Claim Listing:
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`This claim listing reflects all claim amendments and replaces all prior versions, and
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`listings, of claims in the application. Material to be inserted is in bold and underline, and
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`material to be deleted is in strikeeut or,
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`if the deletion is of five or fewer consecutive
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`characters or would be difficult to see, in double brackets [[ ]].
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`In brief, the present communication cancels claims 2, 5, 7, 11-13, 17, 20, 21, 32, 36,
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`39, 59, 75, 89, 102, and 105, without prejudice, and amends claims 1, 4, 10, 15, 16, 22, 23,
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`25, 35, and 101.
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`1.
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`(Currently amended) A method of detecting copy number of a target
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`polynucleotide within a population of genetic material, the method comprising:
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`a) binding a first ligation probe to a first target polynucleotide;
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`b) binding a second ligation probe to a second target polynucleotide;
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`c) subjecting said first and second ligation probes to a ligation reaction te—eletain
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`wherein said ligation reaction ioins a 5’ region of the first ligation probe to a 3’
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`region of the first ligation probe to obtain a circular first ligated product and ioins
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`a 5’ region of the second ligation probe to a 3’ region of the second ligation probe
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`to obtain a circular second ligated product;
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`d) partitioning said circular first and second one—emanate ligated products into
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`two or more partitions, wherein said two or more partitions are aqueous droplets;
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`e) amplifying a region within said circular first and second ene—eemere ligated
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`products to obtain amplified products, wherein the amplifying occurs in said two or more
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`partitions;
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`f) detecting said partitions to determine a number of said partitions that contain
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`said amplified products; and
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`g) calculating a copy number of said first target polynucleotide based on said
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`number of said partitions.
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`2.
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`(Canceled)
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`3.
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`(Previously presented) The method of claim 1, wherein during said
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`amplification process said two or more partitions remain intact or stable.
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`4.
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`(Currently amended) The method of claim 1, wherein during said detecting
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`detemqining of step (f), said two or more partitions remain intact or stable.
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`5.
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`(Canceled)
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`6.
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`(Previously presented) The method of claim 1, wherein said partitioning of
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`step (d) does not comprise partitioning said first and second target polynucleotides.
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`7.
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`(Canceled)
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`8.
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`(Original) The method of claim 1, wherein said first
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`ligation probe is
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`designed to bind to a polynucleotide sequence that is conserved between individuals
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`within a species.
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`9.
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`(Canceled)
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`10.
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`(Currently amended) The method of claim 1, wherein a continuous oil phase
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`encloses comprises said aqueous droplets.
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`11-13. (Canceled)
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`14.
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`(Previously presented) The method of claim 1, wherein said first target
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`polynucleotide is not identical to said second target polynucleotide.
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`15.
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`(Currently amended) The method of claim 14, wherein said first target
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`polynucleotide is a test polynucleotide ehremeseme and said second target
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`polynucleotide is a reference polynucleotide ehremeseme.
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`16.
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`(Currently amended) The method of claim 15, wherein said test
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`polynucleotide is provided by a chromosome [[is]] selected from the group consisting
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`of[[:]] chromosome 21, chromosome 13, chromosome 18, and an X chromosome.
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`17.
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`(Canceled)
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`18.
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`(Original) The method of claim 1, wherein said first target polynucleotide is
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`a segment of a chromosome.
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`19.
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`(Previously presented) The method of claim 18, wherein said segment of a
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`chromosome is associated with fetal aneuploidy.
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`20.
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`(Canceled)
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`21.
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`(Canceled)
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`22.
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`(Currently amended) The method of claim 1 [[20]], wherein said 5' region
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`and said 3' region of said first
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`ligation probe are [[each]] designed to bind adjacent
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`sequences within said first target polynucleotide.
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`23.
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`(Currently amended) The method of claim 1 [[20]], wherein said 5' region
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`and said 3' region of said first ligation probe are [[each]] designed to bind neighboring
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`sequences within said first target polynucleotide.
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`24.
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`(Previously presented) The method of claim 23, wherein said neighboring
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`sequences are separated by at least one nucleotide.
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`25.
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`(Currently amended) The method of claim 24, wherein said ligation reaction
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`further comprises a template-driven gap fill
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`reaction to incorporate one or more
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`nucleotides in a region between said 5' region and said 3' region of said first ligation probe.
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`26.
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`(Original) The method of claim 1, wherein said first ligation probe comprises
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`a site cleavable by an enzyme.
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`27.
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`(Previously presented) The method of claim 26, wherein said site cleavable
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`by an enzyme comprises one or more uracils.
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`28.
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`(Previously presented) The method of claim 26, wherein said site cleavable
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`by an enzyme comprises a restriction site.
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`29.
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`(Original) The method of claim 1, wherein said first
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`ligation probe is a
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`padlock probe.
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`30.
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`(Original) The method of claim 1, wherein said first
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`ligation probe is a
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`molecular inversion probe.
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`31.
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`(Original) The method of claim 1,
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`further comprising performing an
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`enzymatic reaction to remove linear polynucleotides.
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`32.
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`(Canceled)
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`33.
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`(Previously presented) The method of claim 1, wherein said first ligation
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`probe is conjugated to a first signaling agent and wherein said second ligation probe is
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`conjugated to a second signaling agent.
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`34.
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`(Previously presented) The method of claim 33, wherein said first signaling
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`agent is a fluorescent marker of a first color and said second signaling agent is a
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`fluorescent marker of a second color.
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`35.
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`(Currently amended) The method of claim 1, wherein said detecting
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`detemqining of step (f) comprises detecting said first ligation probe with a first signaling
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`agent and detecting said second ligation probe with a second signaling agent.
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`36.
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`(Canceled)
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`37.
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`(Original) The method of claim 35, wherein said first target polynucleotide
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`is a test chromosome and said second target polynucleotide is a reference chromosome.
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`38.
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`(Original) The method of claim 14, wherein said first and second ligation
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`probes are conjugated to a signaling agent with the same signaling color.
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`39-100.
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`(Canceled).
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`101.
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`(Currently amended) The method of claim 1, further comprising performing
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`an enzymatic reaction to remove said first and second target polynucleotidesrwherein
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`amplification step.
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`102-105.
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`(Canceled)
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