araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Evaluation of NAATs for Detection of C. Trachomatis and N. Gonorrhoeae From Pharynx, Rectum, Glans & Urethra of MSM

Summary: Julius Schachter, PhD, from the Department of Laboratory Medicine at UCSF, and Jeffrey Klausner, MD, from the Department of Public Health, are conducting a study to evaluate a type of test (nucleic acid amplification test) for the detection of two sexually transmitted diseases, Chlamydia trachomatis and Neisseria gonorrhoeae, in men who have sex with men (MSM), using urine samples and swabs taken from the throat (pharynx), tip of penis (glans), and rectum. The use of nucleic acid amplification tests on these swabs is experimental, which means that the use of the tests for this purpose have not been approved by the Food & Drug Administration.

Detailed description: For all subjects enrolled in the study, the following clinical data information will be obtained: 1) reason for exam, 2) subject's signs and symptoms and 3) clinical assessment.
  For each subject enrolled in the study, three clinician-collected pharyngeal, four rectal swabs (three clinician-collected, 1 self-collected) specimens, one glans swab (self-collected) and a first catch urine specimen (approximately 25 ml) will be obtained. The collection order of the clinician collected swabs will be randomized.
  Three pharyngeal swabs will be tested for: 1) CT/NG NAAT (TMA) at DPH, 2) NG culture at DPH and 3) NAATs for CT/NG (TMA, SDA) and CT culture at UCSF. Four rectal swabs will be tested for: 1) CT/NG NAAT (TMA) at DPH, 2) NG culture at DPH and 3) NAATs for CT/NG on Clinician- and self-collected rectal swab (TMA, SDA) and CT culture at UCSF. Self-collected glans swab and the FCU will be tested by NAATs for CT/NG (TMA, SDA) at UCSF. All NAAT specimens collected in a universal NAAT transport medium. After specimen processing, samples will be frozen at -70 C for discrepant analysis.

Eligibility: Inclusion Criteria:
  -  A subject must be a man who has sex with men (MSM). Subjects must provide verbal consent, must be able to submit all required specimens and must not have urinated within 1 hr prior to providing a study urine specimen.
  Exclusion Criteria:
  -  Subjects are excluded if they do not have sex with men, refuse to give verbal consent, are unable to provide all required specimens and minimum specimen volume, have been on antibiotic therapy within the last 21 days, have urinated within 1 hr prior to submitting study specimens, and have already been evaluated as part of this trial. Subjects will be excluded if specimens are mishandled or inappropriately stored.

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Irinotecan, Gemcitabine and Radiation Therapy for Pancreatic Cancer

Summary: The study hypothesis is that chemoradiation based on 2 drugs will improve local control and long-term survival in patients with locally advanced pancreatic cancer. That is why gemcitabine and irinotecan are combined in an induction phase of 2 months and then this IrinoGem combination is given for 3 more cycles, in reduced doses,concurently with irradiation.


Eligibility: Inclusion Criteria:
  -  locally advanced pancreatic cancer
  -  performance status 0-2
  -  normal blood count and chemistry
  -  no previous chemotherapy or radiotherapy
  Exclusion Criteria:
  -  serious concurrent systemic disease

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Gemcitabine With Curcumin for Pancreatic Cancer

Summary: The study hypotheasis is that curcumin, a natural compound with a potent antiproliferative effect, can improve the efficacy of the standard chemotherapy gemcitabine in patients with advanced pancreatic cancer. That is why the patients are given a daily oral dose of 8 gr of curcumin along the chemotherapeutic protocol of weekly gemcitabine.


Eligibility: Inclusion Criteria:
  -  locally advanced or metastatic adenocarcinoma of the pancreas
  -  no prior chemotherapy
  -  performance status 0-2
  -  adequate hematology and chemistry
  Exclusion Criteria:
  -  serious concurrent medical condition

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Use of Celecoxib in Patients With Intraductal Papillary Mucinous Neoplasms (IPMNs)

Summary: The purpose of the study is to find out whether the drug celecoxib has beneficial effects on people with pre-cancerous lesions of the pancreas.

Detailed description: Efforts at finding a successful chemotherapy for pancreatic cancer have been disappointing. Some patients are at increased risk of pancreatic cancer or may have pre-malignant pancreatic lesions which predispose them to later pancreatic cancer development. In these individuals, chemopreventative measures may block future development of pancreatic cancer. Human tissue studies, cell culture and animal models of pancreatic cancer strongly suggests that cyclooxygenase-2 (COX-2) may be a successful target for chemoprevention. COX-2 is overexpressed in human pancreatic cancers. Elevated COX-2 expression correlates with progression of premalignant precursors of pancreatic cancer in development models of hamster pancreatic cancer. Human tissue studies confirm increases in COX-2 expression with progression of premalignant precursors called intraductal papillary mucinous neoplasms (IPMNs) and pancreatic intraepithelial neoplasms (PanINs). Moreover, COX-2 inhibitors appear to have chemopreventative efficacy in the PC-1 homograft model of hamster pancreatic cancer. Demographic studies have suggested COX-2 inhibitors may confer protection from pancreatic cancer. We propose to conduct a pilot/phase II trial to determine the chemopreventative effects of the COX-2 inhibitor celecoxib in patients with premalignant pancreatic lesions.
  Patients registered to the study will take celecoxib twice daily for 6-8 weeks prior to surgery (if patient decides to have surgery for his/her condition). If subject is not a surgical candidate or puts off surgical treatment, subject will take celecoxib for 6 months.

Eligibility: Inclusion Criteria:
  -  Clinical diagnosis of IPMN
  -  ECOG Performance status of 0, 1, or 2
  -  Adequate liver function, bilirubin < 1.5 times ULN, ALT or AST < 2.5 times ULN
  -  Adequate renal function: creatinine < 1.8
  -  Must be at least 18
  Exclusion Criteria:
  -  Use of COX-2 selective inhibitors within the last month
  -  More than occasional use of NSAIDS in last month (occasional use defined as up to twice weekly dosing)
  -  CA19-9 levels 1.5 times the ULN
  -  Active pancreatitis
  -  Taking sulphonylureas, fluconazole or lithium concomitantly

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Cancer Detection in Pancreatic Cysts

Summary: The purpose of this study is to assist with early and accurate diagnosis of cancer in pancreatic cysts based on the analysis of DNA obtained by endoscopic ultrasound guided fine needle aspiration

Detailed description: The study of pancreatic diseases is hindered by the organ's deep seated location and especially lack of symptoms during the early stages of disease development and progression e.g. pancreatic cancer. This is particularly true of pancreatic cysts, the variety and the malignant potential of which encompass a broad spectrum. The radiological features distinguishing a benign from a pre-malignant to a frankly malignant cyst in the pancreas are frequently underwhelming and have lead to the clinical practice of sampling all but the most obvious. The yield of the aspirate in turn is frequently not of a quality upon which a clinical decision can be based.
  Most would agree that the best approach for management of pancreatic cystic neoplasm lies in early diagnosis, ideally at a precancerous stage. The effectiveness and applicability of this study is the based on the ability of the cyst DNA analysis to stratify the patients at risk of developing pancreatic cancer based on the extent of accumulated mutational damage.

Eligibility: Inclusion Criteria:
  -  Previously scheduled for Endoscopic ULtrasound for evaluation of pancreatic cyst
  Exclusion Criteria:
  -  Any condition that would preclude safe performance of EUS/FNA

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Pilot Study Using Neoadj Chemo-Rad & EGFR-tyrosine Kinase Inhibitor for Potentially Resectable Pancreatic Cancer

Summary: To determine the feasibility and toxicity of neoadjuvant hypofractioned radiotherapy concurrently with weekly gemcitabine and an EGFR tyrosine-kinase inhibitor (OSI-774, Tarceva) in the treatment of patients with resectable pancreatic cancer.

Detailed description: To determine the feasibility and toxicity of neoadjuvant hypofractioned radiotherapy concurrently with weekly gemcitabine and an EGFR tyrosine-kinase inhibitor (OSI-774, Tarceva) in the treatment of patients with resectable pancreatic cancer.

Eligibility: Inclusion Criteria:
  -  pathologically confirmed adenocarcinoma of the pancreas
  -  resectable disease
  -  tumor </= 6cm diameter
  -  ECOG performance 0-1
  -  Organ system fxn: granulocytes (>/=1800/uL); plt ct >/=100K; bili</=2mg; liver enzymes <2.5ULN; crt </=1.5;
  -  Normal CXR
  -  Negative pregnancy test
  Exclusion Criteria:
  -  metastatic disease or peritoneal seeding based on cross-sectional imaging
  -  previous irradiation to the planned field
  -  prior chemotherapy or immunotherapy
  -  active infection
  -  active PUD

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Three New Methods for Diagnosing Pancreas Cancer

Summary: The purpose of this project is to evaluate and compare three new methods for diagnosis, staging, operability evaluation and treatment control of pancreas cancer. The investigators use contrast-enhanced ultrasound combined with the gastrointestinal hormones Secretin and Cholecystokinin, which triggers the enzyme production of pancreas. The hormones induce an increased metabolism and thus an increased blood flow through healthy pancreas tissue, however, not in tumor tissue. The investigators hope to be able to use this effect diagnostically. The patients included will also have a 64-slice-CT in order to evaluate, if an increased diagnostic safety can be reached compared to an older CT scanning method. All patients will also be examined for the tumor marker CA 19-9. Further, the investigators will examine if contrast-enhanced ultrasound can contribute with information in treatment control after either surgery or medical treatment.


Eligibility: Inclusion Criteria:
  -  suspicion of cancer of the pancreas

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: GEMOX: Oxaliplatin in Pancreatic Cancer

Summary: Primary objective:
  -  To evaluate overall response rate (based on RECIST criterion)
  Secondary objective:
  -  To evaluate time to progression, clinical benefit, quality of life and safety


Eligibility: Inclusion Criteria:
  -  Histologically proven adenocarcinoma of the pancreas
  -  Metastatic or locally advanced, non resectable disease(Non resectable disease will be determined by the investigators with clinical data)
  -  Uni-dimensionally measurable disease as defined by RECIST (primary or secondary tumors>2cm using conventional CT scan or ≥1cm with spiral CT scan)
  -  No previous chemo or radiotherapy, but postoperative radiotherapy as a adjuvant therapy for non-target lesion is permitted
  -  Karnofsky Performance Status (KPS) ≥60
  -  No known Central Nervous System metastases
  -  No sensory neuropathy at inclusion
  -  Biological and hematological evaluation < 2 weeks prior to treatment administration:
  -  Neutrophils ≥ 1500/ mm3
  -  Platelets ≥ 100,000/mm3
  -  Alkaline phosphatases< 5X ULN(upper Limits of Normal) and Bilirubin < 1.5X ULN
  -  SGOT,SGPT <2.5 X ULN if no liver metastasis
  -  SGOT,SGPT <5 X ULN if liver metastasis
  -  Creatinine < 1.5 X ULN
  -  Baseline imaging (CT scan or Magnetic Resonance Imaging) <3 weeks before treatment administration
  -  Men and women who are fertile must use a medically acceptable contraceptive throughout the treatment period and for 3 months following cessation of treatment with oxaliplatin. Subjects must be made aware, before entering this trial of the risk of becoming pregnant or in fathering children
  Exclusion Criteria:
  -  Corticotherapy except for anti-emetic purpose
  -  Pregnant or breast feeding women (Documentation of a negative pregnancy test must be available for premenopausal women with intact reproductive organs)
  -  Uncontrolled congestive heart failure or angina pectoris, or hypertension or arrhythmia
  -  Uncontrolled or persistent hypercalcemia
  -  History of significant neurologic or psychiatric disorders
  -  Vater ampulomas and biliary tract adenocarcinomas
  -  Other -non cured- malignancies
  The above information is not intended to contain all considerations relevant to a patient's potential participation in a clinical trial.

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Z-360 in Unresectable Advanced Pancreatic Cancer in Combination With Gemcitabine Treatment

Summary: To evaluate the safety of two doses of Z-360 with Gemcitabine administration for subjects with unresectable advanced pancreatic cancer in order to determine the optimal dosage for PhaseII study


Eligibility: Inclusion Criteria:
  -  Subjects with unresectable locally advanced or metastatic pancreatic cancer
  -  KPS > 70%
  -  Life expectancy of at least 3 months
  Exclusion Criteria:
  -  received previous chemotherapy for the current indication
  -  received previous radiotherapy for the current indication
  -  Currently receiving chemotherapy

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: EAP (Expanded Access Protocol) Of Lapatinib Combined With Capecitabine In Metastatic Breast Cancer

Summary: This study will provide pre-approval drug access to lapatinib, in combination with capecitabine, to patients whose breast cancer had progressed on other therapies


Eligibility: Inclusion criteria:
  -  May have received prior lapatinib in another trial. Previous capecitabine (as previous agent or non-lapatinib containing regimen) is also permitted.
  -  Prior treatment with hormonal therapy is allowed.
  -  Must have advanced or metastatic breast cancer with progression (as assessed by modified RECIST) after prior therapy, which must include all of the following: prior treatment with an anthracycline, a taxane, and trastuzumab alone or in combination with other therapy. Trastuzumab must have been administered in the adjuvant, or locally advanced or metastatic setting.
  -  Must have tumors that overexpress ErbB2 defined as +3 by IHC or FISH positive for ErbB2 gene amplification. The status of ErbB2 expression must be documented prior to study entry.
  -  Must be >/= 18 years of age
  -  Life expectancy of > 8 weeks
  -  Must have recovered from side effects of previous treatment
  -  Patients with CNS mets are eligible provided treatment with prohibited medications as listed in the protocol are not required
  -  Cardiac ejection fraction must be within the institutional range of normal as measured by ECHO. MUGA scans are allowed if ECHOs cannot be performed
  -  Able to swallow and retain oral medications
  -  Must have adequate hematologic, hepatic and renal function
  Exclusion criteria:
  -  Pregnant or lactating females
  -  Malabsorption syndrome, disease significantly affecting GI function, or resection of the stomach or bowel, or ulcerative colitis
  -  Concurrent disease or condition that would make the patient inappropriate for study participation
  -  Unresolved or unstable toxicity from prior administration of another investigational drug and/or prior cancer treatment
  -  Uncontrolled infection
  -  Active cardiac disease defined as history of uncontrolled or symptomatic angina; history of arrhythmias requiring medication, or clinically significant, with the exception of asymptomatic atrial fibrillation requiring anticoagulation; MI < 6 months from study entry; uncontrolled or symptomatic CHF; ejection fraction below the institutional normal limit; any other cardiac condition that would make this protocol unreasonably hazardous for the patient
  -  Receiving concurrent chemotherapy (other than capecitabine), radiation therapy, immunotherapy, biologic therapy or hormonal therapy for cancer. Concurrent therapy with bisphosphonates is allowed
  -  History of allergic reaction attributed to compounds of similar composition to lapatinib or any excipients
  -  History of allergic reactions attributed to compounds of similar chemical composition to capecitabine, fluorouracil or excipients
  -  Known DPD deficiency

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Genetic Analysis of Familial Melanoma

Summary: In collaboration with members of The International Melanoma Consortium, we propose to study melanoma in families lacking mutations in the cyclin-dependent kinase inhibitor 2 (CDKN2 or p16) gene, or the cyclin-dependant kinase 4 (CDK4). CDKN2 and CDK4 are both genes that encode presumed tumor suppressor genes, mutant forms of which are known to cause increased susceptibility to melanoma. The purpose of the present study then is to confirm the existence of and to identify additional gene(s) involved in heritable melanoma (cutaneous and ocular) and their precursor lesions (atypical nevi) by linkage analysis and gene mapping strategies. It is clear that the risk to develop atypical nevi and/or melanoma is strongly influenced by genetic and environmental factors (e.g. sun exposure). Characterization of such genes could provide important insights into the inheritance, pathogenesis, and treatment of this increasingly important disease.

Detailed description: In collaboration with members of The International Melanoma Genetics Consortium, we propose to study melanoma in families lacking mutations in the cyclin-dependent kinase inhibitor 2 (CDKN2A), or the cyclin-dependant kinase 4 (CDK4) genes. CDKN2 and CDK4 are both genes that encode presumed tumor suppressor genes, mutant forms of which are known to cause increased susceptibility to melanoma. The purpose of the present study then is to confirm the existence of and to identify additional gene(s) involved in heritable melanoma (cutaneous and ocular) and their precursor lesions (atypical nevi) by linkage analysis and gene mapping strategies. It is clear that the risk to develop atypical nevi and/or melanoma is strongly influenced by genetic and environmental factors (e.g. sun exposure). Characterization of such genes could provide important insights into the inheritance, pathogenesis, and treatment of this increasingly important disease.

Eligibility: -  INCLUSION CRITERIA:
  Inclusion into this study was restricted to families containing at least three CMM cases with DNA available for genotyping, and CDKN2A and CDK4 involvement and had been excluded.
  All families must be mutation negative for both CDKN2A and CDK4.
  This study will also include families with at least one case of ocular and two cases of other cutaneous melanomas, or at least 2 ocular melanomas (except where they occur in parent and child).
  EXCLUSION CRITERIA:
  Any family showing evidence of haplotype sharing in the 9p21-p22 region, where CDKN2A is located, was also excluded.

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Changes in Muscle Tissue in Patients With Pancreatic Cancer

Summary: RATIONALE: Measuring changes in muscle tissue in patients with cancer may help doctors predict how well patients will respond to treatment, and may help the study of cancer in the future.
  PURPOSE: This pilot study is evaluating changes in muscle tissue in patients with pancreatic cancer.

Detailed description: OBJECTIVES:
  -  Demonstrate a decrease/increase of fat-free mass (FFM) by 10% from baseline, based on tumor progression/regression, within each patient with inoperable locally advanced or metastatic pancreatic carcinoma.
  -  Determine the correlation between changes in FFM and 6-month survival.
  -  Confirm the frequency of lymphocytopenia in patients with inoperable locally advanced or metastatic pancreatic carcinoma.
  -  Demonstrate an interaction between pretreatment total lymphocyte count, treatment response, and 6-month survival in patients with inoperable locally advanced or metastatic pancreatic carcinoma.
  -  Collect adjuvant information, such as weight, body mass index, age, ECOG performance status, gait speed, concomitant medications, CA19-9, and total lymphocyte count, in these patients.
  OUTLINE: This is a pilot study.
  Patients will have weight, body mass index, age, ECOG performance status, gait speed, concomitant medications, CA19-9, and total lymphocyte count measured before start of cancer treatment of the patient's choosing.
  Patients will be re-assessed at approximately 2 months, 4 months, 6 months, and with any change in tumor burden.
  PROJECTED ACCRUAL: A total of 17 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Biopsy-proven inoperable locally advanced or metastatic pancreatic adenocarcinoma
  PATIENT CHARACTERISTICS:
  -  ECOG performance status 0-3
  -  Must be able to stand unassisted on a scale
  -  Must not have pacemaker or implanted defibrillator
  PRIOR CONCURRENT THERAPY:
  -  Prior chemotherapy or radiotherapy allowed
  -  No concurrent use of any of the following:
  -  Corticosteroids
  -  Steroids as anti-emetics associated with chemotherapy allowed
  -  Anabolic steroids
  -  Thalidomide
  -  Megesterol
  -  Eicosapentaenoic acid (EPA)
  -  Nutritional supplements without EPA allowed
  -  Juven
  -  Concurrent enrollment in other clinical trials allowed

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: AZD6244 vs. Capecitabine (Xeloda®) in Patients With Advanced or Metastatic Pancreatic Cancer, Who Have Failed First Line Gemcitabine Therapy

Summary: The purpose of this study is to assess the efficacy and safety of AZD6244 (ARRY-142886)versus capecitabine in patients with advanced or metastatic pancreatic cancer who have failed first-line therapy with gemcitabine. Following baseline assessments, a minimum of 64 patients in approximately 5-6 centers from the US will be treated with either AZD6244 or capecitabine. Treatment will be continued for as long as the patients receive clinical benefit. The status of all patients will be checked (whether they are still taking treatment or not) approximately 3 months after the last patient has entered the study.


Eligibility: Inclusion Criteria:
  -  Confirmed with pancreatic cancer
  -  Have failed first line gemcitabine therapy
  Exclusion Criteria:
  -  Previous therapy with EGFR inhibitor, MEK inhibitor or capecitabine.
  -  Any recent surgery, unhealed surgical incision or severe condition such as uncontrolled cardiac disease or chronic gastrointestinal diseases.

Relevance to patient case: not relevant