araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: A Study of PLX3397 in Patients With Unresectable or Metastatic KIT-mutated Melanoma

Summary: The purpose of this Phase I/II study is to evaluate safety, pharmacokinetics, and preliminary efficacy of the investigational drug PLX3397 in subjects with unresectable or metastatic KIT-mutated melanoma.


Eligibility: Inclusion Criteria:
  -  Age ≥ 18 years
  -  Unresectable stage III or stage IV melanoma which is histologically confirmed at the treating institution with KIT mutation(s) not known to be resistant to PLX3397
  -  Presence of measurable lesions by Response Evaluation Criteria in Solid Tumors
  -  Eastern Cooperative Oncology Group (ECOG) performance Status (PS) 0-2
  -  Life expectancy ≥ 3 months
  -  Adequate organ and bone marrow function
  -  Women of child-bearing potential must have a negative serum pregnancy test at Screening and must agree to use an effective form of contraception from the time of the negative pregnancy test up to 3 months after the last dose of study drug. Women of non-child-bearing potential must have been postmenopausal for ≥ 1 year or surgically sterile.
  -  Fertile men must agree to use an effective method of birth control during the study and for up to 3 months after the last dose of study drug.
  -  Willingness and ability to provide written informed consent prior to any study-related procedures and to comply with all study requirements
  Exclusion Criteria:
  -  Prior treatment with a KIT inhibitor for melanoma
  -  Presence of NRAS or BRAF mutation
  -  Exposure to any investigational drug within 28 days or unresolved adverse effects from previous therapy
  -  Symptomatic brain metastases.
  -  Active secondary malignancy unless the malignancy is not expected to interfere with the evaluation of safety and is approved by the Sponsor
  -  Concomitant treatment with other anti-neoplastic agents (hormonal therapy acceptable)
  -  Uncontrolled intercurrent or infectious illness
  -  Major surgical procedure or significant traumatic injury within 14 days of initiating study drug or anticipation of the need for major surgery during the study
  -  Previous radiotherapy to 25% or more of the bone marrow and/or radiation therapy within 28 days prior to study entry
  -  Inability to swallow capsules, or refractory nausea and vomiting, malabsorption, an external biliary shunt, or significant bowel resection that would preclude adequate absorption
  -  Congestive heart failure (CHF) New York (NY) Heart Association class III or IV; unstable coronary artery disease (myocardial infarction [MI] more than 6 months prior to study entry is permitted); or serious cardiac arrhythmia
  -  Baseline QTcF ≥ 450 msec (for males) or ≥ 470 msec (for females) at Screening
  -  Active or chronic infection with human immunodeficiency virus (HIV), hepatitis C virus (HCV), or hepatitis B virus (HBV)
  -  Known chronic liver disease
  -  Women who are breast-feeding or pregnant

Relevance to patient case: possibly relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Study of 1cm Versus 2cm Margins for the Surgical Treatment of cT2N0M0 Melanoma

Summary: This is a randomized non-blinded pilot study for patients with melanoma staging cT2N0M0 who are candidates for surgical resection. The primary objective is to determine the feasibility of randomizing participants with cT2N0M0 malignant melanoma to surgical treatment with 1cm versus 2cm margins. Study will try to determine overall survival for cT2N0M0 malignant melanoma after surgical treatment with 1cm versus 2cm margins.

Detailed description: After randomization, participants will undergo surgery with wide local excision with either 1cm or 2cm margins. The margin will be based upon the previous biopsy site or area of pigmentation. The skin and subcutaneous tissue (down to fascia) will be resected. Closure considerations may require removal of additional tissue for non-oncologic purposes. As per standard of care, sentinel lymph node biopsy will be performed using a dual tracer technique (technetium radiolabeled sulfur colloid and isosulfan blue) with or without lymphoscintigraphy.

Eligibility: Inclusion Criteria:
  -  Biopsy proven T2 malignant melanoma.
  -  Eastern Cooperative Oncology Group (ECOG) score of 0-2.
  Exclusion Criteria:
  -  Visible additional disease that suggests a greater than T2 malignant melanoma
  -  Unable to tolerate general anesthesia
  -  Evidence of distant metastatic disease
  -  Melanoma located on face or digits

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: A Retrospective Pharmacokinetics and Pharmacogenomics Research of Imatinib in Gastrointestinal Stromal Tumor Treatment

Summary: For patients of GIST (Gastrointestinal Stromal Tumor), Imatinib has been widely used in GIST with KIT or PDGFRA sensitive mutations. From clinical points of view, individual differences often occur between different patients, leading diverse effect in ADR and drug effect. Meanwhile, the drug effect and adverse drug reaction was significantly influenced by the pharmacokinetic factors and pharmacodynamic and other factors. In this research, we try to establish a more sensitive method to detect sensitive mutations in plasma and discover the correlation between somatic and germline mutations, plasma trough concentration and drug effect, the association between ADME-associated SNP, Target/Receptor/Pathway-associated SNP, trough concentration and TKI adverse effect. Furthermore, in vivo and in vitro research is also crucial for rational explanation for these clinical phenomenon.

Detailed description: The plasma concentration of Imatinib were established. The ADME-associated SNPs included are CYP3A4, CYP3A4, CYP1A1, CYP2C9, CYP2C19, ABCB1, ABCG2, ABCC4, SLC22A1, SLCO1B3 and so on. The Target/Receptor/Pathway-associated SNP s included KIT, PDGFRA, PDGFRB, FLT1, FLT3, MAPK1, SHC1, CCL5, CXCL14 and so on. The somatic mutations included are KIT, PDGFRA, BRAF and so on.

Eligibility: Inclusion Criteria:
  -  The main patient entry criteria included: age≥ 18 years; histologically and cytologically proved GIST; Eastern cooperative oncology group performance status (ECOGPS)≤2; adequate hematological,renal,and hepatic functions.
  Exclusion Criteria:
  -  uncontrolled systemic disease,and other chemotherapy at the time of inclusion. The protocol was approved by the Ethical Committee of Cancer Center of Sun Yat-Sen University (CCSU), and written informed consent was obtained form each patient.

Relevance to patient case: not relevant
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: NF2 Natural History Consortium

Summary: OBJECTIVES:
  I. Define the growth rates and clinical course of NF2-related tumors in patients with neurofibromatosis type 2. Associate growth rate with physical function.

Detailed description: PROTOCOL OUTLINE: Data on the clinical course and growth rate of NF2-related tumors in patients with neurofibromatosis 2. Patients are evaluated each year on a cranial and a spinal MRI, eye tests, hearing tests, quality of life, neurological tests, and physical functioning.

Eligibility: PROTOCOL ENTRY CRITERIA:
  --Disease Characteristics--
  -  Diagnosed with neurofibromatosis 2 on or after 01/01/93
  -  Must meet one of the following conditions:
  Bilateral vestibular schwannoma OR Family history of neurofibromatosis 2 (first degree family relative) AND Unilateral vestibular schwannoma at under 30 years OR Any 2 of the following: Meningioma Glioma Schwannoma Juvenile posterior subcapsular lenticular opacity/juvenile cortical cataract
  -  No plans to treat vestibular schwannoma in next 12 months
  --Prior/Concurrent Therapy--
  -  Not specified
  --Patient Characteristics--
  -  Age: 5 and over

Relevance to patient case: not relevant
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: Nitrocamptothecin in Treating Patients With Metastatic Melanoma

Summary: RATIONALE: Drugs used in chemotherapy use different ways to stop tumor cells from dividing so they stop growing or die.
  PURPOSE: Phase II trial to study the effectiveness of nitrocamptothecin in treating patients who have metastatic melanoma.

Detailed description: OBJECTIVES: I. Assess the efficacy and toxicity of nitrocamptothecin in patients with metastatic melanoma.
  OUTLINE: Patients are stratified according to disease (choroidal vs nonchoroidal). Patients receive oral nitrocamptothecin daily on days 1-5. Treatment continues weekly for at least 8 weeks (2 courses) in the absence of disease progression or unacceptable toxicity.
  PROJECTED ACCRUAL: A total of 28-74 patients (14-37 per stratum) will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS: Histologically or cytologically confirmed metastatic melanoma Choroidal (no prior chemotherapy required) OR Nonchoroidal No more than 3 chemotherapy regimens Bidimensionally measurable disease No symptomatic uncontrolled CNS involvement including extensive brain metastases, spinal cord compression, or meningeal carcinomatosis Not eligible for treatment protocol of higher priority
  PATIENT CHARACTERISTICS: Age: Over 16 Performance status: Zubrod 0-2 Life expectancy: Greater than 8 weeks Hematopoietic: Absolute neutrophil count at least 1,000/mm3 Platelet count at least 100,000/mm3 Hepatic: Bilirubin no greater than 1.5 times upper limit of normal (ULN) Transaminase no greater than 3 times ULN Renal: Creatinine no greater than 2.0 mg/dL Other: Not pregnant or nursing Negative pregnancy test Fertile patients must use effective contraception during and for 1 year after study No serious concurrent illness
  PRIOR CONCURRENT THERAPY: Biologic therapy: Not specified Chemotherapy: See Disease Characteristics At least 3 weeks since prior chemotherapy and recovered Endocrine therapy: Not specified Radiotherapy: At least 3 weeks since prior radiotherapy and recovered Surgery: Not specified

Relevance to patient case: not relevant
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: Diagnostic Study to Predict the Risk of Developing Metastatic Cancer in Patients With Stage I or Stage II Melanoma

Summary: RATIONALE: Diagnostic procedures that analyze surgically-removed tumor tissue and lymph node samples may help doctors identify patients with melanoma who are at risk for developing metastatic cancer.
  PURPOSE: This clinical trial is studying tumor tissue and lymph node samples to see how well they work in predicting the development of metastatic cancer in patients with stage I or stage II melanoma.

Detailed description: OBJECTIVES:
  -  Correlate degree of melastatin gene expression with risk of developing local regional metastases in patients with primary stage I or II melanoma.
  -  Correlate melastatin expression prospectively with event-free survival of these patients.
  OUTLINE: This is a multicenter study.
  Melastatin mRNA expression is determined by in situ hybridization using tissue from primary tumor and lymph nodes. Tissue is also examined by immunohistochemical staining using antibodies to S-100 and MART-1. Patients do not receive the results of these tests nor do the results influence individual therapy.
  Patients are followed every 4 months for 3.5 years.
  PROJECTED ACCRUAL: A total of 300 patients will be accrued for this study within 3.5 years.

Eligibility: 1. Histologically documented primary AJCC stage I or II melanoma. Evidence of ulceration, vertical growth phase, regression, lymphocytic infiltration, vascular invasion, microscopic satellitosis, and mitotic rate shall be noted.
  2. Patients planning to undergo a sentinel lymph node biopsy, or an elective lymph node dissection of an anatomic draining region from the index primary melanoma.
  3. ≥18 years of age
  4. Patients must be registered prior to planned surgery. The surgery must be performed within 45 days following registration.
  5. No concurrent active malignancy other than carcinoma in situ of the cervix and basal cell carcinoma of the skin, or history of any other primary malignancy including previously primary melanoma.
  6. Tissue blocks: one of primary tumor tissue taken from region of greatest Breslow thickness. Note: If blocks cannot be sent due to institutional policy, slides may be substituted for the locks per the protocol.

Relevance to patient case: not relevant
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: Safety and Efficacy Study of INGN 241 Gene Therapy in Patients With In Transit Melanoma

Summary: This is a research study to look at the ways in which a treatment called INGN241 can kill melanoma cells or help the patient's immune system kill melanoma cells.

Detailed description: INGN 241 is an adenoviral vector carrying the MDA-7 cDNA. MDA-7 is a novel tumor suppressor molecule with cytokine properties, recently designated as IL-24. Over expression of MDA-7 in melanoma cells in vitro has been shown to inhibit cellular proliferation and induce apoptosis. Loss of MDA-7 expression in human melanomas has been shown to correlate with invasion and metastasis. The INGN 241 gene transfer construct has been previously used in human subjects in an ongoing open label Phase I study using intratumoral administration, and has been well tolerated to date. The primary objectives of the present study are to determine if INGN 241, injected into a melanoma in transit lesion, can induce apoptosis in regional uninjected lesions and initiate systemic immune activation. Secondary objectives include examination of specific immunity and of clinical response and toxicity.

Eligibility: Inclusion Criteria:
  -  Histologically proven melanoma, must have 3 regional metastatic lesions that are in transit
  Exclusion Criteria:
  -  Central nervous system involvement by melanoma

Relevance to patient case: not relevant
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: Vaccine Therapy in Treating Patients With Malignant Melanoma

Summary: RATIONALE: Vaccines made from tumor cells may help the body build an effective immune response to kill tumor cells.
  PURPOSE: This phase II trial is studying vaccine therapy to see how well it works in treating patients with malignant melanoma.

Detailed description: OBJECTIVES:
  -  Determine the response in patients with in-transit cutaneous malignant melanoma treated with active immunotherapy comprising polyvalent melanoma vaccine (Canvaxin™).
  OUTLINE: This is an open-label, multicenter study.
  Patients receive polyvalent melanoma vaccine (Canvaxin™) subcutaneously to the armpit and groin areas every 2 weeks for approximately 10 weeks (5 doses) and then every 4 weeks for up to approximately 1 year of total treatment (total of 15 doses). Patients with no evidence of response at week 24 receive no further treatment. Patients whose disease continues to respond after completion of study treatment are eligible for a new study in which they will continue treatment with polyvalent melanoma vaccine (Canvaxin™).
  After completion of study treatment, patients are followed at 30 days.
  PROJECTED ACCRUAL: A total of 100 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically confirmed malignant melanoma
  -  At least 1 in-transit skin lesion measuring 3-10 mm in the longest diameter
  PATIENT CHARACTERISTICS:
  Age
  -  18 to 80
  Performance status
  -  Not specified
  Life expectancy
  -  Not specified
  Hematopoietic
  -  Not specified
  Hepatic
  -  Not specified
  Renal
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  Biologic therapy
  -  Not specified
  Chemotherapy
  -  Not specified
  Endocrine therapy
  -  Not specified
  Radiotherapy
  -  Not specified
  Surgery
  -  Not specified

Relevance to patient case: not relevant
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: Study of Metastatic Ocular Melanoma

Summary: This study evaluates treatment with combination versus monotherapy for patients with metastatic ocular melanoma.

Detailed description: Treatment of patients with metastatic ocular melanoma with combination chemotherapy Gemcitabine and Treosulfan versus monotherapy with Treosulfan as first-line chemotherapy.

Eligibility: Inclusion Criteria:
  -  Metastatic ocular melanoma
  Exclusion Criteria:
  -  Prior treatment with chemotherapy
  -  Active 2nd malignancy
  -  Cerebral metastasis

Relevance to patient case: not relevant
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: Dendritic Cell Based Therapy of Malignant Melanoma

Summary: The aim of the study is to show if vaccination with autologous dendritic cells pulsed with peptides or tumor lysate in combination with adjuvant cytokines and Cyclophosphamide can induce a measurable immune response in patients with metastatic malignant melanoma, and to evaluate the clinical effect (objective response rate) of the vaccination regime.

Detailed description: Eligible patients receive vaccination with tumor antigen pulsed autologous monocyte-derived mature dendritic cells with a fixed interval. The dendritic cells are generated from leukapheresis products and frozen after antigen loading.
  HLA A2 positive patients are treated with PADRE and oncopeptide pulsed DC; p53, survivin and telomerase peptides. HLA A2 negative patients are treated with KLH and tumorlysate pulsed DC; autologous or allogeneic. Each patient is given 6 immunizations with at least 5x106 peptide/lysate pulsed autologous DC. Vaccination 1-4 is given weekly and 4-6 at 2-week intervals. Those patients who exhibit stable disease, partial response or complete response after 6 injections will be given 4 more vaccinations at 2-week interval. The vaccine is applied by intradermal injection near the inguinal region.
  IL-2 2 MIU s.c. day 2-6, Cyclophosphamide (Sendoxan®, Baxter A/S) 50 mg twice a day bi-weekly and 200 mg Celecoxib (Celebra®, Pfizer) daily are used. Scans and re-staging tests are performed at scheduled intervals throughout the study.

Eligibility: Inclusion Criteria:
  -  Histologically proven progressive metastatic or locally advanced melanoma
  -  No standard treatment indicated
  -  Age: > 18
  -  WHO-Performance Status 0-1
  -  At least tone measurable tumor lesions according to the RECIST criteria.
  -  Life expectancy more than 3 months
  -  Acceptable CBC and blood chemistry results
  -  Written informed consent
  Exclusion Criteria:
  -  Patients with a history of any other neoplastic disease less than 5 years ago (excepting treated carcinomas in situ of the cervix and basal/squamous cell carcinomas of the skin).
  -  Patients with metastatic disease in the central nervous system (CNS).
  -  Patients with other significant illness including severe allergy, asthma, angina pectoris or congestive heart failure.
  -  Patients with acute or chronic infection including HIV, hepatitis and tuberculosis.
  -  Patients who are pregnant.
  -  Patients who have received antineoplastic therapy including chemotherapy or immunotherapy less than 4 weeks before beginning the trial.
  -  Patients who receive corticosteroids or other immunosuppressive agents.
  -  Baseline serum LDH greater than 2.5 times the upper limit of normal.
  -  Patients with active autoimmune diseases such as lupus erythematosus, rheumatoid arthritis or thyroiditis.

Relevance to patient case: not relevant
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: Vaccination With Tumor mRNA in Metastatic Melanoma - Fixed Combination Versus Individual Selection of Targeted Antigens

Summary: The purpose of the vaccination protocol is to induce specific immune responses against melanoma associated antigens by intradermal injections of mRNA coding for the corresponding antigen.

Detailed description: vaccination protocol to induce clinically specific immune responses against melanoma associated antigens by intradermal injections of mRNA coding for the corresponding antigens. Half of patients is treated with mRNA coding for Melan-A, Mage-A1, Mage-A3, Survivin, GP100 and Tyrosinase. The other half of patients is treated with an individualized selection of mRNAs after analysis of overexpressed melanoma antigens in autologous tumor tissue. GM-CSF is used as an adjuvants. Phase I/II clinical trial to analyse safety and immune responses in stage III/IV melanoma patients.

Eligibility: Inclusion Criteria:
  -  malignant melanoma stage III/IV
  -  fresh frozen tumor tissue available
  -  informed consent given
  -  Karnofsky >= 70%
  Exclusion Criteria:
  -  brain metastasis
  -  parallel chemotherapy
  -  systemic treatment with glucocorticoids
  -  other malignancies

Relevance to patient case: not relevant
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: Pegylated Interferon-alpha-2a in Patients With Malignant Melanoma Stage IIA-IIIB

Summary: The purpose of this study is to evaluate the efficacy and safety of adjuvant treatment with pegylated interferon-α-2a (PEG-IFN) vs. 'low dose' interferon-α-2a in patients with malignant melanoma in stage IIA (T3a) - IIIB.
  A total of 880 will be randomized up to three months after first surgical management of their melanoma to either: PEG-IFN-α-2a or low-dose interferon-α-2a.


Eligibility: Inclusion Criteria:
  -  Histologically proven cutaneous melanoma
  -  ≥ 18 years of age and < 75 years of age
  -  Have confirmed stage IIa (T3a), IIB, IIC, IIIA or IIIB (AJCC 2002) melanoma (lymph node staging either per sentinel node biopsy or elective lymph node dissection)
  -  Have a Karnofsky performance status of ≥ 80%
  -  Negative pregnancy test
  -  Start of therapy within three months after surgery
  -  Informed consent
  Exclusion Criteria:
  -  Pregnant or lactating women
  -  Unwillingness or inability to employ an effective barrier method of birth control throughout the study and for up to 3 months after end of treatment in female or male patients
  -  Mucous membrane or ocular melanoma
  -  Any evidence of distant metastasis (CT-scan of brain, Chest X ray or CT, abdominal ultrasound or CT and ultrasound of regional lymph nodes at screening)
  -  Patients who have received chemotherapy or vaccines for melanoma
  -  Patients with tumor progression under a previous adjuvant interferon therapy or within three months after termination of interferon therapy (patients previously receiving adjuvant interferon therapy in another tumor stage without disease progression may be included)
  -  History of any other malignancy within the last ten years (except basal cell carcinoma or squamous cell carcinoma of the skin and carcinoma in situ of the cervix)
  -  Patients with severe cardiac disease (e.g. NYHA Functional Class III or IV, myocardial infarction within 6 months, ventricular tachyarrhythmias requiring ongoing treatment, unstable angina), severe liver disease or severe renal disease.
  -  ALAT or ASAT > 2 x ULN
  -  Bilirubin > 2 x ULN
  -  Creatinine > 2 x ULN
  -  Patients who have a history of depression or other psychiatric diseases requiring hospitalisation
  -  Patients with seizure disorders requiring anticonvulsant therapy
  -  Any of the following abnormal baseline hematologic/laboratory values:
  -  Hb <10g/dl
  -  WBC <3.0 x 109 /l
  -  Platelets <100x109/l
  -  Neutrophils < 1.5 x 109/l
  -  History or presence of autoimmune disease (i.e. autoimmune hepatitis, thyroid auto-immune dysfunction, systemic lupus erythematodes)
  -  Unwilling or unable to comply with the requirements of the protocol for the duration of the study
  -  Known infection with HBV, HCV, HIV
  -  Evidence of allergy or hypersensitivity against IFN or pegylated interferon
  -  Thyroid disease poorly controlled on prescribed medications
  -  Systemic corticosteroid therapy for any reason (>1 month)

Relevance to patient case: not relevant