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

Clinical trial: An Investigational Immuno-therapy Study of Nivolumab, and Nivolumab in Combination With Other Anti-cancer Drugs, in Colon Cancer That Has Come Back or Has Spread

Summary: The purpose of this study is to examine if Nivolumab by itself, or Nivolumab in combination with other anti-cancer drugs, will result in meaningful tumor size reduction, in patients with colon cancer that has come back or has spread, and who have a specific biomarker in their tumors.

Detailed description: Allocation: The Microsatellite Instability High (MSI-High) and C4 and C6 Cohort Parts of the trial are Non-randomized, The Non-MSI high Dose Escalation Phase part of the trial contained a randomized portion

Eligibility: For more information regarding BMS clinical trial participation, please visit www.BMSStudyConnect.com
  Inclusion Criteria:
  -  Men and women ≥ 18 years of age
  -  Eastern Cooperative Oncology Group (ECOG) performance status 0 to 1
  -  Histologically confirmed recurrent or metastatic colorectal cancer
  -  Measurable disease by CT or MRI
  -  Testing for MSI Status (by an accredited lab)
  1. Subjects with microsatellite instability high (MSI-H) tumors will enroll in the MSI-H Cohort (mStage and cStage groups), the C3 Cohort, and the C5 Cohort.
  2. Subjects with phenotypes that are non-microsatellite instability high (non-MSI-H) will enroll in the non- MSI-H Safety Cohort and the C6, C4 Cohorts.
  -  Adequate organ function as defined by study-specific laboratory tests
  -  Must use acceptable form of birth control throughout the study. After the final dose of study drug, an acceptable form of birth control must be used for 23 weeks for women of childbearing potential (WOCBP) and 31 weeks for men who are sexually active with WOCBP
  -  Signed informed consent
  -  Willing and able to comply with study procedures
  -  Subjects enrolled into the C3 Cohort must have not had treatment for their metastatic disease
  Exclusion Criteria:
  -  Active brain metastases or leptomeningeal metastases are not allowed.
  -  Prior treatment with an anti-Programmed Death Receptor (PD)-1, anti-PD-L1, anti-PD-L2, anti-Cytotoxic T-Cell Lymphoma-4 Antigen (CTLA-4) antibody, or any other antibody or drug specifically targeting T-cell co-stimulation or immune checkpoint pathways
  -  Prior malignancy active within the previous 3 years except for locally curable cancers
  -  Subjects with active, known or suspected autoimmune disease
  -  Subjects with a condition requiring systemic treatment with either corticosteroids or other immunosuppressive medications within 14 days of study drug administration
  Other protocol defined inclusion/exclusion criteria could apply

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

Clinical trial: OctavaColon Cancer Blood Tests OctavaGold and OctavaSilver - Blood Tests for the Help in Diagnosis of Colon Cancer Clinical Study Protocol

Summary: The OctavaColon tests are qualitative plasma tests that are indicated to people above 18 years of age suspected with colon abnormality. The blood tests will provide additional information to the doctor in the course of colon cancer diagnosis for both normal population and high risk population

Detailed description: The clinical objective of this study is to develop two antibody-based blood tests for additional information during colon cancer diagnosis -
  1. Highly specific (OctavaGold) - provides additional information to doctors during evaluation of normal population.
  2. Highly sensitive (OctavaSilver) - provides additional information to doctors during evaluation of high risk population.
  The study will be considered successful it can achieve at least one of the following sets of performances -
  1. For the OctavaGold - 95% specificity with at least 50% sensitivity.
  2. For the OctavaSilver - 95% sensitivity with at least 50% specificity. The biological objective of this study is to find the best set of antigens, that when combined with the appropriate algorithm will support each of the above clinical objectives

Eligibility: Inclusion Criteria:
  Subjects 18 years or over. Subjects scheduled for colonoscopy or surgery
  Exclusion Criteria:
  -  Subjects less than 18 years of age
  -  Previous or concurrent synchronous cancers other than previous malignancies of the colon and recovered melanoma
  -  Autoimmune disorders diagnosed subjects
  -  Hematological malignancies
  -  Subjects under active chemotherapy treatment or chemotherapy in the past 6 months
  -  Steroid treatment in the past 3 months
  -  Subject undergoing immunosuppressive treatments
  -  Subject with verified melanoma colon cancer
  -  Subject with verified sarcoma 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: Simultaneaous Detection of Quantitative Somatic Alterations Using the Qantitative Multiplex Pcr of Short Fluorescent Fragments Method (QMPSF) in Stage II-III Colon Cancer: a Prospective Study

Summary: Lymph node involvement remains the main criteria for postoperative chemotherapy in patients with colon cancer (CC) without distant metastasis. To date, the prognostic value of the somatic quantitative molecular alterations such as loss or gain of genomic region is not established in CC.
  AIMS & METHODS: Using the one-step screening method based on the Quantitative Multiplex PCR of Short fluorescent Fragments (QMPSF), we aimed to assess the prognostic role of the simultaneous detection of main quantitative somatic alterations in stage II-III CC.
  Patients and Methods. We enrolled and collected all baseline characteristics of patients operated for a stage II-III CC with storage frozen tissues. The QMPSF was based on a simultaneous amplification of 9 selected target genomic sequences from literature: DCC (18q21); EGFR (7p12); P53 (17p13.1); BLK (8p23-p22); c-myc (8q24.12); APC (5q22.2); ERBB2 (17q12); STK6 (20q13.31); NR21 (14p11.1) and two control: DCOHM (5q31.1); HMBS (11q23.3). Comparison of each amplicon electropherograms obtained from tumour vs normal peritumoral tissue allowed us to identified gain or loss genomic region. The primary end-point was the local and/or distant recurrence and relation between clinical and single or combined molecular alterations and recurrence were evaluated.


Eligibility: Inclusion Criteria:
  -  age over 18
  -  localized colon cancer
  -  proven adenocarcinoma
  -  surgery R0
  -  no metastatic disease
  -  stage II or III
  -  WHO performance status 0, 1 or 2
  -  availaible frozen tissue
  -  written consent
  -  no major co-morbidities
  Exclusion Criteria:
  -  metastatic disease
  -  hereditary colorectal cancer
  -  rectal 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: Low Glycemic Load Diet in Patients With Stage I-III Colon Cancer

Summary: This pilot clinical trial studies the feasibility of a low glycemic load diet in patients with stage I-III colon cancer. A low glycemic load diet includes foods that have low scores on the glycemic index. The glycemic index is a scale that measures how much a certain carbohydrate causes a person's blood sugar to rise. A low glycemic load diet may help decrease the chance of cancer coming back and improve the survival in patients with colon cancer.

Detailed description: PRIMARY OBJECTIVES:
  I. To determine the feasibility of following a low or medium glycemic load diet in patients with stage I-III (local-regional) colon cancer.
  SECONDARY OBJECTIVES:
  I. To determine patient-reported acceptability of diet. II. To determine nutritionist resources utilized. III. To evaluate the effect of lowering dietary glycemic load on body mass index (BMI), lipid metabolism and pro-oncogenic intermediaries of cellular metabolism.
  OUTLINE: Patients are sequentially enrolled in 1 of 4 possible cohorts as needed based on the feasibility of the prior cohort.
  COHORT 1: Patients follow a low glycemic load diet with standard dietary intervention (contact with nutritionist in person every 2 weeks with phone contact on the alternating weeks) for 12 weeks.
  COHORT 2: Patients follow a low glycemic load diet with intensified dietary intervention (contact with nutritionist in person every week) for 12 weeks.
  COHORT 3: Patients follow a medium glycemic load diet with standard dietary intervention for 12 weeks.
  COHORT 4: Patients follow a medium glycemic load diet with intensified dietary intervention for 12 weeks.

Eligibility: Inclusion Criteria:
  -  Patients must have stage I-III colon or rectal cancer and have undergone definitive therapy; definitive therapy may have included surgery alone, or surgery plus neoadjuvant and/or adjuvant therapy
  -  Patients must regularly consume a diet with a glycemic load > 150 as estimated through the 3 day food recall
  -  Patients must readily be available for a 3 month period and agree to participate in regular dietary adherence assessments (surveys and phone interviews)
  Exclusion Criteria:
  -  Current participation in an intervention targeting diet or exercise

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

Clinical trial: Metabiomics Colon Cancer Clinical Research Study

Summary: The specific aim of the study is to determine the false negative rate of the Metabiomics Colon Polyp and Colorectal Cancer Assay for Cancer.

Detailed description: The purpose of this study is to conduct clinical research to investigate the association of the gut microbiome with colonic neoplasia. In this case several types of gut microbiome samples will be collected from patients undergoing colectomy for colonic adenocarcinoma; those samples will be tested by Metabiomics Colon Polyp and Colorectal Cancer Assay and the percentage of false negative (test returns a negative for cancer) results determined.

Eligibility: Inclusion Criteria:
  -  Recently diagnosed with colorectal cancer (CRC) and scheduled for colectomy
  -  Male or female,
  -  Age: 18-95 years,
  -  Able to comprehend, sign, and date the written informed consent form (ICF),
  -  Able to give informed consent in English
  -  Women and minorities will be included.
  Exclusion Criteria:
  -  History of Inflammatory Bowel Disease
  -  Antibiotics within 2 weeks of sample collection.
  -  Colonoscopy, colon prep or bowel contrast agent within 7 days prior to sample collection
  -  Any radiation therapy

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

Clinical trial: Study of Berberine Hydrochloride in Prevention of Colorectal Adenomas Recurrence

Summary: Berberine hydrochloride is a conventional component in Chinese medicine. In recent years, anticancer activity of berberine hydrochloride have been explored. The aim of this study is to investigate the effect of berberine hydrochloride on the recurrence of colorectal adenomas.

Detailed description: Colorectal adenomas are well-known to be precancerous lesions that develop into colorectal cancers on the basis of the adenoma-carcinoma sequence. The effects of screening for colorectal adenomas and removing precancerous lesions on the prevention of colorectal cancer have been established. Because of the high recurrence rates of colorectal adenomas in patients who have undergone polypectomy, the potential chemopreventive agents that may reduce the risk of colorectal adenoma recurrence need to be investigated.
  Berberine hydrochloride is a conventional component in Chinese medicine. In recent years, anticancer activity of berberine hydrochloride have been explored. The aim of this study is to investigate the effect of berberine hydrochloride on the recurrence of colorectal adenomas by conducting a randomized, placebo-controlled, prospective clinical.

Eligibility: Inclusion criteria
  -  Individuals aged 18-75 years
  -  Individuals who had at least one and no more than 6 histologically confirmed CRAs removed within 6 months before recruitment
  -  Individuals who are able to swallow pills
  -  Individuals who voluntarily sign the consent form after being fully informed and understanding the purpose and procedure of this study, characters of the disease, effect of medication, methods of related examinations, and potential risk/benefits of the study 4.2 Exclusion criteria
  -  Individuals whose adenoma was not completely removed during previous colonoscopy
  -  Individuals with a history of familial adenomatous polyposis (FAP) or hereditary non-polyposis colorectal cancer (HNPCC, Lynch syndrome)
  -  Individuals who are taking regularly aspirin, nonsteroidal anti-inflammatory drugs (NSAIDs), cyclo-oxygenase 2 (COX2) inhibitors, calcium or vitamin D
  -  Individuals with a history of subtotal/total gastrectomy or partial bowel resection
  -  Individuals who are intolerant to another colonoscopy examination
  -  Individuals who are hypersensitive or intolerant to the drugs
  -  Individuals with severe heart, liver or kidney disease, or any cancer history
  -  Individuals presenting severe constipation
  -  Pregnant women, women during breast-feeding period, or women with expect pregnancy
  -  Individuals with mental diseases who are not able to cooperate
  -  Individuals who are involved in designing, planning or performing this trial

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

Clinical trial: Pain After Endoscopic Submucosal Dissection

Summary: Endoscopic submucosal dissection (ESD) is widely used for local treatment of gastric neoplasms. Although ESD-related complications such as bleeding and perforation have been reported, data is currently lacking on the development of pain, which is one of the most common adverse events after ESD. Therefore, in the present study, we investigated the incidence and clinicopathologic risk factors of pain after ESD.

Detailed description: A prospective randomized controlled study was conducted evaluating 156 patients with gastric neoplasms treated by ESD at Gangnam Severance Hospital between April 2011 and December 2014. All subjects were randomly assigned to treatment with intravenous proton pump inhibitor (PPI) either before or after ESD.

Eligibility: Inclusion Criteria:
  -  patients undergoing ESD for gastric neoplasms
  Exclusion Criteria:
  -  (1) history of acid suppressive medication within 1 week prior to the procedure; (2) known gastrointestinal disorders, such as peptic ulcer disease, which might impact epigastric pain assessment; (3) current or regular use of pain medication; (4) history of upper gastrointestinal surgery; (5) multiple lesions requiring ESD; (6) perforation during ESD; and (7) significant cardiovascular, renal, hepatic, neurotic, or psychological disorders

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

Clinical trial: A Trial of Aspirin on Recurrence and Survival in Colon Cancer Patients

Summary: The purpose of this study is to determine whether acetylsalicylic acidis effective on the recurrence and survival of colon cancer patients.

Detailed description: The purpose of this study is to determine the effect of 80mg acetylsalicylic acid (given orally once daily for 5 years) on 5 year overall survival (OS) for stage II and III colon cancer patients of 45 years of age and older. Preclinical, epidemiologic and clinical evidence suggest that acetylsalicylic acid use may reduce overall cancer risk and mortality in colon cancer patients. It is a phase III double blind placebo controlled, randomized trial of adjuvant low-dose acetylsalicylic acid in colon cancer patients. Patients will be stratified at randomization by centre, age (<70 and ≥70 years) chemotherapy use (any versus none) and disease stage.

Eligibility: Inclusion Criteria:
  -  Age ≥45 years
  -  Patients must have TNM stage that is one of the following: pT3-4; N0-2 and M0, or pT1-2 and N1-2 (UICC stage II and III) (in case of >1 tumour: largest tumour is stage II or III)
  -  Patients must have completed surgical resection (R0) (both laparoscopic and open surgery) within 12 weeks of randomisation
  Exclusion Criteria:
  -  Patients with rectal cancer (defined as tumour within 15 cm from the anal verge)
  -  Patients currently taking oral anti-coagulants or use of LMWH
  -  Patients currently taking acetylsalicylic acid for any reason
  -  Patients with a history of bleeding disorders or active gastric or duodenal ulcers
  -  Patients currently taking high dose systemic glucocorticoids.(≥ 30 mg predniso(lo)n)
  -  Patients with (suspected) (non-) polyposis syndrome (FAP/AFAP, MAP, Lynch syndrome)
  -  Patients with >100 polyps of the colon or a known hereditary syndrome of the colon in a first degree family member
  -  Allergy or intolerance to salicylates.
  -  Patients with a history of other malignancies in the last 5 years, except for SCC or CIN.
  -  Presence of any psychological, familial, sociological or geographical condition potentially hampering compliance with the study protocol and follow-up schedule; those conditions should be discussed with the patient before registration in the trial

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

Clinical trial: Study of Synapsis and Recombination in Male Meiosis and the Implications in Infertility

Summary: The aim of this study was to assess meiotic recombination in primary spermatocytes, synaptonemal complex length and the correlation with chromosomal abnormalities in testicular spermatozoa from infertile men with idiopathic non-obstructive azoospermia (NOA).

Detailed description: During the first meiotic division in spermatogenesis there are two critical events. First, synapsis between homologous chromosomes and formation of the synaptonemal complex (SC), which regulates sister chromatid cohesion and provides the template for localization of recombination machinery proteins. Secondly, recombination between homologous chromosomes, which is essential for the correct segregation. Errors during these two processes may induce incorrect segregation of chromosomes and are a major cause of gamete aneuploidy. The aim of this study was to assess meiotic recombination in primary spermatocytes, synaptonemal complex length and the correlation with chromosomal abnormalities in testicular spermatozoa from infertile men with idiopathic non-obstructive azoospermia (NOA). Prospective cohort study to assess meiotic progression, total length of SC, frequency of recombination and sperm aneuploidy in samples obtained from testicular biopsies from NOA patients. The study group was compared with a control group from post-vasectomized (OA) patients. Immunocytogenetics with SCYP3, CREST and MLH1 antibodies for meiotic progression, SC length, and recombination. Fluorescence in situ Hybridization (FISH) for chromosomes 1, 4, 6, 13, 16, 18, 21, 22 in primary spermatocytes and chromosomes 13, 18, 21, X, Y on sperm. MicroMeasure 3.3 program was used for SC length.

Eligibility: Inclusion Criteria:
  -  NOA patients undergoing ICSI with testicular sperm
  -  OA post-vasectomized patients undergoing ICSI with testicular sperm
  Exclusion Criteria:
  -  Abnormal Karyotype

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

Clinical trial: Celiac Plexus Radiosurgery for Pain Management

Summary: This prospective study evaluates celiac plexus radiosurgery for pain control in patients with upper abdominal malignancies.

Detailed description: This study aims as primary objective to evaluate short and long term pain relief following the administration of radiosurgery to the celiac plexus in patients with upper abdominal cancer. As secondary objectives it will describe acute and late side effects and quality of life measures of patients undergoing the treatment.
  The study has a prospective, single arm design. It will be composed from an initial run-in safety assessment that will include 6 patients and then continue as a phase II trial. All eligible patients will receive the same protocol of celiac plexus radiosurgery and will be evaluated before, during and following this treatment.
  The treatment duration is one and a half weeks (5 fractions delivered every other weekday).

Eligibility: Inclusion Criteria:
  -  Patients with upper abdominal cancer (pancreatic/gastric/colon/hepato-biliary cancer) with typical retroperitoneal pain syndrome (somatic pain that radiates from the upper abdomen to the back) thought to be secondary to celiac plexus involvement, directly or indirectly, and have high level of pain despite opioids usage (NRS >4). Patients with other cancer types metastatic to the celiac lymph nodes will also be eligible
  -  Recent abdominal imaging (CT, PET or MRI) should be at most 2 months old.
  -  Prior chemotherapy or biological treatment is allowed, but any active oncological treatment should be stopped at least 1 week prior to radiation and renewed at least 1 week following radiation. Following gemcitabine 2 weeks are required between final dose and commencement of radiation
  -  Absence of any psychological, familial, sociological or geographical condition potentially hampering compliance with the study protocol and follow-up schedule; those conditions should be discussed with the patient before registration in the trial
  Exclusion Criteria:
  -  Patients under 18 years of age
  -  Patients who are well balanced in terms of pain control
  -  Patients with life expectancy <8 weeks
  -  Patients with ECOG (Eastern cooperative oncology group) performance status 4
  -  Any concurrent chemotherapy or biologic treatment is prohibited during 1 week before until 1 week following radiotherapy
  -  Special populations: pregnant women, prisoners, patients with major psychiatric illnesses
  -  Previous radiotherapy to upper abdomen
  -  Conditions associated with increased side effects to radiotherapy (IBD (inflammatory bowel disease) for example)

Relevance to patient case: not relevant