araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Urinary Circulating Tumor DNA Detection in Non-small Cell Lung Cancer: a Prospective Study

Summary: This study will evaluate the feasibility and effectiveness of urinary ctDNA detection and dynamic monitoring during treatment of NSCLC patients prospectively,by collecting and detecting tumor tissues, peripheral blood samples and urine samples of NSCLC patients.

Detailed description: Liquid biopsy, specifically through the assessment of circulating tumor DNA(ctDNA) from peripheral blood, has shown great promise in lung cancer diagnosis and therapeutic monitoring.
  Urinary samples are completely non-invasive and easily obtainable compared to blood and tissue extraction. To date, only a limited number of published studies have examined the feasibility of ctDNA detection from urine.
  This study will collect tumor tissues, pretreatment peripheral blood samples and urine samples from different TNM stages of NSCLC patients, and detect EGFR gene mutations in paired samples.

Eligibility: Inclusion Criteria:
  -  Aged 18 to 80 years
  -  Histologically confirmed diagnosis of stage non-small cell lung cancer undergoing surgical resection
  -  Completed and explicit information about TNM staging
  -  Paired specimens including tumor tissues, and both peripheral blood samples and urinary samples before and after surgery.
  -  Patients must have given written informed consent
  Exclusion Criteria:
  -  Unable to comply with the study procedure
  -  Malignant tumor history within the past 5 years
  -  Coexisting small cell lung cancer
  -  Unqualified tissue, blood or urine samples

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Early Diagnosis of Oral Cancer by Detecting p16 Hydroxymethylation

Summary: The purpose of this study is to verify the function of p16 hydroxymethylation diagnostic reagents in early diagnosis of oral cancer.

Detailed description: Background:Oral epithelial dysplasia (OED) is one of the common precancerous lesions among Chinese adults. To investigate the clinical predictive value of p16 hydroxymethylation diagnostic reagents in the early diagnosis of oral cancer, the investigators carried out the prospective multi-center double-blind cohort study.
  Methods:336 patients with histologically confirmed mild or moderate OED were included in the present study. After the bisulfite modification and tet assistant bisulfite modification, MethyLight and Methylation-specific PCR (MSP) assays were used to analyze p16 methylation and status in these patients. Building three follow-up queue by p16-methylated, p16-hydroxymethylation and p16-unmethylated. The Statistical analysis used SPSS16.0. All P-values were two-sided. P<0.05 was considered to test for statistical significance difference.

Eligibility: Inclusion Criteria:
  -  Histopathological diagnosis of oral lesions meet the epithelial diagnostic criteria for mild to moderate grade OED;
  -  No local area stimulate by residual root and crown, sharp cusp, poor restoration and biting cheek or lips;
  -  Without the treatment history by laser , radiation or chemical;
  -  Be able to Sign the informed consent;
  Exclusion Criteria:
  -  Histopathological diagnosis of oral lesions do not meet the epithelium of mild to moderate dysplasia diagnostic criteria; histological diagnosis of severe grade OED or malignant disease;
  -  Pregnancy or breast-feeding women;
  -  Serious heart, lung, liver , kidney and other systemic diseases local area stimulate by residual root and crown, sharp cusp, poor restoration and biting cheek or lips;
  -  OED treatment history by LASER, radiotherapy, or chemotherapy;
  -  Tumor and psychiatric patients;
  -  Patients are unable to cooperate;

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: 18F‐Labeled Picolinamide PET Imaging of Melanoma Diagnosis

Summary: The purpose of this study is to assess the dosimetric properties of the positron emission tomography (PET) imaging probe 18F labeled Picolinamide (18F-P3BZA) and preliminarily evaluate its diagnosis value in melanoma patients.

Detailed description: 50 patients with pathology diagnosed melanoma will be enrolled for the clinical study. If agree to take part in this study, the patient will be performed with 18F-P3BZA PET/CT scan and 18F-FDG PET/CT scan in the other day before and after surgery. Next, all of the resected tissues from the patients will be checked with pathology.
  6 of 50 patients are performed for whole-body PET scans at 0, 15, 30, 45, 60, and 120 minutes and a CT scan at 60 minutes after tracer injection (mean dose, 5.0 ± 0.5 mCi in 2.0 ± 0.5ml) will be performed. During the imaging period, 1 mL blood samples will be obtained for time-activity curve calculations at 1, 5, 10, 30,60, 90, 120, and 180 minutes after injection. The estimated radiation doses will be calculated by using OLINDA/EXM software.
  The images produced by these scans will be compared to see the diagnosis value of 18F-P3BZA.
  Screening Tests:
  Women who decide to take part in this study will be asked if they think they might be pregnant at the start of the study. All of them must have a negative blood pregnancy test (Human chorionic gonadotropin, HCG).
  PET-CT Scan Procedure:
  Before the PET-CT scan is performed, patient will be asked to remove any metallic objects when she/he arrive at the PET-CT Center. After a property rest, he/she will be injected with about 5mCi 18F-P3BZA. The first scan will take at 60 minutes after injection and a delay scan will take at 120 minutes after injection. Each PET/CT scan will take about 20 minutes.
  After 18F-P3BZA scan, the patient will be asked to avoid stressful exercise. Starting about 12 hours before 18F-FDG scan, he/she will be asked to limit the amount of carbohydrates until the scans are done.
  Follow-Up Visits:
  Patients' primary care physician will follow-up them for next 24 hours. After then, they may order additional imaging or surgical results after this study for follow-up purposes. The study doctor will review these results to compare them with the PET-CT images. The study doctors will also review the results of any biopsies you may have had as a result of PET-CT findings.
  This is an investigational study. PET-CT and CT scans are FDA approved and commercially available.

Eligibility: Inclusion Criteria:
  -  patients with melanoma: diagnosed by pathology and ready for surgery
  Exclusion Criteria:
  -  patients with melanoma: refuse or cannot endure surgery
  -  pregnant women

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Purse String Suture for the Closure of Large Thyroidectomy Resulted in Better Cosmetics

Summary: Thyroidectomy for large thyroid tumor poses a problem of cosmetics, especially in terms of wide post-operative scar and prominent neck wrinkles. In this manuscript, we performed purse-string suture for the first time for the closure of skin defect after thyroidectomy of large thyroid tumors which resulted in better cosmetics as compared to the conventional suturing method.

Detailed description: Increasing demand for better cosmetics following thyroidectomy for large thyroid tumor of > 6 cm diameter created a necessity to find an alternative to the conventional technique (CT), which could be addressed by purse string technique (PST). A non-randomized controlled trial was conducted to new thyroid tumor patients at Cipto Mangunkusumo Hospital (RSCM) from October 2013 until December 2014. Thirty patients grouped into two intervention arms of thyroidectomy with PST and CT were assessed for post-operative scar outcomes.

Eligibility: Inclusion Criteria:
  -  New cases of thyroid tumor in Doctor Cipto Mangunkusumo General Hospital
  -  Tumor diameter > 6 cm
  Exclusion Criteria:
  -  Previous surgery in the anterior neck area
  -  Local involvement of lymph nodes requiring nodes dissection

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Genetic Basis of Melanocytic Nevi

Summary: The objective of this protocol is to further elucidate the genetic mutations that drive melanocytic nevi (benign melanocytic neoplasms, moles). This will be performed by whole genome, whole exome, or targeted sequencing of de-identified specimens.
  Herein, we plan to isolate DNA from de-identified skin biopsy specimens and blood samples:
  1. From melanocytic nevi collected by skin biopsy (a shave or punch biopsy). A part of the tissue will be submitted for routine diagnostic dermatopathology and investigational histomorphologic and immunohistochemical analysis.
  2. From corresponding normal tissue (blood). DNA isolated from blood will be used as a normal control when analyzing sequencing data to identify somatic mutations in lesional tissue.


Eligibility: Inclusion criteria:
  -  Male or female subjects that are 18 years or older
  -  Subjects with melanocytic nevi\
  Exclusion criteria:
  -  Patients less than 18 years of age
  -  Patients without melanocytic nevi
  -  Patients with a bleeding disorder or are taking anticoagulation medication

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Risk Stratification Among Individuals Who Have Many Moles on Their Skin

Summary: The investigators are doing this study to improve our ability to identify which people with many moles on their skin are most likely to develop skin melanoma. The investigators hope to identify features of moles that are associated with melanoma risk. The investigators hope to use this information to customize and tailor melanoma screening to the individual patient based on a better estimate of their individual risk.


Eligibility: Inclusion Criteria:
  -  Patients ≥ 18 years of age
  -  High-risk nevus phenotype (≥ 50 nevi and ≥ 1 atypical nevus)
  -  First presented to MSKCC for cutaneous melanoma-related care within the past 12 months
  -  Cases: recent diagnosis (≤ 12 months) of unequivocal invasive cutaneous melanomas (AJCC Stages I-IV) confirmed by MSKCC pathology
  -  Cases: completion of surgical treatment of primary melanoma
  -  Ability to sign informed consent
  Exclusion Criteria:
  -  Known germline high-penetrance melanoma predisposition mutation (that is, CDKN2A and CDK4)
  -  Cases: history of invasive cutaneous melanoma (AJCC Stages I-IV) not confirmed by MSKCC pathology, history of acrolentiginous type of cutaneous melanoma
  -  Cases: history of systemic adjuvant therapy or treatment of metastatic melanoma, including: MEK inhibitors (trametinib, cobimetinib, etc.), BRAF inhibitors (vemurafenib, dabrafenib, etc.), and immunotherapy (pembrolizumab, nivolumab, atezolizumab, ipilimumab, etc.). Controls: history of Stage 0-IV melanoma confirmed by MSKCC pathology
  -  History of limb amputation or other condition (e.g., tattoos, burns) per investigator discretion that would modify nevus phenotype
  -  Physical inability to undergo total body photography or reflectance confocal microscopy imaging (that is, remain relatively still for durations of 3-5 minutes)
  -  Known hypersensitivity to adhesive rings used for reflectance confocal microscopy
  -  Inability to give informed consent
  -  Have skin afflicted with anther skin condition (for example, psoriasis) that would affect ability to characterize nevus phenotype (per investigator discretion)
  -  Familial cutaneous melanoma history (families with at least one invasive melanoma and two or more other diagnoses of invasive melanoma or pancreatic cancer among first- or second-degree relatives on the same side of the family). We will confirm melanoma family history via medical record documentation, whenever possible, as recommended by previous studies that disproved about half of the reported family histories of melanoma among first-degree relatives in case-control studies.

Relevance to patient case: not relevant
Patient case: 55-year-old male with Melanoma. Genetic variant: NRAS (Q61K). Other conditions: Hypertension.

Clinical trial: A Randomized Phase III Trial of Hyperthermic Isolated Limb Perfusion With Melphalan, Tumor Necrosis Factor, and Interferon-Gamma in Patients With Locally Advanced Extremity Melanoma

Summary: Randomized study. Initially, 3 patients will be entered on Arm I as a pilot feasibility study and to standardize the technical aspects of the study. Subsequently, all patients are randomized to Arms I and II.
  Arm I: Regional Hyperthermia plus Regional Single-Agent Chemotherapy. Hyperthermic intravenous limb perfusion, HILP; plus Melphalan, L-PAM, NSC-8806.
  Arm II: Regional Hyperthermia plus Regional Single-Agent Chemotherapy and Biological Response Modifier Therapy. HILP as in Arm I; plus L-PAM; and Tumor Necrosis Factor (Knoll), TNF, NSC-635257; Interferon gamma (Genentech), IFN-G, NSC-600662.

Detailed description: Patients with locally advanced melanoma confined to an extremity (Stage IIIA or Stage IIIAB) will be treated in a randomized Phase III study with hyperthermic isolated limb perfusion. One arm of the study will be a standard 60 minute perfusion with melphalan as a single agent. The second arm of the study will combine melphalan, tumor necrosis factor, and interferon-gamma in the isolated limb perfusion reproducing a regimen shown to have 100% response rates in a Phase II European trial. Patients will be followed for local response rates, duration of response, treatment toxicity, and disease-free survival.

Eligibility: DISEASE CHARACTERISTICS:
  Biopsy-proven Stage IIIA or IIIAB melanoma (M.D. Anderson staging system) of an extremity, as follows:
  Advanced local disease indicated by 2 or more satellite or in-transit metastases.
  Lower limb regional metastases must be distal to the apex of the femoral triangle except inguinal lymph node metastases.
  Upper limb regional metastases must be distal to the deltoid insertion except axillary lymph node metastases.
  No evidence of systemic disease outside the involved extremity.
  Recurrent disease subsequent to prior successful limb perfusion allowed.
  Bidimensional directly measurable dermal or subcutaneous lesion required.
  PRIOR/CONCURRENT THERAPY:
  No prior isolated limb perfusion.
  Biologic Therapy: At least 1 month since Biologic Therapy.
  At least 3 months since regional therapy of the extremity.
  Chemotherapy: At least 1 month since chemotherap.y
  At least 3 months since regional therapy of the extremity.
  Endocrine Therapy: Not specified.
  Radiotherapy: At least 1 month since radiotherapy.
  Surgery: Not specified.
  PATIENT CHARACTERISTICS:
  Age: 18 and over.
  Performance status: ECOG 0 or 1.
  Hematopoietic: Platelets greater than 150,000.
  Hepatic: Bilirubin less than 1.5 mg/dl; Coagulation profile normal.
  Renal: Creatinine less than 2.0 mg/dl.
  Cardiovascular: No evidence of peripheral vascular disease, e.g.:
  No history of claudication.
  OTHER:
  HIV negative.
  No pregnant or nursing women.

Relevance to patient case: not relevant
Patient case: 55-year-old male with Melanoma. Genetic variant: NRAS (Q61K). Other conditions: Hypertension.

Clinical trial: A Phase I Study of gp100 Human Melanoma Peptide Vaccine With Incomplete Freund's Adjuvant

Summary: This is a phase I study of melanoma tumor antigen peptide vaccines. The nine amino acid peptides representing HLA-A2 restricted T cell epitope of the melanoma antigen, gp100 will be administered to patients emulsified in Incomplete Freund's Adjuvant, (IFA). The study is designed to evaluate the toxicity, immunologic effects and potential therapeutic role of repeated doses of gp100 peptide vaccines administered subcutaneously.
  Immune reactivity to the gp100 epitope peptides will be monitored in all patients by analysis of melanoma-specific T cell precursor frequency prior to and after immunization.

Detailed description: This is a phase I study of melanoma tumor antigen peptide vaccines. The nine amino acid peptides representing HLA-A2 restricted T cell epitope of the melanoma antigen, gp100 will be administered to patients emulsified in Incomplete Freund's Adjuvant, (IFA). The study is designed to evaluate the toxicity, immunologic effects and potential therapeutic role of repeated doses of gp100 peptide vaccines administered subcutaneously.
  Immune reactivity to the gp100 epitope peptides will be monitored in all patients by analysis of melanoma-specific T cell precursor frequency prior to and after immunization.

Eligibility: DISEASE CHARACTERISTICS:
  Metastatic melanoma that is HLA-A2 positive.
  No primary melanoma of ocular or mucosal origin.
  Measurable or resected metastatic disease required.
  PRIOR/CONCURRENT THERAPY:
  BIOLOGIC THERAPY: No prior (greater than 30 days) or concurrent Biologic Therapy.
  CHEMOTHERAPY: No prior (greater than 30 days) or concurrent chemotherapy.
  ENDOCRINE THERAPY: No prior (greater than 30 days) or concurrent hormone therapy.
  No requirement for steroids.
  RADIOTHERAPY: No prior (greater than 30 days) or concurrent radiotherapy.
  SURGERY: Not specified.
  PATIENT CHARACTERISTICS:
  Age: 18 and over.
  Performance Status: ECOG 0 or 1.
  Life Expectancy: More than 3 months.
  HEMATOPOIETIC: No coagulation disorder.
  HEPATIC:
  Bilirubin no greater than 2.0 mg/dL.
  No Hepatitis BsAg antibody.
  RENAL: Creatinine no greater than 2.0 mg/dL.
  CARDIOVASCULAR: No major cardiovascular illness.
  PULMONARY: No major respiratory illness.
  OTHER:
  No previous allergic reaction to incomplete Freund's adjuvant.
  HIV negative.
  No active systemic infection.
  Not pregnant or lactating.

Relevance to patient case: not relevant
Patient case: 55-year-old male with Melanoma. Genetic variant: NRAS (Q61K). Other conditions: Hypertension.

Clinical trial: Immunization of Patients With Metastatic Melanoma Using the GP100 Peptide Preceded by an Endoplasmic Reticulum Insertion Signal Sequence

Summary: Patients with metastatic melanoma who are HLA-A201+ will be immunized with a modified peptide from the gp100 molecule that contains a signal sequence designed to improve peptide presentation by antigen presenting cells. This peptide called gp100:ES209-217 (210M) will be administered either alone or in combination with high or low dose IL-2. Patients will be evaluated for clinical response, as well as undergo studies of the immunologic response to the peptide immunization.

Detailed description: Patients with metastatic melanoma who are HLA-A201+ will be immunized with a modified peptide from the gp100 molecule that contains a signal sequence designed to improve peptide presentation by antigen presenting cells. This peptide called gp100:ES209-217 (210M) will be administered either alone or in combination with high or low dose IL-2. Patients will be evaluated for clinical response, as well as undergo studies of the immunologic response to the peptide immunization.

Eligibility: Any patient age greater than or equal to 18 with measurable metastatic melanoma who has failed standard treatment and has an expected survival of greater than three months will be considered.
  Serum creatinine of 2.0 mg/dl or less.
  Bilirubin 1.6 mg/dl or less.
  WBC 3000/mm(3) or greater.
  Platelet count 90,000 mm(3) or greater.
  Serum AST/ALT less then two times normal.
  ECOG performance status of 0 or 1 or 2.
  Patients of both genders must be willing to practice effective birth control during this trial.
  No patients who are undergoing or have undergone in the past 3 weeks any other form of therapy except surgery for their cancer.
  No patients who have active systemic infections, coagulation disorders, autoimmune disease or other major medical illnesses of the cardiovascular or respiratory systems or any known immunodeficiency disease. Patients with cardiovascular disease will be eligible to receive peptide in IFA alone.
  No patients who require steroid therapy.
  No patients who are pregnant (because of possible side effects on the fetus).
  No patients who are known to be positive for hepatitis BsAG or HIV antibody (because of possible immune effects of these conditions).
  No patients who have any form of primary or secondary immunodeficiency. (The experimental treatment being evaluated in this protocol depends on an intact immune system. Patients who have decreased immune competence may be less responsive to the experimental treatment and more susceptible to its toxicities).

Relevance to patient case: not relevant
Patient case: 55-year-old male with Melanoma. Genetic variant: NRAS (Q61K). Other conditions: Hypertension.

Clinical trial: SWOG-9430: Surgery in Treating Patients With Metastatic Melanoma

Summary: RATIONALE: Surgery may be effective therapy in treating patients with metastatic melanoma.
  PURPOSE: This phase II trial is studying how well surgery works in treating patients with metastatic melanoma.

Detailed description: OBJECTIVES:
  -  Assess overall and progression-free survival in patients with metastatic melanoma (beyond the draining lymph nodes) after complete surgical resection of all known disease.
  -  Determine the ability of the Southwest Oncology Group Melanoma Committee to enroll patients with metastatic melanoma who can be resected to a disease-free state.
  OUTLINE: This is a multicenter study.
  All patients undergo gross total resection of all known disease. Patients whose disease cannot be completely resected or who have disease recurrence after surgery are removed from study. Patients found to have microscopic residual disease after surgery are considered completely resected. Resected tissue is submitted for analysis on protocol SWOG-9431.
  Patients may receive any adjuvant therapy (e.g., radiotherapy, interferon, and/or vaccines) deemed clinically appropriate by the treating physician.
  Patients are followed periodically for 5 years after study entry.
  PROJECTED ACCRUAL: A total of 100 eligible patients with completely surgically resected disease will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically confirmed metastatic melanoma that is deemed grossly surgically resectable
  -  Multiple resected sites or metastatic melanoma of unknown primary allowed provided all known disease can be grossly resected
  -  Recurrence in iliac lymph nodes after inguinal lymph dissection allowed
  -  No metastatic disease beyond the lesions planned for resection
  -  Confirmed by CT scan of chest, abdomen, pelvis, and CT or MRI of brain within 42 days of study
  -  Concurrent registration on protocol SWOG-9431 required
  PATIENT CHARACTERISTICS:
  Age:
  -  18 and over
  Performance status:
  -  SWOG 0-2
  Hematopoietic:
  -  Not specified
  Hepatic:
  -  Not specified
  Renal:
  -  Not specified
  Other:
  -  No other malignancy within the past 5 years except adequately treated basal cell or squamous cell skin cancer, carcinoma in situ of the cervix, or adequately treated stage I or II cancer from which patient is currently disease free
  -  Not pregnant
  PRIOR CONCURRENT THERAPY:
  Biologic therapy:
  -  Prior immunotherapy in the adjuvant or metastatic setting allowed
  Chemotherapy:
  -  Prior chemotherapy in the adjuvant or metastatic setting allowed
  Endocrine therapy:
  -  Prior hormonal therapy in the adjuvant or metastatic setting allowed
  Radiotherapy:
  -  Prior radiotherapy in the adjuvant or metastatic setting allowed
  Surgery:
  -  See Disease Characteristics
  -  At least 14 days since prior surgery in the adjuvant or metastatic setting
  Other:
  -  Recovered from prior therapy

Relevance to patient case: not relevant