Contract analysis

I. EXECUTIVE SUMMARY This memorandum provides an internal analysis of the claim construction issues arising in the above-captioned patent infringement action, prepared in advance of the Markman hearing currently scheduled for September 18, 2026, before the Honorable Judge Jessica W. Langston in the Northern District of California. The purpose of this analysis is to guide our litigation strategy, inform expert prepara

II. BACKGROUND A. The Patents-in-Suit GenomeDx has asserted three related patents in this action, all arising from a common research program directed to genomic classifier methods for prostate cancer prognosis. The patents are summarized below.

1. U.S. Patent No. 10,438,271 ("the '271 Patent") Title: "Methods for Predicting Prostate Cancer Outcomes Using Multi-Gene Expression Classifiers" Filing Date: June 14, 2016 Issue Date: October 8, 2019 Expiration Date: June 14, 2036 Named Inventors: Dr. Rajan Mehta, Dr. Carolyn Xu, Dr. David Petrossian Asserted Claims: Claims 1, 3, 5, 7, 12, and 18 The '271 Patent is the parent patent in the asserted patent family an

2. U.S. Patent No. 11,204,893 ("the '893 Patent") Title: "Genomic Classifier Systems and Methods for Post-Surgical Cancer Prognosis" Filing Date: March 22, 2019 (continuation of the '271 Patent family) Issue Date: December 21, 2021 Expiration Date: June 14, 2036 Named Inventors: Dr. Rajan Mehta, Dr. Carolyn Xu Asserted Claims: Claims 1, 2, 9, 14, and 20 The '893 Patent is a continuation of the '271 Patent and claims

3. U.S. Patent No. 11,891,647 ("the '647 Patent") Title: "Improved Methods for Genomic Risk Stratification in Prostate Cancer Using Combined Biomarker and Clinical Variable Models" Filing Date: September 9, 2021 Issue Date: February 6, 2024 Expiration Date: September 9, 2041 Named Inventors: Dr. Rajan Mehta, Dr. Kevin Ostrowski, Dr. Priya Shah Asserted Claims: Claims 1, 4, 6, 11, and 15 The '647 Patent is the most re

III. LEGAL FRAMEWORK FOR CLAIM CONSTRUCTION Claim construction is a question of law for the court. Markman v. Westview Instruments, Inc., 517 U.S. 370, 372 (1996). The words of a patent claim are generally given their ordinary and customary meaning as understood by a person of ordinary skill in the art ("POSITA") at the time of the invention, in light of the specification and prosecution history. Phillips v. AWH Corp

1. Claim Language. The claims themselves define the scope of the patent right. The analysis begins with the words of the claims, read in the context of the entire claim and in relation to other claims in the same patent. Id. at 1314. The doctrine of claim differentiation creates a rebuttable presumption that different claims have different scope, and that the use of different terms across related claims reflects deli

2. Specification. The specification, including the written description and figures, is "the single best guide to the meaning of a disputed term." Phillips, 415 F.3d at 1315 (quoting Ridgeway & Co. v. Conceptronic, Inc., 90 F.3d 1576, 1582 (Fed. Cir. 1996)). The specification may reveal a special definition given to a claim term or may clarify the meaning of a term in the context of the invention. However, the Federal

3. Prosecution History. The prosecution history provides evidence of how the patent holder and the Patent Office understood the patent during the examination process. Phillips, 415 F.3d at 1317. Statements made during prosecution, including claim amendments and arguments distinguishing prior art, can limit the scope of the claims through prosecution history disclaimer or prosecution history estoppel. The prosecution

IV. DISPUTED CLAIM TERM ANALYSIS A. "Trained Machine-Learning Classifier" ('271 Patent, Claim 1)

1. Claim Language in Context The term "trained machine-learning classifier" appears in the context of the following limitation of Claim 1 of the '271 Patent: "applying a trained machine-learning classifier to generate a risk score" This term appears in all asserted claims of the '271 Patent — Claims 1, 3, 5, 7, 12, and 18. Claim 1 is the key independent claim; the dependent claims add specificity regarding particular

2. GenomeDx's Proposed Construction GenomeDx proposes the following construction for "trained machine-learning classifier": "A computational model that has been trained on labeled data using any supervised or semi-supervised machine-learning algorithm — including but not limited to random forests, gradient-boosted decision trees, support vector machines, neural networks, and logistic regression — to generate a numeri

3. Helios's Anticipated Proposed Construction Based on the August 4, 2025 exchange, Helios proposes the following construction for "trained machine-learning classifier": "A random-forest or support vector machine classifier that has been trained on a specific labeled training dataset as described in the specification." We anticipate that Helios will advance the following arguments in support of this narrower construc

4. Analysis and Recommendation GenomeDx's proposed construction is strongly supported by the intrinsic record and should prevail under controlling Federal Circuit precedent. The '271 Patent specification expressly lists multiple classifier types as examples of the "trained machine-learning classifier" genus. The passage at column 8, lines 15–42, is unambiguous: it identifies random forests, SVMs, and neural networks

1. Claim Language in Context The term "random-forest classifier" appears in the context of the following limitation of Claim 1 of the '893 Patent: "inputting normalized expression values into a random-forest classifier trained on a cohort of at least 500 patient samples" This term appears in all asserted claims of the '893 Patent — Claims 1, 2, 9, 14, and 20. The '893 Patent is a continuation of the '271 Patent, and

2. GenomeDx's Proposed Construction GenomeDx proposes the following construction for "random-forest classifier": "A classifier based on an ensemble of decision trees constructed using random feature selection and bootstrap aggregation (bagging), or a functionally equivalent ensemble-of-trees method." This proposed construction is supported by the following rationale: Specification Support. The '893 Patent specificati

3. Helios's Anticipated Proposed Construction Based on the August 4, 2025 exchange, Helios proposes the following construction for "random-forest classifier": "A classifier that specifically uses the random forest algorithm — i.e., an ensemble of decision trees trained using bootstrap aggregation (bagging) with random feature subsets at each split — and excludes other tree-based ensemble methods such as gradient boos

4. Analysis and Recommendation This is the most critical and highest-risk term for GenomeDx in the claim construction proceedings. Literal Infringement Analysis. The term "random-forest classifier" has a recognized meaning in the art. The random forest algorithm, as described by Breiman (2001), is a specific ensemble method that combines bootstrap aggregation (bagging) with random feature selection at each tree split

1. Claim Language in Context The term "panel of at least 22 genes selected from a predefined gene set" appears in the context of the following limitation of Claim 1 of the '271 Patent: "measuring expression levels of a panel of at least 22 genes selected from a predefined gene set" This term appears in all asserted claims of the '271 Patent — Claims 1, 3, 5, 7, 12, and 18. The specification of the '271 Patent defines

2. GenomeDx's Proposed Construction GenomeDx proposes the following construction: "Measuring the expression levels of 22 or more genes chosen from the gene set identified in the specification (Table 1 of the '271 Patent), which may be a subset of a larger gene panel measured by the accused method." The key aspect of GenomeDx's proposed construction is that the claim requires measurement of "at least 22 genes" that ar

3. Helios's Anticipated Proposed Construction Based on the August 4, 2025 exchange, Helios proposes the following construction: "Measuring expression levels of a panel consisting of at least 22 genes, all of which must be selected from the specific gene set defined in Table 1 of the '271 Patent specification." Helios's construction largely aligns with GenomeDx's on the basic requirement — at least 22 genes from the p

4. Analysis and Recommendation This term presents a significant vulnerability for the '271 Patent infringement theory if the gene overlap is confirmed at only 19 of 24. At the construction level, the parties' proposed constructions are not dramatically different — both require at least 22 genes from the predefined gene set. The real dispute is factual: whether 22 or more ProstaSignal™ genes actually come from the pre

1. Claim Language in Context The term "risk category" appears in the following context in Claim 1 of the '271 Patent: "classifying the patient into a risk category based on the score" The '647 Patent uses similar language in the context of generating a report that includes a risk classification for the patient. The specifications of both patents describe exemplary risk categories as "low risk," "intermediate risk," a

2. GenomeDx's Proposed Construction GenomeDx proposes the following construction: "A discrete classification grouping (e.g., low, intermediate, high, or other prognostic grouping) assigned to a patient based on the generated risk score, using predefined thresholds." GenomeDx contends that this term should be given its plain and ordinary meaning as understood by a POSITA. No special construction is required beyond its

3. Helios's Anticipated Proposed Construction Based on the August 4, 2025 exchange, Helios proposes the following construction: "A clinically validated risk grouping based on thresholds determined from the same training cohort used to develop the classifier, corresponding to distinct clinical outcomes." Helios's proposed construction imports two significant limitations not found in the claim language. First, it requi

4. Analysis and Recommendation GenomeDx's proposed construction is well-supported by the intrinsic record and should prevail. The claim language imposes no "clinical validation" requirement. Claim 1 simply recites "classifying the patient into a risk category based on the score." There is no mention of clinical validation, threshold derivation methodology, or correlation with specific clinical outcomes. Helios's atte

1. Claim Language in Context The term "composite risk metric" appears in the context of the following limitation of Claim 1 of the '647 Patent: "generating a composite risk metric and transmitting it to a healthcare provider" This limitation follows the step of "combining the genomic risk score with at least two clinical covariates selected from Gleason score, PSA level, surgical margin status, and pathological stage

2. GenomeDx's Proposed Construction GenomeDx proposes the following construction: "A single numerical or categorical output that integrates the genomic risk score with the selected clinical covariates into a unified prognostic assessment." This construction is supported by the '647 Patent specification, which describes the composite risk metric as an "integrated prognostic output" that provides enhanced predictive va

3. Helios's Anticipated Proposed Construction Based on the August 4, 2025 exchange, Helios proposes the following construction: "A single numerical score derived from a mathematical combination (e.g., weighted sum, regression model) of the genomic risk score and clinical covariates, as opposed to merely presenting the genomic score alongside clinical variables in a report." Helios's construction adds a critical limit

4. Analysis and Recommendation GenomeDx's proposed construction is broader and more consistent with the claim language, which recites "generating a composite risk metric" without specifying the mathematical method of generation. The term "composite" implies integration — combining multiple inputs into a single output — but does not require a specific mathematical operation such as a weighted sum or regression model.