DETAILED ACTION
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 .
Status of claims: 100-119 are pending below.
Response to Arguments
Applicant’s arguments with respect to claims 100-119 have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
Applicant’s remarks – (page 4-5) Applicant argued Statement of Common Ownership, establishing that the present application and Staker were commonly owned or subject to an obligation of assignment to Apton Biosystems, Inc. not later than the effective filing date of the present application. Applicant notes that while the present application and Staker have since been assigned to a different entity - Illumina Cambridge Limited - these patent properties remain commonly owned and were commonly owned or subject to assignment to the same entity (i.e., Apton Biosystem, Inc.) not later than the September 19, 2018 effective date of the present application. Accordingly, Staker is disqualified as prior art under 35 U.S.C. 102(b)(2)(C). See MPEP 717.02(a). As Staker is not prior art under 35 USC 102(a)(1) and is disqualified as 35 USC 102(a)(2) prior art under 35 USC 102(b)(2)(C). Please see Remarks for further detail.
Examiner’s response – Examiner respectfully agree. And updated search has provided a new combination of prior arts that teaches the instant invention. Please see the Office Action below for further details.
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.
Claims 100-118 are rejected under 35 U.S.C. 103 as being unpatentable over Quake (2006/0019267) in view of KLEIN et al (US 2017/0128365) and Hesselberth (US 2015/0087526).
Claim 100:
Quake (2006/0019267) teaches the following subject matter:
A method of controlling a center-to-center distance of two molecules on a substrate, wherein the substrate is coupled to an optical system, the method comprising (figure 2 and 0056; 0122 detail optical instruments for imaging surface of substrate):
(b) placing the two molecules onto a substrate (figure 2 and 0122 detail concentration of cations, e.g., Mg.sup.2+, can be used to screen the electrostatic repulsion between the negatively-charged polynucleotides and the negatively-charged PEM surface); and
(c) imaging the substrate; wherein the center-to-center distance of the two molecules in an image is less than a diffraction limit of the optical system (figure 2 and 0122 detail bind such a small number of molecules to the surface that they are separated by more than the diffraction limit of optical instruments and thus able to be visualized individually.).
Quake et al teaches all the subject matter above, but not the following:
(a) treating the two molecules with an attractant or a repellant.
KLEIN et al (US 2017/0128365) teaches the following subject matter:
(a) treating the two molecules with an attractant or a repellant (0315 detail use of zwitterion as an electrostatic attraction).
Quake et al and KLEIN et al are both in the field of image analysis, especially analysis of molecules on a substrate regarding measurement of centers (KLEIN et al detail in 0311) such that the combine outcome is predictable.
Therefore it would have been obvious to one having ordinary skill before the effective filing date to modify Quake et al by KLEIN et al regarding attractant or repellant prove an effect highly effective lubrication hydrated charged groups as disclosed by KLEIN et al in 0312.
Quake et al and KLEIN et al both teach all the subject matter above, but not the following:
Separate from each other.
Hesselberth (US 2015/0087526) teaches the following subject matter: Separate from each other (0124 detail step (c) attaching each of said plurality of peptides to a surface such that each peptide is spatially separated enough to allow single-molecule detection, which is before (d) imaging each of said plurality of peptides using single-molecule detection, and 0129 and 0135).
Quake et al and KLEIN et al and Hesselberth are all in image analysis, especially imaging molecules with optical system on substrate for processing such that the combine outcome is predictable.
Therefore it would have been obvious to one having ordinary skill before the effective filing date to modify Quake et al and KLEIN et al by Hesselberth enables to determined by bioinformatic analysis based on the encoded amino acid sequence further provides peptide derivatization and immobilization strategies to enable the sequencing and identification of a single peptide or a plurality of peptides as disclosed by Hesselberth in 0136.
Claim 101:
KLEIN et al teach:
The method of claim 100, wherein the repellant or the attractant comprises zwitterionic features (0315).
Claim 102:
KLEIN et al teach:
The method of claim 100, wherein the repellant or the attractant comprises PEG (0443), a polysaccharide (0342), ampholine ampholytes, sulphobetaine, BSA, or any combination thereof.
Claim 103:
KLEIN et al teach:
The method of claim 100, wherein the treating the two molecules with the attractant or the repellant comprises encasing the two molecules in a shell of the attractant or the repellant (0499 detail coverage/encasing).
Claim 104:
KLEIN et al teach:
The method of claim 103, further comprising removing the shell of the two molecules prior to imaging the substrate (0458 detail rinsed in de-ionized water to remove; 0551 detail attributed to removal of residual intact).
Claim 105:
KLEIN et al teach:
The method of claim 100, wherein the placing of the two molecules onto the substrate comprises dragging or pulling the two molecules (0315 detail use of zwitterion as an electrostatic attraction).
Claim 106:
Quake teach:
The method of claim 100, further comprising exposing the two molecules placed onto the substrate to a gas-liquid interface such that the two molecules form a monolayer across the substrate (0131 detail tachment can be achieved by anchoring a hydrophobic chain into a lipidic monolayer or bilayer.).
Claim 107:
Quake teach:
The method of claim 106, wherein the gas-liquid interface is an air-water-interface (figure 6 and interface of glass (expose to air) and water, where refracted light was reflected back and not continued in the liquid phase as the critical angel for total internal reflection).
Claim 108:
Quake teach:
The method of claim 100, wherein the two molecules comprise concatemers (0333 comparing of sequence with one or more nucleotides downstream of the region of interest,).
Claim 109:
Quake teach:
The method of claim 108, wherein the concatemers are hybridized to ssDNA hairs (0102-0103; 0105-0106; 0117; 0130).
Claim 110:
Quake teach:
The method of claim 108, wherein the attractant or the repellant increases an effective exclusion size of the concatemers without altering a size of the concatemers (0099 detail consideration of various size; 0150; 0180; 0183-0186).
Claim 111:
Quake teach:
The method of claim 108, wherein the concatemers comprise an actively extending end (figure 12 and 0066 detail extending product; 0139 detail primer is extended by a polymerizing agent in the presence of a single type of nucleotide; 0284; 0311-0312).
Claim 112:
KLEIN et al teach:
The method of claim 111, wherein the actively extended away is raised above the substrate (0563).
Claim 113:
Quake teach:
The method of claim 100, wherein the two molecules are proteins or peptides (0090; 0132; 0137-0138; 0234).
Claim 114:
Quake teach:
The method of claim 100, wherein the substrate comprises a patterned surface (0129 detail measuring pattern on template; 0221-0222).
Claim 115:
Quake teach:
The method of claim 100, wherein the substrate comprises an unpatterned surface (0042 detail substrate to be flat (no pattern)).
Claim 116:
Quake teach:
The method of claim 100, wherein a plurality of molecules are disposed on the substrate at a density of about 1 to about 25 molecules per square micron (0024; 0096; 0121; 0269).
Claim 117:
Quake teach:
The method of claim 100, wherein the center-to-center distance between the two molecules is less than 400 nm (0255; 0263-0264; 0269-0270; 0388).
Claim 118:
Quake teach:
The method of claim 100, wherein the center-to-center distance between the two molecules is less than 300 nm (0255; 0263-0264; 0269-0270; 0388).
Claim 119 is rejected under 35 U.S.C. 103 as being unpatentable over Quake (2006/0019267) in view of KLEIN et al (US 2017/0128365).
Claim 119:
Quake (2006/0019267) teach following subject matter:
A method of sequencing a plurality of analytes disposed at high density on a surface of a substrate, comprising:
(i) contacting the plurality of analytes with a plurality of probes, a probe of the plurality of probes comprising a detectable label (0391 detail probes used with labeled and unlabeled); and
(ii) imaging a field of the surface with an optical system to detect an optical signal of a plurality of optical signals from each probe of the plurality of probes brought in contact with the plurality of analytes (0051 detail spatially addressable array, which comprises determining the sequences of a plurality of polynucleotide molecules in an array that has a surface density such that a molecule in said array is in an optically resolvable area; figure 2 and 0056);
(b) determining a peak location of an analyte of the plurality of analytes from each of the plurality of optical signals (figures 5-7 detail graphs where peaks can be determined); and
(c) identifying the analyte from the detectable label of the plurality of probes at the peak location across the plurality of cycles (figures 5-7 detail graph and 0367-0368 detail nice agreement between the expected positions for Cy3 incorporation in the polynucleotide template and the positions of the fluorescence intensity bands.).
Quake et al teaches all the subject matter above, but not the following:
(a) performing a plurality of cycles of probe binding to a substrate comprising a surface, wherein the surface comprises a plurality of analytes immobilized adjacent to the surface in a monolayer due to, at least in part, a repellant of one or more adjacent analytes and a repellant of an analyte of the plurality of analytes, wherein a cycle of the plurality of cycles comprising.
KLEIN et al (US 2017/0128365) teaches the following subject matter:
(a) performing a plurality of cycles of probe binding to a substrate comprising a surface, wherein the surface comprises a plurality of analytes immobilized adjacent to the surface in a monolayer due to, at least in part, a repellant of one or more adjacent analytes and a repellant of an analyte of the plurality of analytes, wherein a cycle of the plurality of cycles comprising (repellant (0315 detail use of zwitterion as an electrostatic attraction).
Quake et al and KLEIN et al are both in the field of image analysis, especially analysis of molecules on a substrate regarding measurement of centers (KLEIN et al detail in 0311) such that the combine outcome is predictable.
Therefore it would have been obvious to one having ordinary skill before the effective filing date to modify Quake et al by KLEIN et al regarding attractant or repellant prove an effect highly effective lubrication hydrated charged groups as disclosed by KLEIN et al in 0312.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Marini et al (US 2006/0148104) Detection Of Ion Channel Or Receptor Activity – 0223: The distance between two particles (or other components) can be measured with respect to any fixed points of the particles (or components), e.g., between the centers of two spherical particles, the centers of mass of two irregularly shaped particles or components.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to TSUNG-YIN TSAI whose telephone number is (571)270-1671. The examiner can normally be reached 7am-4pm.
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, Bhavesh Mehta can be reached at (571) 272-7453. 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.
/TSUNG YIN TSAI/Primary Examiner, Art Unit 2656
