araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: NIR-Guided Sentinel Lymph Node Mapping in Melanoma

Summary: This study will try to define an appropriate dose of the investigational drug indocyanine green (ICG) in combination with near infrared (NIR) imaging to use for future studies.
  ICG is a dye which has been in use since the 50s, and is approved for testing liver function and measuring blood flow from the heart. It has been used in studies to map lymphatic pathways in lung and breast cancer and information from those studies suggest it may help identify lymph nodes associated with melanoma. ICG can be detected within the body using near-infrared light cameras.
  In this study the investigators are looking at how easily ICG can get to the first lymph node (sentinel lymph node [SLN]) associated with melanoma, whether the investigators can see the path of the ICG and the SLN using a near infrared camera, and what dose of ICG works the best. While the current method for SNL mapping, known as lymphoscintigraphy, is effective it does provide a small amount of radiation. This study will compare the investigators results to the standard procedure.

Detailed description: At the time of surgery, you will undergo a lymphoscintigraphic procedure which is standard of care for patients with melanoma. You will also receive a dose of ICG mixed with human serum albumin. This will be administered in four small injections immediately around your tumor or the tumor scar if it has already been removed. Pictures of the ICG solution will be taken with the NIR camera and the progression of the dye along the lymphatic channel from your tumor to the SLN will be monitored.
  As each lymph node is removed, pictures will be taken to see if the ICG dye has entered and colored that node. We will compare this technique with the results from the lymphoscintigraphy to measure accuracy.
  Patients will be followed for at least one hour post injection for adverse events. The patient will then be taken off of the study. The results from each intervention will subsequently analyzed.

Eligibility: Inclusion Criteria:
  -  Histologically confirmed melanoma and an appropriate surgical candidate for a sentinel lymph node biopsy
  -  Stage of disease conducive to sentinel lymph node biopsy as determined by oncologic surgeon
  -  Receiving a planned lymphoscintigraphy procedure
  Exclusion Criteria:
  -  History of allergic reactions attributed to compounds of similar chemical or biologic composition to indocyanine green, including those patients with a history of iodide or seafood allergy
  -  Pregnant or breast-feeding

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

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: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Short Non-coding RNA Biomarkers of Predisposition to Ovarian Cancer

Summary: The purpose of this study is to create new tests to identify biomarkers for ovarian cancer so that a screening test can be developed. For patients who have a diagnosis of ovarian Cancer, researchers will use blood samples before and after treatment to see if disease status can be determined by measuring the amount of biomarker.

Detailed description: Epithelial ovarian cancer is the most lethal female reproductive malignancy, mainly because 80% of tumors have metastasized beyond the ovary at the time of diagnosis. Screening efforts aimed at improved identification of early stage disease have been largely unsuccessful, because of ovarian cancer's propensity for early spread. Our hypothesis is that this obstacle can be circumvented by identifying biomarkers for the precancerous stage of this disease. Since this pre-cancerous stage is currently undetectable, we instead propose to look for biomarkers in women at very high risk for developing ovarian cancer due to genetic mutations. We hypothesize that identification of markers for genetic predisposition to ovarian cancer will also be informative for detection of biological changes that over time lead to sporadic cancers. Given their increasingly recognized role in states of normal and abnormal growth and differentiation, we hypothesize that short non-coding RNAs (sncRNAs) hold significant promise as biomarkers of ovarian cancer predisposition. We will test these hypotheses in two aims. First, we will identify biomarkers for hereditary ovarian cancer risk by comparing serum-derived sncRNAs in women with and without hereditary risk for ovarian cancer. In the second aim we will define serum-derived sncRNAs correlates of ovarian cancer disease status. We will compare sera from ovarian cancer patients at times of highest and lowest disease burden to those of control, cancer-free subjects. Each aim will provide independent, novel, and important information for future investigations. The sncRNAs found to be differentially expressed in both aims will be prioritized for future validation in women under clinical surveillance for hereditary risk of ovarian cancer.

Eligibility: Inclusion Criteria:
  -  Undergoing medical care at UVA
  -  Up to date breast cancer screening
  -  Subjects must fall into one of the following groups:
  -  Women at increased risk of ovarian cancer based on family history, personal history, or genetic factors defined as either BRCA1 or BRCA2 mutations who still retain both fallopian tubes and both ovaries.
  -  Women at average risk for ovarian cancer
  -  Women with known/suspected or recurrent ovarian cancer who are undergoing evaluation and/or treatment at UVA Cancer Center
  Exclusion Criteria:
  -  Subjects with increased risk for ovarian cancer may not have a history of prior malignancy within the last 10 years excluding cervical carcinoma in situ or basal cell carcinoma
  -  Pregnancy (self reported)

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Safety and Tolerability Study of GSK1120212, a MEK Inhibitor, in Combination With Docetaxel, Erlotinib, Pemetrexed, Pemetrexed + Carboplatin, Pemetrexed + Cisplatin, or Nab-Paclitaxel

Summary: The purpose of this study is to determine what dose of GSK1120212 can be given safely in combination with at least one other drug that is already approved to treat cancer. This study will test the safety of up to 6 different GSK1120212 study treatment combinations (GSK1120212 plus either docetaxel, erlotinib, pemetrexed, pemetrexed + carboplatin, pemetrexed + cisplatin, or nab-paclitaxel). The doses identified in this study may be used in future trials to test whether the combination treatment is a safe and effective therapy for subjects with metastatic lung and/or pancreatic cancers.


Eligibility: Inclusion Criteria:
  -  The subject has a solid tumor. Expansion cohorts are limited to non-small cell lung cancer and/or pancreatic cancer with or without a KRAS mutation.
  -  Tumor progression following at least one prior standard therapy, the subject refuses standard therapy, or no standard therapy exists.
  -  The subject has a radiographically measurable tumor.
  -  The subject is able to carry out daily life activities without difficulty.
  -  The subject is able to swallow and retain oral medication.
  -  The subject does not have significant side effects from previous anti-cancer treatment.
  -  The subject has adequate organ and blood cell counts.
  -  Sexually active subjects must use medically acceptable methods of contraception during the course of the study.
  Exclusion Criteria:
  -  The subject has had major surgery or received certain types of cancer therapy within 2-3 weeks before starting the study.
  -  The subject has a brain tumor.
  -  Current severe, uncontrolled systemic disease.
  -  History of clinically significant heart, lung, or eye/vision problems.
  -  The subject has high blood pressure that is not well-controlled with medication.
  -  The subject has a permanent pacemaker.
  -  The subject is pregnant or breastfeeding.
  -  Positive for Hepatitis B, Hepatitis C, or HIV.

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: A Study of BYL719 in Adult Patients With Advanced Solid Malignancies, Whose Tumors Have an Alteration of the PIK3CA Gene

Summary: This is a first-in-man trial, in which BYL719 will be administered to adult patients with advanced solid tumors, whose tumors have an alteration of the PIK3CA gene and whose disease has progressed despite standard therapy or for whom no standard therapy exists. A combination of BYL719 with fulvestrant will also be investigated in post-menopausal patients with locally advanced or metastatic breast cancer whose tumors have an alteration of the PIK3CA gene. The single agent MTD dose expansion cohort and the fulvestrant combination MTD dose expansion cohort will also include ER+/HER2- breast cancer patients whose tumors have the wild type PIK3CA gene


Eligibility: Inclusion Criteria:
  -  Patients with histologically-confirmed, advanced unresectable solid tumors who have progressed within three months before screening/baseline visit Only patients who have confirmed PIK3CA status (wild type, mutation or amplification) will be allowed for screening (patients participating in the combination arm must be eligible for treatment with fulvestrant)
  -  Availability of a representative formalin fixed paraffin embedded tumor tissue sample
  -  At least one measurable or non-measurable lesion
  -  Age ≥ 18 years
  -  World Health Organization (WHO) Performance Status ≤ 2
  -  Good organ (hepatic, kidney, BM) function at screening/baseline visit
  Exclusion Criteria:
  -  Brain metastasis unless treated and free of signs/symptoms attributable to brain metastasis in the absence of corticosteroid therapy (anti-epileptic therapy is allowed).
  -  Prior treatment with PI3K, AKT or mTOR inhibitor and failure to benefit
  -  Patient with peripheral neuropathy NCI-CTC Grade ≥ 3
  -  Patient with diarrhea NCI-CTC Grade ≥ 2
  -  Patient with acute or chronic pancreatitis
  -  Impaired cardiac function or clinically significant cardiac disease incl. unstable angina pectoris ≤ 3 months prior to starting study drug and Acute Myocardial Infarction (AMI) ≤ 3 months prior to starting study drug.
  -  Patients with clinically manifest diabetes mellitus, history of gestational diabetes mellitus or documented steroid-induced diabetes mellitus
  -  Women who are pregnant or breast feeding or adults of reproductive potential not employing an effective method of birth control
  Other protocol-defined inclusion/exclusion criteria may apply

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Nordic Adjuvant IFN Melanoma Trial

Summary: The aim of this study is to evaluate the effect of giving adjuvant treatment with intermediate doses of interferon-alpha2b to patients operated for high risk melanoma. Patients are randomly assigned to either observation only or interferon treatment for 2 different durations. The outcome with respect to overall survival, relapse-free survival, side effects and quality of life is analysed.

Detailed description: This is an open multicenter, prospective randomised phase III trial evaluating the efficacy of two different schedules of Interferon-alpha2b (IFN-alpha2b) administered in an adjuvant setting after adequate surgery in high risk cutaneous melanoma patients (T4N0M0/TxN1-2M0). The patients have been operated for either a thick primary melanoma (> 4 mm) without evidence of distant metastasis or have undergone surgery for regional lymph node metastases.
  The study consists of a control arm (A) and two treatment arms, B and C. The outcome in arms B and C with adjuvant treatment with IFN-alpha2b will be compared to the outcome of arm A in which the patients will only be observed after the surgery. The primary endpoint is overall survival. Secondary endpoints are relapse-free survival, safety-toxicity and health-related quality of life.

Eligibility: Inclusion Criteria:
  -  T4 N0 M0 - Thick primary melanoma: > 4.0 mm Breslow depth, without lymph node involvement, or
  -  Tx N1-2 M0 Primary melanoma of any thickness with regional lymph node metastases confirmed by lymphadenectomy, or
  -  Tx N1-2 M0 Recurrent melanoma in regional lymph node(s) confirmed by lymphadenectomy.
  -  ECOG performance status of 0-1
  -  No active medical or psychiatric disorder requiring therapy that would prevent completion of protocol
  -  Written informed consent
  Exclusion Criteria:
  -  Patients with unknown primary site of melanoma or primary melanoma originating apart from the skin, except subungual melanoma
  -  Patients who have clinical, radiological/laboratory or pathological evidence of incompletely resected melanoma or distant metastatic disease
  -  Patients who have had prior adjuvant radiotherapy, chemotherapy, immunotherapy including preoperative infusion or perfusion therapy
  -  Female patients who are pregnant or lactating

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Interferon Alfa Sensitivity in HIV/HCV Persons Before and After HIV Meds

Summary: The chief purpose of this research is to evaluate interferon alpha sensitivity and cell type specific levels of interferon receptor and interferon stimulated genes and proteins in HIV/ HCV (hepatitis C virus) coinfected persons before and after administration of HIV medications (antiretroviral therapy).

Detailed description: We plan to perform liver biopsy by microlaparoscopy on previously untreated HIV/HCV coinfected persons, then give them a dose of peginterferon alfa 2b. HCV and HIV kinetics will be studied. Afterward, HIV will be treated using antiretroviral therapy and the procedure will be repeated.

Eligibility: Inclusion Criteria:
  -  Adult Human
  -  Able to provide written informed consent
  -  HIV antibody positive
  -  HIV viral load positive
  -  HIV treatment naive
  -  Hepatitis C antibody positive
  -  Hepatitis C viral load positive
  -  Hepatitis C treatment naive
  -  Approved to take HIV medications for minimum 9 months
  -  Willing to use contraception, Life expectancy greater than 2 years
  Exclusion Criteria:
  -  Significant opportunistic infections within 12 month
  -  Hepatitis B positive
  -  Evidence of liver cirrhosis
  -  Decompensated liver disease
  -  Chronic alcohol abuse
  -  Allergy to raltegravir, tenofovir, and/or emtricitabine
  -  Active or suspected malignancy
  -  Sarcoidosis
  -  Active TB
  -  Coronary artery disease
  -  Uncontrolled seizures
  -  Untreated thyroid disease
  -  Untreated diabetes
  -  Weight greater than 125 kg
  -  Severe depression or severe psychiatric disorder
  -  Ongoing alcohol or illicit drug use
  -  Pregnant, nursing, pr planning to become pregnant
  -  Allergy to interferon

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: IL-2 "SELECT" Tissue Collection Protocol in Patients With Advanced Melanoma

Summary: The purpose of this study is to determine which participants with melanoma have a better response to IL-2 and to identify markers that may predict response to IL-2 by collecting participant information (for example; cancer diagnosis and history, prior treatments for cancer, etc.) blood and tumor samples prior to treatment and tumor measurements after treatment.

Detailed description: Original tumor slides will be collected to identify tumor markers that may predict responses to treatment. Blood samples will be obtained prior to treatment with IL-2.

Eligibility: Inclusion Criteria:
  -  Malignant melanoma that is metastatic or unresectable
  -  Eligible to receive high-dose IL-2
  -  Tissue block available with adequate tumor to perform RNA extraction and DASL analysis
  Exclusion Criteria:
  -  Prior immunotherapy for unresectable or metastatic disease
  -  Untreated brain metastases, leptomeningeal disease, or seizure disorder

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

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
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Efficacy and Safety Study of GSK1120212, a MEK Inhibitor, in Subjects With Uveal Melanoma

Summary: The purpose of this study is to determine whether GSK1120212, a MEK inhibitor, is an effective and safe treatment for cancer subjects with metastatic uveal melanoma and mutation-positive GNAQ or GNA11 metastatic melanoma.


Eligibility: Inclusion Criteria:
  -  Histologically or cytologically confirmed diagnosis of metastatic uveal melanoma or previously documented mutation-positive GNAQ or GNA11 metastatic melanoma not previously treated with a MEK inhibitor.
  -  Provide archival tumor tissue or, if tissue blocks are not available, undergo fresh tumor biopsy prior to enrollment.
  -  The patient has a radiographically measurable tumor.
  -  ECOG performance status 0, 1, or 2.
  -  The patient is able to swallow and retain oral medication.
  -  Life expectancy of at least 4 months.
  -  Toxicities from previous anti-cancer therapy (except alopecia) are recovered (Grade 1 or less) at the time of enrollment.
  -  The patient has adequate organ and bone marrow function.
  -  Sexually active patients must use medically acceptable methods of contraception during the course of the study.
  -  Female patients of childbearing potential must have a negative serum pregnancy test at screening.
  Exclusion Criteria:
  -  The patient has had any of the following within 21 days of starting study drug or anticipates the need for any of the following during the course of study treatment: chemotherapy, immunotherapy, biologic therapy, hormone therapy, major surgery, or tumor embolization.
  -  The patient has received experimental therapy within 21 days of starting study drug.
  -  The patient has received nitrosourea or mitomycin C within 42 days of starting study drug.
  -  The patient has received any herbal medications or palliative radiotherapy within 14 days of starting study drug.
  -  The patient is currently receiving anticoagulation therapy that is not well controlled.
  -  Ongoing or newly diagnosed eye abnormality other than symptoms due to uveal melanoma.
  -  History of retinal vein occlusion or central serous retinopathy.
  -  Current severe, uncontrolled systemic disease.
  -  History of leptomeningeal disease or spinal cord compression secondary to metastasis.
  -  Brain metastasis, unless previously treated with surgery, whole-brain radiation or stereotactic radiosurgery and the disease has been stable for at least 3 months without steroid use or on a stable dose of steroids for at least 1 month prior to starting study drug. Stability of brain metastases must be confirmed with imaging.
  -  The patient has a concurrent, active hematological malignancy or other solid tumor malignancy.
  -  History of clinically significant cardiac or pulmonary dysfunction.
  -  Allergy or hypersensitivity to components of the GSK1120212 formulation.
  -  The patient is pregnant or breastfeeding.

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Study of Circulating Tumoral DNA in Metastatic Choroidal Melanoma

Summary: Circulating tumor DNA detection and quantification in patients with metastatic choroidal melanoma.

Detailed description: Technique development: In first step, the different available techniques will be evaluated for specificity and sensibility using serial dilutions of cell lines with or without GNAQ mutation.
  Validation: The tumor DNA detection rate will be estimated from metastatic uveal patient's blood. The investigators will study 40 patients to obtain at least 15 patients bearing a GNAQ mutation in the primitive tumor or in metastasis. With those 15 patients, the investigators will determinate the most sensitive technique and the best cost/efficiency ratio.

Eligibility: Inclusion Criteria:
  -  Age > or = 18 years.
  -  Patient with a metastatic choroidal melanoma.
  -  Patient with tumor or metastasis available for GNAQ (Guanine nucleotide blinding protein) status characterization.
  -  Patient able to stand a blood collection.
  -  Signed written informed consent approved by competent authority and ethic committee.
  Exclusion Criteria:
  -  Patient without social protection/insurance.
  -  Current pregnancy and lactation.
  -  All social, medical, psychological, situations making the study impossible.
  -  Person deprived of liberty.

Relevance to patient case: not relevant