araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 40-year-old female with thyroid cancer; genetic feature: BRAF

Clinical trial: The Oncopanel Pilot (TOP) Study

Summary: The BCCA Oncopanel is a clinical assay being developed to determine genotype status of a prospectively defined set of genes.
  The purpose of this pilot study is to assess the feasibility and effect on clinical-decision-making of the Oncopanel test. Eligible patients are those with advanced lung, colorectal, melanoma and GIST cancers and patients with diagnosed malignancies being considered for clinical trials.

Detailed description: Somatic mutations in solid tumors represent an established means of characterizing malignancies for prognostic, diagnostic and therapeutic purposes. Mutations in EGFR, KRAS, BRAF, and KIT and PDGFRA genes direct therapy in patients with advanced lung, colorectal, melanoma, and GIST tumors, respectively. Known or novel mutations in other genes may also be of clinical significance but are not identified by current genotyping offered to BC Cancer Agency (BCCA) patients. Furthermore, numerous candidate genes have been implicated as potential prognostic and predictive biomarkers in patients with solid tumours. As such, the Oncopanel is a clinical assay being developed to determine genotype status of a prospectively defined set of genes. The following clinically relevant set of genes and exons are included in the Oncpanel: KRAS, EGFR, BRAF, NRAS and HRAS, PIK3CA Signal Transduction Pathway Genes, RAS-RAF-MEK-MAPK Pathway, HER2, IDH1 and IDH2, ALK, TP53, c-KIT, STAT1&3 and PDGFRA. Additional testing on the tumour material will also include analysis of specific gene variants associated with adverse events or response to therapy.
  Numerous studies have documented the presence of circulating tumour DNA (ctDNA) among patients with advanced and early stage malignancies (20-22). The ability to diagnose standard cancer mutations with a blood-based assay (a "liquid biopsy") has not yet been established but presents obvious advantages. The emergence of "resistance" mutations arising in the metastatic tumor or throughout the course of therapy is well documented (21, 22). A blood biopsy may represent more accurate determination of the tumor's genetic features than archival DNA specimen. Adequate tissue specimens can be difficult to obtain from some patients with diagnosed malignancies, particularly lung cancer. A blood biopsy may represent a less invasive and timelier means of diagnosing both standard and translational cancer mutations.

Eligibility: Patients with archival tumor tissue and a known history of invasive malignancies are eligible if they meet one or more of the following criteria:
  -  Advanced colorectal cancer and eligible for standard KRAS testing,
  -  Advanced non-small cell lung cancer and eligible for standard EGFR testing,
  -  Advanced melanoma and eligible for standard BRAF testing,
  -  Gastrointestinal stromal tumors (GISTs) eligible for standard c-KIT and PDGFRA testing,
  -  Being considered for potential eligibility in clinical trial.

Relevance to patient case: not relevant
Patient case: 40-year-old female with thyroid cancer; genetic feature: BRAF

Clinical trial: Use of Exome Sequence Analysis and Circulating Tumour in Assessing Tumour Heterogeneity in BRAF Mutant Melanoma

Summary: Despite recent advances in cancer treatment, little impact has been made on curing as opposed to controlling cancers over the last several decades. Part of the problem is that investigators have an incomplete understanding of how tumours behave as they evolve and in response to treatment. In this trial, the investigators hope to better understand the evolution of BRAF melanoma in response to drugs a patient may have received such as vemurafenib or dabrafenib. Importantly, the investigators want to understand how the tumours evolve resistance to these drugs and whether this can be predicted through blood tests, in particular of the circulating tumour DNA.

Detailed description: Study population: BRAF mutant melanoma patients
  Pre-mortem bloods will be taken from the patient on three occasions at one to thirty days apart from each other, with the first blood draw taking place on the patient's first clinic visit. Six 7 ml EDTA and one 6 ml SST vacutainers of blood (a total of approx. 50 ml of blood) will be taken from the patient.
  When death is expected within the next 48-72 hours, the Medical Oncologist/ Radiation Oncologist/ Hematologist OR delegate will revisit the RAP process with the patient and/or family/substitute decision maker to ensure that they are still in agreement. The patient and the families will also be provided with an additional consent form for participation including blood sampling.

Eligibility: Inclusion Criteria:
  UHN adult patient with BRAF mutant melanoma
  Exclusion Criteria:
  Non BRAF mutant melanoma patient Pediatric patient Non-UHN patient

Relevance to patient case: not relevant
Patient case: 40-year-old female with thyroid cancer; genetic feature: BRAF

Clinical trial: Study of Trametinib and Nab-paclitaxel in Patients With Melanoma

Summary: This study will investigate the combination of two drugs, trametinib and nab-paclitaxel, in patients with advanced unresectable or metastatic melanoma. Each drug has shown activity in trials of patients with melanoma. However, the combination of these two drugs has not been studied. In this trial the investigators will determine the maximum dose of the drug combination to be administered to patients with advanced unresectable or metastatic melanoma and examine the safety profile of the drug combination.

Detailed description: While treatment for melanoma has evolved in the last few years, advanced/metastatic melanoma remains an aggressive disease with poor prognosis. Trametinib and nab-paclitaxel have demonstrated single-agent activity in Phase III trials of patients with melanoma. The investigators propose to investigate this drug combination in patients with advanced unresectable or metastatic melanoma. This open-label Phase I study is designed to determine the maximum tolerated dose (MTD), recommended Phase II dose (RP2D), and safety profile of trametinib and nab-paclitaxel given in combination. Patients with melanoma and known BRAF mutation status will receive escalating doses of trametinib and nab-paclitaxel to determine the MTD. Once the MTD is determined an additional 6 patients will be treated at the MTD to establish the dose for future studies.

Eligibility: Inclusion Criteria:
  -  Adults (≥18 years) with histologically or cytologically-confirmed advanced unresectable or metastatic melanoma. BRAF mutation-positive and wild-type tumors are allowed.
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1
  -  Adequate hematologic, renal, and hepatic function
  -  Life expectancy ≥12 weeks
  -  Any pre-existing neuropathy must be <grade 2 per Common Technology Criteria for Adverse Events (CTCAE) version 4.0
  Exclusion Criteria:
  -  More than 1 prior cytotoxic chemotherapy regimen in the metastatic setting
  -  Prior MEK inhibitor therapy (prior BRAF inhibitor allowed)
  -  Prior nab-paclitaxel (prior taxane allowed)
  -  Use of an investigational anti-cancer drug within 21 days or 5 half-lives (whichever is shorter) prior to first dose. A minimum of 10 days after termination of investigational drug is required. Any drug-related toxicity should have resolved to Grade 1 or baseline.
  -  Symptomatic or untreated brain metastases
  -  History of retinal vein occlusion (RVO)

Relevance to patient case: not relevant
Patient case: 40-year-old female with thyroid cancer; genetic feature: BRAF

Clinical trial: Dexamethasone and Wound Healing After Thyroid Surgery

Summary: Dexamethasone is a potent glucocorticoid with analgesic and anti-emetic effects [1-3]. Perioperative single-dose dexamethasone therapy has been used for several purposes: to reduce post-operative nausea and vomiting (PONV), pain and sore throat. There are also some reports on beneficial effects of less cardiac arrhythmia, improved appetite and less edema from glucocorticoids. Preoperative small dose of dexamethasone was reported to prevent reversal laryngeal nerve injury and improve voice quality after thyroid surgery. While accepted wildly in clinical anesthesia practice, the immune-press related potential risks of side effects associated with dexamethasone, such as delayed wound healing, infection, as well as effects on blood sugar, make the use of perioperative single dose of glucocorticoid controversial. The effect of perioperative dexamethasone on wound healing varied with different types of surgery. The present study will observe the effect of dexamethasone on the safety of thyroid surgery.

Detailed description: Patients who has the thyroid surgery for their thyroid cancer will be randomly allocated into two groups, either dexamethasone group or saline group. In the dexamethasone group, patients will receive 5mg dexamethasone iv right after general anesthesia induction while in the saline group, patients will have 1ml saline iv. The drainage fluid will be collected at 6 hours after surgery and on every morning after operation till the drainage tube is taken out. The total amount of drainage fluid and blood stain area in dressing will be collected and calculated after the operation. The C-reaction protein is checked in drainage fluid and in blood after operation. Besides, the pain scores of incision pain and throat pain will be evaluated. Postoperative nausea and vomit will be checked as well.

Eligibility: Inclusion Criteria:
  -  Elective total thyroidectomy or hemithyroidectomy with lymphadenectomy for thyroid cancer
  Exclusion Criteria:
  -  Age > 65 years, < 18 years
  -  Thyroid tumor with Grave's disease
  -  Thyroid tumor size over 5 cm
  -  Second or more than 2 times for thyroid surgery
  -  Non-traditional pathway for thyroid surgery
  -  ASA > II
  -  Pharyngitis
  -  Smoking, alcohol drinking history
  -  Contraindication or long term use of dexamethasone (allege, ulcer bleeding history, et al)

Relevance to patient case: not relevant
Patient case: 40-year-old female with thyroid cancer; genetic feature: BRAF

Clinical trial: APPLICATION OF MOLECULAR TECHNIQUES FOR IMPROVING THE DIAGNOSIS AND TREATMENT OF NODULAR THYROID LESIONS.

Summary: To determine the improvement in diagnosis of papillary carcinoma by detecting mutation V600E BRAF in retrospective cases with inconclusive cytologic diagnosis (categories III, IV and V of Bethesda System)

Detailed description: Aim of the study To determine the improvement in diagnosis of papillary carcinoma by detecting mutation V600E BRAF in retrospective cases with inconclusive cytologic diagnosis (categories III, IV and V of Bethesda System).
  Design: Retrospective observational study. Scope: The study will be peformed at the Pathology Service, from cytological samples and paraffin file post-diagnosis. Mutations are detected by pyrosequencing technique.
  Subject of study:
  Cases with histological diagnosis of papillary carcinoma (CP) and previous cytological diagnosis in groups III, IV and V Bethesda, collected between October 1989 and July 2014 in Corporació Parc Taulí.
  Methodology:
  -  Identification of cases
  -  Detection of BRAF V600E mutation, initially in histological material from the surgical specimen, and if present, detection in cytological material.
  The statistical analysis will use SPSS. Univariate and bivariate analysis will be done. Results will be presented in the form of frequency tables and percentages for qualitative variables and by average, median and standard deviation for quantitative variables. Pearson chi-square or Fisher's exact test will be applied. The Student t test or the Mann-Whitney test will be performed for quantitative variables.

Eligibility: Inclusion Criteria:
  -  Cases with histological diagnosis of papillary carcinoma (CP) and previous cytological diagnosis in groups III, IV and V Bethesda, collected between October 1989 and July 2014 in Corporació Parc Taulí
  Exclusion Criteria:
  -  Non available cytological or histological material

Relevance to patient case: not relevant
Patient case: 40-year-old female with thyroid cancer; genetic feature: BRAF

Clinical trial: Single-arm Study to Evaluate the Safety and Efficacy of Sorafenib, in Subjects With BRAF Mutation Refractory Solid Tumors

Summary: This is a pilot study of sorafenib in patients with BRAF Mutation Refractory Solid Tumors.
  This study is a single-arm, pilot study of sorafenib in patients with Refractory Solid Tumors harboring BRAF Mutation Sorafenib 400 mg will be administered orally twice a day for 28 days.
  To investigate the efficacy of sorafenib in patients with Refractory Solid Tumors harboring BRAF Mutation.


Eligibility: Inclusion Criteria:
  1. Provision of fully informed consent prior to any study specific procedures.
  2. Patients must be ≥20 years of age.
  3. BRAF mutation Refractory Solid Tumors that has recurred or progressed following standard therapy, or that has not responded to standard therapy, or for which there is no standard therapy.
  4. ECOG performance status 0-2.
  5. Have measurable or evaluated disease based on RECIST1.1. as determined by investigator.
  6. Adequate Organ Function Laboratory Values
  -  Absolute neutrophil count ≥ 1.5 x 109/L, Hemoglobin ≥ 9g/dL, Platelets ≥ 100 x 109/L
  -  bilirubin ≤ 1.5 x upper limit of normal AST/ALT ≤ 2.5 x upper limit of normal (5.0 X upper limit of normal , for subjects with liver metastases)
  -  creatinine ≤1.5 x UNL
  7. Patients of child-bearing potential should be using adequate contraceptive measures (two forms of highly reliable methods) should not be breast feeding and must have a negative pregnancy test prior to start of dosing.
  8. Adequate heart function.
  Exclusion Criteria:
  1. Patients with second primary cancer, except: adequately treated non-melanoma skin cancer, curatively treated in-situ cancer of the cervix, or other solid tumours curatively treated with no evidence of disease for ≤3 years.
  2. Has known active central nervous system (CNS) metastases.
  3. Has an active infection requiring systemic therapy.
  4. Pregnancy or breast feeding
  5. Patients with cardiac problem.
  6. Any previous treatment with sorafenib

Relevance to patient case: possibly relevant
Patient case: 40-year-old female with thyroid cancer; genetic feature: BRAF

Clinical trial: Diagnostic Performance of Ultrasound Elastography for Detection of Thyroid Cancer

Summary: For patients with thyroid gland nodule, fine-needle aspiration biopsy has been proved to be an efficient tool for thyroid cancer diagnosis. However, it is somewhat an invasive procedure and is subject to sampling and analysis uncertainties. Thus, improved, more reliable criteria for determining which nodule should be be aspirated are needed. Ultrasound elastography has been shown to be useful in the differential diagnosis of breast and prostate cancers. Ultrasound elastography also may discriminate malignant from benign nodule.

Detailed description: To prospectively evaluate the elastographic appearance of thyroid cancer and explore the potential sensitivity and specificity of elastography for differentiating benign and malignant tumors, with histopathologic analysis as the reference standard.

Eligibility: Inclusion Criteria:
  - The patients with thyroid nodule who are supposed to take fine needle aspiration biopsy
  Exclusion Criteria:
  - The patients who do not want to participate in the study

Relevance to patient case: not relevant
Patient case: 40-year-old female with thyroid cancer; genetic feature: BRAF

Clinical trial: Detection of BRAF Mutation on FNAB From Papillary Thyroid Carcinoma

Summary: Immunohistochemical detection of the BRAF-V600E mutation on pre-operative fine needle aspiration biopsy (FNAB) from patients suspected for papillary thyroid carcinoma, using the mutation specific antibody VE1.

Detailed description: The BRAF mutation is reported to be present in approximately 50% of papillary thyroid carcinomas (PTC). The mutation has been associated with poor prognosis and more advanced disease stage. Therefore, pre-operative detection of the BRAF-V600E mutation may be of clinical interest in order to individualize treatment of patients with BRAF positive PTC.
  FNABs are performed immediately before the thyroid operation, and BRAF-V600E detection using VE1 is performed on clots. The VE1 stain is compared to the mutation status of the removed cancer or control tissue using the Cobas test.

Eligibility: Inclusion Criteria:
  -  Bethesda system of reporting thyroid cytology (BSRTC) group 5-6 on pre-operative FNAB from the nodule (>1cm)
  -  Undergoing thyroid surgery (histology of index nodule)
  Exclusion Criteria:
  -  Not undergoing thyroid surgery

Relevance to patient case: not relevant
Patient case: 40-year-old female with thyroid cancer; genetic feature: BRAF

Clinical trial: Study of Anlotinib in Patients With Differentiated Thyroid Cancer(ALTER01032)

Summary: The purpose of this study is to compare the effects and safety of Anlotinib with placebo in patients with Differentiated Thyroid Cancer.


Eligibility: Inclusion Criteria:
  1. Signed and dated informed consent
  2. Histological documentation of Differentiated Thyroid Cancer ,With measurable disease (using RECIST1.1)
  3. ECOG PS:0-1,Life expectancy of more than 6 months
  4. Subjects must be 131I-refractory / resistant as defined by at least one of the following:
  -  Lesions that do not demonstrate iodine uptake on any radioiodine scan
  -  Cumulative activity of 131I of >600 mCi or 22 gigabequerels (GBq)
  -  Lesion that demonstrate iodine uptake on any radioiodine scan,but has progressed by RECIST 1.1 within 18 months of 131I therapy
  5. main organs function is normal
  Exclusion Criteria:
  1. Prior treatment with Anlotinib or VEGFR-targeted therapies(such as Vandetanib,Cabozantinib,Lenvatinib,Sunitinib,Sorafenib etc.)
  2. Subjects received radiotherapy external exposure or 131I within 3 months prior to the first dose of study drug or plan to be received any anti-cancer treatment during study
  3. Patients suffering from other malignancies currently or within 5 years, except for cured cervical carcinoma in situ, non-melanoma skin cancers and superficial bladder cancer [ Ta (non-invasive carcinoma), Tis (carcinoma in situ) and T1 (carcinoma invasion into lamina propria) ]
  4. CTCAE(4.0) Grade 1 or higher non-remission toxicity induced by any other previous treatments，excluding alopecia and Grade 2 or lower neurotoxicity induced by oxaliplatin
  5. Patients with factors that could affect oral medication (such as dysphagia etc.)
  6. Patients with pleural effusion or ascites, causing respiratory syndrome (CTCAE Grade 2 or higher dyspnea [Grade 2 dyspnea refers to Shortness of breath with a small amount of activities, affecting Instrumental activities of daily life])
  7. Patients underwent major surgical treatment，open biopsy or significant traumatic injury within 28 days prior to assignment

Relevance to patient case: not relevant
Patient case: 40-year-old female with thyroid cancer; genetic feature: BRAF

Clinical trial: Prospective Study on the Clinical Prognosis of Bilateral Central Lymph Node Dissection in the Patients With Unilateral Thyroid Papillary Carcinoma

Summary: This study recruit the patients with unilateral papillary thyroid cancer before operation,the patients agree to enter the test,and divided into experimental and control group.experimental group patients receive the surgery including unilateral thyroid lobectomy and bilateral central lymph node dissection.and control group receive the surgery including unilateral thyroid lobectomy and unilateral central lymph node dissection.last the investigators compare numbers of patient with tumor recurrence and metastasis rate of 5 years,numbers of metastatic lymph node,and numbers of participants with adverse events related to treatment between two groups in order to evaluate the significance of bilateral lymph node dissection.


Eligibility: according by thyroid carcinoma TNM(tumor,lymph node, metastasis) staging of NCCN (National Comprehensive Cancer Network)
  Inclusion Criteria:
  -  1.Unilateral thyroid papillary carcinoma 2.TNM staging: T1~2N0M0
  Exclusion Criteria:
  -  1.Bilateral thyroid papillary carcinoma 2.isthmus thyroid carcinoma 3.TNM staging: T3orT4 4.Clinic N1orM1

Relevance to patient case: not relevant
Patient case: 40-year-old female with thyroid cancer; genetic feature: BRAF

Clinical trial: Study of Efficacy and Safety of Dabrafenib and Trametinib Combination Therapy in Japanese Patients With BRAF V600E Stage IV NSCLC

Summary: This is an open-label, multicenter, non-randomized, single arm, phase II study to assess efficacy and safety of the dabrafenib and trametinib combination in Japanese patients with any line, stage IV NSCLC harboring a confirmed BRAF V600E mutation.
  Patients will receive oral dabrafenib twice daily and oral trametinib once daily combination therapy. Patients may continue study treatment until disease progression, unacceptable adverse events, start of a new anti-cancer therapy, consent withdrawal, death, or end of the study. Patients who have met the criteria for disease progression (PD) according to RECIST v1.1 may continue to receive study treatment if the investigator believes the patient is receiving clinical benefit and the patient is willing to continue on study treatment. After discontinuation of study treatment, all patients will be followed for survival until death, lost to follow-up, withdrawal of consent, or end of study.


Eligibility: Inclusion Criteria:
  -  Histologically- or cytologically-confirmed diagnosis of NSCLC stage IV (according to AJCC Staging 7th Edition)
  -  Presence of a BRAF V600E mutation in lung cancer tissue. BRAF V600E mutation tested by local laboratory (e.g. study center laboratory, local laboratory company) with proper quality control and license to operation by local health authority is allowed.
  -  Measurable disease according to RECIST v1.1.
  Exclusion Criteria:
  -  Previous treatment with a BRAF inhibitor (including but not limited to dabrafenib, vemurafenib, encorafenib, and XL281/BMS-908662) or MEK inhibitor (including but not limited to trametinib, cobimetinib, binimetinib, AZD6244, and RDEA119) prior to start of study treatment
  -  Patients with brain metastases are excluded if their brain metastases are:
  -  Symptomatic OR
  -  Treated (surgery, radiation therapy) but not clinically and radiographically stable 3 weeks after local therapy (as assessed by contrast enhanced magnetic resonance imaging [MRI] or computed tomography [CT]), OR
  -  Asymptomatic and untreated but >1 cm in the longest dimension
  -  History of malignancy with confirmed activating RAS mutation at any time.
  -  History of interstitial lung disease or pneumonitis
  -  A history or current evidence of retinal vein occlusion (RVO)
  -  Current evidence of unstable aneurysm or one that needs treatment
  Other protocol-defined inclusion/exclusion may apply.

Relevance to patient case: not relevant