araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: Copanlisib Pharmacodynamic Study

Summary: This study aims to analyze what the study drug does to the body and its relationship to drug levels and safety after patients with advanced cancer have been treated with copanlisib in different dose groups.


Eligibility: -  Histologically confirmed diagnosis of the following NHL: follicular lymphoma all grades, lymphoplasmacytic lymphoma / Waldenström macroglobulinemia, transformed indolent lymphoma, diffuse large B-cell lymphoma, Burkitt lymphoma, mantle cell lymphoma, or peripheral T-cell lymphoma, relapsed or refractory, with 1 or more prior chemo-immunotherapy- or immunotherapy-based regimen(s) OR
  -  Advanced and / or refractory solid tumors with high prevalence (≥30%) of PIK3CA or PTEN alteration: Breast and uterine cancers (endometrium cancers but also non-endometrial uterine cancers), lung (squamous cell only), cervical, head and neck, prostate, and ovarian cancers
  -  Biopsy-accessible tumor
  -  Male or female patients equal 18 or more years of age
  -  NHL patients must have at least 1 bi-dimensionally measurable lesion according to the modified Cheson criteria. Patients with solid tumors must have at least 1 solid tumor lesion measurable by computed tomography or magnetic resonance imaging according to the Response Evaluation Criteria in Solid Tumors Version 1.1 (RECIST 1.1) criteria
  -  Eastern Cooperative Oncology Group performance status 2 or <
  -  Life expectancy of at least 3 months
  -  Adequate bone marrow, liver, and renal functions as assessed by laboratory requirements conducted within 7 days before the first dose of study drug
  -  Left ventricular ejection fraction > or equal the lower limit of normal for the institution
  Exclusion Criteria:
  -  Previous or concurrent cancer that is distinct in primary site or histology from NHL or the solid tumor, for which the patient is enrolled into this study, within 5 years before treatment start EXCEPT for curatively treated cervical cancer in situ, non-melanoma skin cancer, in situ breast cancer, in situ prostate carcinoma if Gleason score < or equal to 6 and prostate-specific antigen <10 ng/mL, and superficial bladder tumors [Ta (non-invasive tumor), Tis (carcinoma in situ) and T1 (tumor invades lamina propria)]
  -  Known lymphomatous involvement of the brain or leptomeningeal involvement; solid tumor patients with central nervous system (CNS) metastases if treatment completed <3 months before enrollment or lesions unstable or progressing on magnetic resonance imaging scans performed within 1 month of enrollment or unstable symptoms of the CNS metastases
  -  Any illness or medical condition that is unstable or could jeopardize the safety of the patient or his / her compliance in the study
  -  Current diagnosis of type 1 or type 2 diabetes mellitus with HbA1c < or equal to 8.5% or fasting blood glucose < or equal to 160 mg/dL

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: Length of Tumour Feeding Artery After Colon Cancer Surgery

Summary: The quality of colon cancer surgery is highly debated these years since the mortality of the disease is not declining markedly. Surgery is the main treatment of colon cancer and during surgery it is very important for the surgeon to remove the tumour and all potential ways of tumour spread. As colon cancer first of all spreads to the nearby lymph nodes lying along the tumour feeding artery the surgeon aims to cut the vessel as central as possible. This means that all of the tumour feeding artery should have been removed after surgery.
  In this study the investigators want to measure the length of the tumour feeding artery after surgery as a quality control of the surgery. The investigators hypothesize that the artery will be shorter than 5 mm.
  The investigators wish to CT scan all patients two days after colon cancer surgery and afterwards measure then length of the artery on the images. This study will not inflict with the normal routine for patient information and treatment.


Eligibility: Inclusion Criteria:
  -  Primary colon cancer
  Exclusion Criteria:
  -  Kidney failure, allergy to contrast, pregnancy

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: The Oncopanel Pilot (TOP) Study

Summary: The BCCA Oncopanel is a clinical assay being developed to determine genotype status of a prospectively defined set of genes.
  The purpose of this pilot study is to assess the feasibility and effect on clinical-decision-making of the Oncopanel test. Eligible patients are those with advanced lung, colorectal, melanoma and GIST cancers and patients with diagnosed malignancies being considered for clinical trials.

Detailed description: Somatic mutations in solid tumors represent an established means of characterizing malignancies for prognostic, diagnostic and therapeutic purposes. Mutations in EGFR, KRAS, BRAF, and KIT and PDGFRA genes direct therapy in patients with advanced lung, colorectal, melanoma, and GIST tumors, respectively. Known or novel mutations in other genes may also be of clinical significance but are not identified by current genotyping offered to BC Cancer Agency (BCCA) patients. Furthermore, numerous candidate genes have been implicated as potential prognostic and predictive biomarkers in patients with solid tumours. As such, the Oncopanel is a clinical assay being developed to determine genotype status of a prospectively defined set of genes. The following clinically relevant set of genes and exons are included in the Oncpanel: KRAS, EGFR, BRAF, NRAS and HRAS, PIK3CA Signal Transduction Pathway Genes, RAS-RAF-MEK-MAPK Pathway, HER2, IDH1 and IDH2, ALK, TP53, c-KIT, STAT1&3 and PDGFRA. Additional testing on the tumour material will also include analysis of specific gene variants associated with adverse events or response to therapy.
  Numerous studies have documented the presence of circulating tumour DNA (ctDNA) among patients with advanced and early stage malignancies (20-22). The ability to diagnose standard cancer mutations with a blood-based assay (a "liquid biopsy") has not yet been established but presents obvious advantages. The emergence of "resistance" mutations arising in the metastatic tumor or throughout the course of therapy is well documented (21, 22). A blood biopsy may represent more accurate determination of the tumor's genetic features than archival DNA specimen. Adequate tissue specimens can be difficult to obtain from some patients with diagnosed malignancies, particularly lung cancer. A blood biopsy may represent a less invasive and timelier means of diagnosing both standard and translational cancer mutations.

Eligibility: Patients with archival tumor tissue and a known history of invasive malignancies are eligible if they meet one or more of the following criteria:
  -  Advanced colorectal cancer and eligible for standard KRAS testing,
  -  Advanced non-small cell lung cancer and eligible for standard EGFR testing,
  -  Advanced melanoma and eligible for standard BRAF testing,
  -  Gastrointestinal stromal tumors (GISTs) eligible for standard c-KIT and PDGFRA testing,
  -  Being considered for potential eligibility in clinical trial.

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: Lapatinib Plus Trametinib in KRAS Mutant NSCLC

Summary: This is an open-label phase I/II multi-center study consisting of two parts. Part A of this study is designed to identify the recommended phase 2 dose (RP2D) of lapatinib combined with trametinib in patients with metastatic KRASm and PIK3CA wild-type (PIK3CAwt) non-small cell lung cancer (NSCLC). Part B is designed to perform a randomized comparison of the lapatinib-trametinib combination versus standard of care therapy in patients with metastatic KRASm/PIK3CAwt NSCLC.


Eligibility: Inclusion Criteria:
  -  Histological or cytological proof of metastatic NSCLC; for PART B: treated with first line therapy for metastatic disease only.
  -  Written documentation of a known pathogenic KRAS (exon 2, 3 or 4) mutation and PIK3CA wild-type (exon 9 and 20)
  -  Age ≥ 18 years
  -  Able and willing to give written informed consent
  -  WHO performance status of 0 or 1 (part A and B)
  Exclusion Criteria:
  -  Any treatment with investigational drugs within 30 days prior to receiving the first dose of investigational treatment.
  -  History of another primary malignancy
  -  Symptomatic or untreated leptomeningeal disease
  -  Symptomatic brain metastasis
  -  History of interstitial lung disease or pneumonitis
  -  Uncontrolled infectious disease or known Human Immunodeficiency Virus HIV-1 or HIV-2 type patients
  -  Retinal degenerative disease (hereditary retinal degeneration or age-related macular degeneration), or a history of uveitis, retinal vein occlusion, central serous retinopathy, or retinal detachment
  -  Patients with left ventricular ejection fraction (LVEF) < 50%

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

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: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: Study on Potential Biomarkers Associated With Clinical Phenotype of EGFR-TKIs in No-small Cell Lung Cancer in China

Summary: To understand 295 gene mutation mutation status (include EGFR, HER2, KRAS, BRAF, PIK3CA,ect) by deep sequencing in Chinese patients with pulmonary adenocarcinoma and their relationships with the patients' clinical features (including sex, age, smoking history and adenocarcinoma subtype), specify the predictive significance of the genes mutations for new targeted therapies in NSCLC patients, and better understand the molecular mechanism drug resistance to EGFR-TKIs.

Detailed description: This study is prospective to identify biomarkers to resistant to afatinib，gefitinib and erlotinib in non-small cell lung cancer patients. Mutations of whole exon of 295 gene are analysed by deep sequencing in Chinese patients with non-small cell lung cancer and their relationships with the patients' clinical features (including sex, age, smoking history and adenocarcinoma subtype), specify the predictive significance of the genes mutations for new targeted therapies in NSCLC patients, and better understand the molecular mechanism drug resistance to EGFR-TKIs.

Eligibility: Inclusion Criteria:
  -  Age>18 years,both male and female
  -  Histologically confirmed patients with pulmonary adenocarcinoma (Stage I-IV)
  -  ECOG 0-2
  -  Patients with enough paraffin tissue specimens or fresh tissue for detection
  -  Quality of the DNA extracted from the tissue samples ensures that the DNA can be used in DNA sequencing
  -  Subjects who provide detailed clinical and follow-up information
  Exclusion Criteria:
  -  Patients with other tumors
  -  Patients suffering from other serious diseases like infectious diseases (viral hepatitis, HIV,etc)
  -  Pregnant women shall be excluded

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: Irreversible Electroporation(IRE) For Unresectable Rectal Neoplasms

Summary: The purpose of this study is to evaluate the safety and efficacy of irreversible electroporation (IRE) for unresectable Rectal Neoplasms.

Detailed description: By enrolling patients with unresectable Rectal Neoplasms adapted to enrolled criteria, this study will document for the first time the safety and the short and long term efficacy of percutaneous IRE for unresectable Rectal Neoplasms.

Eligibility: Inclusion Criteria:
  -  Rectal Neoplasms diagnosed by positive biopsy or non-invasive criteria,
  -  Not suitable for surgical resection,
  -  Eastern Cooperative Oncology Group (ECOG) score of 0-1,
  -  A prothrombin time ratio > 50%,
  -  Platelet count > 80x10^9/L,
  -  Ability of patient to stop anticoagulant and anti-platelet therapy for seven days prior to and seven days post NanoKnife procedure,
  -  Able to comprehend and willing to sign the written informed consent form (ICF),
  -  Have a life expectancy of at least 3 months.
  Exclusion Criteria:
  -  Cardiac insufficiency, ongoing coronary artery disease or arrhythmia,
  -  Any active implanted device (eg Pacemaker),
  -  Women who are pregnant or women of child-bearing potential who are not using an acceptable method of contraception,
  -  Have received treatment with an investigational agent/ procedure within 30 days prior to treatment with the NanoKnife™ LEDC System,
  -  Are in the opinion of the Investigator unable to comply with the visit schedule and protocol evaluations.

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: Irreversible Electroporation(IRE) For Uterine Cervical Neoplasms

Summary: The purpose of this study is to evaluate the safety and efficacy of irreversible electroporation (IRE) for unresectable Uterine Cervical Neoplasms.

Detailed description: By enrolling patients with unresectable Uterine Cervical Neoplasms adapted to enrolled criteria, this study will document for the first time the safety and the short and long term efficacy of percutaneous IRE for unresectable Uterine Cervical Neoplasms.

Eligibility: Inclusion Criteria:
  -  Uterine Cervical Neoplasms diagnosed by positive biopsy or non-invasive criteria,
  -  Not suitable for surgical resection,
  -  Eastern Cooperative Oncology Group (ECOG) score of 0-1,
  -  A prothrombin time ratio > 50%,
  -  Platelet count > 80x10^9/L,
  -  Ability of patient to stop anticoagulant and anti-platelet therapy for seven days prior to and seven days post NanoKnife procedure,
  -  Able to comprehend and willing to sign the written informed consent form (ICF),
  -  Have a life expectancy of at least 3 months.
  Exclusion Criteria:
  -  Cardiac insufficiency, ongoing coronary artery disease or arrhythmia,
  -  Any active implanted device (eg Pacemaker),
  -  Women who are pregnant or women of child-bearing potential who are not using an acceptable method of contraception,
  -  Have received treatment with an investigational agent/ procedure within 30 days prior to treatment with the NanoKnife™ LEDC System,
  -  Are in the opinion of the Investigator unable to comply with the visit schedule and protocol evaluations.

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: Irreversible Electroporation(IRE) For Unresectable Prostatic Neoplasms

Summary: The purpose of this study is to evaluate the safety and efficacy of irreversible electroporation (IRE) for unresectable Prostatic Neoplasms.

Detailed description: By enrolling patients with unresectable Prostatic Neoplasms adapted to enrolled criteria, this study will document for the first time the safety and the short and long term efficacy of percutaneous IRE for unresectable Prostatic Neoplasms.

Eligibility: Inclusion Criteria:
  -  Prostatic Neoplasms diagnosed by positive biopsy or non-invasive criteria,
  -  Not suitable for surgical resection,
  -  Eastern Cooperative Oncology Group (ECOG) score of 0-1,
  -  A prothrombin time ratio > 50%,
  -  Platelet count > 80x10^9/L,
  -  Ability of patient to stop anticoagulant and anti-platelet therapy for seven days prior to and seven days post NanoKnife procedure,
  -  Able to comprehend and willing to sign the written informed consent form (ICF),
  -  Have a life expectancy of at least 3 months.
  Exclusion Criteria:
  -  Cardiac insufficiency, ongoing coronary artery disease or arrhythmia,
  -  Any active implanted device (eg Pacemaker),
  -  Women who are pregnant or women of child-bearing potential who are not using an acceptable method of contraception,
  -  Have received treatment with an investigational agent/ procedure within 30 days prior to treatment with the NanoKnife™ LEDC System,
  -  Are in the opinion of the Investigator unable to comply with the visit schedule and protocol evaluations.

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: A Multicenter Study of Active Specific Immunotherapy With OncoVax® in Patients With Stage II Colon Cancer

Summary: OncoVAX® is the first cancer vaccine that both prevents cancer recurrence and
  addresses the diversity of cancer cells. In this pivotal randomized, multicenter Phase
  IIIb study in patients with Stage II colon cancer, OncoVAX is designed to use a patient's
  own cancer cells to mobilize the body's immune system to prevent the return of colon
  cancer following surgery.

Detailed description: OncoVAX is an active specific immunotherapeutic (ASI) stimulating a patient's immune
  response to autologous (patient-specific) tumor cells. It is comprised of sterile, live but
  non-dividing tumor cells obtained following standard-of-care surgical tumor resection for
  Stage II colon cancer. Within 35 days following surgery, patients are immunized with
  OncoVAX to prevent disease recurrence, which is incurable and occurs in up to 35% of
  patients. Patients are given three vaccinations once per week for three weeks, followed
  by a booster vaccination after six months. A previously completed Phase III trial
  published in The Lancet showed that OncoVAX cut the risk of recurrence by 61% in
  patients with Stage II colon cancer. The primary endpoint is Disease-Free Survival:
  defined as the time from curative surgery to the objective test confirming tumor
  recurrence or death due to any cause. The secondary endpoints are Overall Survival
  and Recurrence-Free-Interval. An interim analysis will be performed at a significance
  level of 0.005 once 2/3 of anticipated events have occurred, resulting in a significance
  level of 0.0483 at the end of the study. A total of 550 patients is planned, randomized
  1:1 to receive OncoVAX® plus surgery (n=275) or surgery alone (n=275).

Eligibility: Inclusion Criteria:
  -  Patients must have Stage II (IIA = T3N0M0, IIB = T4aN0M0, IIC = T4bN0M0) disease.
  -  Patients must have undergone curative resection and have no evidence of residual or metastatic disease.
  -  Following curative resection patients must have a CEA within normal limits. If elevated prior to resection, it must return to normal within 21 days post surgery and prior to randomization.
  Exclusion Criteria:
  -  Patients with prior radiation therapy or chemotherapy or a prior malignancy of any type will be excluded. However, subjects with prior, curatively-treated squamous cell or basal cell carcinoma of the skin or carcinoma in situ of the cervix will be eligible for participation in this study.
  -  Patients with more than one malignant primary colon cancer will be excluded.

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: Study to Evaluate the Safety and Efficacy of Everolimus, in Subjects With PIK3CA Amplification, PTEN Loss and PIK3CA Mutation Refractory Solid Tumors

Summary: This study is a single-arm, phase II study of everolimus in patients with PTEN loss ,PIK3CA mutation and PIK3CA amplification Refractory Solid Tumors .
  Everolimus 10 mg will be administered orally qd daily.
  To investigate the efficacy and safety of everolimus in patients with PTEN loss ,PIK3CA mutantion and PIK3CA amplification Refractory Solid Tumors.


Eligibility: Inclusion Criteria:
  1. Provision of fully informed consent prior to any study specific procedures.
  2. Patients must be ≥20 years of age.
  3. PIK3CA amplification, PTEN loss and PIK3CA mutation Refractory Solid Tumors that has recurred or progressed following standard therapy, or that has not responded to standard therapy, or for which there is no standard therapy.
  4. ECOG performance status 0-2.
  5. Have measurable or evaluated disease based on RECIST1.1. as determined by investigator.
  6. Adequate Organ Function Laboratory Values
  -  Absolute neutrophil count ≥ 1.5 x 109/L, Hemoglobin ≥ 9g/dL, Platelets ≥ 75 x 109/L
  -  bilirubin ≤ 1.5 x upper limit of normal AST/ALT ≤ 2.5 x upper limit of normal (5.0 X upper limit of normal , for subjects with liver metastases)
  -  creatinine ≤1.5 x UNL
  7. Patients of child-bearing potential should be using adequate contraceptive measures (two forms of highly reliable methods) should not be breast feeding and must have a negative pregnancy test prior to start of dosing.
  8. Adequate heart function.
  Exclusion Criteria:
  1. Patients with second primary cancer, except: adequately treated non-melanoma skin cancer, curatively treated in-situ cancer of the cervix, or other solid tumours curatively treated with no evidence of disease for ≤5 years.
  2. Has known active central nervous system (CNS) metastases.
  3. Has an active infection requiring systemic therapy.
  4. Pregnancy or breast feeding
  5. Patients with cardiac problem.
  6. KRAS mutation (codon 12 or 13) or BRAF mutation (V600)
  7. Any previous treatment with everolimus

Relevance to patient case: possibly relevant