araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: Detection of CSF Next Generation Sequencing in the Application of Brain Metastases From Lung Adenocarcinoma or Meningeal Metastasis

Summary: This study aimed to detect cell free DNA (cfDNA) in the cerebrospinal fluid and plasma, and to determine whether cfDNA can be used for concomitant diagnosis to improve the treatment efficacy and prognosis of patients with brain (meningeal) metastasis by monitoring tumor-related genetic mutations in cfDNA in the plasma and cerebrospinal fluid.

Detailed description: This study planned to enroll 50 patients with lung cancer diagnosed with brain (meningeal) metastases, and all cases were slated to receive radiotherapy and targeted therapy. Patients' clinical data were collected (including but not limited to: age at diagnosis with brain (meningeal) metastases, KPS score, smoking history, stage of disease at diagnosis, time to progress to brain metastases, number of brain metastases, extracranial metastases (ECM), and systemic disease at the time of brain metastases. Anticoagulated whole blood and anticoagulated cerebrospinal fluid were collected before local treatment (samples of primary cancer tissue and metastatic carcinoma of some patients were preserved) and at 7 days, 1 month, 3 months, as well as 6 months after the treatment (time of sample retention was to be determined, Figure 2). DNA was extracted from tumor tissues, genomic DNA was extracted from leukocytes, and cfDNA was extracted from plasma and cerebrospinal fluid, for complete quantitative detection of DNA, DNA library construction, as well as targeted capture sequencing. Tumor-related genes were analyzed, and changes in the tumor burden during the treatment process were evaluated. The clinical significance of cfDNA in the plasma and cerebrospinal fluid for treatment efficacy and prognosis was evaluated, and compared with that of clinical indicators of treatment efficacy.
  This study involved two stages. The first stage was a pre-experiment: samples were retained from 3-5 cases, and mutations in tumor-related genes in the cfDNA in plasma and cerebrospinal fluid were compared. The investigators analyzed, combined with clinical indicators, whether mutations of cfDNA in plasma accord with that of the cerebrospinal fluid and whether mutations of cfDNA in cerebrospinal can reflect the mutational status of tumor cells. The second phase was conducted by expanding the number of cases, based on the first stage.

Eligibility: Inclusion Criteria:
  1. Patients with confirmed diagnosis of lung adenocarcinoma with brain (meningeal) metastasis.
  2. Samples collection should be allowed.
  Exclusion Criteria:
  1. Pregnant women
  2. Minors (subjects less than 18 years of age)

Relevance to patient case: not relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: Improving Chronic Illness Management With the Apsaalooke Nation: The Baa Nnilah Project

Summary: This is a group randomized trial of an intervention to improve chronic illness self-management.


Eligibility: Inclusion Criteria:
  -  ≥ 25 years
  -  AI
  -  diagnosed with diabetes
  -  hypertension
  -  osteoporosis
  -  liver disease
  -  chronic lung disease (asthma, chronic bronchitis or emphysema)
  -  heart disease (coronary artery disease or congestive heart failure)
  -  stroke (completed cerebrovascular accident with neurologic handicap and normal mentation)
  -  chronic arthritis
  Exclusion Criteria:
  -  major medical illness that precludes their attendance at 7 meetings
  -  <25 years of age

Relevance to patient case: not relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: Early Rebiopsy to Identify Biomarkers of Tumor Cell Survival Following EGFR TKI Therapy

Summary: A comparison of baseline tumor characteristics in EGFR mutant lung cancers to tumor characteristics after early response of EGFR-TKI targeted treatment to allow identification of early adaptive mechanisms of cell survival in the setting of oncogene-targeted therapy. This identification will facilitate targeting and termination of these survival/resistance pathways before they develop with rational combination of therapeutic agents to improve outcomes.


Eligibility: Inclusion Criteria:
  -  Carry a diagnosis of stage IV lung adenocarcinoma with an EGFR activating mutation
  -  Aged 18 - 85 years or older
  -  ECOG 0-2
  -  Have a histologically confirmed diagnosis of lung adenocarcinoma harboring an EGFR sensitizing mutation (including, but not limited to: G719X, del exon 19, or L858R).
  -  No prior therapy for metastatic disease.
  -  Planned treatment with a single agent EGFR TKI including but not limited to:
  1. erlotinib,
  2. gefitinib,
  3. rociletinib (CO-1686),
  4. afatinib, or
  5. osimertinib (AZD-9291).
  -  Patients must have at least one site of measurable disease ≥ least 2cm.
  -  Primary disease site or site of metastatic disease must be amenable to biopsy.
  -  Patients must have the ability to understand and willingness to sign an informed consent document.
  -  Patients must be willing to undergo an initial pre-treatment biopsy of tumor tissue (or have previously collected frozen tissue) and a follow-up biopsy 2 weeks (+/- 1 week) after treatment start
  Exclusion Criteria:
  -  Concurrent health problem which would preclude tissue biopsy (eg hemophilia or other bleeding predisposition).
  -  Patients whose only source of biopsiable disease is:
  1. intracranial,
  2. pleural effusion or any lesion that is deemed unsafe to biopsy by the treating physician or,
  3. interventional radiology.

Relevance to patient case: not relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: Therapeutic ResistAnce and Clonal Evolution Assessed With Liquid Biopsy of NSCLC Patients in China

Summary: To evaluate the concordance of sensitizing mutations detected between paired plasma and tissue samples; the correlation between the clonal status of sensitizing mutations and targeted therapy response; and the prognostic impact of the relative abundance of sensitizing / resistance mutations.

Detailed description: In the study, 500 advanced NSCLC patients will be recruited. All the patients will receive biopsy genotype assay and circultating tumor DNA (ctDNA) liquid biopsy. Patients who carry actionable EGFR mutation, ROS1 fusion, ALK fusion or MET exon 14 skipping mutation will receive TKI treatment according to guidelines. During the TKI treatment, every patients will take liquid biopsy assay to monitor the mutation status. The study will be ended when all the patients had a progressive disease (PD) in their targeted lesion.

Eligibility: Inclusion Criteria:
  -  Provision of informed consent
  -  Newly diagnosed and histological or cytological confirmed stage IIIB-IV lung adenocarcinoma or non-smoking squamous cell carcinoma patients according to the AJCC staging system. The stage IV lung cancer and brain metastasis can be diagnosed by imaging and enhanced CT respectively
  -  ECOG performance status 0-2 with expected more than 6 months of survival time
  -  Willingness to comply with required protocols and give permission to use the data for clinical research and products development
  Exclusion Criteria:
  -  Patients have other primary cancers
  -  Patients have symptomatic brain metastasis, complications that are associated with brain metastasis or cognitive disorders
  -  Patients failed in either plasma or tissue sample QC

Relevance to patient case: not relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: Expanded Access to Entrectinib for Cancers With NTRK1/2/3, ROS1, or ALK Gene Fusions

Summary: Expanded access to entrectinib will be given to patients with cancers harboring NTRK1/2/3, ROS1, or ALK gene fusions who do not qualify for participation in, or who are otherwise unable to access, an ongoing clinical trial for entrectinib.


Eligibility: Inclusion Criteria:
  -  Diagnosis of advanced cancer with an NTRK1, NTRK2, NTRK3, ROS1, or ALK gene fusion
  -  Unable to participate in an ongoing entrectinib (RXDX-101) clinical trial
  -  Willing and able to provide written, signed informed consent
  -  Medically suitable for treatment with entrectinib (RXDX-101)
  Exclusion Criteria:
  -  Currently enrolled in an ongoing clinical study with any other investigational agent

Relevance to patient case: possibly relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: A Phase 1/2 Trial of Trametinib and Erlotinib in Patients With EGFR-Mutant Lung Adenocarcinomas and Acquired Resistance to Erlotinib

Summary: The purpose of this study is to determine the safety, tolerability and overall response rate of trametinib when given in combination with erlotinib in patients with Stage IV or recurrent lung adenocarcinoma that cannot be treated with curative intent.


Eligibility: Inclusion Criteria:
  -  Pathologic evidence of advanced stage IV or recurrent lung adenocarcinoma reviewed at MSKCC
  -  Somatic activating mutation in EGFR Radiographic progression during treatment with erlotinib.
  -  Any number of prior chemotherapy regimens is permitted.
  -  Measurable (RECIST 1.1) indicator lesion not previously irradiated
  -  KPS >/= 70%
  -  Age >18 years old
  -  Must have undergone biopsy after development of acquired resistance to erlotinib with available archived tissue (equivalent of > 10 unstained slides)
  -  Left ventricular Ejection Fraction >/= the lower limit of normal by ECHO or MUGA
  -  Adequate organ function:
  -  AST, ALT </= 2.5 x ULN
  -  Total bilirubin </= 1.5 x ULN
  -  Albumin>/=2.6g/dL - Creatinine < 1.5 x ULN OR calculated creatinine clearance >/=50mL/min
  -  Absolute neutrophil count (ANC) >/= 1,200 cells/mm3
  -  Hemoglobin>/=9.0 g/dL
  -  Platelets >/=100,000/mm3
  Exclusion Criteria:
  -  Patients with symptomatic brain metastasis requiring escalating doses of steroids
  -  Patients with grade 2 or greater diarrhea prior to study initiation despite maximal medical management due to medications or a medical condition such as Crohn's disease or malabsorption
  -  Pregnant or lactating women
  -  Any type of systemic therapy (chemotherapy or experimental drugs) within 2 weeks of starting treatment on protocol except for a EGFR TKI
  -  Patients who have received prior treatment with a MEK inhibitor
  -  Any major surgery or extensive radiotherapy within 21 days of starting treatment on protocol.
  -  A history of clinically significant interstitial lung disease or pneumonitis
  -  Clinically significant cardiac disease including unstable angina, acute myocardial infarction within 6 months from Day 1 of study administration, New York Heart Association Class III or IV congestive heart failure, or symptomatic uncontrolled Arrythmias, prolonged corrected QT interval >480msec, treatment refractory hypertension, presence of a cardiac defibrillator
  -  History of central serous retinopathy or retinal vein occlusion

Relevance to patient case: not relevant
Patient case: 70-year-old male with Lung cancer. Genetic variant: ERBB2 Amplification. Other conditions: Arthritis.

Clinical trial: Biological Therapy in Previously Treated Patients With Non-small Cell Lung Cancer

Summary: RATIONALE: Interleukin-2 may stimulate a person's white blood cells to kill non-small cell lung cancer cells.
  PURPOSE: Phase II trial to study the effect of biological therapy with interleukin-2 in patients with previously treated non-small cell lung cancer.

Detailed description: OBJECTIVES: I. Determine the response rate and median duration of response of interleukin-2 (IL-2) in patients with previously treated non-small cell lung cancer. II. Determine the median survival of patients treated with IL-2. III. Further delineate the toxicity of IL-2 in these patients.
  OUTLINE: This is an open label study. Patients receive bolus interleukin-2 on days 1-5 and 8-12. The cycle repeats every 3 weeks. Patient response is evaluated after 2 cycles. Patients with stable disease, partial, or complete response may be treated with maintenance IL-2 for up to 4 additional cycles. Patient evaluation is performed after every 2 cycles. At this point, patients with stable or responding disease may be treated with IL-2 every 6 weeks until disease progression, intolerable toxic effects, or 2 cycles beyond complete response.
  PROJECTED ACCRUAL: A maximum of 30 patients will be accrued.

Eligibility: DISEASE CHARACTERISTICS: Histologically proven recurrent or refractory non-small cell lung cancer At least one prior systemic therapy OR prior radiation therapy Must have measurable disease Previously irradiated sites of disease are not considered evaluable unless there is radiologic documentation of progression
  PATIENT CHARACTERISTICS: Age: Not specified Performance Status: ECOG 0-2 Life Expectancy: At least 3 months Hematopoietic: WBC at least 3,000/mm3 Hemoglobin greater than 10 g/dL Platelet count greater than 100,000/mm3 Hepatic: Bilirubin less than 2.0 mg/dL Renal: Creatinine less than 2.0 mg/dL Cardiovascular: No prior history of myocardial infarction within previous 6 months No uncompensated congestive heart failure No primary (not due to electrolytes or drugs) cardiac arrhythmias besides premature ventricular contractions Pulmonary: No dyspnea at rest or need for supplemental oxygen Patients with symptomatic lung disease or extensive lung metastases must have oxygen saturation greater than 90% Other: Not pregnant or nursing Negative pregnancy test Patients with elevated temperatures greater than 100.5 F must have no occult infection
  PRIOR CONCURRENT THERAPY: Biologic therapy: No concurrent cyclosporin Chemotherapy: At least 3 weeks since chemotherapy and recovered No concurrent methotrexate See Disease Characteristics Endocrine therapy: No concurrent systemic corticosteroids Radiotherapy: At least 3 weeks since radiotherapy See Disease Characteristics Surgery: Not specified

Relevance to patient case: not relevant
Patient case: 70-year-old male with Lung cancer. Genetic variant: ERBB2 Amplification. Other conditions: Arthritis.

Clinical trial: High-Dose Combination Chemotherapy Followed by Peripheral Stem Cell Transplantation in Treating Patients With Lung Cancer

Summary: RATIONALE: Drugs used in chemotherapy use different ways to stop tumor cells from dividing so they stop growing or die. Combining chemotherapy with peripheral stem cell transplantation may allow the doctor to give higher doses of chemotherapy drugs and kill more tumor cells.
  PURPOSE: Phase II trial to study the effectiveness of high-dose combination chemotherapy followed by peripheral stem cell transplantation in treating patients with lung cancer.

Detailed description: OBJECTIVES: I. Evaluate the response rate of high dose chemotherapy followed by autologous peripheral blood stem cell transplantation in the treatment of lung cancer.
  OUTLINE: Patients undergo stem cell harvesting. Patients receive radiation therapy to primary site and metastatic sites, if necessary. Patients receive a high dose of paclitaxel by 24 hour continuous infusion, then stem cells are infused 72 hours later. After a 3-4 week recovery period, patients receive ifosfamide and carboplatin by daily continuous infusion on days -7, -6, -5, and -4. Etoposide is administered by continuous infusion twice daily on days -7, -6, -5, and -4. Stem cells are again infused on day 0. Filgrastim (granulocyte colony-stimulating factor; G-CSF) begins on day 0. Patients may receive radiotherapy following recovery from chemotherapy. Patients are followed weekly for the first 6 months, then periodically for at least 2 years.
  PROJECTED ACCRUAL: This study will accrue 30 patients in 3 years.

Eligibility: DISEASE CHARACTERISTICS: Histologically or cytologically diagnosed lung cancer including the following: Relapsed limited stage small cell lung cancer (SCLC) Limited stage SCLC responding to conventional radiotherapy Extensive stage SCLC Stage IIIB and IV non-small cell lung cancer (NSCLC) Stages II-IIIA NSCLC who are unable or unwilling to undergo surgery but are acceptable candidates for high dose chemotherapy Cryopreserved peripheral blood stem cells with CD34 count greater than 2000/mm3 No untreated or uncontrolled brain metastases
  PATIENT CHARACTERISTICS: Age: Any age Performance status: Karnofsky 60-100% Life expectancy: Not specified Hematopoietic: Not specified Hepatic: Bilirubin less than 1.5 times normal SGOT less than 1.5 times normal Renal: Creatinine clearance greater than 50 mL/min Pulmonary: Left ventricular ejection fraction greater than 45% DLCO greater than 40% Other: Not pregnant or lactating No medical or psychiatric illness preventing informed consent or intensive treatment
  PRIOR CONCURRENT THERAPY: Concurrent chemotherapy allowed if no evidence of disease progression

Relevance to patient case: not relevant
Patient case: 70-year-old male with Lung cancer. Genetic variant: ERBB2 Amplification. Other conditions: Arthritis.

Clinical trial: Trastuzumab Plus Chemotherapy in Treating Patients With Advanced Non-small Cell Lung Cancer

Summary: RATIONALE: Monoclonal antibodies can locate tumor cells and either kill them or deliver tumor-killing substances to them without harming normal cells. Drugs used in chemotherapy use different ways to stop tumor cells from dividing so they stop growing or die. Combining monoclonal antibody therapy with chemotherapy may kill more tumor cells.
  PURPOSE: Phase II trial to study the effectiveness of the monoclonal antibody trastuzumab plus carboplatin and paclitaxel in treating patients who have advanced non-small cell lung cancer.

Detailed description: OBJECTIVES: I. Assess the toxicity of monoclonal antibody HER2 with carboplatin and paclitaxel in patients with HER2 positive non-small cell lung cancer. II. Determine median time to progression and one year freedom from progression in this patient population. III. Evaluate one year survival rate and overall objective response rate in this patient population.
  OUTLINE: Patients receive paclitaxel IV over 3 hours immediately followed by carboplatin IV over 30 minutes immediately followed by monoclonal antibody HER2 IV over 30-90 minutes on day 1. Patients also receive monoclonal antibody HER2 on days 8 and 15. Treatment is repeated every 3 weeks for 6 courses. After 6 courses of treatment, patients may receive monoclonal antibody HER2 weekly for up to 1 year in the absence of disease progression or unacceptable toxicity. Patients are followed every 3 months for 2 years, every 6 months for 3 years and once a year thereafter until disease progression or death.
  PROJECTED ACCRUAL: A total of 22-44 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS: Histologically confirmed non-small cell lung cancer (NSCLC) Recurrent AND/OR Stage IIIB with pleural or pericardial effusion OR Stage IV Must have at least one bidimensionally measurable lesion Must be HER2 positive (1-3+) Brain metastases allowed, if symptoms controlled and not requiring steroids Prior/Concurrent Therapy-- Biologic therapy: Not specified Chemotherapy: No prior chemotherapy for NSCLC Endocrine therapy: No concurrent steroids Radiotherapy: At least 2 weeks since prior radiotherapy Surgery: Not specified
  PATIENT CHARACTERISTICS: Age: 18 and over Performance status: ECOG 0-1 Life expectancy: Not specified Hematopoietic: Absolute neutrophil count at least 1,500/mm3 Platelet count at least 100,000/mm3 Hepatic: Bilirubin no greater than 1.5 mg/dL Transaminases no greater than 5 times upper limit of normal Renal: Creatinine no greater than 2 mg/dL Cardiovascular: No uncontrolled angina pectoris and arrhythmias No myocardial infarction within past 3 months No uncompensated congestive heart failure Ejection fraction at least 45% Other: No active infections Not pregnant or nursing Fertile patients must use effective contraception HIV negative No other active malignancies No evidence of peripheral sensory neuropathy of at least grade 2

Relevance to patient case: definitely relevant
Patient case: 70-year-old male with Lung cancer. Genetic variant: ERBB2 Amplification. Other conditions: Arthritis.

Clinical trial: Two Rebeccamycin Analogue Regimens in Treating Patients With Advanced or Recurrent Non-small Cell Lung Cancer

Summary: RATIONALE: Drugs used in chemotherapy use different ways to stop tumor cells from dividing so they stop growing or die. It is not yet known which regimen of rebeccamycin analogue is more effective in treating non-small cell lung cancer.
  PURPOSE: Randomized phase II trial to compare the effectiveness of two rebeccamycin analogue regimens in treating patients who have stage IIIB, stage IV, or recurrent non-small cell lung cancer.

Detailed description: OBJECTIVES:
  -  Compare the efficacy, in terms of response rate, in patients with advanced or recurrent non-small cell lung cancer treated with rebeccamycin analogue via 1 infusion vs 5 daily infusions every 3 weeks.
  -  Compare the response duration in patients treated with these regimens.
  -  Compare the toxicity profiles of these two regimens in these patients.
  OUTLINE: This is a randomized, multicenter study. Patients are stratified according to performance status (0 or 1 vs 2) and participating center. Patients are randomized to one of two treatment arms.
  -  Arm I: Patients receive rebeccamycin analogue IV over 1 hour on day 1.
  -  Arm II: Patients receive rebeccamycin analogue IV over 1 hour on days 1-5. Treatment for both arms repeats every 3 weeks for 6-8 courses in the absence of disease progression or unacceptable toxicity.
  Patients are followed every 3 months.
  PROJECTED ACCRUAL: A total of 36-64 patients (18-32 per arm) will be accrued for this study at a rate of 3-4 patients per month.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically proven stage IIIB (with pleural effusions), IV, or recurrent non-small cell lung cancer with failure on 1 prior chemotherapy regimen
  -  Measurable disease
  PATIENT CHARACTERISTICS:
  Age:
  -  Not specified
  Performance status:
  -  0-2
  Life expectancy:
  -  At least 12 weeks
  Hematopoietic:
  -  WBC at least 3,000/mm^3
  -  Granulocyte count at least 1,500/mm^3
  -  Platelet count at least 100,000/mm^3
  -  Hemoglobin greater than 10 g/dL
  Hepatic:
  -  Bilirubin no greater than 1.5 mg/dL
  -  AST and ALT less than 2 times normal
  Renal:
  -  Creatinine normal OR
  -  Creatinine clearance at least 60 mL/min
  Cardiovascular:
  -  No New York Heart Association class III or IV heart disease
  Other:
  -  Not pregnant or nursing
  -  Negative pregnancy test
  -  Fertile patients must use effective contraception
  -  No concurrent illness that would preclude study
  PRIOR CONCURRENT THERAPY:
  Biologic therapy:
  -  Not specified
  Chemotherapy:
  -  See Disease Characteristics
  -  No more than 1 prior chemotherapy regimen
  -  At least 4 weeks since prior chemotherapy
  Endocrine therapy:
  -  Not specified
  Radiotherapy:
  -  Not specified
  Surgery:
  -  Not specified
  Other:
  -  No concurrent combination antiretroviral therapy for HIV

Relevance to patient case: not relevant