Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
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.
Claim 1 rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being incomplete for omitting essential structural cooperative relationships of elements, such omission amounting to a gap between the necessary structural connections. See MPEP § 2172.01. The omitted structural cooperative relationships are: “the sample comprises template molecules of a nucleic acid” and “fluorescently labeled nucleotides”. The flowcell receives a sample of template molecules of nucleic acid but then the detector detects fluorescently labeled nucleotides from that same surface. It is unclear if they are overlapping, both present, or not connected. Clarification is required.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of pre-AIA 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a) the invention was known or used by others in this country, or patented or described in a printed publication in this or a foreign country, before the invention thereof by the applicant for a patent.
(b) the invention was patented or described in a printed publication in this or a foreign country or in public use or on sale in this country, more than one year prior to the date of application for patent in the United States.
Claims 1, 2, 3, 4, 5, 7, 9, 10, 11, 12, 13, and 15 are rejected under pre-AIA 35 U.S.C. 102(b) as being anticipated by Feng U.S. Publication 2006/0209309.
With respect to claim 1, Feng discloses a system of facilitating focusing an optical scanner comprising:
A flowcell having a surface to receive a sample, wherein the sample comprises template molecules of nucleic acids (flowcell = slide, P.0050, P.0044, P.0041-42)
An optical assembly to relatively scan the surface in a x or y direction (P.0064)
A detector to detect fluorescently labeled nucleotides on the surface of the flowcell (P.0043, P.0028)
A system controller configured to carry out cycles of a sequencing process on the template molecules of nucleic acids, wherein each cycle of the sequencing process comprises contacting the template molecules with a sequencing reagent of the fluorescently labeled nucleotides (P.0044)
Determine a focus score of the detected fluorescently labeled nucleotides on a region of the surface of the flowcell (P.0068, focus score = correction amount)
Adjust a focus setting for a region of the surface of the flowcell based upon the determined focus score by shifting a z direction distance between the optical assembly and the surface of the flowcell (P.0058)
With respect to claim 2, 3, 5, and 7, Feng discloses all of the limitations as applied to claim 1 above. In addition, Feng discloses:
2- The optical assembly is configured to perform line scanning (Figure 2, P.0025, P.0064)
3- The optical assembly is configured to perform step-and-shoot scanning (P.0064, section by section)
4- the detector is configured to detect the fluorescently labeled nucleotides on the surface of the flowcell by deriving spots from images of the fluorescently labeled nucleotides (P.0044, spot = particular array location)
5- the focus score is determined based upon one or more image quality parameters selected from the group consisting of image contrast (P.0067)
It should be noted that the limitation in claim 7 that the fluorescently labeled nucleotides possess a reversible termination property fails to limit the device and distinguish over prior art since the fluorescently labeled nucleotides are not a component of the system but rather an intended use of the detector.
With respect to claim 9, Feng discloses a method for facilitating focusing of an optical scanner comprising:
Receiving a sample by a surface of flowcell, wherein the sample comprises template molecules of nucleic acids (P.0044, P.0050)
Relatively scanning the surface in a x or y direction by the optical assembly (P.0025)
Detecting fluorescently labeled nucleotides on a surface of the flowcell (P.0044, P.0073)
Carrying out cycles of a sequencing process on the template molecules of nucleic acids, wherein each cycle of the sequencing process comprises contacting the template molecules with a sequencing reagent of the fluorescently labeled nucleotides (P.0044)
Determining a focus score of the detected fluorescently labeled nucleotides on a region of the surface of the flowcell (P.0022, focus score = correction function)
Adjusting a focus setting for a region of the surface of the flowcell based upon the determined focus score by shifting a z direction distance between the optical assembly and the surface of the flowcell (P.0022, P.0052, P.0067)
With respect to claim 10, 11, 12, 13, and 15, Feng discloses all of the limitations as applied to claim 9 above. In addition, Feng discloses:
10- The optical assembly is configured to perform line scanning (Figure 2, P.0025, P.0064)
11- The optical assembly is configured to perform step-and-shoot scanning (P.0064, section by section)
12- the detector is configured to detect the fluorescently labeled nucleotides on the surface of the flowcell by deriving spots from images of the fluorescently labeled nucleotides (P.0044, spot = particular array location)
13- the focus score is determined based upon one or more image quality parameters selected from the group consisting of image contrast (P.0067)
It should be noted that the limitation of claim 15 that “the fluorescently labeled nucleotides possess a reversible termination property” is not limiting methodically on the method claim. The limitation is a structural characteristic that does not affect the manner in which the method is performed.
Claim Rejections - 35 USC § 103
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained through the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim 6 and 14 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Feng U.S. Publication 2002/0061529 in view of Batchelder et al. U.S. Patent #5,133,602.
With respect to claim 6 and 14, , Feng fails to disclose the spot size is measured as a full width half maximum of the spots.
Batchelder discloses determining locations of particles comprising:
6- measuring a spot size of a particle as a full width half maximum of the spots to analyze focus (Col.7, l 36-50)
It would have been obvious to one of ordinary skill in the art at the time of the invention to use the full width half maximum calculation of Batchelder for the focus score calculations in Feng since FWHM is well known in the art as an accurate yet simple manner of determining a point spread for analyzing how focused a light beam or an object in an image is from raw data.
Claim 8 and 16 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Feng U.S. Publication 2002/0061529 in view of Turcatti et al. “A new class of cleavable fluorescence nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis”.
With respect to claim 8 and 16, Feng discloses all of the limitations as applied to claims 1 and 9 above. However, Feng fails to disclose sequencing comprises sequencing by synthesis.
Turcatti discloses sequencing of fluorescence nucleotides comprising:
8, 16- the sequencing process comprises sequencing by synthesis (abstract)
It would have been obvious to one of ordinary skill in the art at the time of the invention to use sequencing by synthesis for the sequencing of Feng since SBS approaches were known at the time of invention, available as a suitable option for someone sequencing fluorescent nucleotides like Feng, and provides the benefit of being cost effective, efficient, and thorough.
Citation
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
Bridgham et al. U.S. Publication 2006/0061529 discloses sequential processing of analytes.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to REBECCA CAROLE BRYANT whose telephone number is (571)272-9787. The examiner can normally be reached M-F, 12-4 pm.
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/REBECCA C BRYANT/Primary Examiner, Art Unit 2877
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