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 .
DETAILED ACTION
This Non-Final Office Action is responsive to the communication received 12/20/2023.
Claims 11-19 are pending.
Claims 11-19 are under examination in this Office Action.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
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Claims 11-19 are rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 1-10 of U.S. Patent Number 11098360.
Although the conflicting claims are not identical, they are not patentably distinct from each other because the present claim 11 is drawn to a method for enriching from a sample a plurality of structurally different target polynucleotides, wherein individual target polynucleotides of the plurality comprise immune cell receptor V, and J gene regions, the method comprising: a) providing a reaction mixture comprising: i) the plurality of structurally different target polynucleotides; and ii) a plurality of immune cell receptor J gene specific primers, wherein the plurality of immune cell receptor J gene specific primers having the following regions from 5′ to 3′: [5′-Phos], [SPLINT], [BARCODE], and [FW], wherein: [5′-Phos] comprises a 5′ phosphate; [SPLINT] comprises an adaptor hybridization site of 2-8 nucleotides in length; [BARCODE] comprises a barcode region of at least 6 nucleotides in length, wherein each nucleotide of the barcode region is independently selected from the group consisting of N and W; and [FW] of each immune cell receptor J gene specific primer comprises a structurally distinct region that specifically hybridizes to an immune cell receptor J gene, wherein the immune cell receptor J gene specific primers are hybridized to the J gene regions of the target polynucleotides; b) extending the hybridized immune cell receptor J gene specific primers with a polymerase, and then removing un-extended immune cell receptor J gene specific primers, if present, wherein the extended immune cell receptor J gene specific primers comprise at least a portion of the immune cell receptor J region and at least a portion of the immune cell receptor V region; c) hybridizing a first universal adaptor to the [SPLINT] adaptor hybridization site of the extended immune cell receptor J gene specific primers, wherein said first universal adaptor is a double-stranded adaptor comprising a single-stranded overhang region that hybridizes to the [SPLINT] adaptor hybridization site of said extended primers; d) ligating the hybridized first universal adapters to the extended immune cell receptor J gene specific primers, and then removing un-ligated adapters, if present; e) hybridizing a plurality of immune cell receptor V gene specific primers to the V region portions of the extended immune cell receptor C gene specific primers, wherein the immune cell receptor V gene specific primers comprise a 3′ V gene hybridizing region and a 5′ second universal adapter region; and f) extending the hybridized immune cell receptor V gene specific primers with a polymerase, thereby forming a plurality of structurally different double-stranded products, each comprising at least a portion of the immune cell receptor V region and at least a portion of the immune cell J region flanked by a first and second universal adapter sequence and claim 1 in U.S. Patent Number 11098360 is drawn to a method for enriching from a sample a plurality of structurally different target polynucleotides, the method comprising: a) providing a reaction mixture comprising: i) a plurality of structurally different target polynucleotides, wherein individual target polynucleotides of the plurality comprise immune cell receptor V, J, and optionally C or D gene regions; and ii) a plurality of immune cell receptor V gene specific primers, wherein the immune cell receptor V gene specific primers comprise at least 10 structurally distinct primers having the following regions from 5′ to 3′: [SPLINT], [BARCODE], and [FW], wherein: [SPLINT] comprises an adaptor hybridization site of 2-8 nucleotides in length; [BARCODE] comprises a barcode region of at least 6 nucleotides in length, wherein each nucleotide of the barcode region is independently selected from the group consisting of N and W; and [FW] of each immune cell receptor V gene specific primer comprises a structurally distinct region that specifically hybridizes to a framework 1, framework 2, or framework 3 region of an immune cell receptor V gene, wherein the immune cell receptor V gene specific primers are hybridized to the V gene regions of the target polynucleotides; b) extending the hybridized immune cell receptor V gene specific primers with a polymerase, and then removing un-extended immune cell receptor V gene specific primers, if present, wherein the extended immune cell receptor V gene specific primers comprise at least a portion of the immune cell receptor V region, optionally the immune cell receptor D region, at least a portion of the immune cell receptor C region, and at least a portion of the immune cell receptor J region; c) hybridizing a first universal adaptor to the [SPLINT] adaptor hybridization site of the extended immune cell receptor V gene specific primers; d) hybridizing a plurality of immune cell receptor J gene specific primers to the J region portions of the extended immune cell receptor V gene specific primers, wherein the immune cell receptor J gene specific primers comprise a 3′ J gene hybridizing region and a 5′ second universal adapter region or hybridizing a plurality of immune cell receptor C gene specific primers to the C region portions of the extended immune cell receptor V gene specific primers, wherein the immune cell receptor C gene specific primers comprise a 3′ C gene hybridizing region and a 5′ second universal adapter region; and e) extending the hybridized immune cell receptor J gene specific primers or C gene specific primers with a polymerase, thereby forming a plurality of structurally different double-stranded products, each comprising at least a portion of the immune cell receptor V region, optionally the immune cell receptor D region, and at least a portion of the immune cell receptor J region or C region flanked by a first and second universal adapter sequence.
Therefore, the present claims are obvious in view of the claims of U.S. Patent Number 11098360.
Claims 11-19 are rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 1-10 of U.S. Patent Number 11725307.
Although the conflicting claims are not identical, they are not patentably distinct from each other because the present claim 11 is drawn to a method for enriching from a sample a plurality of structurally different target polynucleotides, wherein individual target polynucleotides of the plurality comprise immune cell receptor V, and J gene regions, the method comprising: a) providing a reaction mixture comprising: i) the plurality of structurally different target polynucleotides; and ii) a plurality of immune cell receptor J gene specific primers, wherein the plurality of immune cell receptor J gene specific primers having the following regions from 5′ to 3′: [5′-Phos], [SPLINT], [BARCODE], and [FW], wherein: [5′-Phos] comprises a 5′ phosphate; [SPLINT] comprises an adaptor hybridization site of 2-8 nucleotides in length; [BARCODE] comprises a barcode region of at least 6 nucleotides in length, wherein each nucleotide of the barcode region is independently selected from the group consisting of N and W; and [FW] of each immune cell receptor J gene specific primer comprises a structurally distinct region that specifically hybridizes to an immune cell receptor J gene, wherein the immune cell receptor J gene specific primers are hybridized to the J gene regions of the target polynucleotides; b) extending the hybridized immune cell receptor J gene specific primers with a polymerase, and then removing un-extended immune cell receptor J gene specific primers, if present, wherein the extended immune cell receptor J gene specific primers comprise at least a portion of the immune cell receptor J region and at least a portion of the immune cell receptor V region; c) hybridizing a first universal adaptor to the [SPLINT] adaptor hybridization site of the extended immune cell receptor J gene specific primers, wherein said first universal adaptor is a double-stranded adaptor comprising a single-stranded overhang region that hybridizes to the [SPLINT] adaptor hybridization site of said extended primers; d) ligating the hybridized first universal adapters to the extended immune cell receptor J gene specific primers, and then removing un-ligated adapters, if present; e) hybridizing a plurality of immune cell receptor V gene specific primers to the V region portions of the extended immune cell receptor C gene specific primers, wherein the immune cell receptor V gene specific primers comprise a 3′ V gene hybridizing region and a 5′ second universal adapter region; and f) extending the hybridized immune cell receptor V gene specific primers with a polymerase, thereby forming a plurality of structurally different double-stranded products, each comprising at least a portion of the immune cell receptor V region and at least a portion of the immune cell J region flanked by a first and second universal adapter sequence and claim 1 in U.S. Patent Number 11725307 is drawn to a method for enriching from a sample a plurality of structurally different target polynucleotides, the method comprising: a) providing a reaction mixture comprising: i) a plurality of structurally different target polynucleotides, wherein individual target polynucleotides of the plurality comprise immune cell receptor V, J, and optionally C or D gene regions; and ii) a plurality of immune cell receptor V gene specific primers, wherein the immune cell receptor V gene specific primers comprise at least 10 structurally distinct primers having the following regions from 5′ to 3′: [SPLINT], [BARCODE], and [FW], wherein: [SPLINT] comprises an adaptor hybridization site of 2-8 nucleotides in length; [BARCODE] comprises a barcode region of at least 6 nucleotides in length, wherein each nucleotide of the barcode region is independently selected from the group consisting of N and W; and [FW] of each immune cell receptor V gene specific primer comprises a structurally distinct region that specifically hybridizes to a framework 1, framework 2, or framework 3 region of an immune cell receptor V gene, wherein the immune cell receptor V gene specific primers are hybridized to the V gene regions of the target polynucleotides; b) extending the hybridized immune cell receptor V gene specific primers with a polymerase, and then removing un-extended immune cell receptor V gene specific primers, if present, wherein the extended immune cell receptor V gene specific primers comprise at least a portion of the immune cell receptor V region, optionally the immune cell receptor D region, at least a portion of the immune cell receptor C region, and at least a portion of the immune cell receptor J region; c) hybridizing a first universal adaptor to the [SPLINT] adaptor hybridization site of the extended immune cell receptor V gene specific primers; d) hybridizing a plurality of immune cell receptor J gene specific primers to the J region portions of the extended immune cell receptor V gene specific primers, wherein the immune cell receptor J gene specific primers comprise a 3′ J gene hybridizing region and a 5′ second universal adapter region or hybridizing a plurality of immune cell receptor C gene specific primers to the C region portions of the extended immune cell receptor V gene specific primers, wherein the immune cell receptor C gene specific primers comprise a 3′ C gene hybridizing region and a 5′ second universal adapter region; and e) extending the hybridized immune cell receptor J gene specific primers or C gene specific primers with a polymerase, thereby forming a plurality of structurally different double-stranded products, each comprising at least a portion of the immune cell receptor V region, optionally the immune cell receptor D region, and at least a portion of the immune cell receptor J region or C region flanked by a first and second universal adapter sequence.
Therefore, the present claims are obvious in view of the claims of U.S. Patent Number 11725307.
Closest Prior Art
The following is the closest prior art:
Dewitt et al. (5/19/2016) US Patent Application Publication 2016/0138011 A1 cited in the 06/28/2023 IDS (hereinafter known as "Dewitt") represents the closest prior art. Dewitt teaches a method for estimating the absolute abundance individually for each unique rearranged lymphocyte receptor in a mixed sample (see [0016], [0027], [0034], [0135] and claims 1, 3-5, 7, 16, 18-20 and 24-25). Dewitt does not explicitly teach a method for enriching from a sample a plurality of structurally different target polynucleotides, wherein individual target polynucleotides of the plurality comprise immune cell receptor V, and J gene regions, the method comprising: a) providing a reaction mixture comprising: i) the plurality of structurally different target polynucleotides; and ii) a plurality of immune cell receptor J gene specific primers, wherein the plurality of immune cell receptor J gene specific primers having the following regions from 5′ to 3′: [5′-Phos], [SPLINT], [BARCODE], and [FW], wherein: [5′-Phos] comprises a 5′ phosphate; [SPLINT] comprises an adaptor hybridization site of 2-8 nucleotides in length; [BARCODE] comprises a barcode region of at least 6 nucleotides in length, wherein each nucleotide of the barcode region is independently selected from the group consisting of N and W; and [FW] of each immune cell receptor J gene specific primer comprises a structurally distinct region that specifically hybridizes to an immune cell receptor J gene, wherein the immune cell receptor J gene specific primers are hybridized to the J gene regions of the target polynucleotides; b) extending the hybridized immune cell receptor J gene specific primers with a polymerase, and then removing un-extended immune cell receptor J gene specific primers, if present, wherein the extended immune cell receptor J gene specific primers comprise at least a portion of the immune cell receptor J region and at least a portion of the immune cell receptor V region; c) hybridizing a first universal adaptor to the [SPLINT] adaptor hybridization site of the extended immune cell receptor J gene specific primers, wherein said first universal adaptor is a double-stranded adaptor comprising a single-stranded overhang region that hybridizes to the [SPLINT] adaptor hybridization site of said extended primers; d) ligating the hybridized first universal adapters to the extended immune cell receptor J gene specific primers, and then removing un-ligated adapters, if present; e) hybridizing a plurality of immune cell receptor V gene specific primers to the V region portions of the extended immune cell receptor C gene specific primers, wherein the immune cell receptor V gene specific primers comprise a 3′ V gene hybridizing region and a 5′ second universal adapter region; and f) extending the hybridized immune cell receptor V gene specific primers with a polymerase, thereby forming a plurality of structurally different double-stranded products, each comprising at least a portion of the immune cell receptor V region and at least a portion of the immune cell J region flanked by a first and second universal adapter sequence.
Conclusion
No claim is allowed.
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/CHRISTIAN C BOESEN/Primary Examiner, Art Unit 1684
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