araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: A Randomised Trial of Chemotherapy Plus Surgery for Recurrent Non-Small Cell Lung Cancer

Summary: The purpose of this study is to determine if the commonly administered chemotherapeutic agents including cisplatin, carboplatin, oxaliplatin, docetaxel and gemcitabine for solid tumors in clinical oncology, either a single format or given as combinations followed by surgery are effective in the treatment of relapsed and refractory non-small cell lung cancer patients.

Detailed description: Lung carcinoma is a malignant disease characterized by uncontrolled alveolar type II epithelial cell growth in lung tissues. Worldwide in 2012, lung cancer occurred in 1.8 million people and resulted in 1.6 million deaths, making it the most common cause of cancer-related death in men and second most common in women after breast cancer. The most common age at diagnosis is 70 years, and less than 20% of people diagnosed with lung cancer can survive five years post diagnosis. The two main types of lung carcinomas are small cell lung carcinoma (SCLC) and non-small cell lung carcinoma (NSCLC). NSCLC represents the most common type of lung cancers, and approximately 85% of lung cancers are NSCLC. Squamous cell carcinoma, adenocarcinoma, and large cell carcinoma are all subtypes of NSCLC, the latter associated with high mortality in overall cancer populations with limited treatment options.
  In this study, the investigators performed a Phase I, open label, agent-combination exploration, multicenter clinical trial to establish the treatment efficacy of several chemotherapeutic agents in patients with recurrent NSCLC who have undergone prior surgery for the primary disease. Up to four cohorts have been enrolled to determine the effectiveness and safety of single or combinational therapeutic strategy. Besides the five-year disease-free survival, overall survival and five-year metastasis-free survival post treatment, the investigators also take into account the anticancer agent-induced tumor stroma damage extent, which may provide further evidence to support the treatment efficacy and assess the potential influence of a damaged tumor microenvironment on disease progression or regression in clinical settings.

Eligibility: Inclusion Criteria:
  -  Age ≤ 75 years with histologically proven NSCLC
  -  No severe major organ dysfunction
  -  WHO performance status of 0 or 1
  -  No prior cancer chemotherapy
  -  A Clinical Stage ≥ IA (T1a, N0, M0) of lung disease but without diagnosed distant metastasis (according to the 1997 revision of the International Union Against Cancer TNM staging system) as determined by a preoperative evaluation that included a pleural computed tomography (CT) scan.
  Exclusion Criteria:
  -  Age ≥ 76
  -  Severe major organ dysfunction
  -  WHO performance status of >1
  -  Prior cancer chemotherapy
  -  Stage IV

Relevance to patient case: not relevant
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: Lipusu Advanced Squamous Cell Carcinoma of Lung Study Carboplatin in Advanced Squamous Cell Carcinoma of Lung

Summary: The purpose of this study is to investigate the efficacy and the safety of paclitaxel liposome injection and carboplatin compared with gemcitabine and carboplatin as first-line therapy in advanced squamous cell carcinoma of lung.

Detailed description: The purpose of this study is to investigate the efficacy and the safety of paclitaxel liposome injection and carboplatin compared with gemcitabine and carboplatin as first-line therapy in advanced squamous cell carcinoma of lung. This study is the Superiority Trial.

Eligibility: Inclusion Criteria:
  1. Aged 18-75 years old, both gender;
  2. ECOG: 0-1;
  3. Histologically or cytologically confirmed diagnosis of squamous non-small-cell lung cancer (stage IIIB or IV);
  4. No prior chemotherapy, biological therapy or immunotherapy; or subjects have recurrence and metastasis more than 6 months after the end of chemotherapy, but not gemcitabine or paclitaxel;
  5. At least one radiographically measurable or assessable lesion on chest CG according to RECIST1.1 (response evaluation criteria of solid tumors); regional lymph node metastases may also be measured or assessed by imaging (mediastinal lymph nodes);
  6. Life expectancy of at least 12 weeks;
  7. Before treatment, blood tests or biochemical measurements must meet the following criteria:
  -  White blood cell count (WBC)≥ 4.0*109/L;
  -  Neutrophil count (ANC)≥ 2.0*109/L;
  -  Platelet count (PLT)≥ 100*109/L;
  -  Hemoglobin (Hb)≥ 100g/L;
  -  Hepatic function: serum bilirubin ≤ 1.5 times the upper normal limit, aspartate aminotransferase (AST) and alanine aminotransferase (ALT) ≤ 2.5 times the upper normal limit;
  -  Renal function: creatinine ≤ 1.5 times the upper normal limit;
  8. Signed informed consent.
  Exclusion Criteria:
  1. Hypersensitivity reaction to the interventional drugs;
  2. Pregnant or breastfeeding;
  2.

Relevance to patient case: not relevant
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: A Study to Evaluate the Efficacy and Safety of Pemigatinib (INCB054828) in Subjects With Myeloid/Lymphoid Neoplasms With FGFR1 Rearrangement - (FIGHT-203)

Summary: The purpose of this study is to evaluate the efficacy and safety of pemigatinib (INCB054828) in subjects with myeloid/lymphoid neoplasms with fibroblast growth factor receptor (FGFR) 1 rearrangement.


Eligibility: Inclusion Criteria:
  -  Documented lymphoid or myeloid neoplasm with 8p11 rearrangement known to lead to FGFR1 activation, based on standard diagnostic cytogenetic evaluation performed locally, before signing informed consent for this study.
  -  Subjects must be relapsed/refractory. Prior stem cell transplantation is allowed.
  -  Life expectancy ≥ 12 weeks.
  -  Eastern Cooperative Oncology Group (ECOG) performance status 0 to 2.
  Exclusion Criteria:
  -  Prior receipt of a selective FGFR inhibitor.
  -  History and/or current evidence of ectopic mineralization/calcification, including but not limited to soft tissue, kidneys, intestine, myocardia, or lung, except calcified lymph nodes and asymptomatic arterial or cartilage/tendon calcifications.
  -  Current evidence of corneal disorder/keratopathy, including but not limited to bullous/band keratopathy, corneal abrasion, inflammation/ulceration, and keratoconjunctivitis, as confirmed by ophthalmologic examination.
  -  Use of any potent cytochrome P450 3A4 inhibitors or inducers within 14 days or 5 half-lives (whichever is shorter) before the first dose of study drug.

Relevance to patient case: not relevant
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: Vistusertib (AZD2014) Monotherapy in Relapsed Small Cell Lung Cancer Patients Harboring RICTOR Amplification

Summary: [Study Design] This study is a single arm, multi-center phase II study of vistusertib monotherapy in patients with relapsed small cell lung cancer (SCLC) harboring RICTOR amplification. Patients will receive vistusertib monotherapy (50 mg BID per os every 12 hours) until they demonstrate objective disease progression or they meet any other discontinuation criteria.
  [Primary Objective] To investigate the efficacy of vistusertib monotherapy in patients with relapsed SCLC patients harboring RICTOR amplification as 2nd or 3rd line therapy


Eligibility: [Inclusion Criteria]
  -  Provision of informed consent prior to any study specific procedures
  -  Men and women aged at least 18 years
  -  Small cell lung cancer harboring RICTOR amplification
  -  Patients are willing and able to comply with the protocol for the duration of the study including undergoing treatment and scheduled visits and examinations.
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 to 1 with no deterioration over the previous 2 weeks
  -  Minimum life expectancy of 12 weeks
  -  Patients must have acceptable bone marrow, liver and renal function measured within 14 days prior to administration of study treatment as defined below:
  -  At least one measurable lesion that can be accurately assessed by imaging or physical examination at baseline and follow up visits.
  -  No history of non-autologous bone marrow transplant.
  Exclusion Criteria:
  -  Participation in another clinical study with an investigational product during the last 21 days.
  -  Prior chemotherapy, biological therapy, radiation therapy, androgens, thalidomide, immunotherapy, other anticancer agents within 21 days of starting study treatment. Prior use of an investigational monoclonal antibody therapy within 3 months.
  -  Major surgery within 4 weeks prior to study entry (excluding placement of vascular access), or minor surgery (excluding tumour biopsies) within 14 days of first dose of study treatment.
  -  Exposure to strong or moderate inhibitors or inducers of CYP3A4/5, Pgp (MDR1) and BCRP if taken within the stated washout periods before the first dose of study treatment (see Appendix 1)
  -  Exposure to specific substrates of the drug transporters OATP1B1, OATP1B3, MATE1 and MATE2K within the appropriate wash-out period
  -  Any haemopoietic growth factors within 14 days prior to receiving study treatment.
  -  Pre-treatment with other PI3K, AKT, dual PI3K/mTRO and mTOR inhibitors
  -  Spinal cord compression and/or brain metastases unless asymptomatic or treated and stable off steroids for at least 4 weeks prior to start of study treatment.

Relevance to patient case: not relevant
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: Lung Transplant HCV, Pilot Study

Summary: In this study HCV negative recipients will be transplanted with HCV positive lungs. Investigators will attempt to decrease infectivity rates by performing Normothermic Ex vivo Lung Perfusion (EVLP), which is an approved method of donor lung preservation, assessment and treatment, and could be an excellent platform to reduce/eliminate hepatitis C virus. Patients will be treated by the standard approved direct-acting antivirals (DAAs) if infection occurs. It is planned to enrolled 20 patients from the Lung transplant wait list in this study. Patients will be followed for 6 months. This will be a single center pilot study.

Detailed description: The success of lung transplantation (LTx) is significantly hindered by the lack of sufficient number of available donors. Many potential donor lungs cannot be utilized in clinical transplantation because donors have chronic viral infections such as hepatitis C (HCV) infection. This study will test the possibility of safely transplanting lungs from HCV positive donors. Donor lungs will be subjected to Normothermic Ex vivo Lung Perfusion (EVLP) for 6 hours for organ assessment and reduction of viral load prior to transplantation. After transplantation, recipients will be carefully monitored for HCV infection and if infection occurs, they will be promptly treated with highly effective antiviral therapy using newly approved DAAs. The aim of the study is to show that transplantation of lungs from HCV positive donors is safe in the era of DAAs. The hypothesis is that the rate of HCV transmission to recipients will be lower than previously described due to EVLP pre-treatment and any HCV transmission that does occur will be readily treatable and curable. If successful, the knowledge from this study can have a large impact to patients with end stage organ diseases by providing a large novel source of donors for lung and potentially other organ transplantations.

Eligibility: Inclusion Criteria:
  -  Recipients listed for single or bilateral lung transplant
  -  HCV Nucleic Acid Amplification Testing (NAT) negative
  -  Ability to provide written informed consent
  Exclusion Criteria:
  -  Participation in another interventional clinical trial

Relevance to patient case: not relevant
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: Circulating Tumor Cells in Solid Tumors

Summary: The purpose of this study is to identify circulating tumor cells in patients with solid tumors. Quantify and characterize these cells, collect patient information in regards to the patient's cancer. Develop a database and a sample repository where future analysis could be done.

Detailed description: The primary purpose of this correlative study is to create a prospective database documenting the quantity and characterization of circulating tumor cells (CTCs) in solid tumor patients as identified by a various laboratory techniques and analyses. The investigators are developing this resource to provide data to achieve the following objectives: 1) correlate CTCs with known prognostic factors, 2) correlate CTCs with burden of disease, 3) evaluate the ability of CTCs to be used in the surveillance of disease recurrence, and 4) evaluate CTCs ability to be used as a biomarker for treatment response.

Eligibility: Inclusion Criteria:
  -  Age ≥ 18 years of age
  -  Biopsy proven solid tumor malignancy
  -  Seen at UNC Chapel Hill Hospital and Health Care System
  -  Consents to abstraction of their medical records
  -  Signed an institutional review board (IRB)-approved informed consent document for this protocol
  Exclusion Criteria:
  -  < 18 years of age
  -  Dementia, altered mental status, incarceration or any psychiatric condition that would prohibit the understanding or rendering of informed consent.

Relevance to patient case: not relevant
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: Relevance of Peripheral Cells in the Pathophysiology of Chronic Myelomonocytic Leukemia (CMML)

Summary: Chronic Myelomonocytic Leukemia (CMML) is the most frequent of myelodysplastic/myeloproliferative syndromes, as defined by the WHO classification of myeloid malignancies. The median age at diagnosis is around 70 years with a strong male predominance. CMML is a clonal disease of the bone marrow hematopoietic stem cell mainly characterized by persistent monocytosis (>1x109/L) and the presence of immature dysplastic granulocytes in the peripheral blood of CMML patients. Allogeneic stem cell transplantation (ASCT) remains the only curative option in CMML. However, CMML patients are rarely eligible for this kind of therapy, mainly due to their advanced age. The gold standard treatment of CMML thus remains hydroxyurea, which is usually initiated when the disease becomes proliferative, and demethylating agents, which could be efficient in the most aggressive forms of CMML. Nevertheless, the pathogenesis of CMML remains poorly understood and new therapies are urgently needed for patients in treatment failure.
  In recent years, a large numbers of gene mutations have been discovered in CMML, none of which are specific of this entity, as they can be encountered with different frequencies in other myeloid neoplasms. These mutated genes encode signaling molecules (NRAS, KRAS, CBL, JAK2, FLT3 and several members of the Notch pathway), epigenetic regulators (TET2, ASXL1, EZH2, IDH1, IDH2,.) and splicing factors (SF3B1, SRSF2, ZRSF2). Mutations in the transcription regulators RUNX1, NPM1 and TP53 have also been reported in CMML. However, the role of these mutations in leukemogenesis is still unclear. CMML is also characterized by defects in monocyte to macrophage differentiation. These defects in monocyte differentiation can be attributed to the presence of immature dysplastic granulocytes that secrete high levels of alpha-defensins HNP1-3 that antagonize the purinergic receptor P2RY6 in CMML patients. These CD14-/CD15+/CD24+ immature granulocytes that belong to the same clone than the leukemic monocytes seem to have immunosuppressive properties ressembling those of the myeloid-derived suppressor cells (MDCS) described in solid tumours. Whether these immature granulocytes contribute to autoimmune manifestations or immunoescape and progression of CMML is a conendrum and remains to be determined.
  In this context, the proposed project aims at identifying news insights into the pathophysiology of CMML through a better definition of the phenotype and function of monocytes and immature granulocytes that characterize this pathology.


Eligibility: Inclusion Criteria:
  -  Patients newly diagnosed or undergoing treatment in the Clinical Hematology department of the participating establishments
  Exclusion Criteria:
  -  NA

Relevance to patient case: not relevant
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: Five Fraction SABR Dose Escalation for Early Stage Squamous Cell Carcinoma of the Lung

Summary: The purpose of this study is to test whether 5 fraction stereotactic ablative body radiation (SABR) is safe and improves local control for early state squamous cell carcinoma of the lung. While three fraction SABR is effective for the treatment of early stage non small cell lung carcinoma (NSCLC) of all histologies, it is not safe for many patients. While four and five fraction SABR is safe, recently published data and our institutional data suggests that local control for early stage squamous cell carcinoma of the lung using the current four or five fraction SABR is suboptimal.

Detailed description: 1. Primary Objectives During Phase I study - Determine the safety and maximum tolerated radiation dose for five fraction SABR for squamous cell cancer of the lung.
  During Phase II study - Determine 2 year local control of dose escalated five fraction SABR vs. institutional historical control standard dose SABR in squamous cell cancer of the lung.
  2. Phase II Secondary Objectives
  -  Determine overall survival, progression free survival and patterns of failure after SABR.
  -  Determine tolerability of dose escalated SABR.

Eligibility: Inclusion Criteria
  1. Age ≥ 18 at time of consent.
  2. Ability to provide written informed consent and HIPAA authorization.
  3. Pathological diagnosis of squamous cell carcinoma of the lung.
  4. Staging PET/CT (invasive mediastinal staging strongly encouraged but not required).
  5. Tumors < 7cm
  6. N0 M0 disease
  7. Baseline PFTs available or will be obtained prior to treatment start
  Exclusion Criteria
  1. Previous radiation therapy to the lung per investigator discretion.
  2. Inability to comply with treatment per investigator discretion.
  3. Inability to follow standard of care follow up recommendations per investigator discretion.

Relevance to patient case: not relevant
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: Donation of Post Mortem Tumor Tissues

Summary: DONUM is an observational prospective independent protocol for patients with advanced lung cancer, colorectal cancer or cancer of unknown primary, willing to donate their tumor tissue samples post mortem for biomedical research purposes. All patients who fulfill the inclusion criteria will be eligible for the study after giving their Informed consent. Informed Consent will be obtained in two steps. During the pre-information step patients will be acquainted with the existence of a post-mortem cancer tissue donation research program governed by the DONUM protocol. If the patients manifest interest to participate into the program (in writing) during the pre-information step, they will proceed to step 2 and undergo the final informed consent process.

Detailed description: Despite the recent technological advancement in genomic and proteomic, the molecular understanding of clonal evolution in solid tumor patients is hampered by intra tumor heterogeneity (ITH), while remaining essential to the effective treatment of patients. Recent evidence suggests that branched evolutionary tumor growth may contribute to ITH both within a primary tumor and between primary and metastatic tumors. To study the full extent and consequences of ITH, and grasp clonal evolution, the investigators need to have access not only to circulating biomarkers (circulating tumor DNA) but also, simultaneously and separately, to the primary tumor and all its derived metastases. However multiple biopsies in live patients are neither medically feasible, nor ethical acceptable. A lesser known tissue collection method is through rapid tissue donation (RTD), which is the procurement of 'fresh' tissue within 2 hrs following the death of a patient. RTD-based research provides an effective way to investigate advance tumors biology in a manner not possible by any other means. With an RTD approach, the full extent and consequences of tumor heterogeneity can be evaluated by deep sequencing and global analysis of genetic alterations at the protein level of simultaneous core biopsies from several areas of the primary tumor and metastases and correlation with clinical outcome. To investigators' knowledge, no such studies have been done in Italy and are currently being pursued only in selected USA and UK cancer centers.

Eligibility: Inclusion Criteria:
  -  Adult patients with confirmed metastatic non-small cell lung cancer (NSCLC), colorectal cancer (CRC), CUP (cancer of unknown origin syndrome) with life expectancy less than or equal to 3/4 months;
  -  Age ≥18;
  -  Signed informed consent from patient to enter the study and to undergo post-mortem tissue sampling.
  Exclusion Criteria:
  -  Medical, or psychological conditions that would preclude informed consent;
  -  History of high-risk infections (e.g. HIV-positive, hepatitis C, tuberculosis and Creutzfeldt-Jacob disease).

Relevance to patient case: not relevant