araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

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: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Ceritinib (LDK378) for Patients Whose Tumors Have Aberrations in ALK or ROS1 (SIGNATURE)

Summary: The purpose of this signal seeking study is to determine whether treatment with ceritinib demonstrates sufficient efficacy in select pathway-activated solid tumors and/or hematologic malignancies to warrant further study.


Eligibility: Inclusion Criteria:
  -  Patient has a confirmed diagnosis of a select solid tumor (except ALK+ NSCLC) or hematological malignancy and is in need of treatment because of radiologic progression or relapse.
  -  Patient must have been pre-identified as having a tumor with an ALK or ROS1 positive mutation, translocation, rearrangement or amplification. The qualifying alteration must be assessed and reported by a CLIA-certified laboratory. ALK positivity as assessed by IHC or FISH are allowed.
  -  Patient must have received at least one prior treatment for recurrent, metastatic and/or locally advanced disease and for whom no standard therapy options are anticipated to result in a durable remission.
  -  Patient has progressive and measurable disease as per RECIST 1.1 or other appropriate hematological guidelines.
  -  Patient has an Eastern Cooperative Oncology Group (ECOG) performance status ≤ 1.
  Exclusion Criteria:
  -  Patient has received prior treatment with ceritinib.
  -  Patients with symptomatic CNS metastases who are neurologically unstable or have required increasing doses of steroids within the 2 weeks prior to study entry to manage CNS symptoms.
  -  Patient has received chemotherapy or anticancer therapy ≤ 4 weeks (6 weeks for nitrosourea, monoclonal antibodies or mitomycin-C) prior to starting study drug.

Relevance to patient case: definitely relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Non Invasive Detection of Lung and Breast Cancer by Odor Signature

Summary: The investigators have developed an early detection solution for lung and breast cancer. A system which can distinguish between different medical odors based on biosensors. Our product is user-friendly noninvasive, nonradioactive and nontoxic to the patients. The technology enables a high level of sensitivity and provides users with a quick lab response and a simple yes or no answer.
  The aim of this study is to contribute and detect the patient at the earliest possible stage, in a noninvasive, nonradioactive and nontoxic way. Exhaled breath and urine samples are a promising approach towards future possible lung and breast cancer screening method.

Detailed description: Early detection of cancer can dramatically improve the survival chances. to date, there is no efficient diagnostic tool for detection of lung cancer in early stages. Regarding breast cancer, the common screening tool us mammography, which suffer from low sensitivity and high false positive. Thus, there is an urgent need for developing a screening tool for early stages lung and breast cancer.
  The sense of smell depends on the ability of specialized sensory cells of the nose to perceive volatile compounds (VOCs). Diseases such as infections and malignancies can be associated with changes in host metabolism, accompanied by production of different VOCs, and thus a different odor. Several studies have shown that different cancers secrete different VOCs, thus produce different smell.
  We have developed a system which uses biosensors that can scent the VOCs that lung and breast cancer cell produce, thus distinguish between healthy control and lung or breast cancer. These biosensors can detect low stages lung and breast cancer.
  Patients will supply urine samples and exhaled breath samples using a kit that we will supply. The samples will be shipped to our lab, where they will be processed and the VOCs will be separated from the head space of the samples. The biosensors will be exposed to the VOCs samples and will report whether the specific sample id cancerous (lung or breast) or not.
  The Data will be collected from all samples and statistical analysis will be calculated, in order to test the specificity and sensitivity of our biosensors to detect cancerous samples.

Eligibility: Inclusion Criteria:
  -  Diagnosed Lung Cancer patients
  -  Diagnosed Breast Cancer patients
  Exclusion Criteria:
  -  Cancer patients who were treated using chemotherapy
  -  Cancer patients who were treated using radiation
  -  Cancer patients who were treated using biological treatments
  -  Cancer patients who were treated with chemotherapy
  -  Cancer patients who were treated with any anti- cancer therapies
  -  Cancer patients who use drugs that affect the immune system

Relevance to patient case: not relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Study to Evaluate Real-world Pharmacoeconomics of Crizotinib in NSCLC Patients

Summary: This is a phase IV multicenter trial to evaluate the pharmacoeconomic (PE) impact of crizotinib and its companion diagnostic test used in a real-life setting in advanced ALK-positive non-small cell lung cancer (NSCLC) patients.
  NSCLC represent 80% of all new cases of lung cancer. One molecular subtype of NSCLC is the ALK-positive subtype. The anaplastic lymphoma kinase (ALK) is a transmembrane receptor tyrosine kinase. Activation of ALK occurs through the formation of gene fusions and in NSCLC, the gene fusion partner for ALK is primarily EML4. The resulting fusion protein is capable of activating the ALK kinase domain, leading to cell growth. The estimated prevalence for ALK rearrangements in NSCLC is 3-5%, and is more commonly found amongst patients with adenocarcinoma histology, in never smokers and in those who are known to be wild type for EGFR and KRAS.
  Crizotinib is a potent inhibitor of ALK and is approved for the treatment of advanced ALK+ NSCLC patients. This is an example of personalized medicine, where patients are selected for treatment based upon a molecular assay, and are provided a specific therapy (crizotinib) for their disease. The pharmacoeconomic impact of using genetic information in early treatment decisions in NSCLC has not been determined.
  The study will enable real-life Heath Economics and Outcome Research (HEOR).
  Approximately 90 patients will be recruited. Patients will be asked to complete quality-of-life questionnaires at regular intervals in a real-life setting of treatment with crizotinib.


Eligibility: Inclusion Criteria:
  -  Patients with histologically confirmed locally advanced or metastatic NSCLC
  -  Presence of the ALK-fusion oncogene (ALK+) as determined using a validated testing platform
  -  Planned first or second-line treatment with crizotinib
  -  Signed and dated IRB-approved informed consent document
  -  Ability to read and understand English or French
  -  18 years of age or older

Relevance to patient case: not relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Comprehensive Genomic Analysis in Tissue and Blood Samples From Young Patients With Lung Cancer

Summary: This research trial studies genomic analysis in tissue and blood samples from young patients with lung cancer. Identifying specific gene mutations (changes in deoxyribonucleic acid [DNA]) may help doctors tailor treatment to target the specific mutations and help plan effective treatment.

Detailed description: PRIMARY OBJECTIVES:
  I. To perform comprehensive genomic analysis of young lung cancer patients' samples to facilitate delivery of targeted therapies and clinical trial enrollment.
  II. To characterize the impact of young age at lung cancer diagnosis on the genomic landscape of primary lung cancer.
  III. To establish a prospective registry of young lung cancer patients for both tumor and germline next generation sequencing.
  OUTLINE:
  Tissue and blood samples are analyzed via next generation sequencing and whole exome sequencing.
  After completion of study, patients are followed up every 3 months for up to 3 years.

Eligibility: Inclusion Criteria:
  -  COHORT 1: LUNG CANCER PATIENTS
  -  Pathologically confirmed bronchogenic lung carcinoma (small cell lung cancer [SCLC] or non-small cell lung cancer [NSCLC] of any stage) at any treatment time point
  -  For individuals diagnosed with advanced disease (stage IV or recurrent) enrollment must occur within 2 years of diagnosis
  -  For appropriate patients (stage IV non-squamous NSCLC) epidermal growth factor receptor (EGFR ) and anaplastic lymphoma kinase (ALK) genotyping performed by a Clinical Laboratory Improvement Amendments (CLIA) certified laboratory is recommended prior to participation
  -  Provision of written informed consent
  -  Willingness to undergo a single blood draw
  -  Individuals who are under 18 are eligible for study if they meet the defined criteria for cohort 1; in addition, consent for participation must be given by a legal guardian or parent
  -  NOTE: to be eligible for genomics, availability of 10 unstained slides (plus hematoxylin and eosin [H&E] slide) or an adequate formalin-fixed paraffin-embedded (FFPE) tumor block from clinically indicated interventional procedures is required
  -  COHORT 2: DECEASED INDIVIDUALS
  -  Deceased individuals diagnosed with lung cancer at any age less than 40 may be studied on a case by case basis depending upon Institutional Review Board (IRB) approval at a participating institution; inclusion will require availability of adequate archived FFPE tissue and release of tissue and records by next of kin, if available
  Exclusion Criteria:
  -  Compromise of patient diagnosis or staging if tissue is used for research

Relevance to patient case: not relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Pharmacokinetic and Safety Study of Lower Doses of Ceritinib Taken With a Low-fat Meal Versus 750 mg of Ceritinib in the Fasted State in Adult Patients With (ALK-positive) Metastatic Non-small Cell Lung Cancer (NSCLC)

Summary: A Phase I study to assess the systemic exposure, effiacy, and safety of 450 mg ceritinib taken with a low-fat meal and 600 mg ceritinib taken with a low-fat meal as compared with that of 750 mg ceritinib taken in the fasted state in adult patients with ALK rearranged (ALK-positive) metastatic non-small cell lung cancer (NSCLC)


Eligibility: Inclusion:
  1. Histologically or cytologically confirmed diagnosis of stage IIIB (and is not a candidate for definitive multimodality therapy) or IV ALK-positive NSCLC.
  2. Patients may have received one prior treatment regimen with crizotinib (all other ALK inhibitors are excluded).
  3. Patients may have received prior chemotherapy, biologic therapy, or other investigational agents. ALK inhibitors other than crizotinib are excluded.
  4. Patient has a World Health Organization (WHO) performance status 0-2.
  Exclusion:
  1. Prior treatment with an ALK inhibitor other than crizotinib.
  2. History of carcinomatous meningitis.
  3. Presence or history of a malignant disease other than an ALK-positive advanced tumor that has been diagnosed and/or required therapy within the past 3 years.
  5. Clinically significant, uncontrolled heart disease and/or recent cardiac event (within 6 months) 6. Patient has history of interstitial lung disease or interstitial pneumonitis, including clinically significant radiation pneumonitis (i.e., affecting activities of daily living or requiring therapeutic intervention).
  7. Patient has other severe, acute, or chronic medical conditions 8. Patient is currently receiving treatment with warfarin sodium (Coumadin®) or any other coumarin-derivative anticoagulants.

Relevance to patient case: definitely relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Personalized Sequence for Thoracic, Esophageal, and H&N Cancer

Summary: The next generation of personalized medical treatment according to the type of personal genetic information are evolving rapidly. The genome analysis needs systematic infra and database based on personal genetic information Therefore, a big data of genome-clinical information is important.

Detailed description: To determine the feasibility of the use of tumor's molecular profiling and targeted therapies in the treatment of advanced cancer and to determine the clinical outcome(PFS, duration of response and overall survival) of patients with advanced cancer, the investigators are going to take a fresh tissue of patients and process molecular profiling.

Eligibility: Inclusion Criteria:
  -  metastatic, histologically confirmed NSCLC, head & Neck Cancer, Esophageal cancer
  Exclusion Criteria:

Relevance to patient case: definitely relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Early Palliative Care in Metastatic Lung Cancer in Northern France

Summary: Single-center, prospective, controlled, open-label, randomized, two parallel arms comparing early Palliative care versus Standard care in patients with non-small-cell metastatic lung cancer

Detailed description: 144 patients will be included; 72 per arm.
  -  "Standard" Control arm: patient supported by the onco-respiratory service.
  -  Intervention arm: patients benefit from early palliative care in addition to standard onco-pneumologic care.
  The main criterion of judgment is the TOI score measured at 12 weeks.
  FACTL questionnaires, HADS and PHQ-9 will be filled out before randomization , at 12 weeks and 21 weeks

Eligibility: Inclusion Criteria:
  -  Being diagnosed with non-small cell lung cancer
  -  Proven histologically
  -  Metastatic proven imaging (MRI, CT Scanner, PET scan)
  -  Stage IV (any T, any N, M1)
  -  prior to secondary chemotherapy treatment.
  -  Age> 18 years
  -  PS ≤2
  -  Patient able to understand the nature, purpose and methodology of the study
  -  signed Informed consent
  Exclusion Criteria:
  -  Age <18 years
  -  Patient already supported by palliative care
  -  Patient with an activating EGFR mutation or EML4-ALK rearrangement
  -  Patient under trusteeship / guardianship

Relevance to patient case: not relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: An epidemiOlogy Study to deteRmine the Prevalence of EGFR (Epidermal Growth Factor Receptor) muTations in RUSsian Patients With Advanced NSCLC (Non-Small Cell Lung Cancer).

Summary: This is a multicentre, non-interventional, prospective study to be carried out in representative oncology departments / institutions in order to determine the prevalence of EGFR mutations in treatment-naive Russian patients with cytologically verified advanced NSCLC in Russia.

Detailed description: This is a multicentre, non-interventional, prospective study to be carried out in representative oncology departments / institutions in order to determine the prevalence of EGFR mutations in treatment-naive Russian patients with cytologically verified advanced NSCLC in Russia. No additional procedures besides those already used in the routine clinical practice will be applied to the patients. Treatment assignment will be done according to the current practice.
  It is planned to enrol approximately 300 subjects in Russian Federation. Approximately 60 EGFR m+ (mutation-positive) patients will be followed for 1.5 years.
  EGFR mutations rate before treatment in cytology and plasma samples in treatment-naive patients with advanced NSCLC in Russia is considered as the primary outcome variable in this study.

Eligibility: Inclusion Criteria:
  -  Cytologically verified advanced (stages IIIB - IV) nonsquamous (adenocarcinoma, large cell carcinoma) and mixed subtypes of NSCLC and NSCLC-NOS), diagnosed before enrolment into the study
  -  Quality and quantity of the cytological sample material meeting the requirements of the molecular-genetic testing
  -  No previous/ ongoing treatment for NSCLC at the moment of recruitment
  Exclusion Criteria:
  -  Squamous NSCLC cytologically confirmed subtype of cancer
  -  Any medical condition which on the opinion of the investigator may interfere the patient's participation in the study
  -  Quality and quantity of the cytological sample material insufficient for the molecular-genetic testing

Relevance to patient case: not relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Prevalence of Sleep Apnea in Patients Undergoing Surgery for Colorectal Cancer

Summary: 300 patients with colorectal cancer will be investigated before surgery and 60 of them will also be investigated in the same manner after surgery. Investigations will include polysomonographic sleep apnea recordings during one night, lung function measurements, blood gas samples and a questionnaire, but only before surgery including questions on sleep, sleep apnea, lung disorders.
  Outcome: side effects of surgery and mortality rate, association with cancer type.
  Prevalence of sleep apnea, sleep quality, hypoxemia and lung function before and after surgery.

Detailed description: Group 1. Inclusion: 240 patients with colorectal cancer scheduled for surgery. Exclusion: Dementia, CPAP treated sleep apnea Methods: Patients are investigaged before surgery with Lung-function measurements, blood-gas sample, questionnaire, Overnight polysomnographic sleep apena recordings including oro-nasal airflow, thoraco-abdominal respiration belts, chin-EMG, EOG, EEG, ECG (V5) and body position.
  Outcome variables: complications of surgery including anastomosis insuficiency and wound infections. Short and long term mortality, Sleep apnea, hypxoia, hyprecapnia and effect on lungfunction (VC, FEV1). Detailed morphologic analysis of cancer type.
  Group 2. Inclusion: 35 patients with colorectal cancer scheduled for open surgery, Exclusion: Dementia, CPAP treated sleep apnea Methods: Patients are investigaged before and 2 days after surgery with Lung-function measurements, blood-gas sample, questionnaire (only before surgery), Overnight polysomnographic sleep apena recordings including oro-nasal airflow, thoraco-abdominal respiration belts, chin-EMG, EOG, EEG, ECG (V5) and body position.
  Outcome variables: Effect on sleep apnea, sleep parameters, blood-gas and lungfunction before and after surgery. Complications of surgery including anastomosis insuficiency and wound infections. Short and long term mortality. Detailed morphologic analysis of cancer type.
  Group 3. Inclusion: 25 patients with colorectal cancer scheduled for laparoscopic or robot surgery.
  Exclusion: Dementia, CPAP treated sleep apnea Methods: Patients are investigaged before and 2 days after surgery with Lung-function measurements, blood-gas sample, questionnaire (only before surgery), Overnight polysomnographic sleep apena recordings including oro-nasal airflow, thoraco-abdominal respiration belts, chin-EMG, EOG, EEG, ECG (V5) and body position.
  Outcome variables: Effect on sleep apnea, sleep parameters, blood-gas and lungfunction before and after surgery. Complications of surgery including anastomosis insuficiency and wound infections. Short and long term mortality. Detailed morphologic analysis of cancer type.

Eligibility: Inclusion Criteria:
  -  Patients scheduled for surgery of colorectal cancer
  Exclusion Criteria:
  -  Dementia, CPAP treatment for obstructive sleep apnea

Relevance to patient case: not relevant