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 .
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Claim Rejections - 35 USC § 103
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1 and 2 are rejected under 35 U.S.C. 103 as being unpatentable over Hoffman (US 9,752,183 B2; IDS reference) in view of Remacle (US 2008/0085515 A1).
Regarding claim 1, Hoffman teaches a device capable of performing a method for the detection of more than one target molecule through the combination of digital PCR and DNA microarrays (Hoffman, abstract, C7 L50-55).
Figure 2 of Hoffman illustrates the design of this device and is shown below:
PNG
media_image1.png
360
755
media_image1.png
Greyscale
PNG
media_image2.png
316
790
media_image2.png
Greyscale
Of note, there is a base surface (Hoffman, Fig. 2, #1) with many cavities (Hoffman, Fig. 2, #4) which are filled by a pre-diluted sample of interest, thereby dividing the overall sample into the many cavities, which is then covered by a DNA microarray (Hoffman: Fig. 2, #2; C10 L66 – C11 L4; C17 L14-16).
The test sample can be diluted in series so that different cavities are filled with progressively lesser amounts of target molecules (Hoffman, C15 L23-36). This diluted and divided sample is equivalent to the first sample of the instant application. Digital PCR (dPCR) is performed in each of the cavities, generating an equivalent to the “second sample” of the instant application (Hoffman, C8 L20).
Hoffman teaches that the detection of the second sample can occur either on the surface of the covering device or the base surface (Hoffman, C9 L1-3). When the detection occurs on the surface of the covering device, multiple methods can be utilized without needing to perform any inventive activity, as a person skilled in the art would know which method is best used for their particular target molecule (Hoffman, C9 L8-29).
One such method is the detection of the hybridization of fluorescent PCR products (i.e. the second sample) on complementary solid-phase primers (Hoffman, C9 L8-17) through the use of a standard device used for reading out DNA microarrays, such as an array scanner (Hoffman, C16 L6-7).
Since the presence of target molecules can be inferred from the detection of the product of their amplification (Hoffman, C11 L5-10), by applying a statistical method (such as the most probable number), the positive results of the dilution series can be used to determine the initial DNA concentration of the sample (Hoffman, C8 L33-42).
However, Hoffman does not teach the application of this technique to the detection of microorganisms or that the detection of PCR products occurs via hybridization to microorganism-specific probes affixed to spots on an array.
Remacle discloses a method for detecting and/or quantifying different microorganisms through PCR amplification of pertinent nucleotide sequences followed by the hybridization of the PCR product to specific immobilized probes on an array (Remacle, pg1 ¶ 005).
PNG
media_image3.png
520
617
media_image3.png
Greyscale
Figure 5 of Remacle shows the use of this method to identify two different target sequences (Sa and Sg). The targets are amplified by specific primer pairs (SP 1/2a and SP 1/2g), the product of which is hybridized to their specific capture probe (Ca and Cg). In this specific embodiment, the primers contain a universal amplifying region that is the same across all primers which is incorporated into the PCR product and used to further amplify the targets using primers specific for that universal amplifying region (U) (Remacle, pg4 ¶ 0043].
Remacle states that their invention is well suited for miniaturized assays capable of detecting a large number of microorganisms using a small amount of input sample (Remacle, pg3 ¶ 0030]. Remacle further teaches that is it possible for the PCR chamber and the array chamber to be the same (Remacle, pg24 ¶ 0335).
Therefore, it would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to apply the method and devices of Hoffman to the purpose of detecting microorganisms in a sample. Remacle showed that there was clear interest in detecting microorganisms, specifically disease-causing microorganisms (Remacle, pg3 ¶ 0031) in the manner of Hoffman, e.g. miniaturized assays. Using the detection method of Remacle (capture of amplified microbial targets on a probe array) would have been further obvious as this was a known detection method and therefore, as noted by Hoffman, one skilled in the art would know which detection method is best used for their particular target molecule without needing to perform any inventive activity (Hoffman, C9, L24-29).
Known work in one field of endeavor may prompt variations of it for use in either the same field or a different one based on design incentives or other market forces if the variations are predictable to one of ordinary skill in the art. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143, F.).
Regarding claim 2, Hoffman and Remacle both teach the use of matching primers and probes for the detection of specific nucleic acids (Hoffman, C15 L16-19; Remacle, Figure 5).
Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Hoffman and Remacle and further in view of Yu (Yu M, et al, Anal Chem, 2019, 91(14), 8751-8755; IDS reference).
Regarding claim 3, Hoffman and Remacle teach a device capable of quantitatively measuring amounts of various microorganisms present in a test sample through PCR amplification of targeted nucleic acids and subsequent hybridization of the amplified product to complementary probes on an array, as discussed in detail in the claim 1 rejection. This hybridization can be detected by a standard device used for reading out DNA microarrays, such as an array scanner, which can be interpreted as equivalent to the measurement device of the instant application. The amount of positive signal resulting from the hybridization step can be used to determine the amount of starting target material via a statistical method such as the most probable number.
While much of the device of Hoffman and Remacle is equivalent to the pretreatment device described in claim 3 of the instant application, neither teach a device is capable of actually performing serial dilution and partitioning, with Hoffman simply stating that the test sample should be diluted prior to its addition onto the device.
However, Yu teaches a device capable of performing this function. Yu describes how setting up serial dilutions in nanoliter volumes was historically challenging and presents a multistep SlipChip (sd-SlipChip) microfluidic device as the solution (Yu, abstract). Through a series of sliding motions, Yu’s device is able to generate serial dilutions with dilution ratios of up to 1:4 (Yu, abstract) through the transfer of liquid between microwells via fluidic ducts (Yu, pg8752, C1 ¶2). Therefore, the overall dilution capabilities of Yu’s device is dependent on the number of microwells present on the device (more microwells = more dilutions).
Figure 1 (Yu), included below, demonstrates the mechanism of this device:
PNG
media_image4.png
219
500
media_image4.png
Greyscale
Two plates, each with microwells and ducts, are assembled so that the wells and ducts on the top and bottom partially overlap. The solution to be diluted is added to Type-1 ducts, and the dilutant is added to Type II ducts. By moving the plates side-to-side, the sample is first partitioned. Then, each subsequent up-down movement results in the completion of a dilution step. For exemplarily purposes, Yu includes a photo of a four-step sd-SlipChip with blue dye that has been diluted.
Yu further demonstrates that this device can be used to quantify hepatitis B virus (HBV) through digital loop-mediated isothermal amplification (LAMP) of a target nucleic acid. According to Yu, LAMP is just one of many digital nucleic acid amplification methods (NAA), which are generally limited by droplet volume and total number of partitions; a limitation that can be overcome by the sd-SlipChip (Yu, pg8752, C1 ¶1-3). While the instant application does not claim one particular amplification method, ¶0061 of the specification states that the type of reaction performed can include, but is not limited to, PCR, LAMP, RCA, etc.
Therefore, it would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to improve the device of Hoffman and Remacle through the incorporation of the device of Yu. This device would be capable of diluting and dividing a sample, performing a NAA method on that sample, and finally hybridizing the amplified sample to a DNA probe array. By using a variety of probes and primers, this system would be capable of detecting multiple target nucleic acids simultaneously, thus achieving the goal of the instant application.
A rationale to support a conclusion that a claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination would have yielded nothing more than predictable results to one of ordinary skill in the art. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395 (2007) (see MPEP §§ 2143, A. and 2143.02).
Allowable Subject Matter
No claims are allowable at this time.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Kara N Kovach whose telephone number is (571)272-8134. The examiner can normally be reached Monday - Friday, 9am - 3pm.
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, Gary Benzion can be reached at (571) 272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/K.N.K./Examiner, Art Unit 1681
/SAMUEL C WOOLWINE/Primary Examiner, Art Unit 1681