy controls in which the differences in methylation densities can provide valuable insight on the state of disease (paragraph [0367] lines 1-8).
Tsai and Lo are considered to be analogous to the claimed invention because they are all in the same field of analysis of repeat sequences with sequencing. 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 of enriching a target (repeat) region and analyzing epigenetic modifications (methylation) in a nucleic acid sample in Tsai to incorporate the conversion of unmethylated cytosines to uracils prior to sequencing as taught in Lo because Lo teaches that doing so would provide insight on diseased samples with higher methylation densities in repeat regions.
Claim(s) 17 & 18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Tsai (WO 2016/028887 A1) in view of Bhatt (Bhatt & Chalmers; Nucleic Acids Research, Vol. 47, pages 8126-8135, June 2019).
The teachings of Tsai with respect to claim 34 are discussed above and incorporated herein.
Regarding amended claim 17 & claim 18, Tsai does not teach cleaving with a transposase.
Bhatt teaches a method of creating a deactivated Cas9 (dCas9) transpose fusion protein that when provided with guide RNA can be used to target and cleave nucleic acid regions of interest (pg. 8129 column 2 2nd full paragraph lines 10-12; pg. 8131 column 1 1st full paragraph lines 1-3 & 14-16). In addition, Bhatt teaches that dCas9 is an attractive candidate for transposon targeting because of its high affinity and long dwell time at its target site (abstract lines 21-24; pg. 8133 column 1 1st full paragraph lines 1-3).
Tsai and Bhatt are considered to be analogous to the claimed invention because they are all in the same field of Cas9-transposase targeting of target nucleic acid regions for cleaving. 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 of cleaving the target (repeat) region with Cas9 in Tsai to incorporate cleaving with the dCas9-transposase fusion protein as taught in Bhatt because Bhatt teaches that doing so would provide a high affinity and long dwell time at the dCas9-transposase’s target site.
Response to Arguments
The response traverses the rejection. The response asserts that claim 4 is not obvious over Tsai in view of Lo at least for the reason that the claim depends from and includes all of the elements of claim 34 and recites additional elements of particular advantage and utility. Further, the response asserts that Tsai does not teach all of the elements of claim 34, much less the combination of elements of claim 4, and Lo does not cure the above-mentioned deficiencies of Tsai. This argument has been thoroughly reviewed but was not found persuasive. First, as discussed above, the recitation of “wherein identifying uses the UMI sequence to identify a separate sequence for the target nucleic acid product” in lines 17-18 of the claim is unclear what is required by the recitation of “uses the UMI to identify a separate sequence for the target nucleic acid product”. Therefore, for the purposes of this rejection, the claim is given its broadest reasonable interpretation to encompass the UMI in the first and second adapters to identify the original target nucleic acid sequence (separate sequence from the target nucleic acid product) from which the target nucleic acid product is enriched from. Tsai teaches linking stem-loop adapters to the at the cleaved ends of the nucleic acid sample (cleaved target nucleic acids) to form adapter-ligated fragments (target nucleic acid product) wherein the adapter sequences (first and second adapter nucleic acids) can contain barcodes (unique molecule index (UMI)) to provide information about the sample from which the adapter-ligated fragments (target nucleic acid products) were enriched (using the UMI sequence to identify a separate sequence for the target nucleic acid product). Second, the response asserts that Tsai also teaches using the barcoded adapter sequence to link the data from the two strands [of the original nucleic acid] during data analysis in which the original nucleic acid is a separate sequence that the target nucleic acid product (using the UMI sequence to identify a separate sequence for the target nucleic acid product). Therefore, Tsai does teach using the UMI sequence to identify a separate sequence for the target nucleic acid product as claim 34, as currently amended, recites.
The response also asserts that claims 17 & 18 are not obvious over Tsai in view of Bhatt at least for the reason that the claim depends from and includes all of the elements of claim 34 and recites additional elements of particular advantage and utility. Further, the response asserts that Tsai does not teach all of the elements of claim 34, much less the combination of elements of claims 17 & 18, and Bhatt does not cure the above-mentioned deficiencies of Tsai. This argument has been thoroughly reviewed but was not found persuasive for the reasons set forth above.
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 2, 4, 7, 8, 10, 13, 14, 16-19, 23, 27-31, & 34 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