Contract analysis

1. GenomeDx brings this action for patent infringement against Helios under the patent laws of the United States, 35 U.S.C. § 1 et seq. This action seeks injunctive relief, compensatory damages, enhanced damages for willful infringement, and other relief arising from Helios's unauthorized making, using, selling, and offering for sale of a genomic classifier test that infringes three of GenomeDx's United States patent

2. GenomeDx is a pioneer in the field of molecular diagnostics, with particular expertise in the development, validation, and clinical deployment of genomic-classifier methods for prostate cancer prognosis. GenomeDx holds a robust and valuable patent portfolio comprising forty-seven (47) issued United States patents, twelve (12) pending United States patent applications, and nineteen (19) international family members

3. GenomeDx's proprietary Decipher® Prostate genomic classifier test is the market-leading prognostic tool for prostate cancer recurrence and metastasis prediction following radical prostatectomy. The Decipher® test is the product of more than a decade of intensive research, development, clinical validation, and commercialization efforts by GenomeDx. The Decipher® test has been validated in more than forty peer-revie

4. GenomeDx brings this action to enforce three of its United States patents — 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") — against Helios's competing ProstaSignal™ Genomic Classifier test. Helios commercially launched the ProstaSignal™ test on October 7, 2024. The ProstaSignal

5. Plaintiff Genome Dx Therapeutics Inc. is a corporation organized and existing under the laws of the State of Delaware. GenomeDx is qualified to do business in the State of California and maintains its principal place of business and corporate headquarters at 4750 Torrey Pines Road, Suite 300, San Diego, California 92130. GenomeDx's registered agent in Delaware is Pacific Registered Agents, Inc., located at 1209 Or

6. GenomeDx was founded in 2011 and is a molecular diagnostics company focused on the development and commercialization of genomic classification technologies for cancer prognosis. GenomeDx's core competency lies in the application of advanced machine-learning techniques to multi-gene expression data to generate clinically actionable prognostic information for cancer patients and their treating physicians.

7. GenomeDx is led by a team of experienced scientists and executives, including Dr. Miriam Langford, PhD, Chief Executive Officer; Dr. Rajan Mehta, PhD, Chief Technology Officer and a named inventor on two of the three Patents-in-Suit; and Victoria Sung, JD, General Counsel. GenomeDx employs approximately eight hundred twenty (820) people, including approximately three hundred forty (340) laboratory and research and

8. GenomeDx is the sole and exclusive owner and assignee of all right, title, and interest in and to the Patents-in-Suit, including the right to sue for and recover damages for past and ongoing infringement. GenomeDx has standing to bring this action and to seek the relief requested herein. Defendant Helios Precision Diagnostics, Inc.

9. Defendant Helios Precision Diagnostics, Inc. is a corporation organized and existing under the laws of the State of Delaware. Helios is qualified to do business in the Commonwealth of Massachusetts and in the State of California. Helios maintains its principal place of business and corporate headquarters at 200 CambridgePark Drive, Suite 600, Cambridge, Massachusetts 02140.

10. Helios operates a Clinical Laboratory Improvement Amendments ("CLIA")-certified laboratory located at 9830 Mesa Rim Road, Suite 140, San Diego, California 92121. The accused ProstaSignal™ Genomic Classifier test is performed at this San Diego laboratory facility.

11. Helios was founded in 2019 and is a molecular diagnostics company. Helios is led by Dr. Nathan Ashford, MD, PhD, Chief Executive Officer, and Dr. Elaine Kossack, PhD, Chief Scientific Officer. Helios employs approximately two hundred fifteen (215) people.

12. Helios is the maker, user, seller, and offeror for sale of the accused ProstaSignal™ Genomic Classifier test, which is the subject of the infringement allegations set forth in this Complaint.

13. Upon information and belief, Helios has performed approximately eight thousand four hundred (8,400) ProstaSignal™ tests between the October 7, 2024 commercial launch date and March 2025. Upon information and belief, Helios has generated estimated revenue of approximately thirty-two million eighty-eight thousand dollars ($32,088,000) from sales of the ProstaSignal™ test during this period, based on an average reim

14. This Court has subject matter jurisdiction over this action pursuant to 28 U.S.C. § 1331, as this action arises under the laws of the United States, and pursuant to 28 U.S.C. § 1338(a), as this action arises under the patent laws of the United States, specifically the Patent Act, 35 U.S.C. § 1 et seq. Personal Jurisdiction.

15. This Court has personal jurisdiction over Helios. Helios is subject to personal jurisdiction in this judicial district and in the State of California for the following reasons: (a) Helios is qualified to do business and conducts substantial business within the State of California. (b) Helios operates a CLIA-certified laboratory located at 9830 Mesa Rim Road, Suite 140, San Diego, California 92121, which is within

16. The exercise of personal jurisdiction over Helios is consistent with the requirements of the Due Process Clause of the Fourteenth Amendment to the United States Constitution. Venue.

17. Venue is proper in this judicial district pursuant to 28 U.S.C. § 1400(b) because Helios has committed acts of infringement within this judicial district and has a regular and established place of business within this judicial district, specifically its CLIA-certified laboratory located at 9830 Mesa Rim Road, Suite 140, San Diego, California 92121. Helios maintains permanent personnel, laboratory equipment, and f

18. Alternatively, venue is proper in this judicial district because Helios is subject to personal jurisdiction in this judicial district, and the requirements of 28 U.S.C. § 1400(b) are otherwise satisfied. FACTUAL BACKGROUND GenomeDx and the Decipher® Prostate Genomic Classifier

19. GenomeDx was founded in 2011 with the mission of developing and commercializing advanced genomic classification technologies to improve cancer patient outcomes. Over the past fourteen years, GenomeDx has invested hundreds of millions of dollars in research and development, clinical validation, and commercialization of its proprietary genomic-classifier technologies. GenomeDx has become a recognized leader in the

20. GenomeDx developed the Decipher® Prostate genomic classifier test, a proprietary twenty-two (22)-gene expression-based prognostic test used to predict the likelihood of clinical recurrence and metastasis following radical prostatectomy for prostate cancer. The Decipher® test represents a breakthrough in the field of prostate cancer management, providing physicians and patients with clinically validated, objective

21. The Decipher® test involves the following key steps: (a) Obtaining a biological sample containing tumor RNA from formalin-fixed paraffin-embedded ("FFPE") prostate tissue. The use of FFPE tissue, rather than fresh-frozen tissue, is a critical feature of GenomeDx's technology, as it allows the test to be performed on routinely archived surgical specimens without requiring special tissue handling at the time of sur

22. In addition to the genomic risk score and risk category classification, the Decipher® test provides an integrated prognostic report that combines the genomic risk score with relevant clinical covariates, including Gleason score, pre-operative prostate-specific antigen ("PSA") level, surgical margin status, and pathological stage. This integrated approach — combining genomic and clinical data into a single, action

23. The Decipher® test is a laboratory-developed test ("LDT") performed exclusively at GenomeDx's CLIA-certified, College of American Pathologists ("CAP")-accredited laboratory. The Decipher® test is reimbursed by the Centers for Medicare & Medicaid Services ("CMS") under the Molecular Diagnostic Services ("MolDX") program. GenomeDx obtained a unique Multianalyte Assays with Algorithmic Analyses ("MAAA") code (0047M)

24. GenomeDx submitted a De Novo classification application with the United States Food and Drug Administration ("FDA") for the Decipher® test on August 15, 2024. That application is currently pending review. GenomeDx's pursuit of FDA authorization further demonstrates the significant investment and commitment GenomeDx has made in its proprietary technology.

25. Prior to the commercial launch of Helios's ProstaSignal™ test in October 2024, GenomeDx held a commanding market position with approximately seventy-four percent (74%) market share in the genomic prostate cancer prognostic testing market in the United States. GenomeDx's market leadership was the result of its pioneering scientific innovations, its extensive clinical validation program, its strong payor relationsh

26. GenomeDx generated three hundred eighty-seven million six hundred thousand dollars ($387,600,000) in revenue in fiscal year 2024, with the vast majority of this revenue derived from Decipher® test reimbursements. GenomeDx's substantial revenue base reflects the significant clinical and commercial value of its proprietary genomic-classification technology. GenomeDx's Patent Portfolio and the Patents-in-Suit

27. GenomeDx holds a robust and comprehensive patent portfolio consisting of forty-seven (47) issued United States patents, twelve (12) pending United States patent applications, and nineteen (19) international family members. This portfolio covers GenomeDx's proprietary genomic-classifier methods, including methods for gene-expression profiling from FFPE tissue specimens, machine-learning-based classification algori

28. GenomeDx has invested substantial resources in developing, prosecuting, maintaining, and enforcing its patent portfolio. GenomeDx's patent portfolio represents the culmination of years of scientific research, bioinformatics analysis, clinical validation, and innovation by GenomeDx's scientists and engineers. The patent portfolio is a critical intellectual property asset of GenomeDx.

29. The three Patents-in-Suit — the '271 Patent, the '893 Patent, and the '647 Patent — represent core innovations in genomic classification methods for prostate cancer prognosis. These patents cover fundamental aspects of GenomeDx's proprietary Decipher® technology, including the methods for multi-gene expression-based classification, the specific machine-learning classifier architectures and training methodologies

30. Helios was founded in 2019, approximately eight years after GenomeDx. Upon information and belief, Helios was founded with the objective of developing and commercializing molecular diagnostic tests for cancer prognosis, including tests that compete directly with GenomeDx's Decipher® test.

31. On or about October 7, 2024, Helios commercially launched the ProstaSignal™ Genomic Classifier, a twenty-four (24)-gene expression-based prognostic test for prostate cancer patients who have undergone radical prostatectomy. The ProstaSignal™ test was designed and marketed as a direct competitor to GenomeDx's Decipher® test and targets the same clinical use case — post-prostatectomy prognostic risk stratification.

32. Upon information and belief, the ProstaSignal™ test uses a twenty-four (24)-gene expression panel. Of the twenty-four genes in the ProstaSignal™ panel, nineteen (19) genes overlap with GenomeDx's patented gene set used in the Decipher® test. This extensive overlap — comprising approximately seventy-nine percent (79%) of the ProstaSignal™ gene panel — is not coincidental and reflects Helios's deliberate copying of

33. Upon information and belief, the ProstaSignal™ test applies a gradient-boosted decision tree classifier — which is a type of trained machine-learning classifier — to the measured gene-expression data to generate a numerical prognostic score designated by Helios as the "ProstaScore." The ProstaScore is a numerical value ranging from 0 to 100, with higher scores indicating greater risk of clinical recurrence and me

34. Upon information and belief, the ProstaSignal™ test combines the ProstaScore with clinical covariates, including Gleason grade group and pre-operative PSA level, to generate an integrated prognostic report that is transmitted to the ordering healthcare provider. This integrated reporting approach mirrors the methodology invented by GenomeDx and claimed in the Patents-in-Suit.

35. Helios obtained a MAAA code (0239M) for the ProstaSignal™ test from the American Medical Association in September 2024, approximately one month before the commercial launch. The ProstaSignal™ test is performed at Helios's CLIA-certified laboratory located at 9830 Mesa Rim Road, Suite 140, San Diego, California 92121.

36. Since its commercial launch on October 7, 2024, the ProstaSignal™ test has captured significant market share from GenomeDx. GenomeDx's market share in the genomic prostate cancer prognostic testing market has declined from approximately seventy-four percent (74%) prior to the ProstaSignal™ launch to approximately sixty-eight percent (68%) as of the filing of this Complaint, a decline of approximately six (6) perc

37. On October 8, 2019, the United States Patent and Trademark Office ("USPTO") duly and lawfully issued U.S. Patent No. 10,438,271, entitled "Methods for Predicting Prostate Cancer Outcomes Using Multi-Gene Expression Classifiers" (the "'271 Patent"). A true and correct copy of the '271 Patent is attached hereto as Exhibit A and is incorporated herein by reference.

38. The application that matured into the '271 Patent was filed on June 14, 2016. The '271 Patent has an expiration date of June 14, 2036.

39. The named inventors of the '271 Patent are Dr. Rajan Mehta, Dr. Carolyn Xu, and Dr. David Petrossian, each of whom conceived and developed the inventions claimed therein during the course of their employment with GenomeDx. Each named inventor assigned all right, title, and interest in the '271 Patent to GenomeDx. GenomeDx is the sole and exclusive owner of the '271 Patent, including the right to sue for and recov

40. The '271 Patent is valid, enforceable, and currently in force. All maintenance fees and other obligations necessary to maintain the '271 Patent in force have been timely paid and satisfied.

41. GenomeDx asserts Claims 1, 3, 5, 7, 12, and 18 of the '271 Patent against Helios in this action.

42. Claim 1 of the '271 Patent recites: A method for prognosing the likelihood of clinical recurrence following radical prostatectomy comprising: (a) obtaining a biological sample containing tumor RNA; (b) measuring expression levels of a panel of at least 22 genes selected from a predefined gene set; (c) applying a trained machine-learning classifier to generate a risk score; and (d) classifying the patient into a r

43. Claim 3 of the '271 Patent depends from Claim 1 and further specifies that the predefined gene set comprises genes associated with cell proliferation, cell adhesion, immune response, androgen signaling, and stromal response pathways, thereby defining the functional categories from which the at least twenty-two genes are selected.

44. Claim 5 of the '271 Patent depends from Claim 1 and further specifies that the trained machine-learning classifier is a random-forest classifier trained on a cohort of at least five hundred patient samples with known five-year clinical outcomes, including known metastasis status.

45. Claim 7 of the '271 Patent depends from Claim 1 and further specifies that the biological sample is a formalin-fixed paraffin-embedded tissue specimen from which RNA is extracted using an acid-guanidinium-phenol extraction protocol or equivalent nucleic acid isolation method.

46. Claim 12 of the '271 Patent depends from Claim 1 and further specifies that the risk categories comprise at least three categories — Low, Intermediate, and High — with defined score thresholds that stratify patients according to their predicted probability of clinical recurrence within a five-year post-surgical period.

47. Claim 18 of the '271 Patent depends from Claim 1 and further specifies that the method includes generating a prognostic report comprising the risk score, the risk category, and at least one clinical covariate selected from the group consisting of Gleason score, PSA level, surgical margin status, and pathological stage, and transmitting the report to a healthcare provider. U.S. Patent No. 11,204,893 ("the '893 Pat

48. On December 21, 2021, the USPTO duly and lawfully issued U.S. Patent No. 11,204,893, entitled "Genomic Classifier Systems and Methods for Post-Surgical Cancer Prognosis" (the "'893 Patent"). A true and correct copy of the '893 Patent is attached hereto as Exhibit B and is incorporated herein by reference.

49. The application that matured into the '893 Patent was filed on March 22, 2019, as a continuation application in the same patent family as the '271 Patent. The '893 Patent claims priority through the same priority chain as the '271 Patent and has an expiration date of June 14, 2036.

50. The named inventors of the '893 Patent are Dr. Rajan Mehta and Dr. Carolyn Xu, each of whom conceived and developed the inventions claimed therein during the course of their employment with GenomeDx. Each named inventor assigned all right, title, and interest in the '893 Patent to GenomeDx. GenomeDx is the sole and exclusive owner of the '893 Patent, including the right to sue for and recover damages for infringe

51. The '893 Patent is valid, enforceable, and currently in force. All maintenance fees and other obligations necessary to maintain the '893 Patent in force have been timely paid and satisfied.

52. GenomeDx asserts Claims 1, 2, 9, 14, and 20 of the '893 Patent against Helios in this action.

53. Claim 1 of the '893 Patent recites: A method comprising: normalizing gene-expression data from a formalin-fixed paraffin-embedded prostate tissue sample using a reference gene panel; inputting normalized expression values into a random-forest classifier trained on a cohort of at least 500 patient samples; and outputting a numerical prognostic score correlated with metastasis risk within 5 years.

54. Claim 2 of the '893 Patent depends from Claim 1 and further specifies that the normalization step comprises quantile normalization using a reference gene panel comprising at least five housekeeping genes, followed by batch-effect correction using a linear model.

55. Claim 9 of the '893 Patent depends from Claim 1 and further specifies that the random-forest classifier comprises at least five hundred individual decision trees, each trained on a bootstrap sample of the training cohort, and that the prognostic score is computed as the average of the individual tree predictions.

56. Claim 14 of the '893 Patent depends from Claim 1 and further specifies that the training cohort of at least five hundred patient samples comprises samples from at least three independent clinical study cohorts, with at least twenty-four months of follow-up data for each sample.

57. Claim 20 of the '893 Patent depends from Claim 1 and further specifies that the numerical prognostic score is a continuous score between 0 and 1, and that the method further comprises converting the continuous score into a categorical risk classification comprising at least three risk strata with clinically validated score thresholds. U.S. Patent No. 11,891,647 ("the '647 Patent")

58. On February 6, 2024, the USPTO duly and lawfully issued U.S. Patent No. 11,891,647, entitled "Improved Methods for Genomic Risk Stratification in Prostate Cancer Using Combined Biomarker and Clinical Variable Models" (the "'647 Patent"). A true and correct copy of the '647 Patent is attached hereto as Exhibit C and is incorporated herein by reference.

59. The application that matured into the '647 Patent was filed on September 9, 2021. The '647 Patent has an expiration date of September 9, 2041.

60. The named inventors of the '647 Patent are Dr. Rajan Mehta, Dr. Kevin Ostrowski, and Dr. Priya Shah, each of whom conceived and developed the inventions claimed therein during the course of their employment with GenomeDx. Each named inventor assigned all right, title, and interest in the '647 Patent to GenomeDx. GenomeDx is the sole and exclusive owner of the '647 Patent, including the right to sue for and recove