araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 64-year-old male with Cholangiocarcinoma. Genetic variant: IDH1 (R132H). Other conditions: Neuropathy.

Clinical trial: The Application of Soluble Triggering Receptor Expressed on Myeloid Cells-1 in Sepsis & Relevant Acute Kidney Injuries

Summary: Triggering receptor expressed on myeloid cells-1 is a member of the immunoglobulin superfamily of receptors that is specifically expressed on the surfaces of monocytes and neutrophils.TREM-1 expression is increased in infectious diseases and is associated with the release of soluble TREM-1 (sTREM-1).There has been demonstrated that the value of plasma sTREM-1 levels as an indicator of sepsis was superior, although other studies reported that the value of sTREM-1 for diagnosing sepsis was inferior.An increasing number of studies indicate that there are increased levels of sTREM-1 in body fluid samples for the following diseases and conditions: sepsis, pneumonia, pleural effusion, septic arthritis, meningitis, peritonitis, and uterine cavity infection.
  Inflammation is now believed to play a major role in the pathophysiology of AKI. It is hypothesized that the initial insult results in morphological and/or functional changes in vascular endothelial cells and/or in tubular epithelium in sepsis models. Then, leukocytes including neutrophils, macrophages, natural killer cells, and lymphocytes infiltrate into the injured kidneys and induce the generation of inflammatory mediators. Whether urine sTREM-1 could also be detected and its significance in sepsis and AKI has not been reported yet.
  The present study focused on the value of serum & urine sTREM-1 for sepsis identification, severity and prognosis assessments, and potential sepsis-related AKI. We also made comparisons between sTREM-1 and WBC counts, serum CRP, serum PCT, urine output,CC SCr, and BUN among sepsis patients.


Eligibility: Inclusion Criteria:
  1. Male and female aged 18 years old and over;
  2. clinically suspected infection;
  3. fulfilled at least two criteria of systemic inflammatory response syndrome (a) core temperature higher than 38 °C or lower than 36 °C (b)respiratory rate above 20/min, or PCO2 below 32 mmHg (c) pulse rate above 90/min, and (d) white blood cell count greater than 12,000/μl or lower than < 4,000/μl or less than 10% of bands.
  Exclusion Criteria:
  Those who fulfilled one below:
  -  neutropenia (≤ 500 neutrophils/mm3)
  -  HIV infection, and
  -  patients or their relatives refused

Relevance to patient case: not relevant
Patient case: 64-year-old male with Cholangiocarcinoma. Genetic variant: IDH1 (R132H). Other conditions: Neuropathy.

Clinical trial: Stereotactic Body Radiotherapy for Liver Tumors

Summary: This study will evaluate the local control rate as well as acute and late toxicity rates of stereotactic body radiotherapy for the treatment of liver metastases and unresectable primary liver tumors such as hepatocellular carcinoma and intrahepatic cholangiocarcinoma.

Detailed description: This study is a single site, non-randomized, prospective, phase IV trial.
  Composed of 4 patient groups:
  1. Oligometastases (1-3) with aggregate tumor diameter < 6 cm
  2. Metastases from neuroendocrine tumors with functional endocrine syndromes
  3. Unresectable hepatocellular carcinoma (HCC)
  4. Unresectable intrahepatic cholangiocarcinoma (IHCC) Data collected will include patient demographics, pathology data, tumor stage, SBRT dose fractionation scheme, dose received by adjacent critical normal tissues, tumor recurrence data, and acute and late toxicities. Follow up data will be collected during the patient's standard office visits. The anticipated duration of this study is 5 years.

Eligibility: Inclusion Criteria:
  -  Patient age >= 18 years
  -  Zubrod performance status of 0-3
  -  Oligometastases (1-3) with aggregate tumor diameter < 6 cm
  -  Metastases from neuroendocrine tumors with functional endocrine syndromes for symptom palliation
  -  Unresectable hepatocellular carcinoma (HCC)
  -  Unresectable intrahepatic cholangiocarcinoma (IHCC)
  -  Maximum tumor diameter < 6 cm
  -  Adequate liver function:
  Total bilirubin < 3 mg/dL Serum albumin > 2.5 g/dL Serum levels of liver enzymes < 3 times the upper limit of normal Normal PT and PTT unless patient is receiving anticoagulant medication
  - Signed study-specific consent form
  Exclusion Criteria:
  -  Maximum tumor diameter > 6 cm
  -  Prior radiotherapy to the liver
  -  Pregnant or lactating women, due to potential exposure of the fetus to RT and unknown effects of RT on lactating females
  -  Patients with psychiatric or addictive disorder that would preclude obtaining informed consent

Relevance to patient case: not relevant
Patient case: 64-year-old male with Cholangiocarcinoma. Genetic variant: IDH1 (R132H). Other conditions: Neuropathy.

Clinical trial: Proton Radiation Therapy for Gliomas

Summary: In this research study the investigators are looking at a type of radiation called proton radiation. Proton radiation has been shown to deliver virtually no radiation beyond the area of the tumor, sparing surrounding normal tissue from exposure. This may reduce side effects that patients would normally experience with conventional radiation therapy.
  In this research study the investigators are looking to determine if proton radiation with a reduced field size will be as effective in controlling tumor growth as photon therapy, while reducing the treatment-related side effects observed in patients with brain tumors.

Detailed description: Proton radiation will be delivered daily for approximately 6 weeks. Subjects will be assessed weekly for side effects. Each visit will take about 15 minutes.
  Subjects will have follow-up visits at 3, 6, 12, 24, 36, 48, 60, 72, and 84 months after their last proton radiation treatment. They will receive a physical exam, MRI, have blood tests (about 4 teaspoons) and answer questionnaires regarding medical history, quality of life, and emotional well-being. Subjects will also receive a neurocognitive exam annually.

Eligibility: Inclusion Criteria:
  -  Histologically confirmed low-grade gliomas OR Grade III anaplastic glioma with either or both IDH1 mutation or 1p/19q codeletion
  -  Subject must be indicated for radiation therapy
  -  Life expectancy greater than 5 years
  -  Willing to participate in rigorous neurocognitive evaluations at baseline and serially following treatment
  -  Able to speak and comprehend English
  -  Recovered from adverse events due to agents administered more than 4 weeks before entering study
  -  Able to undergo MRI scans
  Exclusion Criteria:
  -  Prior cranial radiation therapy
  -  Chemotherapy within 4 weeks prior to entering study
  -  Pregnant or breastfeeding
  -  Known brain metastases
  -  Baseline neurocognitive or emotional disorders
  -  Uncontrolled intercurrent illness
  -  History of a different malignancy unless disease-free for at least 5 years
  -  HIV positive on antiretroviral therapy

Relevance to patient case: not relevant
Patient case: 64-year-old male with Cholangiocarcinoma. Genetic variant: IDH1 (R132H). Other conditions: Neuropathy.

Clinical trial: Second-line Therapy of Unresectable Cholangiocarcinoma by RADIOEMBOLIZATION

Summary: Cholangiocarcinoma (CCK) is a rare tumor (2000 new cases/year in France) with very poor prognosis (overall survival < 3% at 5 years). Less than 20% of patients may benefit from curative surgical resection and most patients have medical treatment by palliative treatment by palliative chemotherapy. It is not standard first-line chemotherapy validated for unresectable CCK, but the best objective response rate (OR) and overall survival (OS) are observed with gemcitabine and platinum associations (OR 24 to 36% and OS between 9.5 to 15.4 months). In case of tumor progression ater this first line therapy, no treatment is currently being validated.
  RADIOEMBOLIZATION (RE) is a new, transarterial approach to radiation therapy using 90 Yttrium microspheres.
  In the patients with unresectable CCK , the first pilot studies showed interesting results with rates of OR 45 to 90% and a median OS of 14.9 mots and an acceptable safety.
  Study Hypothesis : RE could help achieve tumor stabilization in patients with intra-hepatic CCK in tumor progression after first-line therapy.

Detailed description: Extended description of the protocol, including information not already contained in other fields, such as comparison studied.
  It is a pilot study including 20 patients with unresectable intra-hepatic CCK in tumor progression after first-line therapy.
  Description of the protocol :
  1. Information and signed CONSENTMENT
  2. Preparatory phase : pre-treatment mesenteric angiography and technetium-99m macroaggregated albumin scans are performed to assess gastrointestinal flow and lung shunting.
  3. Therapeutic phase : intra-arterial administration of resin-based microspheres ( SIRSPHERES, SIRTEX). The RE can be performed in 2 sessions, especially if liver disease is bi-lobar.
  4. Follow up to J15,M1,M2,M4 and M6 : clinical examination and imaging evaluation ( scans and /or MRI)

Eligibility: Inclusion Criteria:
  -  Unresectable intra-hepatic CCK histologically proven
  -  Tumor progression documented on imaging evaluation ( CT or MRI) according to RECIST criteria version 1.1 after first-line therapy
  -  Performance status < 2 ; 4) Bilirubin < 36 micromol/l
  -  age > 18 years
  Exclusion Criteria:
  -  Extra-hepatic metastases
  -  Uncontrolled biliary obstruction
  -  Contra-indications to RE.

Relevance to patient case: not relevant
Patient case: 64-year-old male with Cholangiocarcinoma. Genetic variant: IDH1 (R132H). Other conditions: Neuropathy.

Clinical trial: Biomarkers in Blood Samples From Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Studying samples of blood from patients with cancer in the laboratory may help doctors identify and lean more about biomarkers related to cancer.
  PURPOSE: This research study is studying biomarkers in blood samples from patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  Primary
  -  To determine if serum 2-hydroxyglutarate (2HG) is only detected in acute myeloid leukemia (AML) patients with isocitrate dehydrogenase (IDH) mutations.
  Secondary
  -  To determine if the level of serum 2HG impacts leukemia-free survival (LFS).
  -  To determine if the level of serum 2HG impacts overall survival (OS).
  -  To determine if serum 2HG is undetectable at the time of documented clinical remission (CR) in IDH-mutated patients.
  OUTLINE: Archived serum samples are analyzed for 2-hydroxyglutarate expression by reverse-phase liquid chromatography coupled to mass spectrometry. Results are then compared with presence or absence of an IDH mutation, patients' clinical outcome, as well as age, sex, white blood cell count at diagnosis, platelet count, bone marrow blast percentage at diagnosis, circulating (serum) percentage at diagnosis, cytogenetic risk group, presence of FLT3, NPMN1, and/or TET2 mutations, specific IDH mutation, and randomization treatment group allocation.

Eligibility: DISEASE CHARACTERISTICS:
  -  Morphologically confirmed acute myeloid leukemia (AML)
  -  Newly diagnosed with AML
  -  Serum samples from patients enrolled on the ECOG-1900 clinical trial between 2002 and 2008
  -  Patients with or without isocitrate dehydrogenase (IDH) mutations
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Received 2 different doses of standard induction chemotherapy on ECOG-1900

Relevance to patient case: not relevant
Patient case: 64-year-old male with Cholangiocarcinoma. Genetic variant: IDH1 (R132H). Other conditions: Neuropathy.

Clinical trial: Biomarker Study of Chemotherapy Resistance and Outcomes in Samples From Older Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Studying blood samples from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer.
  PURPOSE: This research trial studies biomarkers related to chemotherapy resistance and outcomes in samples from older patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  -  Delineate the spectrum of genetic and epigenetic lesions occurring in elderly patients with acute myeloid leukemia (AML).
  -  Determine the biological functions perturbed by these lesions.
  -  Identify and validate lesions or pathways that are most highly associated with chemo-sensitive and chemo-refractory disease, and with adverse outcome in elderly AML.
  -  Identify potential classifiers and biomarker lesions that we can then evaluate prospectively in the E2906 trial which is about to begin enrollment.
  OUTLINE: DNA and RNA extracted from cell samples are analyzed for genetic and epigenetic expression by Agilent SureSelect sequencing, Illumina HiSeq2000 platform coding and sequencing, DNA methylation, and microarray assays. Results are then associated with patients' overall survival, progression-free survival, and complete response rate. Results are also analyzed assessing the prognostic relevance of known mutations and epigenetic alterations that have shown to have an impact on overall survival and response to therapy in younger patients with acute myeloid leukemia (AML) in E1900 including, but not limited to, FLT3, DNMT3A, IDH1, IDH2, TET2, ASXL1, WT1, and MLL, and 15-gene DNA methylation classifier, and with novel recurrent mutations identified by other AML-profiling efforts.

Eligibility: DISEASE CHARACTERISTICS:
  -  Subset of patients diagnosed with acute myeloid leukemia (AML) enrolled on E3999
  -  AML resistant or sensitive to chemotherapy
  -  Mononuclear cell samples available
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 64-year-old male with Cholangiocarcinoma. Genetic variant: IDH1 (R132H). Other conditions: Neuropathy.

Clinical trial: Study of Gemcitabine With TheraSphere® (Yttrium-90)in Patients With Hepatic Tumors of Pancreatobiliary Origin

Summary: Therasphere is a form of treatment that has been designed to selectively deliver radiation to the cancer within the patient's liver. This form of treatment has been used in a number of clinical trials and has been approved for use in the treatment of liver cancer.
  The investigators want to test the safety of using Gemcitabine (a chemotherapy drug) with TheraSphere (radioactive beads that are injected directly into the blood vessel supplying the tumor in the liver) in patients with advanced pancreatobiliary tumors such as pancreatic cancer or cholangiocarcinoma (bile duct tumors) involving the liver.

Detailed description: Patients with liver predominant cholangiocarcinoma or pancreatic cancer will be considered for the trial. The patients wre being treated in groups of thre patients. Each three patients receive a pre-specified dose of gemcitabine with full dose radioembolization using theraspheres. If no significant side effects are observed then three additional three patients will be treated with a higher dose of gemcitabine. The purpose to identify the highest dose of gemcitabine that can be safely combined with theraspheres.

Eligibility: Inclusion Criteria:
  1. Histologic or cytologic diagnosis of pancreatic cancer or cholangiocarcinoma
  2. Liver predominant disease defined as
  - Cholangiocarcinoma: liver disease should be unresectable
  - Limited extra hepatic metastasis defined as: i. Lung metastasis: 6 or less nodules with no nodule greater than 1.5 cm.
  ii. Abdominal lymph nodes iii. Pancreatic primary as long as the size is less than 4 cm in size iv. Bone metastasis
  3. No prior systemic therapy for advanced stage disease
  4. Measurable target tumors using standard imaging techniques
  5. Lung shunting less than 20%
  6. ECOG performance status 0-1 (See Appendix )
  7. Age ≥ 18 years
  8. No other investigational agents while on protocol
  9. Signed informed consent
  Exclusion Criteria:
  1. Inadequate hepatic function: AST/ALT > five times upper limit of normal, Bilirubin >2.0 mg/dl or history of hepatic encephalopathy
  2. Inadequate renal function Creatinine > 2.0 mg/dL
  3. Inadequate bone marrow function: platelets < 100,000/mL or absolute neutrophil count <1500/mL
  4. Contraindication to angiography
  5. Prior external beam radiotherapy to the upper abdomen
  6. Clinical evidence of peritoneal metastasis or ascites
  7. Patients with extensive tumor replacement in the liver defined as >50% of liver involved with tumor
  8. Any serious ongoing extra-hepatic disease such as infections.

Relevance to patient case: not relevant
Patient case: 64-year-old male with Cholangiocarcinoma. Genetic variant: IDH1 (R132H). Other conditions: Neuropathy.

Clinical trial: Phase 1 Study of Pazopanib With GSK1120212 in Advanced Solid Tumors, Enriched With Patients With Differentiated Thyroid Cancer, Soft-tissue Sarcoma, and Cholangiocarcinoma

Summary: The purpose of this study is to determine the safety and toxicity of the combination of pazopanib and GSK1120212 in patients with solid tumors and identify the maximum tolerated dose (MTD) of this combination for phase II study.


Eligibility: Inclusion Criteria:
  -  Dose escalation cohort for all solid tumors is closed to enrollment.
  -  Expansion cohorts: Soft-tissue sarcoma, cholangiocarcinoma, and differentiated thyroid cancer (DTC) cohorts are closed to enrollment. Patients in the DTC cohort must have disease that is able to be biopsied.
  -  Must have measurable disease.
  -  Tumor progression in the 6-month period prior to study drug initiation.
  -  DTC patients: must have radioiodine non-avid lesions, OR radioiodine avid lesions that have not responded to treatment with radioactive iodine.
  -  ECOG performance status less than or equal to 1.
  -  Life expectancy >3 months.
  -  Blood pressure <140 mmHg and <90 mmHg.
  -  LVEF is >= 50%
  -  Must be able to swallow pills.
  Exclusion Criteria:
  -  Chemotherapy, radiotherapy, other investigational therapy, or major surgery within 4 weeks.
  -  Sarcoma and cholangiocarcinoma ONLY: Prior VEGF-targeted TKI therapy.
  -  Pregnant or currently breastfeeding.
  -  Unresolved toxicity greater than grade 1.
  -  Evidence of active hepatitis or HIV.
  -  Significant cardiovascular disease.
  -  Taking medications known to be strong inducers or inhibitors of CYP3A enzymes.
  -  Clinically significant gastrointestinal abnormalities that may increase the risk for gastrointestinal bleeding.
  -  History of gastrointestinal condition causing malabsorption or obstruction.
  -  Cerebrovascular accident including transient ischemic attack (TIA), pulmonary embolism or untreated deep vein thrombosis (DVT) within past 6 months.
  -  Known endobronchial lesions and/or lesions infiltrating major pulmonary vessels that increase risk of pulmonary hemorrhage.
  -  Hemoptysis within 6 months of starting treatment.
  -  History of retinal vein occlusion (RVO) or central serous retinopathy (CSR), or predisposing factors to RVO or CSR as assessed by ophthalmic exam.
  -  Known brain mets that are not stable for at least 8 weeks prior to treatment, or patient is on glucocorticoids for brain mets.

Relevance to patient case: not relevant
Patient case: 64-year-old male with Cholangiocarcinoma. Genetic variant: IDH1 (R132H). Other conditions: Neuropathy.

Clinical trial: Comparison of Biliary Stenting Alone vs. Stenting With Photodynamic Therapy (PDT) During ERCP

Summary: This study entails retrospective and prospective review of data from a database protocol. Data gathered will be then analyzed for a set amount of patients. In this study, the investigators will compare biliary stenting vs. biliary stenting plus photodynamic therapy (PDT) and assess if PDT can improve quality of life and prolong survival.

Detailed description: Successful palliation of biliary obstruction is the main goal for reducing morbidity and mortality in patients with biliary disease and biliary obstruction related to cholangiocarcinoma. Surgical biliary bypass is unfortunately complicated by a 30-day postoperative mortality rate of between 7 and 24%. Moreover, because of recovery time the quality of life following surgery is only improved in a minority. At present endoscopic insertion of a plastic or metal stent is the method of choice to relieve obstructive jaundice without the high morbidity and mortality associated with surgery. But this relief is unfortunately temporary since stents tend to become obstructed and the fact that effective biliary drainage in the proximal lesion is challenging. Photodynamic Therapy (PDT) is a new therapeutic approach that specifically targets neoplastic cells. This therapy involves the intravenous administration of a photosensitizing agent followed by activation of the agent by illumination with non-thermal light of a specific wavelength, resulting in cell death from direct cytotoxicity and ischemic necrosis. Cytotoxicity is directly proportional to tissue oxygenation.
  A prospective, randomized and controlled trial study by Ortner et all confirmed the significant advantage of PDT with regard to relief of jaundice, quality of life, and survival. The improvement of survival in the randomized PDT group was so impressive that it was believed unethical to continue with randomization after the first 39 patients (20 and 19 in each group).Previously, the principal investigator conducted such a study (and also conducted Endoscopic Retrograde Cholangiopancreatography with PDT) at the University of Virginia, and would continue to conduct these procedures, as well as the study at WCMC.

Eligibility: Inclusion Criteria:
  -  Any patient who has undergone ERCP (Endoscopic Retrograde Cholangiopancreatography) and Biliary stenting with or without Photodynamic Therapy.
  -  Biliary disorder or obstruction due to Cholangiocarcinoma.
  -  Above 18 years of age.
  Exclusion Criteria:
  -  Any patient who has not undergone ERCP and biliary stenting.
  -  Not diagnosed with Cholangiocarcinoma.
  -  Below 18 years of age

Relevance to patient case: not relevant
Patient case: 64-year-old male with Cholangiocarcinoma. Genetic variant: IDH1 (R132H). Other conditions: Neuropathy.

Clinical trial: Long Time Follow up After HJ Following Iatrogenic Bile Duct Injuries

Summary: Introduction: Bile duct injury (BDI) after cholecystectomy remains a serious complication with major implications for patient outcome. For most major BDIs, the recommended method of repair is a hepaticojejunostomy (HJ). We conducted a retrospective review from 5 Danish hepatobiliary centres aiming to examine the perioperative and the long-term outcome after reconstructive HJ.


Eligibility: Inclusion Criteria:
  -  All patients with iatrogenic Bile duct injury (BDI) after cholecystectomy reconstructed with hepatojejunostomy/choledochojejunostomy.
  Exclusion Criteria:
  -  Patients with non-cholecystectomy-related BDI or with cholecystectomy-related BDI that had been definitively managed by other techniques.

Relevance to patient case: not relevant