araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 71-year-old female with lung cancer; genetic feature: ROS1

Clinical trial: Assessment of Labile Plasma Iron (LPI) in Myelodysplastic Syndromes (MDS) and Primary Myelofibrosis

Summary: Recently, it has been demonstrated that iron overload is associated with the appearance of labile plasma iron (LPI).
  LPI is redox active and is rapidly taken up by cells, leading to a rise in the labile iron pool (LIP) and catalyzing generation of reactive oxygen species (ROS), which can lead to cellular damage.
  The LPI data are mostly derived from thalassemia iron overload research , however, there are a few data describing LPI and its correlations with the classical iron overload parameters (ferritin, TSAT) in acute anemias such as MDS Therefore we are going to assess LPI in iron overloaded myelodysplastic syndromes (MDS) (low and high risk) and primary myelofibrosis, in order to assess whether it can be used as alternative to the routinely used parameters; TSAT and ferritin levels.

Detailed description: Approximately 60-80% of patients with myelodysplastic syndromes (MDS) present with symptomatic anemia and 80-90%, of these, will require red blood cell (RBC) transfusions. Excess transfusional iron causes iron overload (IO) which is characterized by elevated serum ferritin (> 1000ng/ml) and transferrin saturation (TSAT > 50%) levels.
  Assessment of IO using serum ferritin and TSAT levels is not accurate enough and this is due to changes in serum ferritin and TSAT during any inflammatory condition.
  Since serum ferritin is considered as a positive acute phase reactant and therefore inflammatory state can lead to an increase in serum ferritin levels and so does not reflect the exact amount of iron overload.
  In contrast TSAT can decrease during inflammation and in addition it follows diurnal variations.The aim of our present study is to asses the levels of LPI in patients with in iron overloaded MDS patients (low and high risk), and also patients with primary myelofibrosis, in order to find out any laboratory correlations between LPI, TSAT and srum ferritin levels.
  Methods:
  The study will contain 50 patients low+high risk MDS patients and patients with primary myelofibrosis with iron overloaded. The risk stratification of these patients will be calculated according to the WPSS (WHO adapted Prognostic Scoring System)
  After ICF (Informed Consent Form) has been signed by the patients the following laboratory tests will be taken once during the study:
  -  Ferritin (local laboratory)
  -  Transferrin Saturation (local laboratory)
  -  CRP (local laboratory)
  -  LPI (feROS™ eLPI from Aferrix Ltd., Tel- Aviv, Israel)

Eligibility: Inclusion Criteria:
  -  age > 18 years old
  -  MDS patients (low and high risk )
  Exclusion Criteria:
  -  age < 18 years old

Relevance to patient case: not relevant
Patient case: 71-year-old female with lung cancer; genetic feature: ROS1

Clinical trial: Assessment of 4D 18F-FDG PET-CT in Radiotherapy for Non Small Cell Lung Cancers

Summary: Computed tomography (CT) images, used for radiotherapy planning, are often caught out in lung target volumes delineation because of their inability to differentiate between neoplasia, inflammation and atelectasia. Positron Emission Tomography (PET) is a new functional imaging modality and is currently used in the diagnosis and the staging of lung cancers. The aim of this study is to evaluate the impact of 4D 18F-FDG-PET-CT on radiotherapy planning for lung cancers.

Detailed description: Many PET studies have been interested in lung radiotherapy volumes definition, however lacking any standardisation. Effectively, the use of PET images is difficult because of the poor image quality resulting from noise and partial volume effects induced blurring. Moreover, due to the long duration of PET acquisitions, respiratory motions are inevitable and result in artifacts in the PET images affecting the volumes and contrast of the tumour: tumours may appear larger while their activity can be lower. To overcome these limitations, we propose to use a 4D PET-CT, ie a PET-CT acquisition system synchronized with respiration in order to compare CT-simulation target volumes and PET target volumes after application of different approaches for partial volume effect correction, respiratory motion correction and automatic segmentation method of functional volumes. For this purpose, patients with a non small cell lung cancer and having to be treated with radiotherapy or radio-chemotherapy underwent CT-simulation and 4D PET-CT in radiotherapy treatment position. The target volumes and the dosimetries obtained with both modalities were compared.

Eligibility: Inclusion Criteria:
  -  age ≥ 18 years old
  -  patients with unresectable non small cell lung cancer having to be treated with radiotherapy or radio-chemotherapy
  Exclusion Criteria:
  -  neo-adjuvant treatment
  -  patient treated previously with thoracic radiation
  -  patient unable to support 4D PET-CT
  -  pregnant or breast-feeding woman

Relevance to patient case: not relevant
Patient case: 71-year-old female with lung cancer; genetic feature: ROS1

Clinical trial: Individualized Chemotherapy Based on BRCA1 and RRM1 mRNA for Advanced Non-small Cell Lung Cancer (NSCLC)

Summary: Gemcitabine, docetaxel, CPT-11 and cisplatin are effective in 1st line treatment of advanced non-small cell lung cancer (NSCLC). Platinum-based doublets including gemcitabine, docetaxel or CPT-11 are standard 1st regimens. BRCA1 and RRM1 expression levels are reported to be associated with sensitivity of the tumor cells to cytotoxic agents. Some Phase II or III trials did prove feasibility of customized chemotherapy based upon expression levels of one or two biomarkers in the NSCLC patients. The investigators think customized chemotherapy may further improve efficacy of chemotherapy in advanced NSCLC. But there is no randomised trial to compare efficacy of standard chemotherapy with individualized chemotherapy in this setting. So, the investigators plan to initiate this phase II trial to compare efficacy between standard chemotherapy of gemcitabine/cisplatin versus customized chemotherapy in chemonaive NSCLC patients.

Detailed description: Primary end point:ORR Secondary end point:PFS,OS,safety,QOL,etc.

Eligibility: Inclusion Criteria:
  1. Written informed consent,
  2. Histologically confirmed stage M1a or M1b NSCLC,
  3. Aged over 18 years old,
  4. Measurable disease,
  5. Life expectancy of at least 12 weeks,
  6. No prior chemotherapy or target therapy,
  7. No brain metastases or spinal cord compression,
  8. Less than 10% body weight loss,
  9. ECOG performance status 0-2,
  10. Adequate vital organ function (haematological, renal, hepatic, etc).
  11. Enough tissue for detection of BRCA1 and RRM1 expression.
  Exclusion Criteria:
  1. Prior systemic cytotoxic chemotherapy or EGFR TKI therapy,
  2. Positive pregnancy test,
  3. Another active malignancy, other than superficial basal cell and squamous cell or carcinoma in situ of the cervix, within the last 5 years,
  4. Patients with brain metastases or spinal cord compression,
  5. Allergy to gemcitabine, cisplatin, docetaxel, CPT-11,
  6. Any unstable systemic disease including active infection,
  7. No enough tissue for detection of BRCA1 and RRM1

Relevance to patient case: not relevant
Patient case: 71-year-old female with lung cancer; genetic feature: ROS1

Clinical trial: SPI-1005 for Prevention and Treatment of Chemotherapy Induced Hearing Loss

Summary: Chemotherapy treatment with platinum based agents is well noted to cause ototoxicity. It is the objective of this study to determine the safety and efficacy of SPI-1005 at three dose levels when delivered orally twice daily for 3 days, surrounding each cycle of platinum chemotherapy in head and neck or non-small cell lung cancer patients to prevent and treat chemotherapy induced hearing loss and tinnitus.

Detailed description: Chemotherapy treatment with the platinum containing chemotherapies (e.g. cisplatin, carboplatin) are well noted and studied for their ability to cause ototoxicity which includes hearing loss, tinnitus, vertigo, or dizziness. It is the objective of this study to determine the safety and efficacy of SPI-1005 at three dose levels when delivered orally twice daily for 3 days, surrounding each cycle of platinum chemotherapy for head and neck or non-small cell lung cancer patients to prevent and treat chemotherapy induced hearing loss and tinnitus.
  SPI-1005, a proprietary oral formulation of ebselen is a small molecule mimic and inducer of the enzyme Glutathione Peroxidase. GPx reduces reactive oxygen species (ROS) by reacting with glutathione. SPI-1005 has been shown to reduce cisplatin induced hearing threshold shift in animal studies.

Eligibility: Inclusion Criteria:
  -  Adult male and female subjects, 19-80 years of age;
  -  Confirmed diagnosis of advanced head and neck cancer or advanced lung cancer
  -  Voluntarily consent to participate in the study
  -  Females of childbearing potential should either be sexually inactive (abstinent) for 14 days prior to screening and throughout the study or be using one of the following acceptable birth control methods:
  -  IUD in place for at least 3 months prior to study;
  -  Barrier method (condom or diaphragm) with spermicide for at least 14 days prior to screening through study completion;
  -  Stable hormonal contraceptive for at least 3 months prior to study through completion of study;
  -  Surgical sterilization (vasectomy) of partner at least 6 months prior to study.
  -  Females of non-childbearing potential should be surgically sterile (bilateral tubal ligation with surgery at least 6 months prior to study, hysterectomy, or bilateral oophorectomy at least 2 months prior to study).
  Exclusion Criteria:
  -  Subjects previously treated with chemotherapy, antibiotics, or diuretics known to cause hearing loss in the last 90 days
  -  History or presence of significant cardiovascular, pulmonary, hepatic, renal, hematologic, gastrointestinal, endocrine, immunologic, dermatologic, neurologic, otologic, or psychiatric disease
  -  Presence of alcoholism or drug abuse
  -  Participation in another investigational drug or device clinical trial within 30 days prior to the study
  -  Female subjects who are pregnant or lactating

Relevance to patient case: not relevant
Patient case: 71-year-old female with lung cancer; genetic feature: ROS1

Clinical trial: Mindfulness for Lung Cancer Patients and Partners

Summary: The aim of the current study is to examine the (cost)effectiveness of mindfulness based stress reduction (MBSR) in comparison with treatment as usual for patients with lung cancer and their partners.

Detailed description: Receiving a diagnosis of cancer is a major cause of distress and is usually characterized by anxiety and depression. Compared to patients with other cancer diagnoses, patients with lung cancer report higher levels of distress, which probably can be explained by the poor prognosis. At the time of diagnosis, lung cancer is often locally or systematically advanced and 5-year survival is only 15 percent.
  Mindfulness based stress reduction (MBSR) is a recently developed psychological intervention that appears to be promising in terms of reducing psychological distress in cancer patients. It consists of 8 weekly group sessions in which formal and informal mindfulness practices are practiced. As most of the earlier studies have been conducted in patients with breast cancer, it is important to examine the effectiveness of this approach in patients with other types of cancer, such as lung cancer. Furthermore, a diagnosis of cancer is not only highly distressing for the patient but also for the partner and family.
  In this study, the (cost)effectiveness of MBSR compared with treatment as usual will be investigated in 110 patients with lung cancer and 110 partners.

Eligibility: Inclusion Criteria:
  -  Cytologically or histologically proven non-small cell lung cancer and small cell lung cancer.
  -  Patients can participate after lung cancer diagnosis, from start of treatment or after treatment.
  -  Sufficient understanding of Dutch language.
  Exclusion Criteria:
  -  Former participation in MBSR or MBCT course.
  -  Current psychological treatment by psychologist or psychiatrist.
  -  Cognitive impairments hampering participation in MBSR and completion of questionnaires.
  -  Physical impairments prohibiting participation in MBSR training.

Relevance to patient case: not relevant
Patient case: 71-year-old female with lung cancer; genetic feature: ROS1

Clinical trial: Study Assessing Safety, Pharmacokinetics and Efficacy of CC-223 With Either Erlotinib or Oral Azacitidine in Advanced Non-Small Cell Lung Cancer

Summary: The main purpose of this first study combining an investigational dual mTOR inhibitor, CC-223, with other agents (erlotinib or the investigational agent, oral azacitidine) is to establish a maximum tolerated dose level for each combination in order to evaluate their effects in future clinical trials for advanced non-small cell lung cancer.


Eligibility: Inclusion Criteria:
  1. Men and women, 18 years or older, with histologically or cytologically-confirmed, Stage IIIB/IV Non-Small Cell Lung Cancer (NSCLC) with tumor progression following at least one prior treatment regimen [(either chemotherapy or an Epidermal Growth Factor Receptor inhibitor (EGFR)] for advanced disease. There is no restriction on the number of prior treatment regimens allowed.
  2. Eastern Cooperative Oncology Group (ECOG) Performance Score of 0 to 1.
  3. Adequate organ function.
  4. Adequate contraception (if appropriate).
  5. Consent to retrieve archival tumor tissue.
  6. Consent to repeated tumor biopsy (dose expansion phase).
  Exclusion Criteria:
  1. Prior systemic cancer-directed treatments or investigational drugs within 4 weeks or 5 half lives, whichever is shorter except erlotinib which may be continued with intervention in subjects allocated in Arm A.
  2. Symptomatic central nervous system metastases.
  3. Acute or chronic pancreatitis.
  4. Persistent diarrhea or malabsorption > Grade 2, despite medical management.
  5. Impaired cardiac function or significant cardiac disease.
  6. Diabetes on active treatment, fasting blood glucose > 126 mg/dL, (glycated haemoglobin) HbA1c > 6.5%.
  7. Known Human Immunodeficiency Virus (HIV), chronic hepatitis B or C infection.
  8. Prior treatment with an investigational dual target of ripamycin 1 (TORC1)/ target of ripamycin 2 (TORC2), Phosphatidylinositol 3-Kinase (PI3K), or protein kinase B (Akt) inhibitor. Prior treatment with analogs of rapamycin (rapalogs) is allowed.
  9. Major surgery < 2 weeks prior to starting study drugs. No specific wash out is required for radiotherapy. Subjects must have recovered from any effects of recent therapy that might confound the safety evaluation of study drug.
  10. Pregnant or breastfeeding, inadequate contraception.
  11. History of concurrent second malignancies requiring ongoing systemic treatment.

Relevance to patient case: not relevant
Patient case: 71-year-old female with lung cancer; genetic feature: ROS1

Clinical trial: ARQ 197 Plus Erlotinib in Patient With Locally Advanced or Metastatic EGFR Mutation-positive Non-small-cell Lung Cancer

Summary: The primary objective of this study is to examine if the combination regimen of ARQ 197 with erlotinib is active in subjects with locally advanced or metastatic NSCLC with activating mutation EGFR who progressed on EGFR-TKI monotherapy.


Eligibility: Key Inclusion Criteria:
  -  Histologically or cytologically confirmed surgically unresectable locally advanced or metastatic (stage IIIB/IV) NSCLC with EGFR activating mutation.
  -  Measurable disease and documented disease progression following the first and immediate EGFR-TKI monotherapy.
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1.
  -  Adequate organ function
  Key Exclusion Criteria:
  -  Prior therapy with a c-Met inhibitor.
  -  Any systemic anti-tumor treatment for NSCLC within 7 days prior to randomization.
  -  Major surgical procedure within 4 weeks prior to randomization
  -  Known symptomatic brain metastases.

Relevance to patient case: not relevant
Patient case: 71-year-old female with lung cancer; genetic feature: ROS1

Clinical trial: Phase II Study of S-488410 to Treat Non-small Cell Lung Cancer

Summary: The investigators identified three cancer-testis antigens, as targets for cancer vaccination against lung cancer. In this clinical study, the investigators examine using a combination of three peptides from these three antigens (S-488410) the safety, immunogenicity, and antitumor effect of vaccine treatment for advanced non-small cell lung cancer patients.

Detailed description: The purpose of this study is to evaluate the clinical efficacy and safety of S-488410 for advanced non-small cell lung cancers who failed to standard therapy.
  The investigators previously identified three novel HLA-A*2402-restricted epitope peptides, which were derived from three cancer-testis antigens, as targets for cancer vaccination against lung cancer. In this phase II trial, we examine using a combination of these three peptides the safety, immunogenicity, and antitumor effect of vaccine treatment for HLA-A*2402-positive advanced small cell lung cancer patients who failed to standard therapy.

Eligibility: Inclusion Criteria:
  -  Advanced NSCLC that cannot undergo curative surgery.
  -  Patients that are refractory to standard chemotherapy or cannot be treated with further therapy due to severe adverse effects of chemotherapy.
  -  Histologically diagnosed NSCLC.
  -  Clinical efficacy can be evaluated by radiologic methods within 4 weeks prior to receiving treatment.
  -  ECOG performance status 0-2 within 2 weeks prior to receiving treatment.
  -  Life expectancy > 3 months.
  -  Age between 20 to 79
  -  Male or Female.
  -  In patients or out patients.
  -  Able and willing to give valid written informed consent.
  Exclusion Criteria:
  -  Other malignancy requiring treatment
  -  radiation, immunotherapy, hyperthermia, or surgery.
  -  Active and uncontrolled infectious disease
  -  Active and uncontrolled hepatic dysfunction, kidney dysfunction, cardiac disease, or lung disease (i.e. interstitial pneumonia).
  -  Autoimmune disease.
  -  HIV-Ab or antigen positive
  -  Prior anti-cancer therapy within 4 weeks
  -  Laboratory values as follows: 2000<mm3 < WBC < 15000/mm3, Platelet count < 50000/mm3, Asparate transaminase > 5 X cutoff value, Alanine transaminase > 5 X cutoff value, Total bilirubin > 3 X cutoff value, and Serum creatinine > 3X cutoff value.
  -  Patients knows HLA-A type.
  -  Breastfeeding and Pregnancy (woman of child bearing potential)
  -  Refusal of pregnancy conception.
  -  Treated with S-488401, S-488402, or S-488403.
  -  Treated with other investigational drug within 3 months prior to receiving S-48810 treatment.
  -  Decision of nonenrollment of the patients by principal investigator or physician-in-charge from the view point of patient's safety.

Relevance to patient case: not relevant
Patient case: 71-year-old female with lung cancer; genetic feature: ROS1

Clinical trial: Clinical Relevance of ROS (V-ros UR2 Sarcoma Virus Oncogene Homolog) Aberrations in Solid Tumours

Summary: Alterations involving the ROS (v-ros UR2 sarcoma virus oncogene homolog 1) gene such as mutations, overexpression and gene rearrangements has been implicated in carcinogenesis and has been demonstrated to be a relevant target for ALK inhibitors. While emerging reports have demonstrated the role of ROS rearrangement in non-small cell lung cancer and cholangiocarcinoma, the functional significance of ROS dysregulation in solid tumors remain largely unstudied. The investigators aims are: (1) To characterize the frequency of ROS gene fusion, ROS protein overexpression and ROS gene mutations in cell lines and tumors from patients with hepatocellular carcinoma, colorectal, gastric, breast, ovarian, cholangiocarcinoma and non-small cell lung cancer, (2) To identify novel ROS gene variants in human solid tumors harboring ROS aberrations using next generation sequencing (NGS), (3) To determine the functional relevance of novel ROS gene variants identified with NGS, (4) To characterize the sensitivity of cells with functionally relevant ROS aberrations using ROS tyrosine kinase inhibitors. ROS fusions and protein overexpression will be screened in a panel of cell lines and primary tumors using Fluorescence In-situ Hybridization and immunohistochemistry respectively. Targeted next-generation sequencing will be applied to identify ROS variants in matching cancer types demonstrating high levels of gene fusion and protein overexpression. Functional characterization of novel ROS variants will be performed by silencing (shRNA) and overexpressing candidate cell lines with the respective ROS mutations/fusions, and evaluating their effects on biological functions including cell proliferation, migration, invasion and apoptosis, as well as sensitivity against ROS/ALK inhibitors. The investigators anticipate findings from this study will improve the investigators understanding of aberrant ROS signaling in an expanded group of cancer types, and potentially identifying a larger group of cancer patients that will benefit from ROS targeted therapy.
  Further insight of the role of ROS receptor tyrosine kinase will confirm it as a therapeutic target in human solid tumors and hence expand the indication of crizotinib and other dual ALK/ ROS inhibitors. Furthermore, given the rarity of ROS fusion receptor tyrosine kinase in reported cancers, defining the epidemiology of ROS aberrations in other unreported cancers harboring ROS pathway activation is essential to properly design future clinical trials of ROS inhibitors. The validation of ROS receptor tyrosine kinase will also provide a new therapeutic target in the treatment of cancer and expand the role of novel targeted agents. Findings from this study will further the investigators knowledge on the oncogenic functions of the ROS and the application of ROS inhibitors in an extended group of solid tumors.


Eligibility: Inclusion Criteria:
  - Patients with cancer

Relevance to patient case: not relevant
Patient case: 71-year-old female with lung cancer; genetic feature: ROS1

Clinical trial: Detection of Chromosomal Aberrations in Non-small Cell Lung Cancer (NSCLC) Using Fluorescent in Situ Hybridization (FISH) (ALK Test)

Summary: The purpose of the study is the identification of chromosomal aberrations in non-small cell lung cancer (NSCLC) .
  The imaging system is intended for diagnostic use as an aid to the pathologist in the detection, counting and classifying ALK FISH stained lung samples.

Detailed description: The ALK Break Apart FISH test detects chromosomal aberrations via fluorescence in situ hybridization (FISH) in formalin-fixed paraffin-embedded (FFPE) non-small cell lung cancer (NSCLC) tissue specimens. The FDA approved ALK kit is designed to detect rearrangements involving the ALK gene (2p23). Results from the ALK Kit are intended for use, in conjunction with and not in lieu of current standard diagnostic procedures, as an aid for the pathologist in the identification of patients eligible for treatment with XALKORI® (crizotinib).

Eligibility: Inclusion Criteria:
  -  Well stained slides with bright FISH signals
  Exclusion Criteria:
  -  Very old slides that were already bleached

Relevance to patient case: not relevant