araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 64-year-old male with bladder cancer; genetic feature: FGFR3 (S249C)

Clinical trial: Study to Evaluate the Effect of XmAb®5871 on Disease Activity in Patients With IgG4-Related Disease (RD)

Summary: The purpose of this Phase 2 study is to investigate the effect of XmAb5871 on IgG4-Related Disease (RD) activity


Eligibility: Inclusion Criteria:
  -  Active IgG4-RD
  -  Compatible pattern of organ involvement consistent with IgG4-RD that cannot be attributed to other causes
  -  Histopathologically-proven diagnosis of IgG4-RD
  -  Peripheral blood plasmablast count >900 cells/mL and/or elevated IgG4-RD levels during screening
  -  Able and willing to complete the entire study according to the study schedule
  -  Able and willing to provide written informed consent
  Exclusion Criteria:
  -  History or evidence of a clinically unstable/uncontrolled disorder, condition or disease other than IgG4-RD that, in the opinion of the Investigator would pose a risk to the patient safety or interfere with the study evaluation, procedures or completion
  -  Malignancy within 5 years (except successfully treated in situ cervical cancer, resected squamous cell or basal cell carcinoma of the skin, or prostate cancer with no recurrence ≥3 years following prostatectomy)
  -  Presence of recurrent or chronic infections, defined as ≥3 infections requiring antimicrobials over the past 6 months prior to screening
  -  Active infection requiring hospitalization or treatment with parenteral antimicrobials within the 60 days prior to randomization or oral antimicrobials within the 21 days prior to enrollment
  -  Patient is taking >40 mg of prednisone QD
  -  Prior use of rituximab (or other B cell depleting agents) within 6 months of enrollment. Prior use of any B cell depleting agent greater than 6 months from enrollment is allowed if the CD19+ B cell count is within the normal reference range during screening
  -  Use of any investigational agent within 5 half-lives of the agent (or 6 months if the half-life is unknown) prior to enrollment
  -  Immunosuppressive agent use within the three months prior to enrollment
  -  Has received live vaccines within 2 months of enrollment
  -  Patient is pregnant or breast feeding, or planning to become pregnant while enrolled in the study, up to end-of-study visit
  -  Unable or unwilling to partake in the follow-up assessments or required protocol procedures

Relevance to patient case: not relevant
Patient case: 64-year-old male with bladder cancer; genetic feature: FGFR3 (S249C)

Clinical trial: External Beam Radiotherapy for Muscle Invasive Bladder Cancer

Summary: In this phase 1 trial, the investigators will prospectively evaluate 3 different external beam radiotherapy (EBRT) schedules. In every schedule, the whole bladder will be treated to 40 Gray (Gy) in 20 fractions, 5 fractions/week, 4 weeks in total. Based on the summation of abnormalities seen on pre- (initial tumor region) and post transurethral resection zone of fibrosis Diffusion weighted-magnetic resonance imaging (MRI) images the tumor region is delineated and defined as a gross tumor volume (GTV). The GTV will be treated using a simultaneous integrated boost (SIB): without extending the 4-weeks treatment period, 3 different dose levels will be implemented in order to increase the biological equivalent dose (BED), as muscle invasive bladder cancer has been shown to be dose-sensitive.

Detailed description: 3 different dose levels will be implemented in order to increase the biological equivalent dose (BED), as muscle invasive bladder cancer has been shown to be dose-sensitive.
  -  Level 1: 57.6 Gray (Gy) (20 x 2.88 Gy, 5 fractions/week, 4 weeks); BED: 61 Gy.
  -  Level 2: 60 Gy (20 x 3.00 Gy, 5 fractions/week, 4 weeks); BED: 64 Gy
  -  Level 3: 62.4 Gy (20 x 3.12Gy, 5 fractions/week, 4 weeks); BED: 67 Gy. Fiducials will be implanted at the edges of the postoperative bed during the second transurethral resection of the bladder to improve visualization of the gross tumor volume (GTV) during external beam radiotherapy (EBRT) and consequently improve treatment delivery accuracy. In order to further improve the treatment accuracy, 5 planning Computed Tomographies and plans, with different bladder fillings will be made upfront in our study. During treatment the plan corresponding best with bladder filling at time of EBRT will be selected and delivered.

Eligibility: Inclusion Criteria:
  -  histological proven diagnosis of muscle invasive bladder cancer
  -  stage <T3b tumours with pathological lymph nodes after extended pelvic lymph node dissection
  -  World Health Organisation performance state 0-2
  -  signed informed consent
  Exclusion Criteria:
  -  contra-indication for Diffusion-Weighted-Magnetic resonance imaging

Relevance to patient case: not relevant
Patient case: 64-year-old male with bladder cancer; genetic feature: FGFR3 (S249C)

Clinical trial: Analysis of Oncogenes in Intrahepatic Cholangiocarcinoma or Mixed Hepatocellular-Cholangiocarcinoma in Tumor Tissue Samples

Summary: The primary objective of this study is to estimate the frequency of FGFR2 fusions in archived intrahepatic cholangiocarcinoma (iCCA) or mixed hepatocellular-cholangiocarcinoma (HCC-CCA) tumor samples

Detailed description: This is a non-interventional, observational study of archived human tissue samples; no surgical procedures will be required and no treatment will be provided as part of this study. Approximately 150 archived tissue samples obtained from patients with iCCA or mixed HCC-CCA will be analyzed for somatic alteration status and will include cholangiocarcinoma-specific FGFR2 fusion isoforms.

Eligibility: Inclusion Criteria:
  -  If required by law or local regulations (i.e., the sample is from an identifiable subject), signed written informed consent should be granted prior to use of the sample in the study
  -  ≥ 18 years of age
  -  Histologically or cytologically confirmed iCCA or mixed HCC-CCA, who are/were eligible for systemic therapy (samples collected prior to initiation of the systemic therapy may be submitted for testing)
  -  Have one or more formalin fixed and paraffin embedded blocks available. If blocks are not evaluable, 7-10 unstained, non-baked slides with 5-micron thick sections with at least 20% tumor tissue should be available. (Potential participants who are scheduled to undergo surgical treatment may agree to provide surplus of tissues not required for diagnosis and have to provide informed consent prior to the surgery.)
  Exclusion Criteria:
  -  Not applicable: Patients must meet all of the inclusion criteria.

Relevance to patient case: not relevant
Patient case: 64-year-old male with bladder cancer; genetic feature: FGFR3 (S249C)

Clinical trial: Pathophysiology Analysis of "Costello Syndrome" on Cellular Models

Summary: The objective is to collect skin biopsies rom patients with Costello syndrome to analyze the molecular mechanisms responsible for this syndrome caused by a mutation in the HRAS gene and the effects of this mutation on energy metabolism and mitochondrial physiology.


Eligibility: Inclusion Criteria:
  -  Children aged over 2 years and under 18
  -  Children with a Costello Syndrome or Syndrome Cardio-Facio-Cutaneous
  Exclusion Criteria:
  -  Previous history allergic to anesthetics

Relevance to patient case: not relevant
Patient case: 64-year-old male with bladder cancer; genetic feature: FGFR3 (S249C)

Clinical trial: Urinary Markers of Detrusor Overactivity in Spina Bifida Patients

Summary: The purpose of this study is to assess diagnostic performance of urinary markers of detrusor overactivity (Nerve Growth Factor (NGF), Brain-Derived Neurotrophic Factor (BDNF), adenosine triphosphate (ATP), Prostaglandine E2) in detected high pressure bladder un spina bifida patients.


Eligibility: Inclusion Criteria:
  Study arm:
  -  Spina bifida patient
  -  Seen consecutively in outpatient clinics
  -  Age > 18 years-old
  Control arm:
  -  Patients with multiple sclerosis or spinal cord injury or overactive bladder
  -  Seen consecutively in urodynamics
  -  with lower urinary tract symptoms
  -  Age > 18 years-old
  Exclusion Criteria:
  -  Positive urine culture
  -  History of urologic neoplasms
  -  History of interstitial cystitis

Relevance to patient case: not relevant
Patient case: 64-year-old male with bladder cancer; genetic feature: FGFR3 (S249C)

Clinical trial: A Study to Evaluate the Efficacy and Safety of Pemigatinib (INCB054828) in Subjects With Urothelial Carcinoma - (FIGHT-201)

Summary: The purpose of this study is to evaluate the overall response rate (ORR) of pemigatinib as a monotherapy in the treatment of metastatic or surgically unresectable urothelial carcinoma harboring FGF/FGFR alterations.


Eligibility: Inclusion Criteria:
  -  20 years and older in Japan
  -  Histologically documented metastatic or surgically unresectable urothelial carcinoma; may include primary site from urethra, ureters, upper tract, renal pelvis, and bladder.
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0-2.
  -  Life expectancy ≥ 12 weeks.
  -  Radiographically measurable per RECIST v1.1.
  -  Documented FGF/FGFR alteration and have either 1a) failed at least 1 previous treatment for their metastatic or surgically unresectable urothelial carcinoma (ie, chemotherapy, immunotherapy) or 1b) have not received chemotherapy due to poor ECOG status or 2) have insufficient renal function.
  Exclusion Criteria:
  -  Prior receipt of a selective FGFR inhibitor.
  -  Use of any potent CYP3A4 inhibitors or inducers within 14 days or 5 half-lives (whichever is shorter) before the first dose of study drug.
  -  Inability or unwillingness to swallow pemigatinib or significant gastrointestinal disorder(s) that could interfere with the absorption, metabolism, or excretion of pemigatinib.

Relevance to patient case: possibly relevant
Patient case: 64-year-old male with bladder cancer; genetic feature: FGFR3 (S249C)

Clinical trial: CART19 in Adult Patients With Minimal Residual Disease During Upfront Treatment for ALL

Summary: This is a single center, single arm, open-label phase 2 study to determine the efficacy of autologous T cells expressing CD19 chimeric antigen receptors expressing tandem TCRζ and 4-1BB (TCRζ/4-1BB) co-stimulatory domains (referred to as "CART19" cells) in adults with minimal residual disease (MRD) during upfront treatment for CD19+ acute lymphoblastic leukemia.


Eligibility: Inclusion Criteria:
  1. Patients with CD19+, B cell Acute Lymphoblastic Leukemia (B-ALL) who have 0.01%≤MRD<10% during upfront treatment
  2. Patients must be within 18 months of initial ALL diagnosis
  3. Age ≥18 years
  4. Adequate organ function defined as:
  1. Creatinine ≤ grade 2
  2. ALT/AST ≤3x upper limit of normal range for age
  3. Direct bilirubin ≤2.0 mg/dl
  4. Adequate pulmonary function defined as ≤ grade 2 dyspnea and ≤ grade 2 hypoxia
  5. Cardiac Left Ventricle Ejection Fraction (LVEF) ≥ 40% confirmed by ECHO/MUGA
  5. Patients with CNS3 disease will be eligible if CNS disease is responsive to therapy.
  6. Expression of CD19 on leukemic blasts demonstrated by flow cytometry or immunohistochemistry of bone marrow or peripheral blood
  7. Adequate performance status defined as ECOG Performance Status 0 or 1
  8. Provides written informed consent
  9. Subjects of reproductive potential must agree to use acceptable birth control methods, as described in protocol
  Exclusion Criteria:
  1. Active, uncontrolled infection
  2. Active hepatitis B or hepatitis C
  3. HIV Infection
  4. Class III/IV cardiovascular disability according to the New York Heart Association Classification (see Appendix 2)
  5. Subjects with clinically apparent arrhythmia or arrhythmias who are not stable on medical management within two weeks of enrollment.
  6. Pregnant or nursing (lactating) women
  7. Patients with a known history or prior diagnosis of optic neuritis or other immunologic or inflammatory disease affecting the central nervous system, and unrelated to leukemia or previous leukemia treatment.

Relevance to patient case: not relevant
Patient case: 64-year-old male with bladder cancer; genetic feature: FGFR3 (S249C)

Clinical trial: A Study of Comparing Effects of Thulium Laser en Bloc Resection and Electrical Transurethral Resection of the Non-muscle Invasive Bladder Cancer

Summary: This study is to verify the short-term efficacy and long-term prognosis of thulium laser resection compared with conventional transurethral resection of non-muscular invasive bladder cancer. Half of participants will receive thulium laser resection of bladder cancer, while the other half will receive electrical transurethral resection of bladder cancer.


Eligibility: Inclusion Criteria:
  1. Pathological or histological diagnosis of primary non-muscle invasive bladder urothelial carcinoma (TaTisT1);
  2. Imaging examinations showed the bladder muscle has not been affected, no lymph node metastasis or distant metastasis;
  3. Patients who agree to TURBT surgery, and will be effected to the postoperative follow-up treatment such as conventional infusion after the operation;
  4. Function of main organs (heart, liver, lung, kidney) should be normal, PS score 0-2;
  5. Bladder capacity≥ 200ml.
  Exclusion Criteria:
  1. Find distant metastasis ,infiltration of the surrounding organs or relapse before operation.Metastatic bladder cancer or other cancers involve the bladder;
  2. Received chemotherapy or BCG perfusion therapy in the nearly 3 months;
  3. Patients who can not tolerate the serious side effects during the bladder perfusion treatment process (bladder irritation and other symptoms);
  4. Patients during pregnancy ,critical care patients and patients who have other cases of surgical contraindications.Such as serious cardiovascular disease,coagulation abnormalities,non-transitional epithelial tumors( such as adenocarcinoma and squamous cell carcinoma),acute cystitis,can not be supine because of spinal deformity,untreated urethral stricture.

Relevance to patient case: not relevant
Patient case: 64-year-old male with bladder cancer; genetic feature: FGFR3 (S249C)

Clinical trial: A Study of Chimeric Antigen Receptor T Cells Combined With Interventional Therapy in Advanced Liver Malignancy

Summary: The purpose of this study is to collect the date on the safety and potential effectiveness of CART cells combined with interventional therapy in patients with advanced liver malignancy.

Detailed description: Designer T cells are prepared by PBMC which from patients or suitable donator by leukapheresis, and then activated and re-engineered to express chimeric antigen receptors (CARs). There are three options for CAR-targets: GPC3 for hepatocellular carcinoma; mesothelin for pancreatic cancer metastatic; CEA for colorectal cancer metastatic. Cells are expanded in culture and returned to the participant by vascular interventional therapy or by intra-tumor injection at the dose of （1.25~4）×107 CAR positive T cells/cm3 tumor bulk. The volume of cell products and the time of cell perfusion process lasted would depend on the ways of cell perfused.

Eligibility: Inclusion Criteria:
  -  tumor histological examination confirmed as GPC3/ mesothelin/CEA positive expression;
  -  persistent cancer after at least one prior standard of care chemotherapy, has no willing for surgery or cannot be suitable for surgery patients
  -  life expectancy greater than 6 months
  -  satisfactory organ and bone marrow function as defined by the following: (1) creatinine <1.5mg/dl; (2) cardiac ejection fraction of >55%; (3) hemoglobin>9g/dl, bilirubin 2.0×the institution normal upper limit
  -  without bleeding disorder or coagulation disorders
  -  Don't allergy to Radiocontrast agent
  -  birth control
  -  Adequate venous access for apheresis, and no other contraindications for leukapheresis
  -  Voluntary informed consent is given
  Exclusion Criteria:
  -  Pregnant or lactating women
  -  Concurrent use of systemic steroids. Recent or current use of inhaled steroids is not exclusionary
  -  patients in the situation of: (1) 30 days before apheresis is still in the period of other antitumor drug observation; (2) patient dont recuperate from earlier acute adverse influence brought by any treatments accepted before
  -  Four weeks before recruit accepted radiation therapy
  -  Previously treatment with any gene therapy products
  -  Feasibility assessment during screening demonstrates<30% transduction of target lymphocytes, or insufficient expansion (<5-fold) in response to CD3/CD28 costimulation
  -  Any serious, uncontrolled diseases (including, but not limit to, unstable angina pectoris, congestive heart failure, grade III or IV cardiac disease, serious arrhythmia, liver and kidney disorders or metabolic diseases, CNS diseases)
  -  Patient with severe acute hypersensitive reaction
  -  Taking part in other clinical trials
  -  Study leader considers not suitable for this tiral

Relevance to patient case: not relevant
Patient case: 64-year-old male with bladder cancer; genetic feature: FGFR3 (S249C)

Clinical trial: Urine-DNA Biomarkers in Detecting Bladder Cancer

Summary: DNA biomarkers in urine are important diagnostic and prognostic indicators for bladder cancer. Many genetic alterations have been identified in the urinary DNA. However, not all bladder tumors harbor mutations in the most commonly altered oncogenes. Thus, to reach satisfactory sensitivity and specificity a new diagnostic test should include multiple biomarkers. The investigators will conduct a prospective evaluation of a panel of mutations in urine-DNA test for the detection of urothelial bladder carcinoma in patients with gross hematuria for cystoscope.

Detailed description: Urinary DNA representative of the tumour genome provide a promising resource as a liquid biopsy for non-invasive genomic profiling of urothelial bladder cancers. Voided urine samples will be collected prior to cystoscopy. Cell free DNA and cellular DNA will both be extracted and analyzed. A blood sample will be taken. In patients with bladder wall findings suspicious of cancer, a bladder wall biopsy will be taken and submitted for histopathology examination, according to clinical standard practice. Next generation sequencing will be applied and hotspots mutations in DNA from urine, blood and tumor. Logistic regression was used to analyze the association between predictor variables and bladder cancer. The investigators will confirm a couple of common mutations occured in urine-DNA and blood-derived DNA simultaneously and verify the specificity and sensitivity of individual variance or mutation combinations to establish an predictive model with optimal robustness in diagnosis of bladder cancer. Moreover, external consistency test will be performed on subsequent patients collection.

Eligibility: Inclusion Criteria:
  -  patients with gross hematuria or other clinical sympton suspected of bladder cancer.
  -  male or female patients aged >= 18 years.
  -  available tumor tissue, urine and blood sample.
  -  signed informed consent form.
  Exclusion Criteria:
  -  prior diagnosis of cancer except bladder cancer
  -  age under 18 years
  -  individuals unwilling to sign the IRB-approved consent form
  -  comorbidities that would prohibit or make serial urine collection and cystoscopy examine difficult or impossible.

Relevance to patient case: not relevant
Patient case: 64-year-old male with bladder cancer; genetic feature: FGFR3 (S249C)

Clinical trial: Trial of SK-1404 for Nocturia Due to Nocturnal Polyuria in Japanese Subjects

Summary: The purpose of this trial is to demonstrate efficacy of SK-1404 against placebo for the treatment of subjects with nocturia due to nocturnal polyuria, during 4 weeks of treatment.


Eligibility: Inclusion Criteria:
  -  5 > nocturnal voids ≥2
  -  NPI >0.33
  Exclusion Criteria:
  -  Polydipsia
  -  Cardiac failure
  -  Syndrome of inappropriate antidiuretic hormone secretion
  -  Hyponatraemia
  -  Uncontrolled diabetes mellitus
  -  Uncontrolled hypertension
  -  Moderate or severe over-active bladder (OAB)
  -  Severe benign prostate hyperplasia (BPH)
  -  Sleep apnoea
  -  Interstitial cystitis
  -  Stress urinary incontinence
  -  Diabetes insipidus
  -  Complication or a history of urological cancer

Relevance to patient case: not relevant
Patient case: 64-year-old male with bladder cancer; genetic feature: FGFR3 (S249C)

Clinical trial: TracelT Hydrogel in Localizing Bladder Tumors in Patients Undergoing Radiation Therapy for Bladder Cancer

Summary: This pilot clinical trial studies how well TracelT hydrogel works in localizing bladder tumors in patients undergoing radiation therapy for bladder cancer. TracelT hydrogel marks the location of a bladder tumor and makes it more visible during imaging tests. Using TracelT hydrogel tissue marker may help doctors learn more about tumor location and altering radiation dosage for bladder cancer.

Detailed description: PRIMARY OBJECTIVES:
  I. To utilize the TraceIT hydrogel tissue marker in localizing bladder tumors during transurethral resection of bladder tumors (TURBT).
  II. To improve identification of gross tumor or tumor bed location in patients receiving chemoradiation treatment for bladder cancers.
  SECONDARY OBJECTIVES:
  I. To report adverse events surrounding the placement of the TraceIT tissue marker.
  II. To calculate the actual dose received by the bladder tumor bed, as delineated by the hydrogel.
  III. To compare the dosimetric impact to the tumor bed of daily patient alignment to the pelvic bones, versus alignment to the whole bladder, versus alignment to the hydrogel markers.
  IV. To calculate the amount of normal tissue radiation dose decrease achievable without losing tumor coverage, with better tumor targeting with hydrogel placement.
  OUTLINE:
  Patients undergo transurethral resection of bladder tumors and receive TracelT hydrogel via injection. Patients undergo standard of care radiation therapy within 8 weeks of TracelT hydrogel placement.

Eligibility: Inclusion Criteria:
  -  Histologically confirmed malignancy of the bladder
  -  No prior cystectomy
  -  Treatment plan for bladder must include at least 4 weeks of daily radiation treatment (most patients will receive chemotherapy concurrent with radiation, but this is not required for trial enrollment)
  -  Patient must undergo TraceIT hydrogel placement within 8 weeks prior to starting radiation therapy for bladder cancer
  -  Participants must have a complete history and physical examination within 60 days of study entry
  -  Participants must be able to provide informed consent for treatment and trial participation
  -  No restrictions on prior treatment to be eligible
  Exclusion Criteria:
  -  Prior cystectomy
  -  Unable to have TraceIT hydrogel placement < 8 weeks prior to beginning radiation treatment
  -  Treatment for metastatic bladder cancer

Relevance to patient case: not relevant