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

Clinical trial: Efficacy and Safety Evaluating Study of CT-P6 in Her2 Positive Early Breast Cancer

Summary: This study will determine whether CT-P6 and Herceptin are equivalent in patients with early-stage breast cancer undergoing neoadjuvant chemotherapy. Our hypothesis is that the pathologic complete response rate will be equivalent in patients treated with neoadjuvant CT-P6 or Herceptin. Patients will receive 8 cycles of neoadjuvant systemic therapy and up to 10 cycles of therapy in the adjuvant setting.


Eligibility: Inclusion Criteria:
  -  Patient who has histologically confirmed and newly diagnosed breast cancer
  -  Patient who has clinical stage I, II, or IIIa operable breast cancer according to AJCC (American Joint Committee on Cancer) Breast Cancer Staging 7th edition
  -  Patient who has HER2-positive status confirmed locally, defined as 3+ score by IHC (immuno-histochemistry).
  Exclusion Criteria:
  -  Patient who has bilateral breast cancer
  -  Patient who has received prior treatment for breast cancer, including chemotherapy, biologic therapy, hormone therapy, immunotherapy, radiation or surgery, including any prior therapy with anthracyclines.

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

Clinical trial: The Oncopanel Pilot (TOP) Study

Summary: The BCCA Oncopanel is a clinical assay being developed to determine genotype status of a prospectively defined set of genes.
  The purpose of this pilot study is to assess the feasibility and effect on clinical-decision-making of the Oncopanel test. Eligible patients are those with advanced lung, colorectal, melanoma and GIST cancers and patients with diagnosed malignancies being considered for clinical trials.

Detailed description: Somatic mutations in solid tumors represent an established means of characterizing malignancies for prognostic, diagnostic and therapeutic purposes. Mutations in EGFR, KRAS, BRAF, and KIT and PDGFRA genes direct therapy in patients with advanced lung, colorectal, melanoma, and GIST tumors, respectively. Known or novel mutations in other genes may also be of clinical significance but are not identified by current genotyping offered to BC Cancer Agency (BCCA) patients. Furthermore, numerous candidate genes have been implicated as potential prognostic and predictive biomarkers in patients with solid tumours. As such, the Oncopanel is a clinical assay being developed to determine genotype status of a prospectively defined set of genes. The following clinically relevant set of genes and exons are included in the Oncpanel: KRAS, EGFR, BRAF, NRAS and HRAS, PIK3CA Signal Transduction Pathway Genes, RAS-RAF-MEK-MAPK Pathway, HER2, IDH1 and IDH2, ALK, TP53, c-KIT, STAT1&3 and PDGFRA. Additional testing on the tumour material will also include analysis of specific gene variants associated with adverse events or response to therapy.
  Numerous studies have documented the presence of circulating tumour DNA (ctDNA) among patients with advanced and early stage malignancies (20-22). The ability to diagnose standard cancer mutations with a blood-based assay (a "liquid biopsy") has not yet been established but presents obvious advantages. The emergence of "resistance" mutations arising in the metastatic tumor or throughout the course of therapy is well documented (21, 22). A blood biopsy may represent more accurate determination of the tumor's genetic features than archival DNA specimen. Adequate tissue specimens can be difficult to obtain from some patients with diagnosed malignancies, particularly lung cancer. A blood biopsy may represent a less invasive and timelier means of diagnosing both standard and translational cancer mutations.

Eligibility: Patients with archival tumor tissue and a known history of invasive malignancies are eligible if they meet one or more of the following criteria:
  -  Advanced colorectal cancer and eligible for standard KRAS testing,
  -  Advanced non-small cell lung cancer and eligible for standard EGFR testing,
  -  Advanced melanoma and eligible for standard BRAF testing,
  -  Gastrointestinal stromal tumors (GISTs) eligible for standard c-KIT and PDGFRA testing,
  -  Being considered for potential eligibility in clinical trial.

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 Study Of PF-05280014 Or Trastuzumab Plus Taxotere® And Carboplatin In HER2 Positive Breast Cancer In The Neoadjuvant Setting (REFLECTIONS B327-04)

Summary: The current study will compare PK, efficacy, safety, and immunogenicity of PF-05280014 (Trastuzumab-Pfizer) in combination with Taxotere® and Carboplatin (Paraplatin) versus Herceptin® (Trastuzumab-EU) approved in the EU in combination with Taxotere® and Carboplatin (Paraplatin) in patients with operable HER2 positive, breast cancer in the neoadjuvant setting. The hypothesis to be tested in this study is the percentage of patients with steady state Cycle 5 Ctrough (Cycle 6 pre-dose) >20 µg/mL of trastuzumab-Pfizer is similar to EU-approved trastuzumab, using a margin of -12.5%.


Eligibility: Inclusion Criteria:
  -  Histologically confirmed HER2 overexpressing invasive breast cancer.
  -  Plan for definitive surgical resection of breast tumor (i.e., lumpectomy or mastectomy, and sentinel node (SN) biopsy or axillary lymph node dissection (ALND).
  -  Plan for neoadjuvant chemotherapy.
  -  Measurable disease in the breast after diagnostic biopsy, defined as longest diameter ≥ 2.0 cm.
  Exclusion Criteria:
  -  Bilateral breast cancer.
  -  Inflammatory breast cancer.
  -  Presence of known distant metastases.
  -  Received prior treatment, including chemotherapy, endocrine therapy, biologic therapy, radiation or surgery with the exception of diagnostic biopsy for primary breast cancer.

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

Clinical trial: LEE011 for Patients With CDK4/6 Pathway Activated Tumors (SIGNATURE)

Summary: The purpose of this signal seeking study is to determine whether treatment with LEE011 demonstrates sufficient efficacy in CDK4/6 pathway activated solid tumors and/or hematologic malignancies to warrant further study.


Eligibility: Inclusion Criteria:
  -  Patient has a confirmed diagnosis of a select solid tumor (except breast cancer (however, triple negative will be included), liposarcoma, CRPC, melanoma and teratoma) or hematological malignancy (except mantle cell lymphoma).
  -  Patient must have been pre-identified as having a tumor with CDK4 amplification or mutation, CDK6 amplification or mutation, Cyclin D1 (CCND1) amplification, Cyclin D3 (CCND3) amplification, or p16 (CDKN2A) mutation
  -  Patient has received at least one prior treatment for recurrent, metastatic and /or locally advanced disease and for whom no standard therapy options are anticipated to result in a durable remission.
  -  Patient has progressive and measurable disease as per RECIST 1.1. or other appropriate hematological guidelines.
  -  Patient has an Eastern Cooperative Oncology Group (ECOG) performance status ≤ 1
  Exclusion Criteria:
  -  Patients has received prior treatment with LEE011.
  -  Patient has clinically significant resting bradycardia (heart rate < 50 at rest), tachycardia (heart rate > 90 at rest), PR interval > 220 msec, QRS interval > 109 msec, or QTcF > 450 msec.
  -  Patients has primary CNS tumor or CNS tumor involvement
  -  Patient has received chemotherapy or anticancer therapy ≤ 4 weeks prior to starting study drug

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

Clinical trial: Improving Adherence to Recommended Surveillance in Breast Cancer Survivors

Summary: Evidence-based guidelines recommend cancer surveillance procedures for breast cancer survivors including physical examination, mammography, breast self-exam, and gynecologic follow-up. The early detection of recurrent and new cancers can best be achieved through the combined, on schedule use of these surveillance procedures. Yet, data suggest that up to 55% of breast cancer survivors do not undergo these procedures as recommended. This study tests a telephone-based psychosocial intervention aimed at improving adherence to recommended surveillance in breast cancer survivors. The psychosocial intervention for improving adherence is compared to treatment as usual.


Eligibility: Inclusion Criteria:
  -  21 years of age or older
  -  Diagnosis of Stage I to IIIA breast cancer
  -  Within 1 to 5 years post primary cancer treatment (i.e., surgery, chemotherapy, and/or radiation therapy)
  -  No diagnosis of recurrent breast cancer or a new primary cancer
  -  Able to provide meaningful consent
  Exclusion Criteria:
  -  < 21 years of age
  -  Unable to provide meaningful consent
  -  Surgically treated with bilateral mastectomy

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

Clinical trial: Non Invasive Detection of Lung and Breast Cancer by Odor Signature

Summary: The investigators have developed an early detection solution for lung and breast cancer. A system which can distinguish between different medical odors based on biosensors. Our product is user-friendly noninvasive, nonradioactive and nontoxic to the patients. The technology enables a high level of sensitivity and provides users with a quick lab response and a simple yes or no answer.
  The aim of this study is to contribute and detect the patient at the earliest possible stage, in a noninvasive, nonradioactive and nontoxic way. Exhaled breath and urine samples are a promising approach towards future possible lung and breast cancer screening method.

Detailed description: Early detection of cancer can dramatically improve the survival chances. to date, there is no efficient diagnostic tool for detection of lung cancer in early stages. Regarding breast cancer, the common screening tool us mammography, which suffer from low sensitivity and high false positive. Thus, there is an urgent need for developing a screening tool for early stages lung and breast cancer.
  The sense of smell depends on the ability of specialized sensory cells of the nose to perceive volatile compounds (VOCs). Diseases such as infections and malignancies can be associated with changes in host metabolism, accompanied by production of different VOCs, and thus a different odor. Several studies have shown that different cancers secrete different VOCs, thus produce different smell.
  We have developed a system which uses biosensors that can scent the VOCs that lung and breast cancer cell produce, thus distinguish between healthy control and lung or breast cancer. These biosensors can detect low stages lung and breast cancer.
  Patients will supply urine samples and exhaled breath samples using a kit that we will supply. The samples will be shipped to our lab, where they will be processed and the VOCs will be separated from the head space of the samples. The biosensors will be exposed to the VOCs samples and will report whether the specific sample id cancerous (lung or breast) or not.
  The Data will be collected from all samples and statistical analysis will be calculated, in order to test the specificity and sensitivity of our biosensors to detect cancerous samples.

Eligibility: Inclusion Criteria:
  -  Diagnosed Lung Cancer patients
  -  Diagnosed Breast Cancer patients
  Exclusion Criteria:
  -  Cancer patients who were treated using chemotherapy
  -  Cancer patients who were treated using radiation
  -  Cancer patients who were treated using biological treatments
  -  Cancer patients who were treated with chemotherapy
  -  Cancer patients who were treated with any anti- cancer therapies
  -  Cancer patients who use drugs that affect the immune system

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

Clinical trial: FBnTP Imaging of Breast Cancer

Summary: Our preclinical studies suggest the capacity of the positron emission tomography imaging agent 18F-fluorobenzyl triphenyl phosphonium (FBnTP) to detects early-stage small breast tumors (e.g., DCIS), and differentiates benign from malignant masses with better accuracy than that obtained by existing breast imaging tools.

Detailed description: Breast cancer is the most widespread type of cancer among women in the USA, and the second leading cause of death. The National Cancer Institute estimates that in 2013, in the USA, 226,870 women will be diagnosed with breast cancer and 39,510 women will die of breast cancer, most of them of progressive metastatic disease. Early detection and treatment of the disease, when the tumor is still localized and at a high curability state, is the outmost important determinant of disease-free survival of breast cancer patients. Survival rate of women first diagnosed with pure early-stage noninvasive tumor (ductal carcinoma in situ- DCIS) is nearly 98%, which drops to 48% in patients with advanced disease.Yet, early detection of breast cancer is relatively poor. This is best exemplify by the astonishing percentage of benign biopsies; 80% of 1.7 million biopsies in the USA, at a cost of $3 billion; whereas, only small fraction (~20%) of newly diagnosed women are found to have pure DCIS.
  Our preclinical studies suggest the capacity of the positron emission tomography (PET) imaging agent 18F-fluorobenzyl triphenyl phosphonium (FBnTP) to detects early-stage small breast tumors (e.g., DCIS), and differentiates benign from malignant masses with better accuracy than that obtained by existing breast imaging tools. Accordingly, the present protocol is designed to extend the preclinical findings into clinical studies in breast cancer women, and to assess the effectiveness of 18F-FBnTP in detecting breast malignant lesions, in comparison with magnetic resonance imaging and fluorodeoxyglucose PET imaging.

Eligibility: Inclusion Criteria:
  -  Female patients with newly-diagnosed invasive and/or intraductal breast cancer detected by core needle or vacuum-assisted biopsy (i.e., index cancer)
  -  Age > 25 Ability and willingness to sign informed consent prior to any study procedure.
  -  Positive indication of disease on mammogram or MRI scan.
  -  Candidate for breast cancer surgery on the basis of recommendation of a breast cancer surgeon.
  -  Ability to undergo up to 90 minutes of PEM imaging.
  Exclusion Criteria:
  -  Any active or chronic illness that, in the opinion of the investigators, would make the study unsafe or limit compliance with study procedures.
  -  Past or present history of active substance abuse (drug or alcohol).
  -  Inability to tolerate venous access.
  -  Pregnant females are excluded from this study. All females of child-bearing potential will undergo a serum pregnancy test within 48 hours prior to FBnTP administration.

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

Clinical trial: Surveillance Imaging Modalities for Breast Cancer Assessment

Summary: The purpose of this study is to determine the effectiveness of surveillance breast MRI compared to mammography alone in women with a personal history of breast cancer

Detailed description: Our overall aim is to find out how well MRI works compared with mammography for surveillance in women who have previously had breast cancer. Specifically, our goals are to:
  1. Understand doctors' and patients' experiences with surveillance mammography and MRI
  2. Provide evidence on which outcomes are more or less likely to occur
  3. Develop patient decision aids to help women and their doctors choose the surveillance method that is right for them
  How we will conduct the study: We will work with patients, doctors, policy makers, advocacy groups, and researchers to improve surveillance for women who have a personal history of breast cancer. Through focus groups with patients and interviews with doctors, we will gain insights into women's experience with surveillance mammography and MRI. We will also compare mammography to MRI using data from the Breast Cancer Surveillance Consortium—the largest collection of breast cancer surveillance data in the nation. We will use data from more than 13,000 women diagnosed with breast cancer between 2005 and 2012 to determine how well each test works. We will measure the tests' effectiveness at finding second cancers, and estimate the likelihood of different outcomes. We will also determine whether one test appears to work better than the other to detect second breast cancers among different groups of women. We will then develop patient decision aids to help women and their doctors make more-informed choices about surveillance.
  What we hope to achieve: We hope this study will improve medical decision making and care for the 3 million women in the United States who have a history of breast cancer. Specifically, our results will help women and their doctors make clearer, better choices about the surveillance method that is right for them.

Eligibility: Inclusion Criteria: Surveillance imaging exams in women included in the Breast Cancer Surveillance Consortium who are 18+ years of age at the the of a Stage 0-III incident breast cancer diagnosis between January 1, 2005 and December 31, 2012.
  Exclusion Criteria:
  -  Women with a diagnosis of lobular carcinoma in situ
  -  Women with missing cancer staging data from Surveillance, Epidemiology and End Results (SEER) Program records
  -  Women with Stage 4 breast cancer at time of diagnosis
  -  Women with a diagnosis of a second breast cancer event within six months of the primary diagnosis
  -  Women who die within six months of primary diagnosis
  -  Women who have had a double mastectomy

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

Clinical trial: Gemcitabine, Trastuzumab, and Pertuzumab in the Treatment of Metastatic HER2-Positive Breast Cancer After Prior Trastuzumab/Pertuzumab, or Pertuzumab Based Therapy

Summary: The purpose of this study is to see if a combination of drugs can help to treat breast cancer. This is a Phase II study which will test whether this combination of drugs is effective and will provide further information on side effects and safety. A standard chemotherapy, gemcitabine, will be combined with 2 other drugs that target the HER2 receptor. The HER2 receptor is a growth protein on the surface of some breast cancer cells that provides messages telling the breast cancer cell to grow. The standard chemotherapy will be gemcitabine.. The other two drugs work against HER2. One is called trastuzumab (Herceptin) and it is commonly given to women with advanced and early HER2 positive breast cancer. The other drug, pertuzumab (Perjeta), is also given to women with advanced HER2 positive breast cancer. The drugs in this study are each individually approved for the treatment of metastatic breast cancer. However, this study is looking at the effectiveness of gemcitabine with trastuzumab and pertuzumab when given to women who have advanced HER2 positive breast cancer who have had prior trastuzumab + pertuzumab or pertuzumab-based therapy.


Eligibility: Inclusion Criteria:
  -  Age ≥ to 18
  -  Stage IV HER2 (+) breast cancer
  -  Histologically documented HER2 (+) breast cancer as defined as IHC 3+ or FISH amplification of ≥ 2.0 of primary or metastatic site; results from the local lab are acceptable.
  -  lECOG performance status 0 -1
  -  Prior treatment with trastuzumab + pertuzumab (HP)-based therapy or pertuzumab-based in the neoadjuvantadjuvant, unresectable, locally advanced, or metastatic setting.
  -  ≤ 3 prior chemotherapies in the metastatic setting. Prior anthracycline, taxane, gemcitabine, and anti-HER2 agents (i.e. trastuzumab, pertuzumab, lapatinib, neratinib, TDM-1, etc.) are allowed. If patients received prior gemcitabine, it could not have been combined with pertuzumab. Patients should have progression of disease on current therapy.
  -  Measurable or non-measurable disease.
  -  LVEF ≥ 50%
  -  Hematologic parameters: white blood cell (WBC) count of ≥ 3000/ul, absolute neutrophil count (ANC) ≥ 1000/ul, platelets ≥ 100,000/ul, hemoglobin ≥10.0 g/dl
  -  Non-hematologic parameters: bilirubin ≤ 1.5 mg/dl, AST/ALT≤ 2.5 x upper limit of normal (ULN), alkaline phosphatase ≤ 5 x ULN.
  -  Creatinine ≤ 1.5 mg/dl
  -  Patients with "treated and stable" brain lesions of a duration of ≥ 2 months may be enrolled.
  Exclusion Criteria:
  -  History of prior unstable angina, myocardial infarction, CHF, uncontrolled ventricular arrhythmias within 12 months
  -  History of prior ≥ G 3 hypersensitivity (HSR) or any toxicity to trastuzumab or pertuzumab that warranted permanent cessation of this agent
  -  History of hepatitis B or C
  -  Pregnant patients

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

Clinical trial: Eradication of Malignant Carcinoma in the Breast Tissue

Summary: The purpose of this study is to confirm the findings of an early study and expand our knowledge of treating Malignant Carcinoma in the Breast Tissue Using an ATP (Adenosine-5'-Triphosphate) Inhibitor.


Eligibility: Inclusion Criteria:
  -  Clinical diagnosis of breast cancer
  -  Referred to the study by their treating physician
  Exclusion Criteria:
  -  Any type of treatment for breast cancer before starting the 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: Triple Negative Breast Cancer and Germline Hereditary Breast and Ovarian Cancer Mutation Carrier Registry

Summary: PROGECT is a registry for patients with Triple Negative breast cancer (TNBC) or patients who have an identified germline mutations (such as a mutation on the BRCA1 or BRCA2 genes).

Detailed description: This study is being done to collect cancer-related information from patients with triple negative breast cancer and patients with hereditary genetic mutations. This information will help us better understand the link between genetic changes and cancer outcome in patients with triple negative breast cancer.

Eligibility: Inclusion criteria include:
  Triple Negative Breast Cancer
  -  ER/PR <10% and HER negative per current ASCO/CAP guidelines
  -  Stages I-IV
  -  Any age at diagnosis
  -  Patient must be within 5 years of diagnosis
  -  Eligible regardless of genetic testing status
  -  Genetic testing recommended for patients meeting NCCN and Medicare guidelines
  AND/OR
  Germline mutation Carriers
  -  Patients with deleterious or uncertain mutations in HBOC genes (BRCA, PTEN, P53, -PALB2 etc) are eligible regardless of type/site of cancer
  -  Healthy patients harboring mutations also eligible
  -  There is no time limit from the time of diagnosis of cancer and enrollment.
  -  Eligible regardless of personal history of cancer
  Exclusion Criteria include:
  Triple Negative Breast Cancer -Patient is not within five years of diagnosis
  Germline mutation Carriers:
  -Patient only carries a HBOC mutation that is classified as "polymorphism" of "favor polymorphism"

Relevance to patient case: not relevant