araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: Safety and Efficacy of AZD4547 in Combination With Fulvestrant vs. Fulvestrant Alone in ER+ Breast Cancer Patients

Summary: The purpose of this study is to assess the safety and effectiveness of AZD4547 in combination with fulvestrant vs. fulvestrant alone in ER+ breast cancer patients with FGFR1 polysomy (FISH4/5) or gene amplification (FISH 6)


Eligibility: Inclusion Criteria:
  -  Post-menopausal women (either through bilateral oophorectomy or amenorrhoeic for 24 months)
  -  Histological confirmation of Breast Cancer with documented ER+ receptor status
  -  Safety run-in: Relapsing during/within 12 months of completion of a single regimen of adjuvant endocrine therapy with non-steroidal AI and/ tamoxifen or progression following 1st line endocrine therapy with non-steroidal AL
  -  Rand phase IIa: Received at least 1 prior endocrine therapy in the metastatic setting or have relapsed during/ within 6 months of completion of adjuvant endocrine therapy (either non-steroidal AI or tamoxifen or a combination of both). Chemotherapy administered in the adjuvant setting is permitted.
  -  Rand phase IIa: Mandatory provision of tumour sample to confirm FGFR1 polysomy or gene amplification. At least one measurable lesion that can be accurately assessed by CT/MRI/x-ray at baseline and follow up visits
  Exclusion Criteria:
  -  Prior exposure to exemestane (safety run-in) / fulvestrant (randomized phase IIa), or any agent known to inhibit FGFRs.
  -  More than 1 prior regimen of chemotherapy for breast cancer
  -  ECG recordings that demonstrate significant abnormalities in cardiac rate, rhythm or conduction
  -  History of hypersensitivity to active or inactive excipients of AZD4547 or exemestane (safety run-in ) or fulvestrant (Randomized phase), including castor oil, or drugs with a similar chemical structure or class to AZD4547 or exemestane or fulvestrant.
  -  Randomized phase IIa: bleeding/blood clotting conditions that would prevent the administration of the fulvestrant injection into the buttocks

Relevance to patient case: definitely relevant
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: Endoscopic Breast Surgery in Treating Patients With Breast Cancer

Summary: RATIONALE: Endoscopic breast surgery (EBS) is a less invasive type of surgery for breast cancer and may have fewer side effects and improve recovery. PURPOSE: This clinical trial studies endoscopic breast surgery in treating patients with breast cancer.

Detailed description: PRIMARY OBJECTIVES: I. To determine the surgical complication rate in patients undergoing EBS for benign or malignant disease and the 5-year local recurrence rate following endoscopic breast surgery among subjects undergoing EBS for breast cancer at USC. SECONDARY OBJECTIVES: I. To evaluate the safety, breast cosmesis and patient quality of life following EBS. OUTLINE: Patients undergo endoscopic breast surgery. After completion of study treatment, patients are followed up every 6 months for 5 years.

Eligibility: Inclusion Criteria:
  -  Breast cancer or prophylactic mastectomy requiring axillary nodal staging
  -  Breast disease (e.g., fibroadenoma, ADH)
  -  Ability to read and/or comprehend consent form and questionnaires
  -  Ability to follow-up per protocol
  -  Not pregnant or breastfeeding
  Exclusion Criteria:
  -  Pregnant or breastfeeding
  -  Evidence of chest wall or skin* involvement
  -  NOTE: *may be endoscopy-assisted

Relevance to patient case: not relevant
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: Safety, Tolerability & Potential Anti-cancer Activity of Increasing Doses of AZD5363 in Different Treatment Schedules

Summary: This study is designed to investigate the safety and tolerability of a new drug, AZD5363, in patients with advanced cancer - and to identify a dose and schedule that can be used in the future. This study will also investigate how the body handles AZD5363 (ie, how quickly the body absorbs and removes the drug). This study will also investigate anti-tumour activity of AZD5363 in patients with advanced / metastatic breast, gynaecological cancers or other solid cancers bearing either AKT1 / PIK3CA or PTEN mutation.

Detailed description: A Phase I, Open-Label, Multicentre Study to Assess the Safety, Tolerability, Pharmacokinetics and Preliminary Anti-tumour Activity of Ascending Doses of AZD5363 under Adaptable Dosing Schedules in Patients with Advanced Solid Malignancies.

Eligibility: Inclusion Criteria:
  -  Aged at least 18 years.
  -  Parts A,B: The presence of a solid, malignant tumour, excluding lymphoma, that is resistance to standard therapies or for which no standard therapies exist.
  -  ER+/HER2+ breast, ovarian, cervical, endometrial cancer, or other solid cancers, resistance to standard therapies with a PIK3CA gene mutation (Part C), AKT1 gene mutation (Part D) or a dysregulatory aberration on the PIK/AKT pathway (Part D), advanced or metastatic ER+ positive breast cancer that has an AKT1 gene mutation (Part E) or advanced or metastatic ER+ positive breast cancer that has a PTEN gene mutation (Part F).
  -  The presence of at least one lesion that can be accurately assessed at baseline by CT, MRI or plain X-ray and is suitable for repeated assessment. Estimated life expectancy of more than 12 weeks.
  -  Estimated life expectancy of more than 12 weeks.
  Exclusion Criteria:
  -  Clinically significant abnormalities of glucose metabolism.
  -  Spinal cord compression or brain metastases unless asymptomatic, treated and stable (not requiring steroids).
  -  Evidence of severe or uncontrolled systemic diseases, including active bleeding diatheses or active infections including hepatitis B, C and HIV.
  -  Evidence of clinically significant cardiac abnormalities, uncontrolled hypotension, left ventricular ejection fraction below the lower limit of normal for the site or experience of significant cardiac interventional procedures.
  -  A bad reaction to AZD5363 or any drugs similar to it in structure or class.

Relevance to patient case: possibly relevant
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: Blood Oxygen Level Dependent Magnetic Resonance Imaging (BOLD MRI) and Fluorothymidine Positron Emission Tomography (FLT PET) in Patients With Locally Advanced Breast Cancer Undergoing Neoadjuvant Chemotherapy

Summary: The objective of this pilot study is to determine the effectiveness of Fluorothymidine Positron Emission Tomography (FLT PET) and Blood Oxygen Level Dependent Magnetic Resonance Imaging (BOLD MRI) in assessing tumour response to neoadjuvant chemotherapy (NA CT) in women with locally advanced breast cancer.


Eligibility: Inclusion Criteria:
  -  Histologic proof of breast cancer (invasive ductal or lobular carcinoma). Breast sarcoma and lymphoma are not eligible.
  -  Clinical diagnosis of locally advanced breast cancer (Stage IIB (T3,N0,M0), Stage IIIA, IIIB, or IIIC, according to American Joint Committee on Cancer (AJCC) Tumour-Node-Metastasis (TNM) Cancer Staging), including inflammatory breast cancer.
  -  Ability to undergo neoadjuvant chemotherapy.
  Exclusion Criteria:
  -  Evidence of metastatic disease (identified on chest x-ray, liver ultrasound, bone scan or other imaging tests);
  -  Previous chemotherapy or hormonal therapy for breast cancer;
  -  Significant concurrent medical problems that result in the patient being unfit for surgery (e.g. uncontrolled diabetes, active cardiac disease, severe chronic obstructive pulmonary disease);
  -  Known pregnancy or lactating female (e.g. positive serum beta human chorionic gonadotropin (B-hCG) pregnancy test);
  -  Inability to lie supine for imaging with Positron Emission Tomography (PET);
  -  Any contraindication to undergoing Magnetic Resonance Imaging (MRI) or PET;
  -  Currently receiving Antabuse;
  -  Inability to provide informed consent (e.g. dementia or severe cognitive impairment).

Relevance to patient case: not relevant
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: Breast Cancer Registry - National University Health System, Singapore

Summary: The Breast Cancer Registry aims to collect clinical data of all breast cancer patients diagnosed and/or treated in the National University Hospital, with the goal of understanding risk factors, presenting symptoms, diagnosis, treatment, and outcome data of breast cancer in Singapore. This information will contribute to improving management of breast cancer patients.


Eligibility: Inclusion Criteria:
  - All breast cancer patients who were diagnosed or managed in NUH.
  Exclusion Criteria:
  - Non breast cancer patients.

Relevance to patient case: not relevant
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: Safety and Efficacy of INCB007839 With Trastuzumab and Vinorelbine in Patients With Metastatic HER2+ Breast Cancer

Summary: This Phase I/II study is designed to assess the safety and therapeutic effect of INCB007839 in combination with trastuzumab and vinorelbine in patients with metastatic HER2+ breast cancer.


Eligibility: Inclusion Criteria:
  -  Subject with diagnosis of metastatic (or locally recurrent-inoperable) breast cancer
  -  Subject with histological HER2+ status as determined by FISH with a gene amplification score of ≥ 2.2
  -  Subject with availability of archival biopsy tissue from primary tumor or metastatic lesions
  -  Subject with presence of measurable disease based on RECIST 1.1
  -  Subject who has received no more than three prior HER2-directed therapeutic regimens for advanced breast cancer
  Exclusion Criteria:
  -  Subject with Left ventricular ejection fraction (LVEF) below institutional normal range
  -  Subject with metastasis to the central nervous system UNLESS asymptomatic and clinically stable
  -  Subject with current active malignancy other than breast cancer
  -  Subject with prior history of other malignancy except for cancers from which the patient is currently disease free
  -  Subject with significant renal or hepatic dysfunction
  -  Subject with history of venous or arterial thrombosis or risk factor for thrombosis other than history of malignancy
  -  Subject with insufficient bone marrow function
  -  Subject with contraindication to vinorelbine, trastuzumab, aspirin and/or warfarin therapy.
  -  Subject with current active bacterial, Hepatitis B or C, and/or HIV infections

Relevance to patient case: not relevant
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: Eribulin With Trastuzumab as First-line Therapy for Locally Recurrent or Metastatic HER2 Positive Breast Cancer

Summary: This is a multicenter phase 2 study designed to evaluate the safety and efficacy of eribulin mesylate in combination with trastuzumab as first line treatment in female subjects with locally recurrent or metastatic human epidermal growth factor receptor (HER2) positive breast cancer.


Eligibility: Key Inclusion criteria:
  -  Age 18 years or older
  -  Histologically or cytologically proven adenocarcinoma of the breast
  -  Subjects who have locally recurrent or metastatic disease with at least one measurable lesion
  -  HER2 positive as determined by score of 3 on immunohistochemistry (IHC) staining or gene amplification by fluorescence in situ hybridization (FISH).
  -  Eastern Cooperative Oncology Group (ECOG) performance status (PS) score of 0, 1 or 2
  -  At least 12 months since prior neoadjuvant or adjuvant chemotherapy
  -  At least 2 weeks since prior radiotherapy, endocrine therapy, trastuzumab, or lapatinib, with complete recovery from the effects of these interventions
  -  Adequate renal function
  -  Adequate bone marrow function
  -  Adequate liver function
  -  Adequate cardiac function
  Key Exclusion criteria:
  -  Prior chemotherapy, biologic therapy, or investigational therapy for locally recurrent or metastatic HER2 breast cancer.
  -  Subjects who have had a prior malignancy other than carcinoma in situ of the cervix, or nonmelanoma skin cancer
  -  Prior exposure to greater than 360 mg/m2 doxorubicin or liposomal doxorubicin, greater than 120 mg/m2 mitoxantrone, greater than 90 mg/m2 idarubicin, or greater than 720 mg/m2 epirubicin
  -  Inflammatory breast cancer
  -  Prior history of hypertensive crisis or hypertensive encephalopathy
  -  Clinically significant cardiovascular impairment
  -  Subjects with known central nervous system (CNS) disease are not eligible, except for those subjects with treated brain metastasis.
  -  Subjects with metastatic disease limited to bone are ineligible unless there is at least one lytic lesion with identifiable soft tissue components that can be evaluated by computed tomography (CT) or magnetic resonance imaging (MRI)
  -  Pulmonary lymphangitic involvement that results in pulmonary dysfunction requiring the use of oxygen
  -  History of bleeding diasthesis
  -  Currently pregnant or breast-feeding.
  -  Subjects with preexisting Grade 3 or 4 neuropathy. Any peripheral neuropathy must recover to Grade less than or equal to 2 before enrollment

Relevance to patient case: not relevant