DETAILED ACTION
Applicant’s response filed 12/16/2025 has been fully considered. The following rejections and/or objections are either reiterated or newly applied.
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 .
Claim Status
Claims 2, 4-5 and 8 are cancelled by Applicant
Claims 1, 3, 6-7 and 9-16 are currently pending and are herein under examination.
Claims 1, 3, 6-7 and 9-16 are rejected.
Claims 1 and 14-15 are objected.
Priority
The instant application claims domestic benefit as a continuation of international application PCT/EP2019/086156 filed 12/19/2019, which claims domestic benefit to U.S. Provisional Application No. 62/783,801 filed 12/21/2018. The claims to domestic benefit are acknowledged for claims 1, 3, 6-7 and 9-16. As such, the effective filing date for claims 1, 3, 6-7 and 9-16 is 12/21/2018.
Drawings
The objection to the drawings is withdrawn in view of amendments to specification filed 12/16/2025. The drawings filed 06/18/2021 are accepted.
Claim Objections
The objections to claims 1, 5, 11 and 14 are withdrawn in view of claim amendment.
Claims 1 and 14-15 are objected to because of the following informality:
Claim 1, step (d)(iii), recites “obtain a remaining” which should recite “obtain remaining”.
Claim 14, step (d)(iii), recites “obtain a remaining” which should recite “obtain remaining”.
Claim 15, line 6, recites “a method of claim 1” which should be “the method of claim 1”. Appropriate correction is required.
Withdrawn Rejections
35 USC 112(b)
The rejection of claims 4, 8-12 and 14 under 35 USC 112(b) is withdrawn in view of claim amendments. Applicant’s arguments are acknowledged (pg. 10, sec. 3 of Applicant’s remarks filed 16/16/2025).
35 USC 102
The rejection of claims 1-2, 5-7 and 15-16 under 35 U.S.C. 102(a)(1) as being anticipated by Mouliere et al. is withdrawn in view of claim amendments. Applicant argues that claim 1 now recites the limitations of claim 8 that were found to be free from the prior art (pg. 12, sec. 5 of Applicant’s remarks filed 16/16/2025). Applicant’s argument is persuasive.
35 USC 103
The rejection of claim 3 under 35 U.S.C. 103 as being unpatentable over Mouliere et al. in view of Li et al. is withdrawn in view of the withdrawn rejection of claim 1.
The rejection of claims 4 and 11-12 under 35 U.S.C. 103 as being unpatentable over Mouliere et al. in view of Nance et al. is withdrawn in view of the withdrawn rejection of claim 1.
The rejection of claim 13 under 35 U.S.C. 103 as being unpatentable over Mouliere et al. in view of Tie et al. is withdrawn in view of the withdrawn rejection of claim 1.
The rejection of claim 14 under 35 U.S.C. 103 as being unpatentable over Mouliere et al. in view of Tie et al. is withdrawn in view of claim amendments. Applicant argues that claim 14 now recites the limitations of claim 8 that were found to be free from the prior art (pg. 12, sec. 5 of Applicant’s remarks filed 16/16/2025). Applicant’s argument is persuasive.
35 USC 101
The rejection of claim 16 under 35 USC 101 for reciting non-statutory subject matter is withdrawn in view of claim amendment.
Claim Rejections - 35 USC § 112
35 USC 112(b)
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.
Claim 14 is 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.
This rejection is newly recited as necessitated by claim amendments.
Claim 14, line 9, recites the phrase “the two or more scores” which renders the claim indefinite. It is unclear which scores are being referenced because in step (a) scores are calculated for three features. It is also unclear if the phrase means that each feature has more than one score or if it means that each feature has only one score. To overcome this rejection, clarify which scores are being referenced and how many scores are generated per feature.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1, 3, 6-7 and 9-16 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea and a natural phenomenon without significantly more.
Any newly recited portions herein are necessitated by claim amendment.
Step 2A, Prong 1:
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomena (Step 2A, Prong 1). In the instant application, claims 1, 3, 6-7 and 9-13 recite a method, claim 14 recites a method, claim 15 recites a system, and claim 16 recites a CRM. The instant claims recite the following limitations that equate to one or more categories of judicial exception:
Claims 1 and 15-16 recite “A method for screening for cancer without relying on mutation detection, comprising: (b) calculating … three metrics from at least a majority of the plurality of genome sequence reads, wherein the three metrics are: (i) a fragment size of the cell free DNA, (ii) relative read depth of the plurality of whole genome sequence reads, and (iii) germline allelic imbalance; (c) inputting … the three metrics into a classifier to obtain a first prediction for a first class and a second prediction for a second class, wherein the first class is the sample of cell free DNA that includes circulating tumor DNA and the second class is the sample of cell free DNA that does not include the circulating tumor DNA; and (d) classifying … the sample of cell free DNA as the first class or the second class based on the first prediction and the second prediction; wherein the fragment size of the cell free DNA is a statistical fragment score calculated by: (i) normalizing cell free DNA fragment sizes obtained in the sample thereby obtaining a probability density function value; (ii) determining a log of values for the cell free DNA fragment sizes and calculating differences between each values of consecutive cell free DNA fragment size; (iii) removing at least 20 of lowest cell free DNA fragment sizes to obtain a remaining cell free DNA fragment sizes; and (iv) determining a first principal component axis of the remaining cell free DNA fragment sizes as compared to cell free DNA that does include the circulating tumor DNA and a cell free DNA that does not include the circulating tumor DNA.”
Claim 3 recites “wherein the classifier is a linear discriminant analysis.”
Claim 6 recites “wherein the fragment size of the cell free DNA comprises a ratio of regions within a probability density function.”
Claim 7 recites “wherein the ratio of regions within the probability density function comprises a ratio of probability of cell free DNA fragment size of between about 116 and about 156 nucleotides in length and a ratio of probability of cell free DNA fragment size around a mode of between about 164 and about 168 nucleotides in length.”
Claim 9 recites “wherein the relative read depth of the plurality of whole genome sequence reads is calculated by: (ii) determining a median read depth per chromosome arm for the set of normalized cell free DNA fragment size sequence read counts; and (iii) determining a maximum value among the median read depths determined for the per chromosome arms to obtain a copy number amplification score.”
Claim 11 recites “wherein the germline allelic imbalance is calculated using a statistical model which is a binomial probability model to determine a median probability value for one or more germline allelic imbalance sites in the sample of cell free DNA, and to obtain an allelic imbalance score.”
Claim 12 recites “wherein if the median probability value for the one or more germline allelic imbalance sites is below a predetermined significance level, the median probability value is indicative of an allelic imbalance at the one or more germline sites in the sample of cell free DNA”
Claim 13 recites “further comprising predicting … whether the subject has minimal residual disease based on the classification of the sample of cell free DNA as the first class or the second class.”
Claim 14 recites “calculating … scores for features of whole genome sequence data obtained from a sample of cell free DNA from a subject, wherein the features include: (i) a fragment size of the cell free DNA, (ii) relative read depth of the whole genome sequence reads, and (iii) germline allelic imbalance; (b) inputting … the two or more scores into a classifier to obtain a first prediction for a first class and a second prediction for a second class, wherein the first class is the sample of cell free DNA includes circulating tumor DNA and the second class is the sample of cell free DNA does not include the circulating tumor DNA; (c) classifying … the sample of cell free DNA as the first class or the second class based on the first prediction and the second prediction; and (d) determining … whether the subject has minimal residual disease based on the classification of the sample of cell free DNA as the first class or the second class; wherein the fragment size of the cell free DNA is a statistical fragment score calculated by: (i) normalizing cell free DNA fragment sizes obtained in the sample thereby obtaining a probability density function value; (ii) determining a log of values for the cell free DNA fragment sizes and calculating differences between values of consecutive cell free DNA fragment sizes; (iii) removing at least 20 of lowest cell free DNA fragment sizes to obtain a remaining cell free DNA fragment sizes; and (iv) determining a first principal component axis of the remaining cell free DNA fragment sizes as compared to cell free DNA that includes the circulating tumor DNA and cell free DNA that does not include the circulating tumor DNA.”
Limitations reciting a mental process.
Claims 1, 3, 6, 9-11 and 13-16 contain limitations recited at such a high level of generality that they equate to a mental process because they are similar to the concepts of collecting information, analyzing it, and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), which the courts have identified as concepts that can be practically performed in the human mind. The paragraphs below discuss the broadest reasonable interpretation (BRI) of the limitations in these claims that recite a mental process.
Regarding claims 1, 3, 6, 11 and 13-16, the BRI of calculating a metric for a fragment size of cfDNA includes counting paired-end reads that correspond to a fragment length. The BRI of calculating a metric for relative read depth includes performing the following calculation: (# of reads X average read length) / genome size. The BRI of calculating a metric for germline allelic imbalance includes performing the calculation described in Sherbina et al. (“Sherbina”; BMC Research Notes 14 (2021): 1-8; previously cited on PTO892 mailed 06/16/2025) or using a binomial probability model as recited in claim 11. Sherbina discloses an equation to calculate allelic imbalance (pg. 2, col. 1, para. 3 – col. 2, para. 6). A human can input numerical values into a classifier, such as a logistic regression or a linear discriminant analysis, to classify a sample as containing ctDNA or as healthy cfDNA. A human can use pen and paper to calculate a probability density function value, ratios of probability, and log values. A human can determine differences between consecutive log values. A human can remove fragment sizes that are lowest and make predictions of minimal residual disease based on a classification.
Regarding claims 9-10, the BRI of determining a median read depth and a maximum value of the median read depths includes making mental determinations and performing calculations.
Limitations reciting a mathematical concept.
Claims 1, 3, 6, 9-11 and 14-16 recite limitations that equate to a mathematical concept because they are similar to the concepts of organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)), which the courts have identified as mathematical concepts. The paragraphs below discuss the broadest reasonable interpretation (BRI) of the limitations in these claims that recite a mathematical concept.
Claims 1 and 14-16 recite mathematical concepts of calculating metrics for fragment size, relative read depth, and germline allelic imbalance. For example, using the statistical fragment score, calculating median read depths, and using the binomial probability model. The classifier in claim 1 may be a linear discriminant analysis as described in claim 3, which is a function that performs calculations. Calculating a probability density function, principal component axis, ratios, a statistical fragment score, median read depth, maximum read depth, copy number amplification score, using a statical model such as a binomial probability model to determine median probability values to determine allelic imbalance score are all limitations that include performing calculations under their BRI.
Limitations reciting a natural phenomenon.
The above cited limitations in claims 1 and 13-16 of correlating fragment size and germline allelic imbalance to detect presence of ctDNA and or predict minimal residual disease equates to a natural phenomenon because these limitations are similar to the concept of a correlation between the presence of myeloperoxidase in a bodily sample (such as blood or plasma) and cardiovascular disease risk in Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1361, 123 USPQ2d 1081, 1087 (Fed. Cir. 2017), which the courts have established as a natural phenomenon.
As such, claims 1, 3, 6-7 and 9-16 recite an abstract idea and a natural phenomenon (Step 2A, Prong 1: Yes).
Step 2A, Prong 2:
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). The judicial exception is not integrated into a practical application because the claims do not recite additional elements that reflect an improvement to a computer, technology, or technical field (MPEP § 2106.04(d)(1) and 2106.5(a)), require a particular treatment or prophylaxis for a disease or medical condition (MPEP § 2106.04(d)(2)), implement the recited judicial exception with a particular machine that is integral to the claim (MPEP § 2106.05(b)), effect a transformation or reduction of a particular article to a different state or thing (MPEP § 2106.05(c)), nor provide some other meaningful limitation (MPEP § 2106.05(e)). Rather, the claims include limitations that equate to an equivalent of the words “apply it” and/or to instructions to implement an abstract idea on a computer (MPEP § 2106.05(f)), insignificant extra-solution activity (MPEP § 2106.05(g)), and field of use limitations (MPEP § 2106.05(h)). The instant claims recite the following additional elements:
Claims 1 and 15-16 recite “(a) obtaining, by a data processing system, whole genome sequence data from a sample of cell free DNA from a subject, wherein the whole genome sequence data includes a plurality of whole genome sequence reads; (b) … by the data processing system …; (c) … by the data processing system …; (d) … by the data processing system …”
Claim 9 recites “(i) preprocessing of cell free DNA fragment size sequence read counts to obtain a set of normalized cell free DNA fragment size sequence read counts;”
Claim 10 recites “wherein the preprocessing comprises: (i) mapping sequence read counts from various samples into windows having predetermined sizes; (ii) filtering sequence read counts in each window based on one or more factors to obtain a set of remaining cell free DNA fragment size sequence read counts for each window; (iii) correcting for guanine-cytosine content and mappability biases in each window; and (iv) normalizing remaining cell free DNA fragment size sequence read counts in each window against sequence data from cell free DNA samples that do include circulating tumor DNA.”
Claims 13-14 recite “by the data processing system”
Claim 15 recites “A system comprising: one or more processors; and a memory accessible to the one or more processors, the memory storing a plurality of instructions executable by the one or more processors, the plurality of instructions comprising instructions that when executed by the one or more processors cause the one or more processors to perform a method of claim 1.”
Claim 16 recites “A computer product comprising a non-transitory computer readable medium storing a plurality of instructions for controlling a computer system to perform a method of claim 1.”
Regarding the above cited limitations in claims 1 and 13-16 of a data processing system, a system comprising a processor and memory, and a computer readable medium for controlling a computer system. The BRI of a data processing system includes it being a generic computer that has memory and a processor as stated in para. [41] of the specification. There are no limitations that these components require anything other than a generic computer and/or generic computing system. Therefore, these limitations equate to mere instructions to implement an abstract idea on a generic computer, which the courts have established does not render an abstract idea eligible in Alice Corp. 573 U.S. at 223, 110 USPQ2d at 1983.
Regarding the above cited limitations in claims 1 and 15-16 of obtaining whole genome sequencing data, this limitation equates to insignificant extra-solution activity of necessary data gathering. This limitation gathers data to perform the judicial exception of calculating metrics.
Regarding the above cited limitations in claims 9-10, these limitations equate to insignificant, extra-solution activity because they merely gather data that is used in performing the abstract idea of inputting data into a classifier and classifying samples into categories.
As such, claims 1, 3, 6-7 and 9-16 are directed to an abstract idea and a natural phenomenon (Step 2A, Prong 2: No).
Step 2B:
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). These claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because these claims recite additional elements that equate to instructions to apply the recited exception in a generic way and/or in a generic computing environment (MPEP § 2106.05(f)) and to well-understood, routine and conventional (WURC) limitations (MPEP § 2106.05(d)). The instant claims recite the following additional elements:
Claims 1 and 15-16 recite “(a) obtaining, by a data processing system, whole genome sequence data from a sample of cell free DNA from a subject, wherein the whole genome sequence data includes a plurality of whole genome sequence reads; (b) … by the data processing system …; (c) … by the data processing system …; (d) … by the data processing system …”
Claim 9 recites “(i) preprocessing of cell free DNA fragment size sequence read counts to obtain a set of normalized cell free DNA fragment size sequence read counts;”
Claim 10 recites “wherein the preprocessing comprises: (i) mapping sequence read counts from various samples into windows having predetermined sizes; (ii) filtering sequence read counts in each window based on one or more factors to obtain a set of remaining cell free DNA fragment size sequence read counts for each window; (iii) correcting for guanine-cytosine content and mappability biases in each window; and (iv) normalizing remaining cell free DNA fragment size sequence read counts in each window against sequence data from cell free DNA samples that do include circulating tumor DNA.”
Claims 13-14 recite “by the data processing system”
Claim 15 recites “A system comprising: one or more processors; and a memory accessible to the one or more processors, the memory storing a plurality of instructions executable by the one or more processors, the plurality of instructions comprising instructions that when executed by the one or more processors cause the one or more processors to perform a method of claim 1.”
Claim 16 recites “A computer product comprising a non-transitory computer readable medium storing a plurality of instructions for controlling a computer system to perform a method of claim 1.”
Regarding the above cited limitations in claims 1 and 13-16 of a data processing system, a system comprising a processor and memory, and a computer readable medium for controlling a computer system. The BRI of a data processing system includes it being a generic computer that has memory and a processor as stated in para. [41] of the specification. There are no limitations that these components require anything other than a generic computer and/or generic computing system. Therefore, these limitations equate to instructions to implement an abstract idea on a generic computing environment, which the courts have established does not provide an inventive concept in Intellectual Ventures I LLC v. Capital One Bank (USA), 792 F.3d 1363, 1367, 115 USPQ2d 1636, 1639 (Fed. Cir. 2015).
The limitation in claims 1, 9-10 and 15-16 when viewed individually and in combination equate to WURC limitations as disclosed by Qian et al. (“Qian”; bioRxiv (2018): 411256; previously cited on PTO892 mailed 06/16/2025) and Risberg et al. (“Risberg”; The Journal of Molecular Diagnostics 20, no. 6 (2018): 883-892; previously cited on PTO892 mailed 06/16/2025). Qian discloses calculating ctDNA fraction in cfDNA using whole genome sequencing data (pg. 32, para. 2; abstract). Qian discloses filtering reads with low mapping quality, dividing the whole genome into non-overlapping bins, calculating read depth count (RDC) of each bin by counting reads with start positions in the bin, correcting for GC content, using mean of centralized RDCs at each bin across control samples to generate reference data that is used to normalize centralized RDC of test samples (section 2.1). Qian discloses several computer-implemented software such as Picard-tools and Samtools, indicating that their method is WURC when combined with a generic computer (pg. 6, para. 2).
Risberg discloses a method for sample processing on ctDNA analysis (abstract). Risberg collected whole genome sequencing data of cfDNA from healthy and cancer patients (pg. 885, col. 2, para. 3). Sequence reads were filtered for containing duplicates along with reads of low mapping quality and supplementary alignments (pg. 885, col. 2, last para. – pg. 886, col. 1, para. 1). Sequence reads were allocated into equally sized nonoverlapping bins throughout the length of the genome, and read counts in each bin were corrected to account for GC content and mappability (pg. 886, col. 1). The sequence reads were further normalized by removing regions corresponding to artifacts and probable germline changes by using a cohort of 45 health controls (pg. 886, col. 1). Several computer-implemented software such as CNAclinic and Samtools, indicating that their method is WURC when combined with a generic computer (pg. 885, col. 1 – pg. 886, col. 1).
Regarding the above cited limitations in claim 1 and 15-16 of obtaining whole genome sequence data, the BRI of this limitation includes it being performed on a generic computer (i.e. the data processing system) and thus equates to receiving/transmitting data over a network, which the courts have established as WURC limitation of a generic computer in buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014).
When these additional elements are considered individually and in combination, they do not provide an inventive concept because they all equate to WURC functions/components of a generic computer and/or generic computing system and to a WURC method of preprocessing sequence reads using a computer as taught above by Qian and Risberg. Therefore, these additional elements do not transform the claimed judicial exception into a patent-eligible application of the judicial exception and do not amount to significantly more than the judicial exception itself (Step 2B: No).
As such, claims 1, 3, 6-7 and 9-16 are not patent eligible.
Response to Arguments under 35 USC 101
Applicant's arguments filed 12/16/2025 have been fully considered but they are not persuasive.
Applicant argues an improvement to the field of genomic diagnostics (pg. 11, 2nd full para. of Applicant’s remarks). Applicant’s arguments are not persuasive for the following reasons:
It’s unclear which limitations Applicant refers to that confer the alleged improvement. If Applicant refers to the limitations listed on pg. 11, 1st full para., of Applicants’ remarks, these limitations recite an abstract idea. The steps of a statistical fragment score, determining log values, calculating differences, removing 20 lowest fragment sizes, and determining a principal component axis all recite an abstract idea. MPEP 2016.05(a) recites “the judicial exception alone cannot provide the improvement.”
If Applicant refers to the limitations in specification para. [61], it is noted that claim 1 does not recite a 3-fold cross validated linear discriminate analysis, which would make the alleged improvement not commensurate in scope with the claimed invention. Even if claim 1 were to recite the 3-fold cross validated linear discriminate analysis, it would likely be identified as at least a mathematical concept.
Applicant argues that a claim is not abstract if it uses specific rules to achieve an improved result in a technological field, referring to McRO (pg. 11, 2nd full para. of Applicant’s remarks). Applicant’s arguments are not persuasive for the following reasons:
Applicant has not specifically identified which additional elements, alone or in combination, that confer the alleged improvement, nor has Applicant explained how the judicial exception interacts with an additional element to confer the alleged improvement.
In McRO, the specific set of rules were applied to the additional element of animating lip synchronization and facial expression of 3D characters, which resulted in an improvement in 3D character animation. In contrast to McRO, the instant claims appear to recite an improved abstract idea. However, the judicial exception alone cannot provide an improvement (MPEP 2106.05(a)).
Applicant argues that the claims contain additional elements that are not conventional (pg. 11, last para. – pg. 12, para. 1 of Applicant’s remarks). Applicant’s arguments are not persuasive for the following reasons:
The limitations of claim 8 imported into claim 1 are not being analyzed for their conventionality because they recite an abstract idea. Only additional elements are evaluated for their conventionality (MPEP 21-6.05(d)).
The only additional elements in claim 1 are the data processing system and obtaining whole genome sequence data via the data processing system. As discussed above, these limitations equate to transmitting/receiving data over a network and mere instructions to implement an abstract idea on computer. Under Step 2B, these do not provide significantly more. See MPEP 2106.05(f) and 2106.05(d)(II)(i).
Conclusion
No claims are allowed.
Claims 1 and 14-16 are free from the prior art because claims 1 and 14 now recite the limitations of claim 8, which were found to be free from the prior art. See the Conclusion section of the Office action mailed 06/16/2025.
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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/N.A.A./Examiner, Art Unit 1687
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685