araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: Oral Vitamin D Substitution Weekly or Monthly and Adherence

Summary: Vitamin D deficiency (defined as 25(OH)-vitamin D serum level <50 nmol/l) is cured with supplementation by mouth. National guidelines recommend the administration of 800 IU cholecalciferol daily for an effective treatment, especially during the winter (poor sun exposition). Commercially available pharmaceutical forms are liquid in Switzerland (drops) and solid forms in Germany (tablets and capsules). Because therapeutic range of vitamin D3 is wide and toxicity is seldom reached, even after the consumption of 200'000 IU, and because the administration of 8 drops daily is inconvenient, weekly and monthly administrations of the cumulative amount (i.e., 5'600 IU weekly or 24'000 IU monthly) have been investigated. Both administration schedules are therapeutic equivalent. The study aims to investigate which form (liquid or solid) and which schedule (weekly or monthly) procure the highest adherence behavior with outpatients under polypharmacy i.e., with 4 or more medications daily. The investigators will use commercially available Swiss and German products.

Detailed description: Intervention study in patients with serum vitamin D <50 nmol/l and polypharmacy, defined as ≥4 medicaments/day. Treatment duration: 6 months. Treatment groups are defined as Lm (liquid monthly 24'000 IU); Lw (liquid weekly 5'600 IU); Sm (solid monthly 20'000 IU) and Sw (solid weekly 5'600 IU). Cross-over design with identical form (liquid or solid) and switching frequence, i.e. from weekly to monthly treatment and vice versa, for 3 months each.

Eligibility: Inclusion Criteria:
  -  vitamin D deficiency by serum level <50 nmol/l
  -  polypharmacy defined as 4 daily medicines or more
  -  speaking German or Swiss German
  Exclusion Criteria:
  -  hypercalcaemia
  -  substitution treatment with cholecalciferol in the past 3 months
  -  medication intake provided by a third person and not by the patient himself

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: Phase II Trial of AZD2014 in RICTOR Amplified Solid Cancer Patients Refractory to Standard Chemotherapy

Summary: Patients with RICTOR amplified refractory solid cancer will receive vistusertib(AZD2014). Study-arm is composed of 27 patients.
  Vistusertib(AZD2014) 50mg BD continuous schedule of a 28 day cycle Tumour evaluation using RECIST 1.1 will be conducted at screening (within 28 days prior to first dose) and every 8 weeks relative to the date of first dose, up to week 40, then every 16 weeks until objective disease progression (within a window of +/- 7 days of the scheduled date).

Detailed description: Patients with RICTOR amplified refractory solid cancer will receive vistusertib(AZD2014). Study-arm is composed of 27 patients.
  Vistusertib(AZD2014) 50mg BD continuous schedule of a 28 day cycle Tumour evaluation using RECIST 1.1 will be conducted at screening (within 28 days prior to first dose) and every 8 weeks relative to the date of first dose, up to week 40, then every 16 weeks until objective disease progression (within a window of +/- 7 days of the scheduled date).
  Study treatment will be continued until objective disease progression (unless other criteria for treatment discontinuation are met). Patients may continue vistusertib(AZD2014) beyond progression (according to RECIST 1.1), at the discretion of the investigator if they are clinically benefiting from the treatment and they do not meet any other discontinuation criteria.
  If a patient discontinues study treatment prior to disease progression, they should continue to be assessed using RECIST 1.1 until disease progression and then followed up for survival.
  Assessments for survival should be made every 8 weeks following objective disease progression. The details of first and subsequent therapies for cancer, after discontinuation of treatment, will be collected.

Eligibility: Inclusion Criteria:
  1. Advanced solid cancers (including histologically or cytologically documented gastric cancer, colorectal cancer, hepatoma, biliary tract cancers, pancreatic cancer and rare cancers.) that has progressed after standard chemotherapy.
  - Rare cancers are defined as sarcoma, neuroendocrine carcinoma
  2. Provision of tumor sample tumor sample tumor sample tumor sampletumor sample (from either a resection or biopsy)
  3. Patients with RICTOR amplification through NGS.
  4. Patients are willing and able to comply with the protocol for the duration of the study including undergoing treatment and scheduled visits and examinations.
  Exclusion Criteria:
  1. Patients not having received recommended treatment-lines and chemotherapy regimen for the treatment of each tumor type in the advanced setting.
  2. Any previous treatment with PIK3CA, AKT or mTOR inhibitor or agents with mixed PI3K / mTOR activity.
  3. HER2 positive AGC patients (defined by HER2 3+ by immunohistochemistry or HER2 SISH +)

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: Relevance of Peripheral Cells in the Pathophysiology of Chronic Myelomonocytic Leukemia (CMML)

Summary: Chronic Myelomonocytic Leukemia (CMML) is the most frequent of myelodysplastic/myeloproliferative syndromes, as defined by the WHO classification of myeloid malignancies. The median age at diagnosis is around 70 years with a strong male predominance. CMML is a clonal disease of the bone marrow hematopoietic stem cell mainly characterized by persistent monocytosis (>1x109/L) and the presence of immature dysplastic granulocytes in the peripheral blood of CMML patients. Allogeneic stem cell transplantation (ASCT) remains the only curative option in CMML. However, CMML patients are rarely eligible for this kind of therapy, mainly due to their advanced age. The gold standard treatment of CMML thus remains hydroxyurea, which is usually initiated when the disease becomes proliferative, and demethylating agents, which could be efficient in the most aggressive forms of CMML. Nevertheless, the pathogenesis of CMML remains poorly understood and new therapies are urgently needed for patients in treatment failure.
  In recent years, a large numbers of gene mutations have been discovered in CMML, none of which are specific of this entity, as they can be encountered with different frequencies in other myeloid neoplasms. These mutated genes encode signaling molecules (NRAS, KRAS, CBL, JAK2, FLT3 and several members of the Notch pathway), epigenetic regulators (TET2, ASXL1, EZH2, IDH1, IDH2,.) and splicing factors (SF3B1, SRSF2, ZRSF2). Mutations in the transcription regulators RUNX1, NPM1 and TP53 have also been reported in CMML. However, the role of these mutations in leukemogenesis is still unclear. CMML is also characterized by defects in monocyte to macrophage differentiation. These defects in monocyte differentiation can be attributed to the presence of immature dysplastic granulocytes that secrete high levels of alpha-defensins HNP1-3 that antagonize the purinergic receptor P2RY6 in CMML patients. These CD14-/CD15+/CD24+ immature granulocytes that belong to the same clone than the leukemic monocytes seem to have immunosuppressive properties ressembling those of the myeloid-derived suppressor cells (MDCS) described in solid tumours. Whether these immature granulocytes contribute to autoimmune manifestations or immunoescape and progression of CMML is a conendrum and remains to be determined.
  In this context, the proposed project aims at identifying news insights into the pathophysiology of CMML through a better definition of the phenotype and function of monocytes and immature granulocytes that characterize this pathology.


Eligibility: Inclusion Criteria:
  -  Patients newly diagnosed or undergoing treatment in the Clinical Hematology department of the participating establishments
  Exclusion Criteria:
  -  NA

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: Study of AG-120 and AG-881 in Subjects With Low Grade Glioma

Summary: Study to evaluate the suppression of 2-HG (2-hydroxyglutarate) in IDH-1 mutant gliomas in resected tumor tissue following pre-surgical treatment with AG-120 or AG-881.

Detailed description: A phase-1, multi-center study in recurrent non-enhancing gliomas with IDH1 R132H mutation for patients who require surgery. The purpose of this study is to evaluate the suppression of 2-HG by comparing the concentration of 2-HG in resected tumors from IDH1 mutant glioma subjects following AG-120 or AG-881 treatment with the 2-HG concentration in untreated, control tumors. The safety, tolerability, PK/PD, and anti tumor activity data from the study in subjects with recurrent non-enhancing Grade 2/3 LGG with an IDH1 R132H mutation for whom surgical resection is indicated will identify the recommended dose of AG-120 and AG-881 for future studies in glioma.

Eligibility: Inclusion Criteria:
  1. Be ≥18 years of age.
  2. Have histologically or cytologically confirmed recurrent Grade 2 or 3 LGG (oligodendroglioma or astrocytoma according to World Health Organization 2016 classification).
  3. Have documented IDH1 R132H gene mutation by local testing and known 1p19q or ATRX mutation status by local testing.
  4. Have central confirmation of primarily non-enhancing disease by MRI with less than or equal to 5 mm slice thickness and up to 1 mm interslice gap on either 2D T2 weighted image, 3D T2 weighted image, or FLAIR, with at least 1 non-enhancing tumor measuring 1×1×1 cm.
  5. Be candidates for clinical resection but for whom surgery is not urgently indicated (eg, for whom surgery within the next 2-4 months is appropriate).
  6. Have KPS of ≥60%
  7. Have expected survival of ≥12 months.
  Exclusion Criteria:
  1. Have received prior systemic anti-cancer therapy within 1 month of the first dose of AG-120 or AG-881 or have received an investigational agent <14 days prior to their first dose of AG-120 or AG-881. In addition, the first dose of AG-120 or AG-881 should not occur before a period of ≥5 half-lives of the investigational agent has elapsed.
  2. Have had radiation within 6 months of the first dose of AG-120 or AG-881. (Note: Prior biopsy or surgery is allowed.)
  3. Have received any prior treatment with an IDH inhibitor.
  4. Have received any prior treatment with bevacizumab (Avastin).

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: Screening of IDH1 and IDH2 Gene Mutations in Adult Acute Myeloid Leukemia for Possible Targeted Therapy

Summary: 1. To assess the incidence of IDH1 and IDH2 mutations in adult AML patients, and to explore their associations with the patients' clinical, cytogenetic, and molecular characteristics as well as with treatment response and outcome.
  2. To delineate the similarities and distinctions among mutations at IDH1-R132, IDH2-R140 and IDH2-R172 in AML, both clinically and molecularly (including cytogenetics, immunophenotyping, mutation co-occurrence patterns).
  3. The results can be references for future selection of targeted therapy (targeting IDH mutant proteins).

Detailed description: Isocitrate dehydrogenases (IDH) are enzymes that catalyze oxidative decarboxylation of isocitrate into alpha-ketoglutarate (α-KG). IDH1 and IDH2 mutations in AML give the enzymes neomorphic enzymatic activity to transform α-KG to D-2HG, an oncometabolite which acts as a competitive inhibitor of dioxygenases, and causes dysregulation of TET2 and histone demethylases, consequently leading to epigenetic reprogramming of a cell, blocking differentiation and contributing to a transformed phenotype, and leukemogenesis. Investigators plan to recruit 300 adult AML patients (newly diagnosed or relapsed). 10mL of peripheral blood or marrow blood will be obtained from routine practice blood/marrow sampling specimens (no extra venipuncture or bone marrow aspiration would be required) and sent for routine tests such as cytogenetics, immunophenotyping, and gene mutation analyses. IDH1 R132, IDH2 R140, and IDH2 R172 mutations will be screened by PCR followed by Sanger sequencing, as previously described.
  Investigators will first assess the incidence of IDH1 and IDH2 mutations in adult AML patients, and then explore their associations with the patients' clinical course, cytogenetic, and molecular characteristics as well as with treatment response and outcome. Investigators also seek to delineate the similarities and distinctions among IDH mutation variants at IDH1-R132, IDH2-R140 and IDH2-R172, both clinically and molecularly (including cytogenetics, immunophenotyping, mutation co-occurrence patterns).

Eligibility: Inclusion criteria:
  1. Patients ≥20 Years with Diagnosed Acute Myeloid Leukemia
  2. Willing to provide voluntary written informed consent before study related procedures
  Exclusion criteria:
  1. Not acute myeloid leukemia patients
  2. Patients <20 Years with Diagnosed Acute Myeloid Leukemia

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: Radiotherapy Concurrent With Apatinib in Advanced Soft Tissue and Bone Sarcomas of Head and Neck--RASS Study

Summary: This is a non-randomized, phase II, open label study of radiotherapy concurrent with Apatinib Mesylate after surgery in patients with advanced head and neck soft tissue and bone sarcomas. The primary purpose of this study is to evaluate the efficacy and safety of Apatinib Mesylate in patients with head and neck soft tissue and bone sarcomas.


Eligibility: Inclusion Criteria:
  1. Histologic diagnosis of head and neck soft tissue sarcoma (undifferentiated pleomorphic sarcoma, synovial sarcoma, alveolar soft part sarcoma, clear cell sarcoma, angiosarcoma, epithelioid hemangiosarcoma, solitary fibrous tumor and epithelioid sarcomas) or bone sarcoma (osteosarcoma/high grade bone sarcoma, Ewing sarcoma or dedifferentiated chondrosarcoma) confirmed by central pathology review.
  2. Gross total resection, with Invasive cancer seen on microscopic evaluation of the resection margin, or with gross tumor residual, or surgically unresectable and/or refuse surgery.
  3. Eastern Cooperative Oncology Group (ECOG) Performance Status of 0-1
  4. Adequate hepatic, renal, cardiac, and hematologic function.
  5. Patients must provide written informed consent prior to performance of study-specific procedures and must be willing to comply with treatment and follow-up.
  Exclusion Criteria:
  1. Evidence of distant metastasis
  2. Prior chemotherapy or anti-cancer biologic therapy for any type of cancer, or prior radiotherapy to the head and neck region
  3. Other previous cancer, except for in situ cervical cancer and cutaneous basal cell carcinoma
  4. Pregnant or breast-feeding females, or females and males of childbearing potential not taking adequate contraceptive measures
  5. Presence of an uncontrolled concomitant illness including, but not limited to, ongoing or active infection, symptomatic congestive heart failure, unstable angina pectoris, or cardiac arrhythmia
  6. Suffered from grade II or above myocardial ischemia or myocardial infarction, uncontrolled arrhythmias (including QT interval male ≥ 450 ms, female ≥ 470 ms). Grade III-IV cardiac insufficiency according to New York Heart Association (NYHA) criteria or echocardiography check: left ventricular ejection fraction (LVEF)<50%
  7. Patients who have had prior allergic reaction to Apatinib

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: Registry of Patients With MPNs in Taiwan

Summary: Myeloproliferative neoplasms (MPNs) are a group of clonal hematologic malignancies with great variation in reported patient life expectancy and are characterized by a relatively indolent course which can be complicated by thromboembolic events and transformation to acute myeloid leukemia (AML).
  The MPNs in the 2016 World Health Organization (WHO) classification of myeloid neoplasms consist of polycythemia vera (PV), essential thrombocythemia (ET), primary myelofibrosis (PMF) including prefibrotic/early stage and over fibrotic stage, chronic myeloid leukemia, other (rare) disorders such as chronic neutrophilic leukemia and chronic eosinophilic leukemia and MPN unclassifiable (MPN-U).
  The prevalence and genetic characteristics of patients with MPNs in Taiwan are still unknown. Molecular tests which are required for the diagnosis of MPNs are not available in many hospitals which hamper the accurate diagnosis and subtype classification of MPNs. Moreover, the information of current therapeutic strategy for MPNs in most medical centers in Taiwan is also not available. The purpose of this MPN registry is to collect clinical data, molecular characteristics, treatment details and response to therapy, occurrence of complications during the course, disease progression to secondary myelofibrosis from PV or ET and secondary AML (sAML) transformation as well as survival. The clinical and molecular data including the high molecular risk (HMR) genes will be examined and correlated with treatment outcomes in Taiwanese MPN patients.
  The Molecular Diagnostic Laboratory at Chang Gung Memorial Hospital-Linkou is a College of American Pathologists (CAP)-accredited lab which provides high quality of molecular genetic tests for hematologic malignancies. The three driver gene mutations are the major criteria for the diagnosis of MPN, the methodologies of mutational analyses have been well set up for the clinical use in this lab. In addition, this lab is also equipped with facilities for the detection of mutated genes which were recently identified as HRM category (presence of any of ASXL1, EZH2, SRSF2, IDH1 or IDH2), and mutations of other epigenetic regulators or splicing factors.


Eligibility: Inclusion Criteria:
  1. Male and female patients aged ≥ 20 years.
  2. Patient who had a confirmed diagnosis according to the 2016 revised WHO criteria with a Ph (-) MPN.
  Exclusion Criteria:
  1. Patients do not fulfill the diagnostic criteria of MPN by WHO 2016 classification.
  2. Patients unwilling to sign informed consent.

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: Study Comparing the Safety and Efficacy of IDP-120 Gel and IDP-120 Vehicle Gel in the Treatment of Acne Vulgaris

Summary: study designed to assess the safety, tolerability, and efficacy of IDP-120 Gel and IDP-120 Vehicle Gel

Detailed description: This is a multi-center, randomized, double-blind, vehicle-controlled, 12-week study designed to assess the safety, tolerability, and efficacy of IDP-120 Gel and IDP-120 Vehicle Gel at Weeks 2, 4, 8, and 12. To be eligible for the study subjects must be at least 9 years of age and have a clinical diagnosis of moderate to severe acne

Eligibility: Inclusion Criteria:
  1. Male or female at least 9 years of age and older;
  2. Written and verbal informed consent must be obtained. Subjects less than age of consent must sign an assent for the study and a parent or a legal guardian must sign the informed consent (if subject reaches age of consent during the study they should be re-consented at the next study visit);
  3. Subject must have a score of 3 (moderate) or 4 (severe) on the Evaluator's Global Severity Score (EGSS) assessment at the baseline visit;
  4. Subjects with facial acne inflammatory lesion (papules, pustules, and nodules) count no less than 20 but no more than 50;
  5. Subjects with facial acne non-inflammatory lesion (open and closed comedones) count no less than 25 but no more than 100;
  6. Subjects with two or fewer facial nodules
  Exclusion Criteria:
  1. Use of an investigational drug or device within 30 days of enrollment or participation in a research study concurrent with this study;
  2. Any dermatological conditions on the face that could interfere with clinical evaluations such as acne conglobata, acne fulminans, secondary acne, perioral dermatitis, clinically significant rosacea, gram-negative folliculitis, dermatitis, eczema;
  3. Any underlying disease(s) or some other dermatological condition of the face that requires the use of interfering topical or systemic therapy or makes evaluations and lesion count inconclusive;
  4. Subjects with a facial beard or mustache that could interfere with the study assessments;
  5. Subjects with more than two (2) facial nodules;
  6. Evidence or history of cosmetic-related acne

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: Molecular and Cellular Characterization of Skull Base Tumors

Summary: The purpose of the study is to analyze biological samples and genetic material for basic science research investigating the molecular and cellular characterization of skull base tumors.

Detailed description: The overall goal of this proposal is to determine new molecular and cellular features that define tumor subtypes that are clinically actionable, may drive important changes in patient management, and/or elucidate novel chemotherapeutic options. Skull base tumors are currently diagnosed based on histopathologic criteria, on which post-operative management is based. However, the investigators hypothesize that each tumor type (eg. chordoma or chondrosarcoma) will have molecular and/or cellular subcategories that will redefine how to categorize and diagnose patients, predict clinical outcome, and optimally design a patient-specific management strategy. In addition, we aim to catalogue changes that occur after treatment after surgical resection, chemotherapy, and/or radiation by comparing primary and recurrent tumors.

Eligibility: Inclusion Criteria:
  -  Diagnosis of a skull base tumor
  Exclusion Criteria:
  -  Insufficient tumor sample at time of resection

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: Synovial Chondrosarcoma: a Single Institution Experience

Summary: single institution cases series review of histological, radiological and clinical data

Detailed description: single institution cases series review of histological, radiological and clinical data. Investigators will retrieve from the archives of the Rizzoli institute all the cases with a histological diagnosis of synovial chondrosarcoma.

Eligibility: Inclusion Criteria:
  -  Male and female patients treated at Rizzoli Institute from 01 January 1982 to 31 December 2017
  -  Diagnosis of synovial chondrosarcoma
  -  Age ≥ 18 years
  -  Histological slides / formalin-fixed paraffin-embedded tissue tumor (FFPE) blocks from archive available to perform the histology analysis
  -  Written informed consent prior to any study-specific analysis and/or data collection
  Exclusion Criteria:
  -  Patients with histological diagnosis different from synovial chondrosarcoma

Relevance to patient case: definitely relevant