araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 73-year-old male with melanoma; genetic feature: tumor cells negative for PD-L1 expression

Clinical trial: Study of Tumor Tissue Samples From Patients With Stage I, Stage II, or Stage III Malignant Melanoma

Summary: RATIONALE: Studying the genes expressed in samples of tumor tissue from patients with cancer may help doctors identify biomarkers related to cancer.
  PURPOSE: This research study is looking at tumor tissue samples from patients with stage I, stage II, or stage III malignant melanoma.

Detailed description: OBJECTIVES:
  -  Determine the genetic profile of primary melanomas with and without synchronous regional nodal involvement by examining for 1) activating mutations B-Raf and N-Ras associated with melanoma development, and 2) allelic imbalances across the genome.
  -  Compare the genetic profile of primary melanomas from patients with and without lymph node involvement.
  -  Determine the combinations of genetic lesions that correlate with nodal metastasis by adopting a statistical machine learning approach to build a lesion-based classifier for nodal metastasis.
  OUTLINE: Laser capture microdissection is performed on the archived tissue samples to isolate melanoma cells. DNA is then purified from the samples and amplified using PCR. Matrix-assisted laser desorption/ionization (MALDI)-time of flight mass spectrometry technology is used to detect mutations of B-Raf and N-Ras. Single nucleotide polymorphism arrays are also performed.
  Information about the patient's demographics (e.g., TNM staging, sex, age, and tissue collection dates) will be gathered by chart review or from the Multidisciplinary Melanoma Conference at University Hospitals tumor conference report in order to match cases.

Eligibility: Inclusion Criteria:
  -  Node positive Group (experimental group)
  -  Primary melanoma > 2 mm in depth
  -  Metastasis must be > 0.1 mm and detectable by IHC or hematoxylin and eosin (H&E) to be considered node positive
  -  Slides and block for primary and node must be archived in UH dermatopathology
  -  Node Negative Group (control group)
  -  Primary melanoma > 2 mm in depth
  -  A negative sentinel lymph node must be negative by IHC and H&E
  -  No stage IV disease
  -  No acral and mucosal histology
  -  No history of prior invasive melanoma
  -  Underwent primary excision and sentinel lymph node biopsy within 3 months of each other
  -  Archived tissue available
  -  Slides and block for primary tumor and node biopsy must be archived in University Hospitals Case Medical Center (UH) dermatopathology
  Exclusion Criteria:
  -  Acral and mucosal histology
  -  Previous diagnosis of invasive melanoma
  -  previous chemotherapy or immunotherapy
  -  patients who are found to have stage IV disease during workup

Relevance to patient case: not relevant
Patient case: 73-year-old male with melanoma; genetic feature: tumor cells negative for PD-L1 expression

Clinical trial: Ultraviolet Light Exposure and Immunosuppression in Cutaneous Melanoma

Summary: This project seeks to understand differences in the serum vitamin D levels and immune status in cutaneous malignant melanoma patients with different UV exposure histories in New Mexico.

Detailed description: It is well established that ultraviolet radiation (UV) exposure is related to the development of melanoma. There is also evidence that immune reactions are altered after UV exposure in the skin (locally) and perhaps throughout the body (systemically). Additionally, while the role of vitamin D and melanoma development has not been fully established, UV-B exposure is essential for vitamin D production in the skin. Increased sun exposure is also related to the presence of solar elastosis, which might protect (1) or improve survival from melanoma. Thus, melanoma represents a unique model for studying UV exposure, the immune system, and vitamin D. Malignant melanoma is an antigenic cancer; therefore, the role of UV exposure-induced immunosuppression and vitamin D production in the recognition, destruction and growth inhibition of cancerous melanocytes is worth further study.
  To underscore the importance of this project, the Scientific Advisory Committee of the Melanoma Research Foundation and the Steering Committee of the Society of Melanoma Research have indicated a need to collect more human data on the host immune response mechanisms in melanoma and also to focus on the skin as a whole microenvironment, moving away from only in vitro experiments.

Eligibility: Inclusion Criteria:
  -  Resident of New Mexico
  -  Age between the 1 and 95
  -  Newly diagnosed with cutaneous invasive melanoma; any stage permitted (ICDO C44.0-9) between September 1, 2008 and December 31, 2011.
  -  SSM (superficial spreading melanoma) and NM (nodular melanoma) histological subtypes are allowed
  -  Access to a telephone or be able to participate in a personal interview at the clinic
  -  Physically and mentally competent to complete a 1-hour telephone or personal interview
  Exclusion Criteria:
  -  Ocular melanoma, LMM (lentigo maligna melanoma) or ALM (acral lentigo melanoma), and mucosal melanoma cases.
  -  No access to a telephone or is not able to meet with the interviewer.

Relevance to patient case: not relevant
Patient case: 73-year-old male with melanoma; genetic feature: tumor cells negative for PD-L1 expression

Clinical trial: The Identification of Novel Prognostic Markers in Melanoma

Summary: The purpose of this project is to analyze tumour tissue from a group of subjects with malignant melanoma, who have been treated at the Royal Marsden Hospital.

Detailed description: Background - The Royal Marsden Hospital and the Institute of Cancer Research constitute the largest comprehensive cancer centre in Europe. In addition to an in-house drug development program, phase I - phase III clinical trials of novel anti-cancer agents are hosted. In order to investigate the optimal use of novel molecularly targeted agents, access to clinical tumour samples is needed in order to determine which particular cancer type expresses a molecular "signature" that may indicate potential therapeutic utility. Understanding such signatures should accelerate the registration of new drugs for routine cancer therapy; offering the potential of selecting those patients with tumour types most likely to benefit from therapy. Furthermore, new insights into disease biology may be gained.
  Main research question/ objective - Are there features of primary melanoma or lymph node metastases that predict subsequent clinical outcome better than existing markers?

Eligibility: Inclusion Criteria:
  -  Diagnosis of melanoma
  -  Adequate paraffin-embedded material available for analysis.
  -  Adequate clinical follow-up information
  -  Written informed consent where applicable
  Exclusion Criteria:
  -  Inadequate paraffin-embedded material available
  -  Inadequate clinical follow-up information.

Relevance to patient case: not relevant
Patient case: 73-year-old male with melanoma; genetic feature: tumor cells negative for PD-L1 expression

Clinical trial: Survey Study - Sensitivity Comparison Between MelaFind and Physician Group

Summary: This survey study purposes to determine and compare the biopsy/referral sensitivity and specificity of MelaFind to the average biopsy/referral sensitivity and specificity of dermatologists. 241 subjects logged into system but only 183 signed consents and completed the intake survey. Out of these 183, 155 were accounted for in the data analysis after exclusions were removed from the pool of subjects.

Detailed description: Early detection of melanoma is critical for favorable prognosis, since patients with earlier stage melanomas have a much higher probability of survival than with later stages. The traditional method of early detection has been with serial total body skin exams where the health care provider examines all skin surfaces, including mucosa, for suspicious pigmented lesions. Studies have demonstrated that the diagnostic accuracy of physicians for melanoma depends on the level of dermatological training. More important than being able to make a diagnosis of melanoma on clinical impression is the ability to make an appropriate decision to biopsy the lesion. Primary care physicians (PCPs) are often expected to screen for melanoma and only refer to dermatologists when there is a high clinical suspicion of melanoma. However, if PCPs are not adept at diagnosing melanoma, then opportunities for early diagnosis and treatment could be missed. Conversely, the morphology of benign pigmented lesions can often mimic that of early melanomas, resulting in potentially unnecessary dermatology referrals, biopsies, and patient anxiety. Studies have indicated that there is great variability in the ability of PCPs to make a correct decision to biopsy/refer a pigmented lesion (1.5 times greater than dermatologists) as well as for diagnosing melanoma (over 2.5 times greater than dermatologists). To aid in detection of early melanomas, new technologies are being developed.
  One such technology is MelaFind, an investigational device that has been developed to give a recommendation for biopsy (or not) of pigmented skin lesions to rule out melanoma. Our hypothesis is that MelaFind will have equal or better sensitivity than pigmented lesion experts in making an appropriate recommendation for biopsy (i.e., MelaFind will be at least as accurate as dermatologists in recommending biopsy for melanomas).

Eligibility: Inclusion Criteria:
  -  Board Certified physicians or equivalent
  Exclusion Criteria:
  -  Did not participate in EOS Protocols 20061 or 20081

Relevance to patient case: not relevant
Patient case: 73-year-old male with melanoma; genetic feature: tumor cells negative for PD-L1 expression

Clinical trial: Study of BMS-650032 With Peginterferon Alfa-2a Plus Ribavirin

Summary: The purpose of this study is to identify one or more doses of BMS-650032 that, when used in combination with pegylated-interferon alpha and ribavirin are safe and demonstrate sufficient activity against hepatitis C virus (Genotypes 1 and 4).


Eligibility: Inclusion Criteria:
  -  Subjects chronically infected with HCV genotype 1 (Phase 2a and Phase 2b)
  -  Subjects chronically infected with HCV genotype 4 (Phase 2b only)
  -  HCV RNA viral load of ≥ 10*5* IU/mL at screening
  -  BMI of 18 - 35 kg/m² at screening
  Exclusion Criteria:
  -  Cirrhosis (Phase 2a only)
  -  Decompensated cirrhosis (Phase 2b)
  -  Co-infection with HBV or HIV
  -  Hepatocellular carcinoma
  -  Prior treatment with anti-HCV drugs

Relevance to patient case: not relevant
Patient case: 73-year-old male with melanoma; genetic feature: tumor cells negative for PD-L1 expression

Clinical trial: Early Diagnosis of Malignant Transformation of Pigmentary Skin Lesions

Summary: Malignant Melanoma is a deadly skin cancer that can be cured if diagnosed early. To date atypical pigmented skin lesions are diagnosed by appearance alone and many moles and lesions are excised unnecessarily and on the other hand malignant lesions are missed and diagnosed too late. In this study a protein conjugated to a florescent dye is spread on a suspicious pigmented lesion, the hypothesis is that this protein binds to malignant cells only and thus with a special camera that picks up the dye we can find pigmented lesions with early malignant transformation.


Eligibility: Inclusion Criteria:
  -  pigmented lesion indicated for surgical excision
  -  over 18 years of age
  Exclusion Criteria:
  -  pregnancy

Relevance to patient case: not relevant
Patient case: 73-year-old male with melanoma; genetic feature: tumor cells negative for PD-L1 expression

Clinical trial: A Study Evaluating INIPARIB in Combination With Chemotherapy to Treat Triple Negative Breast Cancer Brain Metastasis

Summary: The purpose of the study is to investigate the response rate for triple negative breast cancer patients with brain metastasis when INIPARIB is used in combination with irinotecan.
  Based on data generated by BiPar/Sanofi, it is concluded that iniparib does not possess characteristics typical of the PARP inhibitor class. The exact mechanism has not yet been fully elucidated, however based on experiments on tumor cells performed in the laboratory, iniparib is a novel investigational anti-cancer agent that induces gamma-H2AX (a marker of DNA damage) in tumor cell lines, induces cell cycle arrest in the G2/M phase in tumor cell lines, and potentiates the cell cycle effects of DNA damaging modalities in tumor cell lines. Investigations into potential targets of iniparib and its metabolites are ongoing.


Eligibility: Inclusion Criteria -
  1. Histologically-confirmed, ER negative, PR negative and Her2 negative adenocarcinoma of the breast with brain lesion on radiographic imaging.
  2. ECOG Performance Status of 0-2.
  3. Life expectancy of >12 weeks.
  4. No limit to prior therapies with last anti-cancer treatment ≥ 2 weeks from initiation of protocol-based therapy provided all toxicities (other than alopecia) have resolved to ≤Grade 1 or baseline.
  5. No active serious infection or other comorbid illness which would impair ability to participate in the trial.
  6. Stable or decreasing dose of steroids for ≥ 7 days.
  7. Interval ≥ 4 weeks between open brain biopsy and initiation of protocol-based therapy.
  8. Patients must have adequate organ function.
  Exclusion Criteria -
  1. Pregnant or breast-feeding
  2. Prior allergic reaction to INIPARIB
  3. Prior allergic reaction to irinotecan.
  4. Evidence of hemorrhage or impending herniation on baseline brain imaging
  5. Evidence of diffuse leptomeningeal disease on brain MRI or by previously documented CSF cytology-NOTE: discrete dural metastases are permitted.
  6. Clinically significant cardiac, renal, hepatic, infectious or pulmonary disease which might affect trial participation.
  7. Concurrent or planned radiation, hormonal, chemotherapeutic, experimental or targeted biologic therapy.
  8. Contraindication to gadolinium-enhanced MRI imaging.
  9. Inability to comply with study and/or follow-up procedures.

Relevance to patient case: not relevant
Patient case: 73-year-old male with melanoma; genetic feature: tumor cells negative for PD-L1 expression

Clinical trial: A Study Investigating the Predictive Value of Philadelphia Positive Stem Cell Properties in Newly Diagnosed Patients With Chronic Myeloid Leukemia in Chronic Phase Receiving Treatment With Imatinib

Summary: Imatinib (IM) is first-line treatment for patients with newly diagnosed CML in chronic phase. The drug is associated with high rates of cytogenetic responses with minimal toxicity in approximately 80% of patients. In 20% of patients however, the disease is either initially unresponsive to IM (Imatinib), resistance develops within a few months, or blast crisis occurs early and unexpectedly following an initial response. An increasing body of clinical evidence indicates that single agent molecularly targeted therapy (as in Gleevec/Imatinib) will not cure most patients with CML, as molecular remissions are rare. There is currently no clinically useful predictive tests to identify AT DIAGNOSIS those patients who are destined to be IM failures. The authors of this study have recently demonstrated that CML stem/progenitor cells are biologically insensitive to IM and are also genetically unstable and rapidly generate IM-resistant mutants in vitro and in vivo. The team recently discovered that the CD34 stem/progenitor cells of newly diagnosed CML patients who subsequently fail to respond to IM treatment show a reduced response to IM and a higher frequency of BCR-ABL mutations by comparison of 14 IM non-responders with 11 IM-responders. If this finding can be validated in a larger prospective cohort of patients, this predictive test could be used to more rationally design treatment plans with early addition of alternative therapies ie: Dasatinib or combination therapies for patients according to their individual risk profiles.
  Hypothesis:
  The clinical response of newly diagnosed chronic phase CML patients to IM can be predicted by certain biological properties of their CD34 stem/progenitor cells which are variable among patients.


Eligibility: Inclusion Criteria:
  -  Diagnosis of CML in chronic phase.
  -  ECOG <2.
  -  Normal organ function and ULN Total bili, AST and ALT.
  -  Must have the ability to understand and sign a written consent form
  Exclusion Criteria:
  -  Patients may not be receiving any other investigational agents.
  -  May not have prior treatment with Imatinib, Dasatinib, Nilotinib or other tyrosine kinase inhibitors.
  -  Patients must not have uncontrolled intercurrent illness including, but not limited to, ongoing or active infections, symptomatic congestive heart failure, unstable angina pectoris, cardiac arrhythmias, or psychiatric illness/social situations that would limit compliance with study requirements.
  -  Pregnant or nursing mothers
  -  Patients must have no prior malignancies except for; adequately treated non-melanoma skin cancer, cervical carcinoma-in-situ, adequately treated Stage I or II cancer from which the patient is in complete remission, or any other cancer from which the patient has been disease free for 5 years

Relevance to patient case: not relevant
Patient case: 73-year-old male with melanoma; genetic feature: tumor cells negative for PD-L1 expression

Clinical trial: A Study Of PF-05082566 As A Single Agent And In Combination With Rituximab

Summary: A study of PF-05082566, a 4-1BB agonist monoclonal antibody (mAb), in patients with solid tumors or b-cell lymphomas, and in combination with rituximab in patients with CD20 positive Non-Hodgkin's Lymphoma (NHL).


Eligibility: Inclusion Criteria
  -  Portion A: Histological or cytological diagnosis of advanced/metastatic solid tumor malignancy or B cell lymphoma, for which no curative therapy is available. Portion A expansion includes patients who have documented disease progression on a checkpoint inhibitor (anti CTLA 4, anti PD1/PD L1 antibodies) per RECIST criteria. Tumor types include metastatic melanoma, renal cell carcinoma (RCC), non-small cell lung cancer (NCSLC) and squamous cell carcinoma of the head and neck (SCCHN). Patients in the dose expansion stage are required to provide archival or baseline (obtained during the screening period) tumor biopsies.
  -  Portion B: Histological confirmed relapsed or refractory CD20 positive NHL for which no curative therapy is available. Patients enrolled in the expansion cohort must have archival tissue available, sampled within 6 months of study entry. The Expansion cohort includes patients with FL or DLBCL with relapsed or refractory disease.
  -  Measurable disease with at least one extranodal tumor mass >1.0 cm in the greatest transverse diameter (GTD) or in the case of malignant lymph nodes >1.5 cm in the GTD.
  -  ECOG performance status of ≤ 1.
  -  Adequate bone marrow function, for Portion A: absolute neutrophil count (ANC) ≥ 1.5 x 109/L, platelet count ≥100 x 109/L, hemoglobin >9.0 g/dL. For Portion B: ANC ≥ 1.0 x 109/L, platelet count ≥ 75 x 109/L, and hemoglobin ≥ 8.0 g/dL. In both cases, patients must be transfusion independent at least 14 days prior to screening.
  -  Serum creatinine ≤ 2 x ULN or estimated creatinine clearance ≥ 50 ml/min.
  -  Total serum bilirubin ≤ 1.5 x ULN unless the patient has documented Gilbert syndrome and AST and ALT ≤ 2.5 x ULN.
  Exclusion Criteria
  -  Patients with known symptomatic brain metastases requiring steroids.
  -  Prior allogeneic hematopoietic stem cell transplant.
  -  Immunosuppressive regimens involving systemic corticosteroids within 14 days before the first dose of study treatment.
  -  Therapeutic or experimental monoclonal antibodies within 28 day or prior radiation therapy within 14 days of the first dose of study drug.
  -  Autoimmune disorders and other diseases that compromise or impair the immune system.
  -  Unstable or serious concurrent medical conditions in the previous 6 months.
  -  Prior therapy with any anti CD137 monoclonal antibody.

Relevance to patient case: not relevant
Patient case: 73-year-old male with melanoma; genetic feature: tumor cells negative for PD-L1 expression

Clinical trial: Detection of Choroidal Nevus Cells in Vitrectomy Fluid

Summary: The purpose of this study is to determine if the investigators can detect the presence of choroidal nevi cells in the vitreous fluid of humans, as this may improve the diagnosis and classification of choroidal nevi and melanomas in the future.

Detailed description: Approximately 7% of the population has a choroidal nevus, or "freckle," in the back of the eye. Like a nevus on the skin, there is potential for malignant change to a melanoma. Dermatologists have the ability to quickly and easily biopsy suspicious skin lesions while ophthalmologists currently have no way of determining the malignant potential of choroidal nevi other than a fine needle aspiration (which is invasive and has the potential complications of bleeding and retinal detachment). This study's sole aim is to see if choroidal nevi cells are present in the inside fluid of the eye. The investigators plan to analyze the fluid of the eye, which is routinely removed during retina surgery, to detect any nevus cells. If the investigators are able to detect these cells, then future studies may allow us to better classify choroidal nevi for potential malignant change.

Eligibility: Inclusion Criteria:
  -  Patients with a choroidal nevus who are undergoing routine vitrectomy surgery for another indication (such as epiretinal membrane or macular hole repair).
  Exclusion Criteria:
  -  Patients without a choroidal nevus
  -  Children under the age of 18
  -  Pregnant and nursing females

Relevance to patient case: not relevant