DETAILED ACTION
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 13 March 2026 has been entered.
Claim Rejections - 35 USC § 112
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.
Claims 1-3, 7-10, 14-16 and 23 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
With respect to independent claim 1, the limitation “having captured thereon single-stranded genomic DNA of a single cell while the single-stranded genomic DNA is being amplified by polymerase in an amplification reaction at the first DNA capture array” is unclear. More specifically, the phrases “having captured…” and “while the single-stranded genomic DNA is being amplified…” are process terms that describe an ongoing reaction that happens while the claimed device is being used. It is therefore unclear if the claims are intended to specifically read on a microfluidic device while it is being used during a select period of time, but not on the same device before or after the amplification reaction.
With respect to independent claim 1, it is unclear if the term “genomic DNA of a single cell” in line 12 is intended to refer to the “single cell” introduced in claim 9, or, alternatively, to a different single cell. It is believed that the term should instead read “genomic DNA of the single cell”.
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 1-3, 7-10, 14-16 and 23 are rejected under 35 U.S.C. 103 as being unpatentable over Craighead (US 20140194313) in view of Southern (US 20090098541), Soper (US 20180074039) and Hagiwara (US 20060257878).
With respect to claim 1, Craighead discloses a microfluidic device (Figure 7:10) for performing whole genome amplification comprising a solid substrate (Figure 7:20) having a microfluidic channel system formed therein. The microfluidic channel system includes an intake region that increases in width and comprises a single microchannel (Figure 1:30) configured to receive a plurality of cells. The microchannel includes a cell capture site (Figure 1:41, see tapered region in Fig. 1), (“FIG. 3 provides a close view of multiple cells 60 (particularly hematopoietic stem-cells) immobilized by micropillars 41 of the micropillar array of one embodiment of a microfluidic device of the present invention. FIGS. 4-6, 11-13, and 15 include photomicrographs that show cells entrapped by the micropillars (by size exclusion)…the micropillar array includes micropillars that are spatially configured to entrap, by size exclusion, at least one cell”, see paragraphs [0058] and [0059]). The microchannel further includes a DNA capture array (Figure 1:40a,b) comprising a plurality of micropillars configured to immobilize genomic DNA. The DNA capture array terminates in a collection region (Figure 1:45) for collecting DNA amplification products. The whole genome amplification system further includes an input port (Figure 1:22) and an output reservoir (Figure 1:24). This is disclosed in at least paragraphs [0053]-[0063]. Paragraphs [0051] and [0109] teach that the micropillars have a diameter between 0.5 to 15 microns and that the spacing between micropillars narrows in a downstream manner (“a micropillar width of about 4 µm").
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Craighead, however, does not expressly state that a plurality of these microchannels 30 originate from a single intake microchannel, or that the cell capture site is configured to capture a single cell.
Southern discloses a microfluidic device comprising a solid substrate having one or more microfluidic channel systems therein. See at least Fig. 1. The microfluidic channel system includes a single intake microchannel (Figure 53:110) configured to receive a cell suspension comprising a plurality of cells. A plurality of cell segregation microchannels (Figure 53:115) extend from the single intake region, and a plurality of cell capture sites (Figure 54:120) are located downstream of each cell segregation microchannel and include a structural barrier effective for physically capturing a single cell and arresting any further movement of the single cell through the microfluidic channel system. This is disclosed in at least paragraphs [0029]-[0099], [0268] and [0269] (“Single cells are trapped, their contents are released, and the contents of individual cells are then analyzed along a channel containing suitable analytical components e.g. immobilized nucleic acid probes, immobilized antibodies, etc. Analysis of a single cell's genome, transcriptome, proteome, etc. thus becomes possible. Moreover, by arranging multiple channels on the same device, multiple cells can simultaneously be treated and analyzed in parallel, allowing individual cells within a population to be compared rapidly and conveniently. Where the multiple channels share a common input line, a population of cells can easily be separated into single cells, with one cell being associated with each channel”). Southern additionally states that a DNA capture array is positioned downstream from each cell capture site and that the array may include micropillars (Figure 36:60) (see paragraph [0082], “Preferred channels include a series of different immobilized nucleic acids for hybridizing to specific nucleic acids within a cell's contents”).
Before the effective filing date of the claimed invention, it would have been obvious to duplicate the Craighead microchannels 30 so that a plurality of identical cell segregation microchannels are split off from a common intake microchannel. Southern teaches that this is an effective way to simultaneously trap and lyse a plurality of individual cells in order to release intracellular analytes for further analysis using separate and independent downstream DNA capture arrays. The benefits of this configuration are described in paragraph [0009] and throughout the reference (“Single cells are trapped, their contents are released, and the contents of individual cells are then analyzed along a channel containing suitable analytical components e.g. immobilized nucleic acid probes, immobilized antibodies, etc. Analysis of a single cell's genome, transcriptome, proteome, etc. thus becomes possible. Moreover, by arranging multiple channels on the same device, multiple cells can simultaneously be treated and analyzed in parallel, allowing individual cells within a population to be compared rapidly and conveniently. Where the multiple channels share a common input line, a population of cells can easily be separated into single cells, with one cell being associated with each channel”).
Craighead additionally teaches that amplification occurs at the plurality of micropillars. See paragraph [0079] (“this method further involves analyzing the immobilized DNA while the DNA is maintained within the micropillar array. As set forth herein, any technique or tool used in the art to analyze such immobilized DNA can be used herein. In a particular embodiment, the analyzing step involves conducting techniques that include, without limitation, nucleic acid amplification”). Accordingly, it is believed that Craighead requires amplifying single-stranded DNA at the DNA capture array.
In the event that this is not inherently taught by Craighead, Hagiwara and Soper each teach that single-stranded DNA is prepared during a denaturation step to enable subsequent annealing and elongation. Hagiwara discloses a microfluidic device comprising a DNA capture array (Figure 2:3) comprising microbeads configured to capture target single-stranded genomic DNA for amplification. This is described in paragraphs [0085]-[0086]. Soper discloses a DNA capture array (Figure 1B:1) comprising micropillars (Figure 1B:4) configured to capture single-stranded target DNA. Single-stranded target DNA is then amplified at the capture array to create an amplified product. This is described in paragraphs [0068]-[0071] and [0189]-[0199]. Accordingly, it would have been obvious to ensure that the Craighead micropillars are configured to capture DNA released from single cells and facilitate amplification while the single stranded DNA remains in the capture array. Hagiwara and Soper describe different amplification strategies that each require single stranded DNA to be captured and amplified at a capture site for purposes of separation from contaminants and the generation of a detectable amplified product.
With respect to claims 2, 3 and 8, Craighead, Southern, Soper and Hagiwara disclose combination as described above. The inlet and outlet ports of Craighead and Southern are depicted as extending into and out of the solid substrate in order to introduce cells into the microfluidic channel system and collect DNA amplification products.
With respect to claim 7, Craighead, Southern, Soper and Hagiwara disclose combination as described above. Soper recognizes the use of Phi29 polymerase1 in at least paragraph [0175].
With respect to claim 9, Craighead, Southern, Soper and Hagiwara disclose combination as described above. Each of these references describe providing a flow of buffer for amplification. Furthermore, this limitation describes how the claimed device is intended to be used. Apparatus claims cover what a device is, not what a device does. A claim containing a recitation with respect to the manner in which a claimed apparatus is intended to be employed does not differentiate the claimed apparatus from a prior art apparatus if the prior art apparatus teaches all the structural limitations of the claim. See MPEP 2114.
With respect to claim 10, Craighead, Southern, Soper and Hagiwara disclose combination as described above. Soper describes different isothermal amplification techniques that do not require annealing to form a duplex DNA. Furthermore, this limitation describes how the claimed device is intended to be used. Apparatus claims cover what a device is, not what a device does. A claim containing a recitation with respect to the manner in which a claimed apparatus is intended to be employed does not differentiate the claimed apparatus from a prior art apparatus if the prior art apparatus teaches all the structural limitations of the claim. See MPEP 2114.
With respect to claim 14, Craighead, Southern, Soper and Hagiwara disclose combination as described above. Craighead additionally shows in Fig. 1 that the micropillars are arranged in a gradient so that the spacing between micropillars narrows in a downstream manner. This approach produces at least 2 distinct regions 40a,b. This is taught in at least paragraph [0060].
With respect to claims 15 and 16, Craighead, Southern, Soper and Hagiwara disclose combination as described above. Southern teaches that the substrate and micropillars are made from PDMS, glass and/or plastics in at least paragraphs [0030]-[0032].
With respect to claim 23, Craighead, Southern, Soper and Hagiwara disclose combination as described above. Soper teaches in paragraphs [0074] and [0075] that the micropillars may have a diameter between about 1.5 to microns. It would have been within the ability of one of ordinary skill in the art to optimize micropillar diameter to arrive at the most effective value (for example, 1.5-2 microns) through routine experimentation. Craighead does not specify a required micropillar diameter range, and the example diameter of 4 microns is close to the claimed range of 1.5-2 microns. A prima facie case of obviousness exists where the claimed ranges or amounts do not overlap with the prior art but are merely close. See MPEP 2144.05.
Response to Arguments
In response to Applicant’s amendments filed 13 March 2026, the previous rejections have been withdrawn. However, upon further consideration, a new ground of rejection is made over Craighead in view of Southern, Soper and Hagiwara. A new 35 U.S.C. 112 rejection has also been made to address the new claim language.
Conclusion
This is a non-final rejection.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NATHAN ANDREW BOWERS whose telephone number is (571)272-8613. The examiner can normally be reached M-F 7am-5pm.
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/NATHAN A BOWERS/ Primary Examiner, Art Unit 1799
1 Phi29 polymerase is considered to be notoriously well known. See https://en.wikipedia.org/wiki/Φ29_DNA_polymerase