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

Clinical trial: Study of Oral RXDX-101 in Adult Patients With Locally Advanced or Metastatic Cancer Targeting NTRK1, NTRK2, NTRK3, ROS1, or ALK Molecular Alterations.

Summary: Entrectinib (RXDX-101) is an orally available inhibitor of the tyrosine kinases TrkA (coded by the gene NTRK1), TrkB (coded by the gene NTRK2), TrkC (coded by the gene NTRK3), ROS1 (coded by the gene ROS1), and ALK (coded by the gene ALK). Molecular alterations to one or more of these targets are present in several different tumor types, including non-small cell lung cancer (NSCLC), colorectal cancer (CRC), prostate cancer, papillary thyroid cancer, pancreatic cancer, and neuroblastoma. Patients with locally advanced or metastatic cancer with a detectable molecular alteration in targets of interest may be eligible for enrollment.
  Phase 1 will assess safety and tolerability of entrectinib via standard dose escalation scheme and determine the recommended Phase 2 dose. Safety and efficacy will be assessed in the dose expansion portion of the study.


Eligibility: Key Inclusion Criteria:
  -  Histologically or cytologically confirmed diagnosis of locally advanced or metastatic solid tumors that have a NTRK1, NTRK2, NTRK3, ROS1, or ALK molecular alteration.
  -  Measurable disease according to RECIST version 1.1.
  -  Prior cancer therapy is allowed, including crizotinib, ceritinib, and investigational drugs.
  -  Prior radiotherapy is allowed
  -  Patients with controlled asymptomatic central nervous system involvement are allowed.
  -  Resolution of all acute toxic effects (excluding alopecia) of any prior anti-cancer therapy to National Cancer Institute Common Terminology Criteria for Adverse Events (NCI CTCAE) Version 4.03 Grade less than or equal to 1.
  -  Eastern Cooperative Oncology Group (ECOG) performance status (PS) ≤ 2.
  -  Adult patients age 18 years or older.
  -  Life expectancy of at least 3 months.
  Key Exclusion Criteria:
  -  Current participation in another therapeutic clinical trial.
  -  Prior treatment with entrectinib.
  -  History of prolonged QTc interval (e.g., repeated demonstration of a QTc interval > 450 milliseconds).
  -  History of additional risk factors for torsade de pointes (e.g., family history of long QT syndrome).
  -  Known active infections (bacterial, fungal, viral including HIV positivity).
  -  Gastrointestinal disease (e.g., Crohn's disease, ulcerative colitis, or short gut syndrome) or other malabsorption syndromes that would impact on drug absorption.
  -  Known interstitial lung disease, interstitial fibrosis, or history of tyrosine kinase inhibitor-induced pneumonitis.
  -  Peripheral neuropathy ≥ Grade 2.

Relevance to patient case: definitely relevant
Patient case: 71-year-old female with lung cancer; genetic feature: ROS1

Clinical trial: A Study to Assess the Efficacy and Safety of the VEGFR-FGFR Inhibitor, Lucitanib, Given to Patients With Advanced/Metastatic Lung Cancer and FGF, VEGF, or PDGF Related Genetic Alterations

Summary: The purpose of this study is to determine whether lucitanib is safe and effective in the treatment of patients with advanced/metastatic lung cancer and fibroblast growth factor (FGF), vascular endothelial growth factor receptor (VEGF), or platelet derived growth factor (PDGF) related genetic alterations.

Detailed description: Lucitanib is an oral inhibitor of the tyrosine kinase activity of FGFR 1-3, VEGFR 1-3, and PDGFR α/β. Lucitanib has demonstrated potent anti-tumor and anti-angiogenic activity in vitro proliferation assays and in vivo using human tumor xenograft models, with a trend for stronger efficacy in those with genomic aberrancies of FGF or PDGF. Abnormalities in the FGF, VEGF, and PDGF-related genes are observed across lung cancer histologies.
  The first in human trial of lucitanib demonstrated that daily lucitanib is clinically active in patients with advanced solid tumors. Specifically, patients with FGFR1-amplification appeared to derive particular benefit from lucitanib.
  Based on these results, this study is designed to explore the safety and anti-tumor activity of daily lucitanib in lung cancer patients with FGF, VEGF, and PDGF genetic alterations.

Eligibility: Inclusion Criteria:
  -  Histologically or cytologically confirmed advanced/metastatic SCLC or NSCLC
  -  Any of the following tumor tissue based genetic alterations: FGFR1, FGFR2, FGFR3, VEGFA, or PDGFRα amplification; Any FGFR1, FGFR2, or FGFR3 gene fusion; FGFR1, FGFR2, or FGFR3 activating mutation
  -  Availability of tumor tissue sample suitable for the central confirmation of the genetic alteration and exploratory analyses
  -  Eastern Cooperative Oncology Group (ECOG) of 0 or 1
  -  Measurable disease per RECIST 1.1
  -  Documented radiographic disease progression following at least one line of therapy in the advanced/metastatic setting
  Exclusion Criteria:
  -  Tumors that are invading a major vessel; NSCLC tumors abutting to a major vessel
  -  Uncontrolled hypertension, defined as SBP ≥ 140 mmHg and/or DBP ≥ 90 mmHg with optimized anti-hypertensive therapy
  -  Uncontrolled hypothyroidism defined as serum thyroid stimulating hormone (TSH) higher than 5 mIU/mL while receiving appropriate thyroid hormone therapy
  -  Symptomatic and/or untreated central nervous system metastases
  -  Presence of another active cancer
  -  Ongoing adverse events from surgery or prior anti-cancer therapies, including radiation, targeted, or cytotoxic therapies
  -  Pregnant or breastfeeding women

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

Clinical trial: Calypso-based Deep Inspiration Breath Hold (DIBH) Radiation Treatments of Lung Cancer

Summary: The purpose of this study is to test the use of Calypso beacon implants as a way to determine where the lung tumor is located during radiation treatment. The Calypso beacons are small devices that are implanted in the lungs, near the tumor. They are able to send a signal to a tracking system to show where they are, and where the tumor is, as the patient holds their breath for the radiation treatment. The investigators want to find out what effects, good and/or bad, that this has on the patient and the way they treat the cancer in your lungs.


Eligibility: Inclusion Criteria:
  -  Patients must have histologic proof of malignancy suitable for thoracic radiation therapy
  -  Patients planning to undergo radiation therapy for primary or recurrent carcinomas of the lung or oligo-metastatic carcinoma to the lung.
  -  Age ≥ 18 years old
  -  KPS ≥ 60%
  -  Ability to hold their breath for >20 seconds for 5 times
  -  Patients who are able to tolerate flexible bronchoscopy
  -  Patients with life expectancy of at least 12 months
  -  Patients able to have bronchoscopic placement of Calypso as confirmed on a recent (within the past 8 weeks) CT scan.
  -  Patients who are able to comply with the protocol follow-up schedule.
  Exclusion Criteria:
  -  Patients unable to comply with instructions for DIBH
  -  Patients with implants in the chest region that contain metal or conductive materials (e.g., metal implants, rods, or plates) which Calypso Medical considers will interfere with the Calypso System's electromagnetic localization.
  -  Patients with active implanted devices, such as pacemakers, defibrillators, and drug infusion pumps since the effects of the Calypso System operation on these devices are unknown.
  -  Patients with clinically significant active infections.
  -  Patients with bronchiectasis in the region of the intended implantation sites.
  -  Patients with a history of hypersensitivity to nickel.
  -  Patients whose lung tumors are being monitored with MR imaging (MR imaging of the anchored transponders is safe but yields an image artifact around the anchored transponders).
  -  Posterior lesions that would be >19cm distance from Calypso detector plate. Patients may be treated in the prone position in order to meet the required minimum distance.
  -  Patients with any other medical condition or laboratory value that would, at the discretion of the investigator, preclude the patient from participation in this clinical study.
  -  Patients who are deemed unable to safely undergo or tolerate flexible bronchoscopy
  -  Patients who are unable to tolerate anesthesia or sedation
  -  Patients enrolled in any other clinical studies the investigator believes to be in conflict with this investigation.
  -  Female patients who are pregnant or nursing

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

Clinical trial: One Step Nucleic Acid Amplification in Endobronchial Ultrasound-guided Needle Aspiration Samples

Summary: The aim of our study is to investigate if CK19 mRNA-detection via OSNA can accurately detect lymph node metastases in lung cancer patients using EBUS-TBNA samples.

Detailed description: Regional lymph nodes are assessed before tumor resection and before initiation of chemo- or radiotherapy. Endobronchial ultrasound-guided needle aspiration (EBUS-TBNA) is a well-established method for mediastinal and hilar lymph node staging [2, 3]. Samples obtained via this route are much smaller than surgical lymph node biopsies, yet they are able to provide complete and thorough evaluation, this includes current molecular testing.
  One Step Nucleic Acid Amplification (OSNA), a molecular test that utilizes CK 19 mRNA-concentration as a target marker is becoming a rapidly dynamic method in quick detection of sentinel lymph node (SLN) metastases in breast cancer, colon cancer and other cancers.
  In lung cancer, the role of SLN is not well established. However, recent publications suggest an accurate and rapid detection of lymph node metastases in NSCLC. However this requires complete lymph node dissection either with mediastinoscopy or by other surgical means such as thoracotomy.
  The aim of our study is to investigate if CK19 mRNA-detection via OSNA can accurately detect lymph node metastases in lung cancer patients using EBUS-TBNA samples.

Eligibility: Inclusion Criteria:
  -  CT-scan suspicious for lung cancer,
  -  enlarged mediastinal lymph nodes (>10 mm),
  -  EBUS-TBNA to be performed,
  -  age: 18-99 years
  Exclusion Criteria:
  -  age: <18 years

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

Clinical trial: The Impact of Lung Cancer-derived Fibroblasts on Mast Cells Activation

Summary: In addition to their role in allergic inflammation, mast cells are often found at the site of tumors. They have been attributed both to pro- and anti-tumorigenic roles depending on the tumor type. Secretion of mast cell mediators such as histamine, tryptase, fibroblast growth factor (b-FGF), vascular endothelial growth factor (VEGF) and interleukin-8 (IL-8) can enhance tumor growth and angiogenesis while TNF-a and heparin act as tumor suppressors.
  The non-small cell lung cancer constitutes the majority of cases of lung cancer. In lung cancer, mast cell numbers correlate with tumor angiogenesis and poor prognosis.
  In this work, we are interested to determine the factors in lung cancer microenvironment that attribute to mast cell activation. Beside the tumor cells themselves, the cancer microenvironment includes other cells such as fibroblasts. The fibroblasts arising from tumor stroma, called cancer-associated fibroblasts (CAFs), undergo activation, and have different feature compared to normal fibroblasts (NFs). In this work we are interested to determine whether CAF cells derived from lung tumors, together with the lung cancer cells, or microvesicles-derived from these cells, are able to stimulate mast cells to degranulate and/ or to release various cytokines and chemokines.
  For this propose, during surgery of patients with lung cancer, we will take unnecessary sample from the cancer and from normal area for purification of CAF or normal fibroblast cells. Those cells will be co-cultured with both lung cancer cell line (A-549) or microvesicles-derived from these cells, and human mast cell line (LAD2). Supernatants will be collected for determine degranulation and cytokine release from these mast cells.


Eligibility: Inclusion Criteria:
  Patient with non small cell lung carcinoma
  Exclusion Criteria:

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

Clinical trial: ADXS11-001 High Dose HPV+ Cervical Cancer

Summary: To evaluate the tolerability and safety of ADXS11-001 (1 x 10^10 colony forming units [cfu]) administered with prophylactic premedication in repeating 3-dose study cycles in women with persistent, metastatic, or recurrent squamous and non-squamous carcinoma, adenosquamous, or adenocarcinoma of the cervix. To evaluate tumor response and progression-free survival (PFS, time to progression) by immune-related Response Evaluation Criteria in Solid Tumors (irRECIST).


Eligibility: Inclusion Criteria:
  -  Patients with histologically-confirmed, persistent, metastatic or recurrent squamous or non-squamous cell carcinoma, adenosquamous carcinoma, or adenocarcinoma of the cervix with documented disease progression (disease not amenable to surgery or standard radiotherapy).
  -  Patients who have received no more than 1 prior cytotoxic treatment regimen.
  -  Subject may have received ≤2 prior regimens for the treatment of their metastatic disease.
  -  Subject is able to provide written informed consent.
  -  Subject must have an ECOG performance status of 0 or 1.
  Exclusion Criteria:
  -  In the opinion of the investigator, subject has rapidly progressing disease, OR has life expectancy of less than 6 months, OR would be unable to receive at least one cycle of therapy.
  -  Subject has received chemotherapy and/or radiation therapy (except palliative radiation therapy for disease-related pain) within ≤2 weeks of first ADXS11-001 infusion.
  -  Subject has a known additional malignancy that is progressing or requires active treatment. Exceptions include basal cell carcinoma of the skin, squamous cell carcinoma of the skin, or in situ cervical cancer that has undergone potentially curative therapy.
  -  Has a contraindication to administration of trimethoprim/sulfamethoxazole or ampicillin.
  -  Has implanted medical device(s) that pose a high risk for colonization and/or cannot be easily removed (e.g., prosthetic joints, artificial heart valves, pacemakers, orthopedic screw(s), metal plate(s), bone graft(s), or other exogenous implant(s)). NOTE: More common devices and prosthetics which include arterial and venous stents, dental and breast implants, and venous access devices (e.g., Port-a-Cath or Mediport) are permitted. Sponsor must be contacted prior to consenting any subject who has any other device and/or implant.

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

Clinical trial: Ethaselen for the Treatment of Thioredoxin Reductase High Expression Advanced Non-small Cell Lung Cancers

Summary: Thioredoxin reductase plays an critical role in lung cancer patients, in vitro study showed that, ethaselen, specific inhibitor of thioredoxin reductase, could inhibit lung cancer cell growth and induce apoptosis. In China, phase 1 clinical trials of ethaselen showed that 1200 mg dose ethaselen could be well tolerated, in pre-clinical study we found that, approximately 50% non-small cell lung cancers harbored high thioredoxin reductase expression(IHC result ++ or +++), phase 1a/b of ethaselen had finished in 2008, the result showed that 1200mg ethaselen per day was safety and tolerated by Chinese malignant tumor patients.In pre-clinical research, our group found that, elevated of thioredoxin reductase activity was associated with the expression of thioredoxin reductase tested by immunohistochemistry, which means high expression of this enzyme may be a favourite predicted factor of ethaselen, the specific inhibitor of thioredoxin reductase.

Detailed description: This phase 1c study will include patients pathologic diagnosis advanced non-small cell lung cancer who had received more than two lines standard treatment, according to NCCN Non-small cell lung cancer guideline, there were no standard treatment scheme for these patients. Approximately 40 patients will be included in the study, patients will received oral ethaselen dispersible tablet, 600 mg bid dose, primary endpoint of this study is 6 week disease control rate(DCR, CR+PR+SD), secondary endpoints include progression free survival(PFS), overall survival(OS), quality of life(QOL) and drug safety.

Eligibility: Inclusion Criteria:
  -  advanced non-small cell lung cancer, stage IIIB/IV who had received more than 2 standard treatment scheme
  -  18-75 years old, anticipate overall survival more than 3 months, ECOG 0-2
  -  within 4 weeks, not receive chemotherapy, radiotherapy or surgery
  -  HB≥90g/L； ANC ≥1.5×109/L；PLT ≥80×109/L
  -  EGFR/ALK mutation negative
  -  immunohistochemistry test of cancer tissue showed ++ or +++ of thioredoxin reductase
  -  brain metastasis without symptoms
  Exclusion Criteria:
  -  according to NCCN non-small cell lung cancer guidelines (2014 v3), there were standard treatment scheme for the patients
  -  pregnancy or breast-feeding women
  -  any serious disease which could not be controled
  -  urine protein≥++, or 24h urine protein＞1g
  -  received any anti-cancer treatment within 4 weeks

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

Clinical trial: Detection of Oncogenic Tumor Mutations in the Urine and Blood of Lung and Colorectal Cancer Patients

Summary: The purpose of this study is to see whether gene mutations can be found in the urine or blood of lung cancer patients and urine of colorectal cancer patients. Gene mutations are when DNA in a gene is damaged in a way that changes the genetic message carried by that gene. Gene mutations can sometimes cause lung cancers. These gene mutations are only found in lung and colorectal cancer cells, not the normal cells in your body. All lung cancer tumors and colorectal cancer tumors are now tested for different gene mutations as their presence affects lung cancer treatment. Tumor samples obtained from a biopsy or surgery are typically tested for these gene mutations.


Eligibility: Inclusion Criteria:
  Lung cancer:
  For patients participating in Part A (initial testing) and Part B (serial testing):
  -  Patients must have a diagnosis of stage IV lung adenocarcinoma undergoing systemic therapy.
  -  Patients must have had or intend to have EGFR mutation testing (specifically including exon 19 deletions and L858R) performed on their tumor with results available from a CLIA certified laboratory.
  -  ≥ 18 years of age
  Specific to patients participating in Part B (serial testing):
  -  Patients must be planning to receive cancer care at Memorial-Sloan Kettering.
  -  Patients must have a confirmed EGFR mutant lung cancer (exon 19 deletions and L858R) with molecular testing results available from a CLIA certified laboratory.
  -  Must be within 3 months of their diagnosis of metastatic lung cancer.
  -  Treatment plan should include an EGFR tyrosine kinase inhibitor, but may concurrently be on a therapeutic protocol.
  Colorectal Cancer:
  For patients participating in Part A (initial testing) and Part B (serial testing):
  -  Patients must have a diagnosis of stage IV colorectal adenocarcinoma undergoing systemic therapy or have recently progressed on therapy including anti-EGFR based therapy.
  -  Patients must have had or intend to have RAS/RAF mutation testing on their tumor with results available from a CLIA certified laboratory. For the patients who recently progressed on anti-EGFR must have tumor tissue molecular analyses preformed (prior to enrolling or a plan to test it at the time of enrollment).
  -  >18 years of age
  Specific to patients participating in Part B (serial testing):
  -  Patients must be planning to receive cancer care at Memorial-Sloan Kettering.
  -  Patients must have a confirmed RAS/RAF mutant colorectal cancer with molecular testing results available from a CLIA certified laboratory.
  -  Must be within 3 months of their diagnosis of metastatic colorectal cancer.
  Exclusion Criteria:
  lung cancer and colorectal cancer
  -  Comorbidities that would prohibit or make serial urine collection difficult or impossible

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

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