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 .
2. A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on August 8, 2025 has been entered. Any rejections or objections not reiterated herein have been withdrawn.
Claims 1-15 are currently pending and have been examined herein.
Non-Compliant Claim Amendments
3. The Claims filed on August 8, 2025 are non-compliant. MPEP 714(c)(2) recites the following:
(2) When claim text with markings is required. All claims being currently amended in an amendment paper shall be presented in the claim listing, indicate a status of “currently amended,” and be submitted with markings to indicate the changes that have been made relative to the immediate prior version of the claims. The text of any added subject matter must be shown by underlining the added text. The text of any deleted matter must be shown by strike-through except that double brackets placed before and after the deleted characters may be used to show deletion of five or fewer consecutive characters. The text of any deleted subject matter must be shown by being placed within double brackets if strike-through cannot be easily perceived. Only claims having the status of “currently amended,” or “withdrawn” if also being amended, shall include markings. If a withdrawn claim is currently amended, its status in the claim listing may be identified as “withdrawn— currently amended.”
Claim 7 step f. recites “identifying the [disease or disorder] the presence or absence of cancer in the subject”. Based on the reponse filed on August 8, 2025 it appears that the phrase “disease or disorder” was intended to be replaced with “the presence or absence of cancer”. However claim 7 do not have the proper markings to show that the phrase “disease or disorder” was deleted. The text of any deleted matter must be shown by strike-through except that double brackets placed before and after the deleted characters may be used to show deletion of five or fewer consecutive characters. In order to advance prosecution of the application the amendment has been entered despite this deficiency. Correction is required.
Claim Rejections - 35 USC § 101
4. 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 1-15 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more. The claims recite a judical exception that is not integrated into a practical application. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception. The claim analysis is set forth below.
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
The instant claims recite abstract ideas.
The claims recite a step of “determining pairs of sequences associated with at least a portion of the plurality of UMI tagged cfDNA fragments wherein the pair members have the same genomic location and wherein the determining is performed by a computer” (clm 1 step c, clm 7 step c ). This step broadly covers performance of the limitation in the mind but for the recitation of a generic computer. That is, other than reciting “by a computer”, nothing in the claim preculdes the determining step from practically being performed in the human mind. For example, but for the “by a computer” language, the claim encompasses the user comparing a bunch of numbers: genomic locations assoicated with cfDNA fragments. This limitation is a mental process.
The claims recite a step of “determining the subset of these pairs of sequences for which the sequence associated with the cfDNA fragment has more than one genomic location within a reference genome, wherein the determining is performed by a computer” (clm 1 step d, clm 7 step d). This step broadly covers performance of the limitation in the mind but for the recitation of a generic computer. That is, other than reciting “by a computer”, nothing in the claim preculdes the determining step from practically being performed in the human mind. For example, but for the “by a computer” language, the claim encompasses the user comparing a bunch of numbers: genomic locations assoicated with cfDNA fragments. This limitation is a mental process.
The claims recite a step of “determining at least some of the tissues and/or cell types giving rise to the cfDNA fragments as a function of this subset of pairs of sequences are cancer tissue, wherein the determining is performed by a computer and wherein the determination is indicative of the presence or absence of cancer tissue in the subject” (clm 1 step e). This step broadly covers performance of the limitation in the mind but for the recitation of a generic computer. That is, other than reciting “by a computer”, nothing in the claim preculdes the determining step from practically being performed in the human mind. For example, but for the “by a computer” language, the claim encompasses the user taking one kind of infomration (paris of sequence) and turning it into another kind of information (tissue and/or cell type). This limitation is a mental process.
The claims recite “wherein the step of determining at least some of the tissues and/or cell types giving rise to the cfDNA fragments comprises comparing the sequences associated with the cfDNA fragments to one or more reference maps” (clms 2 and 8). Comparing is a mental process.
The claims recite a step of “determining at least some of the tissues and/or cell types giving rise to the cfDNA fragments as a function of this subset of pairs of sequences, wherein the determining is performed by a computer” (clm 7 step e). This step broadly covers performance of the limitation in the mind but for the recitation of a generic computer. That is, other than reciting “by a computer”, nothing in the claim preculdes the determining step from practically being performed in the human mind. For example, but for the “by a computer” language, the claim encompasses the user taking one kind of infomration (paris of sequence) and turning it into another kind of information (tissue and/or cell type). This limitation is a mental process.
The claims recite a step of “identifying the presence or absence of cancer in the subject as a function of the determined by the presence or absence cfDNA, wherein the identifying is performed by a computer and wherein the determination is indicative of the presence or absence of cancer” (clm 7 step f ). This step broadly covers performance of the limitation in the mind but for the recitation of a generic computer. That is, other than reciting “by a computer”, nothing in the claim preculdes the identifying step from practically being performed in the human mind. For example, but for the “by a computer” language, the claim encompasses the user taking one kind of infomration (presence or absence of cfDNA) and turning it into another kind of information (presence or absence of cancer). This limitation is a mental process.
The claims recite “counting UMIs associated with identical cfDNA sequences to produce a vector of counts” (clm 13). Counting is considered to be a mental process. Mental processes are considered to be abstract ideas.
The claims recite “wherein determining at least some of the tissues and/or cell types giving rise to the cfDNA fragments comprises performing a mathematical transformation on the vector of counts” (clm 15). The mathematical transformation is considered to be a mathematical concept. Mathematical concepts are considered to be abstract ideas.
The instant claims recite a law of nature.
Claim 1 recites method of determining the presence or absence of cancer tissues and/or cell types giving rise to cfDNA in a subject based on the properties of cfDNA fragments determined by DNA sequencing. Claim 7 recites a method of identifying the presence or absence of cancer based on the properties of cfDNA fragments determined by DNA sequencing. These types of correlations are a consequence of natural processes, similar to the naturally occurring correlation found to be a law of nature by the Supreme Court in Mayo.
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, claims 1 and 7 recite the additional steps of (a) isolating cfDNA from a biological sample from the subject, the isolated cfDNA comprising a plurality of cfDNA fragments and (b) tagging a UMI to each isolated cfDNA fragment, the UMI comprising an oligomer of at least two nucleotides. These steps do not integrate the judicial exceptions into a practical application because they merely add insignificant extra-solution activity (data gathering necessary to perform the mental steps) to the judicial exception.
In addition to the judicial exceptions claims 6 and 10-11 recites steps of generating reports. Merely presenting the results of a process otherwise unpatentable under section 101 is, however, insufficient to establish eligibility under the statute. See FairWarning IP, LLC v. Iatric Sys., Inc., (Fed. Cir. Oct. 11, 2016) (claim unpatentable despite recitation of the step: "providing notification if [an] event has occurred"). The courts have affirmed that merely collecting data, extracting information from the data and/or storing data are not patent-eligible (see, For example, Content Extraction and Transmission LLC v. Wells Fargo Bank., N.A. 776 F.3d 1343, 112 USPQ2d 1354 (Fed. Cir. 2014) and Electric Power Group LLC v Alstom S.A. CAFC 2015-1778).
Step 2B: Evaluate Whether the Claim Provides an Inventive Concepts
In addition to the judicial exceptions, the claims recite the additional steps of (a) isolating cfDNA from a biological sample from the subject, the isolated cfDNA comprising a plurality of cfDNA fragments and (b) tagging a UMI to each isolated cfDNA fragment, the UMI comprising an oligomer of at least two nucleotides. These steps do NOT amount to significantly more because they simply appends well understood, routine, and conventional activities previously known in the art to the judicial exceptions.
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 (para 0019) teaches
In particular embodiments of the methods, cell-free DNA (cfDNA) is extracted and purified from a source. Extraction and purification can proceed according to techniques known to those of skill in the art. For example, the QIAGEN QIAamp Circulating Nucleic Acid kit is a common method, based on the binding of cfDNA to a silica column, for purification of cfDNA from plasma or urine. An alternative method, phenol-chloroform extraction followed by isopropanol or ethanol precipitation, provides similar results while allowing for more flexibility in the volume of the biological sample.
The prior art also 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 Karlsson (Genomics 105 (2015) pages 150-158, available online 1224/2014) teaches the following:
Here we describe an amplification-free method for sequencing of cell-free DNA, even from low levels of starting material. We evaluated this method in the context of prenatal diagnosis of fetal aneuploidy and compared it with a PCR-based library preparation method as well as a recently described method using unique molecular identifiers (UMI) (abstract).
Another way to nearly eliminate PCR bias is to use unique molecular identifiers [10-14]. This method, where each molecule is made unique either by adding a degenerate barcode or by diluting the sample before amplification, corrects for most types of bias, including sequencing errors and quantitative bias (page 151, col 1).
When there is a need for extremely accurate sequencing and both PCR and sequencing errors need to be corrected for, UMI is the method of choice (page 153, col 2).
The prior art of Karlsson which provides citations back to 5 references that use unique molecular identifiers demonstrates that their use was well known, routine, and conventional in the art.
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);
Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs., 818 F.3d at 1377; 118 USPQ2d at 1546;
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.
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.
Claims 1-15 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.
Regarding Claims 1-6 and 9-15 it is not clear how the recited preamble is intended to breathe life and meaning into the claim. The preamble of the claim recites “A method of determining the presence or absence of cancer tissues and/or cell types giving rise to cell-free DNA (cfDNA) in a subject. The goals of the method set forth by the premable are:
(i) determining the presence or absence of cancer tissue
and/or
(ii) determining cell types giving rise to cfDNA.
Step (e.) recites “determining at least some of the tissues and/or cell types giving rise to the cfDNA fragments”. The final step only accomplishes the second goal that is recited in the preamble. There are no active process steps in the claim that accomplish the first goal of determining the presence or absence of cancer tissue. The claims recite a final wherein clause stating “wherein the determination is indicative of the presence or absence of cancer in the subject”. However, claim scope is not limited by claim language (such as wherein clauses) that suggests or makes optional but does not require steps to be performed. Thus it is not clear if applicant intends to cover only a method of determining cell types giving rise to cfDNA OR if the method is intended to somehow require more to accomplish both goals set forth in the preamble. If it is the later, then it appears that the claims are incomplete, as they fail to provide any active steps that clearly accomplish the first goal of determining the presence or absence of cancer tissue. Clairification is required.
Claims 1-6 and 9-15 are rejected over the recitation of the phrase “the pair members” in claim 1 step c. There is insufficient antecedent basis for this limitation in the claim because although the claim previously refers to “paris of sequences” it does not refer to “pair members”.
Claims 1-6 and 9-15 are rejected over the recitation of the phrase “the subset of these pairs of sequences” in claim 1 step d. There is insufficient antecedent basis for this limitation in the claim.
Claims 1-6 and 9-15 are rejected over the recitation of the phrase “the tissues and/or cell types giving rise to the cfDNA fragments” in claim 1 step e. There is insufficient antecedent basis for this limitation in the claim because although the claim previously refers to “cell types giving rise to cfDNA” it does not refer to “tissues and/or cell types giving rise to the cfDNA fragments”. Claims 2, 13, and 15 also recite the indefinite language.
Claims 1-6 and 9-15 are rejected over the recitation of the phrases
(i) “determining at least some of the tissues and/or cell types giving rise to the cfDNA fragments as a function of this subset of pairs of sequences are cancer tissue” and
(ii) “wherein the determination is indicative of the presence or absence of cancer tissue in the subject” in claim 1 step e.
Regarding (i) it is unclear what the recitation of “as a function of this subset of pairs of sequences are cancer tissue” means. It is unclear if one only needs to determine the cell types giving rise to cfDNA to meet this limitation or if something else is required. Regarding (ii) it is unclear how determining the cell types giving rise to the cfDNA relates to cancer and is being used to determine the presence or absence or cancer? Clairification is required.
Claim 6 is rejected over the recitation of the phrase “generating a report comprising a list of the determined cancer tissues”. This recitation is confusing because the claims do recite any active process steps of determining cancer tissues. Clairification is required.
Claims 7-8 are rejected over the recitation of the phrase “the pair members” in claim 7 step c. There is insufficient antecedent basis for this limitation in the claim because although the claim previously refers to “paris of sequences” it does not refer to “pair members”.
Claims 7-8 are rejected over the recitation of the phrase “the subset of these pairs of sequences” in claim 7 step d. There is insufficient antecedent basis for this limitation in the claim.
Claims 7-8 are rejected over the recitation of the phrase “the tissues and/or cell types giving rise to the cfDNA fragments” in claim 7 step e. There is insufficient antecedent basis for this limitation. The indefinite language is also recited in claim 8.
Claims 7-8 are rejected over the recitation of the phrase “the presence or absence of cfDNA”. This phrase lacks antecedent basis in the claim and is confusing because the claims require that cfDNA is present and isolated.
Claims 7-8 are rejected over the recitation of the phrase “determining at least some of the tissues and/or cell types giving rise to the cfDNA fragments as a function of this subset of pairs of sequences” in claim 7 step e. It is unclear what the recitation of “as a function of this subset of pairs of sequences” means. It is unclear if one only needs to determine the cell types giving rise to cfDNA to meet this limitation or if something else is required.
Claims 7-8 are rejected over the recitation of the following phrases:
(i) “identifying the presence or absence of cancer in the subject as a function of the determined by the presence or absence cfDNA” in claim 7 step f and
(ii) “wherein the determination is indicative of the presence or absence of cancer in the subject” in claim 7 step f.
Regarding (i) it is unclear what the recitation of “as a function of the determined by the presence or absence of cfDNA” means. It is unclear how the presence or absence of cfDNA is used to identify the presence or absence of cancer? Regarding (ii) it is unclear how the determination of the presence or absence of cfDNA is related to the presence or absence of cancer in the claim. Clairification is required.
Claim 9 is rejected over the recitation of the phrase “wherein the reference genome is assoicated with a human”. This recitation is confusing because it is unclear what if means for a genome to be “assoicated” with a human. It is unclear if the clams are limited to human reference genomes or if they could encompass other reference genomes. Clairifcation is required.
Claims 10-11 are rejected over the recitation of the phrase “generating a report comprising a statement identifying the presence or absence of cancer”. This recitation is confusing because the claims do recite any active process steps of determining/identifying the presence or absence of cancer. Clairification is required.
Claim 11 is rejected over the recitation of the phrase “a list of the determined cancer tissues and/or cell types giving rise to the isolated cfDNA”. This recitation is confusing because the claims do recite any active process steps of determining cancer tissues. Clairification is required.
Response To Arguments
6. Regarding the rejection over claims 1-6 and 9-15 about the preamble being unclear, the Applicants argue that the rejection has been overcome by amendment.
The amendment has been fully considered but does not overcome the rejection. The rejection has been modified to address the claims as amended.
Claim Rejections - 35 USC § 112
7. The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-15 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for,
A method comprising:
a. isolating cfDNA from a biological sample from the subject, the isolated cfDNA comprising a plurality of cfDNA fragments;
b. tagging a unique molecular identifier (UMI) to each isolated cfDNA fragment, the UMI comprising an oligomer of at least two nucleotides;
c. determining pairs of sequences associated with at least a portion of the plurality of UMI-tagged cfDNA fragments, wherein the pairs have the same genomic location and wherein the determining is performed by a computer; and
d. identifying a subset of pairs of sequences for which the sequence associated with the cfDNA fragment has more than one genomic location within a reference genome, wherein the determining is performed by a computer.
does not reasonably provide enablement for methods (i) determining/identifying the presence or absence of cancer or (ii) determining cell types giving rise to cell free DNA in a subject. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
Scope of the Claims/Nature of the Invention
The claims encompass methods of
(I) determining the presence or absence of cancer tissues (clm 1);
(II) determining cell types giving rise to cell free DNA in a subject (clm 1); and
(III) identifying the presence or absence of cancer in a subject (clm 7).
Methods (I) and (II) comprise the steps of
(a) isolating cfDNA from a biological sample from the subject, the isolated cfDNA comprising a plurality of cfDNA fragments;
(b) tagging a UMI to each isolated cfDNA fragment, the UMI comprising an oligomer of at least two nucleotides;
(c) determining pairs of sequences associated with at least a portion of the plurality of UMI tagged cfDNA fragments, wherein the pair members have the same genomic location;
(d) determining the subset of these pairs of sequences for which the sequence associated with the cfDNA fragment has more than one genomic location within a reference genome; and
(e1) determining at least some of the tissues and/or cell types giving rise to the cfDNA fragments as a function of this subset of pairs of sequences are cancer tissues, wherein the determination is indicative of the presence or absence of cancer tissue in a subject.
Method (III) comprises the steps of (a)-(d) as recited above and further requires
(e2) determining at least some of the tissues and/or cell types giving rise to the cfDNA fragments as a function of this subset of pairs of sequences; and
(f) identifying the the presence or absence of cancer in the subject as a function of the determined by the presence of absence cfDNA, wherein the determination is indicative of the presence or absence of cancer in the subject.
The nature of the invention requires analysis of tagged cfDNA fragments to determine the presence or absence of cancer in a subject. The nature of the invention requires analysis of tagged cfDNA fragments to determine the cell types giving rise to the cell free DNA.
Teachings in the Specification and Examples
The specification (para 0018) states that provided herein are methods for determining or quantifying the cell types and tissue-of-origin composition of cfDNA in bodily fluids on the basis of transcription factor (TF) footprints in short cfDNA fragments.
The specification (para 0019-0021)describes how cell-free DNA (cfDNA) is extracted and purified. After purification of cfDNA from biological fluids, the fragments can be subjected to one or more enzymatic steps to create a sequencing library. Next the cfDNA fragments are tagged with an oligonucleotide unique molecular identifier (UMI) to facilitate identification of unique fragments.
The specification (paras 0022) teaches that library amplification (e.g. with PCR) and sequencing can each result in the same original cfDNA fragment being sequenced more than once and thus appearing as duplicate reads. However, cfDNA fragments may also be truly biologically duplicated at the sequence level--a possibility that is magnified as fragment length decreases. Disentangling these two scenarios--true biological duplication and technical duplication--is difficult or impossible with conventional DNA sequencing workflows. However, the addition of a UMI to each molecule allows these two scenarios to be disentangled, by uniquely tagging each molecule to allow the identification of technical duplicates (which would carry the same UMI).
The specification (para 0024) teaches that following sequencing, duplicates can be identified by comparing reads on the basis of both their UMIs and their genomic locations and/or sequences. Technical duplicates, which share genomic locations and/or sequences as well as UMIs, can be discarded. Biological duplicates, which share genomic locations and/or sequences but do not share UMIs, can be retained. These remaining sequences can then be partitioned into length classes to enrich for TF footprints in the shortest class(es).
The specification (para 0025) teaches that in certain embodiments, the reads that cannot be uniquely mapped are separated from the reads that can be uniquely mapped. These reads can be computationally compared to existing compendia of TF footprints (also known as "motifs") to identify TFs that are likely to have conferred protection to the fragments from which the reads were derived. The comparison to existing compendia does not require exact sequence matches. In some embodiments, one or more sequence mismatches can be allowed to account for imperfect sequence specificity on the part of the TF. In some embodiments, the comparison is performed by searching for one or more informative subsequences of length k (often called "k-mers"), with gaps ("gapped k-mers) or without gaps. The number of such reads derived from each TF using this comparison is tallied by counting the UMIs, thus allowing the relative frequency of each TF's footprint in the sample of reads to be quantified. By iterating this procedure across a large number of TFs, a vector of TF frequencies can be populated for each biological sample. This vector can then be normalized across biological samples and sequencing datasets (e.g. from multiple individuals, or from the same individual over time) by comparing to counts of uniquely mapped reads within a predefined set of genomic loci in each sample (i.e., accounting both for sequencing coverage and for fragment length biases owing to technical differences between samples).
The specification (para 0026) teaches that in some embodiments, the vector of counts for each TF is then modeled as a mixture of TF profiles found in myriad cell types using orthogonal methods, including ChIP-seq assays such as those performed by the ENCODE project. This modeling can have several embodiments. In one embodiment, the comparison involves a computational search for TF footprints that are present in the biological sample and whose cognate TFs are specific to a single cell type. In another embodiment, the vector of molecular counts described above and derived from a biological sample is modeled as a linear combination of vectors of TF profiles derived from orthogonal methods. The output from each embodiment is a list of contributing cell types, optionally including estimated proportions for each contributor in some embodiments.
The specification (para 0027) teaches that transcription factor utilization is a dynamic process, such that single cells of the same type are not identical with respect to TF occupancy along their genome. Nonetheless, at the aggregate level, the complement of TFs within a cell is known to be cell type-specific. In other words, there are many coordinates in the genome at which the probability of TF occupancy substantially differs between cell or tissue types.
The specification ( para 0028) teaches that the methods provided herein are based, at least in part, on the discovery that short cfDNA fragments, despite typically being discarded because their length challenges unique genomic placement, contain information about the complement of TFs active upon cell death and cfDNA genesis. The addition of unique molecular identifiers enables counting-based relative quantification of these TFs, and can be used to differentiate the relative contributions of two or more tissue or cell types to the composition of cfDNA in bodily fluids. Furthermore, the comparison of TF profiles between individuals and/or samples can be used to diagnose and/or monitor any pathology or clinical conditions in humans in which the tissue-of-origin composition of cfDNA in bodily fluids is substantially altered in a way that consistently correlates with that pathology or clinical condition.
In the instant case the specification provides generic, prophetic guidance. There are no working examples in the specification wherein TF footprints of short cfDNA fragments are identified and used to determine tissues and/or cells types giving rise to cell free DNA. Further there are no working examples in the specification where tissues and/or cells types giving rise to cell free DNA are determined and used to identify a disease or disorder in a subject. The instant claims do not appear to be commensurate in scope with what the invention actually is. For example the specification teaches that the invention is drawn to methods for determining or quantifying the cell types and tissue-of-origin composition of cfDNA in bodily fluids on the basis of transcription factor (TF) footprints in short cfDNA fragments, yet the claims do not require determining transcription factor footprints.
State of the Art and the Unpredictability of the Art
While methods of amplifying and sequencing cfDNA are known in the art, methods of using the sequences cfDNA to determine the tissues/cells giving rise to the cell free DNA and methods of using the tissues/cells giving rise to the cell free DNA to detect the presence or absence of cancer are highly unpredictable. The unpredictability will be discussed below.
The post filing date art of Peng (Briefings in Bioinformatics 22(3) 2021 1-20) teaches that advances in sequencing technologies facilitate personalized disease-risk profiling and clinical diagnosis. In recent years, some great progress has been made in noninvasive diagnoses based on cell-free DNAs (cfDNAs). It exploits the fact that dead cells release DNA fragments into the circulation, and some DNA fragments carry information that indicates their tissues-of-origin (TOOs). Based on the signals used for identifying the TOOs of cfDNAs, the existing methods can be classified into three categories: cfDNA mutation-based methods, methylation pattern-based methods and cfDNA fragmentation pattern-based methods. In cfDNA fragmentation pattern-based methods, cfDNA fragmentation patterns, such as nucleosome positioning or preferred end coordinates of cfDNAs, are used to predict the TOOs of cfDNAs (abstract).
Peng further teaches that it is novel to infer the TOOs of cfDNAs based on the patterns of nucleosome spacing, the tissue-specific preferred ends or the length distribution of cfDNAs. However, this type of method is at its very beginning. The individual differences in tissue-specific nucleosome spacing patterns and tissue-specific preferred ends of cfDNAs should be evaluated, and more samples should be involved to identify tissue-specific nucleosome spacing patterns and tissue-specific preferred ends of cfDNAs. Furthermore, the influence of different sequencing coverages on extracting cfDNA fragmentation patterns should be assessed. Moreover, it is quite important to quantify the cfDNA fragmentation patterns when applying the cfDNA fragmentation pattern-based methods to clinical diagnosis (page 10, col 2).
Additionally Peng teaches that in cfDNA fragmentation pattern-based methods, abundant cfDNA fragmentation patterns, such as tissue-specific nucleosome spacing patterns and tissue-specific preferred ends of cfDNAs, were extracted for three noninvasive diagnoses based on a small number of samples. The results show that these cfDNA fragmentation patterns have limited power to indicate the TOOs of cfDNAs and estimate the corresponding fractions in other samples. Thus, continuous effort is needed to extract cfDNA fragmentation patterns with a strong signal intensity and improve the estimation of tissue-derived cfDNA fractions. In this review, most of these methods are proposed to detect and predict the TOOs of cancers. They are different in the detection sensitivity and accuracy due to the different performances on identifying the TOOs of cfDNAs. Therefore, improving the identification of the TOOs of cfDNAs is a basic but important thing in noninvasive diagnostics (page 14, col 1).
Further Peng teaches that although the cfDNA fragmentation pattern-based methods are at the very beginning stage, they have great potential to provide abundant markers. Therefore, more efforts should be made to identify tissue-specific nucleosome spacing patterns or tissue-specific preferred ends of cfDNAs (para 14, col 2).
Finally reagrding the use of preferred end coordinates, Peng teaches that although the idea is quite innovative, more work needs to be done before applying to clinical diagnosis (page 10, col 1).
The instant specification teaches that the origin of cfDNA is determined on the basis of transcription factor footprints in cfDNA fragments, but this is not being claimed. The specification provides generic prophetic guidance on how to use TF footprints to determine the tissue/cell of origin and detect the presence of cancer in a subject. It is noted that there are no working examples. In the absence of working examples, it is highly unpredictable how to determine the tissues/cell types giving rise to cfDNA in a subject by following the vague guidance in the specification. Based on the teachings of Peng, the technology being used by the inventors is just at the very beginning stage and tissue-specific nucleosome spacing patterns or tissue-specific preferred ends of cfDNAs still need to determined and more work needs to be done before this is applied to clinical diagnosis.
Quantity of Experimentation:
The quantity of experimentation necessary is great, on the order of many man-years, and then with little if any reasonable expectation of successfully enabling the full scope of the claims. In support of this position, it is noted that the claimed methods encompass being able to determine the cell types and tissue-of-origin composition of cfDNA in bodily fluids on the basis of transcription factor (TF) footprints in short cfDNA fragments. The claims further encompass being able to use the origin of the tissues and/or cell types to diagnose the presence or absence of cancer.
In order to practice the claimed invention one of skill in the art would first have to determine the cfDNA TF footprint of a representative number of different types of cells and/or tissues. The specification does not provide step by step guidance on how to do this. It is possible that it could take many years to just identify the cfDNA TE footprints for the representative number of the different types of cells and/or tissues encompassed by the claims.
Then additional experimentation would need to be conducted to determine whether or not the presence of cfDNA from a specific origin could be used to diagnose cancer. It’s not clear how the presence of cfDNA originating from one origin (i.e., the kidney) would allow one to diagnose a specific type of kidney disease or disorder since there are numerous disease/disorders known in the art to effect the kidneys (cancer, interstitial cystitis, glomerulonephritis, prostatitis, nephrosclerosis, bladder cancer, Peyronines disease). The specification has merely provided an invitation for further experimentation.
The amount of experimentation that would be required to practice the full scope of the claimed invention and the amount of time and cost this experimentation would take supports the position that such experimentation is undue. Attention is directed to Wyeth v. Abbott Laboratories 107 USPQ2d 1273, 1275, 1276 (Fed. Cir. June 2013):
Claims are not enabled when, at the effective filing date of the patent, one of ordinary skill in the art could not practice their full scope without undue experimentation. MagSil Corp. v. Hitachi Global Storage Techs., Inc., 687 F.3d 1377, 1380-81 [103 USPQ2d 1769] (Fed. Cir. 2012).
The remaining question is whether having to synthesize and screen each of at least tens of thousands of candidate compounds constitutes undue experimentation. We hold that it does. Undue experimentation is a matter of degree. Chiron Corp. v. Genentech, Inc., 363 F.3d 1247, 1253 [70 USPQ2d 1321] (Fed. Cir. 2004) (internal quotation omitted). Even “a considerable amount of experimentation is permissible,” as long as it is “merely routine” or the specification “provides a reasonable amount of guidance” regarding the direction of experimentation. Johns Hopkins Univ. v. CellPro, Inc., 152 F.3d 1342, 1360-61 [47 USPQ2d 1705] (Fed. Cir. 1998) (internal quotation omitted). Yet, routine experimentation is “not without bounds.” Cephalon, Inc. v. Watson Pharm., Inc., 707 F.3d 1330, 1339 [105 USPQ2d 1817] (Fed. Cir. 2013). (Emphasis added)
In Cephalon, although we ultimately reversed a finding of nonenablement, we noted that the defendant had not established that required experimentation “would be excessive, e.g., that it would involve testing for an unreasonable length of time.” 707 F.3d at 1339 (citing White Consol. Indus., Inc. v. Vega Servo-Control, Inc., 713 F.2d 788, 791 [218 USPQ 961] (Fed. Cir. 1983)). Finally, in In re Vaeck, we affirmed the PTO's nonenablement rejection of claims reciting heterologous gene expression in as many as 150 genera of cyanobacteria. 947 F.2d 488, 495-96 [20 USPQ2d 1438] (Fed. Cir. 1991). The specification disclosed only nine genera, despite cyanobacteria being a “diverse and relatively poorly understood group of microorganisms,” with unpredictable heterologous gene expression. Id. at 496. (Emphasis added)
Additionally, attention is directed to Cephalon at 1823, citing White Consol. Indus., Inc. v. Vega Servo-Control, Inc., 218 USPQ 961, that work that would require 18 months to 2 years so to enable the full scope of an invention, even if routine, would constitute undue experimentation. As stated therein:
Permissible experimentation is, nevertheless, not without bounds. This court has held that experimentation was unreasonable, for example, where it was found that eighteen months to two years’ work was required to practice the patented invention. See, e.g., White Consol. Indus., Inc. v. Vega Servo-Control, Inc., 713 F.2d 788, 791 [218 USPQ 961] Fed. Cir.1983). (Emphasis added)
Attention is also directed to MPEP 2164.06(b) and In re Vaeck, 20 USPQ2d 1438, 1445 (Fed. Cir. 1991).
Where, as here, a claimed genus represents a diverse and relatively poorly understood group of microorganisms, the required level of disclosure will be greater than, for example, the disclosure of an invention involving a “predictable” factor such as a mechanical or electrical element. See Fisher, 427 F.2d at 839, 166 USPQ at 24.
In view of such legal precedence, the aspect of having to work for so many years just to provide the starting materials for minute fraction of the scope of the claimed invention is deemed to constitute both an unreasonable length of time and undue experimentation.
Conclusion:
Taking into consideration the factors outlined above, including the nature of the invention, the breadth of the claims, the guidance presented in the specification and the working examples, the skill of those in the art and the unpredictability of the art, and the quantity of experimentation necessary, it is the conclusion that an undue amount of experimentation would be required to make and use the invention.
Response To Arguments
8. In the response the Applicants traversed the rejection under 35 USC 112(a). The Applicants argue that the claims are limited to the detection of cancer based on cfDNA produced from cancer cells. Furthermore, the use of cfDNA fragment counts incorporating mapping positions has been well established by work prior to the filing date, e.g., Snyder et al, and subsequent work by others, as useful for detecting the presence or absence of cancer in patient. The application does not need to include specific correlation data in order to enable to the person skilled in the art to practice the claimed invention.
This argument has been fully considered but is not persuasive. In the instant case the specification provides generic, prophetic guidance. There are no working examples in the specification wherein TF footprints of short cfDNA fragments are identified and used to determine tissues and/or cells types giving rise to cell free DNA. Further there are no working examples in the specification where tissues and/or cells types giving rise to cell free DNA are determined and used to identify cancer in a subject. Further the instant claims do not appear to be commensurate in scope with what the invention actually is. For example the specification teaches that the invention is drawn to methods for determining or quantifying the cell types and tissue-of-origin composition of cfDNA in bodily fluids on the basis of transcription factor (TF) footprints in short cfDNA fragments, yet the claims do not require determining transcription factor footprints. Applicants are reminded that patent protection is granted in return for an enabling disclosure of an invention, not for vague intimations of general ideas that may or may not be workable (See Brenner v. Manson, 383 U.S. 519, 536, 148 USPQ 689, 696 (1966), Stating, in context of the utility requirement, that "a patent is not a hunting license. It is not a reward for the search, but compensation for its successful conclusion. ") Tossing out the mere germ of an idea does not constitute enabling disclosure. While every aspect of a generic claim certainly need not have been carried out by an inventor, or exemplified in the specification, reasonable detail must be provided in order to enable members of the public to understand and carry out the invention. Considering the limited amount of guidance provided in the instant specification, one skilled in the art would have to engage in excessive and undue amount of experimentation to exercise the invention as claimed. The rejection is maintained.
Claim Rejections - 35 USC § 103
9. 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.
10. Claims 1-15 are rejected under 35 U.S.C. 103 as being unpatentable over Shendure (WO 2016/015058 Pub 1/28/2016 and Filed 7/27/2015) in view of Wang (US 2015/0132754 Pub 5/14/2015) and Kivioja (Nature Methods Vol 9 No 1 January 2012 pages 72-76).
Regarding Claim 1 Shendure teaches a method of determining tissues and/or cell types giving rise to cell-free DNA (cfDNA) in a subject, the method comprising: isolating cfDNA from a biological sample from the subject, the isolated cfDNA comprising a plurality of cfDNA fragments; determining a sequence associated with at least a portion of the plurality of cfDNA fragments; determining a genomic location within a reference genome for at least some cfDNA fragment endpoints of the plurality of cfDNA fragments as a function of the cfDNA fragment sequences; and determining at least some of the tissues and/or cell types giving rise to
the cfDNA fragments as a function of this subset of pairs of sequences (page 73, Ex 7).
Regarding Claim 2 Shendure teaches a method wherein determining at least some of the
tissues and/or cell types giving rise to the cfDNA fragments comprises comparing the
sequences associated with the cfDNA fragments to one or more reference maps (page 73, Ex 8).
Regarding Claim 3 Shendure teaches a method wherein the reference maps comprise binding motifs for at least one transcription factor (page 75, Ex 23-24).
Regarding Claim 4 Shendure teaches a method wherein the reference maps comprise binding locations for at least one transcription factor (page 75, Ex 23-24).
Regarding Claim 5 Shendure teaches a method wherein the binding locations for at least one transcription factor are determined by CHIPseq (page 46)
Regarding Claim 6 Shendure teaches generating a report comprising a list of the determined tissues and/or cell types giving rise to the isolated cfDNA (page 78, Ex 53).
Regardi