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

Clinical trial: Microbiome, Exercise Tracking Study (METS)

Summary: The purpose of this study has 2 aims:
  Aim 1: To demonstrate the feasibility of recruiting and retaining adults at high risk of colorectal cancer to a physical activity intervention trial. Investigators hypothesize that it will be possible to recruit and retain this patient population to a physical activity intervention trial.
  Aim 2: To demonstrate the feasibility of collecting, processing, storing stool samples and analyzing the gut microbiome data. Investigators hypothesize that all of these steps are feasible.

Detailed description: Colorectal cancer (CRC) is the second leading cause of cancer-related deaths in the U.S. and is the third most common cancer in men and women. CRC risk factors include genetic predisposition, host factors and modifiable lifestyle behaviors (e.g., diet, physical activity, obesity). There are very limited data on the differences in the gut microbiota among populations at different levels of CRC risk, as well as the effects of behavioral interventions to alter the gut microbiome.

Eligibility: Inclusion Criteria:
  1. Fluent in English or Spanish;
  2. At high risk of developing colorectal cancer;
  3. No history of colorectal cancer, including germ-line heritable colorectal cancers such as Familial Adenomatous Polyposis (FAP) and Hereditary Nonpolyposis Colorectal Cancer (HNPCC);
  4. No use of antibiotics in the previous 3 months; or current regular use of antibiotics
  5. Access to either smart phone or computer; and
  6. Currently physically inactive.
  Exclusion Criteria:
  Any criterion not met under inclusion.

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

Clinical trial: Epidemiological and Molecular Colorectal Cancer Registry

Summary: This is a Registry that invites patients undergoing colorectal surgery for colorectal cancer. Epidemiological data is collected. The Registry includes tumor tissue and blood banks for analyzing different genetic mutations and disease-specific biomarkers.


Eligibility: Inclusion Criteria:
  -  Adult patients undergoing colorectal surgery for colorectal cancer.
  Exclusion Criteria:
  -  Unwillingness to participate.

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

Clinical trial: A 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: possibly relevant
Patient case: 35-year-old female with Colorectal cancer. Genetic variant: FGFR1 Amplification. Other conditions: None.

Clinical trial: Adjuvant Chemotherapy Combined With Huaier Granule for Treating High-risk Stage II, Stage III Colorectal Cancer

Summary: A randomized, paralleled control clinical study investigating Huaier Granule for prevention of recurrence and metastasis of colorectal cancer after radical surgery, to evaluate the efficacy and safety.


Eligibility: Inclusion Criteria:
  -  The subjects volunteer to sign the informed consent
  -  Aged: 18 to 75 years old
  -  Colorectal cancer (AJCC-TNM, high-risk Stage II and Stage III)
  -  The diagnosis and colorectal cancer has been confirmed by pathological examination after radical surgery
  -  The liver and kidney function satisfies the following conditions within 15 days after surgery (excluding day 15): aspartate aminotransferase (AST), glutamic-oxalacetic transaminase (ALT), alkaline phosphatase (ALP)< 2 upper limit of normal (ULN), total bilirubin ≤ 1.5 ULN, serum creatinine < 1.5 ULN; normal coagulation function
  -  Other laboratory tests meet the following requirements within 15 days after surgery (excluding day 15): white blood cells count ≥ 3.0×109/L, absolute neutrophil count ≥ 1.5×109/L, platelet count ≥ 100×109/L
  -  ECOG：0-2 points
  -  No other previous history of malignancy.
  Exclusion Criteria:
  -  Multiple primary cancer
  -  Not recover from the colorectal surgery
  -  Presence of organ, bone, or skin metastases
  -  Pregnant or lactating women
  -  Those with active bleeding due to various reasons
  -  Those with HIV infection or AIDS-associated diseases
  -  Those with severe acute and chronic diseases
  -  Those with severe diabetes
  -  Those with serious infectious diseases
  -  Those who can not take drugs by oral route
  -  Drug abusers or those with psychological or mental diseases that may interfere with study compliance
  -  Conditions that are considered not suitable for this study investigators

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

Clinical trial: Huaier Granule As Adjuvant Therapy for Colorectal Cancer After Radical Surgery

Summary: A randomized, paralleled control clinical study investigating Huaier Granule for prevention of recurrence and metastasis of colorectal cancer after radical surgery, to evaluate the efficacy and safety.


Eligibility: Inclusion Criteria:
  -  The subjects volunteer to sign the informed consent;
  -  Aged: 18 to 75 years old;
  -  Colorectal cancer (AJCC-TNM, Stage Ⅰ, low-risk Stage Ⅱand Stage Ⅲ; Patients with Stage Ⅲ colorectal cancer refuse to postoperative adjuvant chemotherapy);
  -  The diagnosis and colorectal cancer has been confirmed by pathological examination after radical surgery;
  -  The liver and kidney function satisfies the following conditions within 15 days after surgery (excluding day 15): aspartate aminotransferase (AST), glutamic-oxalacetic transaminase (ALT), alkaline phosphatase (ALP)< 2 upper limit of normal (ULN), total bilirubin ≤ 1.5 ULN, serum creatinine < 1.5 ULN; normal coagulation function;
  -  Other laboratory tests meet the following requirements within 15 days after surgery (excluding day 15): white blood cells count ≥ 3.0×109/L, absolute neutrophil count ≥ 1.5×109/L, platelet count ≥ 100×109/L;
  -  ECOG：0-2 points；
  -  No other previous history of malignancy.
  Exclusion Criteria:
  -  Multiple primary cancer;
  -  Not recover from the colorectal surgery;
  -  Presence of organ, bone, or skin metastases;
  -  Pregnant or lactating women;
  -  Those with active bleeding due to various reasons;
  -  Those with HIV infection or AIDS-associated diseases;
  -  Those with severe acute and chronic diseases;
  -  Those with severe diabetes;
  -  Those with serious infectious diseases;
  -  Those who can not take drugs by oral route;
  -  Drug abusers or those with psychological or mental diseases that may interfere with study compliance;
  -  Conditions that are considered not suitable for this study investigators.

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

Clinical trial: Full-spectrum Endoscopy in Colorectal Cancer Screening

Summary: The purpose of this study is to compare the adenoma detection rates of full-spectrum endoscopy versus standard forward-viewing colonoscopy in colorectal cancer screening programme.

Detailed description: Colorectal cancer is the third most common neoplasia and the second leading cause of cancer death in West countries. Colonoscopy is the gold standard for prevention of colorectal cancer disease. Screening for colorectal cancer with biennial faecal occult blood testing is a widely used strategy followed by colonoscopy for those with a positive test. Colonoscopy identifies polyps during the procedure as well as polyp removal in order to prevent progression to cancer. Although, interval cancer appears after a colonoscopy because of 22-28% of polyp missed rates. Advanced Technology may improve adenoma detection rates so decrease interval cancer and reduce mortally. Full-spectrum endoscopy with 330º angle vision decrease adenoma miss rate in general population.
  The investigators conducted a randomized trial in patients from colorectal cancer screening programme (aged 50-69 years) after faecal immunological test positive. One arm the colonoscopy is performed with standard forward view colonoscopy (170º angle view) and the other arm is performed with full-spectrum endoscopy (EndoChoice) (330º angle view)

Eligibility: Inclusion Criteria:
  -  patient referred for colorectal cancer screening with positive fecal inmunological test.
  -  Age between 50 and 69 years
  Exclusion Criteria:
  -  history of colonic resection,
  -  high risk for colorectal cancer like family history of colorectal cancer o polyposis syndrome,
  -  inflammatory bowel disease,
  -  patients with lower gastrointestinal bleeding symptoms,
  -  acute diverticulitis,
  -  colonic strictures,
  -  poor bowel preparation (Boston scale less than 5 points)

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

Clinical trial: Proteomics of Papillary Thyroid Carcinoma

Summary: Thyroid carcinoma is the common endocrine system malignant neoplasm. At present it has become the malignant neoplasm of fastest growing incidence rate. More than 85% thyroid carcinoma is papillary thyroid carcinoma. Cervical lymph node metastasis is common in papillary thyroid carcinoma patients. This study aim to reveal protein expression differences between papillary thyroid carcinoma with cervical lymph node metastasis and without cervical lymph node metastasis.

Detailed description: 1. Object: Patients aged 18-65 years; newly diagnosed papillary thyroid carcinoma with cervical lymph node metastasis and without cervical lymph node metastasis and undergone thyroidectomy according to the China thyroid association guidelines for the Management of thyroid nodule and thyroid cancer.
  2. Clinical information, examination data: Information is obtained from medical record abstraction.
  3. Samples: Fresh frozen thyroid tissues from each sample group(normal histology, benign disease, papillary thyroid carcinoma with cervical lymph node metastasis, papillary thyroid carcinoma without cervical lymph node metastasis ).

Eligibility: Inclusion Criteria:
  -  Newly diagnosed papillary thyroid carcinoma.
  -  Undergo thyroidectomy according to the China thyroid association guidelines forthe Management of thyroid nodule and thyroid cancer.
  Exclusion Criteria:
  -  Current substance abuse/dependence.
  -  Daily tobacco and alcohol use.
  -  Whole neck irradiation or surgery.
  -  Prior cancer diagnosis or chemotherapy treatment.
  -  Active autoimmune disorder.
  -  Uncontrolled allergic condition or asthma.
  -  Chronic use of oral steroid medication.
  -  Hormone therapy (estrogen, progestin compounds).

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

Clinical trial: Study for Validation of Immunological Biomarkers in Patients With Metastatic Colorectal Cancer

Summary: The investigators recently identified promiscuous HLA-DR-derived epitopes from the human telomerase reverse transcriptase (TERT) called universal cancer peptides (UCP), to study tumor-specific CD4+ T cell responses.
  The investigators found high frequency of naturally occuring UCP-specific TH1 cells in long term survival of metastatic colorectal cancer (CRC) previously treated by 5 fluoro-uracil -oxaliplatin (Folfox) +/- bevacizumab regiment (Godet et al. OncoImmunology 2012 and unpublished data).
  Epitopes-CRC02 is a French prospective multicenter study which will evaluate the post chemotherapy and post surgery modulation of host tumor-specific CD4 TH1 cell responses in metastatic colorectal cancer patients and their correlation with progression-free survival.


Eligibility: Inclusion Criteria:
  -  Performance status ECOG-WHO 0, 1 or 2
  -  Metastatic colorectal cancer Histologically proved
  -  signed written informed consent
  Exclusion Criteria:
  -  previous treatment (chemotherapy, targeted therapy, surgery) for metastatic disease
  -  history of autoimmune disease
  -  patients under immunotherapy systemic treatment or immunosuppressive drugs or stopped for less than 6 months to the enrollment in this study.
  -  corticoids ≥ 1mg/kg
  -  acute or chronic infectious disease during treatment or stopped for less than six months
  -  other malignancy within the last 5 years, except for adequately treated carcinoma in situ of the cervix or squamous carcinoma of the skin, or adequately controlled limited basal cell skin cancer.
  -  pregnancy, breast-feeding or absence of adequate contraception for fertile patients
  -  patient with any medical or psychiatric condition or disease which would make the patient inappropriate for entry into this study.
  -  patient under guardianship, curator or under the protection of justice.

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

Clinical trial: Study Comparing the Role of the Laparoscopy Surgical Staging in the Peritoneal Carcinomatosis to Laparotomic Approach

Summary: The peritoneum is the second most common site of recurrence in patients with colorectal cancer. Cytoreductive surgery with hyperthermic intraperitoneal chemotherapy improve the prognosis of these patients and incorporates surgical removal of all visible disease followed by chemical destruction of microscopic disease through chemoperfusion. The most validated predictors of outcome are preoperative tumor burden measured in terms of the peritoneal carcinomatosis index (PCI) and completeness of cytoreduction (CC score). Diagnostic laparoscopy prior to resection is widely used in hepatopancreaticobiliary and colorectal cancer and has been shown to be effective in excluding unnecessary laparotomy associated with higher morbidity.


Eligibility: Inclusion Criteria:
  -  Patients with Colorectal cancer with a resected minimal synchronous peritoneal carcinomatosis, or ovarian metastases, tumour rupture in the abdominal cavity.
  -  Patients received six months of systemic chemotherapy (currently the Folfox-4 regimen which could be modified if the standard is modified)
  Exclusion Criteria:

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

Clinical trial: Use of ctDNA for Monitoring of Stage III Colorectal Cancer

Summary: This observational study will evaluate circulating tumor DNA (ctDNA) as a prognostic marker and as a monitor of disease recurrence in stage III colorectal cancer (CRC).

Detailed description: Circulating tumor DNA (ctDNA) are small fragments of nucleic acid that originate from apoptotic or necrotic tumor cell turnover. Characteristic of the malignant process, ctDNA can be assessed in plasma and offers the potential of a sensitive and specific biomarker for prognostic information on disease-free or overall survival, and predictive information on chemotherapy resistance and probability of lack of response to treatment. This study will evaluate ctDNA as a prognostic marker and as a monitor of disease recurrence in stage III colorectal cancer (CRC). We will recruit newly diagnosed stage III CRC patients, determine their tumor mutational profile, and systematically collect high volume (>10 ml), serial plasma specimens every 3 months for up to 3 years and every 6 months in years 4-5 for ctDNA and concurrent carcinoembryonic antigen (CEA) measurement. Clinical outcome and survival will be tracked. The resulting data will permit assessment of ctDNA as a prognostic marker for disease-free and overall survival and as a monitor of disease recurrence in comparison with CEA.

Eligibility: Inclusion Criteria:
  -  Men and women with CRC Stage III A, B, or C
  -  Age ≥18 years
  -  Willingness to provide blood samples for research purposes
  -  Ability to understand written informed consent document, and written informed consent provided
  Exclusion Criteria:
  -  Blood sampling would compromise patients overall health such as presence of severe anemia
  -  Unable to give informed consent

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

Clinical trial: Study on Fluids Associated to Lung Cancer

Summary: The diagnosis of lung cancer is the first cause of cancer deaths for man and woman. It requires invasive procedures (at least endoscopy, transthoracic puncture, or surgery).
  This study is about the set up of an innovative test for lung cancer prognosis, based on biopsies and surgical material : LungCancerTest, with the creation of a start-up in progress.
  The main goal of this study is to approve the diagnostic value of the molecular signature of the 26 genes (LungCancerTest) revealed in blood and respiratory fluids among patients with lung cancer.


Eligibility: Inclusion Criterias :
  -  Patients with lung cancer in stage 1-2, lung cancer of all histology kind eligible for surgery (Group 1).
  -  Patients with lung cancer in stage 3-4 (no adenocarcinoma or squamous) receiving classical or targeted chemotherapy on genetic anomalies (Group 2).
  -  Control patients : carriers of non-cancerous radiological anomalies : benign nodules, cicatricial lesions, infectious or inflammatory, paired with the two other groups by age, sex or tobacco (Group 3).
  -  Adults patients : over 18 years.
  -  Persons affiliated to national social security.
  -  Free signed consent.
  Exclusion Criterias :
  -  Persons referred to in articles L1121-5 to L1121-8 of CSP ( protected people) : pregnants, parturients or breastfeeding women, person deprived of liberty by judicial or administrative decision, person under legal protection.

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

Clinical trial: Institut Paoli Calmettes Colorectal Cancer Database

Summary: Database of Institut Paoli-Calmettes patients diagnosed with colorectal cancer


Eligibility: Inclusion Criteria:
  -  Patients with a colorectal cancer diagnosis
  Exclusion Criteria:
  -  Non applicable

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

Clinical trial: EnteroCT With Enteroclysis Versus Enterography-MRI for the Diagnosis of Tumors of the Small Intestine: a Pilot Study

Summary: Early diagnosis of tumors of the small intestine is a challenge for clinicians and for radiologists. The detection of tumors of the small intestine is a field in which the video capsule endoscopy has the lowest performance.
  The entero-CT with enteroclysis is the imaging technique used primarily to explore patients with a strong suspicion of small intestine tumors. However the entero-CT with enteroclysis has disadvantages : it is irradiating, the nasojejunal tube implies a discomfort to the patient and it is a complicated examination in terms of logistics with necessity of specific equipment to insert the nasojejunal tube.
  MRI has been proposed as an alternative imaging technique and satisfactory results have been reported with the MRI enteroclysis. However, this technique has several disadvantages related to nasojejunal tube insertion and the necessity of equipment compatible with the high magnetic fields. The enterography-MRI without enteroclysis, whose principle is to distend the small intestine by ingestion of large quantities of a liquid, has a major and undisputed role in the exploration of Crohn's disease of the small bowel. However, its capacity for distension of the small intestine for optimal tumor detection is questioned and its role in tumor detection is largely unknown.

Detailed description: Evaluate the diagnostic performances of enteroCT with enteroclysis and enterography-MRI without enteroclysis, for the diagnosis of tumor of the small intestine, among patients with suspicion of small intestine tumors.

Eligibility: Inclusion Criteria:
  -  patient clinically suspected of having a tumor of the small intestine
  -  patient consenting to participate to the study
  -  patient enrolled in the national healthcare insurance program
  -  patient older than 18 years
  Exclusion Criteria:
  -  patient with inflammatory bowel disease
  -  patient with contraindication for MRI

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

Clinical trial: Effects of Video Information on Preoperative Anxiety in Patients With Colorectal Cancer

Summary: Patient's anxiety prior to surgery has been linked to more harmful outcome after surgery. The investigators aim to evaluate the effect of video information on preoperative anxiety level in patients with colorectal cancer.


Eligibility: Inclusion Criteria:
  -  Age: 20-75
  -  Elective surgery
  Exclusion Criteria:
  -  History of previous any surgery
  -  emergency surgery
  -  dementia
  -  psychological disease

Relevance to patient case: not relevant