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

Clinical trial: Imatinib as Pre-operative Anti-Colon Cancer Targeted Therapy

Summary: In this proof-of-concept trial the investigators will study the effects of imatinib treatment on the biology of mesenchymal-type colon cancers.

Detailed description: Tumor biopsies from patients with newly diagnosed colon cancer will be pre-screened with an RT-qPCR test to identify tumors of the mesenchymal subtype. Patients with mesenchymal-type tumors that meet the in- and exclusion criteria will be treated with imatinib during the "window period" that normally precedes surgery. Immediately following tumor resection, biopsies will be taken from the surgical specimen. Gene and protein expression of the pre- and post-treatments biopsies will be compared to assess the effects of imatinib therapy on PDGFR- and cKIT-signalling and on the mesenchymal gene expression profile.

Eligibility: Inclusion Criteria:
  1. Male or female aged ≥18 years
  2. Histologically proven adenocarcinoma of the colon;
  3. Completed cancer staging with CT-abdomen and CT-thorax/X-thorax according to hospital's standard of care;
  4. Confirmed eligibility for surgery with curative intent as deemed by the hospital's multidisciplinary board (MDB) review;
  5. An intratumoural gene expression profile of PDGFR-α, PDGFR-β, PDGF-C and KIT, indicative of the mesenchymal phenotype, according to our diagnostic RT-qPCR test (i.e. more than 50% chance of having the mesenchymal phenotype);
  6. Minimum of four properly stored pre-treatment biopsies for gene expression analysis/ELISA;
  7. WHO performance status 0 or 1;
  8. Adequate haematology status and organ function, defined as:
  -  Normal creatinine clearance (≥60 ml/min (MRDR))
  -  ALAT within 2.5x upper limit of normal (ULN)
  -  PT-INR < 1.5
  -  Leukocytes > 1,5*10^9/L; Hb > 6.0 mmol/L; platelets > 100*10^9/L
  9. Willingness and ability to comply with scheduled visits, treatment plans and laboratory tests;
  10. Written informed consent.
  Exclusion Criteria:
  1. The presence of synchronous distant metastases;
  2. Current hospital standard of care dictates that subject should undergo any neoadjuvant therapy;
  3. Concurrent participation in another clinical trial using any medicinal product, or participation in such a trial in the period of three months prior to the current trial;
  4. Women who are pregnant, plan to become pregnant or are lactating during the study or for up to 30 days after the last dose of imatinib;
  5. Known HIV or Hepatitis B/C infection;
  6. Known symptomatic congestive heart failure;
  7. Co-morbidity requiring concomitant treatment with drugs that act as strong inducers of CYP3A4 or with drugs with a narrow therapeutic range influenced by imatinib

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

Clinical trial: Colon Cancer Risk-stratification Via Optical Analysis of Rectal Ultrastructure

Summary: This is a study whose focus is on understanding the clinical utility of rectal ultrastructure in detecting colonic neoplasm. The method uses Low-coherence Enhanced Backscattering Spectroscopy (LEBS).

Detailed description: The investigators use an optic probe which is a small device that uses light to assess the colon tissue. This probe will be used to identify subjects who do and do not have precancerous changes in the colon by capturing the light reflected back from the rectal wall and that will be assessed without the need for colonoscopy and bowel preparation (i.e unprepped). This device may detect early cancerous changes in colon tissue with higher accuracy than current tests.

Eligibility: Inclusion Criteria:
  - Subjects are eligible if they were scheduled for colonoscopy for colon cancer screening or surveillance
  Exclusion Criteria:
  -  age <50
  -  personal/family history of colonic neoplasia
  -  personal history of coagulopathy
  -  (retrospectively) failure to complete or inadequate colonoscopy
  -  any patients harboring non-pathoglocially normal rectum (i.e. presence of lesion, inflammation, polyp, adenomas at 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: A Study of LY3039478 in Participants With Advanced or Metastatic Solid Tumors

Summary: The main purpose of this study is to evaluate the safety of the study drug known as LY3039478 in combination with other anticancer agents in participants with advanced or metastatic solid tumors.


Eligibility: Inclusion Criteria:
  -  For all parts: The participant must be, in the judgment of the investigator, an appropriate candidate for experimental therapy after available standard therapies have failed to provide clinical benefit for their advanced or metastatic cancer.
  -  For dose escalation for all combinations: The participant must have histological or cytological evidence of cancer, either a solid tumor or a lymphoma, which is advanced or metastatic.
  -  For Part A dose confirmation: All participants must have histological evidence of advanced or metastatic soft tissue sarcoma or breast cancer. Breast cancer participants must have prescreened mutations, amplification, or gene/protein expression alterations related to Notch pathway.
  -  For Part B dose confirmation: All participants must have histological evidence of advanced or metastatic colon cancer or soft tissue sarcoma. Colon cancer participants must have prescreened mutations, amplification, or gene/protein expression alterations related to Notch pathway.
  -  For Part C dose confirmation: All participants must have histological evidence of advanced or metastatic breast cancer and prescreened mutations, amplification, or gene/protein expression alterations related to Notch pathway.
  -  For Part D dose confirmation: All participants must have histological evidence of cholangiocarcinoma and prescreened mutations, amplification, or gene/protein expression alterations related to Notch pathway. Participants must not have received >1 line of prior systemic therapy for metastatic or resectable disease (that is, participants may have received adjuvant gemcitabine and then later gemcitabine/cisplatin for recurrent metastatic disease).
  -  For Part E dose confirmation: All participants must have histological evidence of locally advanced or metastatic triple negative breast cancer (TNBC) and prescreened mutations, amplification, or gene/protein expression alterations related to Notch pathway. Participants must not have received >2 lines of systemic treatment for advanced or metastatic TNBC.
  -  Have adequate organ function.
  -  Have a performance status of ≤1 on the Eastern Cooperative Oncology Group (ECOG) scale.
  -  Have discontinued all previous therapies for cancer.
  Exclusion Criteria:
  -  Have current acute leukemia.
  -  Have current or recent (within 3 months of study drug administration) gastrointestinal disease with chronic or intermittent diarrhea, or disorders that increase the risk of diarrhea, such as inflammatory bowel disease.

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

Clinical trial: I-scan for Adenoma Detection

Summary: This study is a randomized controlled trial to determine whether i-scan can improve the detection of conventional adenomas and sessile serrated adenomas/polyps.

Detailed description: This is a randomized controlled trial comparing the use of i-scan (digital surface and contrast enhancement of the mucosa) versus standard high-definition white light for the detection of conventional adenomas and sessile serrated adenomas/polyps. 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 sessile serrated adenomas/polyps (SSA) are located primarily proximal to the splenic flexure. Sessile serrated adenomas/polyps 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. Recent studies have shown that image enhanced endoscopy can highlight the appearance of these lesions. This study will test whether i-scan increases the detection of conventional adenomas and sessile serrated adenomas/polyps in a randomized controlled trial.

Eligibility: Inclusion Criteria:
  -  Age 50-75
  -  Intact colon and rectum
  -  Willing to sign an informed consent form
  Exclusion Criteria:
  -  Subjects less than 50 years of age or greater than 75 years of age
  -  Subjects who are in the inpatient unit
  -  Subjects with diverticulitis,
  -  Subjects with inflammatory bowel disease
  -  Subjects with polyposis syndromes
  -  Subjects with previous surgical resection of any portion of the colon or rectum
  -  Subjects referred for endoscopic resection of previously diagnosed colorectal polyp

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

Clinical trial: Laparoscopic Surgery for T4 Tumor of the Colon Cancer

Summary: The purpose of this study is to compare the short- and long-term survival of laparoscopic surgery and conventional open surgery for T4 colon cancer.

Detailed description: The investigators previous study indicated that laparoscopic surgery is feasible in T4 colon cancers with comparable clinical and oncologic outcomes. Laparoscopy can be considered as an alternative approach for T4 colon cancers with the advantage of faster recovery. However, the clinical value of laparoscopic surgery for T4 colon cancer was only validated in some retrospective study and some prospective study in single institute with small sample of patients. The aim of the present study is to compare the short-and long-term survival outcomes of laparoscopic surgery and conventional open surgery for T4 colon cancer as well as the mortality and the morbidity.
  The number of patients needed to get a 80% power is 1960. The average number of patients/surgical center is approximately 200 in each of 10 surgical centers.
  The preoperative, intraoperative and postoperative period will be in complete accordance with the usual care of the center.
  The baseline demographics and conditions as well as the perioperative items and the postoperative occurrences will be recorded through a prior designed e-questionnaire.
  Systematically analyze and compare the disease free survival rate, the mortality, the morbidity, and the proportion of completion of laparoscopic surgery of the two surgical strategies (laparoscopy VS conventional open surgery).

Eligibility: Inclusion Criteria:
  -  Able to provide written informed consent
  -  Histologically confirmed diagnosis of colon carcinoma
  -  CT or MRI verified as T4 colon cancer without involvement of other organs
  -  Without multiple lesion other than carcinoma in situ
  -  Tumor size < 8 cm
  -  No bowel obstruction
  -  Sufficient organ function
  -  No history of gastrointestinal surgery
  -  18 years of age or older
  -  Performance Status (ECOG) 0, 1 or 2 and life expectancy > 12 weeks
  -  Operable patients
  Exclusion Criteria:
  -  Women who are pregnant (confirmed by serum b-HCG in women of reproductive age) or breast feeding
  -  Unstable or uncompensated respiratory or cardiac disease
  -  Serious active infections
  -  Hypersensitivity to capecitabine/fluorouracil or oxaliplatin
  -  Stomatitis, ulceration in the mouth or gastrointestinal tract
  -  Severe diarrhea
  -  Peripheral sensory neuropathy with functional impairment

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 Study of Prexasertib (LY2606368) in Combination With Ralimetinib in Participants With Advanced or Metastatic Cancer

Summary: The main purpose of this study is to evaluate the safety of the study drug prexasertib in combination with ralimetinib in participants with advanced or metastatic cancer.


Eligibility: Inclusion Criteria:
  -  Advanced or metastatic cancer.
  -  Able to swallow tablets.
  -  For Part B, you will need to have colon cancer or non-small cell lung (NSCLC) cancer with KRAS and/or BRAF mutations.
  -  Discontinued all previous treatments for cancer and recovered from the acute effects from the therapy.
  Exclusion Criteria:
  -  Active infection (fungal, viral, or bacterial).
  -  Active cancer in your brain or spinal cord.
  -  Acute or chronic leukemia.
  -  Serious heart condition.
  -  Disease that requires immunosuppressant therapy.
  -  Diagnosis of inflammatory bowel disease.
  -  Major small bowel resection that interferes with your body's ability to absorb the oral medicine.
  -  Participated in other clinical trials investigating prexasertib or ralimetinib.
  -  Pregnant or breastfeeding.
  -  Other pre-existing conditions or medical history which your doctor will explain to you.

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

Clinical trial: Neoadjuvant Chemotherapy for the Treatment of Resectable Locally Advanced Colon Cancer

Summary: A randomized controlled clinical trial to compare the short and long outcomes of Neoadjuvant chemotherapy with postoperative chemotherapy in patients with resectable locally advanced colon cancer

Detailed description: For resectable locally advanced colon cancer, the preferred treatment is colectomy with en bloc removal of the regional lymph nodes followed by chemotherapy of about 6 months. However, surgery may postpone the administration of chemotherapy due to postoperative complications such as anastomosis leakage, abdominal infection, thus leads to a poor survival. Some scholars suggested that for patients with locally advanced colon cancer, chemotherapy given before surgery might shrink or downstage tumor, facilitate surgery and promote a better oncological outcome. Whether adjuvant chemotherapy benefits these patients with better outcome still remains controversial.
  In this study, eligible patients will be randomly allocated to receive either adjuvant chemotherapy or not. For patients receiving adjuvant chemotherapy, surgery will be performed 3-4 weeks later. Preoperative and postoperative chemotherapy will be given for a total of about 6 months. For patients receiving no preoperative chemotherapy, chemotherapy will be given for about 6 months postoperatively. The recommended chemotherapy regimes includes FOLFOX, CapeOX, FOLFIRI, Capecitabine monotherapy. Patients will be followed up every 3 months for 2 year, every 6 months for 3 years postoperatively.

Eligibility: Inclusion Criteria:
  -  Patients suitable for curative surgery between 18 to 80 years old;
  -  American Society of Anesthesiologists(ASA) grade I-III;
  -  Pathological diagnosis of adenocarcinoma;
  -  Tumor located between the cecum and sigmoid colon;
  -  Enhanced CT scan of chest, abdominal and pelvic cavity: preoperative assessment of tumor stage is T3-T4 N0 or T any N+ (according to the National Comprehensive Cancer Network(NCCN) clinical practice guidelines in oncology: colon cancer version 2.2015);there is no distant metastasis;
  -  Informed consent;
  -  No preoperative chemoradiotherapy;
  -  No history of familial adenomatous polyposis, ulcerative colitis or Crohn's disease.
  Exclusion Criteria:
  -  Pregnant patient;
  -  History of psychiatric disease;
  -  Use of systemic steroids;
  -  Simultaneous multiple primary colorectal cancer;
  -  Preoperative imaging examination results show:
  1. distant metastasis;
  2. unable to perform R0 resection;
  -  Postoperative pathology of T1-T2 N0;
  -  History of any other malignant tumor in recent 5 years;
  -  Patients need emergency operation: mechanic ileus, perforation.

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-Follow up Study

Summary: This is a follow up study which aims to evaluate the correlation between several methylated genes (potential biomarkers) and oral cancers. A prospective case control trial is designed with sample size of at least 300 cases with estimated 200 subjects with precancerous lesion or oral cancer, and 100 subjects with normal oral mucosa. This study is approved by the National Taiwan University Hospital Research Ethics Committee. After signing the informed consent, all subjects will receive an intraoral examination and followed by epithelial cells collection with oral swab. The gDNA will be extracted from the oral swab collected cells and followed by bisulfite conversion procedures. Subsequently, bisulfite converted DNA will be subjected to methylated gene detection by Real-Time PCR. The methylation index (clinical sensitivity and specificity) of oral cancer related genes will be evaluated. For diagnosis confirmation, photos and biopsy specimens will be taken upon observation of abnormal lesion.


Eligibility: Inclusion Criteria:
  -  Subject with age over 20.
  -  Subjects with oral mucosal findings (normal, oral mucosal lichen planus, precancerous lesion, and oral cancer) or subjects who have involved in the previous study (NCT01945697).
  -  Subjects agrees to sign the informed consent form.
  Exclusion Criteria:
  -  Pregnant woman.
  -  Subject disagrees to sign the informed consent form.

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

Clinical trial: Prognostic Impact of Programmed Death Ligand-1 Expression in Advanced Endometrial Cancer

Summary: The aim of this study was to assess the frequency of PD-L1 expression in stage III-IV ECs and to investigate its correlation impact with progression-free survival (PFS), and clinicopathological features including microsatellite instability and quantified stromal and intraepithelial tumor-infiltrating CD8+ lymphocytes (TILs)


Eligibility: Inclusion Criteria:
  -  All patients consecutively enrolled from January 2004 to December 2014 treated for Endometrial cancer
  -  Stage III-IV endometrial cancer with available tissue blocks, including biopsies, hysterectomy specimens and resections of metastatic foci
  Exclusion Criteria:
  -  A patient record captured outside the time frame from January 2004 to December 2014

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

Clinical trial: Diagnosis of Lynch Syndrome Based on Next-generation Sequencing in Colorectal Cancer

Summary: The purpose of this study is to determine the proportion of patients diagnosed with Lynch syndrome in colorectal cancer patients with the loss of staining by immunohistochemistry (IHC) of any of the mismatch repair (MMR) proteins. Besides, this study aims to test the specificity and the sensitivity of detecting microsatellite instability (MSI) by next-generation sequencing, and to find out the consistency between IHC and MSI in colorectal cancer patients in China. In addition, researchers want to analyze the clinical characteristics and germline mutation of Lynch syndrome in Chinese population.

Detailed description: 1. Detect microsatellite instability (by next-generation sequencing and PCR capillary electrophoresis) and germline mutation (by next-generation sequencing) in probands.
  2. Analyze the test outcome with clinical and family information to evaluate the germline mutation status preliminarily: likely pathogenic germline mutation, variant of uncertain significance, non-pathogenic germline mutation.
  3. Verify the germline mutation in blood relatives whose proband has known likely pathogenic germline mutation or variant of uncertain significance.
  4. Diagnose pathogenic germline mutation and non-pathogenic germline mutation based on clinical characteristics, family information and germline mutation test outcomes (including the outcomes of probands and blood relatives). Diagnose Lynch syndrome and the pathogenic germline mutation carriers in the included population.
  5. Analyze the specificity and the sensitivity of detecting microsatellite instability (MSI) by next-generation sequencing; and analyze the consistency between IHC and MSI.
  6. Analyze the clinical characteristics and germline mutation of Lynch syndrome in Chinese population.

Eligibility: For probands, the inclusion criteria:
  All of the following four points should be satisfied:
  -  Histological diagnosis of colorectal cancer;
  -  With the loss of staining by immunohistochemistry of any of the mismatch repair (MMR) proteins (MLH1, MSH2, MSH6, PMS2);
  -  With sufficient tumor tissue and normal tissue to test;
  -  Agree to provide basic information, clinical information and family history of cancer information.
  For probands, the exclusion criteria:
  -  With at least one blood relative with known pathogenic germline mutation(s).
  For blood relatives verifying germline mutation, the inclusion criteria:
  All of the following three points should be satisfied:
  -  First- to second-degree blood relatives of probands with germline mutation(s).
  -  With Sufficient tumor tissue and normal tissue to test.
  -  Agree to provide basic information, clinical information and family history of cancer information.
  For blood relatives verifying germline mutation, the exclusion criteria:
  -  Blood relatives who refuse to test.

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

Clinical trial: Phase Ib Study of PDR001 in Combination With Regorafenib in Adult Patients With Previously Treated Metastatic Colorectal Cancer

Summary: This is a phase Ib study of PDR001 in combination with regorafenib in adult patients with previously treated metastatic microsatellite stable (MSS) colorectal cancer. The study will assess primarily the safety and tolerability of PDR001 in combination with regorafenib.


Eligibility: Key inclusion criteria:
  1. Patients with metastatic colorectal adenocarcinoma.
  2. Patients must provide a newly obtained or an archival tumor sample corresponding to CRC diagnosis (primary tumor) with sufficient tissue quality (qualified) for analysis
  3. Patients must provide a newly obtained tumor tissue sample from a metastatic site
  4. Patients with the presence of at least one lesion with measurable disease as per RECIST
  5. Patients previously treated with two prior regimen as per standard of care and have experienced disease progression (including -VEGF and EGFR targeted therapies (if KRAS wild).
  6. Patient has an Eastern Cooperative Oncology Group (ECOG) performance status 0-1
  Key exclusion criteria:
  1. Patients with MSI-H colorectal adenocarcinoma as defined per local assessment using standard of care testing
  2. Patients with metastatic disease amenable to be resected with potentially curative surgery
  3. Patients who have had chemotherapy, radiation, or biological cancer therapy within 14 days prior to the first dose of study treatment
  4. Patients with a history of prior treatment with anti-PD-1, anti-PD-L1, anti-PDL2, anti- CTLA-4 antibodies, other checkpoint inhibitors
  Other protocol-defined inclusion/exclusion criteria may apply

Relevance to patient case: not relevant