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
Claims 1-20 and 29 are cancelled.
Claims 21-28 and 30-41 are pending and are examined on the merits.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. Priority of US application 62/593,547 filed 12/01/2017 is acknowledged.
Withdrawn Rejections/Objections
The rejection to claims 21-40 under 35 U.S.C. 112(b) in the Office action posted 1/15/2025 is withdrawn in view of claim amendments filed 09/25/2025.
Claim Objections
Claims 21 and 32 are objected to because of the following informalities: “an FLT3 gene” at the connection of the first two lines should read as “a FLT3 gene”.
Claim 40 is objected to because of the following informalities: “an FLT3 gene” at the connection of the 3rd ~4th lines should read as “a FLT3 gene”.
Claim 21 is objected to because of the following informalities: “the insert size of the duplication in the soft-clipped portion is determined based on a distance between duplicated copies;;” (page 3, ending clause of the 1st para), the duplicated “;;” should read as “;”.
Appropriate correction is required.
Double Patenting
This rejection is maintained from a previous Office Action. Minor modifications are necessitated by claim amendments.
Claims 21-18 and 30-40 of this application is patentably indistinct from claims 1-20 of Application No. US11961591 B2. Pursuant to 37 CFR 1.78(f), when two or more applications filed by the same applicant or assignee contain patentably indistinct claims, elimination of such claims from all but one application may be required in the absence of good and sufficient reason for their retention during pendency in more than one application. Applicant is required to either cancel the patentably indistinct claims from all but one application or maintain a clear line of demarcation between the applications. See MPEP § 822.
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).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 21-40 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. US11961591 B2. Although the claims at issue are not identical, they are not patentably distinct from each other because the current claims 21-28 and 30-40 are expected by the reference claims 1-20 respectively.
A side-by-side claim mapping is provided here:
Current claims
US11961591 B2 claims
21
A method for detecting an internal tandem duplication in an FLT3 gene of a sample, comprising:
amplifying a nucleic acid sample in a presence of a primer pool to produce a plurality of template polynucleotide strands, the primer pool including a plurality of target specific primers targeting regions of exons of the FLT3 gene;
disposing the plurality of template polynucleotide strands in a plurality of reaction confinement regions on a sensor array, wherein the sensor array comprises at least 105 sensors in electrical communication with the reaction confinement regions; exposing a plurality of the template polynucleotide strands disposed in the reaction confinement regions on the sensor array to a series of flows of sequencing reagents including nucleotide species and polymerase to obtain raw sequencing data reads for the template polynucleotide strands;
determining base sequences of the raw sequencing data reads by base calling to generate a plurality of reads;
mapping the reads to a reference sequence,
wherein the reference sequence includes the targeted regions of exons of the FLT3 gene, wherein the mapping produces a pileup comprising a plurality of alignments of the reads
with the reference sequence and a plurality of columns corresponding to positions along the reference sequence, wherein a portion of the plurality of
reads are partially mapped to the reference sequence for a plurality of partially mapped reads, wherein a partially mapped read includes a mapped portion, a soft-clipped portion and a breakpoint; analyzing the partially mapped reads intersecting a column of the pileup for tandem duplications, including: detecting a duplication in the soft-clipped portion by comparing a sequence of the soft- clipped portion to a sequence of the mapped portion of the partially mapped read adjacent to the breakpoint;
determining an insert size of the duplication in the soft-clipped portion, wherein if a length of an anchor portion of the soft-clipped portion is greater than or equal to a minimum length, the insert size is determined based on the anchor portion of the soft-clipped portion, wherein if the length of the anchor portion is less than the minimum length, the insert size of the duplication in the soft-clipped portion is determined based on a distance between duplicated copies;
to generate a plurality of categories corresponding to a plurality of insert sizes, each category having a number of members corresponding
to the filtered partially mapped reads having the corresponding insert size; converting the categories into features corresponding to the column, wherein a feature includes the insert size and a sequence of an insert at an insert position; and merging the features corresponding to one or more columns representing a same insert to determine a location and a size of a tandem duplication.
1
A method for detecting an internal tandem duplication in an FLT3 gene of a sample, comprising:
amplifying a nucleic acid sample in a presence of a primer pool to produce a plurality of template polynucleotide strands, the primer pool including a plurality of target specific primers targeting regions of exons of the FLT3 gene;
disposing the plurality of template polynucleotide strands in a plurality of reaction confinement regions on a sensor array, wherein the sensor array comprises at least 105 sensors in electrical communication with the reaction confinement regions;
exposing a plurality of the template polynucleotide strands disposed in the reaction confinement regions on the sensor array to a series of flows of sequencing reagents including nucleotide species and polymerase to obtain raw sequencing data reads for the template polynucleotide strands;
determining base sequences of the raw sequencing data reads by base calling to generate a plurality of reads, wherein the plurality of reads includes a plurality of forward reads and a plurality of reverse reads;
mapping the forward reads and the reverse reads to a reference genome, wherein the reference genome includes the targeted regions of exons of the FLT3 gene, wherein the mapping produces a pileup comprising a plurality of alignments of the forward reads and the reverse reads with the reference genome and a plurality of columns corresponding to positions along the reference genome, wherein a portion of the plurality of forward reads and the plurality of reverse
reads are partially mapped to the reference genome for a plurality of partially mapped reads, wherein a partially mapped read includes a mapped portion, a soft-clipped portion and a breakpoint; analyzing the partially mapped reads intersecting a column of the pileup for tandem duplications, including:
detecting a duplication in the soft-clipped portion by comparing a sequence of the soft-clipped portion to a sequence of the mapped portion of the partially mapped read adjacent to the breakpoint;
determining an insert size of the duplication in the soft-clipped portion;
filtering the detected duplications based on properties of duplicated copies to form filtered partially mapped reads; assigning the filtered partially mapped read to a category based on the insert size
to generate a plurality of categories corresponding to a plurality of insert sizes, each category having a number of members corresponding to the filtered partially mapped reads having the corresponding insert size;
converting the categories into features corresponding to the column, wherein a feature includes the insert size and a sequence of an insert at an insert position; and
merging the features corresponding to one or more columns representing a same insert to determine a location and a size of a tandem duplication.
22
(New) The method of claim 21, wherein the analyzing the partially mapped reads intersecting a column of the pileup further comprises determining whether the partially mapped read intersects the column at the breakpoint representing an end of alignment and a start of the soft-clipped portion, wherein the partially mapped read is a forward read.
2
The method of claim 1, wherein the analyzing the partially mapped reads intersecting a column of the pileup further comprises determining whether the partially mapped read intersects the column at the breakpoint representing an end of alignment and a start of the soft-clipped portion, wherein the partially mapped read is a forward read.
23
(New) The method of claim 21, wherein the analyzing the partially mapped reads intersecting a column of the pileup further comprises determining whether the partially mapped read intersects the column at the breakpoint representing a start of alignment and an end of the soft-clipped portion, wherein the partially mapped read is a reverse read.
3
The method of claim 1, wherein the analyzing the partially mapped reads intersecting a column of the pileup further comprises determining whether the partially mapped read intersects the column at the breakpoint representing a start of alignment and an end of the soft-clipped portion, wherein the partially mapped read is a reverse read.
24
(New) The method of claim 21, wherein the analyzing the partially mapped reads intersecting a column of the pileup further comprises determining an anchor portion of the soft-clipped portion that matches a portion of the reference sequence adjacent to the breakpoint.
4
The method of claim 1, wherein the analyzing the partially mapped reads intersecting a column of the pileup further comprises determining an anchor portion of the soft-clipped portion that matches a portion of the reference genome adjacent to the breakpoint.
25
(New) The method of claim 24, wherein the determining an anchor portion further comprises applying a string-matching method to the soft-clipped portion and an unmapped portion of the reference sequence adjacent to the breakpoint.
5
The method of claim 4, wherein the determining an anchor portion further comprises applying a string-matching method to the soft-clipped portion and an unmapped portion of the reference genome adjacent to the breakpoint.
26
(New) The method of claim 24, wherein the insert size of the duplication is based on a distance from the breakpoint to a position of the anchor portion in the soft-clipped portion.
6
The method of claim 4, wherein the determining an insert size of the duplication is based on a distance from the breakpoint to a position of the anchor portion in the soft-clipped portion.
27
(New) The method of claim 21, wherein the detecting a duplication applies a string- matching method to the soft-clipped portion and the mapped portion adjacent to the breakpoint.
7
The method of claim 1, wherein the detecting a duplication applies a string-matching method to the soft-clipped portion and the mapped portion adjacent to the breakpoint.
28
(New) The method of claim 21, further comprising filtering the categories for each column based on the number of members in the category.
8
The method of claim 1, further comprising filtering the categories for each column based on the number of members in the category.
30
(New) The method of claim 28, wherein the filtering the categories is based on a ratio of the number of members in the category to a coverage at the insert position.
10
The method of claim 8, wherein the filtering the categories is based on a ratio of the number of members in the category to a coverage at the insert position.
31
(New) The method of claim 21, wherein the merging the features further comprises applying a single-link clustering to the features.
11
The method of claim 1, wherein the merging the features further comprises applying a single-link clustering to the features.
32
(New) A system for detecting an internal tandem duplication in an FLT3 gene of a sample, comprising: a plurality of template polynucleotide strands disposed in a plurality of reaction confinement regions on a sensor array, wherein the sensor array comprises at least 105 sensors in electrical communication with the reaction confinement regions, wherein the template polynucleotide strands were obtained from the sample and prepared using multiplex amplification using a set of primers for FLT3 detection;
a machine-readable memory; and a processor configured to execute machine-readable instructions, which, when executed by the processor, cause the system to perform a method, comprising: exposing a plurality of the template polynucleotide strands disposed in the reaction confinement regions on the sensor array to a series of flows of sequencing reagents including nucleotide species and polymerase to obtain raw sequencing data reads for the template polynucleotide strands;
determining base sequences of the raw sequencing data reads by base calling to generate a plurality of reads;
mapping the reads to a reference sequence, wherein the reference sequence
includes targeted regions of exons of the FLT3 gene, wherein the mapping produces a pileup comprising a plurality of alignments of the reads with the
reference sequence and a plurality of columns corresponding to positions along the reference sequence, wherein a portion of the plurality of
reads are partially mapped to the reference sequence for a plurality of partially mapped reads, wherein a partially mapped read includes a mapped portion, a soft-clipped portion and a breakpoint;
analyzing the partially mapped reads intersecting a column of the pileup for tandem duplications, including: detecting a duplication in the soft-clipped portion by comparing a sequence of the soft- clipped portion to a sequence of the mapped portion of the partially mapped read adjacent to the breakpoint;
filtering the detected duplications based on properties of duplicated copies to form filtered partially mapped reads;
assigning the filtered partially mapped read to a category based on an insert size of the duplication
to generate a plurality of categories corresponding to a plurality of insert sizes, each category having a number of members corresponding to the filtered partially mapped reads having the corresponding insert size; converting the categories into features corresponding to the column, wherein a feature includes
the insert size and a sequence of an insert at an insert position; and merging the features corresponding to one or more columns representing a same insert to determine a location and a size of a tandem duplication.
12
A system for detecting an internal tandem duplication in an FLT3 gene of a sample, comprising:
a plurality of template polynucleotide strands disposed in a plurality of reaction confinement regions on a sensor array, wherein the sensor array comprises at least 105 sensors in electrical communication with the reaction confinement regions, wherein the template polynucleotide strands were obtained from the sample and prepared using multiplex amplification using a set of primers for FLT3 detection;
a machine-readable memory; and
a processor configured to execute machine-readable instructions, which, when executed by the processor, cause the system to perform a method, comprising: exposing a plurality of the template polynucleotide strands disposed in the reaction confinement regions on the sensor array to a series of flows of sequencing reagents including nucleotide species and polymerase to obtain raw sequencing data reads for the template polynucleotide strands;
determining base sequences of the raw sequencing data reads by base calling to generate a plurality of reads wherein the plurality of reads includes a plurality of forward reads and a plurality of reverse reads;
mapping the forward reads and the reverse reads to a reference genome, wherein the reference genome includes targeted regions of exons of the FLT3 gene, wherein the mapping produces a pileup comprising a plurality of alignments of the forward reads and the reverse reads with the reference genome and a plurality of columns corresponding to positions along the reference genome, wherein a
portion of the plurality of forward reads and the plurality of reverse reads are partially mapped to the reference genome for a plurality of partially mapped reads, wherein a partially mapped read includes a mapped portion, a soft-clipped portion and a breakpoint;
analyzing the partially mapped reads intersecting a column of the pileup for tandem duplications, including:
detecting a duplication in the soft-clipped portion by comparing a sequence of the soft-clipped portion to a sequence of the mapped portion of the partially mapped read adjacent to the breakpoint;
determining an insert size of the duplication in the soft-clipped portion;
filtering the detected duplications based on properties of duplicated copies to form filtered partially mapped reads;
assigning the filtered partially mapped read to a category based on the insert size
to generate a plurality of categories corresponding to a plurality of insert sizes, each category having a number of members corresponding to the filtered partially mapped reads having the corresponding insert size;
converting the categories into features corresponding to the column, wherein a feature includes the insert size and a sequence of an insert at an insert position; and
merging the features corresponding to one or more columns representing a same insert to determine a location and a size of a tandem duplication.
33
(New) The system of claim 32, wherein the analyzing the partially mapped reads intersecting a column of the pileup further comprises determining whether the partially mapped read intersects the column at the breakpoint representing an end of alignment and a start of the soft-clipped portion, wherein the partially mapped read is a forward read.
13
The system of claim 12, wherein the analyzing the partially mapped reads intersecting a column of the pileup further comprises determining whether the partially mapped read intersects the column at the breakpoint representing an end of alignment and a start of the soft-clipped portion, wherein the partially mapped read is a forward read.
34
(New) The system of claim 32, wherein the analyzing the partially mapped reads intersecting a column of the pileup further comprises determining whether the partially mapped read intersects the column at the breakpoint representing a start of alignment and an end of the soft-clipped portion, wherein the partially mapped read is a reverse read.
14
The system of claim 12, wherein the analyzing the partially mapped reads intersecting a column of the pileup further comprises determining whether the partially mapped read intersects the column at the breakpoint representing a start of alignment and an end of the soft-clipped portion, wherein the partially mapped read is a reverse read.
35
(New) The system of claim 32, wherein the analyzing the partially mapped reads intersecting a column of the pileup further comprises determining an anchor portion of the soft-clipped portion that matches a portion of the reference sequence adjacent to the breakpoint.
15
The system of claim 12, wherein the analyzing the partially mapped reads intersecting a column of the pileup further comprises determining an anchor portion of the soft-clipped portion that matches a portion of the reference genome adjacent to the breakpoint.
36
(New) The system of claim 35, wherein the
insert size of the duplication is based on a distance from the breakpoint to a position of the anchor portion in the soft-clipped portion.
16
The system of claim 15, wherein the determining an
insert size of the duplication is based on a distance from the breakpoint to a position of the anchor portion in the soft-clipped portion.
37
(New) The system of claim 32, wherein the detecting a duplication applies a string- matching method to the soft-clipped portion and the mapped portion adjacent to the breakpoint.
17
The system of claim 12, wherein the detecting a duplication applies a string-matching method to the soft-clipped portion and the mapped portion adjacent to the breakpoint.
38
(New) The system of claim 32, further comprising filtering the categories for each column based on the number of members in the category.
18
The system of claim 12, further comprising filtering the categories for each column based on the number of members in the category.
39
(New) The system of claim 32, wherein the merging the features further comprises applying a single-link clustering to the features.
19
The system of claim 12, wherein the merging the features further comprises applying a single-link clustering to the features.
40
(New) A computer-readable media comprising machine-readable instructions that, when loaded in a machine-readable memory and executed by a processor, are configured to cause a system to perform a method for detecting an internal tandem duplication in an FLT3 gene of a sample, comprising: exposing a plurality of template polynucleotide strands disposed on a sensor array to a series of flows of sequencing reagents including nucleotide species and polymerase to obtain raw sequencing data reads for the template polynucleotide strands, wherein the sensor array comprises at least 105 sensors in electrical communication with reaction confinement regions, wherein the template polynucleotide strands were obtained from the sample and prepared using multiplex amplification using a set of primers for FLT3 detection;
determining base sequences of the raw sequencing data reads by base calling to generate a plurality of reads, wherein the plurality of reads includes a plurality of forward reads and a plurality of reverse reads; mapping the
reads to a reference sequence, wherein the reference sequence includes targeted regions of exons of the FLT3 gene, wherein the mapping produces a pileup comprising a plurality of alignments of the
reads with the reference sequence and a plurality of columns corresponding to positions along the reference sequence, wherein a portion of the plurality of
reads are partially mapped to the reference sequence for a plurality of partially mapped reads, wherein a partially mapped read includes a mapped portion, a soft-clipped portion and a breakpoint;
analyzing the partially mapped reads intersecting a column of the pileup for tandem duplications, including: detecting a duplication in the soft-clipped portion by comparing a sequence of the soft- clipped portion to a sequence of the mapped portion of the partially mapped read adjacent to the breakpoint;
filtering the detected duplications based on properties of duplicated copies to form filtered partially mapped reads;
assigning the filtered partially mapped read to a category based on an insert size of the duplication to generate a plurality of categories corresponding to a plurality of insert sizes, each category having a number of members corresponding to the filtered partially mapped reads having the corresponding insert size; converting the categories into features corresponding to the column, wherein a feature includes the insert size and a sequence of an insert at an insert position; and merging the features corresponding to one or more columns representing a same insert to determine a location and a size of a tandem duplication.
20
A computer-readable media comprising machine-readable instructions that, when loaded in a machine-readable memory and executed by a processor, are configured to cause a system to perform a method for detecting an internal tandem duplication in an FLT3 gene of a sample, comprising:
exposing a plurality of template polynucleotide strands disposed on a sensor array to a series of flows of sequencing reagents including nucleotide species and polymerase to obtain raw sequencing data reads for the template polynucleotide strands, wherein the sensor array comprises at least 105 sensors in electrical communication with reaction confinement regions, wherein the template polynucleotide strands were obtained from the sample and prepared using multiplex amplification using a set of primers for FLT3 detection;
determining base sequences of the raw sequencing data reads by base calling to generate a plurality of reads wherein the plurality of reads includes a plurality of forward reads and a plurality of reverse reads;
mapping the forward reads and the reverse reads to a reference genome, wherein the reference genome includes targeted regions of exons of the FLT3 gene, wherein the mapping produces a pileup comprising a plurality of alignments of the forward reads and the reverse reads with the reference genome and a plurality of columns corresponding to positions along the reference genome, wherein a portion of the plurality of forward reads and the plurality of reverse reads are partially mapped to the reference genome for a plurality of partially mapped reads, wherein a partially mapped read includes a mapped portion, a soft-clipped portion and a breakpoint;
analyzing the partially mapped reads intersecting a column of the pileup for tandem duplications, including:
detecting a duplication in the soft-clipped portion by comparing a sequence of the soft-clipped portion to a sequence of the mapped portion of the partially mapped read adjacent to the breakpoint;
determining an insert size of the duplication in the soft-clipped portion;
filtering the detected duplications based on properties of duplicated copies to form filtered partially mapped reads;
assigning the filtered partially mapped read to a category based on the insert size to generate a plurality of categories corresponding to a plurality of insert sizes, each category having a number of members corresponding to the filtered partially mapped reads having the corresponding insert size;
converting the categories into features corresponding to the column, wherein a feature includes the insert size and a sequence of an insert at an insert position; and
merging the features corresponding to one or more columns representing a same insert to determine a location and a size of a tandem duplication.
As can be seen from the above mapping, the independent claims 21, 32 and 40 in the current invention are slightly broader than their corresponding reference claims. Particularly, 1) reference claims recite “reference genome” while instant corresponding claims recite “reference sequence”; 2) reference claims recite “the plurality of forward reads and the plurality of reverse reads” while instant corresponding claims recite “the plurality of reads”; and 3) reference claims recite “determining an insert size of the duplication in the soft-clipped portion” while instant corresponding claim now recite this limitation with more detail “wherein if a length of an anchor portion of the soft-clipped portion is greater than or equal to a minimum length, the insert size is determined based on the anchor portion of the soft-clipped portion, wherein if the length of the anchor portion is less than the minimum length, the insert size of the duplication in the soft-clipped portion is determined based on a distance between duplicated copies”. This conditional part for inset size determination is considered obvious. Because the reference claims 6 and 16 also teach: “determining an insert size of the duplication is based on a distance from the breakpoint to a position of the anchor portion in the soft- clipped portion”.
In all these three situations the reference claims expect the instant claims. Otherwise all the other dependent claims are patentably identical between the reference claims and their corresponding instant claims.
Therefore, the instant claims 21-28 and 30-40 are obvious over the reference claims 1-20, and are rejected on the ground of nonstatutory double patenting.
Response to Applicant Argument
In the Remarks filed 4/15/2025, Applicant argued (page 9, lower part through page 10 end) that the newly added element “wherein if a length of an anchor portion of the soft-clipped portion is greater than or equal to a minimum length, the insert size is determined based on the anchor portion of the soft-clipped portion, wherein if the length of the anchor portion is less than the minimum length, the insert size of the duplication in the soft-clipped portion is determined based on a distance between duplicated copies” to claims 21, 32 and 40 is not recited in the reference claims.
To response, the newly added element is obvious. A skilled person in art when looking at the cartoon picture covering the joint part of anchor/soft-clip portion, will come up with this conditional calculation of insert length. Because the reference claims 6 and 16 also teach: “determining an insert size of the duplication is based on a distance from the breakpoint to a position of the anchor portion in the soft- clipped portion”.
Hence, the nonstatutory double patenting rejection is maintained.
Claim Rejections - 35 USC§ 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 21-28 and 30-41 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Step 1: Process, Machine, Manufacture or Composition
Claims 21-28, 30-31 and 41 are directed to a process, here a "method," for detecting an internal tandem duplication in an FLT3 gene of a sample, with process steps like “amplifying,” “disposing,” “determining,” “mapping,” “analyzing,” “converting,” and “merging.”
Claims 32-39 is directed to a machine or manufacturer, here a “system,” for detecting an internal tandem duplication in an FLT3 gene of a sample, with structural components like: a plurality of template polynucleotide strands, a sensor array, a machine-readable memory and a processor.
Claim 40 is directed to another machine or manufacturer, here “a computer-readable media,” with structural components like: a computer-readable media and a processor.
Step 2A Prong One: Identification of an Abstract Idea
The claims recite:
Determining base sequences of the raw sequencing data reads by base calling to generate a plurality of reads (claims 21, 32 and 40);
--This step does not specify how exactly “base calling” is performed. Under a Broadest Reasonable Interpretation (BRI), this step recites observing the wavelet curves and mental decide which base (A/G/C/T/N) should be called. Therefore this step recites abstract ideas of mental processes.
Mapping the reads to a reference sequence, wherein the reference sequence includes the targeted regions of exons of the FLT3 gene, wherein the mapping produces a pileup comprising a plurality of alignments of the reads with the reference sequence and a plurality of columns corresponding to positions along the reference sequence, wherein a portion of the plurality of reads are partially mapped to the reference sequence for a plurality of partially mapped reads, wherein a partially mapped read includes a mapped portion, a soft-clipped portion and a breakpoint (claims 21, 32 and 40);
--This step reciting mapping short reads to a specific reference sequence (targeting the FLT3 gene). Under a BRI, this step can be achieved in human mind with perhaps the aid of a pen and paper. Therefore this step recites abstract ideas of mental processes.
Analyzing the partially mapped reads intersecting a column of the pileup for tandem duplications (claims 21, 32 and 40);
--This step does not specify how exactly “analyzing” is done. Under a BRI, this step recites observing the partially aligned (aka “mapped”) reads intersecting a column of the pileup for tandem duplications and make some judgements or decisions. Therefore this step recites abstract ideas of mental processes.
Detecting a duplication in the soft-clipped portion by comparing a sequence of the soft-clipped portion to a sequence of the mapped portion of the partially mapped read adjacent to the breakpoint (claims 21, 32 and 40);
--This step reciting comparing parts of a short sequence and then make some judgements or decisions (“detecting a duplication“). Under a BRI this step can be achieved in human mind with perhaps the aid of a pen and paper. Therefore this step recites abstract ideas of mental processes.
Determining an insert size of the duplication in the soft-clipped portion (claims 21, 32 and 40);
--This step reciting a judgement/decision-making process (“Determining an insert size of the duplication”) following a data observation (of “a duplication“). Therefore this step recites abstract ideas of mental processes.
Assigning the partially mapped read to a category based on the insert size to generate a plurality of categories corresponding to a plurality of insert sizes (claims 21, 32 and 40);
--This step reciting a judgement/decision-making process (“assigning … to a category”) following a data observation (of “the insert size“). Therefore this step recites abstract ideas of mental processes.
Converting the categories into features corresponding to the column, wherein a feature includes the insert size and a sequence of an insert at an insert position (claims 21, 32 and 40);
--This step reciting a data manipulation activity (“Converting the categories into features corresponding to the column”). Therefore this step recites an abstract idea of mental processes.
Merging the features corresponding to one or more columns representing a same insert to determine a location and a size of a tandem duplication (claims 21, 32 and 40);
--This step reciting a data manipulation activity (“Merging the features corresponding to one or more columns representing a same insert”) and a decision-making activity (“to determine”). Therefore this step recites an abstract idea of mental processes.
The abstract ideas recited in claims are evaluated under Broadest Reasonable Interpretations (BRI) and determined to each cover performance by abstract idea in the form of mental processes. The “mental processes” elements are procedures for observing, evaluating, analyzing/judging and organizing information. They can be achieved by a person with the help of a pen and a paper in their simplest embodiments. Hence they fit the definition for mental processes.
Because the steps do not clearly require more than instructions for a user to manually manipulate data using mental processes. The claims must therefore be examined further to determine whether the claims integrate the above-identified abstract ideas into a practical application (MPEP 2106.04(d)).
Step 2A Prong Two: Consideration of Practical Application
The claims result in a process of determining “a location and a size of a tandem duplication”, which reads on generating new data after analyzing existing data. The claims do not recite any additional elements that integrate the abstract idea/judicial exception into a practical application.
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than
a drafting effort designed to monopolize the exception.
Step 2B: Consideration of Additional Elements and Significantly More
The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea. The recited additional elements are drawn to:
Amplifying a nucleic acid sample in a presence of a primer pool to produce a plurality of template polynucleotide strands, the primer pool including a plurality of target specific primers targeting regions of exons of the FLT3 gene (claim 21);
Disposing the plurality of template polynucleotide strands in a plurality of reaction confinement regions on a sensor array, wherein the sensor array comprises at least 105 sensors in electrical communication with the reaction confinement regions (claim 21);
Exposing a plurality of the template polynucleotide strands disposed in the reaction confinement regions on the sensor array to a series of flows of sequencing reagents including nucleotide species and polymerase to obtain raw sequencing data reads for the template polynucleotide strands (claims 21, 32 and 40);
A system (claim 32);
A plurality of template polynucleotide strands disposed in a plurality of reaction confinement regions on a sensor array, wherein the sensor array comprises at least 105 sensors in electrical communication with the reaction confinement regions, wherein the template polynucleotide strands were obtained from the sample and prepared using multiplex amplification using a set of primers for FLT3 detection (claim 32);
A machine-readable memory (claim 32);
A processor (claims 32 and 40); and
A computer-readable media (claim 40).
The claims do not include additional elements that are sufficient to amount of significantly more than the judicial exception because it is routine and conventional to perform the acts of acquiring sequence data through target sequencing experiments. The high density sensor arrays including the 10^5 sensor arrays are commonly used in modern day NGS facilities. Other elements of the method include computer-controlled data acquiring and computerized data analysis, which are recitations of generic computer structure that serves to perform generic computer functions that are well-understood, routine, and conventional activities previously known to the pertinent industry. For example, in MPEP 2106.05(d).II, the courts have recognized and designated a list of laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity. Particularly the following three categories are highly related to the above identified additional elements:
ii. Using polymerase chain reaction to amplify and detect DNA, Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016); Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1377, 115 USPQ2d 1152, 1157 (Fed. Cir. 2015);
v. Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs., 818 F.3d at 1377; 118 USPQ2d at 1546; and
vii. Amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014).
The identified additional elements, can be summarized as amplifying the FLT3 target gene, then sequencing the target, then analyzing the sequenced reads to detect the tandem duplication and hence to provide the FLT3-ITD information. Hence they fit the conventional activities defined above. Additionally, the “sequencing” and “mapping” elements are achieved by commercially available service and commercially available software (Torrent Suite Software (Thermo Fisher Scientific Inc.), which further prove the conventionality of recited additional elements. Hence, at step 2B, the additional elements failed to provide the something to be significantly more.
Viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself.
Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
Claim Rejections - 35 USC § 103
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 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 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.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
Determining the scope and contents of the prior art.
Ascertaining the differences between the prior art and the claims at issue.
Resolving the level of ordinary skill in the pertinent art.
Considering objective evidence present in the application indicating obviousness or non-obviousness.
Claims 21-28 and 30-40 are rejected under 35 U.S.C. 103 as being unpatentable over Park (“Apparatus and Method For Detecting Internal Tandem
Duplication”, US 20160098517A1, 2016-04-07. Cited on the 4/29/2024 IDS), in view of Spencer (“Detection of FLT3 Internal Tandem Duplication in Targeted, Short-Read-Length, Next-Generation Sequencing Data,” The Journal of molecular diagnostics 15.1 (2013): 81-93. Cited on the 4/29/2024 IDS), Rothberg et al. (“Methods and apparatus for measuring analytes using large scale FET arrays”, US7948015B2, Publication of US20090127589A1: 2009-05-21. Newly cited) and Shimizu (“SlideSort: all pairs similarity search for short reads,” Bioinformatics 27.4 (2011): 464-470. Cited on the 4/29/2024 IDS).
Claim 21 is directed to a method for detecting an internal tandem duplication in an FLT3 gene of a sample, comprising:
amplifying a nucleic acid sample in the presence of a primer pool to produce a plurality of amplicons, the primer pool including a plurality of target specific primers targeting regions of exons of the FLT3 gene;
disposing the plurality of template polynucleotide strands in a plurality of reaction confinement regions on a sensor array, wherein the sensor array comprises at least 105 sensors in electrical communication with the reaction confinement regions;
exposing a plurality of the template polynucleotide strands disposed in the reaction confinement regions on the sensor array to a series of flows of sequencing reagents including nucleotide species and polymerase to obtain raw sequencing data reads for the template polynucleotide strands;
determining base sequences of the raw sequencing data reads by base calling to generate a plurality of reads
mapping the forward reads and the reverse reads to a reference genome, wherein the reference genome includes the targeted regions of exons of the FLT3 gene, wherein the mapping produces a pileup comprising a plurality of alignments of the reads with the reference genome and a plurality of columns corresponding to positions along the reference genome, wherein a portion of the plurality of forward/reverse reads are partially mapped to the reference genome for a plurality of partially mapped reads, wherein a partially mapped read includes a mapped portion, a soft-clipped portion and a breakpoint;
analyzing the partially mapped reads intersecting a column of the pileup for tandem duplications, including:
detecting a duplication in the soft-clipped portion by comparing a sequence of the soft- clipped portion to a sequence of the mapped portion of the partially mapped read adjacent to the breakpoint;
determining an insert size of the duplication in the soft-clipped portion;
assigning the partially mapped read to a category based on the insert size to generate a plurality of categories corresponding to a plurality of insert sizes, each category having a number of members corresponding to the partially mapped reads having the corresponding insert size;
converting the categories into features corresponding to the column, wherein a feature includes the insert size and a sequence of an insert at an insert position;
merging the features corresponding to one or more columns representing a same insert to determine a location and a size of a tandem duplication.
With respect to claim 21, Park discloses a method to detect the FLT3 ITD from NGS sequence ([0004-0005]), Spencer discloses a method for Detection of FLT3 Internal Tandem Duplication in Targeted, Short-Read-Length, Next-Generation Sequencing Data. Both Park and Spencer reads on the claim subject matter of detecting an internal tandem duplication in an FLT3 gene of a sample, further:
Park teaches an application of next generation sequencing (NGS) technology for “millions of short DNA fragments from a DNA sample of a certain organism”([0005]), which reads on the claim limitation “…to generate a plurality of reads”. Park did not disclose (a) the amplifying of nucleic acid samples as a prior step to acquire a plurality of amplicons for targeted regions of the FLT3 exons, nor the sequencing method as claimed in step b-d).
Spencer teaches (a) Prepare the sample DNA and amplify the FLT3 ITD by PCR (col 2, section “Samples”, “DNA Preparation” and “FLT3 ITD Testing by PCR and Capillary Electrophoresis” under “Materials and Methods”, page 82); Sequencing the DNA samples to generate many short reads (col 1, section “Targeted Next-Generation Sequencing of FLT3” under “Materials and Methods”, page 83). Spencer is silent in forward reads and reverse reads; Park discloses the sequence reads exist in a forward direction or a reverse direction ([52]) and matching can happen in both the forward and the reverse directions ([54, 60], Table 1).
Rothberg provides (col 13, 3rd para through col 13, 4th para):
“In another aspect, the invention provides a method for sequencing a nucleic acid comprising disposing a plurality of template nucleic acids into a plurality of reaction chambers, wherein the plurality of reaction chambers is in contact with an chemical-sensitive field effect transistor (chemFET) array comprising at least one chemFET for each reaction chamber, and wherein each of the template nucleic acids is hybridized to a sequencing primer and is bound to a polymerase, synthesizing a new nucleic acid strand by incorporating one or more known nucleotide triphosphates sequentially at the 3′ end of the sequencing primer, detecting the incorporation of the one or more known nucleotide triphosphates by the generation of sequencing reaction byproduct, wherein (a) the chemFET array comprises more than 256 sensors, or (b) a center-to-center distance between adjacent reaction chambers (or “pitch”) is 1-10 μm.
Various embodiments apply equally to the methods disclosed herein and they are recited once for brevity. In some embodiments, the center-to-center distance between adjacent reaction chambers is about 2-9 μm, about 2 μm, about 5 μm, or about 9 μm. In some embodiments, the chemFET array comprises more than 256 sensors (and optionally more than 256 corresponding reaction chambers (or wells), more than 103 sensors (and optionally more than 103 corresponding reaction chambers), more than 104 sensors (and optionally more than 104 corresponding reaction chambers), more than 105 sensors (and optionally more than 105 corresponding reaction chambers), or more than 106 sensors (and optionally more than 106 corresponding reaction chambers). In some embodiments, the chemFET array comprises at least 512 rows and at least 512 columns of sensors.”
Rothberg hence teaches (b) disposing the plurality of template polynucleotide strands in a plurality of reaction confinement regions on a sensor array, wherein the sensor array comprises at least 105 sensors in electrical communication with the reaction confinement regions;
Rothberg provides (col 13, last para through col 14, 1st para):
“In some embodiments, the sequencing reaction byproduct is inorganic pyrophosphate (PPi). In some embodiments, PPi is measured directly. In some embodiments, the PPi is measured in the absence of a PPi receptor. In some embodiments, the sequencing reaction byproduct is hydrogen ions. In some embodiments, the sequencing reaction byproduct is inorganic phosphate (Pi). In still other embodiments, the chemFET detects changes in any combination of the byproducts, optionally in combination with other parameters, as described herein.”
Rothberg hence teaches (c) Exposing a plurality of the template polynucleotide strands disposed in the reaction confinement regions on the sensor array to a series of flows of sequencing reagents including nucleotide species and polymerase to obtain raw sequencing data reads for the template polynucleotide strands;
Rothberg provides (col 17, lower part):
“FIG. 71A is a screen capture showing pixels with signal occurring after dATP was added (first) resulting in a 4 base extension in template 4 (see Tables 1 and 2) (left panel) and a plot of voltage versus frame (or time) for the arrowed pixels (right panel).
FIG. 71B is a screen capture showing pixels with signal occurring after dCTP was added next resulting in a 4 base extension in template 1 (see Tables 1, 2) (left panel) and a plot of voltage versus frame (or time) for the arrowed pixels (right panel).”
Rothberg hence teaches (d) Determining base sequences of the raw sequencing data reads by base calling.
Park discloses (e) mapping the sequence reads containing ITDs to a ITD reference sequence which ends up matching portion, nonmatching portion, and one end of a matching portion of each of the plurality of related reads may be mapped at one of the two breakpoints. (Fig. 1, [0020-0023]). The examiner notes that the “nonmatching portion” reads the claim limitation “soft-clipped portion” (see Fig. 3 in the instant application). Park is silent in “pileup” generated in mapping. Spencer teaches Mapping the reads to a reference genome (col 1 and col 2, section “Bioinformatic Analysis”, page 83). Which produce a pileup that partially mapped to the reference genome, a mapped portion, a soft-clipped portion and a breakpoint (Fig 3B, page 87).
Park discloses (f) a “ITD detection apparatus may further include a read mapping unit for mapping the plurality of reads with the reference genome sequence to identify a matching portion and a nonmatching portion of each of the plurality of reads” ([0010}), which reads on the claim limitation “analyzing the partially mapped reads intersecting a column of the pileup for tandem duplications”.
Park discloses (f.i) the detection of ITD in the nonmatching portion and between the two break points as discussed above. Park did not disclose determining the insert size, nor categorizing/featuring the insert size/insert sequence/insert position. Spencer teaches (f.ii) the determining of the ITD sizes (see Spencer Table 2). Spencer also teaches (f.iii) categorizing the ITDs by the ITD size (see Spencer Table 2). Shimizu teaches (f.iv, f.v ) “summarizing short reads for further processing” using “single link clustering” (Shimizu, page 469, left column, section “3.4 Clustering analysis of short reads”). The hierarchical clustering is one of the most frequently used method to summarize the relationships among nucleic acid sequences, and single-link clustering is a hierarchical clustering (examiner note).
Regarding claims 32 and 40, claim 32 is “system” version and claim 40 is the memory disk version of claim 21 (for “method” version). Since Park also teaches an embodiment of a computer program combined with hardware and computer readable storage medium for executing the FLT3 ITD detection method([0029], [0082], [0088]). The art applied to claim 21 also teaches claims 32 and 40.
Regarding claim 22, Park discloses all of the limitations as set forth above. Park further discloses the identification of a breakpoint at the end of a matching portion and a start of nonmatching portion (the soft-clipped portion) in a partially mapped forward read (see Fig. 3).
Regarding claim 23, Park discloses all of the limitations as set forth above. Park further discloses the identification of a breakpoint at the start of a matching portion and an end of nonmatching portion (the soft-clipped portion) in a partially mapped reverse read (see Fig. 3).
Regarding claim 24, Park discloses all of the limitations as set forth above. Park further discloses the identification of a second breakpoint (two breakpoints, [0009]), which reads on the claim limitation “determining an anchor portion”, because the anchor portion is in the reference sequence adjacent to the second breakpoint.
Regarding claim 26, Park discloses the detection of ITD in the nonmatching portion and between the two break points as discussed above. Park did not disclose determining the insert size. Spencer teaches the determining of the ITD sizes (see Table 2).
Regarding claims 25 and 27, Park did not disclose the string-matching method. Spencer’s pindel (page 83, col 2, 1st para) in view of Ye (Ye et al. "Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads." Bioinformatics 25.21 (2009): 2865-2871. Cited on the 4/29/2024 IDS) teaches string-matching (Ye: Page 2865, col 2, 2nd para and 3rd para). Since the string-matching method is effective for detecting the breakpoints, it is reasonable to applies a string-matching method to the soft-clipped portion and the mapped portion adjacent to the breakpoint in expectation of success to detect the duplication, because the duplication is located between the breakpoint and the anchor portion.
Regarding claim 28, and its dependent claim 30, Park did not disclose filtering the ITD detected by a threshold. Spencer teaches “An insertion event is reported if at least two reads support it” (see Spencer Fig 2), it is obvious for any person with ordinary skills in art to set an arbitrary number as the low bound for an insertion to be a qualified insertion. Here the unique insertions are assessed by the insertion size (defined as “categories” in the instant claims).
Regarding claim 30, Park teaches the application of “total number of read sequences with the mismatch ratio equal to or less than a particular value exceeds a preset critical value, it is determined that ITD is present in a genome sample ([0074])”. It is obvious for a person with ordinary skills in art to switch the nominator and denominator and achieve the same filtering effect.
Regarding claim 31, Park did not disclose the sing-link clustering method for summarizing the ITDs. Shimizu teaches “summarizing short reads for further processing” using single link clustering. It would be obvious for a person with ordinary skills in art to summarize the ITDs as the ITDs are short reads.
Claims 33-39 depend on claim 32, just like claims 22-24, 26-28, 31 depend on claim 21. Also, Claims 33-39 are very similar to claims 22-24, 26-28, 31 respectively. The difference between claims 33-39 and claims 22-24, 26-28, 31 lies in that claim 33-39 applied in the framework of a computing system while claims 22-24, 26-28, 31 applied in the framework of a method. Claim 33-39 are rejected as discussed above in claims 22-24, 26-28, 31, respectively.
It would have been prima facie obvious to combine Park’s method which detect the FLT3 ITD from NGS sequence ([0004-0005]), sequencing in a forward direction or a reverse direction ([52]), with Spencer’s method which enriches the target through PCR before NGS sequencing but no paired-end sequencing, because Park does not disclose amplifying of nucleic acid samples as a prior step to acquire a plurality of amplicons for targeted regions of the FLT3 exons but Spencer teaches preparing the sample DNA and amplify the FLT3 ITD by PCR (col 2, section “Samples”, “DNA Preparation” and “FLT3 ITD Testing by PCR and Capillary Electrophoresis” under “Materials and Methods”, page 82). One would reasonably expect success as both Park and Spencer are about detecting FLT3 gene ITDs and Spencer’s target enrichment through PCR will ensure more related sequence reads for ITD detection.
It would have been prima facie obvious to modified the combined Park and Spencer pipeline which detect the FLT3 ITD from target enrichment-NGS sequencing that sequencing in a forward direction or a reverse direction, with Rothberg large-scale FET arrays wherein the sensor array comprises at least 105 sensors in electrical communication with the reaction confinement regions, because Rothberg’s high-throughput sequencing method will ensure rapid, large-scale sequencing for the ITD detection. One would reasonably expect success as Park, Spencer and Rothberg are all using NGS method and Rothberg’s large-scale FET arrays with at least 105 sensors provides a customized solution to the NGS method.
It would have been prima facie obvious to modified the combined Park, Spencer and Rothberg pipeline which detect the FLT3 ITD from target enrichment-NGS sequencing that sequencing in a forward direction or a reverse direction through a customized NGS method, with Shimizu’s “single link clustering” (Shimizu, page 469, left column, section “3.4 Clustering analysis of short reads”) for summarizing short reads of ITDs, because the single-link clustering is a hierarchical clustering (examiner note) and hierarchical clustering is one of the most frequently used method to summarize the relationships among nucleic acid sequences. One would reasonably expect success as the combined Park, Spencer and Rothberg pipeline is about detecting and summarizing the FLT3 ITDs and Shimizu’s method of hierarchical clustering in summarizing the ITD sequences is a good addition to Park’s method to describe an insert by its chromosomal position (chromosomal coordination) and Spencer’s method of using the insert size of the ITD to summarize the ITDs.
Conclusion
No claims are allowed.
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/GL/
Patent Examiner
Art Unit 1686
/Anna Skibinsky/
Primary Examiner, AU 1635