araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 73-year-old female with Pancreatic ductal adenocarcinoma. Genetic variant: ERBB3. Other conditions: Whipple, FNA.

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: 73-year-old female with Pancreatic ductal adenocarcinoma. Genetic variant: ERBB3. Other conditions: Whipple, FNA.

Clinical trial: Stool Testing for Pancreatic Cancer

Summary: The purpose of this study is to determine if pancreatic cancer/pre-cancer can be detected in early stages through the molecular analysis of stool samples. Investigators hypothesize that analysis of stool samples using digital melt curve (DMC) analysis, can be used as a sensitive and specific method to detect the common genetic abnormalities present in pancreatic cancers and pre-cancerous lesions of the pancreas.

Detailed description: Pancreatic ductal adenocarcinoma (PDC) remains the fourth leading cause of cancer-related death in the United States. This is largely due to the fact that most patients present with advanced, unresectable disease, highlighting the critical need for a screening test for this disease. Stool testing is an approach that has not been explored for use in PDC screening. With the advent of stool-based DNA tests, it may be possible to target genetic abnormalities that have been recently characterized in PDC tumorigenesis.
  Aim: The aim of this study is to determine if deoxyribonucleic acid (DNA) alterations present in pancreatic cancer and precancerous intrapapillary mucinous neoplasms (IPMN) can be reliably recovered in matched stool.
  Methods: This is a case-control prospective study to determine the utility of a stool-based digital melt curve (DMC) assay in PDC screening. A total of 30 patients (18 with pancreatic cancer, 12 with IPMN) who will be undergoing pancreatic resection will be enrolled. Pancreatic neoplastic tissue will be isolated from their surgical specimens and the genes most commonly mutated in PDC will be sequenced from extracted DNA. In addition, hypermethylation at common promoter sites will be assessed by methylation-specific PCR. The genetic and epigenetic alterations isolated in pancreatic tissue will be utilized as the targets for stool DMC assay. Blinded technicians will process stool specimens from control patients as well as a matched control. The primary outcomes of this study will be the sensitivity and specificity of the stool DMC assay in detecting genetic mutations present in tumor or IPMN lesions.

Eligibility: Inclusion Criteria:
  -  18 years of age and older.
  -  Tissue-confirmed or radiological evidence of either pancreatic adenocarcinoma or intrapapillary mucinous neoplasm(IPMN).
  -  Scheduled for surgical resection of the adenocarcinoma or IPMN.
  -  Able to give informed consent
  Exclusion Criteria:
  -  History of colorectal, gastric cancer, esophageal, or head-and-neck cancer.
  -  Endoscopic procedure conducted less than 1 week prior to enrollment.
  -  Unwillingness or inability to sign informed consent.

Relevance to patient case: not relevant
Patient case: 73-year-old female with Pancreatic ductal adenocarcinoma. Genetic variant: ERBB3. Other conditions: Whipple, FNA.

Clinical trial: Frequency of Methods of Local Invasion of Pancreatic Adenocarcinoma

Summary: Pancreatic cancer often spreads through local invasion into local structures, including fat, blood vessels, nerves, and nearby organs (stomach, duodenum, spleen, bile duct). Local microscopic invasion is associated with recurrence of pancreatic cancer after pancreatic resection, such that even if the original cancer is surgically removed, microscopic areas of cancer often remain. Data on the patterns of local invasion by pancreatic cancer have not been published. In this study, The investigators hope to investigate the frequency of the various methods of local invasion of pancreatic adenocarcinoma. This would help the investigators better understand how pancreatic cancer spreads, and determine what cancers are not resectable.

Detailed description: Pancreatic cancer is the eighth most common malignancy, and the fifth leading cause of cancer-related death, in the United States. Unfortunately, patients often present late in the course of the disease. Accordingly, the 1- year survival rate is approximately 20%, and the 5-year survival rate is less than 4%. Even in patients with local disease who are surgical candidates, survival at five years remains only 10-25%. Staging for pancreatic adenocarcinoma typically utilizes the TNM classification, where "T" represents tumor size, "N" represents regional lymph node metastasis, and "M" represents distant metastasis. This type of staging can usually only be done after operative resection. Unfortunately, up to 25% of patients are found to be unresectable at the time of surgical exploration. This is most often due to local invasion or metastatic disease. Local microscopic invasion is associated with recurrence of pancreatic cancer after pancreatic resection. Comprehensive data on the patterns of local invasion by pancreatic cancer have not been published. The investigators believe that it would be beneficial to investigate the frequency of the various methods of local invasion of pancreatic adenocarcinoma. A clearer understanding of the natural history of local invasion could potentially lead to a better determination of what constitutes unresectability.

Eligibility: Inclusion Criteria:
  -  Tissue confirmed diagnosis of pancreatic adenocarcinoma.
  -  Underwent surgical resection for adenocarcinoma at the Columbia University Medical Center between 2001-2009.
  Exclusion Criteria:
  -  Did not undergo surgery.

Relevance to patient case: not relevant
Patient case: 73-year-old female with Pancreatic ductal adenocarcinoma. Genetic variant: ERBB3. Other conditions: Whipple, FNA.

Clinical trial: Registry Study - Whipple at the Splenic Artery

Summary: The purpose of this study is to determine how effective Whipple at the Splenic Artery (WATSA).

Detailed description: Primary
  The primary objective of this registry study is to collect clinical data from patients who undergo the WATSA procedure. Specific hypotheses to be tested are
  -  To determine how effective Whipple at the Splenic Artery (WATSA) is at resecting tumors with negative microscopic margins (R0) at the resection line on the pancreas and at the tangential posterior, uncinate, and venous margins.
  -  To determine if WATSA can be performed within the usual range of morbidity and mortality (30 day postoperative mortality) for a standard a Whipple procedure.
  Secondary
  The secondary objectives of this registry study are to
  -  To determine the survival/recurrence rates at 2 years.
  -  To determine the effect of occlusion of the splenic vein at the confluence.

Eligibility: Eligibility Criteria - Prospective Portion:
  -  Patient must have diagnosis of ductal adenocarcinoma of head and/or neck of pancreas, ampullary adenocarcinoma, or pancreatic neuroendocrine tumor confirmed by tissue diagnosis.
  -  Patient must be between 18 to 85 years of age.
  -  Patient must be a candidate for the WATSA procedure or have had the WATSA surgery performed within 1 year.
  -  Patient must be able to understand and willing to sign a written informed consent document.
  Eligibility Criteria - Retrospective Portion:
  Patient underwent WATSA procedure at our institution between 01/01/2009 and 12/31/2011.

Relevance to patient case: not relevant
Patient case: 73-year-old female with Pancreatic ductal adenocarcinoma. Genetic variant: ERBB3. Other conditions: Whipple, FNA.

Clinical trial: Biomarkers of Response in Blood and Tumor Tissue Samples From Patients With Unresectable Stage IV Squamous Cell Cancer of the Head and Neck Previously Treated With Cetuximab, Cisplatin, and Radiation Therapy

Summary: RATIONALE: Studying samples of blood and tumor tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer. It may also help doctors understand how patients respond to treatment.
  PURPOSE: This research study is studying biomarkers of response in blood and tumor tissue samples from patients with unresectable stage IV squamous cell carcinoma of the head and neck previously treated with cetuximab, cisplatin, and radiation therapy.

Detailed description: OBJECTIVES:
  Primary
  -  To expand upon the list of molecular correlates indicated in clinical trial ECOG-E3303, including EGFR expression, EGFR phosphorylation, map kinase, AKT, and STAT3.
  -  To correlate the status or expression level of each biomarker with clinical outcome (response, progression-free survival, overall survival).
  OUTLINE: Archived tumor and blood specimens are analyzed for human papilloma virus and p16 status; EGFR gene amplification; levels of ERCC1, XPF, and c-Met proteins; expression and activation of several signaling pathways including PI3 kinase gene and mTOR; levels of ErbB2, ErbB3, P70S6 kinase, S6 , and Akt; expression of amphiregulin (AR), TGF-alpha (TGF-α), heparin-binding EGF-like growth factor (HB-EGF), EGF, epiregulin and c-Met ligand, and hepatocyte growth factor by fluorescence in situ hybridization (FISH), automated in situ quantitative measurements of protein analysis (AQUA), IHC, PCR, and ELISA.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of squamous cell carcinoma of the head and neck
  -  Stage IV disease
  -  Unresectable disease
  -  Treated with cetuximab, cisplatin, and radiotherapy on clinical trial ECOG-E3303
  -  Archived blood and tumor tissue samples available
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 73-year-old female with Pancreatic ductal adenocarcinoma. Genetic variant: ERBB3. Other conditions: Whipple, FNA.

Clinical trial: Reconstruction Method and Delayed Gastric Emptying After Pancreatic Surgery

Summary: Pancreaticoduodenectomy (whipple procedure) is the standard operation for tumors of the pancreatic head, uncinate process, distal common bile duct as well as the papilla of vater. For reconstruction, pylorus-preservation (PPPD) has been shown to be technically and oncologically equivalent to the traditional whipple operation. One issue with this technique is delayed gastric emptying (DGE), which occurs in 25-70% of patients, usually emerging between day 4 and 14 after surgery. Patients with severe DGE can not only experience prolonged length of hospital stay, but are also at increased risk for other complications like aspiration or other issues related to the inability to ingest nutrition.
  There is vast retrospective evidence and one prospective study indicating that antecolic reconstruction of the duodenojejunostomy can improve the rate and severity of delayed gastric emptying.
  The investigators have conducted a prospective randomized trial in order to test this hypothesis. Patients were randomized to either undergo antecolic or retrocolic reconstruction after PPPD. On day 10 after surgery, DGE was assessed by clinical criteria. In addition, a test meal including 1g paracetamol was administered to check for clinically inapparent DGE. Of these serum samples, kinetics of intestinal peptides like GLP-1, PYY and glucagon was alos measured.


Eligibility: Inclusion Criteria:
  -  verified cancer of the pancreatic head/neck/uncinate process or distal bile duct, radiographically suspicious tumor requiring pancreaticoduodenectomy
  -  pylorus-preserving reconstruction planned
  -  no evidence of distant metastases
  -  written informed consent
  Exclusion Criteria:
  -  age <18 or >90 years
  -  status post surgical resection of stomach or duodenum
  -  locally unresectable:
  -  invasion of the hepatic artery/superior mesenteric artery
  -  >180 deg invasion of portal vein/superior mesenteric vein
  -  gastric invasion
  -  hypersensitivity to paracetamol
  -  clinically significant anastomotic dehiscence
  -  postoperative pancreatitis > day 10
  -  preoperative evidence of gastroparesis

Relevance to patient case: not relevant
Patient case: 73-year-old female with Pancreatic ductal adenocarcinoma. Genetic variant: ERBB3. Other conditions: Whipple, FNA.

Clinical trial: L-CARnitine in the Palliative Treatment of Advanced PANcreatic Cancer (CARPAN)

Summary: The study investigated the role of L-Carnitine supplementation on proinflammatory immune response, malnutrition, cancer cachexia and cancer related fatigue in advanced and inoperable pancreatic cancer, UICC Stage IV .

Detailed description: Pancreatic cancer has the lowest 5-year survival rate of any cancer and ranks as the fourth leading cause of cancer death world wide. Several metabolic changes are present in the whole body in case of cancer so the investigators conducted a placebo controlled, double blinded, randomized, prospective and multicentre study to investigate, whether L-Carnitine supplementation may have an impact on malnutrition, cancer cachexia and cancer related fatigue in advanced pancreatic cancer.
  Study drug: L-Carnitine 4g per day (vers) Placebo Study design: A multi-centre, double blind, and placebo-controlled, randomised, parallel group study
  Patient population: Patients with advanced pancreatic carcinoma Number of patients: Total of 90 patients in two equal groups number of centres: 4 (Greifswald, Magdeburg, Berlin,Heidelberg,all Germany) Duration of dosing: 12 weeks

Eligibility: Inclusion Criteria:
  -  advanced pancreatic cancer (UICC Stage IV)
  -  Karnofsky Index larger than 60
  -  compliance
  -  consent to participate to the study
  Exclusion Criteria:
  -  Child-Pugh classification of liver failure greater than Child B,
  -  a known second malignant tumor
  -  oral or parenteral supplementation with omega-3-fatty acids
  -  treatment with thalidomide or Infliximab
  -  mental or physical disorders

Relevance to patient case: not relevant
Patient case: 73-year-old female with Pancreatic ductal adenocarcinoma. Genetic variant: ERBB3. Other conditions: Whipple, FNA.

Clinical trial: Safety Study of MM-121 in Combination With Multiple Anticancer Therapies in Patients With Advanced Solid Tumors

Summary: To evaluate the safety and tolerability of escalating doses of MM-121 + certain anticancer therapies

Detailed description: This study was a Phase 1 and pharmacologic dose-escalation trial of MM-121 in combination with certain anticancer therapies. The dose-escalation portion of the study employed a 3 + 3 design to assess the safety, tolerability, and pharmacokinetics of MM-121 administered weekly in combination with certain anticancer therapies in patients with advanced/recurrent cancer. Doses of MM-121 and/or the anticancer therapy were escalated until either the MTD is identified or the combination was shown to be tolerable at the highest planned doses.

Eligibility: Inclusion Criteria:
  -  Advanced-stage solid tumors
  -  ≥ 18 years of age
  -  Adequate liver and kidney function
  Exclusion Criteria:
  -  Any other active malignancy
  -  No known HIV, Hepatitis C or B

Relevance to patient case: not relevant
Patient case: 73-year-old female with Pancreatic ductal adenocarcinoma. Genetic variant: ERBB3. Other conditions: Whipple, FNA.

Clinical trial: A Safety Study of MM-121 With Cetuximab and Irinotecan in Patients With Advanced Cancers

Summary: The purpose of this study was to evaluate the safety and tolerability of escalating doses of the MM-121 plus cetuximab and the MM-121 plus cetuximab plus irinotecan combination.

Detailed description: This study was a Phase 1 and pharmacologic dose-escalation trial of MM-121 plus cetuximab plus irinotecan. The study assessed the safety, tolerability, and pharmacokinetics of MM-121, cetuximab and irinotecan.

Eligibility: Inclusion Criteria:
  -  No standard options remaining
  -  Adequate liver and kidney functions
  -  18 years of age or above
  Exclusion Criteria:
  -  History of any secondary active cancer in the last 3 years.
  -  Pregnant or breast feeding
  -  History of severe allergic reactions or contraindications to cetuximab or irinotecan

Relevance to patient case: not relevant
Patient case: 73-year-old female with Pancreatic ductal adenocarcinoma. Genetic variant: ERBB3. Other conditions: Whipple, FNA.

Clinical trial: Resectability of Pancreatic Head Cancer by Contrast-enhanced MDCT:a Multi-center Study

Summary: The purpose of this multicenter and double-blind clinical trial is to prospectively assess the sensitivity, specificity, negative predictive value, positive predictive value, and accuracy in respectability of pancreatic head cancer with contrasted-enhanced MDCT and its various post processing techniques, taking operational and pathological records as the gold standard.


Eligibility: Inclusion Criteria:
  -  Patients with (or suspected) pancreatic head cancer
  -  Being examined by contrasted-enhanced MDCT
  -  Receiving surgical treatment (including palliative surgery) in all research centers
  Exclusion Criteria:
  -  Patients having (or suspected) pregnancy or breast-feeding
  -  Patients having allergic reactions to iodinated contrast agents or Hypersensitivity reactions to allergens(including drugs)
  -  Patients receiving ERCP before contrasted-enhanced MDCT examination
  -  Patients without surgery because of a high degree of surgical risk

Relevance to patient case: not relevant
Patient case: 73-year-old female with Pancreatic ductal adenocarcinoma. Genetic variant: ERBB3. Other conditions: Whipple, FNA.

Clinical trial: A Study of DMOT4039A in Participants With Unresectable Pancreatic or Platinum-Resistant Ovarian Cancer

Summary: This multicenter, open-label, dose-escalating study will assess the safety, tolerability, and pharmacokinetics of DMOT4039A in participants with unresectable pancreatic or platinum-resistant ovarian cancer. Cohorts of participants will receive multiple ascending intravenous doses of DMOT4039A.


Eligibility: Inclusion Criteria:
  -  Eastern Cooperative Oncology Group (ECOG) performance status 0 or 1
  -  Histologically documented, incurable, locally advanced or metastatic disease for which no standard therapy exists, consisting of one of the following: Unresectable pancreatic ductal adenocarcinoma or platinum-resistant ovarian cancer
  -  Measureable disease, defined as at least one bi-dimensionally measurable non-lymph node lesion greater than or equal to (>/=) 1 centimeter (cm) in long-axis diameter on spiral computed tomography (CT) scan or at least one bi-dimensionally measurable lymph node measuring >/= 1.5 cm in short-axis diameter on spiral CT scan
  -  Adequate hematological, renal and liver function
  Exclusion Criteria:
  -  Treatment with anti-tumor therapy, including chemotherapy, biologic, experimental or hormonal therapy, within 4 weeks prior to Day 1
  -  Known active infection
  -  Current Grade >/= 2 toxicity (except for alopecia, anorexia and fatigue) from prior therapy or Grade >/= 2 neuropathy
  -  Untreated or active cerebral nervous system metastases
  -  Pregnant or breastfeeding women

Relevance to patient case: not relevant
Patient case: 73-year-old female with Pancreatic ductal adenocarcinoma. Genetic variant: ERBB3. Other conditions: Whipple, FNA.

Clinical trial: The Significance of MRI in the Development of Diagnostics and Treatment of Breast Cancer

Summary: The purpose of this study is to determine how MRI changes the treatment and diagnostics of ductal breast cancer. 100 women with newly diagnosed breast cancer will participate the study.


Eligibility: Inclusion Criteria:
  -  Tumor size less than 2cm
  -  Ductal carcinoma unifocal
  Exclusion Criteria:
  -  Previous breast cancer

Relevance to patient case: not relevant