araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 35-year-old female with Breast cancer. Genetic variant: NRAS Amplification. Other conditions: None.

Clinical trial: ELBA: Exemestane and Lapatinib in Advanced Breast Cancer

Summary: Aromatase inhibitors are the standard treatment for hormone responsive advanced breast cancer. The combination of the aromatase inhibitor exemestane with with another breast cancer drug that blocks epidermal growth factor receptor (EGFR) and Erb-2 activity (lapatinib) is being studied for the possibility of improving response to therapy, and delaying resistance to endocrine therapy.

Detailed description: The recommended dose of lapatinib will be determined in the first part of the study. In the second part of the study, patients will receive the recommended dose of lapatinib and exemestane daily, taken orally.

Eligibility: Inclusion Criteria:
  -  Histological diagnosis of breast cancer
  -  Indication for hormonal therapy (ER and/or PgR positive)
  -  Stage IV disease
  -  Female gender
  -  Postmenopausal status (patients treated with LHRH analogs are eligible for the Phase II part of the study)
  -  At least one target or non-target lesion according to RECIST criteria
  -  ECOG Performance Status 0-2
  -  Adequate bone marrow (neutrophils > or = 1.500/mm³, platelets > or = 100.000/mm³ and hemoglobin > or = 9 g/dl), hepatic (GOT, GPT < 2.5 e bilirubin <1.25 times the value of upper normal limit) and renal (creatinine < 1.25 times the value of upper normal limit) function
  -  Adequate cardiac function (FEVS > or = 50%)
  -  Able to take oral medications
  -  Life expectancy > 3 months
  -  Signed informed consent
  Exclusion Criteria:
  -  Any previous hormone therapy for metastatic disease
  -  More than one line of chemotherapy for metastatic disease (first line chemotherapy is permitted)
  -  Symptomatic cerebral metastases
  -  Planned concomitant radiation therapy in the first month of therapy (for those patients participating in the dose finding phase of the study)
  -  Previous therapy with exemestane, including as adjuvant therapy (previous therapy with non-steroidal aromatase inhibitors is permitted)
  -  Previous or concurrent malignancy in past 5 years (excluding adequately treated basal cel or spinocellular skin cancer and in situ carcinoma of the cervix)
  -  Treatment with experimental pharmacologic therapy within 4 weeks of enrollment in the study
  -  Unable or unwilling to provide signed informed consent
  -  Any concurrent illness that would, in the Investigator's opinion, contraindicate the use of the study drugs.
  -  Active infection
  -  Assumption of CYP3A4 inhibitors or inducers (ketoconazole, itraconazole, fluconazole, macrolide antibiotics, antidepressives, calcium-antagonists, cimetidine, carbamazepine, phenytoin, barbiturates, rifampicin e glucocorticoids)
  -  Pregnancy or lactation
  -  Unable to comply with follow-up
  -  Active hepatobiliary disease (with the exception of Gilbert's syndrome, asymptomatic biliary calculi, hepatic metastases or stabile chronic hepatopathy)

Relevance to patient case: not relevant
Patient case: 35-year-old female with Breast cancer. Genetic variant: NRAS Amplification. Other conditions: None.

Clinical trial: Limonene Study in Women With Breast Cancer

Summary: Limonene is a major component in the essential oils of citrus fruits. It has demonstrated promising breast cancer preventive and therapeutic effects in preclinical model systems. This early phase clinical study will evaluate the distribution of limonene to the breast tissue and its associated biological activities after 2 to 6 weeks of limonene dosing in women with a recent diagnosis of early stage breast cancer. This study will help evaluate the potentials of developing limonene as a breast cancer preventive agent.


Eligibility: Inclusion Criteria:
  -  Women who are 18 years of age or older
  -  Women electing to undergo excision surgery for early stage breast cancer
  -  A minimum of 2 weeks from enrollment to definitive surgery
  -  Underwent core needle biopsy for breast cancer diagnosis
  -  No clinical evidence of metastatic breast cancer
  -  ECOG performance status 0-1
  -  Participants must have normal organ and marrow function
  -  Women of child-bearing potential must agree to use adequate contraception
  -  Ability to understand and the willingness to sign a written informed consent document
  Exclusion Criteria:
  -  Concurrent chemotherapy or radiation therapy
  -  Use of selective estrogen receptor modifiers or aromatase inhibitors within the past 3 months or concurrently
  -  History of other malignancies within the past 5 years excluding non-melanoma skin cancer and cancers confined to organs with removal as only treatment
  -  Participated in another clinical intervention trial within the past 3 months
  -  Uncontrolled intercurrent illness including, but not limited to, ongoing or active infection, symptomatic congestive heart failure, unstable angina pectoris, cardiac arrhythmia, or psychiatric illness/social situations that would limit compliance with study requirements
  -  Pregnant or breast-feeding women
  -  Use of dietary supplement that contains large amounts of d-limonene (such as Heartburn Free with ROH10 and CoQ with d-limonene) within the past 3 months

Relevance to patient case: not relevant
Patient case: 35-year-old female with Breast cancer. Genetic variant: NRAS Amplification. Other conditions: None.

Clinical trial: Detection of Amplification of Her2 Fluorescent in Situ Hybridization (FISH) in Breast Tissue Sections

Summary: The purpose of the study is the identification of amplification level in human breast tissue. The imaging system is intended for diagnostic use as an aid to the pathologist in the detection, counting and classification of Her2 FISH stained tissue samples.


Eligibility: Inclusion Criteria:
  -  Well stained breast tissue slides with bright Her2 signals
  Exclusion Criteria:
  -  Very old slides that were already bleached

Relevance to patient case: not relevant
Patient case: 35-year-old female with Breast cancer. Genetic variant: NRAS Amplification. Other conditions: None.

Clinical trial: Mindfulness Based Stress Reduction: Supportive Treatment for Adult Patients With Cancer and Their Partners

Summary: The main purpose of this study is to evaluate the effects of the Mindfulness Based Stress Reduction (MBSR) training program that is offered in the investigator hospital, more specifically on quality of life, coping strategies and partner relationship by using questionnaires. To asses the possible impact of this treatment on the latter domain, partners of the patients with a cancer diagnosis are invited to join the training program.

Detailed description: Patients with breast cancer often experience anxiety, depression, stress and reduced quality of life. As such, there is an increased interest in the implementation of the Mindfulness-Based Stress Reduction program as an additional supportive treatment. MBSR is a structured group program that aims at reducing stress levels by enhancing awareness of the present moment in combination with a non-judgemental attitude.
  The study evaluates the effects of an 8-week MBSR program on quality of life, mood, depression, stress and coping skills in breast cancer patients.
  Breast cancer patients of the Breast Clinic of the Universitair Ziekenhuis Brussel participate in the MBSR program. Before and after the training program patients filled out questionnaires evaluating quality of life, coping skills, emotional functioning, stress and aspects of mindfulness.

Eligibility: Inclusion Criteria:
  For patients:
  -  Cancer diagnosis
  -  Between the age of 18 until 70
  -  Dutch speaking
  For partners:
  -  between the age of 18 until 70
  -  dutch speaking
  Exclusion Criteria:
  for patients and partners:
  -  Ongoing radiation therapy
  -  Psychiatric disorders
  -  Previous experience with mindfulness or meditation related techniques
  -  Pregnancy
  -  No or insufficient understanding of the Dutch language

Relevance to patient case: not relevant
Patient case: 35-year-old female with Breast cancer. Genetic variant: NRAS Amplification. Other conditions: None.

Clinical trial: 89Zr-trastuzumab PET for Imaging the Effect of HSP90 Inhibition

Summary: HSP90 inhibition is a potentially new targeted drug modality in the treatment of HER2 positive, trastuzumab refractory breast cancer. Little is known about the pharmacodynamics of HSP90 inhibitors in vivo, but non-invasive PET/CT imaging in a xenograft mouse model could visualize and quantify HER2 reduction after AUY922 treatment by 89Zr-trastuzumab PET imaging. Two doses of 50 mg/kg AUY922 resulted in a decrease in HER2 expression of approximately 50%, quantified 6 days after the last administration of AUY922.
  Visualizing HER2 expression in breast cancer patients before and early following HSP90 inhibition by means of 89Zr-trastuzumab PET, is likely to provide insight in the early in vivo effect of HSP90 inhibition and could potentially support patient tailored therapy.

Detailed description: This study is designed as a side study to the multicenter, international phase I-II trial with the HSP90 inhibitor AUY922 (protocol CAUY922A2101), as part of the biomarker assessment. In protocol CAUY922A2101, section 4, the design of this phase I-II trial is described (p36, 37). Briefly, a dose-escalation study is performed according to phase I design. This part is followed by a dose-expansion study according to a phase II design. In the latter part, breast cancer patients are enrolled that are either refractory to hormone- or trastuzumab treatment (both treatment arms, n=40 patients). Patients with HER2 positive, trastuzumab refractory breast cancer, will receive a 89Zr-trastuzumab PET scan as part of the present side study protocol, which will be performed in collaboration with the Royal Marsden Hospital (United Kingdom).
  To this end, a 89Zr-trastuzumab PET scan will be performed before (baseline) and during treatment with the HSP90 inhibitor AUY922, as described below.
  A minimum of six patients are needed to evaluate whether the 89Zr-trastuzumab PET scan can be used for the detection of a decrease of HER2 expression, induced by HSP90 inhibition.

Eligibility: Inclusion Criteria:
  -  Patients with HER2 positive, trastuzumab (and lapatinib) refractory breast cancer
  -  Participation in the phase I-II trial with HSP90 inhibitor AUY922 (in- and exclusion criteria for this study with AUY922 are described in protocol CAUY922A2101.
  Exclusion Criteria:
  -  No participation in the phase I-II trial with HSP90 inhibitor AUY922 (CAUY922A2101. Clinical trials no. NCT00526045A)

Relevance to patient case: not relevant
Patient case: 35-year-old female with Breast cancer. Genetic variant: NRAS Amplification. Other conditions: None.

Clinical trial: Estrogen for Triple Negative Breast Cancer

Summary: The purpose of this study is to determine the effectiveness of Estradiol treatment for advanced breast cancer that is hormone receptor negative and Her2/neu negative. The study will also use tumor tissue from your original diagnosis or from a biopsy you may have had for your cancer to look at hormone receptors in the lab. The tissue left over from your previous surgery or a previous biopsy will be used for research tests to check whether a different estrogen receptor (estrogen receptor beta) is seen in the tumor and if that makes estrogen work better.


Eligibility: Inclusion Criteria:
  -  histologically or cytologically confirmed breast cancer which is metastatic.
  -  A formalin-fixed paraffin embedded tumor block (preferred) or unstained slides must be available from either a prior biopsy of the primary tumor or a metastatic site. .
  -  Primary tumor or metastatic biopsy lacking estrogen and progesterone receptor and Her2 negative
  -  Patients must have measurable disease.
  -  Eastern Cooperative Oncology Group performance status 0-1.
  -  Patients with bone metastasis at baseline must agree to treatment with intravenous bisphosphonates
  -  Subjects may have had 0-4 lines of prior systemic chemotherapy or targeted therapy regimens administered for treatment of their metastatic breast cancer.
  -  Age >18 years
  -  Life expectancy of greater than 3 months.
  -  Patients must have adequate organ and marrow function as defined below:
  Exclusion Criteria:
  -  systemic chemotherapies, targeted therapies or radiotherapy for their cancer within 2 weeks prior to entering the study
  -  Patients receiving any other investigational agents for breast cancer treatment.
  -  Patients with known brain metastases are excluded 3.2.4 History of allergic reactions attributed to compounds of similar chemical or biologic composition to estradiol.
  -  Patients with any condition of the gastrointestinal tract that is expected to result in an inability to take oral medication
  -  Dysfunctional or post-menopausal vaginal bleeding.
  -  Uncontrolled hypercalcemia/hypocalcemia
  -  Prior history of or active thrombophlebitis, cerebral vascular accident, myocardial infarction, deep venous thrombosis or pulmonary embolism.
  -  History of or active hepatic adenoma.
  -  Uncontrolled intercurrent illness
  -  Pregnant women are excluded from this study
  -  Patients with bone metastasis are excluded if they are unable to receive intravenous bisphosphonate therapy due to the risk for developing hypercalcemia.

Relevance to patient case: not relevant
Patient case: 35-year-old female with Breast cancer. Genetic variant: NRAS Amplification. Other conditions: None.

Clinical trial: Everolimus in Breast Cancer Patients After Pre-operative Chemotherapy

Summary: This is a randomized controlled pilot study investigating signals involved in drug resistance to chemotherapy.
  Patient will be randomized to undergo observation or to receive Everolimus after completion of neoadjvuant treatment (anthracycline and/or taxane-based) and before surgery. The patients will be monitored for efficacy and safety.


Eligibility: Inclusion Criteria:
  -  Women aged ≥ 18 years;
  -  Histologically and/or cytologically confirmed invasive ductal or lobular breast cancer;
  -  Tumor of 3 cm or greater at time of diagnosis
  -  Measurable primary tumor after neoadjuvant treatment before randomization
  -  No prior chemotherapy for breast cancer;
  -  ECOG performance status ≤1 or Karnofsky performace status ≥ 70%
  -  Adequate liver/renal function
  -  Able to swallow whole tablets.
  -  Able to give written informed consent
  -  Able to follow prescription instructions reasonably well
  Exclusion Criteria:
  -  Male patient
  -  Prior history of other malignancy within 5 years of study entry, aside from contralateral breast carcinoma, appropriately treated cervical carcinoma in situ, or adequately treated basal or squamous cell carcinoma of the skin
  -  Distant metastasis, including skin involvement beyond the breast area
  -  Other severe acute or chronic medical or psychiatric condition, or laboratory abnormality that would impart, in the judgment of the investigator, excess risk associated with study participation or study drug administration, or which, in the judgment of the investigator, would make the patient inappropriate for entry into this study

Relevance to patient case: not relevant
Patient case: 35-year-old female with Breast cancer. Genetic variant: NRAS Amplification. Other conditions: None.

Clinical trial: A Retrospective Study of Biomarkers in Non-Small Cell Lung Cancer

Summary: The purpose of this study is:
  1. To characterize the types and frequency of molecular alterations to the epidermal growth factor receptor (EGFR) pathway, FGFR4 and EML-ALK in Asian patients with non-small cell lung cancer
  2. To identify candidate biomarkers of importance in the EGFR and estrogen pathways
  Most, if not all, human malignancies including lung cancer are caused by somatic alterations of the genome, leading to activation of oncogenes or inactivation of tumor suppressor genes and their resultant oncogenic effects. In addition to mutations, increased chromosomal copy number (by amplification or polysomy) and DNA methylation are other mechanisms of oncogene activation and tumour suppressor gene inactivation respectively.
  Little is known about the relationship between these oncogenes of the EGFR family and the recently described oncogenes FGFR4 and fusion gene EML4-ALK. Recent data suggests molecularly defined subgroups of non-small cell lung cancer (NSCLC) exist and can be used to predict for sensitivity to targeted agents (erlotinib or gefitinib) or cytotoxic chemotherapy (pemetrexate, gemcitabine, platinum agents). The findings that estrogen receptors are present in lung tumours and that estrogen can stimulate growth and proliferation of lung cancers in vitro and in vivo are provocative. Further studies to evaluate the role of estrogens and other sex hormones in lung cancer are warranted.
  A further understanding of the molecular indicators of lung cancer prognosis and treatment prediction would improve drug development and patient treatment selection.
  Archived paraffin-embedded and fresh frozen NSCLC tumor tissue will be obtained via the Department of Pathology and the National University Tissue Repository respectively. Clinico-pathological characteristics will be obtained from the case records, Pathology and Tissue Repository. DNA will be isolated using standard techniques. Sequencing of genes in the EGFR signaling pathway: EGFR, KRAS, ErbB2, ErbB3, MET, PI3K, and BRAF as well as FGFR4. Unstained slides from the paraffin-embedded tissue will be obtained and subjected to fluoresce in vitro hybridization (FISH) for breakpoints in the EML4 and ALK genes as previously described. For cases that have been snap-frozen, RNA will be extracted and EML4-ALK fusions will be confirmed using RT-PCR and pre-specified primers. To analyse the expression of proteins of putative relevance to EGFR function (such as EGFR, ErbB2, ErbB3, AKT, MET, STAT, ERK, MAPK, cyclin D1, C/EBPa), downstream effects of EGFR: cell proliferation (Ki-67), angiogenesis (CD34, VEGF-A), apoptosis (bcl-2), metastasis, and hormonal influence (oestrogen and progesterone receptors, aromatase), TMA technology will be utilised. The status of the tumor suppressor genes PTEN and C/EBPa will be analysed.


Eligibility: Inclusion Criteria:
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 35-year-old female with Breast cancer. Genetic variant: NRAS Amplification. Other conditions: None.

Clinical trial: Biomarkers in Tissue Samples From Patients With Breast Cancer Treated With Bevacizumab

Summary: RATIONALE: DNA analysis of tumor tissue may help doctors predict how well patients will respond to treatment.
  PURPOSE: This research study is studying biomarkers in tissue samples from patients with breast cancer treated with bevacizumab.

Detailed description: OBJECTIVES:
  Primary
  -  To demonstrate that vascular endothelial growth factor-A (VEGFA) haplotypes that are associated with an increased VEGFA expression will predict superior outcome for patients with metastatic breast cancer receiving bevacizumab in ECOG-E2100 (but not for the control arm).
  -  To demonstrate that candidate single nucleotide polymorphisms (SNPs) will further improve the predictive capacity of outcome (efficacy and toxicity) in patients enrolled in ECOG-E2100.
  -  To demonstrate that tumor VEGFA amplification or borderline amplification (estimated 14% frequency) will predict superior outcome for patients with metastatic breast cancer receiving bevacizumab on ECOG-E2100 whereas those with VEGFA deletion (estimated 11% frequency) will predict inferior outcome.
  -  To demonstrate that VEGFA amplification/deletion will not predict outcome in the control arm of ECOG-E2100.
  Secondary
  -  To demonstrate that tumor VEGFA amplification will predict increased protein expression as ascertained by IHC.
  -  To demonstrate that a combined algorithm calculated from tumor-specific variability (VEGFA amplification/deletion) and host-specific variability (SNPs) will optimally predict outcome (efficacy) with bevacizumab in patients enrolled on ECOG-E2100.
  OUTLINE: This is a multicenter study.
  Previously collected tumor-derived DNA is analyzed for VEGFA amplification/deletion and haplotype as biomarkers for outcome after bevacizumab treatment. Gene expression, polymorphism, protein expression analysis, and IHC are performed on the samples.

Eligibility: DISEASE CHARACTERISTICS:
  -  Enrolled on ECOG-E2100
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 35-year-old female with Breast cancer. Genetic variant: NRAS Amplification. Other conditions: None.

Clinical trial: Lung Inflammation and Lung Metastases From Breast Cancer

Summary: The purpose of this study is to find out if there is a link between cigarette smoking, inflammation and the spread of breast cancer to the lung. We think that women who are current or former smokers may be at increased risk for breast cancer spreading to the lung compared to women who have never smoked. Smoking causes inflammation in the lung in some women. Researchers at Memorial Sloan-Kettering (MSKCC) think that smoking-related lung inflammation may increase the chance of breast cancer spreading to the lung. In order to find out whether inflammation plays a role in breast cancer spreading to the lung, we will measure a urinary marker of lung inflammation. This will allow us to determine if this marker is more commonly elevated in women with breast cancer that has spread to the lung compared to those without breast cancer in the lung. We will also collect DNA from blood to have the opportunity to determine if there are differences in DNA in women with or without breast cancer that has spread to the other sites including the lung. We will also collect blood to determine if we can identify risk factors for the spread of breast cancer to the lungs.


Eligibility: Inclusion Criteria:
  -  Registered patient at MSKCC
  -  Histologically proven breast cancer. It is not necessary that pathology be reviewed at MSKCC
  -  Age ≥18 years Group 1 (A and B)
  -  Diagnosed with metastatic breast cancer on biopsy or imaging study.
  -  Patients will be considered to have lung metastases, and will be assigned to group 1A if any of the following criteria are met, otherwise patients will be assigned to group 1B "No known Lung Metastases," Biopsy-proven lung metastasis.
  -  Pleural effusion with cytologic evidence of malignancy.
  -  Pleural effusion, exudative in character, without alternative explanation and attributed, in the opinion of the clinician to metastatic disease.
  -  Symptoms attributable to lung metastases and a radiological pattern interpreted by a radiologist as suspicious for metastatic disease.
  -  Any pulmonary nodule on chest radiograph, CT scan, PET-CT or MRI, which is interpreted by the clinician and radiologist to be metastatic in etiology, whether or not a biopsy was performed, and regardless of symptoms.
  -  A radiographic pattern interpreted by a radiologist as consistent with lymphangitic carcinomatosis.
  Group 2 (Controls)
  -  History of early breast cancer and currently no evidence of disease
  Exclusion Criteria:
  -  Inability to provide written informed consent.
  -  Inability to complete smoking and NSAID questionnaire.
  -  Steroid use within the previous 4 weeks.
  -  Radiotherapy to the breast, chest wall or axilla within the previous 3 months.
  -  Men with breast cancer.

Relevance to patient case: not relevant