araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 74-year-old female with melanoma; genetic feature: no tumor infiltrating lymphocytes

Clinical trial: Characterization of the Melanoma-Specific Immune Response

Summary: The aim of this study is to study T-cells. Blood will be collected and the samples will be used to generate T cell clones. Two separate blood draws will be required at the maximum.

Detailed description: The aim of the study is to in-vitro characterize and expand T cells specific for melanoma-derived antigens. Peripheral blood with be collected from 20 volunteers with biopsy proven melanoma and 10 age matched controls. Blood will be collected prior to the initiation of chemotherapy. There will be no more than two blood draws per patient. Most patients will receive a single blood draw; however, some participants may be asked to return for a single additional blood draw if investigators were unable to isolate melanoma-specific immune cells after the first blood draw. Two separate blood draws will be the maximum. The interval between these blood draws will be a minimum of 3 months apart. Blood samples will be used to determine the patient's HLA haplotype via PCR and DNA sequencing. After the patient's haplotype has been established melanoma-specific T cell clones will be generated from the peripheral blood samples and expanded in-vitro. These clones will then be assayed for specificity against commercially available melanoma cell lines. The T cell clones will also be assayed for reactivity to melanocyte differentiation antigens such as MART-1 and gp100. If the volunteer requires a palliative resection of a melanoma tumor then the patient's own tumor cells may also be used to test the specificity of the isolated T cell clones. All experiments will be conducted in-vitro.

Eligibility: Inclusion Criteria:
  -  Biopsy diagnosis of malignant melanoma
  -  Have had a biopsy diagnosis of malignant melanoma in the past
  Exclusion Criteria:
  -  Patients taking immunosuppressive medications

Relevance to patient case: not relevant
Patient case: 74-year-old female with melanoma; genetic feature: no tumor infiltrating lymphocytes

Clinical trial: Validation of a Molecular Prognostic Test for Eye Melanoma

Summary: Up to half of patients with ocular melanoma (also called iris, choroidal or uveal melanoma) develop metastasis. We have found that certain molecular features of the eye tumor can be detected by gene expression profiling and accurately predict which patients will develop metastasis. This molecular test could eventually allow high risk patients to receive preventative therapy to delay or prevent the development of metastasis. The goal of this study is to prospectively validate the predictive accuracy of the gene expression-based molecular test and compare it to monosomy 3, the most common but potentially less accurate molecular marker for metastasis in ocular melanoma.

Detailed description: We have discovered a gene expression profile derived from primary uveal melanomas that accurately predicts which patients will develop metastasis. Tumors with a class 1 gene expression signature have a very low risk, and those with a class 2 signature have a high risk of metastasis. The molecular test was initially performed on tissue obtained from enucleated eyes using commercial microarray platforms. We are now able to perform the molecular test on fine needle biopsy specimens, and we have developed a customized test that has greater dynamic range and sensitivity than commercial microarray platforms. The goal of this study is to validate the prognostic accuracy of the customized platform by performing the molecular test on primary uveal melanomas obtained from enucleation, local tumor resection or fine needle biopsy. Each sample will be diagnosed as either class 1, class 2 or indeterminate. Outcomes will be collected and the ability of the molecular diagnosis to predict metastasis will be evaluated at regular intervals.

Eligibility: Inclusion Criteria:
  -  clinical diagnosis of melanoma of the iris, ciliary body and/or choroid
  -  treatment to include enucleation, radiotherapy or local tumor resection
  Exclusion Criteria:
  -  evidence of marked tumor necrosis

Relevance to patient case: not relevant
Patient case: 74-year-old female with melanoma; genetic feature: no tumor infiltrating lymphocytes

Clinical trial: Melanoma Inhibitory Activity (MIA): A Serological Marker for Metastatic Uveal Melanoma

Summary: Uveal Melanoma is the most common primary intraocular tumor in adults. Most tumors metastasize to the liver. So far no sensitive or specific serological tumor marker is routinely used. The marker "Melanoma inhibitory activity" is a promising marker. Study hypothesis is to detect metastatic lesions in an early stage. This would increase life expectance of our patients

Detailed description: Serum is taken from each melanoma patient at every follow up after signed concent. With ELISA the marker MIA is evaluated. An increase of MIA serum level will lead to search for metastasis by oncologists.

Eligibility: Inclusion Criteria:
  -  uveal melanoma (With/without overt metastatic disease)

Relevance to patient case: not relevant
Patient case: 74-year-old female with melanoma; genetic feature: no tumor infiltrating lymphocytes

Clinical trial: Study of Families With Melanoma

Summary: RATIONALE: A study that evaluates patients' lifestyle, skin, and blood and tissue samples may help doctors understand the risk factors for melanoma relapse.
  PURPOSE: This clinical trial is studying the risk factors for melanoma in families with melanoma.

Detailed description: OBJECTIVES:
  Primary
  -  Determine what lifestyle factors and which genes govern relapse from melanoma.
  Secondary
  -  Compare sun exposure and genes that cause melanoma in patients with melanoma vs healthy participants.
  -  Assess how unusual moles relate to sun exposure and genes that cause melanoma.
  OUTLINE: This is a multicenter, cohort study.
  Patients and healthy participants complete lifestyle questionnaires by mail and telephone. Some patients* and healthy participants undergo a skin examination to count moles and classify skin type (e.g., degree of freckling and wrinkling indicative of sun damage).
  NOTE: *Patients diagnosed with primary invasive melanoma after September 2005 do not need to consent to a skin examination.
  Patients and healthy participants also undergo blood collection for lymphocyte analysis, DNA extraction, and the measurement of minerals, vitamins, and beta carotene. Tissue samples from original diagnosis are examined by immunohistochemistry for gene expression and mutations, including CDKN2A and CDK4.
  Patients and healthy participants are followed annually.
  Peer reviewed and funded or endorsed by Cancer Research UK
  PROJECTED ACCRUAL: A total of 3,700 patients and healthy participants will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Meets 1 of the following criteria:
  -  Newly diagnosed primary invasive melanoma (patient group)
  -  Lentigo maligna malignant melanoma allowed
  -  Rare variants of melanoma allowed, including any of the following:
  -  Acral lentiginous
  -  Subungual
  -  Ear, nose, and throat
  -  Oropharyngeal
  -  Perineal
  -  Vaginal
  -  Vulval
  -  Rectal
  -  Nodal with no known primary
  -  Patients undergoing sentinel node biopsy are eligible
  -  No in situ melanoma, melanocytic intraepidermal neoplasia, or ocular melanoma
  -  Healthy participant meeting either of the following criteria (control group):
  -  Relative of a patient who was diagnosed with melanoma after September 2005
  -  Healthy volunteer who is age- and sex-matched for patients who were diagnosed with melanoma before October 2005
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 74-year-old female with melanoma; genetic feature: no tumor infiltrating lymphocytes

Clinical trial: High-resolution Magnetic Resonance Imaging (MRI) Scans to Look for Spread of Melanoma to Nearby Lymph Nodes

Summary: The study is designed to see if a high-resolution MRI scan of lymph node areas near where a melanoma has been removed from the skin can pick up the spread of melanoma to those lymph nodes with a high degree of accuracy.

Detailed description: When a melanoma of the skin is diagnosed, there is some chance it can spread to nearby lymph nodes, and from there to other parts of the body. Currently, patients with melanoma at low risk for spreading to lymph nodes do not get the lymph nodes assessed except by a physical exam. Those at high risk for spreading to lymph nodes get one or more lymph nodes removed surgically to check for melanoma spread. But physical exam alone will often miss small areas of melanoma in lymph nodes; removal of lymph nodes by surgery is painful and can cause complications. Neither assessment tool is optimal.
  This study is designed to see if use of very high-resolution contrast-enhanced MRI scans of lymph node areas near the primary melanoma site in the skin can accurately detect small areas of melanoma spread to those lymph nodes. If this turns out to be the case, in the future, MRI scans could potentially be an alternative for assessing lymph nodes, compared to physical exams alone or surgical removal of the lymph nodes.
  In this study, patients with low risk melanoma will receive very high-resolution MRI scans of nearby lymph nodes every 6 months for 5 years of follow-up. If the MRI looks abnormal, the lymph nodes will be biopsied, and results from the biopsy compared to the results from the MRI.
  Patients with high risk melanoma will get a baseline MRI of the nearby lymph nodes, and then one or more lymph nodes will be removed (usually by sentinel lymph node biopsy) regardless of the MRI results. Again, results from the biopsy will be compared to the results from the MRI. MRI's will still be repeated every 6 months to assess whether lymph nodes not removed at surgery develop any changes.
  We plan to enroll 200 patients on this study and by the end of the study will have a measure of the sensitivity and specificity of high-resolution MRI scans in the detection of melanoma involvement of regional lymph nodes.

Eligibility: Inclusion Criteria:
  -  history of invasive cutaneous melanoma stages 1-3 within 2 years of treatment of the melanoma by primary excision
  -  eligible whether or not a sentinel lymph node biopsy or regional lymph node dissection has been performed
  -  adequate renal function (creatinine 2 or less)
  -  life expectancy 2 years of more
  Exclusion Criteria:
  -  history of severe claustrophobia precluding MRI scans
  -  known hypersensitivity or other contraindication to gadolinium contrast
  -  known presence of metastatic melanoma at sites beyond regional lymph nodes (stage 4)

Relevance to patient case: not relevant
Patient case: 74-year-old female with melanoma; genetic feature: no tumor infiltrating lymphocytes

Clinical trial: Adoptive Transfer of MART1/Melan-A CTL for Malignant Melanoma

Summary: RATIONALE: Cytotoxic T lymphocytes (CTL) are cells of the immune system that can fight infections and cancer. These CTL can be manipulated in the laboratory so that they can target an individual's cancer.
  PURPOSE: This early phase trial is studying the feasibility and side effects of intravenous infusions of CTL generated in the laboratory. To produce the CTL, the study participant's own immune cells are collected by a procedure called a leukapheresis. The cells then undergo laboratory processing for three weeks. Part of this processing includes mixing the patients immune cells with a new kind of cell that has some extra genes added to it. These extra genes are to "teach" the participant's own immune cells to become anti-tumor CTL that can attack the melanoma.

Detailed description: DETAILED OUTLINE: This is an early phase pilot/feasibility trial.
  Study subjects will be sequentially accrued to three cohorts. Cohorts 1 and 2 will evaluate the safety and feasibility of infusing two different doses of CTL.
  -  Participants in all cohorts will undergo two CTL infusions 5 weeks apart.
  -  Procedures performed during the trial will include physical examinations, laboratory tests, delayed hypersensitivity testing, and skin biopsies.
  -  Between 5 and 8 days after the first CTL infusion, a biopsy or excision of a melanoma lesion may be performed.
  -  Three leukapheresis procedures will be performed: two to collect peripheral blood for CTL production and one for research purposes at the end of the clinical trial.
  -  Radiology tests (including CT scans) will be performed prior to infusion and about 4-5 weeks after the second CTL infusion.

Eligibility: Inclusion Criteria:
  -  Patients with metastatic melanoma: Either unresectable Stage III or any Stage IV
  -  ECOG of 0 or 1
  -  HLA-A*0201 haplotype
  -  Baseline tumor biopsy MART1/Melan-A expression present (in >10% of tumor cells)
  -  Patient provides consent for all required biopsies
  -  Adequate intravenous access for leukapheresis
  -  Absolute lymphocyte count >500/ul at least once within 30 days of leukapheresis
  -  Life expectancy greater than 4 months in the opinion of the study clinician
  -  Negative pregnancy test
  Exclusion Criteria:
  -  Administration of systemic corticosteroids within 28 days of planned leukapheresis
  -  Administration of cytotoxic chemotherapy or anti-tumor immunotherapy within 28 days of planned leukapheresis
  -  Administration of radiotherapy within 28 days of planned leukapheresis with the exception of subjects accrued to Cohort 3
  -  Active autoimmunity requiring systemic immunosuppressive therapy
  -  HIV infection
  -  Previous enrollment on this protocol and infusion of MART1/Melan-A CTL

Relevance to patient case: not relevant
Patient case: 74-year-old female with melanoma; genetic feature: no tumor infiltrating lymphocytes

Clinical trial: MicroRNA Expression and Function in Cutaneous Malignant Melanoma

Summary: Spectrophotometric intracutaneous analysis (SIAscopy) is a new technique for imaging pigmented skin lesions and for diagnosing melanoma and non-melanoma skin cancer. The SIAscope is a portable system comprising of a laptop computer connected to a small handheld skin probe equipped with a light source. The skin lesion is interrogated with light of different wavelengths and the reflection spectra analysed by proprietary algorithms showing distribution, position and quantity of melanin, blood and collagen within the papillary dermis (the SIAgraphs). Earlier studies generated promising results and documented >80% specificity and sensitivity of SIAscopy for melanoma diagnosis. It has been suggested that this technique could be used for the initial screening and selection of pigmented lesion for excision. In this work we addressed the usefulness of SIAscopy for the clinical diagnosis of pigmented malignant melanoma in a prospective, blinded design.


Eligibility: Inclusion Criteria:
  -  Pigmented lesion
  Exclusion Criteria:
  -  No pigmented lesion

Relevance to patient case: not relevant
Patient case: 74-year-old female with melanoma; genetic feature: no tumor infiltrating lymphocytes

Clinical trial: A Phase I, Randomized, Open-label, Cross-over, Pharmacokinetic Study of Genasense With and Without Dacarbazine

Summary: This clinical drug-drug interaction study is being conducted to evaluate the pharmacokinetics of dacarbazine(DTIC) when administered in combination with Genasense


Eligibility: Inclusion Criteria:
  -  Metastatic Stage IV disease, or Stage III disease that is not surgically resectable
  -  ECOG Performance Status of 0, 1, or 2
  -  Life expectancy of at least 12 weeks
  -  Adequate venous access
  -  Agreement to practice effective method of birth control
  Exclusion Criteria:
  -  Less than 3 weeks of recovery from prior major surgery or other therapy, including radiation therapy, chemotherapy, or immunotherapy, or cytokine, biologic, or vaccine therapy
  -  Significant medical disease
  -  Known hypersensitivity to phosphorothioate-containing oligonucleotides
  -  Known hypersensitivity to DTIC
  -  Pregnancy/Lactation

Relevance to patient case: not relevant
Patient case: 74-year-old female with melanoma; genetic feature: no tumor infiltrating lymphocytes

Clinical trial: Pharmacokinetics of G3139 in Subjects With Advanced Melanoma, Including Those With Normal Hepatic Function and Those With Moderate Hepatic Impairment

Summary: This is an open-label, parallel-group study with a total of 16 evaluable subjects. Subjects will be assigned to 1 of the following cohorts: Cohorts I (subjects with normal hepatic function; n+8 and Cohort II (subjects with moderate hepatic impairment, Child-Pugh classification Grade B; n=8). If, for any reason, the Genasense infusion is interrupted or discontinued prior to completion or the rate of administration of the Genasense infusion is changed, the subject will be replaced.


Eligibility: Inclusion Criteria:
  -  Histologically confirmed diagnosis of malignant melanoma
  -  Metastatic Stage IV disease, or Stage III disease that is not surgically resectable
  -  ECOG Performance status of 0,1,or 2
  -  Adequate venous access
  -  Agreement to practice effective methods of birth control
  -  Hepatically impaired consistent with Child-Pugh classification Grade B
  Exclusion Criteria:
  -  Chronic intravascular coagulopathy confirmed by the presence of fibrinogen degradation products, metastases to the liver, or exudative ascites
  -  Prior organ allograft
  -  Requirement for concomitant anticoagulant therapy (with the exception of 1 mg/day of warfarin for central line prophylaxis) while receiving protocol therapy
  -  Known hypersensitive to DTIC
  -  Prior treatment with Genasense

Relevance to patient case: not relevant
Patient case: 74-year-old female with melanoma; genetic feature: no tumor infiltrating lymphocytes

Clinical trial: Treatment With Intravitreal Avastin for Large Uveal Melanomas

Summary: The purpose of this study is to test the safety and effectiveness of Avastin introduced into the inside of the eyeball in causing shrinkage of the uveal melanoma (tumor of the eye). Avastin is an anti-cancer drug specially designed to shrink blood vessels within tumors.


Eligibility: Inclusion Criteria:
  -  Patients diagnosed with large uveal melanomas who elect to undergo enucleation.
  -  Patients diagnosed with uveal melanomas with tumor thickness > 10 mm or basal diameter > 16 mm, as measured by ultrasound examination, funduscopic examination, or transillumination.
  Exclusion Criteria:
  -  Cases that do not meet the above criteria for tumor size will be ineligible to participate in the study.
  -  Patients with history of metastatic cancer (other than melanoma).
  -  Patients not able to provide consent for the study.
  -  Patients with clinical or radiographic evidence of extraocular extension of the tumor.
  -  Patients with a previous history of an adverse reaction to intravitreal injection.
  -  Patients with a poor view of the fundus due to cataract or vitreous hemorrhage.
  -  Patients with intravitreal silicone oil or gas tamponade.
  -  Patients < 18 years of age.
  -  Women known to be pregnant.

Relevance to patient case: not relevant
Patient case: 74-year-old female with melanoma; genetic feature: no tumor infiltrating lymphocytes

Clinical trial: A Pilot Study to Evaluate Optical Spectroscopy of Pigmented Skin Lesions

Summary: The incidence of malignant melanoma has increased dramatically in recent decades. In 1930, the lifetime risk of an individual in the United States developing melanoma was 1 in 1,500. This has been exponentially increasing over the years with the risk estimated to be 1 in 75 in 2000 . According to the American Cancer Society, approximately 59,580 new cases of melanoma will be diagnosed in the United States in 2005 and about 7,770 people are expected to die of the disease.

Detailed description: The researcher ucan use special imaging devices to obtain information about a typical mole and melanoma and use this information to determine the different between malignant and benign melanized lesions. The imaging devices are, Modified Two Layer Diffuse Optical Spectroscopy,multi-spectral imaging, and Spatially Modulated Quantitative Spectroscopy can use to measure atypical moles and melanoma and correlate the results of the biopsy tissue histology.
  The imaging devices can quantify melanin, oxy and deoxy hemoglobin concentration, water, lipid and reduced scattering coefficients and can compare results to histopathologic. Atypical moles and melanoma have a different optical profile based on physiological parameters compared to benign nevus.

Eligibility: Inclusion Criteria:
  -  18 years or older.
  -  Have atypical mole/s and melanoma
  Exclusion Criteria:
  -  Age less than 18 years old.
  -  have NO atypical mole/s and melanoma

Relevance to patient case: not relevant
Patient case: 74-year-old female with melanoma; genetic feature: no tumor infiltrating lymphocytes

Clinical trial: A Phase I Study of BIIB015 in Relapsed/Refractory Solid Tumors

Summary: Phase 1, open-labeled, safety and tolerability study for the treatment of subjects with relapsed or refractory solid tumors.


Eligibility: Inclusion Criteria
  -  Age 18 years or older at the time of informed consent.
  -  Solid tumors that are relapsed or refractory to at least 1 prior anti-cancer systemic therapy and for which no standard therapy exists.
  -  ECOG Performance Status </= 2.
  Exclusion Criteria
  -  History of keratoconjunctivitis, open or closed angle glaucoma, or "dry eye" disease.
  -  New York Heart Association (NYHA) Grade II or greater congestive heart failure.
  -  History of myocardial infarction within 6 months prior to Day 1.
  -  Presence of >/= Grade 2 peripheral neuropathy.
  -  Known presence of central nervous system or brain metastases.
  -  Prior therapy with a conjugated or unconjugated maytansine derivative.

Relevance to patient case: not relevant
Patient case: 74-year-old female with melanoma; genetic feature: no tumor infiltrating lymphocytes

Clinical trial: Human Leukocyte Antigen-A*2402-Restricted Tumor Vessel Specific Peptide Vaccination for Advanced Pancreatic Cancer

Summary: Feasibility and efficacy of combined modality intervention using chemotherapeutic agent gemcitabine with anti-angiogenic peptide vaccination targeting VRGFR1 should be determined in case of advanced/inoperable or therapy-resistant pancreatic cancer patients.
  Gemcitabine 1,000mg/m2 BSA will be administered on day1, day8, day15, day29, day36, day43, respectively.
  HLA-A*2402-restricted VEGFR1-derived peptide (VEGFR1-A24-1084; SYGVLLWEI) emulsified with Montanide ISA51 will be subcutaneously injected twice weekly for 8weeks (total 16 doses).

Detailed description: HLA-A*2402-restricted cytotoxic T lymphocyte (CTL) clones were obtained from healthy volunteer donor peripheral blood.
  These CTL clones showed potent cytotoxicities selectively against VEGFR1-expressing target cells in HLA-class I-restricted manner.

Eligibility: Inclusion Criteria:
  -  Heterozygote or homozygote of HLA-A*2402 allele
  -  Inoperable or recurrent pancreatic cancer with or without any prior therapy
  -  Difficult to continue the prior therapy due to treatment-related toxicities
  -  ECOG performance status 0-2
  -  Evaluable primary or metastatic lesion with RECIST criteria
  -  Clearance period from prior therapy more than 4 weeks
  -  Life expectancy more than 3 months
  -  Laboratory values as follows 2,000/μL<WBC<15,000/μL Platelet count>100,000/μL AST<150IU/L ALT<150IU/L Total bilirubin<3.0mg/dl Serum creatinine<3.0mg/dl
  Exclusion Criteria:
  -  Pregnancy (refusal or inability to use effective contraceptives)
  -  Breastfeeding
  -  Active or uncontrolled infection
  -  Systemic use of corticosteroids or immunosuppressants
  -  Uncontrollable brain metastasis and/or meningeal infiltration
  -  Unhealed external wound
  -  Possibilities of complicated paralytic ileus or interstitial pneumonitis
  -  Decision of not eligible determined by principal investigator or attending doctor

Relevance to patient case: not relevant