DETAILED ACTION
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. This action is in response to the papers filed May 22, 2026. Applicant’s remarks and amendments have been fully and carefully considered but are not found to be sufficient to put the application in condition for allowance. Any new grounds of rejection presented in this Office Action are necessitated by Applicant's amendments. Any rejections or objections not reiterated herein have been withdrawn. This action is made FINAL.
Claims 59, 61-67, and 69 are currently pending and have been examined herein.
Claim Rejections - 35 USC § 101
3. 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 59 and 61-67 are rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exception without significantly more. The claims have been evaluated using the 2019 Revised Patent Subject Matter Eligibility Guidance (see Federal Register Vol. 84, No. 4 Monday, January 7, 2019).
Step 1: The claims are directed to the statutory category of a process.
Step 2A, prong one: Evaluate Whether the Claim Recites a Judicial Exception
Claim 59 recites the following limitation:
(3) detecting, using a computer, Indicator CA regions in the genomic sequence, wherein Indicator CA regions comprise Indicator loss of heterozygosity (LOH) Regions, Indicator telomeric allelic imbalance (TAI) Regions, and Indicator large scale transitions (LSTs), wherein
(a) an Indicator LOH Region is an LOH Region that is longer than 1.5 megabases but shorter than the entire length of the respective chromosome within which the LOH Region is located;
(b) an Indicator TAI Region is a TAI Region with allelic imbalance that (1) extends to one of the subtelomeres, (i1) does not cross the centromere and (iii) is longer than 1.5 megabases; and
(c) an Indicator LST is a ploidy-adjusted somatic copy number breakpoint along the length of a chromosome that is between two regions of at least 6 megabases in length.
The instant claims recite abstract ideas. The claims recite two types of abstract ideas that have been identified in the guidance.
The first type of abstract idea is a mental process. The “detecting” step, as recited in claim 59, is a process that, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of a generic computer. That is, other than reciting “using a computer,” nothing in the claim precludes the determining step from practically being performed in the human mind. Except for the “using a computer” language, the claim encompasses the user reading nucleic acid sequences and thinking about whether the nucleic acid sequences meet the criteria set forth in the claims for a LOH, TAI, and LST region. It is noted that the amount of base pairs that would need to be analyzed and the amount of time required to perform the analysis, is irrelevant for determining whether that procedure is a mental process: "the fact that the required calculations could be performed more efficiently via a computer does not materially alter the patent eligibility of the claimed subject matter. ... Using a computer to accelerate an ineligible mental process does not make that process patent-eligible" (Bancorp v. Sun Life, 103 USPQ2d 1425 at 1433-1434 (CAFC 2012)).
MPEP 2106.04(a)(2)(III)(A) states that claims recite a mental process when they contain limitations that can practically be performed in the human mind, including for example, observations, evaluations, judgments, and opinions. Examples of claims that recite mental processes include:
a claim to “collecting information, analyzing it, and displaying certain results of the collection and analysis,” where the data analysis steps are recited at a high level of generality such that they could practically be performed in the human mind, Electric Power Group v. Alstom, S.A., 830 F.3d 1350, 1353-54, 119 USPQ2d 1739, 1741-42 (Fed. Cir. 2016);
claims to “comparing BRCA sequences and determining the existence of alterations,” where the claims cover any way of comparing BRCA sequences such that the comparison steps can practically be performed in the human mind, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 763, 113 USPQ2d 1241, 1246 (Fed. Cir. 2014);
a claim to collecting and comparing known information (claim 1), which are steps that can be practically performed in the human mind, Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1067, 100 USPQ2d 1492, 1500 (Fed. Cir. 2011)
Further MPEP 2106.04(a)(2)(III)(C) states that a claim that requires a computer may still recite a mental process when the computer is generic.
An example of a case identifying a mental process performed on a generic computer as an abstract idea is Voter Verified, Inc. v. Election Systems & Software, LLC, 887 F.3d 1376, 1385, 126 USPQ2d 1498, 1504 (Fed. Cir. 2018). In this case, the Federal Circuit relied upon the specification in explaining that the claimed steps of voting, verifying the vote, and submitting the vote for tabulation are “human cognitive actions” that humans have performed for hundreds of years. The claims therefore recited an abstract idea, despite the fact that the claimed voting steps were performed on a computer. 887 F.3d at 1385, 126 USPQ2d at 1504. Another example is Versata, in which the patentee claimed a system and method for determining a price of a product offered to a purchasing organization that was implemented using general purpose computer hardware. 793 F.3d at 1312-13, 1331, 115 USPQ2d at 1685, 1699. The Federal Circuit acknowledged that the claims were performed on a generic computer, but still described the claims as “directed to the abstract idea of determining a price, using organizational and product group hierarchies, in the same way that the claims in Alice were directed to the abstract idea of intermediated settlement, and the claims in Bilski were directed to the abstract idea of risk hedging.” 793 F.3d at 1333; 115 USPQ2d at 1700-01.
The second type of abstract idea is mathematical concepts.
The claims recite that the LST region is “ploidy-adjusted”. The specification teaches that the LST Region Score can be modified by adjusting it by ploidy: LSTm=LST-kP, where P is ploidy and k is a constant (in some embodiments, k=15.5) (see paras 0056 and 0351). Thus detecting an Indicator LST that is ploidy adjusted requires performing a mathematical calculation.
Step 2A, prong two: Evaluate Whether the Judicial Exception Is Integrated Into a Practical Application
The claims do NOT recite additional steps or elements that integrate the recited judicial exceptions into a practical application of the exception(s). For example, the claims do not practically apply the judicial exception by including one or more additional elements that the courts have stated integrate the exception into a practical application:
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.
In addition to the judicial exceptions the claims require (1) contacting a ovarian, lung or esophageal cancer cell sample with at least 500 oligonucleotide probes capable of hybridizing to a plurality of polymorphic regions of human genomic DNA; and (2) sequencing, by a sequencer, the human genomic DNA. These steps are not considered to integrate the judicial exception into a practical application because they merely add insignificant extra-solution activity (data gathering) to the judicial exception.
Step 2B: Evaluate Whether the Claim Provides an Inventive Concept
In addition to the judicial exceptions the claims require (1) contacting a ovarian, lung or esophageal cancer cell sample with oligonucleotide probes capable of hybridizing to a plurality of polymorphic regions of human genomic DNA; and (2) sequencing, by a sequencer, the human genomic DNA. These steps do not amount to significantly more because they simply append well understood, routine, and conventional activities previously known in the art, specified at a high level of generality, to the judicial exceptions.
In the instant case the teachings in the specification demonstrate the well understood, routine, conventional nature of additional elements because it teaches that the additional elements are well known or commercially available. For example the specification teaches the following:
[0105] As described herein, identifying CA loci (as well as the size and number of CA Regions) can include, first, determining the genotype of a sample at various genomic loci (e.g., SNP loci, individual bases in large-scale sequencing) and, second, determining whether the loci exhibit any of LOH, TAI or LST. Any appropriate technique can be used to determine genotypes at loci of interest within the genome of a cell. For example, single nucleotide polymorphism (SNP) arrays (e.g., human genome-wide SNP arrays), targeted sequencing of loci of interest (e.g., sequencing SNP loci and their surrounding sequences), and even large-scale sequencing (e.g., whole exome, transcriptome, or genome sequencing) can be used to identify loci as being homozygous or heterozygous.
[0110] In some cases, targeted sequencing of known polymorphic loci (e.g., SNPs and surrounding sequences) can be done as an alternative to microarray analysis. For example, the genomic DNA can be enriched for those fragments containing a locus (e.g., SNP location) to be analyzed using kits designed for this purpose (e.g., Agilent SureSelect™, Illumina TruSeq Capture™, and Nimblegen SeqCap EZ Choice™). For example, genomic DNA containing the loci to be analyzed can be hybridized to biotinylated capture RNA fragments to form biotinylated RNA/genomic DNA complexes. Alternatively, DNA capture probes may be utilized resulting in the formation of biotinylated DNA/genomic DNA hybrids. Streptavidin coated magnetic beads and a magnetic force can be used to separate the biotinylated RNA/genomic DNA complexes from those genomic DNA fragments not present within a biotinylated RNA/genomic DNA complex. The obtained biotinylated RNA/genomic DNA complexes can be treated to remove the captured RNA from the magnetic beads, thereby leaving intact genomic DNA fragments containing a locus to be analyzed. These intact genomic DNA fragments containing the loci to be analyzed can be amplified using, for example, PCR techniques. The amplified genomic DNA fragments can be sequenced using a high-throughput sequencing technology or a next-generation sequencing technology such as Illumina HiSeq™, Illumina MiSeq™, Life Technologies SoLID™ or Ion Torrent™, or Roche 454™
Additionally the prior art demonstrates the well understood, routine, conventional nature of additional elements because it teaches that the additional elements are well known or commercially available.
For example Mertes (Briefings in Functional Genomics, Vol 10, Issue 6, November 2011 pages 374-386) is a review article that discusses the latest targeted enrichment methods and aspects of their utilization along with second-generation sequencing for complex genome analysis (abstract). Mertes teaches that hybrid capture is a technique for targeted enrichment. Mertes teaches that in this technique nucleic acid strands derived from the input sample are hybridized specifically to preprepared DNA fragments complementary to the targeted regions of interest, either in solution or on a solid support, so that one can physically capture and isolate the sequences of interest (page 375, 377). Mertes teaches that recently, an increasing number of protocols and vendors have begun offering out of the box solutions for hybrid capture, meaning, the researcher need not do development work but merely choose between a preset targeted enrichment regions (e.g. whole exome) or specify their own custom enrichment region. Example vendors include: Agilent (SureSelect product), NimbleGen (SeqCap EZ product), Flexgen and MycroArray (page 379). Mertes teaches that following targeted enrichment the DNA is sequenced using a sequencer (page 374-375).
Further it is noted that the courts have recognized the following 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.
Determining the level of a biomarker in blood by any means, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017);
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);
Detecting DNA or enzymes in a sample, Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157); Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017);
Immunizing a patient against a disease, Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1063, 100 USPQ2d 1492, 1497 (Fed. Cir. 2011);
Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs., 818 F.3d at 1377; 118 USPQ2d at 1546;
Freezing and thawing cells, Rapid Litig. Mgmt. 827 F.3d at 1051, 119 USPQ2d at 1375;
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)
For the reasons set forth above the claims are not directed to patent eligible subject matter.
Response To Arguments
4. In the response the Applicants traversed the rejection under 35 USC 101. In the response the Applicants argue that claim 59 does not recite a mental process. In particular they argue that the recited “detecting” step cannot be practically performed in the human mind. To perform the “detecting” step of claim 59 just for Indicator LOH Regions in the human mind, every nucleotide base pair over at least 1.5 megabases would need to be evaluated and compared to a control (e.g., a reference genome) to determine the presence of a LOH Region longer than 1.5 megabases but shorter than the entire length of the respective chromosome within which the LOH Region is located. Even assuming a human mind takes only 1 second to detect the presence of loss of heterozygosity at each nucleotide base pair, over 1.5 megabases this would take approximately 17 days to be performed in the human. Extrapolating this calculation over the approximately 240 million nucleotide base pairs of chromosome 1 as an example, detecting the presence of only Indicator LOH Regions in only one pair of human chromosomes would take approximately 7.5 years in the human mind.
This argument has been fully considered but is not persuasive. The amount of information that a data processing procedure involves, or the amount of time required to perform it, is irrelevant for determining whether that procedure is a mental process: "the fact that the required calculations could be performed more efficiently via a computer does not materially alter the patent eligibility of the claimed subject matter. ... Using a computer to accelerate an ineligible mental process does not make that process patent-eligible" (Bancorp v. Sun Life, 103 USPQ2d 1425 at 1433-1434 (CAFC 2012)). Analyzing 15 bases of a nucleic acid sequence to detect LOH compared to a reference sequence at each position can easily be performed mentally. Hence, analyzing 1.5 megabases can also be performed mentally; it just takes more total time. While the examiner generally agrees that the time required to analyze 1.5 megabases makes the process infeasible or cost-prohibitive to perform without a computer, infeasibility and cost-prohibitiveness are irrelevant to the determination of whether or not a claim element is, legally, a mental process. There is no threshold of complexity, infeasibility or cost above which a mental process ceases to be a mental process.
Additionally the Applicants argue that the claims do not recite mathematical concepts. They argue that the recitation of “ploidy-adjusted” does not explicitly set forth or recite a particular calculation, formula, or equation using word or mathematical symbols, even if such calculation might underpin or be encompassed within the claims. They argue that while the claims might “involve” a mathematical concept, they do not “recite” one.
This argument has been fully considered but is not persuasive. The claims recite that the LST region is “ploidy-adjusted”. The specification teaches that the LST Region Score can be modified by adjusting it by ploidy: LSTm=LST-kP, where P is ploidy and k is a constant (in some embodiments, k=15.5) (see paras 0056 and 0351). It’s not clear how one would be able to detect ploidy-adjusted LST without performing this calculation. Thus detecting an Indicator LST that is ploidy adjusted requires performing a mathematical calculation.
The Applicants argue that any alleged judicial exceptions are integrated into a practical application. The Applicants argue that the claims are eligible for the same reasons that claim 3 of Example 47 was found to be eligible. Applicants argue that the human mind is not equipped to detect Indicator CA regions in the genomic sequence comprising the particularly recited features. They argue that the claims, as a whole, represent their discovery that "using a combined analysis of two or more types of CA Regions (including two or more types of Indicator CA regions)" can be used "to assess (e.g., detect, diagnose) HRD in a sample." Specification as filed, paragraph [0051]. Such information can identify cancer patients that are likely to respond to a particular cancer treatment regimen. They argue that the claims do not “recite” a judicial exception, and that they provide an improvement to technology.
This argument has been fully considered but is not persuasive. As discussed above, it is maintained that step (3) is a judicial exception. In addition to the judicial exception step (3), the claims recite steps of (1) “contacting” and (2) “sequencing”. These steps do not provide integration because they merely add insignificant extra-solution activity (data gathering) to the judicial exception. In response to the argument that the claims provide improvements to the technical field of cancer therapy, it is noted that “technology” used by the claim is targeted amplification and sequencing. The additional elements cited by the Applicants, do not improve the technology of targeted amplification and sequencing and do not improve any other technology. The additional elements, do not make the technology of targeted amplification and sequencing work better and do not make any other technology work better. Detecting the combination of LOH, TAI, and LST cannot provide integration of the method into a practical application because the detecting step is the judicial exception. Therefore, it is maintained that judicial exceptions are not integrated into a practical application and do not provide an inventive step.
Claim Rejections - 35 USC § 112
5. The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 69 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 69 is rejected as being indefinite. The claim requires sequencing, by a sequencer, the human genomic DNA, thereby obtaining a genomic sequence comprising Indicator CA regions. The claim then states that the human genomic DNA comprises one or more Indicator CA regions comprising Indicator loss of heterozygosity (LOH) Regions, Indicator telomeric allelic imbalance (TAI) Regions, and Indicator large scale transitions (LSTs). The claim then states that Indicator LSTs are a ploidy-adjusted somatic copy number breakpoint along the length of a chromosome that are between two regions of at least 6 megabases in length. The claims are considered indefinite because it is unclear what it means for genomic DNA to “comprise” a ploidy-adjusted somatic copy number breakpoint. Clarification is required.
Claim Rejections - 35 USC § 103
6. 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 of this title, 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.
Claim 69 is rejected under 35 U.S.C. 103 as being unpatentable over Silver (WO 2013/0130347 Pub 9/6/2013 and Filed 2/22/2013 with priority to 61/602,460 Filed 2/23/2012 and 61,604,810 Filed 2/29/2012) in view of Sulonen (Genome Biology 2011 12:R94).
Regarding Claim 69 Silver teaches a method comprising determining a global chromosomal aberration score (GCAS), comprising obtaining a biological sample from the subject and determining whether a plurality of chromosomal regions displaying a chromosomal aberration exists within a plurality of chromosomal loci, wherein said chromosomal aberrations are allelic imbalance (AI) and loss of heterozygosity (LOH) relative to a control (para 0007). Silver teaches that the chromosomal loci are analyzed by next generation sequencing methods (para 0018, 0079). Silver teaches using a computer to analyze the sequence results (para 00211). Silver teaches that the biological sample comprises a cancer cell (para 0011). Silver teaches that cancer cell is from ovarian cancer, lung cancer, esophageal cancer (para 00157). Silver teaches the chromosomal regions being assayed are on at least two pairs of human chromosomes (para 00217 clms 29, 34). Silver defines a LOH region as a region of loss of heterozygosity that is longer than a first length but shorter than the length of the whole chromosome, wherein the first length is about 1.5 or more megabases (para 0029). Silver teaches that one type of AI that can be measured is telomeric imbalance. Silver defines a TAI region as a region of allelic imbalance that extends toward the telomere but does not cross the centromere, wherein the TAI region is 2 or more megabases (para 0081). Silver teaches that the GCAS is determined by adding together the number of individual chromosomal aberrations (para 0064). Silver teaches that a genome wide count of abnormal chromosomal regions in tumors can indicate the degree of DNA repair incompetence, independent of knowledge of any specific causative DNA repair detect (para 0094). Thus Silver teaches a method of sequencing, by a sequencer, human genomic DNA, thereby obtaining a genomic sequence comprising Indicator chromosomal aberration (CA) regions wherein the human genomic DNA comprises one or more Indicator CA regions comprising LOH regions or TAI regions.
Silver does not teach a method wherein the sample is contacted with at least 500 oligonucleotide probes capable of hybridizing to human genomic DNA at a plurality of polymorphic regions prior to sequencing.
However Sulonen is a review article that compares solution based exome capture methods for next generation sequencing. Sulonen compares kits sold by Agilent and NimbleGen. Sulonen teaches that Agilent SureSelect includes 346,500 and SureSelect 50MB 635,250 RNA probes (page 2, Table 1).
Accordingly, it would have been obvious to one of ordinary skill in the art at the time the invention was made to have modified the method of Silver by first contacting the sample is contacted with at least 500 oligonucleotide probes capable of hybridizing to human genomic DNA at a plurality of polymorphic regions prior to sequencing as suggested by Sulonen. The skilled artisan would have been motivated to capture exome sequences prior to sequencing since this is more cost effective and faster than sequencing the entire genome.
Double Patenting
7. 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 §§ 706.02(l)(1) - 706.02(l)(3) 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 USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The 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/process/file/efs/guidance/eTD-info-I.jsp.
8. Claim 69 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 37, 39-51, 53-64 of US Application 19/088496 in view of Sulonen (Genome Biology 2011 12:R94). Although the claims at issue are not identical, they are not patentably distinct from each other.
Regarding Claim 69 both sets of claims are drawn to a method that comprises sequencing human genomic DNA, thereby obtaining a genomic sequence comprising Indicator CA regions that comprise one or more Indicator CA regions comprising LOH, TAI, and LSTs (see clm 51 of the copending application). Both sets of claims encompass LOH Regions that are longer than 15 megabases but shorter than the entire length of the respective chromosome within which the LOH Region is located (see clm 51 of the copending application). Both sets of claims encompass TAI Regions that are regions with allelic imbalance that (i) extends to one of the subtelomeres, and (iii) is longer than 11 megabases (see clm 51 of the copending application). The instant claim is different from the copending ones because it requires contacting the sample with at least 500 oligonucleotide probes capable of hybridizing to human genomic DNA at a plurality of polymorphic regions prior to the sequencing step. However, Sulonen teaches this limitation (see 103 rejection above). It would have been obvious to modify the method of the copending application in view of Sulonen for the same reasons discussed in the 103 rejection.
9. Claim 69 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-6 of US Patent 10,400,278 in view of Sulonen (Genome Biology 2011 12:R94). Although the claims at issue are not identical, they are not patentably distinct from each other.
Regarding Claim 69 both sets of claims are drawn to a method that comprises sequencing human genomic DNA, thereby obtaining a genomic sequence comprising Indicator CA regions that comprise one or more Indicator CA regions comprising LOH, TAI, and LSTs (see clm 1 and 6 of the Patent). Both sets of claims state that a LOH Region is longer than 1.5 megabases but shorter than the entire length of the respective chromosome within which the LOH Region is located (see clm 1 of the Patent). Both sets of claims state that an TAI Region is a region with allelic imbalance that (i) extends to one of the subtelomeres, and (iii) is longer than 1.5 megabases (see clm 1 of the Patent). The instant claim is different from the claims of the patent because it requires contacting the sample with at least 500 probes capable of hybridizing to the human and sequencing the human genomic DNA. However Sulonen has been relied upon to teach this limitation (see 103 rejections above). It would have been obvious to modify the Patent by performing exome capture followed by sequencing to detect the regions since this method was known in the art at the time of the invention.
10. Claim 69 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 37-56 of US Application 19/048,611 in view of Sulonen (Genome Biology 2011 12:R94). Although the claims at issue are not identical, they are not patentably distinct from each other.
Regarding Claim 69 both sets of claims are drawn to a method that comprises sequencing human genomic DNA, thereby obtaining a genomic sequence comprising Indicator CA regions that comprise one or more Indicator CA regions comprising LOH, TAI, and LSTs (see clm 37 of the copending application). Both sets of claims state that a LOH Region is longer than 1.5 megabases but shorter than the entire length of the respective chromosome within which the LOH Region is located (see clm 37 of the copending application). Both sets of claims state that an TAI Region is a region with allelic imbalance that (i) extends to one of the subtelomeres, and (iii) is longer than 1.5 megabases (see clm 37 of the copending application). The instant claim is different from the copending ones because it requires contacting the sample with at least 500 oligonucleotide probes capable of hybridizing to human genomic DNA at a plurality of polymorphic regions prior to the sequencing step. However, Sulonen teaches this limitation (see 103 rejection above). It would have been obvious to modify the method of the copending application in view of Sulonen for the same reasons discussed in the 103 rejection.
11. Claim 69 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 74-76, 78-80, 85-87, 91-92, and 95 of US Application 18/076,279 in view of Sulonen (Genome Biology 2011 12:R94. Although the claims at issue are not identical, they are not patentably distinct from each other.
Regarding Claim 68 both sets of claims are drawn to a method that comprises sequencing human genomic DNA, thereby obtaining a genomic sequence comprising Indicator CA regions that comprise one or more Indicator CA regions comprising LOH, TAI, and LSTs (see clm 74 of the copending application). Both sets of claims state that a LOH Region is longer than 1.5 megabases but shorter than the entire length of the respective chromosome within which the LOH Region is located (see clm 75 of the copending application). Both sets of claims state that an TAI Region is a region with allelic imbalance that (i) extends to one of the subtelomeres, and (iii) is longer than 1.5 megabases (see clm 78 of the copending application). The instant claim is different from the copending ones because it requires contacting the sample with at least 500 oligonucleotide probes capable of hybridizing to human genomic DNA at a plurality of polymorphic regions prior to the sequencing step. However, Sulonen teaches this limitation (see 103 rejection above). It would have been obvious to modify the method of the copending application in view of Sulonen for the same reasons discussed in the 103 rejection.
12. Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMANDA HANEY whose telephone number is (571)272-8668. The examiner can normally be reached Monday-Friday, 8:15am-4:45pm EST.
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/AMANDA HANEY/Primary Examiner, Art Unit 1682
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