araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: Gene Therapy in Treating Patients With Cancer

Summary: RATIONALE: Inserting a gene that has been created in the laboratory into a person's white blood cells may make the body build an immune response to kill cancer cells.
  PURPOSE: Phase I trial to study the effectiveness of gene therapy in treating patients who have cancer that has not responded to previous therapy.

Detailed description: OBJECTIVES:
  -  Determine the safety and maximum tolerated dose of T cells activated in vitro and modified with chimeric anti-CEA immunoglobulin T cell receptors (Ig TCR) in patients with CEA expressing adenocarcinoma.
  -  Determine the pharmacokinetics of this regimen by the persistence of modified T cells in the blood of these patients.
  -  Evaluate the immunogenicity of murine sequences in chimeric anti-CEA Ig TCR.
  -  Assess immunologic parameters which correlate with the efficacy of this regimen in these patients.
  -  Evaluate, in a preliminary manner, the efficacy of this regimen in patients with CEA bearing tumors.
  OUTLINE: This is a dose escalation study.
  Peripheral blood lymphocytes (PBL) are harvested. PBL are activated in vitro and then modified with recombinant chimeric anti-CEA immunoglobulin T cell receptors (Ig TCR). Ig TCR modified T cells are reinfused over 30-60 minutes.
  The estimated maximum tolerated dose (MTD) is defined as the dose at which 2 of 6 patients experience unacceptable toxicity. If the MTD is not reached within the first cohort, a second cohort of 3 patients then receives 4 doses of modified T cells at a higher dose.
  Patients are followed every 2 weeks for 2 months.
  PROJECTED ACCRUAL: A total of 6-9 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically proven CEA expressing adenocarcinoma
  -  Serum CEA levels greater than 10 ng/mL
  -  Failed standard therapy
  -  Measurable disease
  PATIENT CHARACTERISTICS:
  Age:
  -  18 and over
  Performance status:
  -  0-2
  Life expectancy:
  -  Greater than 2 months
  Hematopoietic:
  -  Not specified
  Hepatic:
  -  No significant hepatic disease
  -  Bilirubin no greater than 3 mg/dL
  -  No active clinical disease caused by hepatitis B
  Renal:
  -  No significant renal disease
  -  Creatinine no greater than 3 mg/dL
  Cardiovascular:
  -  No significant cardiovascular disease
  Pulmonary:
  -  No significant pulmonary disease
  Other:
  -  Not pregnant
  -  Negative pregnancy test
  -  Fertile patients must use effective contraception
  -  No significant endocrine, rheumatologic, or allergic disease
  -  No active clinical disease caused by cytomegalovirus or tuberculosis
  -  HIV negative
  PRIOR CONCURRENT THERAPY:
  Biologic therapy:
  -  Not specified
  Chemotherapy:
  -  At least 4 weeks since prior chemotherapy
  Endocrine therapy:
  -  Not specified
  Radiotherapy:
  -  At least 4 weeks since prior radiotherapy
  Surgery:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: PTEN and IGFBP-3 Correlation in Ovarian Carcinoma Invasion

Summary: We have identified insulin-like growth factor binding protein (IGFBP)-3 as an invasion suppressor gene in ovarian endometrioid carcinoma, and showed association with lower cancer migration, invasion and metastasis. Recently, a novel model of ovarian EC formation from endometriosis was reported, and PTEN was found to be a major protein involved. Inactivation of PTEN has been reported in some ovarian EC tumors and methylation was suggested as one of the major epigenetic changes. This tumorigenesis model has lots of similarity to our established invasion model. Therefore, we plan to study the important of PTEN expression in ovarian EC and if inactivation of PTEN and IFGBP-3 is through methylation. Furthermore, by studying the signal transduction pathways using PTEN and IGFBP-3 transfection, we plan to study the mutual interaction between PTEN and IGFBP-3 on the suppression of tumor invasion in ovarian EC.

Detailed description: We have successfully established an ovarian cancer cell line (OVTW-59), which was derived from an ovarian endometrioid carcinoma (EC), and have also established an ovarian EC invasion model. By using cDNA microarray and quantitative reverse-transcriptase polymerase chain reaction, we identified insulin-like growth factor binding protein (IGFBP)-3 as an invasion suppressor gene, which were associated with lower cancer migration, invasion and metastasis. Clinically, lower IGFBP-3 was found associated with significantly higher tumor grade, advanced stage and poor survival in patients with EC tumors. Furthermore, we have proved IGFBP-3 expression correlated with lower Erk activation, but with no effect on the activation of Akt. All these two signal transduction proteins have crucial roles in cancer invasion. Recently, a novel model of ovarian EC formation from endometriosis was reported, and PTEN was found to be a major protein involved. Inactivation of PTEN has been reported in some ovarian EC tumors and methylation was suggested as one of the major epigenetic changes. This tumorigenesis model has lots of similarity to our established invasion model. Therefore, we plan to study the important of PTEN expression in ovarian EC and if inactivation of PTEN and IFGBP-3 is through methylation. Furthermore, by studying the signal transduction pathways using PTEN and IGFBP-3 transfection, we plan to study the mutual interaction between PTEN and IGFBP-3 on the suppression of tumor invasion in ovarian EC.

Eligibility: Inclusion Criteria:
  Clinical diagnosis of ovarian endometrioid carcinoma
  Exclusion Criteria:
  other types of ovarian epithelial carcinoma

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: Chart Review: Unresectable/Metastatic Cholangiocarcinoma Treated With Irinotecan, Capecitabine and Celecoxib

Summary: Chart Review on Patients with unresectable/metastatic cholangiocarcinoma treated in the UNM Cancer Center with a combination of irinotecan, capecitabine and celecoxib.

Detailed description: As above.

Eligibility: Inclusion Criteria:
  -  Patients with unresectable/metastatic cholangiocarcinoma treated in the UNM Cancer Center with a combination of irinotecan, capecitabine and celecoxib.
  Exclusion Criteria:
  -  Not specified.

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: Coregistration of 18F-FDG-PET and MRI in the Staging of Potentially Resectable Hilar Cholangiocarcinoma: a Pilot Study

Summary: To evaluate the feasibility and performance of coregistered 18F-FDG-PET/MRI in the staging of potentially respectable hilar cholangiocarcinoma.


Eligibility: Inclusion Criteria:
  -  Hilar cholangiocarcinoma assessed by conventional imaging modalities (triphasic CT scan of the liver) and thought to be potentially resectable.
  Exclusion Criteria:
  -  Biliary drain inserted.
  -  Contraindication for MRI.
  -  Pregnant or breast-feeding.
  -  Uncontrolled diabetes (over 9.7 mmol/L).

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: Everolimus in Treating Patients With Relapsed or Refractory Multiple Myeloma

Summary: RATIONALE: Everolimus may stop the growth of cancer cells by blocking some of the enzymes needed for cell growth and by blocking blood flow to the cancer.
  PURPOSE: This phase II trial is studying how well everolimus works in treating patients with relapsed or refractory multiple myeloma.

Detailed description: OBJECTIVES:
  Primary
  -  To assess the response rate in patients with relapsed or refractory multiple myeloma treated with everolimus.
  Secondary
  -  To evaluate the toxicity of everolimus in patients with multiple myeloma.
  -  To study the tumor cells and blood from patients entering this trial for laboratory correlates.
  OUTLINE: Patients receive oral everolimus once daily on days 1-28. Treatment repeats every 4 weeks for up to 12 courses in the absence of disease progression or unacceptable toxicity.
  Patients undergo bone marrow aspirate, biopsy, and blood sample collections periodically. Samples are assessed for the following: cyclin D1, phospho-AKT, phospho-p70 S6 kinase, and phospho-S6 by western blot; checkpoint regulators PTEN, p53, pRB, and p27 by immunoblotting; p53, Rb, p16, PTEN, p27, and cyclin D1 by DNA analysis; caspases 3 and 9 by immunoblotting and Annexin/PI by flow cytometry; unknown molecular markers by protein profiling; and microvessel density.
  After completion of study treatment, patients are followed every 3-6 months for up to 2 years.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of multiple myeloma, meeting 1 of the following criteria:
  -  Monoclonal protein in the serum of ≥ 1 g/dL
  -  Monoclonal light chain in the urine protein electrophoresis of ≥ 200 mg/24 hours
  -  Measurable light chains by free light chain assay of ≥ 10 mg/dL
  -  Measurable plasmacytoma
  -  Must have received prior therapy and have relapsed or refractory disease
  PATIENT CHARACTERISTICS:
  -  ECOG performance status 0-2
  -  Life expectancy ≥ 12 weeks
  -  ANC ≥ 1,000/mm³
  -  Platelet count ≥ 75,000/mm³
  -  Hemoglobin ≥ 8.0 g/dL
  -  Total bilirubin ≤ 2.0 mg/dL (if total bilirubin is elevated, direct bilirubin must be normal)
  -  AST ≤ 3 times upper limit of normal (ULN)
  -  Creatinine ≤ 1.5 times ULN
  -  Calcium < 11 mg/dL
  -  No uncontrolled infection
  -  Not pregnant or nursing
  -  Negative pregnancy test
  -  Fertile patients must use effective contraception
  -  No HIV positivity
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics
  -  At least 3 weeks since prior cytotoxic chemotherapy
  -  At least 2 weeks since prior biologic therapy or radiotherapy
  -  At least 2 weeks since prior corticosteroids
  -  Concurrent chronic corticosteroids allowed for treatment of disorders other than myeloma
  -  No other concurrent chemotherapy, immunotherapy, radiotherapy, or any ancillary therapy considered investigational

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: Gemcitabine/Oxaliplatin and Photodynamic Therapy in Cholangiocarcinoma

Summary: In patients with cholangiocarcinoma therapeutic effects have been reported for Gemcitabine/Oxaliplatin. Furthermore, photodynamic therapy (PDT) has significantly improved patients survival in two randomised trials. PDT induces tumor necrosis only in an area of few millimetres, while tumor parts which are located beyond this area remain untreated. An additive effect could result from PDT as a local therapy in combination with systemic chemotherapy.

Detailed description: Patients entered in the study receive a sequential therapy consisted of photodynamic therapy followed by systemic chemotherapy (Gemcitabine/Oxaliplatin) 4 weeks later. Systemic chemotherapy every 2 weeks is scheduled 9 times in each cycle. Thereafter, another cycle of PDT followed by chemotherapy is intended.

Eligibility: Inclusion Criteria:
  -  Histologic/cytologic verified cholangiocarcinoma or cholangiocarcinoma-typical findings in >= 2 diagnostic methods
  -  Bile duct stenoses which are technically successful treated with biliary drainage
  -  Irresectability/inoperability
  -  Karnofsky-Index >= 60%
  -  Age >= 18
  -  Written consent
  Before chemotherapy:
  -  Bilirubin <= 5 mg/dl
  -  GOT/GPT < 5x upper standard
  -  Creatinine < 2x upper standard
  -  Thrombocytes > 100 G/l
  -  Neutrophils > 2,00 G/l
  -  Haemoglobin > 9 g/dl
  -  No occurence of complications during endoscopic procedures (abscess, bilioma, cholecystitis, cholangitis, pancreatitis, biliary leakage)
  Exclusion Criteria:
  -  Implantation of a metal stent in the bile duct
  -  Previous PDT or chemotherapy
  -  Neoplasia
  -  Porphyria
  -  Pregnant or breastfeeding women
  -  Women of childbearing age and potent men who are not using highly effective contraceptives

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: Efficacy and Cost Analysis of Plastic Stent Compare to Metallic Stent in Hilar Cholangiocarcinoma

Summary: The purpose of this study is to compare the adequacy of unilateral endoscopic biliary drainage using metallic stent with plastic stent in unresectable, complex, hilar, cholangiocarcinoma and cost analysis.

Detailed description: There are two types of biliary stents: 1) the plastic stent made from polyethylene or polytetrafluoroethylene; and, 2) the metal stent braided in the form of a tubular mesh from surgical-grade stainless steel alloy and designed to expand to a maximum diameter of 10 mm. The main drawback of the plastic stent is the relatively high occlusion rate, but its advantage is the lower cost. The use of a metal stent for hilar tumor has many theoretical advantages: 1) the flexible open-mesh design should allow drainage of secondary duct branches; and, 2) its larger diameter may provide better drainage and longer patency (~3-9 months).
  Whether one type of stent is superior in terms of adequacy of drainage or cost-effectiveness remains undefined. Therefore, we would conduct this study to assess the efficacy of drainage of endoscopically-inserted, unilateral, plastic stents vs. metallic stents in unresectable, complex, hilar cholangiocarcinoma patients.

Eligibility: Inclusion Criteria:
  -  Unresectable complex hilar cholangiocarcinoma which diagnosis and staging based on computed tomography(CT) or magnetic resonance cholangiopancreatography (MRCP)
  Exclusion Criteria:
  -  Patients with ASA 4 or 5
  -  Patients with liver failure.
  -  Patients unable to comply with follow-up

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: Surgical Treatment of Hilar Cholangiocarcinoma: Minor or Major Liver Resection?

Summary: The investigators conducted a prospective study to determine the safety and efficacy of minor and major hepatectomy selected by predetermined criteria in 138 patients with hilar cholangiocarcinoma. In selected patients, minor liver resection was a good treatment.

Detailed description: Objective: To determine the safety and efficacy of minor and major hepatectomy selected by predetermined criteria in patients with hilar cholangiocarcinoma (HC).
  Summary Background Data: For HC treated with hepatectomy, the extent of liver resection remains controversial despite extensive studies.
  Methods: From January 2000 to December 2007, we prospectively studied patients who received surgical treatment for HC. Of the 187 patients who were surgically treated, 138 (73.8%) underwent resection with a curative intent. Minor hepatectomy was carried out in 93 patients who had Bismuth-Corlette types I, II and III HC without hepatic artery/portal vein invasion; and major hepatectomy in 45 patients who had type III HC with hepatic artery/portal vein invasion, or type IV HC.

Eligibility: Inclusion Criteria:
  -  Criteria for resectability were absence of peritoneal or liver metastases, tumor extension to beyond secondary biliary branches bilaterally, tumor extension to secondary portal venous branches bilaterally
  Exclusion Criteria:
  -  not in accordance with the above criteria

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: Molecular Features Predicting Response/Resistance to Trastuzumab in Metastatic Breast Cancer Patients

Summary: Aim of the study is to assess the impact on response to Herceptin-based therapy in patients with advanced breast cancer. Tumor specimens from primary breast cancer will be analized for several biological factors potentially involved in Herceptin sensitivity.
  Tests that will be performed include: FISH analyses of EGFR, HER-2, HER-3, C-MYC, PTEN, MET, IGFR-1. Immunofluorecence of P95HER2. Mutation analyses of EGFR, HER-2, MET, C-MYC, PTEN, KRAS, PIK3CA, IGFR-1. Immunohistochemistry of the same biomarkers.


Eligibility: Inclusion Criteria:
  -  Hystological diagnosis of breast cancer
  -  Availability of tumor tissue
  -  Availability to assess the response to Trastuzumab according to RECIST criteria
  -  Availability of clinical data
  Exclusion Criteria:
  -  Unavailability of tumor tissue
  -  Impossibility to assess the response to Trastuzumab according to RECIST criteria

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: Safety Study of XL765 (SAR245409) in Combination With Erlotinib in Adults With Solid Tumors

Summary: The purpose of this study is to evaluate the safety and tolerability of XL765 in combination with erlotinib (Tarceva®) in subjects with solid tumors. XL765 is a new chemical entity that inhibits the kinases PI3K and mTOR. In preclinical studies, inactivation of PI3K has been shown to inhibit growth and induce apoptosis (programmed cell death) in tumor cells, whereas inactivation of mTOR has been shown to inhibit the growth of tumor cells. Erlotinib is an orally administered inhibitor of EGFR (also known as HER1) tyrosine kinase. It was approved by the FDA as a single agent for the treatment of patients with locally advanced or metastatic non-small-cell lung cancer (NSCLC) after failure of at least one prior chemotherapy regimen and in combination with gemcitabine for first line treatment of patients with locally advanced, unresectable or metastatic pancreatic cancer.


Eligibility: Inclusion Criteria:
  -  Confirmed diagnosis of:
  -  Advanced solid tumor that is no longer responding to therapies OR
  -  Advanced or metastatic NSCLC that has previously been treated with erlotinib or gefitinib
  -  ECOG Performance Status 0-1
  -  Adequate organ and bone arrow function as defined by hematological and serum chemistry limits
  -  At least 18 years old
  -  Both men and women must practice adequate contraception
  -  Informed consent
  Exclusion Criteria:
  -  Restriction of some therapies/medications within specific timeframes prior to enrollment and during the study including prior therapy with PI3K, cytotoxic chemotherapy, biologic agents, nitrosoureas or mitomycin C, small-molecule kinase inhibitors, non-cytotoxic hormonal agents
  -  Erlotinib intolerant
  -  Taking oral corticosteroids chronically or > 1 mg/day warfarin
  -  Not recovered from the toxic effects of prior therapy
  -  History of diabetes mellitus and an HgbA1c > 7%
  -  Uncontrolled intercurrent illness
  -  Pregnant or breastfeeding
  -  Congestive heart failure, unstable angina, or a myocardial infarction within 3 months of entering the study.
  -  HIV positive
  -  Diagnosis of another malignancy may exclude subject from study

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: DNA Analysis of Tumor Tissue Samples From Patients With Human Papilloma Virus-Associated Cancer of the Oropharynx

Summary: RATIONALE: Studying samples of tumor tissue in the laboratory from patients with cancer may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer.
  PURPOSE: This laboratory study is looking at the DNA in tumor tissue samples from patients with human papilloma virus-associated cancer of the oropharynx.

Detailed description: OBJECTIVES:
  -  Analyze PIK3CA expression and mutation and p110α amplification and expression in tumor tissue samples from patients with human papilloma virus positive (HPV+) and human papilloma virus negative (HPV-) squamous cell carcinoma (SCC) of the oropharynx.
  -  Determine proliferation and survival after PI3K inhibition in HPV(+) and HPV(-) oropharyngeal SCC cell lines and in HPV E6 and E7 expressing cells.
  -  Determine proliferation and survival after PI3K inhibition in short-term cultures of tumor tissue samples from patients with HPV(+) and HPV(-) primary SCC of the oropharynx.
  OUTLINE: Previously collected tumor tissue samples are analyzed for HPV DNA by PCR amplification and direct sequencing of PCR products; expression of E6 protein and relative expression of PIK3CA by qRT-PCR; amplification of PIK3CA by Southern blotting; mutation of PIK3CA; expression of p110α, phospho-AKT, total AKT, and FOXO1 by polyacrylamide gel electrophoresis (PAGE) and immunoblotting; and the effect of PI3K inhibition on cell cycle and apoptosis by flow cytometry. Pharmacological studies are performed on oropharyngeal squamous cell carcinoma cell lines and short-term cultures and HPV E6 and E7 expressing cells using LY 294002 in vitro to analyze response to PI3K inhibition. Results of response to PI3K inhibition will be correlated with HPV status, PIK3CA expression, amplification, and mutation, and p110α expression.
  PROJECTED ACCRUAL: A total of 20 HPV(+) and 20 HPV(-) tumor tissue specimens from patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Undergoing operative procedures for biopsy and/or resection of squamous cell carcinoma (SCC) of the oropharynx
  -  Tumor tissue sample available from the Head and Neck Tissue Repository and Clinical Database of Vanderbilt University
  -  No tumors with human papilloma virus (HPV) DNA sequences but no expression of E6
  PATIENT CHARACTERISTICS:
  -  See Disease Characteristics
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: Photodynamic Therapy (PDT) Trial for Palliation of Cholangiocarcinoma

Summary: This research study is a phase III double arm, multicenter, randomized controlled clinical trial comparing endoscopic retrograde cholangiopancreatography (ERCP) and stenting plus photodynamic therapy (PDT) versus ERCP with stenting alone in adult patients with unresectable cholangiocarcinoma.
  The study objectives are to investigate the efficacy of photodynamic therapy (PDT) in increasing the survival time of patients with unresectable cholangiocarcinoma and to assess the effect of PDT on both cholestasis and health-related quality of life (HRQoL).

Detailed description: The study objectives are to investigate the efficacy of photodynamic therapy (PDT) in increasing the survival time of patients with unresectable cholangiocarcinoma and to assess the effect of PDT on both cholestasis and health-related quality of life (HRQoL).

Eligibility: Inclusion Criteria:
  -  Patient is age 18 years or older
  -  Patient is diagnosed with non-resectable cholangiocarcinoma, as determined by CT within 30 days of enrollment and CT shows Bismuth Tumor Stage as: IIIa, IIIb, IV (Bismuth tumor stage I and II are not eligible to participate)
  -  Patients must have adequate organ and marrow function as defined below:
  -  Patient's INR ≤ 2 within 30 days of treatment
  -  Patient's platelets > 50,000/cmm within 30 days of treatment
  -  Patient's Absolute Neutrophil Count (ANC) > 1,500/cmm within 30 days of treatment
  -  Patient's creatinine ≤ 3 mg/dL within 30 days of treatment
  -  Patient has the ability to understand and the willingness to comply with the study procedures and provide written informed consent to participate in the study
  Exclusion Criteria:
  -  Patient was diagnosed with cholangiocarcinoma more than 3 months ago
  -  Patient has any metastatic disease
  -  Patient has acute porphyria
  -  Subjects exhibiting neurologic or cutaneous symptoms will undergo urinary delta-aminolevulinic acid and porphobilinogen dosage tests to determine severity.
  -  Patient is pregnant (Women of child bearing age must have a negative pregnancy test prior to registration and must agree to use adequate contraception during study therapy)
  -  Patient has a concurrent non solid malignancy

Relevance to patient case: not relevant