araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: A Gene Hunting Study for Familial Papillary Thyroid Cancer

Summary: The aim of this project is to identify genetic risk factors associated with familial papillary thyroid carcinoma (PTC). Papillary thyroid cancer is a type of cancer that shows high heritability. However, the specific genetic factors that cause an increased risk have been elusive.

Detailed description: The aim of this project is to identify genetic risk factors associated with familial papillary thyroid carcinoma (PTC). This can be accomplished in several ways, including loss of heterozygosity studies as well as comparative gene expression analysis. When possible, linkage analysis on families with multiple individuals affected with PTC may also help identify the putative gene(s).
  Study participants will be asked to:
  1. Complete family history and medical history questionnaires
  2. Sign a medical record release so that thyroid cancer pathology reports can be obtained
  3. Supply a blood sample for genetic studies
  4. Provide study related information to family members who are needed for family studies

Eligibility: Eligibility Criteria:
  -  Patients with a diagnosis of PTC and a family history of PTC
  -  Affected and unaffected family members of the proband*
  -  For familial cases (families with 2 or more cases of PTC), participation will be offered to all living family members with PTC or benign thyroid disease as well as selected unaffected first and second degree relatives. Participation may also be offered to spouses when needed for analyzing parent/offspring samples.

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: Proteomics of Papillary Thyroid Carcinoma

Summary: Thyroid carcinoma is the common endocrine system malignant neoplasm. At present it has become the malignant neoplasm of fastest growing incidence rate. More than 85% thyroid carcinoma is papillary thyroid carcinoma. Cervical lymph node metastasis is common in papillary thyroid carcinoma patients. This study aim to reveal protein expression differences between papillary thyroid carcinoma with cervical lymph node metastasis and without cervical lymph node metastasis.

Detailed description: 1. Object: Patients aged 18-65 years; newly diagnosed papillary thyroid carcinoma with cervical lymph node metastasis and without cervical lymph node metastasis and undergone thyroidectomy according to the China thyroid association guidelines for the Management of thyroid nodule and thyroid cancer.
  2. Clinical information, examination data: Information is obtained from medical record abstraction.
  3. Samples: Fresh frozen thyroid tissues from each sample group(normal histology, benign disease, papillary thyroid carcinoma with cervical lymph node metastasis, papillary thyroid carcinoma without cervical lymph node metastasis ).

Eligibility: Inclusion Criteria:
  -  Newly diagnosed papillary thyroid carcinoma.
  -  Undergo thyroidectomy according to the China thyroid association guidelines forthe Management of thyroid nodule and thyroid cancer.
  Exclusion Criteria:
  -  Current substance abuse/dependence.
  -  Daily tobacco and alcohol use.
  -  Whole neck irradiation or surgery.
  -  Prior cancer diagnosis or chemotherapy treatment.
  -  Active autoimmune disorder.
  -  Uncontrolled allergic condition or asthma.
  -  Chronic use of oral steroid medication.
  -  Hormone therapy (estrogen, progestin compounds).

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: Investigation of Efficacy and Safety of Three Dose Levels of Subcutaneous Semaglutide Once Daily Versus Placebo in Subjects With Non-alcoholic Steatohepatitis.

Summary: Investigation of efficacy and safety of three dose levels of subcutaneous semaglutide once daily versus placebo in subjects with non-alcoholic steatohepatitis


Eligibility: Inclusion Criteria: - Informed consent obtained before any trial-related activities. Trial-related activities are any procedures that are carried out as part of the trial, including activities to determine suitability for the trial except for protocol described pre-screening activities which require a separate informed consent. - Male or female, aged 18-75 years (both inclusive) (for Japan: male or female aged 20-75 years (both inclusive)) at the time of signing informed consent - Local histological diagnosis of NASH followed by histological confirmation of NASH based on central pathologist evaluation of a liver biopsy obtained up to 21 weeks before screening - Histologic evidence of NASH based on central pathologist evaluation of a liver biopsy obtained up to 21 weeks before screening. - NASH fibrosis stage 1, 2 or 3 according to the NASH CRN fibrosis staging system based on central pathologist evaluation Exclusion Criteria: - Known or suspected abuse of alcohol (above 20 g/day for women or above 30 g/day for men), alcohol dependence* or narcotics. (* = assessed by the Alcohol Use Disorders Identification Test (AUDIT questionnaire)) - Diagnosis of type 1 diabetes according to medical records - HbA1c above 10% at screening - History or presence of pancreatitis (acute or chronic) - Calcitonin equal or above 50 ng/L at screening - Family or personal history of multiple endocrine neoplasia type 2 or medullary thyroid carcinoma. Family is defined as a first degree relative - Body Mass Index (BMI) ≤ 25.0 kg/sqm at the screening visit (visit 1) - Female who is pregnant, breast-feeding or intends to become pregnant or is of childbearing potential and not using an adequate contraceptive method (adequate contraceptive measures as required by local regulation or practice)

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: Early Rebiopsy to Identify Biomarkers of Tumor Cell Survival Following EGFR, ALK, ROS1 or BRAF TKI Therapy

Summary: A comparison of baseline tumor characteristics in oncogene-driven cancers to tumor characteristics after early response to Tyrosine Kinase Inhibitor (TKI) targeted treatment will allow identification of early adaptive mechanisms of cell survival. This will facilitate targeting and termination of these survival/ resistance pathways before they develop with rational combinations of therapeutic agents to improve outcomes.


Eligibility: Inclusion Criteria:
  -  Carry a diagnosis of stage IV lung adenocarcinoma with an activating mutation determined to respond to an estimated glomerular filtration rate (EGFR) TKI, alkaline phosphatase (ALK) or ROS Proto-Oncogene 1 (ROS1) fusion or BRAF V600E.
  -  Aged 18 - 85 years or older
  -  ECOG 0-2
  -  Have a histologically confirmed diagnosis of lung adenocarcinoma harboring an EGFR sensitizing mutation (including, but not limited to: G719X, del exon 19, or L858R).
  -  No prior therapy for metastatic disease.
  -  Planned treatment with a single agent EGFR TKI including but not limited to:
  1. erlotinib,
  2. gefitinib,
  3. rociletinib (CO-1686),
  4. afatinib, or
  5. osimertinib (AZD-9291).
  -  Patients must have at least one site of measurable disease ≥ least 2cm.
  -  Primary disease site or site of metastatic disease must be amenable to biopsy.
  -  Patients must have the ability to understand and willingness to sign an informed consent document.
  -  Patients must be willing to undergo an initial pre-treatment biopsy of tumor tissue (or have previously collected frozen tissue) and a follow-up biopsy 2 weeks (+/- 1 week) after treatment start
  Exclusion Criteria:
  -  Concurrent health problem which would preclude tissue biopsy (eg hemophilia or other bleeding predisposition).
  -  Patients whose only source of biopsiable disease is:
  1. intracranial,
  2. pleural effusion or any lesion that is deemed unsafe to biopsy by the treating physician or,
  3. interventional radiology.

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: Profiling Biospecimens From Cancer Patients to Screen for Molecular Alterations Related to Treatment Selection

Summary: Many patients are treated for advanced cancer without knowledge of underlying molecular features that might indicate FDA approved therapies or potential eligibility for biomarker-selected clinical trials. Strata Oncology is initiating the Strata Trial (STR-001-001) with the primary goal of understanding the proportion of subjects available for clinical trials and approved targeted therapies in advanced cancer while assessing the feasibility of using a large-scale NGS screening program to match subjects for eligibility assessments in clinical trials and/or for approved targeted therapies. The Strata Trial does not require additional procedures but rather uses surplus, or leftover tumor specimens for molecular profiling.

Detailed description: The Strata Trial is a precision oncology collaboration structured as an observational master screening protocol with the aim to match patients to genomically-guided therapeutic protocols and/or approved therapies. Subjects enrolled on the Strata trial will submit surplus, clinical formalin fixed paraffin-embedded (FFPE) tumor specimens for molecular profiling and a test report will be provided back to the investigator. For those subjects identified as having molecular variants associated with an affiliated therapeutic protocol and/or approved targeted therapy, the Strata report will provide additional relevant information.
  All molecular profiling will be performed in the Strata Oncology CLIA-certified laboratory (Ann Arbor, MI). The molecular profiling assays will include targeted next generation sequencing (NGS) of DNA and RNA covering a range of actionable genomic variants, such as gene mutations (e.g. those in EGFR and BRAF), gene amplifications (e.g. ERBB2) and gene fusions (e.g. ALK).
  Subjects who have been identified with genetic alterations relevant to a trial or targeted therapy will be followed for treatment changes for three years from the time of signed informed consent.

Eligibility: Inclusion Criteria:
  -  Subjects must be ≥ 18 years of age.
  -  Subjects must have histologically documented solid tumors or lymphoma.
  -  Specific criteria for individual tumor types are as follows:
  1. Subjects with glioblastoma.
  2. Subjects with pancreatic cancer are eligible at any stage of disease.
  3. Subjects with rare tumors (i.e. cancer started in an unusual place in the body, it is unusual type and requires special treatment) are eligible at stages II-IV
  4. Subjects with other tumor types must have recurrent, relapsed, refractory, metastatic or advanced stages III or IV cancer.
  -  Subjects must have an adequate formalin-fixed paraffin-embedded tumor specimen for genomic sequencing.

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

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: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: PACE4 in Thyroid Cancer

Summary: The investigation of thyroid nodules is limited by the fact that up to 49% of the fine needle aspirations (FNA) performed are of "indeterminate cytological signification". Moreover, no fully reliable molecular marker for thyroid cancer have been described. The goal of this project is to study the expression of a specific kind of protein convertase in benign and in malignant thyroid nodules to determine its potential as a biomarker.

Detailed description: Patients that underwent thyroidectomy at the CIUSSS de l'Estrie-CHUS will be recruited and classified according to the pathological diagnosis. An immunohistochemistry technique, developed and calibrated for the specific protein convertase studied, will be undertaken. Results will be interpreted by a specialized pathologist.

Eligibility: Inclusion Criteria:
  -  Men of women, aged 18-100 y.-o.
  -  History of subtotal or total thyroidectomy at the "Centre intégré universitaire de santé et de services sociaux de l'Estrie - Centre hospitalier universitaire de Sherbrooke" (CIUSSS de l'Estrie - CHUS) between January 2010 and May 2016.
  Exclusion Criteria:
  -  Refusal to participate to the study.
  -  Unavailability of the formalin-fixed, paraffin-embedded tissues.
  -  Uncertain pathological diagnosis.

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: Bone Healing Study

Summary: The aim of the research is to identify structural tissue changes in the early fracture hematomas.

Detailed description: The fracture hematomas obtained during reconstructive bone surgery from patients with bone fractures will be examined. Histological methods and ultra-thin sections for electron microscopy will be used to identify structural tissue changes in the granulation tissue in different period of time after bone fracture. Immunohistochemical analysis will be performed to estimate the dynamic of proliferation, differentiation and cell migration during granulation and reticulofibrosis bone tissues development.

Eligibility: Inclusion Criteria:
  -  Patients with fractures of the upper and lower extremities
  -  Patients for whom the surgical bone reconstruction are indicated

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: BRAF V600E and Redifferentiation Therapy in Radioiodine-refractory Papillary Thyroid Cancer

Summary: Papillary thyroid cancer (PTC) is the most common neoplasia in the thyroid gland. The combination of surgery, followed by radioiodine therapy (RIT) and thyroid-stimulating hormone (TSH) suppressive therapy is usually a curative option for differentiated thyroid cancer (DTC). Although DTC has a good prognosis generally, it is problematic when dedifferentiation is suspected and radioiodine refractoriness presumed. One possible therapy option for redifferentiation is the pretreatment with retinoids. From 2008 to 2014 there were 13 patients with PTC who were treated with retinoids after thyroidectomy before a further course of radioiodine. A recent study has shown that the efficacy of Selumetinib, another option for redifferentiation depends on the mutational status of the treated patient. In this retrospective study the investigators looked for a similar association between BRAF V600E and redifferentiation therapy with retinoids. As retinoids have fewer side effects compared to TKI, it is worth performing studies to assess the importance of genetic marker for the response and to estimate the chances of this specific patient collective. BRAF V600E seems to be associated with better long-term response after redifferentiation therapy with 13-cis RA in RAI-R PTC. Therefore, evaluation of BRAF mutational status prior to redifferentiation therapy could be beneficial for predicting response.


Eligibility: Eligible criteria for radioiodine-refractory patients included:
  -  PTC
  -  no response to former RIT
  -  decrease or loss of initial sufficient RI-Uptake
  -  redifferentiation therapy with 13-cis-RA
  -  available FFPE tissue.
  Eligible criteria for radioiodine-sensitive patients included:
  -  PTC
  -  cured after a maximum of two RIT
  -  no redifferentiation therapy necessary
  -  available FFPE tissue.
  Exclusion criteria
  -  DTC other than PTC
  -  patients lost to follow-up
  -  other redifferentiation therapy than retinoids
  -  anaplastic or medullary thyroid cancer
  -  benign thyroid disease, no available FFPE tissue
  -  more than two RITs in the control group
  -  insufficient clinical information.

Relevance to patient case: definitely relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: Radiofrequency Ablation of Low Risk Papillary Thyroid Microcarcinoma

Summary: This is a single center prospective clinical trial with regard to efficacy and safety of radiofrequency ablation of papillary thyroid microcarcinoma.

Detailed description: For treatment of papillary thyroid microcarcinoma (PTMC), radiofrequency ablation (RFA) will be performed with the supine position and neck extended under ultrasonogrphic guidance. Before RFA, local anesthesia will be performed. RFA system including radiofrequency generator (VIVA RF system, STARmed, Goyang-si, Korea) and internally cooled electrode (18G with 0.5cm-1cm active tip, star RF electrode, STARmed, Goyang-si, Korea) will be used. With regard to RFA procedure, moving shot technique and hydrodissection, if indicated, will be used. After RFA, follow-up will be performed using ultrasonography, serum thyroid function test, and questionnaire for quality of life by face-to-face interview at 2 months, 6, 12, 18, 24 months during the first 2 years after RFA, and yearly afterwards.

Eligibility: Inclusion Criteria:
  -  who agrees to the consent form
  -  aged from 18 to 60 years old
  -  who has been diagnosed with Bethesda category V or VI by fine needle aspiration or needle biopsy
  -  whose thyroid cancer is 1 cm or smaller than 1 cm length
  -  who does not have lymph node or distant metastasis
  -  whose thyroid cancer does not have extrathyroidal extension
  -  in whom it seems technically possible to completely ablate thyroid cancer using RF
  Exclusion Criteria:
  -  who cannot routinely followed up according to the study schedule
  -  who has been with Bethesda category I, II, III, or IV by fine needle aspiration or needle biopsy.
  -  who has hyperthyroidism that requires treatment
  -  who has bleeding tendency
  -  multifocal papillary thyroid microcarcinoma
  -  who is pregnant

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: Comparison Between Robotic, Endoscopic and Traditional Open Surgery in Thyroidectomy

Summary: Comparison of endoscopic thyroidectomy, robotic thyroidectomy and conventional open surgery, the safety of the operation, the timing of the operation and the complications.

Detailed description: With the further development of endoscopic technique, thyroid surgery of the robot has emerged, which may become a trend of endoscopic technology due to its convenience and accuracy.In this study, the advantages and disadvantages of endoscopic thyroidectomy and robotic thyroid surgery were compared, and the experience in the transition stage of thyroid surgery in robotic and endoscopic thyroidectomy was summarized.

Eligibility: Inclusion Criteria:
  -  Thyroid papillary carcinoma.
  -  The tumor diameter is less than or equal to 1cm.
  -  The lymph nodes are limited to the VI level.
  -  Voluntary choice of endoscopy or robotic surgery.
  Exclusion Criteria:
  -  Patients without beauty needs.
  -  There is lateral neck or mediastinal lymph node metastasis.
  -  The tumor invades the nerve and surrounding organs.

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: Study of Dabrafenib+Trametinib in the Adjuvant Treatment of Stage III BRAF V600+ Melanoma After Complete Resection to Evaluate the Impact on Pyrexia Related Outcomes

Summary: This is an open-label Phase IIIb study of dabrafenib in combination with trametinib in the adjuvant treatment of melanoma after complete resection to evaluate the impact on pyrexia related outcomes of an adapted pyrexia AE-management algorithm, as well as safety, efficacy and health-related outcomes.
  Approximately 600 subjects will be enrolled to receive dabrafenib (150 mg BID) and trametinib (2 mg once daily) combination therapy for 12 months. At enrollment, subjects will be instructed on the pyrexia management algorithm.
  This study consists of two Periods for Enrolled subjects:
  -  Treatment Period - subjects will receive up to 12 months of treatment.
  -  Follow-up Period - subjects will be followed through 24 months from their first dose date for relapse, and through end of study for overall survival. Follow-up will start once treatment is complete or is prematurely discontinued and continue through the end of the study, regardless of disease recurrence.


Eligibility: Inclusion Criteria:
  -  Completely resected histologically confirmed cutaneous melanoma stage IIIA (LN metastasis >1 mm), IIIB, IIIC, IIID [AJCC (ed 8)]
  -  V600E/K mutation positive using a validated local test
  -  Subjects presenting with initial resectable lymph node recurrence after a diagnosis of Stage I or II melanoma are eligible.
  -  Subjects who have previously had Stage III melanoma at any time are not eligible.
  -  Subjects with an unknown primary melanoma are not eligible.
  -  Recovered from definitive surgery (e.g. no uncontrolled wound infections or indwelling drains).
  -  Eastern Cooperative Oncology Group (ECOG) Performance Status of 0-1
  Exclusion Criteria:
  -  Uveal or mucosal melanoma
  -  Evidence of metastatic disease including unresectable in-transit metastasis
  -  Received any prior adjuvant or neoadjuvant treatment, including but not limited to chemotherapy, checkpoint inhibitors, targeted therapy [e.g., BRAF and/or MEK inhibitors], biologic therapy, vaccine therapy, investigational treatment, or radiotherapy for melanoma
  -  Malignant disease, other than that being treated in this study. Exceptions to this exclusion include the following: malignancies that were treated curatively and have not recurred within 2 years prior to study treatment; completely resected basal cell and squamous cell skin cancers and any completely resected carcinoma in situ
  -  History or current evidence of cardiovascular risk
  -  A history or current evidence/risk of retinal vein occlusion (RVO) or central serous retinopathy

Relevance to patient case: not relevant