araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 49-year-old female with Gastrointestinal stromal tumor. Genetic variant: KIT Exon 9 (A502_Y503dup). Other conditions: None.

Clinical trial: Serum Caspase 3, Annexin a2 and Soluble Fas Levels and Endometriosis

Summary: The study population will comprise of 90 women age varying between 15-55 years, those are candidate for laparoscopic surgery due to definition of >4 cm endometrioma or any other benign ovarian cysts such as mature teratoma or simple serous cysts on ultrasound examination, chronic pelvic pain, infertility. The blood samples will be drawn for analysis of serum biomarkers.

Detailed description: The participants will be accepted for the study between 1st of August 2016 to 30th June 2017. 2 cc blood samples will be drawn from the antecubital vein for serum analysis of caspase 3, annexin a2 and soluble fas levels before the operations. The patients will divide into three groups. The group 1 will comprise of 30 patients with benign ovarian cysts such as mature teratoma or simple serous cysts on ultrasound examination. The group 2 will comprise of 30 patients with diagnosis of stage 1-2 endometriosis in guidance with the revised American Society for Reproductive Medicine classification. The group 3 will comprise of 30 patients with diagnosis of stage 3-4 endometriosis in guidance with the revised American Society for Reproductive Medicine classification. The blood samples will be kept in -80 C degree after centrifuge till at the end of the study.The relation between serum caspase 3, annexin a2 and soluble fas levels and severity of endometriosis will be analysed.

Eligibility: Inclusion Criteria:
  -  The women ages varying between 15-55 years, those are candidate for laparoscopic surgery due to definition of >4 cm endometrioma or any other benign ovarian cysts such as mature teratoma or simple serous cysts on ultrasound examination, chronic pelvic pain, infertility.
  Exclusion Criteria:
  -  The women with malignant diseases, chronic bowel disease, other defined cause of infertility.

Relevance to patient case: not relevant
Patient case: 49-year-old female with Gastrointestinal stromal tumor. Genetic variant: KIT Exon 9 (A502_Y503dup). Other conditions: None.

Clinical trial: Long Outcome of Endoscopic Submucosal Dissection for Small Gastrointestinal Stromal Tumors (<2cm)

Summary: Data are currently insufficient to guide the management of very small gastrointestinal stromal tumors（GISTs）（< 2 cm) discovered incidentally on endoscopy,this study is designed to collect the medical records of patients in different treatment group with long-term follow-up data,and attempts to evaluate the usefulness of regular endoscopic ultrasound（EUS）surveillance and the necessity,safety and feasibility of endoscopic submucosal dissection（ESD）for small GISTs,thus provide evidence for the revision of the guideline.

Detailed description: OBJECTION:to evaluate the usefulness of regular endoscopic ultrasound（EUS） surveillance and the necessity,safety and feasibility of endoscopic submucosal dissection（ESD） for small GISTs(<2cm),thus providing evidences for the revision of the guideline.
  OUTLINE:This is a randomized controlled trial. Eligible patients are divided into 2 group with 45 in each.The experimental group undergo ESD for GISTs,while the investigators do no treatment to the control group.Then,the 2 groups will be follow up for 5 years.All data are analysed with the Statistical Product and Service Solutions（SPSS）statistical software.

Eligibility: Inclusion Criteria:
  1. Male or female chinese patients of 18-70 years old.
  2. Patients with very small gastric GISTs (< 2 cm) with no high-risk EUS features.
  3. Patients voluntarily join this study with informed consents.
  Exclusion Criteria:
  1. Patients with the tumors involving the serosa layer or grow outside the lumen obviously that are not eligible for endoscopic treatment.
  2. Patients with distant metastasis on computed tomography(CT)scan.
  3. patients with an extremely poor general condition or a very short life expectancy.
  4. Patients presenting with severe gastrointestinal tract bleeding that require immediate surgery.

Relevance to patient case: not relevant
Patient case: 49-year-old female with Gastrointestinal stromal tumor. Genetic variant: KIT Exon 9 (A502_Y503dup). Other conditions: None.

Clinical trial: A Retrospective Pharmacokinetics and Pharmacogenomics Research of Imatinib in Gastrointestinal Stromal Tumor Treatment

Summary: For patients of GIST (Gastrointestinal Stromal Tumor), Imatinib has been widely used in GIST with KIT or PDGFRA sensitive mutations. From clinical points of view, individual differences often occur between different patients, leading diverse effect in ADR and drug effect. Meanwhile, the drug effect and adverse drug reaction was significantly influenced by the pharmacokinetic factors and pharmacodynamic and other factors. In this research, we try to establish a more sensitive method to detect sensitive mutations in plasma and discover the correlation between somatic and germline mutations, plasma trough concentration and drug effect, the association between ADME-associated SNP, Target/Receptor/Pathway-associated SNP, trough concentration and TKI adverse effect. Furthermore, in vivo and in vitro research is also crucial for rational explanation for these clinical phenomenon.

Detailed description: The plasma concentration of Imatinib were established. The ADME-associated SNPs included are CYP3A4, CYP3A4, CYP1A1, CYP2C9, CYP2C19, ABCB1, ABCG2, ABCC4, SLC22A1, SLCO1B3 and so on. The Target/Receptor/Pathway-associated SNP s included KIT, PDGFRA, PDGFRB, FLT1, FLT3, MAPK1, SHC1, CCL5, CXCL14 and so on. The somatic mutations included are KIT, PDGFRA, BRAF and so on.

Eligibility: Inclusion Criteria:
  -  The main patient entry criteria included: age≥ 18 years; histologically and cytologically proved GIST; Eastern cooperative oncology group performance status (ECOGPS)≤2; adequate hematological,renal,and hepatic functions.
  Exclusion Criteria:
  -  uncontrolled systemic disease,and other chemotherapy at the time of inclusion. The protocol was approved by the Ethical Committee of Cancer Center of Sun Yat-Sen University (CCSU), and written informed consent was obtained form each patient.

Relevance to patient case: not relevant
Patient case: 54-year-old male with Gastric cancer. Genetic variant: PIK3CA (E545K). Other conditions: Depression.

Clinical trial: The Effect of Stomach Acid on Foscarnet

Summary: To see if ranitidine, by reducing stomach acidity, can enhance the effectiveness of foscarnet, by making foscarnet more available to the body.
  Foscarnet is an antiviral compound. Laboratory studies have shown it to be active against HIV. However, only 12 - 22 percent of an oral foscarnet dose is absorbed by the body. Ranitidine suppresses gastric acid output, increasing gastric pH. Thus by increasing gastric pH (decreasing stomach acidity), less foscarnet is expected to be decomposed or broken down in the stomach. Thus, more foscarnet should be absorbed into the body.

Detailed description: Foscarnet is an antiviral compound. Laboratory studies have shown it to be active against HIV. However, only 12 - 22 percent of an oral foscarnet dose is absorbed by the body. Ranitidine suppresses gastric acid output, increasing gastric pH. Thus by increasing gastric pH (decreasing stomach acidity), less foscarnet is expected to be decomposed or broken down in the stomach. Thus, more foscarnet should be absorbed into the body.
  Six asymptomatic HIV-infected males, or those with limited symptoms of early AIDS-related complex ( ARC ), will receive one dose intravenously of ranitidine in distilled water and one dose of placebo (distilled water alone), followed in 1 hour by foscarnet in oral solution. The order of ranitidine and placebo is randomized and the two foscarnet doses are separated by at least 72 hours. A nasogastric pH probe is placed on each morning of drug administration to monitor gastric pH.

Eligibility: Inclusion Criteria
  Concurrent Medication:
  Allowed:
  -  Acetaminophen and sedatives.
  Patient must be able to give informed consent.
  Exclusion Criteria
  Patients with the following are excluded:
  -  Unintentional weight loss in excess of 10 pounds or 10 percent of usual body weight within 2 years prior to study.
  -  Unexplained temperature above 38 degrees Celsius on more than 5 consecutive days or on more than 10 days in any 30 days in 2 years prior to expected study entry.
  -  Unexplained diarrhea defined by two or more stools/day for at least 14 days during a 120-day interval.
  Prior Medication:
  Excluded within 1 week of entry into study:
  -  Probenecid, aspirin, or diuretics.

Relevance to patient case: not relevant
Patient case: 54-year-old male with Gastric cancer. Genetic variant: PIK3CA (E545K). Other conditions: Depression.

Clinical trial: Cryosurgery in Treating Patients With Liver Cancer or Liver Metastases

Summary: RATIONALE: Cryosurgery kills cancer cells by freezing them during surgery.
  PURPOSE: Phase I/II trial to study the effectiveness of cryosurgery in treating patients with unresectable primary liver cancer or liver metastases.

Detailed description: OBJECTIVES: I. Assess the safety and efficacy of liquid nitrogen necrosis of liver lesions using a commercially available intraoperative cryosurgical system, with placement of the cryoprobe and subsequent monitoring by high-resolution ultrasound. II. Use this technique on selected patients with surgically unresectable metastatic or primary liver cancer whose disease appears confined to the liver and who are potentially curable if all tumor in the liver can be destroyed. III. Quantitate the quality and duration of survival, identify recurrence of hepatic malignant disease, and identify any morbidity from the procedure.
  OUTLINE: Cryosurgery. Liquid nitrogen freezing of tumor using a cryoprobe placed and maintained under ultrasound guidance.
  PROJECTED ACCRUAL: 50 patients will be treated.

Eligibility: DISEASE CHARACTERISTICS: Biopsy-proven metastatic or primary malignant disease of the liver No extrahepatic regional or distant metastases No primary tumors commonly associated with local spread or metastases to other sites, e.g.: Gastric cancer Pancreatic cancer Breast cancer Lung cancer Liver lesions considered unresectable because of location in relation to major vascular structures or involvement of multiple hepatic segments Tumor extent and location such that cryosurgery expected to destroy all tumor and render patient disease-free Tumor volume no greater than 50% of total hepatic volume on CT No more than 12 lesions
  PATIENT CHARACTERISTICS: Age: Over 21 Other: Overall health permitting safe laparotomy Blood/body fluid analyses and imaging/exams for tumor measurement within 1 month prior to registration
  PRIOR CONCURRENT THERAPY: Prior liver resection, radiotherapy, or chemotherapy allowed

Relevance to patient case: not relevant
Patient case: 54-year-old male with Gastric cancer. Genetic variant: PIK3CA (E545K). Other conditions: Depression.

Clinical trial: High-Dose Chemotherapy in Treating Patients With Advanced Stomach Cancer

Summary: RATIONALE: Drugs used in chemotherapy use different ways to stop tumor cells from dividing so they stop growing or die. Combining more than one drug and giving higher doses may kill more tumor cells.
  PURPOSE: Randomized phase II trial to study the effectiveness of high-dose chemotherapy in treating patients with advanced stomach cancer.

Detailed description: OBJECTIVES: I. Determine the response rates in patients with advanced gastric cancer treated with high-dose fluorouracil (5-FU) with vs without high-dose leucovorin (CF) vs high-dose 5-FU/CF/cisplatin. II. Determine the toxic effects of these regimens in these patients. III. Assess the symptomatic improvement in these patients treated with these regimens.
  OUTLINE: This is a randomized, multicenter study. Patients are stratified according to participating center, WHO performance status (0 or 1 vs 2), and disease stage (metastatic vs locally advanced). Patients are randomized to 1 of 3 treatment arms. Arm I: Patients receive fluorouracil (5-FU) IV over 24 hours weekly for 6 weeks. Arm II: Patients receive leucovorin calcium (CF) IV over 2 hours followed by 5-FU IV over 24 hours weekly for 6 weeks. Arm III: Patients receive CF and 5-FU as in arm II and cisplatin IV over 1 hour on days 1, 15, and 29. Treatment repeats every 7 weeks for a maximum of 4 courses in the absence of unacceptable toxicity or disease progression. Patients are followed every 8 weeks.
  PROJECTED ACCRUAL: A total of 65-135 patients (21-45 per arm) will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS: Histologically confirmed gastric cancer that is either metastatic or locally advanced and inoperable Bidimensionally measurable disease No CNS metastasis
  PATIENT CHARACTERISTICS: Age: 75 and under Performance status: WHO 0-2 Life expectancy: At least 3 months Hematopoietic: Granulocyte count at least 2,000/mm3 Platelet count at least 100,000/mm3 Hepatic: Bilirubin no greater than 1.7 mg/dL Renal: Creatinine no greater than 1.3 mg/dL Creatinine clearance greater than 60 mL/min Cardiovascular: No myocardial infarction within past 12 months No coronary heart disease requiring drug therapy Congestive heart failure or arrhythmia treatable with standard medication allowed Other: No active infection No history of severe mental disorder No other malignancy within past 10 years except carcinoma in situ of the cervix or nonmelanoma skin cancer Not pregnant
  PRIOR CONCURRENT THERAPY: Biologic therapy: Not specified Chemotherapy: No prior chemotherapy Endocrine therapy: Not specified Radiotherapy: No prior radiotherapy Surgery: Not specified

Relevance to patient case: not relevant
Patient case: 54-year-old male with Gastric cancer. Genetic variant: PIK3CA (E545K). Other conditions: Depression.

Clinical trial: Study of Tadalafil for the Treatment of Diabetic Patients With Symptoms of Upset Stomach and Delayed Stomach Emptying

Summary: The purposes of this study are to determine whether an experimental drug known as tadalafil can reduce symptoms of dyspepsia (fullness after eating, inability to finish a regular meal, bloating, discomfort or pain in the upper abdomen, belching after meals, nausea, vomiting) in diabetic patients, and/or reduce the amount of time the stomach takes to empty the contents of a standard meal. The safety of tadalafil given once daily for 8 weeks in this population will also be studied.


Eligibility: Inclusion Criteria:
  -  Diagnosis of diabetes mellitus
  -  Delayed gastric emptying
  -  3 month minimum history of chronic upper abdominal discomfort
  -  Symptoms of dyspepsia (upset stomach)
  Exclusion Criteria:
  -  Major gastrointestinal surgery or medical conditions known to affect gastric motility
  -  Irritable Bowl Syndrome
  -  Medications known to affect gastric motility
  -  Angina treated with nitrates
  -  Uncontrolled diabetes mellitus and history of certain heart problems

Relevance to patient case: not relevant
Patient case: 54-year-old male with Gastric cancer. Genetic variant: PIK3CA (E545K). Other conditions: Depression.

Clinical trial: S-1 and Cisplatin Before Surgery in Treating Patients With Stage IV Gastric Cancer

Summary: RATIONALE: Drugs used in chemotherapy, such as S-1 and cisplatin, work in different ways to stop tumor cells from dividing so they stop growing or die. Combining more than one drug may kill more tumor cells. Giving combination chemotherapy before surgery may shrink the tumor so that it can be removed.
  PURPOSE: This phase II trial is studying how well giving S-1 together with cisplatin works in treating patients who are undergoing surgery for stage IV gastric cancer.

Detailed description: OBJECTIVES:
  Primary
  -  Determine the efficacy and feasibility of neoadjuvant chemotherapy comprising S-1 and cisplatin in patients with stage IV gastric adenocarcinoma.
  -  Determine the overall survival of patients treated with this regimen.
  Secondary
  -  Determine the time to progression and types of initial recurrence in patients treated with this regimen.
  -  Determine tumor response in patients treated with this regimen.
  -  Determine mortality and morbidity related to treatment in these patients.
  -  Determine the toxicity of this regimen in these patients.
  OUTLINE: This is a multicenter study.
  Patients receive oral S-1 on days 1-21 and cisplatin IV over 2 hours on day 8. Treatment repeats every 35 days for 2 courses in the absence of disease progression or unacceptable toxicity. Patients then undergo gastrectomy with lymphadenectomy. Patients resume oral S-1 after surgery.
  PROJECTED ACCRUAL: A total of 50 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically confirmed gastric adenocarcinoma
  -  Stage IV disease meeting 1 of the following staging criteria according to Japanese gastric cancer classification:
  -  T4, N2
  -  T4, N3
  -  P1, CY1
  -  CT scan and laparoscopic staging required
  PATIENT CHARACTERISTICS:
  Age
  -  20 and over
  Performance status
  -  ECOG 0-1
  Life expectancy
  -  Not specified
  Hematopoietic
  -  WBC ≥ 4,000/mm^3 AND < 12,000/mm^3
  -  Granulocyte count ≥ 2,000/mm^3
  -  Platelet count ≥ 100,000/mm^3
  -  Hemoglobin ≥ 9.0 g/dL
  Hepatic
  -  AST and ALT ≤ 2.5 times upper limit of normal
  -  Bilirubin ≤ 1.5 mg/dL
  Renal
  -  Creatinine clearance ≥ 50 mL/min
  Pulmonary
  -  PaO_2 ≥ 70 mm Hg on room air
  Other
  -  Able to swallow oral medication
  PRIOR CONCURRENT THERAPY:
  Biologic therapy
  -  Not specified
  Chemotherapy
  -  No prior chemotherapy for gastric cancer
  Endocrine therapy
  -  Not specified
  Radiotherapy
  -  No prior radiotherapy for gastric cancer
  Surgery
  -  No prior surgery for gastric cancer
  Other
  -  No other prior therapy for gastric cancer

Relevance to patient case: not relevant
Patient case: 54-year-old male with Gastric cancer. Genetic variant: PIK3CA (E545K). Other conditions: Depression.

Clinical trial: S-1 and Irinotecan in Treating Patients Who Are Undergoing Surgery for Locally Advanced Stomach Cancer

Summary: RATIONALE: Drugs used in chemotherapy, such as S-1 and irinotecan, work in different ways to stop the growth of tumor cells, either by killing the cells or by stopping them from dividing. Giving more than one drug (combination chemotherapy) may kill more tumor cells. Giving chemotherapy before surgery may shrink the tumor so that it can be completely removed.
  PURPOSE: This phase II trial is studying how well giving S-1 together with irinotecan works in treating patients who are undergoing surgery for locally advanced stomach cancer.

Detailed description: OBJECTIVES:
  Primary
  -  Determine the efficacy of neoadjuvant S-1 and irinotecan in patients with locally advanced gastric cancer.
  Secondary
  -  Determine the histological response in patients treated with this regimen.
  -  Determine the overall survival of patients treated with this regimen.
  -  Determine the progression-free survival of patients treated with this regimen.
  -  Determine the toxicity of this regimen in these patients.
  -  Determine postoperative morbidity in patients treated with this regimen.
  -  Determine the rate of potentially curative surgery in patients treated with this regimen.
  OUTLINE: This is a multicenter study.
  Patients receive oral S-1 on days 1-21 and irinotecan IV over 90 minutes on days 1 and 15. Treatment repeats every 28 days for 2 courses in the absence of disease progression or unacceptable toxicity. Patients then undergo gastrectomy with lymphadenectomy. After surgery, patients resume treatment with S-1 alone as before for 1 year.
  PROJECTED ACCRUAL: A total of 70 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically confirmed gastric adenocarcinoma
  -  Locally advanced disease
  -  Clinical stage T3-4, N0-3, M0 (according to the Japanese gastric cancer classification)
  -  Planning to undergo curative surgery after neoadjuvant chemotherapy
  PATIENT CHARACTERISTICS:
  Age
  -  20 to 75
  Performance status
  -  ECOG 0-1
  Life expectancy
  -  Not specified
  Hematopoietic
  -  WBC 4,000-12,000/mm^3
  -  Granulocyte count ≥ 2,000/mm^3
  -  Platelet count ≥ 100,000/mm^3
  -  Hemoglobin ≥ 9.0 g/dL
  Hepatic
  -  AST and ALT ≤ 100 U/L
  -  Bilirubin ≤ 1.5 mg/dL
  Renal
  -  Creatinine normal OR
  -  Creatinine clearance ≥ 50 mL/min
  Pulmonary
  -  PaO_2 > 60 mm Hg on room air
  Other
  -  Able to swallow oral medication
  PRIOR CONCURRENT THERAPY:
  Biologic therapy
  -  No prior biologic therapy for gastric cancer
  Chemotherapy
  -  No prior chemotherapy for gastric cancer
  Endocrine therapy
  -  No prior endocrine therapy for gastric cancer
  Radiotherapy
  -  No prior radiotherapy for gastric cancer
  Surgery
  -  No prior surgery for gastric cancer
  Other
  -  No other prior therapy for gastric cancer

Relevance to patient case: not relevant
Patient case: 54-year-old male with Gastric cancer. Genetic variant: PIK3CA (E545K). Other conditions: Depression.

Clinical trial: A Study of 5-FUci Versus CPT-11 Plus CDDP Versus S-1 Alone in Advanced Gastric Cancer

Summary: To investigate the superiority of a combination of irinotecan and cisplatin and the non-inferiority of S-1 compared to continuous infusion of 5-FU in advanced gastric cancer

Detailed description: From the results of our previous phase III study (JCOG9205), continuous infusion of 5-fluorouracil has remained to be a control arm of this study. This study investigates the superiority of a combination of irinotecan plus cisplatin and non-inferiority of S-1, a oral fluoropyrimidine, compared to continuous infusion of 5-fluorouracil at the point of overall survival, and the planned number of enrolled patients is 690 (230/arm).

Eligibility: Inclusion Criteria:
  1. unresectable or recurrent histologically proved gastric cancer
  2. adequate oral intake
  3. age 20 or older and 75 or younger
  4. Performance Status (ECOG):0, 1, 2
  5. measurable or unmeasurable lesions
  6. preserved organ functions
  7. no severe medical condition
  8. no prior chemotherapy for gastric cancer
  9. written informed consent
  Exclusion Criteria:
  1. patient with marked infection or inflammation
  2. patient with severe peritoneal metastasis
  3. patient with massive pleural effusion
  4. patient with metastasis to CNS
  5. patient with diarrhea 4 or more times per day
  6. patient severe medical condition
  7. patient with other concurrent malignancy affecting on survival or adverse events
  8. pregnant or nursing patient or with intent to bear baby
  9. patient evaluated to be inadequate by a attending doctor
  10. patient requiring nutritional support

Relevance to patient case: not relevant