araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: Narrow-Band Imaging Versus Standard White Light for the Detection of Serrated Lesions in the Proximal Colon

Summary: This is a study to determine if using Narrow-Band Imaging of the colon, rather than the usual white light on the colon, will improve the detection of a type of polyp called serrated. The polyps are called serrated because of their appearance under the microscope after they have been removed. They tend to be located up high in the colon, far away from the rectum. They have been definitely shown to be a type of precancerous polyp and it is possible that using Narrow-Band Imaging will make it easier to see them, as they can be quite difficult to see with standard white light.

Detailed description: This is a randomized controlled trial comparing the use of Narrow-Band Imaging (illumination of the colon in blue light)versus standard white light for the detection of serrated lesions in the proximal colon (the colon proximal to the splenic flexure). Recent studies have indicated that colonoscopy is more effective in preventing cancer in the left side of the colon than the right side of the colon. The reasons for this difference may be partly biologic, in that a special group of polyps known as serrated polyps, particularly sessile serrated adenomas, are located primarily proximal to the splenic flexure. These lesions share molecular features with a group of cancers that occur primarily in the proximal colon. These molecular features include CpG island methylator phenotype (CIMP) and microsatellite instability. These lesions are endoscopically subtle in that they are often flat, have the same color as the surrounding mucosa, and are hard to differentiate from normal mucosa. Narrow-Band Imaging has anecdotally been used to highlight the appearance of these lesions. This study will test whether Narrow-Band Imaging increases the detection of serrated lesions in a randomized controlled trial.

Eligibility: Inclusion Criteria:
  -  Age 50-85
  -  Intact colon and rectum
  -  American Society of Anesthesiology risk class 1, 2 or 3
  Exclusion Criteria:
  -  No prior surgical resection of colon or rectum

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: Mutation Analysis and Copy Number Changes of KRAS and BRAF Gene in Taiwanese Cases of Biliary Tact Adenocarcinoma

Summary: Cholangiocarcinoma is a fatal malignant neoplasm originating from biliary tracts and constitutes about 5-10% of primary liver cancers, characterized by a poor prognosis. High prevalence in southeast and eastern Asia has been observed. At present, the cellular and molecular mechanisms leading to oncogenesis of cholangiocarcinoma remain unclear.
  The RAS gene product has a key role in controlling cell growth and differentiation through its intrinsic GTPase activity. Point mutations that activate the RAS protein and its downstream cascade have been observed in human tumors. Both KRAS and BRAF are members of the RAS-RAF-MEK-ERK-MAP kinase pathway which mediates cellular response to growth signals. Somatic KRAS mutations are found at high rates in leukemia, colon cancer, pancreatic cancer and lung cancer. Studies from European and Japanese groups have recently described that activating KRAS/ BRAF mutations may play a role in the carcinogenesis of cholangiocarcinoma of the biliary tracts, but our preliminary data demonstrated low frequency of KRAS and BRAF mutation in the same tumor as well as the results from Thailand. In this study, the investigators hypothesize copy number changes rather than genetic mutation of either KRAS or BRAF genes may be the key findings of Taiwanese cases of the adenocarcinoma from the biliary tracts.


Eligibility: Inclusion Criteria:
  -  The patients diagnosed as biliary tact adenocarcinoma.

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: Efficacy Study of Robotic Surgery for Rectal Cancer

Summary: After introducing minimally invasive surgery, robotic surgery has been increasingly used in colorectal cancer. However, there is a few prospective study for robotic surgery. The aim of this trial is to evaluate the effectiveness and safety of robotic surgery in mid or low rectal cancer.

Detailed description: This study was designed as randomized phase II trial (laparoscopic versus robotic). The primary end point is quality of mesorectal excision.

Eligibility: Inclusion Criteria:
  -  mid or low rectal cancer (within 9cm from anal verge)
  -  pathologically proven as adenocarcinoma
  -  written informed consent
  -  no severe functional disability in lung and heart
  Exclusion Criteria:
  -  invading adjacent organ
  -  distant metastasis (lung, liver, brain, bone, distant lymph nodes etc.)
  -  lateral pelvic lymph node metastasis
  -  Have severe concomitant disease that might limit compliance or completion of the protocol.
  -  Have any other malignancy that might impact 5-year survival or might be potentially confused with rectal cancer.
  -  If female, be pregnant or breast feeding.
  -  Hereditary colorectal cancer (HNPCC, FAP etc)
  -  emergency operation

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: PK/PD Investigation of Modufolin® in Plasma, Tumor and Adjacent Mucosa in Patients With Colon Cancer

Summary: The purpose of this study is to compare the concentration of [6R] 5,10-methylene-THF, 5-formyl-THF, 5-methyl-THF and THF in the tumor, in adjacent mucosa and in plasma in patients with colon cancer receiving two different does of Modufolin® and Levoleucovorin (Isovorin®) respectively (60 and 200 mg/m2).


Eligibility: Inclusion Criteria:
  Patients must have operable colon cancer that is amenable to curative surgery.

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: Efficacy and Safety Study of Complete Mesocolic Excision for Colon Cancer

Summary: In 2009, Prof. Hohenberger proposed complete mesocolic excision (CME) as standardized, in which the same principle of TME in rectal cancer has been applied to the colon. More and more surgeons pay attention to the rationality of this surgical approach. However, the clinical application researches are still few, in particular the prospective controlled study is still none. This clinical trial will compare the CME group and non-CME group to evaluate the outcome and safety of CME for apply in clinic.

Detailed description: Materials and Methods:
  All the patients with colon cancer will undergo elective radical operation. The observations were recorded during the operation and on the postoperative specimens. Intra-operative photographs were taken at various stages, as were photographs of the postoperative specimen. According to the CME operation keypoints, all the photographs will accept third-party assessment of the expert group, while the third-party expert group will not participate in the management of patients. Both of The evaluators and research doctors are double-blind state. The postoperative patients will divided into two groups according to the results of the assessment. The clinical and pathological data of the patients as well as follow-up information will be recorded and collected.
  1. Outcome of CME By comparison to clinicopathologic variables, and precise tissues morphometry of two groups, the prognosis, lymph nodes harvest and removal of the mesocolic area were investigated. Outcomes of interest also include disease-free survival, local recurrence-free survival, recurrence rate. In addition, we analyzed the correlation between mesocolic area and height, weight, body surface area and body mass index.
  2. Safety of CME CME group and non-CME group were compared the differences of security, included operation time, blood loss, postoperation complications, flatus restoring time, defecation restoring time, drainage removal time, Diet restoring time, drainage volume in three days after surgery, hospital deaths, the exhaust time, hospitalization time and hospitalization costs. In addition, the feasibility of CME techniques as the surgical approach of choice for elderly patients was also evaluated.

Eligibility: Inclusion Criteria:
  -  Clinical diagnosis of colon cancer;
  -  Clinical stage Ⅰ ~ Ⅲ;
  -  Undergoing colorectal surgery for the first time;
  -  Accept laparotomy;
  -  Accept radical resection;
  -  More than 18 years.
  Exclusion Criteria:
  -  Emergency surgery;
  -  Preoperative neoadjuvant chemoradiotherapy history;
  -  Combined with other malignant diseases;
  -  Pathological stage Ⅳ patients with colon cancer.

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: Narrow Band Imaging for Diagnosis of Proximal Serrated Polyps

Summary: Although colonoscopy is considered the gold standard for diagnosis of colonic polyps, the missed rate for colonic adenoma ranged from 15-32%. In particular, missed colonic polyps in the right side colon have been suggested to be the cause for interval cancer that developed after a prior negative colonoscopy.
  Different endoscopic image enhanced modules like the narrow band imaging (NBI) have been developed to improve colonic polyp detection. However, it remains controversial whether the previous version of NBI helps to improve colonic polyp detection. The new generation colonoscope is equipped with high definition and improved narrow band imaging (NBI) which gives at least twice the viewable distance and contrast. The images obtained are far brighter with better resolution than the previous version. It however remains to be determined whether this enhanced imaging technique could help to improve colonic polyps detection.
  Hypothesis:
  The new generation NBI increases the detection rate of proximal serrated polyps and reduces the missed rate of all colorectal polyps.
  Aims:
  -  To determine whether the new generation NBI improve the detection rate of proximal serrated polyps.
  -  To determine whether the new generation NBI improve the detection rate of all colorectal adenoma and polyps.
  -  To determine whether the new generation NBI reduce the miss rate of colorectal adenoma and polyps.

Detailed description: Design:
  Prospective randomized trial
  Inclusion:
  • All patients scheduled to have screening or scheduled colonoscopy
  Exclusion:
  -  History of Crohn's or ulcerative colitis
  -  Surveillance for known polyposis syndrome (FAP or HNPCC)
  -  Previous colonic resection (except appendectomy)
  -  Refused consent
  -  Deranged coagulation profile that preclude polypectomy

Eligibility: Inclusion Criteria:
  -  All patients scheduled to have colonoscopy
  Exclusion Criteria:
  -  History of Crohn's or ulcerative colitis
  -  Surveillance for known polyposis syndrome (FAP or HNPCC)
  -  Previous colonic resection (except appendectomy)
  -  Refused consent
  -  Deranged coagulation profile that preclude polypectomy

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: Peripheral Blood DNA Methylation Markers for the Early Detection of Colorectal Carcinoma in the Egyptian Population

Summary: The incidence of colorectal cancer (CRC) is on the rise on a global scale. The number of cancer-related deaths related to CRC is also rising to an alarming level. This picture is similarly seen in Egypt where the incidence of colorectal carcinoma is increasing annually, moreover, CRC in Egypt exhibits an alarming characteristic which is the affection of much younger patients than their counterparts worldwide. Fortunately, the early detection of CRC and its precursor (adenoma) has been shown to markedly decrease morbidity and mortality related to this tumor, this has prompted the development of robust screening programs for CRC in several western countries. The implementation of a CRC screening program in Egypt has been hampered by the low compliance of the patients and the relatively high cost of colonoscopy. There is a need for an affordable, non-invasive, simple, accurate and socially accepted screening test to allow such a program to succeed in Egypt. Recent studies have shown that DNA is the future target of screening tests for several malignancies. Particularly for CRC a few preliminary studies have shown encouraging results with separate DNA methylation markers both in blood and stool. In our efforts to develop a screening test with the criteria stated above, the investigators have decided to join the forces of 2 of the largest medical centers in Egypt and the middle-east: Kasr-Alaini hospital and the National cancer institute (NCI). The investigators plan to test a panel of 7 DNA methylation markers in peripheral blood for their performance as an early marker for CRC and colorectal adenomas. Data from this study will pave the way for the development of a screening test for CRC "tailored" to the Egyptian population, moreover, it will supply essential data about the genetic alterations occurring in CRC in Egyptian patients.


Eligibility: Inclusion Criteria:
  -  Patients undergoing colonoscopy as part of their clinical care or part of screening program.
  -  Complete endoscopic examination (up to the caecum)
  -  Adequate colonic preparation
  Exclusion Criteria:
  -  - Incomplete colonoscopic examination due to technical causes e.g. difficult colonoscopy, patient intolerance (N.B. a neoplastic mass causing lumen stenosis will not be excluded.)
  -  Poor colonic preparation obscuring adequate mucosal examination.
  -  Patients who have received any treatment for CRC and/or adenomas.
  -  Patients with known malignancy elsewhere (i.e. non-colorectal malignancy)

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: Molecular Screening for Lynch Syndrome in Denmark

Summary: A clinically applicably strategy for molecular screening for Lynch Syndrome is being implemented in Denmark.
  Based on sequential analysis with immunohistochemistry and methylation analysis, patients with possible hereditary colorectal cancer are identified. These patients are offered genetic risk assessment and counselling.
  The study hypothesis is that molecular screening will identify more patients with Lynch Syndrome than the family history alone.
  Prospective data collection is performed using established clinical databases.


Eligibility: Inclusion Criteria:
  -  Histological diagnosis of colorectal adenocarcinoma
  -  Diagnosed at one of the departments of pathology in Denmark
  Exclusion Criteria:
  -  None

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: Early Recovery After Surgery (ERAS) Versus Conventional Protocol After Laparoscopic Gastrectomy

Summary: Enhanced Recovery After Surgery (ERAS) programs have been introduced with purposes of reducing the surgical stress response and obtaining optimal recovery after surgery.

Detailed description: There is strong evidence of the usefulness of the ERAS programs in patients undergoing colorectal surgery in terms of significantly reduced postoperative complications and shorter length of hospital stay, compared to the patients of conventional treatment.
  However, few studies exist about the implication of ERAS programs in the laparoscopic gastrectomy.
  The aim of this study was to compare the recovery rate, morbidity, and quality of life in the patients undergoing laparoscopic gastrectomy for gastric cancer, receiving either ERAS protocol or conventional postoperative cares.

Eligibility: Inclusion Criteria:
  -  Elective surgery
  -  American Society of Anesthesiologists (ASA) scores < 3
  -  20 < Age < 80
  -  Gastric cancer, adenocarcinoma, possible to perform laparoscopic distal gastrectomy
  -  Informed consent
  -  No other treatment (Radiation, Chemotherapy or Immunotherapy) on this gastric cancer or other type of cancer.
  -  No systemic inflammatory disease
  Exclusion Criteria:
  -  Emergency operation

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: Validation of DNA Methylation Biomarkers for Oral Cancer Detection

Summary: The aim of this study is to evaluate the association between several methylated genes and oral cancers. A prospective case control trial is designed with sample size estimated at least 160 cases. It is expected to enroll at least 100 subjects with precancerous lesion or oral cancer, and ~60 subjects with normal oral mucosa. This study is approved by the National Taiwan University Hospital Research Ethics Committee. After signing the informed consent, all of the subjects will receive an intraoral examination and the oral epithelial cells will be collected. If abnormal oral lesion is observed, it will be photographed, and the biopsy will be performed to confirm the diagnosis. For methylated gene detections, the gDNA will be extracted from the collected cells and standardized assay will be performed. Clinical sensitivity and specificity for these methylated genes will be evaluated.


Eligibility: Inclusion Criteria:
  -  Subject with age over 20.
  -  Subject agrees to sign the informed consent form.
  Exclusion Criteria:
  -  Subjects have history of head and neck cancer.
  -  Subjects have had received chemotherapy for cancers.
  -  Pregnant Woman
  -  Subjects whose has oral mucosal lichen planus.
  -  Subjects whose oral mucosal findings is abnormal, but the diagnosis is unknown.

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: The Cancer of the Pancreas Screening-5 CAPS5)Study

Summary: Johns Hopkins clinical research office quality assurance group will monitor and audit this study at Johns Hopkins. The Sub Investigator at each site will be responsible for internal monitoring at their site.

Detailed description: The Sub Investigator at each site will be responsible for internal monitoring at their site. The site sub Investigator and study team will report any serious adverse events to Principal Investigator and annually report adverse events.

Eligibility: Inclusion Criteria:
  -  Hereditary Pancreatitis or
  -  Peutz-Jeghers Syndrome or
  -  Strong family history of pancreas cancer on one side of the family tree or
  -  Confirmed germline mutation carrier (BRCA2, FAMMM, PALB2, BRCA1, HNPCC, PRSS1/2, or CTRC
  -  Endoscopic evaluation of pancreas scheduled
  Exclusion Criteria:
  -  Medical comorbidities or coagulopathy that contraindicate endoscopy
  -  Prior surgery that prevent optimal endoscopic ultrasound such as partial or complete gastrectomy with Bilroth or Roux-en-Y anastomosis
  -  Stricture or obstruction in the upper GI tract that does not allow passage of the echoendoscope
  -  Poor performance status
  -  Inability to provide informed consent
  -  Pregnancy.

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: Circulating Cell-free DNA as a Predictive Biomarker for Hepatocelluar Carcinoma.

Summary: Circulating free cell DNA (cfDNA) is extracellular fragmentation of nucleic acids that occurs both in plasma and serum. This kind of DNA which derived from the apoptotic/necrotic cells or the lysis of circulating tumor cells (CTCs) can be detectedin the patients with a variety of diseases. Emerging evidence suggests that cfDNA from patients exhibits characteristicchanges of tumors, suchas mutations, insertions/deletions, methylations,microsatellite aberrations, and copy number variations, etc. All of these reveal a visible difference between the benign conditions, and thus may be useful in the diagnosis of cancer, identification of targeted therapy, monitor responses to treatments, and early detection of relapse. The purpose for this study is to explore these characteristic changes in the patients withhepatocellular carcinoma (HCC) and expect to guide targeted therapy and identify non-invasive biomarkers of cancer diagnosis and prognosis which can be easily isolated from the circulation.

Detailed description: In cancer, cfDNA can be detected a higher concentration in the circulation because of the necrosis of neoplasm cells with the rapid enlargement and relatively shortage of blood supply. So, identifying tumor-specific genetic and epigenetic changes in cfDNA on this status, such as gene mutations, deletions, methylation alterations and microsatellite alterations, may be more specific for us to diagnose the neoplasms in early phase. This phenomenon also appears in the patients with hepatocellular carcinoma (HCC). Studies have shown that cfDNA level is associated with intrahepatic and extrahepatic metastasis in HCC patients and examined some cfDNAcharacteristic changes, such as p161NK4A, RTL, RASSF1A, LINE-1 and GSTP1. Thus is useful for us to explore the specific cfDNA in HCC. For a high sensitivity and specificity detection, we will use technologiesdeveloped at Stanford Genome Technology Centerto find more characteristic gene mutations, methylation alterations or other changes (3). In this study, we willinvestigate thesecharacteristic changesin cfDNA and primary tumor lesions.
  Study arrangement:
  Collect the DNA samples from the plasma, blood cells and solid tumor tissues in the patients with HCC.
  Detect the DNA sequence from the samples of plasma, blood cells and solid tumor tissues.
  Identify cancer specific variations in cfDNA and primary tumor lesions. Date analysis and investigate these characteristic changes. Evaluate the application in early diagnosis, treatment monitoring and prognosis for HCC.

Eligibility: Inclusion Criteria:
  Age≥18years and ≤80 years; Histologically and cytologically proven Hepatocellular carcinoma Child-Pugh：child A-B Adequate hematological, renal, cardiac and pulmonary functions Tumor in any segment of liver
  Exclusion Criteria:
  Uncontrolled systemic disease Reject the surgical treatment Metastatic carcinoma Child-Pugh：child C

Relevance to patient case: not relevant