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 .
Drawings
The drawings as submitted by Applicant on 12/12/2023 have been accepted.
Disposition of Claims
Claims 1-26 are pending in the instant application. No claims have been added. Claims 2,4,6,7,9,14-19, and 21-26 have been amended. Claims 3, 10-13, and 20 have been cancelled. The rejection of pending claims 1, 2, 4-9, 14-19, and 21-26 is hereby made non-final.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 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)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1, 2, 4-9, 14-19, and 21-26 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by McGall et al (US 2017/0016063).
Regarding claim 1, the prior art discloses a method for characterizing polynucleotides in a sample, the method comprising: hybridizing first polynucleotides coupled to a first substrate to second polynucleotides in a sample (see at least paragraph [0223] to McGall et al); adding first labeled nucleotides to the first polynucleotides using a sequence of the second polynucleotides (see at least paragraph [0249] to McGall et al); measuring a first signal intensity from the first labeled nucleotides (see at least paragraph [0033] to McGall et al); adding second labeled nucleotides to the first polynucleotides using the sequence of the second polynucleotides (see at least paragraph [0251] to McGall et al); measuring a second signal intensity from the second labeled nucleotides (see at least paragraph [0033] to McGall et al); and normalizing the first signal intensity using the second signal intensity, the normalized first signal intensity characterizing the second polynucleotides in the sample (see at least paragraph [0181] to McGall et al).
Regarding claim 2, the prior art discloses the method of claim 1, wherein the second labeled nucleotides are added after the first labeled nucleotides are added, or wherein the second labeled nucleotides are added before the first labeled nucleotides are added (see at least paragraph [0251] to McGall et al).
Regarding claim 4, the prior art discloses the method of claim 1, further comprising: hybridizing third polynucleotides coupled to a second substrate to fourth polynucleotides in the sample; adding third labeled nucleotides to the third polynucleotides using a sequence of the fourth polynucleotides; measuring a third signal intensity from the third labeled nucleotides; adding fourth labeled nucleotides to the third polynucleotides using the sequence of the fourth polynucleotides; measuring a fourth signal intensity from the fourth labeled nucleotides; and normalizing the third signal intensity using the fourth signal intensity, the normalized third signal intensity characterizing the fourth polynucleotides in the sample (see at least paragraph [0255] to McGall et al).
Regarding claim 5, the prior art discloses the method of claim 4, further comprising calculating a difference or ratio between an amount of the second polynucleotides in the sample and an amount of the fourth polynucleotides in the sample using a difference or ratio between the normalized first signal intensity and the normalized third signal intensity (see at least paragraph [0210] to McGall et al, wherein one of skill in the art would appreciate that may be desirable to vary difference parameters such as surface properties to optimize molecular combing on an oligo chip or array).
Regarding claim 6, the prior art discloses the method of claim 4, wherein the fourth polynucleotides have a different sequence than the second polynucleotides (see at least paragraph [0179] to McGall et al, wherein he first and second adaptor sequences can be the same or can be different).
Regarding claim 7, the prior art discloses the method of claim 4, wherein the first substrate comprises a first bead, and wherein the second substrate comprises a second bead (see at least paragraph [0255] to McGall et al, wherein when the emulsion is broken, amplified fragments remain bound to the beads. The methods can include a step of rendering the nucleic acid bound to the beads single stranded or partially single stranded).
Regarding claim 8, the prior art discloses the method of claim 7, wherein the first bead is located within a first well, and the second bead is located within a second well (see at least paragraph [0255] to McGall et al, wherein the beads can be enriched and loaded into wells of a fiber optic slide so that there is approximately 1 bead in each well).
Regarding claim 14, the prior art discloses the method of claim 4, wherein the normalizing corrects for a difference between the first signal intensity and the third signal intensity that is caused by a number of the second polynucleotides coupled to the first substrate or a number of the fourth polynucleotides coupled to the second substrate (see at least paragraph [0255] to McGall et al, wherein the combination of signal intensity and positional information generated across the plate allows software to determine the DNA sequence).
Regarding claim 15, the prior art discloses the method of claim 4, wherein the normalized first signal intensity corresponds to an amount of a first single nucleotide polymorphism (SNP) in the sample, and the normalized third signal intensity corresponds to an amount of a second, different SNP in the sample (see at least paragraph [0087] to McGall et al, wherein where a genetic disease is any disease that can be linked to a genetic variation such as mutations, insertions, additions, deletions, translocation, point mutation, trinucleotide repeat disorders and/or single nucleotide polymorphisms (SNPs)).
Regarding claim 16, the prior art discloses the method of claim 4, wherein the normalized first signal intensity corresponds to an amount by which a first base is methylated in the sample, and the normalized third signal intensity corresponds to an amount by which the first base is not methylated in the sample (see at least paragraph [0255] to McGall et al, wherein the combination of signal intensity and positional information generated across the plate allows software to determine the DNA sequence).
Regarding claim 17, the prior art discloses the method of claim 1, wherein the first and second polynucleotides are hybridized to one another in solution (see at least paragraph [0170] to McGall et al, wherein the template nucleic acids can be single-stranded, and can be made double-stranded by primer extension. The primers used for primer extension can be in solution).
Regarding claim 18, the prior art discloses the method of claim 1, wherein the first substrate comprises a bead (see at least paragraph [0119] to McGall et al, wherein examples of surfaces include flow cells, sequencing flow cells, flow channels, microfluidic channels, capillary tubes, piezoelectric surfaces, wells, microwells, microwell arrays, microarrays, chips, wafers, non-magnetic beads, magnetic beads, ferromagnetic beads, paramagnetic beads, superparamagnetic beads, and polymer gels).
Regarding claim 19, the prior art discloses the method of claim 18, further comprising capturing the bead within a well, wherein the first and second labeled nucleotides are added after the bead is captured in the well (see at least paragraph [0119] to McGall et al, wherein examples of surfaces include flow cells, sequencing flow cells, flow channels, microfluidic channels, capillary tubes, piezoelectric surfaces, wells, microwells, microwell arrays, microarrays, chips, wafers, non-magnetic beads, magnetic beads, ferromagnetic beads, paramagnetic beads, superparamagnetic beads, and polymer gels).
Regarding claim 21, the prior art discloses the method of claim 19, wherein the first and second signal intensities are measured using a complementary metal oxide semiconductor (CMOS) sensor on which the well is disposed (see at least paragraph [0253] to McGall et al, wherein sequencing technique that can be used in the methods described herein is semiconductor sequencing provided by Ion Torrent (e.g., using the Ion Personal Genome Machine (PGM)). Ion Torrent technology can use a semiconductor chip with multiple layers, e.g., a layer with micro-machined wells, an ion-sensitive layer, and an ion sensor layer and paragraph [0119] to McGall et al).
Regarding claim 22, the prior art discloses the method of claim 1, wherein the second labeled nucleotide is added to a position adjacent to where the first labeled nucleotide is added (see at least paragraph [0251] to McGall et al, “labeled nucleotide probes”).
Regarding claim 23, the prior art discloses the method of claim 1, further comprising adding one or more additional nucleotides to positions between where the first and second labeled nucleotides respectively are added (see at least paragraph [0251] to McGall et al, “sequencing primer to determine which of the four bases are at those positions”).
Regarding claim 24, the prior art discloses the method of claim 1, wherein the first and second labeled nucleotides respectively comprise first and second fluorophores (see at least paragraph [0222] to McGill et al, “labeled with fluorophores”).
Regarding claim 25, the prior art discloses the method of claim 1, wherein characterizing the second polynucleotides in the sample comprises determining an amount of the second polynucleotides in the sample, identifying the first nucleotide, or both determining an amount of the second polynucleotides in the sample and identifying the first nucleotide (see at least paragraph [0134] to McGall et al).
Regarding claim 26, the prior art discloses the method of claim 1, wherein the second labeled nucleotide is coupled to a primer hybridized to a barcode oligonucleotide coupled to the first substrate (see at least paragraph [0081]to McGall et al, “barcoded oligo array”).
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
The examiner has considered all references listed on the Notice of References Cited, PTO-892.
The examiner has considered all references cited on the Information Disclosure Statement submitted by Applicant, PTO-1449.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to TALIA F CRAWLEY whose telephone number is (571)270-5397. The examiner can normally be reached on Monday thru Thursday; 8:30 AM-4:30 PM EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Fahd A Obeid can be reached on 571-270-3324. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/TALIA F CRAWLEY/ Primary Examiner, Art Unit 3627
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