Contract analysis

1. GenomeDx admits that this Court has subject matter jurisdiction over the patent-related claims and counterclaims asserted in this action pursuant to 28 U.S.C. §§ 1331 and 1338(a), which confer original jurisdiction on federal district courts over civil actions arising under the patent laws of the United States.

2. GenomeDx admits that, to the extent Helios seeks a declaratory judgment of non-infringement, invalidity, or unenforceability of the patents-in-suit, the Declaratory Judgment Act, 28 U.S.C. §§ 2201–2202, provides a procedural mechanism by which this Court may adjudicate such claims, and GenomeDx does not contest that an actual controversy exists between the parties within the meaning of the Declaratory Judgment Act

3. GenomeDx admits that venue is proper in the Northern District of California pursuant to 28 U.S.C. §§ 1391 and 1400(b).

4. GenomeDx admits that Helios is subject to personal jurisdiction in this judicial district, based upon, among other things, Helios's systematic and continuous business activities in the State of California, including the operation of a CLIA-certified laboratory in San Diego, California, and the marketing, sale, and performance of its ProstaSignal™ Genomic Classifier test within this district. B. Responses to Party

5. GenomeDx admits that it is a corporation organized and existing under the laws of the State of Delaware, with its principal place of business at 4750 Torrey Pines Road, Suite 300, San Diego, California 92130, and that it is qualified to do business in the State of California.

6. GenomeDx admits that Helios is a corporation organized and existing under the laws of the State of Delaware, with its principal place of business at 200 CambridgePark Drive, Suite 600, Cambridge, Massachusetts 02140, and that Helios is qualified to do business in the Commonwealth of Massachusetts and the State of California. GenomeDx further admits that Helios operates a CLIA-certified clinical laboratory located

7. GenomeDx admits that it is the owner by assignment of all right, title, and interest in and to U.S. Patent No. 10,438,271 ("the '271 Patent"), U.S. Patent No. 11,204,893 ("the '893 Patent"), and U.S. Patent No. 11,891,647 ("the '647 Patent") (collectively, the "patents-in-suit"), and that GenomeDx holds the exclusive right to enforce those patents and to collect damages for any infringement thereof.

8. GenomeDx denies any allegation, characterization, or implication contained in Helios's Counterclaims that any of the patents-in-suit is invalid, unenforceable, or not infringed by Helios's products, services, or activities. Each of the patents-in-suit was duly and lawfully issued by the United States Patent and Trademark Office ("USPTO") after full and thorough examination, and each is entitled to a presumption of

9. GenomeDx admits that U.S. Patent No. 10,438,271 is titled "Methods for Predicting Prostate Cancer Outcomes Using Multi-Gene Expression Classifiers," that the application leading to the '271 Patent was filed on June 14, 2016, and that the '271 Patent was duly issued by the USPTO on October 8, 2019.

10. GenomeDx admits that the named inventors of the '271 Patent are Dr. Rajan Mehta, Dr. Carolyn Xu, and Dr. David Petrossian.

11. GenomeDx admits that in the present action it asserts Claims 1, 3, 5, 7, 12, and 18 of the '271 Patent against Helios.

12. GenomeDx denies any allegation that the '271 Patent or any asserted claim thereof is invalid, unenforceable, or otherwise not entitled to full patent protection under the laws of the United States. The '271 Patent speaks for itself, and any characterization of the '271 Patent, its claims, its specification, or its prosecution history that is inconsistent with the patent document as issued is denied. Regarding U.S

13. GenomeDx admits that U.S. Patent No. 11,204,893 is titled "Genomic Classifier Systems and Methods for Post-Surgical Cancer Prognosis," that the application leading to the '893 Patent was filed on March 22, 2019, as a continuation of the application that issued as the '271 Patent and is part of the same patent family, and that the '893 Patent was duly issued by the USPTO on December 21, 2021.

14. GenomeDx admits that the named inventors of the '893 Patent are Dr. Rajan Mehta and Dr. Carolyn Xu.

15. GenomeDx admits that in the present action it asserts Claims 1, 2, 9, 14, and 20 of the '893 Patent against Helios.

16. GenomeDx denies any allegation that the '893 Patent or any asserted claim thereof is invalid, unenforceable, or otherwise not entitled to full patent protection. The '893 Patent speaks for itself, and any characterization of the '893 Patent, its claims, its specification, or its prosecution history that is inconsistent with the patent document as issued is denied. Regarding U.S. Patent No. 11,891,647 ("the '647 P

17. GenomeDx admits that U.S. Patent No. 11,891,647 is titled "Improved Methods for Genomic Risk Stratification in Prostate Cancer Using Combined Biomarker and Clinical Variable Models," that the application leading to the '647 Patent was filed on September 9, 2021, and that the '647 Patent was duly issued by the USPTO on February 6, 2024.

18. GenomeDx admits that the named inventors of the '647 Patent are Dr. Rajan Mehta, Dr. Kevin Ostrowski, and Dr. Priya Shah.

19. GenomeDx admits that in the present action it asserts Claims 1, 4, 6, 11, and 15 of the '647 Patent against Helios.

20. GenomeDx denies any allegation that the '647 Patent or any asserted claim thereof is invalid, unenforceable, or otherwise not entitled to full patent protection. The '647 Patent speaks for itself, and any characterization of the '647 Patent, its claims, its specification, or its prosecution history that is inconsistent with the patent document as issued is denied.

21. GenomeDx denies any allegation that the terminal disclaimer filed during prosecution of the '647 Patent over the '271 and '893 Patents affects the validity of any asserted claim of the '647 Patent. The terminal disclaimer was filed to overcome a non-substantive double-patenting rejection and does not constitute an admission regarding the scope or validity of any claim of any patent-in-suit. D. Responses to Allega

22. GenomeDx states that the prosecution histories of the '271, '893, and '647 Patents are public records maintained by the USPTO that speak for themselves. GenomeDx denies any characterization of the prosecution histories that is incomplete, misleading, or otherwise inconsistent with the actual contents of those prosecution records.

23. Regarding the prosecution of the '271 Patent, GenomeDx acknowledges that the Examiner initially raised a rejection under 35 U.S.C. § 101 based on the framework set forth in Mayo Collaborative Services v. Prometheus Laboratories, Inc., 566 U.S. 66 (2012), and Alice Corp. Pty. Ltd. v. CLS Bank International, 573 U.S. 208 (2014). GenomeDx further acknowledges that the applicant amended the claims to recite specific

24. Regarding the prosecution of the '893 Patent, GenomeDx acknowledges that the Examiner raised a rejection under 35 U.S.C. § 102 based on Nakamura et al. (U.S. Patent No. 9,617,340) and that the applicant overcame that rejection by distinguishing the random-forest classifier training methodology and minimum cohort size recited in the claims from what was disclosed in Nakamura. GenomeDx denies any implication by Hel

25. Regarding the prosecution of the '647 Patent, GenomeDx acknowledges that the Examiner raised rejections under 35 U.S.C. § 103 based on combinations of Nakamura et al. and Gagnon (WO 2018/065413), and that the applicant overcame those rejections through, among other things, a declaration under 37 C.F.R. § 1.132 submitted by Dr. Rajan Mehta, which established unexpected results achieved by the combined genomic-clin

26. GenomeDx admits that it markets and sells the Decipher® Prostate genomic classifier test, which is a clinical-grade diagnostic assay that utilizes a 22-gene expression panel to assess the risk of metastasis in men with prostate cancer following radical prostatectomy.

27. GenomeDx admits that it obtained Multianalyte Assays with Algorithmic Analyses ("MAAA") code 0047M from the American Medical Association for the Decipher® test in 2018, and that this code is used for billing and reimbursement purposes.

28. GenomeDx admits that the Decipher® test is performed as a laboratory-developed test ("LDT") under the Clinical Laboratory Improvement Amendments ("CLIA") regulatory framework, consistent with standard industry practice for genomic diagnostic assays.

29. GenomeDx admits that it submitted a De Novo classification request to the U.S. Food and Drug Administration ("FDA") on August 15, 2024, regarding the Decipher® test, and that such application remains pending before the FDA as of the date of this Answer.

30. GenomeDx denies any allegation by Helios that characterizes GenomeDx's commercial activities, marketing practices, licensing strategies, or enforcement of its intellectual property rights as anticompetitive, monopolistic, or otherwise improper under the antitrust laws, unfair competition laws, or any other body of law. GenomeDx's business activities are lawful in all respects, and GenomeDx's enforcement of its va

31. GenomeDx admits that Helios commercially launched its ProstaSignal™ Genomic Classifier on or about October 7, 2024.

32. GenomeDx admits that, based on publicly available information, ProstaSignal™ uses a 24-gene expression panel to assess prostate cancer prognosis.

33. GenomeDx admits that Helios obtained MAAA code 0239M for ProstaSignal™ from the American Medical Association in September 2024.

34. GenomeDx states that it lacks sufficient knowledge or information to admit or deny allegations regarding the internal workings, proprietary algorithms, specific computational methodologies, validation datasets, or other technical details of the ProstaSignal™ test that have not been publicly disclosed or produced in discovery, and on that basis denies such allegations. GenomeDx reserves the right to amend its resp

35. GenomeDx denies that ProstaSignal™ does not infringe the patents-in-suit. As set forth in GenomeDx's Complaint (Dkt. No. 1) and as will be demonstrated through discovery and at trial, Helios's ProstaSignal™ Genomic Classifier practices each and every limitation of the asserted claims of the '271, '893, and '647 Patents, either literally or under the doctrine of equivalents. RESPONSES TO COUNTERCLAIM COUNTS Respon

36. GenomeDx denies that Helios is entitled to a declaration of non-infringement of any asserted claim of U.S. Patent No. 10,438,271. GenomeDx incorporates by reference each and every admission, denial, and averment set forth above as though fully restated herein.

37. GenomeDx denies that Helios's ProstaSignal™ Genomic Classifier does not practice any element of Claims 1, 3, 5, 7, 12, or 18 of the '271 Patent. To the contrary, GenomeDx avers that ProstaSignal™ performs each step and satisfies each limitation recited in the asserted claims of the '271 Patent, including, without limitation, the use of a trained machine-learning classifier applied to a multi-gene expression panel

38. GenomeDx specifically denies Helios's contention that the use of a 24-gene expression panel in ProstaSignal™ avoids infringement of the '271 Patent. The asserted claims of the '271 Patent recite the measurement of expression levels of "at least 22 genes" from a defined panel. A 24-gene expression panel satisfies the "at least 22 genes" limitation. Helios's argument to the contrary lacks any basis in claim constru

39. GenomeDx further denies Helios's contention that the use of a gradient-boosted decision tree classifier in ProstaSignal™ avoids infringement of the '271 Patent claims reciting a "trained machine-learning classifier." The claims of the '271 Patent are not limited to any particular type or implementation of machine-learning classifier. A gradient-boosted decision tree is a type of trained machine-learning classifie

40. GenomeDx denies that Helios is entitled to a declaration of non-infringement of any asserted claim of U.S. Patent No. 11,204,893. GenomeDx incorporates by reference each and every admission, denial, and averment set forth above as though fully restated herein.

41. GenomeDx denies that Helios's ProstaSignal™ Genomic Classifier does not practice any element of Claims 1, 2, 9, 14, or 20 of the '893 Patent. GenomeDx avers that, to the extent any limitation of the '893 Patent claims—including the recitation of a "random-forest classifier"—is not literally met by Helios's use of a gradient-boosted decision tree classifier, infringement nonetheless exists under the doctrine of eq

42. GenomeDx denies that ProstaSignal™ does not normalize gene-expression data derived from FFPE prostate tissue samples using a reference gene panel. Based on publicly available information regarding the ProstaSignal™ test, including Helios's published technical white papers and its MAAA code application materials, ProstaSignal™ performs normalization of raw gene-expression data using reference housekeeping genes, c

43. GenomeDx denies that ProstaSignal™ does not output a numerical prognostic score correlated with the risk of metastasis within five years following radical prostatectomy. Based on available information, ProstaSignal™ generates a "ProstaScore" that is a numerical value on a continuous scale intended to predict the probability of metastatic progression within a defined time horizon, satisfying this claim limitation.

44. GenomeDx denies that Helios is entitled to a declaration of non-infringement of any asserted claim of U.S. Patent No. 11,891,647. GenomeDx incorporates by reference each and every admission, denial, and averment set forth above as though fully restated herein.

45. GenomeDx denies that Helios's ProstaSignal™ Genomic Classifier does not practice any element of Claims 1, 4, 6, 11, or 15 of the '647 Patent. GenomeDx avers that ProstaSignal™ combines its ProstaScore genomic risk score with clinical covariates—specifically, Gleason grade group and pre-operative prostate-specific antigen ("PSA") level—to generate a composite risk metric that is transmitted to ordering healthcare

46. GenomeDx denies that any asserted claim of the '271 Patent is invalid under 35 U.S.C. § 101 as lacking patent-eligible subject matter. GenomeDx incorporates by reference each and every admission, denial, and averment set forth above as though fully restated herein.

47. GenomeDx denies that the asserted claims of the '271 Patent are directed to abstract ideas, laws of nature, or natural phenomena. The claims of the '271 Patent are directed to specific, concrete diagnostic improvements in the field of prostate cancer prognosis, including particular technical steps that go well beyond any abstract idea or natural correlation. Specifically, the asserted claims recite: (a) obtaining

48. GenomeDx avers that the asserted claims of the '271 Patent are distinguishable from the claims at issue in Mayo Collaborative Services v. Prometheus Laboratories, Inc., 566 U.S. 66 (2012), and Association for Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. 576 (2013). Unlike the claims in Mayo, which recited only the observation of a natural correlation between drug metabolite levels and therapeutic effica

49. GenomeDx further states that the USPTO examined the claims of the '271 Patent under § 101, initially raised a rejection on patent-eligibility grounds, and subsequently withdrew that rejection after the applicant demonstrated that the claims recited patent-eligible subject matter. The '271 Patent claims are therefore entitled to a presumption of validity under 35 U.S.C. § 282, which Helios must overcome by clear a

50. GenomeDx denies that any asserted claim of the '893 Patent is invalid under 35 U.S.C. § 101. GenomeDx incorporates by reference each and every admission, denial, and averment set forth in its responses to Counts I through IV above, including its responses to Count IV, as though fully restated herein.

51. GenomeDx avers that the asserted claims of the '893 Patent recite specific technical limitations that, individually and as an ordered combination, render the claims patent-eligible. These limitations include, without limitation: (a) normalization of gene-expression data from FFPE prostate tissue using a defined reference gene panel; (b) input of the normalized expression data into a random-forest classifier that

52. GenomeDx denies that the inclusion of machine-learning classification methodology renders the claims of the '893 Patent abstract. The machine-learning classifier recited in the claims is not an end in itself but is integrated into a specific diagnostic method that transforms raw biological data into actionable clinical information through a series of defined technical steps. Response to Count VI: Declaratory Judg

53. GenomeDx denies that any asserted claim of the '647 Patent is invalid under 35 U.S.C. § 101. GenomeDx incorporates by reference each and every admission, denial, and averment set forth in its responses to Counts I through V above, as though fully restated herein.

54. GenomeDx avers that the asserted claims of the '647 Patent recite an integrated method that combines genomic data with clinical data to generate a composite risk metric for post-prostatectomy cancer prognosis. This integration of genomic and clinical variables represents a specific, practical application of any underlying natural relationship between gene expression and clinical outcomes. The claims do not merely

55. GenomeDx notes that this Court, in its Order dated January 13, 2026, denied Helios's Motion to Dismiss GenomeDx's infringement claims (Counts II and III of GenomeDx's Complaint) on § 101 grounds, finding that Helios's patent-eligibility challenges were premature in the absence of full claim construction. That ruling is relevant to the question of whether Helios's § 101 invalidity counterclaims can be adjudicated

56. GenomeDx denies that any asserted claim of the '271 Patent is anticipated by any prior art reference under 35 U.S.C. § 102, including Nakamura et al. (U.S. Patent No. 9,617,340) or any other reference identified or relied upon by Helios. GenomeDx incorporates by reference each and every admission, denial, and averment set forth above as though fully restated herein.

57. GenomeDx avers that Nakamura et al. does not disclose each and every element of any asserted claim of the '271 Patent, arranged as claimed. Without conceding the relevance or materiality of Nakamura to the asserted claims, GenomeDx states that Nakamura discloses a different gene panel, a different classification methodology, and a different clinical application than those recited in the '271 Patent claims. The '2

58. GenomeDx denies that any other prior art reference not yet identified by Helios anticipates the asserted claims of the '271 Patent, and reserves the right to respond to any additional prior art references identified by Helios during the course of discovery and in accordance with any scheduling orders entered by the Court. Response to Count VIII: Declaratory Judgment of Invalidity Under 35 U.S.C. § 103

59. GenomeDx denies that any asserted claim of any patent-in-suit is obvious under 35 U.S.C. § 103 in view of any combination of prior art references, whether taken individually or in combination. GenomeDx incorporates by reference each and every admission, denial, and averment set forth above as though fully restated herein.

60. GenomeDx specifically denies that the asserted claims of any patent-in-suit would have been obvious in view of Nakamura et al. (U.S. Patent No. 9,617,340), Gagnon (WO 2018/065413), Thornberry et al. ("Ensemble Machine Learning Methods for Predicting Cancer Recurrence," Journal of Computational Oncology, Vol. 14, No. 3, pp. 287–301, March 2015), and Klein et al. ("A Genomic Classifier Improves Prediction of Metast