araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 35-year-old female with Colorectal cancer. Genetic variant: FGFR1 Amplification. Other conditions: None.

Clinical trial: Changes in Stem Cells of the Colon in Response to Increased Risk of Colorectal Cancer

Summary: Colorectal cancer is a common disease worldwide. Increasing evidence is demonstrating that colorectal cancers arise from 'cancer stem cells.' Stem cells in the colon reside at the bottom of thousands of microscopic crypts throughout the wall of the colon. They create all the cells lining the bowel wall. These cells are created in the base of the crypt and ascend to the top acquiring the characteristics of mature cells of the bowel wall as they ascend.
  It is now thought that colorectal cancer cells arise from stem cells where the genetic material regulating growth and division of the stem cell has become defective. This leads to unregulated production of cells which in turn have defective genetic information and cancer formation.
  Prior studies have demonstrated that the earliest changes before a cancer develops are changes in cellular proliferation. Now that reliable markers to identify stem cells have been found, the researchers aim to investigate stem cell numbers and changes in distribution in those at normal risk of colorectal cancer and those at higher risk. The researchers hypothesise that changes in cellular proliferation at the top of the crypt in individuals at higher risk of colorectal cancer are due to a change in the number of stem cells in the crypt base.


Eligibility: Inclusion Criteria:
  -  Referred for endoscopy at participating centre
  Exclusion Criteria:
  -  Age <16 or >85
  -  Familial polyposis syndrome
  -  Lynch syndrome
  -  Known colorectal tumour
  -  Previous colorectal resection
  -  Pregnancy
  -  Chemotherapy in last 6 months
  -  Therapy with aspirin/other nonsteroidal anti-inflammatory drug (NSAID)
  -  Other immunosuppressive medication
  -  Incomplete left sided examination
  -  Colorectal carcinoma found at endoscopy
  -  Iatrogenic perforation at endoscopy
  -  Colorectal cancer on histology
  -  Microscopic colitis on histology
  For the colitis group
  -  Simple clinical colitis activity index (SCCAI) score > 5

Relevance to patient case: not relevant
Patient case: 35-year-old female with Colorectal cancer. Genetic variant: FGFR1 Amplification. Other conditions: None.

Clinical trial: A Retrospective Study of Biomarkers in Non-Small Cell Lung Cancer

Summary: The purpose of this study is:
  1. To characterize the types and frequency of molecular alterations to the epidermal growth factor receptor (EGFR) pathway, FGFR4 and EML-ALK in Asian patients with non-small cell lung cancer
  2. To identify candidate biomarkers of importance in the EGFR and estrogen pathways
  Most, if not all, human malignancies including lung cancer are caused by somatic alterations of the genome, leading to activation of oncogenes or inactivation of tumor suppressor genes and their resultant oncogenic effects. In addition to mutations, increased chromosomal copy number (by amplification or polysomy) and DNA methylation are other mechanisms of oncogene activation and tumour suppressor gene inactivation respectively.
  Little is known about the relationship between these oncogenes of the EGFR family and the recently described oncogenes FGFR4 and fusion gene EML4-ALK. Recent data suggests molecularly defined subgroups of non-small cell lung cancer (NSCLC) exist and can be used to predict for sensitivity to targeted agents (erlotinib or gefitinib) or cytotoxic chemotherapy (pemetrexate, gemcitabine, platinum agents). The findings that estrogen receptors are present in lung tumours and that estrogen can stimulate growth and proliferation of lung cancers in vitro and in vivo are provocative. Further studies to evaluate the role of estrogens and other sex hormones in lung cancer are warranted.
  A further understanding of the molecular indicators of lung cancer prognosis and treatment prediction would improve drug development and patient treatment selection.
  Archived paraffin-embedded and fresh frozen NSCLC tumor tissue will be obtained via the Department of Pathology and the National University Tissue Repository respectively. Clinico-pathological characteristics will be obtained from the case records, Pathology and Tissue Repository. DNA will be isolated using standard techniques. Sequencing of genes in the EGFR signaling pathway: EGFR, KRAS, ErbB2, ErbB3, MET, PI3K, and BRAF as well as FGFR4. Unstained slides from the paraffin-embedded tissue will be obtained and subjected to fluoresce in vitro hybridization (FISH) for breakpoints in the EML4 and ALK genes as previously described. For cases that have been snap-frozen, RNA will be extracted and EML4-ALK fusions will be confirmed using RT-PCR and pre-specified primers. To analyse the expression of proteins of putative relevance to EGFR function (such as EGFR, ErbB2, ErbB3, AKT, MET, STAT, ERK, MAPK, cyclin D1, C/EBPa), downstream effects of EGFR: cell proliferation (Ki-67), angiogenesis (CD34, VEGF-A), apoptosis (bcl-2), metastasis, and hormonal influence (oestrogen and progesterone receptors, aromatase), TMA technology will be utilised. The status of the tumor suppressor genes PTEN and C/EBPa will be analysed.


Eligibility: Inclusion Criteria:
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 35-year-old female with Colorectal cancer. Genetic variant: FGFR1 Amplification. Other conditions: None.

Clinical trial: Patients With Metastatic Colorectal Cancer Treated With Regorafenib or Placebo After Failure of Standard Therapy

Summary: This is a randomized, double-blind, placebo-controlled multi-center phase III study to evaluate efficacy and safety of regorafenib in patients with metastatic colorectal cancer (CRC) who have progressed on/after all approved drugs for CRC

Detailed description: All participants received Best Supportive Care. Acronyms used in Adverse events section: Gastrointestinal (GI), Genitourinary (GU), Not Otherwise Specified (NOS), Absolute Neutrophil Count (ANC), Aspartate aminotransferase (AST), Alanine aminotransferase (ALT), Common Terminology Criteria for Adverse Events (CTCAE), International Normalized Ratio (INR), Central nervous system (CNS), Acute respiratory distress syndrome (ARDS), Cranial nerves (CN), Disseminated Intravascular Coagulation (DIC), Cardiac troponin T (cTnT).
  Abbreviation used in Results section: Data Monitoring Committee (DMC). Adverse event collection will be covered in Adverse events section.

Eligibility: Inclusion Criteria:
  -  Histological or cytological documentation of adenocarcinoma of the colon or rectum
  -  Progression during or within 3 months following the last administration of approved standard therapies. Patients treated with oxaliplatin in an adjuvant setting should have progressed during or within 6 months of completion of adjuvant therapy
  -  Patients with measurable or non measurable disease
  -  Eastern Cooperative Oncology Group (ECOG) Performance Status of </= 1
  -  Life expectancy of at least 3 months
  -  Adequate bone marrow, liver and renal function
  Exclusion Criteria:
  -  Unstable/uncontrolled cardiac disease
  -  History of arterial or venous thrombotic or embolic events
  -  Symptomatic metastatic brain or meningeal tumors
  -  Patients with evidence or history of bleeding diathesis
  -  Interstitial lung disease - Persistent proteinuria >/= grade 3
  -  Unresolved toxicity > grade 1 attributed to any prior therapy/procedure excluding alopecia and oxaliplatin induced neurotoxicity </= Grade 2

Relevance to patient case: not relevant
Patient case: 35-year-old female with Colorectal cancer. Genetic variant: FGFR1 Amplification. Other conditions: None.

Clinical trial: A Post-Marketing Surveillance Study On Erbitux® (Cetuximab) In Patients With Metastatic Colorectal Cancer Refractory To Irinotecan Containing Treatment

Summary: A post marketing surveillance, prospective study to collect safety information from 250 subjects with epidermal growth factor receptor (EGFR) expressing, KRAS wild-type metastatic colorectal cancer treated with Erbitux as final evaluable cases.


Eligibility: Inclusion Criteria:
  -  EGFR expressing, KRAS wild-type subjects with metastatic colorectal cancer, who are indicated for Erbitux treatment according to the nationally authorized label (in combination with irinotecan, metastatic colorectal cancer after failure of irinotecan-including cytotoxic therapy)
  Exclusion Criteria:
  -  Subjects who are not eligible for Erbitux treatment according to the indication in national label; or with hypersensitivity reactions (grade 3 or 4) to Erbitux

Relevance to patient case: not relevant
Patient case: 35-year-old female with Colorectal cancer. Genetic variant: FGFR1 Amplification. Other conditions: None.

Clinical trial: Safety and Efficacy of AZD4547 in Combination With Fulvestrant vs. Fulvestrant Alone in ER+ Breast Cancer Patients

Summary: The purpose of this study is to assess the safety and effectiveness of AZD4547 in combination with fulvestrant vs. fulvestrant alone in ER+ breast cancer patients with FGFR1 polysomy (FISH4/5) or gene amplification (FISH 6)


Eligibility: Inclusion Criteria:
  -  Post-menopausal women (either through bilateral oophorectomy or amenorrhoeic for 24 months)
  -  Histological confirmation of Breast Cancer with documented ER+ receptor status
  -  Safety run-in: Relapsing during/within 12 months of completion of a single regimen of adjuvant endocrine therapy with non-steroidal AI and/ tamoxifen or progression following 1st line endocrine therapy with non-steroidal AL
  -  Rand phase IIa: Received at least 1 prior endocrine therapy in the metastatic setting or have relapsed during/ within 6 months of completion of adjuvant endocrine therapy (either non-steroidal AI or tamoxifen or a combination of both). Chemotherapy administered in the adjuvant setting is permitted.
  -  Rand phase IIa: Mandatory provision of tumour sample to confirm FGFR1 polysomy or gene amplification. At least one measurable lesion that can be accurately assessed by CT/MRI/x-ray at baseline and follow up visits
  Exclusion Criteria:
  -  Prior exposure to exemestane (safety run-in) / fulvestrant (randomized phase IIa), or any agent known to inhibit FGFRs.
  -  More than 1 prior regimen of chemotherapy for breast cancer
  -  ECG recordings that demonstrate significant abnormalities in cardiac rate, rhythm or conduction
  -  History of hypersensitivity to active or inactive excipients of AZD4547 or exemestane (safety run-in ) or fulvestrant (Randomized phase), including castor oil, or drugs with a similar chemical structure or class to AZD4547 or exemestane or fulvestrant.
  -  Randomized phase IIa: bleeding/blood clotting conditions that would prevent the administration of the fulvestrant injection into the buttocks

Relevance to patient case: not relevant
Patient case: 35-year-old female with Colorectal cancer. Genetic variant: FGFR1 Amplification. Other conditions: None.

Clinical trial: Molecular Determinants Affecting Fluoro-L-thymidine (FLT) Positron Emission Tomography (PET) in Rectal Cancer

Summary: The purpose of this study is to determine if positron emission tomography (PET) imaging with an imaging agent called 18F-fluorodeoxythymidine([18F]-FLT) will allow investigators to measure how well tumor(s) respond to treatment without taking a tissue sample (biopsy). Additionally, the investigators want to determine if it is possible to predict how well tumor(s) might respond to treatment with [18F]-FLT PET imaging.


Eligibility: Inclusion Criteria:
  -  Subjects with known rectal cancer.
  -  Subjects must have signed an approved consent form.
  -  Subjects must be 18 years of age or older.
  Exclusion Criteria:
  -  Children less than 18 are excluded.
  -  Pregnant women and women who are breast feeding will be excluded from this study. A serum beta HCG will also be performed for each pre-menopausal female subject.
  -  Patients who are acutely ill who are deemed by their treating physician as not suitable candidates for this study

Relevance to patient case: not relevant
Patient case: 35-year-old female with Colorectal cancer. Genetic variant: FGFR1 Amplification. Other conditions: None.

Clinical trial: Diagnostic Value of C-reactive Protein and White Blood Cell Counts for Early Detection of Inflammatory Complications After Open Resection of Colorectal Cancer

Summary: Although widely used, there is a lack of evidence concerning diagnostic value of C-reactive protein (CRP) and white blood cell counts (WBC) in the postoperative course. The aim of this study was to evaluate the diagnostic accuracy of CRP and WBC for postoperative inflammatory complications after open resection of colorectal cancer.


Eligibility: Inclusion Criteria:
  -  all patients with resection of colorectal cancer
  Exclusion Criteria:
  -  lack of measurement of C-reactive protein
  -  lack of measurement of white blood cell counts

Relevance to patient case: not relevant
Patient case: 35-year-old female with Colorectal cancer. Genetic variant: FGFR1 Amplification. Other conditions: None.

Clinical trial: Using Videos in Advance Care Planning for Patients With Advanced Cancer

Summary: To compare the decision making of subjects with advanced cancer having a verbal advance care planning discussion compared to subjects using a video.

Detailed description: A.1. Aim 1: To recruit 150 subjects with advanced cancer and randomly assign these subjects to one of two advance care planning (ACP) modalities: 1. a video visually depicting CPR (intervention) or 2. a verbal narrative describing the CPR.
  Hypothesis 1: It is feasible to recruit and randomize 150 subjects with advanced cancer.
  A.2. Aim 2: To compare the care preferences for CPR among 150 subjects randomized to video vs. verbal narrative intervention.
  Hypothesis 2: Subjects randomized to the video intervention will be significantly more likely to opt NOT to have CPR compared to those randomized to the verbal narrative.
  A.3. Aim 3: To compare knowledge assessment of CPR for 150 subjects randomized to video vs. verbal narrative intervention.
  Hypothesis 3: When compared to subjects randomized to the verbal narrative arm, subjects in the video group will have higher knowledge assessment scores when asked questions regarding their understanding of CPR.

Eligibility: Inclusion Criteria:
  1. diagnosis of cancer that falls under one of the following: A. All patients with brain cancer, inoperable hepatocellular/bile duct/gallbladder cancer, incurable non-small cell lung carcinoma (wet IIIb or IV), extensive stage small cell lung cancer, inoperable mesothelioma, inoperable pancreatic cancer or; metastatic gastric or esophageal cancer, metastatic melanoma, OR B. Patients with the following cancers, if first-line therapy has failed and limited response is expected to second-line therapy: breast cancer, colorectal cancer, head and neck cancer, leukemia, ovarian cancer, prostate cancer, renal cancer, sarcoma, lung cancer, myeloma, or lymphoma, OR C. Less than one year prognosis.
  2. ability to provide informed consent,
  3. cognitive ability to participate in the study
  4. ability to communicate in English.
  Exclusion Criteria:
  1. inability to make decisions,
  2. non-English speaking,
  3. new patient visit

Relevance to patient case: not relevant
Patient case: 35-year-old female with Colorectal cancer. Genetic variant: FGFR1 Amplification. Other conditions: None.

Clinical trial: Cytokine Changes After Colorectal Cancer Resection

Summary: Based on our previous research, this study aims to determine reliable surgical stress response markers in patients undergoing radical resection of colorectal cancer.

Detailed description: Every surgical intervention represents a stress for patient's organism. During the operation, numerous changes in the patient's metabolism take place, that are termed surgical stress response. Leading cause of surgical stress response is tissue destruction that always accompanies operations. Surgical stress response is effected through activation of hypothalamus-pituitary-adrenal axis and through sympathetic activation.
  The consequences of surgical stress response are numerous. Surgical stress response is essential to uneventful postoperative recovery. On the other hand, excessive surgical stress response may lead to serious postoperative complications, such as heart and kidney failure, venous thrombosis, disruption of operative wound and wound infection.
  In prior studies the investigators have shown the kinetics of postoperative serum interleukin changes after radical resection of gastric cancer.
  This study aims at determining reliable markers of surgical stress response severity in patients undergoing radical resection of colorectal cancer.

Eligibility: Inclusion Criteria:
  -  Pathohistologically verified colorectal cancer
  Exclusion Criteria:
  -  Distant metastases noticed before or during surgery
  -  History of autoimmune diseases or immunodeficiencies
  -  Use of immunomodulatory drugs within 1 year prior to surgery

Relevance to patient case: not relevant
Patient case: 35-year-old female with Colorectal cancer. Genetic variant: FGFR1 Amplification. Other conditions: None.

Clinical trial: An Observational Study on The Correlation Between Time of Initiation of Avastin (Bevacizumab) Treatment And Progression-Free Survival in Patients With Colorectal Cancer (CRONOS 1)

Summary: This single arm, prospective, observational study will assess the correlation between the time from start of chemotherapy to the start of Avastin (bevacizumab) treatment with progression-free survival in patients with previously untreated metastatic colorectal cancer. Patients will be followed for up to 12 months after progressive disease occurs.


Eligibility: Inclusion Criteria:
  -  Adult patients, >/= the 18 years of age
  -  Previously untreated metastatic colorectal cancer
  -  Scheduled to start 1st line chemotherapeutic treatment
  -  ECOG performance status 0-1
  Exclusion Criteria:
  -  Any conditions included in contraindication list for Avastin
  -  Prior chemotherapy for metastatic colorectal cancer
  -  Adjuvant/neoadjuvant chemotherapy or radio-chemotherapy of non-metastatic colorectal cancer completed <6 months prior to treatment start

Relevance to patient case: not relevant
Patient case: 35-year-old female with Colorectal cancer. Genetic variant: FGFR1 Amplification. Other conditions: None.

Clinical trial: A Trial of Capecitabine (Xeloda), Oxaliplatin and Irinotecan in Combination With Bevacizumab in 1st Line Treatment of Metastatic Colorectal Cancer

Summary: A Phase I-II Trial of Capecitabine (Xeloda), Oxaliplatin and Irinotecan in Combination with Bevacizumab in 1st Line Treatment of Metastatic Colorectal Cancer

Detailed description: A Phase I-II Trial of Capecitabine (Xeloda), Oxaliplatin and Irinotecan in Combination with Bevacizumab in 1st Line Treatment of Metastatic Colorectal Cancer

Eligibility: Inclusion Criteria:
  -  Patients with diagnosed Metastatic Colorectal Cancer
  Exclusion Criteria:
  -  Patients with diagnosis other than Metastatic Colorectal Cancer

Relevance to patient case: not relevant
Patient case: 35-year-old female with Colorectal cancer. Genetic variant: FGFR1 Amplification. Other conditions: None.

Clinical trial: Perfusion and Diffusion Magnetic Resonance Imaging, and Phosphorylation of Circulation Endothelial Cells to Determine Anti-anogenic Effect of Chemotherapeutic Regimens in Colorectal Liver Metastasis Patients

Summary: The purpose of our study is to establish the accuracy of the perfusion MRI parameters and the availability of the VEGFR2 signaling assay using phosphospecific flow cytometry in predicting the response of liver metastasis from colorectal cancer to treatment with antiangiogenic agent.

Detailed description: The purpose of our study is to establish the accuracy of the perfusion MRI parameters and the availability of the VEGFR2 signaling assay using phosphospecific flow cytometry in predicting the response of liver metastasis from colorectal cancer to treatment with antiangiogenic agent.
  IRB approval will be obtained to enroll 60 naïve patients (30 patients who will get antiangiogenic agent (Avastin) combined chemotherapy and 30 patients who will get chemotherapy without antiangiogenic agent) with liver metastasis from colorectal cancer. MRI and blood test (VEGFR2 signaling assay) will be undergoing at three time points in the patients with Avastin chemotherapy; at baseline (pretreatment), 3 days after Avastin alone treatment, 3 days after Avastin combined chemotherapy (about 10 days after initial Avastin alone treatment). MRI and blood test (VEGFR2 signaling assay) will be undergoing at two time points in the patients who will get chemotherapy without antiangiogenic agent; at baseline (pretreatment), 3 days after chemotherapy.

Eligibility: Inclusion Criteria:
  -  Patients who have single or multiple liver metastasis from colorectal cancer
  -  Patients willing to undergo the study procedure
  -  Patients who are fully informed about the study and have signed the informed consent form
  -  60 patients (30 patients who will get antiangiogenic agent(Avastin) combined chemotherapy and 30 patients who will get chemotherapy without antiangiogenic agent)
  Exclusion Criteria:
  -  Patients (men or women) under 20 years of age
  -  Patients who have previously entered this study
  -  Patients who have received or will receive any investigational drug 48 hours before injection of the study drug or during study participation
  -  Women who are pregnant, lactating or who are of childbearing potential and have not had a negative pregnancy test at baseline visit
  -  Patients not eligible to contrast media injection according to product labeling
  -  Patients with a contraindication for MRI or CT
  -  Patients with impaired renal function (e.g. acute renal failure) or patients on dialysis

Relevance to patient case: not relevant