DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. Applicant’s election without traverse of Group 2 in the reply filed on August 12, 2026 is acknowledged.
Claims 1-10 and 19-25 are currently pending.
Claims 1-3 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on August 12, 2026.
Nucleotide and/or Amino Acid Sequence Disclosures
3. Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - Sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.831(c). Sequence identifiers for sequences (i.e., “SEQ ID NO:X” or the like) must appear either in the drawings or in the Brief Description of the Drawings. See Figure 8B.
Required response – Applicant must provide:
Amended drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers (i.e., “SEQ ID NO:X” or the like) into the Brief Description of the Drawings, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Claim Rejections - 35 USC § 103
4. The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
5. Claims 4-9 are rejected under 35 U.S.C. 103 as being unpatentable over Ma (Scientific Reports 3:2730 9/24/2013) in view of Meddeb (Clinical Chemistry 65:5 pages 623-633 (2019)) and Anand (Analytica Chimica Acta 1166 (2021) 338547).
Regarding Claim 4 Ma discloses an impedance-based integrated biosensor for suspended DNA characterization (title). The structure of the biosensor is shown in Fig 1. Ma teaches that they used this biochip-based system to measure the impedance of DNA solutions with different concentrations. Concentrated single-stranded DNA fragments from herring sperm with a uniform length of approximately 700 base pairs were obtained. This sample comprised DNA molecules without any additional buffer. The molecules were dissolved in deionized (DI) water and diluted to six different concentrations: 12 ng/ml, 30 ng/ml, 60 ng/ml, 120 ng/ml, 240 ng/ml and 600 ng/ml. The results are shown in Figure 2. In particular Figure 2C shows the relationship between the ssDNA concentration and the solution impedance. As shown below, concentrated solutions had lower impedance. Higher impedance indicates that the solution has lower conductivity. (see pages 2-3).
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Thus Ma teaches a method of performing impedance spectroscopy. The method comprises loading test sample (different concentrations of DNA diluted in deionized water) over a plurality of electrodes enclosed inside a microchamber, measuring the electrical conductivity of the test sample using an impedance analyzer, and analyzing a difference between the electrical conductivity of a test sample (12 ng/µl) and the electrical conductivity of a control sample (60 ng/µl).
Ma teaches a method of performing impedance spectroscopy to detect the concentration of DNA in a sample. Ma exemplifies detection of DNA fragments ranging from 148 bp to 2129 bp (page 4). However Ma does not teach detection of cfDNA fragments. It is noted that cfDNA fragments are 120-220 bp. Ma does not teach a method further comprising collecting a biological sample and extracting cfDNA from the biological sample (clm 4). Ma does not teach a method wherein the biological sample comprises a biological fluid selected from whole blood, plasma, platelets, saliva, white blood cells, serum, and urine (clm 5). Ma does not teach a method wherein the biological sample comprises plasma, the method further comprising: separating the plasma from whole blood via double centrifugation, the double centrifugation comprising a first cycle at 1500g to 2500g for 7-12 minutes, and a second cycle at 15000-17000g for 7-12 minutes (clm 6).
However Meddeb discusses the analysis of circulating cell free DNA. Meddeb teaches that there are many reasons why one would want to quantify cfDNA. Meddeb teaches the following clinical applications of cfDNA quantification: cancer, transplant, cardiovascular disease, autoimmune disease, sepsis, and exercise (see Table 1). Meddeb teaches that cfDNA can be extracted from plasma samples (Fig 1, page 629). Meddeb teaches that plasma can be separated from whole blood via double centrifugation. Meddeb recommends that the first centrifugation be carried out for 800 to 1200g at 4 °C for 10 min and the second centrifugation for 14000 to 16000g at 4 °C for 10 min (page 627).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Ma by using the impedance spectroscopy to determine the concentration of cfDNA is a sample as suggested by Meddeb. One of skill in the art would have been motivated to determine the concentration of cfDNA in sample since Meddeb teaches that this has many clinical applications such as: cancer, transplant, cardiovascular disease, autoimmune disease, sepsis, and exercise (see Table 1). One of skill in the art would have had more than a reasonable expectation of success of being able to determine the concentration of cfDNA in a sample since cfDNA is 120-220 bp and Ma teaches that impedance spectroscopy can be used detect DNA fragments ranging from 148 bp to 2129 bp (page 4). Further one skill in the art would have been motivated to obtain the cfDNA from a plasma sample since Meddeb teaches that serum and plasma have been used as biological sources for cfDNA (page 626). Finally one of skill in the art would have been motivated to separate plasma from whole blood using the double centrifugation method of Meddeb since this 2-step plasma separation procedure has been validated and is now established as the optimal procedure of choice (see page 627).
Ma teaches a method of performing impedance spectroscopy, wherein the DNA is present in deionized water or PBS (see page 2 of the article and page 13 of the supplementary information). However Ma does not teach a method wherein the DNA is suspended in a zwitterionic buffer (clm 4). Ma does not teach a method wherein the zwitterionic buffer is selected from (4-(2- hydroxyethyl)-1-piperazineethanesulfonic acid), piperazine-1,4-bis(2-hydroxypropanesulfonic acid), and 4-(2-Hydroxyethyl)-1-piperazinepropanesulfonic acid (clm 7). Ma does not teach a method wherein the zwitterionic buffer comprises (4-(2- hydroxyethyl)-1-piperazineethanesulfonic acid) (clm 9).
However Anand teaches that zwitterionic buffers show improved performance over standard electrolyte buffers (e.g. PBS) currently widely used in impedance spectroscopy measurements of bacterial suspensions (abstract). Anand teaches that 4-(2 hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffer is a zwitterionic buffer (page 2).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Ma such that the DNA is present in a zwitterionic buffer (e.g., HEPES) as suggested by Anand. In the instant case Anand teaches that that impedance measurements can be performed in zwitterionic buffer, PBS buffer, and tris-HCl buffer (page 2). Anand further teaches that zwitterionic buffers lead to enhanced impedance sensing ability (page 1). Based on the teachings in Anand, it would have been obvious to a person of ordinary skill in the art to try using a zwitterionic buffer with a DNA sample in an attempt to enhance impedance sensing ability of DNA, as the person with ordinary skill has good reason to pursue the known options within his or her technical grasp. Further the claim is obvious because the substitution of one known buffer for impedance measurements (the PBS of Ma) for another (the HEPEs of Anand) would have yielded predictable results to one of ordinary skill in the art at the time of the invention.
Regarding the recitation in claim 8 that the method can be used for quantitative and qualitative detection of cf DNA, it is noted that the recitation merely sets forth an intended use of the method but does not actually require active process steps of quantitating or qualitating DNA.
Regarding the recitation in claim 9 that the method has a limit of detection of 0.4 ng/ml or 5.14 pM and a sensitivity and specificity each of about 95%, it is noted that recitation merely sets forth a property of the claimed method and does not require any additional steps to be performed.
6. Claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over Ma (Scientific Reports 3:2730 9/24/2013) in view of Meddeb (Clinical Chemistry 65:5 pages 623-633 (2019) and Anand (Analytica Chimica Acta 1166 (2021) 338547) as applied to claim 4 above and in further view of Ye (2022 IEEE International Symposium on Circuits and Systems (ISCAS), Austin, TX, USA, 2022, pp. 1347-1351).
The teachings of Ma, Meddeb, and Anand are presented above.
Ma teaches a impedance based integrated biosensor for suspended DNA characterization within a few minutes (abstract). However the combined references do not specification teach a method wherein the measuring and analyzing the electrical conductivity is performed in less than 5 minutes and preferably less than 1 minute.
However Ye teaches a portable biosensing system consisting of a bioimpedance measurement circuit and an IDE chip. This system can be modified to detect various biomolecules, including DNA, antigen/antibody, proteins, metabolites, etc. The bioimpedance measurement circuit has a fast measurement speed (obtaining single frequency impedance result within 1.1 milliseconds), and its error levels are within 0.5% and 0.1% in terms of accuracy and precision, respectively. The proposed system can function similarly to the commercialized electrochemical workstation (Biologic SP-200). Meanwhile, the proposed system is 36 times faster in terms of measurement from 10 Hz to 1 MHz (72 seconds vs 3 seconds). Furthermore, the system has the potential to be a point-of-care diagnostic tool because of its low-cost and portability (abstract).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Ma, Meddeb, and Anand by using a impedance spectroscopy system that can perform measurements and obtain results within less than 5 min as suggested by Ye. One of skill in the art would have been motivated to use such a system especially in busy point of care settings where it is desirable to quickly test a subject for an illness.
7. Claims 19-24 are rejected under 35 U.S.C. 103 as being unpatentable over Ma (Scientific Reports 3:2730 9/24/2013) in view of Thermo Fisher Scientific (Isolating Genomic DNA from Whole Blood 2008 found online at https://www.argentalab.pl/argenta-lab/pdf/Nota-1-Izolacja-genomowego-DNA-z-krwi-1.pdf) and Anand (Analytica Chimica Acta 1166 (2021) 338547).
Regarding Claim 19 Ma discloses an impedance-based integrated biosensor for suspended DNA characterization (title). The structure of the biosensor is shown in Fig 1. Ma teaches that they used this biochip-based system to measure the impedance of DNA solutions with different concentrations. Concentrated single-stranded DNA fragments from herring sperm with a uniform length of approximately 700 base pairs were obtained. This sample comprised DNA molecules without any additional buffer. The molecules were dissolved in deionized (DI) water and diluted to six different concentrations: 12 ng/ml, 30 ng/ml, 60 ng/ml, 120 ng/ml, 240 ng/ml and 600 ng/ml. The results are shown in Figure 2. In particular Figure 2C shows the relationship between the ssDNA concentration and the solution impedance. As shown below, concentrated solutions had lower impedance. Higher impedance indicates that the solution has lower conductivity. (see pages 2-3).
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Thus Ma teaches a method of performing impedance spectroscopy. The method comprises loading test sample (different concentrations of DNA diluted in deionized water) over a plurality of electrodes enclosed inside a microchamber, measuring the electrical conductivity of the test sample using an impedance analyzer, and analyzing a difference between the electrical conductivity of a test sample (12 ng/µl) and the electrical conductivity of a control sample (60 ng/µl).
Ma does not teach a method further comprising collecting a biological sample and extracting a DNA fraction from the biological sample (clm 19). Ma does not teach a method wherein the DNA fraction comprises genomic DNA (clm 20). Ma does not teach a method wherein biological sample comprises a biological fluid selected from whole blood, plasma, platelets, saliva, white blood cells, serum, and urine (clm 21). Ma does not teach a method wherein the biological sample comprises whole blood and the method further comprises: separating a buffy coat layer from the whole blood (clm 22).
However Thermo Fisher discloses a method of isolating genomic DNA from whole blood samples (title). Thermo Fisher teaches that DNA was extracted from the buffy coat layer of whole blood samples from 10 patients for downstream analysis (page 1 col 2).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Ma by collecting a blood sample from a subject and extracting genomic DNA from a fraction of the blood sample as suggested by Thermo Fisher. One of skill in the art would have been motivated to extract genomic DNA from a fraction of a blood sample since Thermo Fisher teaches that it is possible to obtain high yield, high purity DNA this way, which can be used for DNA profiling and real time PCR (page 2 col 2).
Ma teaches a method of performing impedance spectroscopy, wherein the DNA is present in deionized water or PBS (see page 2 of the article and page 13 of the supplementary information). However Ma does not teach a method wherein the DNA is suspended in a zwitterionic buffer (clm 19). Ma does not teach a method wherein the zwitterionic buffer is selected from (4-(2- hydroxyethyl)-1-piperazineethanesulfonic acid), piperazine-1,4-bis(2-hydroxypropanesulfonic acid), and 4-(2-Hydroxyethyl)-1-piperazinepropanesulfonic acid (clm 23).
However Anand teaches that zwitterionic buffers show improved performance over standard electrolyte buffers (e.g. PBS) currently widely used in impedance spectroscopy measurements of bacterial suspensions (abstract). Anand teaches that 4-(2 hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffer is a zwitterionic buffer (page 2).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Ma and Thermo Fisher such that the DNA is present in a zwitterionic buffer (e.g., HEPES) as suggested by Anand. In the instant case Anand teaches that that impedance measurements can be performed in zwitterionic buffer, PBS buffer, and tris-HCl buffer (page 2). Anand further teaches that zwitterionic buffers lead to enhanced impedance sensing ability (page 1). Based on the teachings in Anand, it would have been obvious to a person of ordinary skill in the art to try using a zwitterionic buffer with a DNA sample in an attempt to enhance impedance sensing ability of DNA, as the person with ordinary skill has good reason to pursue the known options within his or her technical grasp. Further the claim is obvious because the substitution of one known buffer for impedance measurements (the PBS of Ma) for another (the HEPEs of Anand) would have yielded predictable results to one of ordinary skill in the art at the time of the invention.
Regarding the recitation in claim 24 that the method can be used for quantitative and qualitative detection of DNA, it is noted that the recitation merely sets forth an intended use of the method but does not actually require active process steps of quantitating or qualitating DNA.
8. Claim 25 is rejected under 35 U.S.C. 103 as being unpatentable over Ma (Scientific Reports 3:2730 9/24/2013) in view of Thermo Fisher Scientific (Isolating Genomic DNA from Whole Blood 2008 found online at https://www.argentalab.pl/argenta-lab/pdf/Nota-1-Izolacja-genomowego-DNA-z-krwi-1.pdf) and Anand (Analytica Chimica Acta 1166 (2021) 338547) as applied to claim 19 above and in further view of Ye (2022 IEEE International Symposium on Circuits and Systems (ISCAS), Austin, TX, USA, 2022, pp. 1347-1351)
The teachings of Ma, Thermo Fisher, and Anand are presented above.
Ma teaches a impedance based integrated biosensor for suspended DNA characterization within a few minutes (abstract). However the combined references do not specification teach a method wherein the measuring and analyzing the electrical conductivity is performed in less than 5 minutes and preferably less than 1 minute.
However Ye teaches a portable biosensing system consisting of a bioimpedance measurement circuit and an IDE chip. This system can be modified to detect various biomolecules, including DNA, antigen/antibody, proteins, metabolites, etc. The bioimpedance measurement circuit has a fast measurement speed (obtaining single frequency impedance result within 1.1 milliseconds), and its error levels are within 0.5% and 0.1% in terms of accuracy and precision, respectively. The proposed system can function similarly to the commercialized electrochemical workstation (Biologic SP-200). Meanwhile, the proposed system is 36 times faster in terms of measurement from 10 Hz to 1 MHz (72 seconds vs 3 seconds). Furthermore, the system has the potential to be a point-of-care diagnostic tool because of its low-cost and portability (abstract).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Ma, Meddeb, and Anand by using a impedance spectroscopy system that can perform measurements and obtain results within less than 5 min as suggested by Ye. One of skill in the art would have been motivated to use such a system especially in busy point of care settings where it is desirable to quickly test a subject for an illness.
9. Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMANDA HANEY whose telephone number is (571)272-8668. The examiner can normally be reached Monday-Friday, 8:15am-4:45pm EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Shen can be reached at 571-272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/AMANDA HANEY/Primary Examiner, Art Unit 1682
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