DETERMINATION OF LYMPHOCYTE ABUNDANCE IN MIXED SAMPLES

§101 §102 §103 §112 §DOUBLEPATENT

DETAILED ACTION Notice of Pre-AIA or AIA Status 1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . Claim status 2. Claims 1-21 are currently pending and under exam herein. Claims 1-21 are rejected. Claim 6 is objected to. Priority 3. This application is a continuation of International Application No. PCT/EP2022/070694, which designated the United States and was filed on 22 July 2022. Claimed benefit of foreign priority to GB20110555.06, filed on 22 July 2021 and GB2203451.06 filed 11 March 2022 is acknowledged. In this action, all claims are examined as though they had an effective filing date of 22 July 2021. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further analysis of the disclosure(s) of the priority application(s). Information Disclosure Statement 4. The information disclosure statements (IDSs) submitted on 19 January 2024, 24 April 2024 and 6 April 2026 are being considered by the examiner except where references lined through. Two references were lined through on the IDS submitted on 19 January 224 because they were duplicate references and one reference was lined through on the IDS submitted on 24 April 2024 because it was not found in the application. Drawings 5. The drawing submitted on 12 August 2024 are accepted by the examiner. Claim Interpretation 6. Claims 1 and 10 refer to a region of interest that is ‘likely’ to be deleted. Although ‘likely’ is a term of degree, it is not considered indefinite in this case because it provides enough certainty to one of ordinary skill in the art in the context of the claim. In addition, examples of establishing if a region of interest is likely to be deleted is provided in the specification (p. 9, line 28-p. 10, line 31). Claim 18, recites: “the method of claim 1, further comprising providing a prognosis for a subject that has been diagnosed as having cancer by determining the lymphocyte fraction in one or mor tumor samples from the subject”, which is interpreted to mean that the prognosis is based on the lymphocyte fraction determined using the method of claim 1. Claim Objections 7. Claim 6 is objected to because of the following informalities: Claim 6 recites: “wherein a read depth profile is obtained”, but ‘a read depth profile’ has already been introduced in the preceding claim family in claim 1. Therefore, it is not clear if this is a second ‘read depth profile’ or the same ‘read depth profile’ previously introduced. A possible correction is to change claim 6 to “wherein the read depth profile is obtained” or “wherein a second read depth profile is obtained”. For the purpose of examination, ‘a read depth profile’ in claim 6 will be considered to be the same read depth profile obtained in claim 1. Appropriate correction is required. Claim Rejections - 35 USC § 112 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. 8. Claims 2-5, 10, 14 and 17 are 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 2 refers to Table 8 of the specification. This is improper claim form because claims should be complete in themselves without incorporation by reference to drawings or the specification (see MPEP 2173.05(s)). Claims 3-5 are also rejected by virtue of their dependence on claim 2 and for failing to resolve the indefiniteness issue. Claim 10 recites “(such as e.g. all D segments)”. It is unclear if the limitation in parentheses is intended to be a limitation or not and if it is a limitation, it includes exemplary language. Claim 14 has two ‘wherein’ clauses but it is unclear if both clauses are required because there is no conjunction between them. Both conjunctions have been deleted in the amended claims. Claim 17 uses the term ‘for example’, which is exemplary claim language that can lead to confusion over the intended scope of the claim (see MPEP 2173.05(d)). 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. 9. Claims 1-21 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. Step 2A, Prong 1 In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea: Claims 1 and 21 recite: obtaining a plurality of read depth ratios (r1) by normalising the read depths along the predetermined region of interest by reference to a baseline read depth derived from a subset of the region of interest Claims 1 and 21 recite: obtaining a summarised read depth ratio value (rVDJ) for a subset of the region of interest that is likely to be deleted through VDJ recombination Claims 1 and 21 recite: determining the fraction of lymphocytes (f) in the sample as a function of the summarised read depth ratio value (rvDJ) Claim 7 recites: the method of claim 1, wherein determining the fraction of lymphocytes (f) in the sample as a function of the summarised read depth ratio value (rVDJ) comprises determining the fraction of lymphocytes (f) in the sample as a function of the summarised read depth ratio value (rVDJ), the fraction of abnormal cells (p) in the mixed sample, wherein abnormal cells are those that are aneuploid in the predetermined region of interest, and a copy number of the abnormal cells in the predetermined region of interest(ψT) Claim 8 recites: the method of claim 7, wherein determining the fraction of lymphocytes (f) in the sample comprises determining the value of f as f = 1 - p + γ 2 ψ T - ( 1 - p +   γ 2 ψ T ) 2 r V D J T wherein γ is a constant. Claim 9 recites: the method of claim 1, wherein determining the fraction of lymphocytes (f) in the sample comprises determining the value of f as f = 1 - 2 r V D J γ wherein γ is a constant Claim 10 recites: the method of claim 1, wherein the subset of the region of interest that is likely to be deleted through VDJ recombination comprises a region located between the end of a last V segment of the genomic locus that undergoes VDJ recombination, and the start of a J segment of the genomic locus that undergoes VDJ recombination, wherein the subset of the region of interest that is likely to be deleted through VDJ recombination comprises one or more D segments (such as e.g. all D segments) of the genomic locus that undergoes VDJ recombination. Claim 11 recites: the method of claim 1, further comprising fitting a model to the plurality of read depth ratios Claim 11 recites: wherein obtaining a summarised read depth ratio value (rVDJ) for a subset of the region of interest that is likely to be deleted through VDJ recombination comprises obtaining a summarised read depth ratio value based on the value of the model in the subset of the region of interest that is likely to be deleted through VDJ recombination Claim 11 recites: wherein the model is a general linear model, a piecewise constrained linear model with a plurality of breakpoints selected to correspond to locations of a plurality of V and J genes in the region of interest, or a Bayesian model modelling segment usage from the read depth and a prior distribution of usage of each of a plurality of V and J genes in the region of interest Claim 12 recites: the method of claim 1, further comprising obtaining a baseline read depth from a subset of the region of interest, wherein the baseline read depth is a summarised read depth value across a subject of the region of interest Claim 13 recites: the method of claim 1, wherein the subset of the region of interest used to obtain the baseline read depth is a subset of the region of interest that is unlikely to be deleted through VDJ recombination Claim 14 recites: the method of claim 13, wherein the subset of the region of interest that is unlikely to be deleted through VDJ recombination comprise the n first V segments of the genomic locus that undergoes VDJ recombination, wherein the subset of the region of interest that is unlikely to be deleted through VDJ recombination comprises a C segment of the genomic locus that undergoes VDJ recombination Claim 15 recites: smoothing the read depth values, wherein smoothing the read depth values comprises replacing the raw read depth values by a corresponding rolling median over a window of a predetermined width Claim 18 recites: the method of claim 1, further comprising providing a prognosis for a subject that has been diagnosed as having cancer, by determining the lymphocyte fraction in one or more tumour samples from the subject Claim 19 recites: the method of claim 1, further comprising determining whether a subject that has been diagnosed as having cancer is likely to respond to immunotherapy by determining the lymphocyte fraction in one or more tumour samples from the subject Claim 20 recites: the method of claim 1, further comprising determining whether a subject has T cell lymphopenia by determining the lymphocyte fraction in one or more samples from the subject The limitations regarding normalising the read depths, obtaining a summarised read depth ratio value, determining the fraction of lymphocytes in the sample, determine the value of f, fitting a model to the plurality of read depth ratios, obtaining a summarised read depth ratio, obtaining a baseline read depth and replacing the raw read depth values by a corresponding rolling median are verbal equivalents that describe a mathematical calculation that is performed as the limitation and are so simple that they could be performed (in the human mind) with pen and paper. Therefore, these limitations fall under the "Mathematical concepts" and "Mental processes" groupings of abstract ideas. The limitations that further limit whether abnormal cells are accounted for in the calculation of lymphocyte fraction, which region of genome is used as ‘likely’ or ‘unlikely’ to be deleted through recombination, the algorithm type of the model, and which genomic region is used to obtain a baseline of read depth, merely further limit the judicial exceptions , but do not change their positions as abstract ideas. The limitations directed to ‘determining whether a subject is likely to respond to immunotherapy’, ‘providing a prognosis’ and ‘determining whether a subject has T cell lymphopenia’ are generically recite data analysis steps that can be practically performed in the human mind because the human mind is capable of identifying relevant information, comparing values, determining information from other values and categorizing data. Therefore, these limitations fall under the "Mental processes" groupings of abstract ideas. Furthermore, the limitation ‘providing a prognosis’ also falls into the “Organizing human activity” grouping of abstract ideas because it is directed to managing an interaction between a patient and a doctor. While claim 21 recites performing some aspects of the analysis with a processor, there are no additional limitations that indicate that this processor requires anything other than carrying out the recited mental process or mathematical concept in a generic computer environment. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then if falls within the "Mental processes" grouping of abstract ideas. Furthermore, claims 19-20 directed to ‘ determining whether a subject is likely to respond to immunotherapy by determining the lymphocyte fraction’ in tumor samples from the subject and ‘determining whether a subject has T cell lymphopenia’ by determining the lymphocyte fraction in one or more samples from the subject are also considered to be in the ‘natural phenomenon’ category of judicial exceptions because they reflect a natural relationship between the level of recombination in a tumor and the prognosis and response to treatment of the patient. As such, claims 1-21 recite one or more judicial exceptions (Step 2A, Prong 1: YES). Step 2A, Prong 2 Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). This judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology or applies or uses the recited judicial exception in some other meaningful way. Rather, the instant claims recite additional elements that amount to mere instructions to implement the abstract idea in a generic computing environment or insignificant extra-solution activity. Specifically, the claims recite the following additional elements: Claim 1 recites: a method of determining a fraction of lymphocytes in a mixed sample comprising genomic material from multiple cell types Claims 1 and 21 recite: obtaining a read depth profile for the sample comprising read depths along a predetermined genomic region of interest, wherein the predetermined genomic region of interest includes at least a portion of a genomic locus that undergoes VDJ recombination Claim 2 recites: the method of claim 1, wherein a genomic locus that undergoes VDJ recombination is selected from TCRA, TCRB, TCRG, TCRD, IGH, IGL or IGK gene locus, and wherein the fraction of lymphocytes is a fraction of T lymphocytes, a fraction of B lymphocytes, a fraction of αβ T lymphocytes, a fraction of γδ T lymphocytes, a fraction of B cells or T cells including any gene segment in the TCRA, TCRB, TCRG, TCRD, IGH, IGL or IGK gene locus, or a fraction of B cells or T cells including any gene segments listed in Table 8 Claim 3 recites: the method of claim 2, wherein the predetermined region of interest includes one or more exons from the TCRA, TCRB, TCRG, TCRD, IGH, IGL or IGK gene locus Claim 4 recites: the method of claim 2, wherein the predetermined region of interest includes a plurality of exons from the TCRA, TCRB, TCRG, TCRD, IGH, IGL or IGK gene locus, wherein the plurality of exons comprise at least one exon corresponding to each of a V, D and C segment of the respective gene locus Claim 5 recites: the method of claim 4, wherein the plurality of exons comprise exons corresponding to multiple V segments of the respective gene locus Claim 6 recites. the method of claim 1, wherein a read depth profile is obtained from sequencing data, whole genome sequencing, or panel sequencing data Claim 15 recites: the method of claim 1, wherein obtaining a read depth profile comprises obtaining a plurality of raw read depth values across the predetermined region of interest Claim 16 recites: The method of claim 1, wherein the mixed sample is a blood sample or a tumour sample Claim 16 recites: wherein the method further comprises obtaining a mixed sample comprising genomic material from multiple cell types, from a subject, or obtaining read depth data from a mixed sample comprising genomic material from multiple cell types, from a subject through one or more in vitro steps Claim 17 recites: the method of claim 1, further comprising providing to a user, for example through a user interface, the determined lymphocyte fraction and/or any value derived therefrom Claim 21 recites: a system comprising: a processor; and a computer readable medium comprising instructions that, when executed by the processor, cause the processor to perform operations The limitations for ‘obtaining a read depth profile’, ‘wherein a read depth profile is obtained’, ‘obtaining a plurality of raw read depth values’, ‘obtaining a mixed sample’ and ‘obtaining read depth data’ merely serve to gather data that is used an input for the judicial exception. Therefore, these limitations are mere data gathering activities. As set forth in MPEP 2106.05(g), mere data gathering activity has been identified by the courts as insignificant extra-solution activity that does not provide a practical application. The limitations that limit the type of sample used to derive genomic material, from where the genomic material is derived and which predetermined genomic loci that undergo recombination are included in the obtained data merely further limit the type of data received, but do not change the position of receiving the measurements as a data gathering activities. Furthermore, limitations to particular data types amount to the ‘field-of-use’ in which to apply the judicial exception and do not amount to significantly more than the exception itself, and thus cannot integrate a judicial exception into a practical application. (MPEP 2106.05(h)). There are no limitations that indicate that the processor requires anything other than a generic computing system. As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. The limitation for ‘providing to a user the determined lymphocyte fraction or related value’ are post-solution activity steps that merely serve to output data from the judicial exception. As set forth in MPEP 2106.05(g), output activity that is incidental to the primary process are insignificant extra-solution activity that do not have a practical application. The limitations that limit the type of data output fail to integrate the judicial exception into a practical application because they merely further limit the tangential output activities but do not change their position as output activities. The above recited additional elements do not provide a practical application of the recited judicial exception. As such, claims 1-21 are directed to an abstract idea (Step 2A, Prong 2: NO). Step 2B Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that equate to mere instructions to apply the recited exception in a generic computing environment or well-understood, and conventional activity. The limitations of claims 1, 6, 15-16 and 21, directed to obtaining data, and the limitations of claim 17, directed to outputting data do not include additional elements that are sufficient to amount to significantly more than the judicial exception. As set forth in MPEP section 2106.05(g), the courts have decided that limitations that merely add an insignificant extra-solution activity, do not amount to an inventive concept, particularly when the activities are well-understood and conventional. As set forth in MPEP section 2106.05(d), the courts have recognized that limitations directed to data gathering that are claimed as insignificant extra-solution activity are routine, well understood and conventional including 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); (Mayo Collaborative servs. V. Prometheus Labs., Inc., 566 U.S. at 79, 101 USPQ2d at 1968), and analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546. Additionally, outputting data (i.e. storing and retrieving information from memory) has also been deemed well-understood, routine and conventional activity (Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015). The limitations of claim 21, pertaining to the computer system (processor and computer readable medium and instructions) used to execute the method, is directed to performing judicial exceptions with a generic computing system on a generic computer. These limitations are not sufficient to amount to significantly more than the judicial exception because, as set forth in the MPEP section 2106.05(d)(II)), using a generic computing environment or generic computer to perform the judicial exception, has been deemed well-understood, routine and conventional activity including receiving or transmitting data over a network (Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362), performing repetitive calculations (Bancorp Services v. Sun Life, 687 F.3d 1266, 1278, 103 USPQ2d 1425, 1433 (Fed. Cir. 2012)), and storing and retrieving information in memory (Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015)). Simply appending well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception are insufficient to provide significantly more. The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: No). As such, claims 1-21 are not patent eligible. 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 (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status. The following is a quotation of 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 factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows: 1. Determining the scope and contents of the prior art. 2. Ascertaining the differences between the prior art and the claims at issue. 3. Resolving the level of ordinary skill in the pertinent art. 4. Considering objective evidence present in the application indicating obviousness or nonobviousness. This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention. 10. Claims 1-6, 10, 12-14, 16 and 18-21, are rejected under 35 U.S.C. 103 as being unpatentable over Zoutman et al. (WO202107358A1, filed 10 October, 2020, 19 January 2024 IDS), in view of Levy et al. (Scientific Reports, 2016, Vol. 6, p. 1-10, 19 January 2024 IDS), as evidenced by Market (PloS Biology, 2003, Vol. 1, p. 24-27). The italicized text corresponds to the instant claim limitations. Regarding claim 21, Zoutman et al. discloses software that enables optimal analysis of cell counts and instructions for carrying out the method of the invention. As Zoutman et al. discloses software, they inherently also disclose a processor and computer readable medium that can perform the operations (p. 45, lines 20-28; a system comprising: a processor; and a computer readable medium comprising instructions that, when executed by the processor, cause the processor to perform operations). Pertaining to claim 1, Zoutman et al. discloses methods and kits for quantifying immune cells, specifically B-cells and T-cells, in a sample based on detecting structural changes at the DNA level that are unique to B- and T-cells (p. 1, lines 1-5; p. 3, lines 21-30; a method for determining a fraction of lymphocytes in a mixed sample comprising genomic material from multiple cell types). Pertainnig to claims 1 and 21, Zoutman et al. disclose a method for determining the VDJ rearranged human B-cell fraction in a sample, the method comprised of quantifying, in the sample, the amount of a diploid reference DNA marker and a B-cell DNA marker comprising an intergenic sequence between IGHD7-27 and IGHJ1 at chromosome 14q32.33. Zoutman et al. further discuses a method of determining the VDJ rearranged human T-cell fraction in a sample, comprising quantifying the amount of a diploid reference DNA marker, a T-cell receptor (TCR) DNA marker (including an intergenic region between Dδ2 and Dδ3 on chromosome 14q11.2 or between Dβ1 and Jβ1.1 on chromosome 7q34) and a DNA regional corrector of the TCR marker. Zoutman et al. further discloses performing the analysis by multiplex digital PCR based on the absolute quantification of the target sequence versus the reference sequence (p. 3, line 32-p. 4, line 1, p. 5, lines 21-26; p. 10, line 36 – p. 11, line 13; p. 12, lines 1-21; Fig. 2-3, Fig. 7C; obtaining a read depth profile for the sample comprising read depths along a predetermined genomic region of interest, wherein the predetermined genomic region of interest includes at least a portion of a genomic locus that undergoes VDJ recombination). Pertaining to claims 1 and 21, Zoutman et al. teaches that digital PCR is performed to obtain an absolute quantification of a B-cell marker and a copy number stable reference gene (REF). Zoutman et al. teaches the absolute loss of the B-cell marker compared to the REF (i.e. a ratio of B-cell level versus REF level) reflects the presence of B-cells (p. 12, lines 17 – 21; Fig. 7C; obtaining a plurality of read depth ratios (r1) by normalising the read depths along the predetermined region of interest by reference to a baseline read depth derived from a subset of the region of interest). Regarding claims 1 and 21, ‘summarized read depth ratio’ as disclosed in the specification can be from a plurality of read depth ratios (ri) that have been normalized along the predetermined region of interest by reference to a baseline read depth derived from a subset of the region of interest. This could be a mean or median value or a log read depth ratio. In general, a summarised value may be a median, average, trimmed average or any other known statistical metric of centrality of a plurality of values (p. 3, line 32 – p. 4, line 10; p. 6, line 27 – p. 7, line 14). With respect to claims 1 and 21, Zoutman et al. teaches determining the VDJ rearranged human T-cell fraction in a sample based on quantification the amount of diploid reference DNA marker, a TCR DNA marker and a DNA regional corrector of the TCR marker (claim 1; determining the fraction of lymphocytes (f) in the sample as a function of the summarised read depth ratio value (rvDJ)). With respect to claims 1 and 21, Zoutman et al. is silent to obtaining a summarised read depth ratio value (rVDJ) for a subset of the region of interest that is likely to be deleted through VDJ recombination. However, this limitation was known in the art at the time of the effective filing date of the invention as taught by Levy et al. Regarding claims 1 and 21, Levy et al. discloses identifying the fraction of tumor infiltrating lymphocytes in breast tumor samples by determining the fraction of TCRB sequence in the sample, a metric they call an immune DNA (iDNA) signature. Levy et al. further discloses generating iDNA scores by analyzing exome sequencing data of the complement determining region 2 (CDR3) region of TCRB locus and generating a smoothed and normalized CDR3 read content for each tumor to generate scores. Levy et al. further discloses that iDNA scores range from 0-10, wherein scores of 0 have no CDR3 reads and scores of 1-10 have increasing deciles of the distribution of normalized CDR3 read count (CDR3 RPM). Levy et al. further discloses that normalized CDR3 reads is the number of CDR3 reads detected normalized by the total number of reads sequenced for that sample. iDNA scores in this context is a type of summarized read depth ratio (abstract; p. 8, para. 2; p. 4, para. 1; obtaining a summarised read depth ratio value (rVDJ) for a subset of the region of interest that is likely to be deleted through VDJ recombination). Regarding claim 2, Zoutman et al. discloses performing their method on genomic loci within TRB and TRD genes (DD and DB marker regions) and in fractions of Tcells and on genomic loci within IGH genes in fractions of B cells (DH and DS marker regions) (Fig. 12 – 14; p. 13, line 37 – p. 14, lines 1-3; p. 55, line 33 – p. 56, line 8; the method of claim 1, wherein a genomic locus that undergoes VDJ recombination is selected from TCRA, TCRB, TCRG, TCRD, IGH, IGL or IGK gene locus, and wherein the fraction of lymphocytes is a fraction of T lymphocytes, a fraction of B lymphocytes, a fraction of αβ T lymphocytes, a fraction of γδ T lymphocytes, a fraction of B cells or T cells including any gene segment in the TCRA, TCRB, TCRG, TCRD, IGH, IGL or IGK gene locus, or a fraction of B cells or T cells including any gene segments listed in Table 8). Regarding claim 3, Zoutman et al. discloses that their method includes detecting class-switch recombination (CSR) of the IGH gene cluster in samples with B-cell fractions, the method comprising: a) quantifying, in the sample, the amount of: a diploid reference DNA marker; and a class-switched B-cell DNA marker comprising a sequence of IGHD at chromosome 14q32.33; and b) determining the class-switched human B-cell fraction in the sample based on the quantification obtained in step a). Zoutman et al. further discloses that the DS IGHD marker is in a coding region (i.e. the CH segment δ of the human immunoglobulin heavy (IGH) locus on chromosome 14 (IGHD) gene), whereas DH is in an intragenic region between IGHD7-27 and IGHJ1. Zoutman et al. further discloses that in contrast to other non-B-cells, the IGH marker DH is lost in VDJ rearranged B-cells, whereas, DS is specifically lost in switched (memory and plasma) VDJ rearranged B-cells. Zoutman et al. further discloses that other coding regions (i.e. exons) are analyzed in their assays including the regional corrector for DH and DS, which is in the coding region of IGHA2 in the IGH locus. Zoutman et al. further disclose that switched B-cells are VDJ rearranged B-cells (Fig. 7A-B; p. 12, lines 1-21; Table 1; p. 50, lines 1-7; the method of claim 2, wherein the predetermined region of interest includes one or more exons from the TCRA, TCRB, TCRG, TCRD, IGH, IGL or IGK gene locus). Pertaining to claim 10, Zoutman et al. discloses that one region of interest, DH (IGHD7-27 – (GHJ1) on 14q32.33 is within the D segment and before the J segment of a VDJ region (FIG 7B, the method of claim 1, wherein the subset of the region of interest that is likely to be deleted through VDJ recombination comprises a region located between the end of a last V segment of the genomic locus that undergoes VDJ recombination, and the start of a J segment of the genomic locus that undergoes VDJ recombination, wherein the subset of the region of interest that is likely to be deleted through VDJ recombination comprises one or more D segments (such as e.g. all D segments) of the genomic locus that undergoes VDJ recombination). Pertaining to claim 13, Zoutman et al. discloses analyzing abundances of two additional DNA regions in the analysis of VDJ recombination quantification: 1) the “diploid reference DNA marker”, which is a DNA region present in two copies on a pair of chromosomes in a given cell. It is in a region of the genome that is stable and is not prone to copy number alterations and is a positive genomic marker for all cells in a sample. It is not a DNA region of a gene encoding any portion of either a T-cell receptor or a B-cell receptor which may be involved in VDJ recombination as T-cells and/or B-cells mature resulting in the DNA regions of the genes being excised such that they would not be present in all cells within a sample, and 2) an “additional regional corrector”, refers to a DNA marker that is in the local vicinity of the B-cell (or T-Cell) marker (i.e. on the same chromosomal arm as the marker used in the quantification but is sufficiently distal as to not be removed from the chromosome during VDJ recombination. This ‘regional corrector’ corrects for CNVs involving the marker loci of T-cells (or CNVs involving the marker loci of B-cells, see below), such that the copy number variation is corrected for (p. 23, lines 4 – 19; p. 29, lines 12-31; p. 17, lines 10-22; the method of claim 1, wherein the subset of the region of interest used to obtain the baseline read depth is a subset of the region of interest that is unlikely to be deleted through VDJ recombination). Regarding claim 14, Zoutman et al. and Levy et al. are silent to the method of claim 13, wherein the subset of the region of interest that is unlikely to be deleted through VDJ recombination comprise the n first V segments of the genomic locus that undergoes VDJ recombination, wherein the subset of the region of interest that is unlikely to be deleted through VDJ recombination comprises a C segment of the genomic locus that undergoes VDJ recombination. However, this would be obvious to try. Regarding claim 14, Zoutman et al. implements a “DNA regional corrector”, which is a marker in the in the local vicinity of the B-cell (or T-cell) DNA marker used in the quantification (i.e. located on the same chromosomal arm) that is sufficiently distal from the B-cell (or T-cell) DNA marker to avoid being removed from the chromosome during VDJ recombination (for example, a neighboring IGHA2 gene) (p. 29, line 12-31, equation 28; p. 29, line 33 – p. 30 line 11; p. 23, lines 24-35). Zoutman et al. further discloses that the regional correction factor is needed to adjust for possible copy number alterations in the TCR DNA marker region (TCR being the region that is modified during VDJ recombination). Zoutman et al. further discloses that this regional corrector can be used as the reference marker (i.e. the denominator in the ratio of equation 28) (p. 23, lines 24-35). Zoutman et al. does not suggest using the first n V segments and the C segments of VDJ regions as ‘DNA regional correctors’ (i.e. regions that are unlikely to recombine), but this would be obvious to try because there are a finite number of genomic positions that are distal to the TCR region (that is likely to recombine) and these positions include the first n V segments and the C segments of VDJ regions (as evidenced by Market et al. (Figure 1)). One of ordinary sill in the art would have recognized that using the regions taught by Market et al. as ‘DNA regional correctors’ (i.e. regions unlikely to recombine) in the method of Zoutman et al. and Levy et al. would have reasonable expectation of success because both disclosures pertain to stable regions distal to regions of VDJ that are modified during recombination (see MPEP 2143(I)(A)). The invention is therefore prima facia obvious. Pertaining to claim 16, Zoutman et al. discloses that the sample may comprise all or a portion of a tumour that contains adaptive immune cells and cells that are not adaptive immune cells (including tumour cells) and may take the form of a variety of tissue and biological fluid samples including bone marrow, thymus, lymph glands, lymph nodes, peripheral tissues and blood. Zoutman et al. further discloses the sample may be processed before determining the VDJ rearranged B-cell or T-cell fraction by extracting DNA from a mixed population of cells from a sample, such as any neoplastic tissue sample or other sample such as blood (p. 38, lines 25-29; p. 39, lines 6-11; the method of claim 1, wherein the mixed sample is a blood sample or a tumour sample, wherein the method further comprises obtaining a mixed sample comprising genomic material from multiple cell types, from a subject, or obtaining read depth data from a mixed sample comprising genomic material from multiple cell types, from a subject through one or more in vitro steps). Pertaining to claim 18, Zoutman et al. discloses that the methods and kits may be used to monitor disease progression, determine the effect of a medicament used in the treatment of a disease, determine disease prognosis, and/or diagnose disease and that the disease may be cancer. Zoutman et al. further discloses that the method may be used to determine the amount of tumor infiltrating lymphocytes (TILs) in a tumor sample to provide diagnostic and/or prognostic information (p. 1, lines 3-6; p. 22, lines 29-33; p. 5, line 10; p. 44, lines 26-29; the method of claim 1, further comprising providing a prognosis for a subject that has been diagnosed as having cancer, by determining the lymphocyte fraction in one or more tumour samples from the subject). Regarding claim 19, Zoutman et al. discloses that by determining the amount of tumor infiltrating lymphocytes (TILs) in a tumor tissue may provide diagnostic and/or prognostic information, including information regarding the potential efficacy of a therapeutic regimen or regarding the optimal dosing regimen. Zoutman et al. further discloses the therapy may be Rituximab (p. 44, lines 26-34; the method of claim 1, further comprising determining whether a subject that has been diagnosed as having cancer is likely to respond to immunotherapy by determining the lymphocyte fraction in one or more tumour samples from the subject). Pertaining to claim 20, Zoutman et al. discloses that the sample analyzed can be a tumor sample or a blood sample including a peripheral blood sample. Zoutman et al. further discloses that their method is useful for aiding in diagnosis and/or minimal residual disease detection. Zoutman et al. further discloses that minimal disease may be encountered in a diagnostic situation, and they provide the example of using their assay to determine the presence of low levels of monoclonal B-cells in patients presenting clinically with cytopenia to aid in a diagnosis of myelodysplastic syndrome (with low B-cell numbers). Zoutman et al. further disclose that their method can detect either B-cells or T-cells. Therefore, it would be obvious to simply substitute an assay to detect a B-cell fraction in a mixed tumor sample to detect myelodysplastic syndrome to one to detect T-cell fraction in order to detect T-cell lymphopenia based on the determination of low levels of T-cells in patients presenting clinically with cytopenia, since their assay is designed to detect B-cell or T-cell fractions. One of ordinary skill in the art could have substituted determining the B-cell fraction for determining the T-cell fraction in the clinical application taught by Zoutman et al. with reasonable expectation of success because Zoutman et al discloses that their method can detect either B-cell or T-cell fractions (p. 38, lines 25-35; p. 43, lines 15-27; abstract; the method of claim 1, further comprising determining whether a subject has T cell lymphopenia by determining the lymphocyte fraction in one or more samples from the subject). Pertaining to claim 4, Zoutman et al. discloses that their region of interest in their disclosed assay includes interrogating both the IGHD coding region (in the DS assay) and the IGHA2 coding region (as a regional corrector for the DH and DS assays) (Table 1; the method of claim 2, wherein the predetermined region of interest includes a plurality of exons from the TCRA, TCRB, TCRG, TCRD, IGH, IGL or IGK gene locus). Regarding claim 4-6 and 12, Zoutman et al. is silent to wherein the plurality of exons comprise at least one exon corresponding to each of a V, D and C segment of the respective gene locus (claim 4) the method of claim 4, wherein the plurality of exons comprise exons corresponding to multiple V segments of the respective gene locus (claim 5); the method of claim 1, wherein a read depth profile is obtained from sequencing data, whole genome sequencing, or panel sequencing data (claim 6); the method of claim 1, further comprising obtaining a baseline read depth from a subset of the region of interest, wherein the baseline read depth is a summarised read depth value across a subject of the region of interest (claim 12). However, these limitations were known in the art at the time of the effective filing date of the invention as taught by Levy et al. Regarding claim 4, Levy et al. discloses identifying CDR3 reads for analysis by first selecting those that mapped to the human TCRB region (hg19: chr7:142,000,817– 142,510,993). Levy et al. further discloses that to identify CDR3 reads, reads in the larger region were manually aligned to the V and J segments on the conserved motifs of TCRA, B, and G (from GenBank), then segments from before or after the conserved motifs were separated out. Therefore, all conserved regions of TCRB were retained, which would include V, D, J and C regions. (p. 8, para. 2; wherein the plurality of exons comprise at least one exon corresponding to each of a V, D and C segment of the respective gene locus). Pertaining to claim 5, Levy et al. discloses using whole exome sequencing and identifying the exome reads to those specific to CDR3 for their analysis based only on presence of conserved motifs. Levy et al. also discloses that the typical exome sequencing coverage depth is 100 fold. Therefore, their method implicitly includes multiple exons corresponding to each of the conserved (V, D, J and C) segments and multiple V segments (p. 8, para. 2; p. 3, para. 2; the method of claim 4, wherein the plurality of exons comprise exons corresponding to multiple V segments of the respective gene locus). Regarding claim 6, Levy et al. discloses identifying CDR3 reads in breast tumor exome sequencing data from TCGA repository and validating it using deep TCRB sequencing (p. 2, para. 1; the method of claim 1, wherein a read depth profile is obtained from sequencing data, whole genome sequencing, or panel sequencing data). Pertaining to claim 12, Levy et al. discloses that CDR3 reads used to identify rearranged TCR regions were selected from reads that mapped to the human TCBR region (hg19: chr7:142,000,817-142,510,993) based on homology to conserved motifs. Levy et al. further discloses that in determining fraction of CDR3 reads, the number of CDR3 reads detected was normalized by the total number of reads sequenced for that sample (p. 8, para. 2; the method of claim 1, further comprising obtaining a baseline read depth from a subset of the region of interest, wherein the baseline read depth is a summarised read depth value across a subject of the region of interest). An invention would have been prima facie obvious to one of ordinary skill in the art at the effective filing date of the invention if some motivation in the prior art would have led that person to combine the prior art teachings to arrive at the claimed invention. Levy et al. taught that their iDNA score has clinical utility as a predictive marker of Her2+ breast cancer and that it has higher value over global histological measurement of TILs in Her2+ patients (p. 6, para. 3). Therefore, one of ordinary skill in the art would have been motivated to utilize the DNA exome sequencing/iDNA scoring method taught by Levy et al. in the determination of lymphocyte abundance by droplet PCR taught by Zoutman et al., to improve prediction of Her2+ breast cancer. Furthermore, one of ordinary skill in the art would predict that the exome sequencing based method taught by Levy et al. could be readily added to the method of Zoutman et al. with a reasonable expectation of success because they both pertain to methods of predicting the fraction of tumor infiltrating lymphocytes by analyzing fraction of VDJ rearrangement in T-cells by genomic analysis. The invention is therefore prima facie obvious. 11. Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over Zoutman et al. (WO202107358A1, filed 10 October, 2020, 19 January 2024 IDS), in view of Levy et al. (Scientific Reports, 2016, Vol. 6, p. 1-10, 19 January 2024 IDS) as applied to claims 1-6, 10, 12-14, 16 and 18-21 above, and further in view of Hicks et al. (Biostatistics, 2018, 19, 2, p. 185–198). The italicized text corresponds to the instant claim limitations. The limitations of claims 1-6, 10, 12-14, 16 and 18-21 were taught by Zoutman et al. and Levy et al. above. Regarding claim 15, Zoutman et al. and Levy et al. are silent to wherein smoothing the read depth values comprises replacing the raw read depth values by a corresponding rolling median over a window of a predetermined width. However, this limitation was known in the art at the time of the effective filing date of the invention as taught by Hicks et al. Pertaining to claim 15, Hicks et al. discloses a method called smooth quantile normalization for genomic data analysis which is a method of between-sample normalization to remove systematic bias and unwanted technical variation in high-throughput data. Hicks et al. further discloses that it is based on the assumption that the statistical distribution of each sample should be the same (or have the same distributional shape) within a biological group (or condition), but that the distribution may differ between groups. Hicks et al. further discloses that the method calculates a weight for each quantile ranging from 0-1, which determines whether to apply standard quantile normalization or normalizing only within distinct sample groups. At each specific quantile, the initial weight can suffer from high local variance, therefore, to smooth out these spikes, the algorithm computers a rolling median across a window of adjacent quantiles, the window being of a predetermined width (p. 185, para. 1; p. 188, para. 1; wherein smoothing the read depth values comprises replacing the raw read depth values by a corresponding rolling median over a window of a predetermined width). An invention would have been prima facie obvious to one of ordinary skill in the art at the effective filing date of the invention if some motivation in the prior art would have led that person to combine the prior art teachings to arrive at the claimed invention. Hicks et al. taught that smooth quantile normalization solves two problems in quantitative analysis of high throughput genomic data: 1) the problem of global differences in the statistical distribution between biological conditions or groups and 2) the problem of external information such as negative or control features not being available for normalization. Hicks et al. further shows improvement of the normalization to large scale genomic dataset analysis including RNA-seq and DNA methylation arrays (p. 185, para. 1; p. 194, para. 6- p. 195, para. 3). Therefore, one of ordinary skill in the art would have been motivated to utilize the smooth quantile normalization taught by Hicks et al. in the determination of lymphocyte abundance from exome sequencing taught by Zoutman et al. and Levy et al., in order to improve whole exome analysis when there are several biological groups or conditions to compare. Furthermore, one of ordinary skill in the art would predict that the exome sequencing based method taught by Hicks et al. could be readily added to the method of Zoutman et al. and Levy et al. with a reasonable expectation of success because they both pertain to analysis of quantitative large-scale genomic datasets. The invention is therefore prima facie obvious. 12. Claim 17 is rejected under 35 U.S.C. 103 as being unpatentable over Zoutman et al. (WO202107358A1, filed 10 October, 2020, 19 January 2024 IDS), in view of Levy et al. (Scientific Reports, 2016, Vol. 6, p. 1-10, 19 January 2024 IDS) as applied to claims 1-6, 10, 12-14, 16 and 18-21 above, and further in view of Madison et al. (US20250283167A1, effective filing date 22 June 2021) The italicized text corresponds to the instant claim limitations. The limitations of claims 1-6, 10, 12-14, 16 and 18-21 were taught by Zoutman et al. and Levy et al. above. Regarding claim 17, Zoutman et al. and Levy et al. are silent to the method of claim 1, further comprising providing to a user, for example through a user interface, the determined lymphocyte fraction and/or any value derived therefrom. However, this limitation was known in the art at the time of the effective filing date of the invention as taught by Madison et al. Regarding claim 17, Madison et al. discloses a method that determines an allele fraction or comparison (e.g. a ratio) of the abundance of an allele relative to the abundance of other alleles in a tumor sample to provide quantitative measures of enrichment. Madison et al. further discloses providing a comprehensive genomic aberration analysis to the oncologist with a comprehensive description of what aberrations may be driving the tumor and could be useful for informing the oncologists treatment decisions. Madison et al. further discloses that this can be done in electronic, web-based or paper format (abstract; para. 0784; 0675; 0682; 0732; the method of claim 1, further comprising providing to a user, for example through a user interface, the determined lymphocyte fraction and/or any value derived therefrom). An invention would have been prima facie obvious to one of ordinary skill in the art at the effective filing date of the invention because it would involve simply combining prior art elements according to known methods to yield predictable results. The user interface taught by Madison et al. and the determination of lymphocyte abundance from exome sequencing was taught by Zoutman et al. and Levy et al. were both known in the art and one of ordinary skill in the art could have combined the elements as claimed because each element merely performs the same function as it does separately. Furthermore, one of ordinary skill in the art would predict that the user interface taught by Madison et al. could be readily added to the method of Zoutman et al. and Levy et al. with a reasonable expectation of success because they both pertain to quantifying fractions of tumor samples by genomic analysis and both methods can have an impact on the treatment or prognosis of cancer. The invention is therefore prima facie obvious (see MPEP 2143(I)(A)). 13. Claims 7-9 are rejected under 35 U.S.C. 103 as being unpatentable over Zoutman et al. (WO202107358A1, filed 10 October, 2020, 19 January 2024 IDS), in view of Levy et al. (Scientific Reports, 2016, Vol. 6, p. 1-10, 19 January 2024 IDS) as applied to claims 1-6, 10, 12-14, 16 and 18-21 above, and further in view of Van Loo et al. (PNAS, 2010, Vol. 107, p. 16910-16915). The italicized text corresponds to the instant claim limitations. The limitations of claims 1-6, 10, 12-14, 16 and 18-21 were taught by Zoutman et al. and Levy et al. above. Regarding claim 7, Levy et al. discloses identifying the fraction of tumor infiltrating lymphocytes in breast tumor samples by determining the fraction of TCRB sequence in the sample, a metric they call an immune DNA (iDNA) signature. Levy et al. further discloses generating iDNA scores by analyzing exome sequencing data of the complement determining region 2 (CDR3) region of TCRB locus and generating a smoothed and normalized CDR3 read content for each tumor to generate scores. Levy et al. further discloses that iDNA scores range from 0-10, wherein scores of 0 have no CDR3 reads and scores of 1-10 have increasing deciles of the distribution of normalized CDR3 read count (CDR3 RPM). Levy et al. further discloses that normalized CDR3 reads is the number of CDR3 reads detected normalized by the total number of reads sequenced for that sample. iDNA scores in this context is a type of summarized read depth ratio (abstract; p. 8, para. 2; p. 4, para. 1; the method of claim 1, wherein determining the fraction of lymphocytes (f) in the sample as a function of the summarised read depth ratio value (rVDJ) comprises determining the fraction of lymphocytes (f) in the sample as a function of the summarised read depth ratio value (rVDJ)). Regarding claim 7, Levy et al. and Zoutman et al. are silent to a function of the fraction of abnormal cells (p) in the mixed sample, wherein abnormal cells are those that are aneuploid in the predetermined region of interest, and a copy number of the abnormal cells in the predetermined region of interest(ψT). However, this limitation was known in the art at the time of the effective filing date of the invention as taught by Van Loo et al. Regarding claim 7, Van Loo et al. teaches an approach called ASCAT to accurately determine the allele-specific copy number fraction (allele-specific frequency) in breast tumor samples, which takes into account both aneuploidy of the tumor cells and nonaberrant cell infiltration. The ASCAT algorithm accounts for the genomic location (region of interest), and calculates the average ploidy of the sample, the aberrant cell fraction of a sample and models allele-specific copy number as a function of the data and the parameters. The equation to calculate the relative abundance of allele A versus allele B (also called bi or BAF) provides the same information as read depth ratio value. Van Loo et al. further disclose that on the basis of the two equations, they can express the allele-specific copy number estimates as a function of the data and the parameters (equations 1 and 2, p. 16914, col. 2, para. 3-4; p. 16910, col. 1, para. 2-col. 2, para. 1; the method of claim 1, wherein determining the fraction of lymphocytes (f) in the sample as a function of the summarised read depth ratio value (rVDJ) comprises determining the fraction of lymphocytes (f) in the sample as a function of the summarised read depth ratio value (rVDJ), the fraction of abnormal cells (p) in the mixed sample, wherein abnormal cells are those that are aneuploid in the predetermined region of interest, and a copy number of the abnormal cells in the predetermined region of interest(ψT)). Pertaining to claim 8, Van Loo et al. teaches a set of equations underlying ASCAT (mixture/log-read-depth equation and the p/copy-number framework) that underlie the claimed equation. Van Loo et al. further teach that the ASCAT method can be applied to either point mutations or to complex rearrangements (Supporting information, Equations S4-S6; Supporting information, p. 1, col. 1, para. 1-6; p. 16913, col. 1, para. 4; the method of claim 7, wherein determining the fraction of lymphocytes (f) in the sample comprises determining the value of f as f = 1 - p + γ 2 ψ T - ( 1 - p +   γ 2 ψ T ) 2 r V D J T wherein γ is a constant). Regarding claim 9, Van Loo et al. teaches a set of equations underlying ASCAT (mixture/log-read-depth equation and the p/copy-number framework) that underlie the equation of claim 8. Van Loo et al. further teach that the ASCAT method can be applied to either point mutations or to complex rearrangements. The claimed equation of claim 9 is equivalent to the one claimed in claim 8 except that it is restricted to wherein the fraction of abnormal cells (p and ψ) is 0 such as with germline cells. Van Loo et al. discloses that their equation models tumor ploidy but that Eq. S6 is valid for mutations that are heterozygous in the germline (and thus nonaberrant cell) DNA. Van Loo et al. further disclose omitting the corresponding terms from the equations for analyzing genomic locations that are germline homozygous (Supporting information, Equations S4-S6; Supporting information, p. 1, col. 1, para. 1-6; p. 16913, col. 1, para. 4; the method of claim 1, wherein determining the fraction of lymphocytes (f) in the sample comprises determining the value of f as f = 1 - 2 r V D J γ wherein γ is a constant). An invention would have been prima facie obvious to one of ordinary skill in the art at the effective filing date of the invention if some motivation in the prior art would have led that person to combine the prior art teachings to arrive at the claimed invention. Van Loo et al. discloses that it is difficult to accurately determine genome-wide copy number profiles of tumors from high-throughput data because tumor cells are often aneuploid and tumor samples contain multiple populations of both tumor and nontumor cells and that ASCAT solves this problem (p. 16912, col. 2, para. 3 – p. 16913, col.1, para. 4). Therefore, one of ordinary skill in the art would have been motivated to utilize the algorithm for accounting for ploidy and aberrant cell fraction taught by Van Loo et al. in the determination of lymphocyte abundance from VDJ/TCR deletion in exome sequencing taught by Zoutman et al. and Levy et al., in order to improve accuracy in determining the fraction of VDJ recombined cells in a tumor sample. Furthermore, one of ordinary skill in the art would predict that the ASCAT algorithm taught by Van Loo et al. could be readily added to the method of Zoutman et al. and Levy et al. with a reasonable expectation of success because they both pertain to determining the fraction of a genomic alteration in a tumor sample. Furthermore, Van Loo et al. disclose that their ASCAT method should work for determining the fraction of complex rearrangements (as VDJ recombination taught by Zoutman et al. and Levy et al.) as well as point mutations (p. 16913, col. 1, para. 4). The invention is therefore prima facie obvious. Double Patenting The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969). 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. 14. Claims 1 and 10-11 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 7, 12 and 15 of U.S. Patent No. 19/481,873. Although the claims at issue are not identical, they are not patentably distinct from each other because: Claim 7 of the reference teaches claim 1 of the instant application. Claim 7 of the reference teaches claim 10 of the instant application. Claim 12 of the reference teaches claim 1 of the instant application. Claims 15 and 16 of the reference teach claim 11 of the instant application (contingent on correction of antecedent basis issue for the expression ‘obtaining a further summarised read depth ratio (rB) for a subset of the region of the IGH locus that is likely to be deleted through VDJ recombination’ in claim 15 of the reference). This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented. Conclusion 15. No claims are allowed. Claim 11 was examined under 35 U.S.C. 102 and 103 and is free from the prior art of record but is not otherwise in condition for allowance. By the effective filing date, there was no prior art teaching fitting a model to the read dept ratios in a method of determining fraction of VDJ recombination to estimate lymphocyte fraction in a sample. E-mail Communications Authorization 16. 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WISE/Supervisory Patent Examiner, Art Unit 1685