araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 58-year-old female with adenoid cystic carcinoma; genetic feature: KIT

Clinical trial: A Study to Determine Safety, Pharmacokinetics and Pharmacodynamics of Intravenous TKM 080301 in Neuroendocrine Tumors (NET) and Adrenocortical Carcinoma (ACC) Patients

Summary: This study will be a Phase I/II, open-label, non-randomized, dose-finding trial conducted at multiple clinical centers. The study is designed to determine the safety, tolerability and PK of TKM-080301 in adult patients with solid tumors or lymphomas that are refractory to standard therapy or for whom there is no standard therapy. After the determination of the maximum tolerated dose this dose will be utilized in an expansion cohort or subjects with refractory neuroendocrine tumors (NET) or adrenocortical carcinoma (ACC) tumors.


Eligibility: Inclusion Criteria:
  -  Patients must have a histologically and cytologically confirmed solid tumor that is refractory to standard therapy or for which no standard therapy is known to exist, or who are not candidates for standard therapy, or non-Hodgkin's lymphoma or Hodgkin's disease that is refractory to standard therapy (i.e., patients have relapsed following at least 2 prior therapies) or for which no standard therapy is known to exist. For the Neuroendocrine (NET) and adrenocortical carcinoma (ACC) expansion cohort subjects must have histologically or cytologically confirmed, measurable (per RECIST 1.1) NET or ACC tumor that is refractory to standard therapy or for which no standard therapy is known to exist, or who are not candidates for standard therapy.
  -  Patient has an ECOG performance status of 0 - 1,
  -  Patient has adequate hematologic, hepatic and renal function,
  -  Patient is seronegative for hepatitis B virus (HBV) and hepatitis C virus (HCV),
  -  Patients must have a life expectancy of at least 12 weeks.
  Exclusion Criteria:
  -  Unresolved toxicities (> Grade 1) of previous chemotherapy,
  -  Patients with primary tumors of the central nervous system (CNS),
  -  Prophylactic hematologic growth factors administered </= 2 weeks prior to start of therapy,
  -  Patient has history of or existing clinically significant cardiovascular disease,
  -  Patient has a history of clinically significant asthma or COPD requiring daily medication within the last 6 months,
  -  Patient has a seizure disorder not controlled on medication,
  -  Patient has a known or suspected viral, parasitic, or fungal infection,
  -  Patient has known hypersensitivity or previous severe reactions to oligonucleotide- or lipid-based products, including liposomal drug products and phospholipid-based products,
  -  Patient has been treated with any investigational drugs, biologics, or devices within 28 days prior to study treatment.

Relevance to patient case: not relevant
Patient case: 58-year-old female with adenoid cystic carcinoma; genetic feature: KIT

Clinical trial: Detection of Chromosomal Aberrations in Urine Samples Using Fluorescent in Situ Hybridization (FISH) (UroVysion Test)

Summary: The purpose of the study is the identification of chromosomal aberrations in urine samples.
  The imaging system is intended for diagnostic use as an aid to the pathologist in the detection, counting and classification of UroVysion FISH stained Urine samples.

Detailed description: The FISH test detect chromosomal aberrations in urine specimens from persons with hematuria suspected of having bladder cancerous using the UroVysion® Bladder Cancer Kit (UroVysion Kit) which is FDA approved. This kit is designed to detect aneuploidy for chromosomes 3, 7, 17, and loss of the 9p21 locus. Results from the UroVysion Kit are intended for use, in conjunction with and not in lieu of current standard diagnostic procedures, as an aid for initial diagnosis of bladder carcinoma in patients with hematuria and subsequent monitoring for tumor recurrence in patients previously diagnosed with bladder cancer.

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

Relevance to patient case: not relevant
Patient case: 58-year-old female with adenoid cystic carcinoma; genetic feature: KIT

Clinical trial: Study to Evaluate the Safety and Efficacy of BA058 (Abaloparatide) for Prevention of Fracture in Postmenopausal Women

Summary: The purpose of this study is to determine whether BA058 (abaloparatide), a parathyroid hormone-related peptide, is effective in preventing fractures in postmenopausal women with severe osteoporosis who are at risk of fractures.

Detailed description: This is a randomized, double-blind, placebo-controlled, comparative Phase 3, multicenter international study to evaluate the efficacy and safety of BA058 (abaloparatide) 80 µg in the prevention of fracture in otherwise healthy ambulatory postmenopausal women with severe osteoporosis.

Eligibility: Inclusion Criteria:
  -  Healthy ambulatory postmenopausal (≥ 5 years) women from 50 to 85 years of age (inclusive) with a diagnosis of osteoporosis
  -  The women are to have a bone mineral density (BMD) T score ≤ -2.5 and > -5.0 at the lumbar spine or hip (femoral neck) by dual energy x-ray absorptiometry (DXA) and radiological evidence of 2 or more mild or one or more moderate lumbar or thoracic vertebral fractures, or history of low trauma forearm, humerus, sacral, pelvic, hip, femoral, or tibial fracture within the past 5 years. Postmenopausal women older than 65 who meet the above fracture criteria but have a T score ≤ -2.0 and > -5.0 may be enrolled. Women older than 65 who do not meet the fracture criteria may also be enrolled if their T score is ≤ -3.0 and > -5.0
  -  Normal physical exam, vital signs, electrocardiogram (ECG) and medical history
  -  Laboratory tests within the normal range including serum calcium, PTH(1-84), serum phosphorus and alkaline phosphatase
  Exclusion Criteria:
  -  History of more than 4 mild or moderate spine fractures or any severe fracture
  -  Abnormality of the spine or hip that would prohibit assessment of bone mineral density (BMD)
  -  Unexplained elevation of serum alkaline phosphatase, history of bone disorders (such as Paget's disease) or a diagnosis of cancer within the last 5 years (with the exception of basal cell or squamous cancer of the skin)
  -  History of thyroid, parathyroid, or adrenal disorders, or malabsorptive syndromes or any chronic or recurrent diseases or disturbances that would interfere with the interpretation of study data or compromise the safety of the patient
  -  Prior treatment with parathyroid hormone (PTH) or parathyroid hormone-related peptid (PTHrP)
  -  Prior treatment with bisphosphonates, fluoride, or strontium within the past five years or treatment with androgens, anabolic steroids, corticosteroids or selective estrogen receptor modulators within the past 12 months (except hormone replacement therapy)
  -  Prior treatment with an investigational drug within the past 12 months
  -  History of nephrolithiasis or urolithiasis within the past five years, or history of osteosarcoma at any time

Relevance to patient case: not relevant
Patient case: 58-year-old female with adenoid cystic carcinoma; genetic feature: KIT

Clinical trial: Qualitative and Quantitative HIV RNA Detection in Saliva Using the Oragene RNA Kit

Summary: The purpose of this study is to determine if the Oragene.RNA kit is able to detect HIV RNA in saliva.

Detailed description: There is an important need for a rapid, non-invasive, sensitive and specific method for detection of HIV RNA, particularly in clinical settings in which patients at risk for HIV exposure are assessed and screened. A rapid and non-invasive method for quantitative testing of HIV RNA would be also valuable to monitor suppression of HIV RNA as a primary surrogate marker of combination antiretroviral therapy efficacy. An Ottawa-based biotech company (DNA Genotek Inc) has developed and sells to research and clinical labs world-wide a kit (Oragene� DNA Self-collection kit) that permits the collection, stabilization at room temperature, and purification of DNA present in saliva. They have recently developed a kit (Oragene��RNA) that is purported to stabilize RNA in saliva, a non-invasive source of a biological fluid.

Eligibility: Inclusion Criteria:
  -  Four groups of 10 patients each will be recruited:
  -  Controls (HIV and HCV seronegative by previous testing)
  -  HIV seropositive with HIV RNA &gt;1000 copies/mL and not on combination antiretroviral therapy. No concurrent HCV infection.
  -  HIV seropositive with HIV RNA &lt;50 copies/mL as a consequence of combination antiretroviral therapy use. No concurrent HCV infection.
  -  HIV seropositive with HIV RNA &gt;1000 copies/mL and not on combination antiretroviral therapy. HCV RNA positive and not on antiviral therapy.
  Exclusion Criteria:
  -  Not fitting one of the 4 groups

Relevance to patient case: not relevant
Patient case: 58-year-old female with adenoid cystic carcinoma; genetic feature: KIT

Clinical trial: A Study of Sunitinib In Young Patients With Advanced Gastrointestinal Stromal Tumor

Summary: Children and young adults with gastrointestinal stromal tumors (GIST) will be treated with sunitinib. The safety (including pharmacokinetics) and tolerability of sunitinib will be studied in these patients. In addition, tumor responses and overall survival will be assessed.


Eligibility: Inclusion Criteria:
  -  Histological diagnosis of GIST.
  -  Patients must have demonstrated either disease progression or intolerance to imatinib mesylate, have non-mutant Stem Cell Factor Receptor gene (KIT) GIST, or cannot obtain imatinib in their country
  -  Measurable by Response Evaluation Criterion in Solid Tumors (RECIST) or evaluable disease.
  Exclusion Criteria:
  -  Current treatment with another investigational agent.
  -  Prior sunitinib treatment.
  -  Prior therapy with known risk for cardiovascular complications.

Relevance to patient case: not relevant
Patient case: 58-year-old female with adenoid cystic carcinoma; genetic feature: KIT

Clinical trial: Transoral Robotic Surgery in Treating Patients With Benign or Malignant Tumors of the Head and Neck

Summary: This pilot clinical trial studies transoral robotic surgery (TORS) in treating patients with benign or malignant tumors of the head and neck. TORS is a less invasive type of surgery for head and neck cancer and may have fewer side effects and improve recovery

Detailed description: To conduct a pilot single-arm study to assess transoral robotic surgery (TORS) for oral and laryngopharyngeal benign and malignant lesions using the Da Vinci Robotic Surgical System.

Eligibility: Inclusion Criteria:
  -  Patient must present with indications for diagnostic or therapeutic approaches for benign and/or malignant diseases of the oral cavity or laryngopharynx (including the neoplastic lesions of the tongue, tongue base, retromolar trigone, tonsils, palate, posterior and lateral pharynx, glottic, supraglottic and subglottic larynx)
  -  Patients must have adequate transoral exposure of the oral cavity and laryngopharynx for TORS instrumentation
  -  Written informed consent and/or Consent waiver by institutional review board (IRB)
  Exclusion Criteria:
  -  Unexplained fever and/or untreated, active infection
  -  Patient pregnancy
  -  Previous head and neck surgery that would preclude transoral/robotic procedures. This is at the investigator's discretion. This is not an exclusion criterion for the non-surgical arm.
  -  The presence of medical conditions contraindicating general anesthesia or transoral surgical approaches
  -  Inability to grant informed consent
  -  INTRAOPERATIVE EXCLUSION CRITERIA:
  -  Inability to adequately visualize anatomy to perform the diagnostic or therapeutic surgical approach transorally

Relevance to patient case: not relevant
Patient case: 58-year-old female with adenoid cystic carcinoma; genetic feature: KIT

Clinical trial: Genome-wide Association Study to Predict Treatment Response for Molecular Targeted Therapy in Hepatocellular Carcinoma and Renal Cell Carcinoma

Summary: All Hepatocellular carcinoma and Renal cell carcinoma patients who receive molecular targeted therapy will be candidates for the study.
  No additional treatment or intervention will be conducted except for blood sampling that will be limited to one time only.
  Blood samples (10 cc in volume) will be collected from all study participants once they provided written informed consent form. DNA will be extracted from peripheral blood samples using DNA isolation kit.


Eligibility: Inclusion Criteria:
  -  All Hepatocellular carcinoma and Renal cell carcinoma patients who receive molecular targeted therapy will be candidates for the study

Relevance to patient case: not relevant
Patient case: 58-year-old female with adenoid cystic carcinoma; genetic feature: KIT

Clinical trial: Biomarkers in Tissue Samples From Patients With Recurrent or Metastatic Head and Neck Cancer Treated on ECOG-E1395 and ECOG-E3301

Summary: RATIONALE: Studying samples of tissue from patients with cancer in the laboratory may help doctors predict how well patients will respond to treatment.
  PURPOSE: This research study is studying biomarkers in tissue samples from patients with recurrent or metastatic head and neck cancer treated on ECOG-E1395 and ECOG-E3301.

Detailed description: OBJECTIVES:
  -  To investigate the association between biomarkers (HPV tumor status and ERCC1 expression) and clinical outcomes in a population of patients with recurrent or metastatic head and neck cancer.
  -  To develop the ability to select patients likely to respond to therapy and to avoid treatment with ineffective therapies, especially since these therapies have substantial toxicity.
  -  To estimate response and survival rates of HPV-negative and -positive patients in each study. (exploratory)
  OUTLINE: Tumor HPV status is determined by in situ hybridization (ISH) and all samples also undergo immunostaining for p16. ERCC1 expression is evaluated with AQUA, a quantitative IHC analysis.
  Samples are classified into two categories based on their biomarker status: HPV tumor status (negative versus positive), and ERCC1 expression level (low versus high).

Eligibility: DISEASE CHARACTERISTICS:
  -  Tissue specimens from patients with recurrent or metastatic head and neck cancer treated on ECOG-E1395 and ECOG-E3301
  -  Stage III, IV, or recurrent disease
  -  Squamous cell disease
  -  Any of the following diagnoses:
  -  Lip and oral cavity
  -  Oropharynx
  -  Hypopharynx
  -  Larynx
  -  Paranasal sinus and nasal cavity
  -  Squamous neck cancer
  -  Salivary gland
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 58-year-old female with adenoid cystic carcinoma; genetic feature: KIT

Clinical trial: Self-sampling and Human Papillomavirus (HPV)-Testing for Unscreened Women in Cervical Cancer Prevention

Summary: Scientific Context:
  High-risk types of human papillomavirus (HPV) are the causative agents for cervical cancer. Cervical cancer screening strategies rely on periodic Papanicolaou (Pap) testing. It's well-known that this test has significantly contributed to the reduction of mortality and morbidity due to cervical cancer. In France, it now seems that the screening strategy could be optimized. The two main ways are to reach the 7 million underscreened women (organized screening, self-sampling for HPV DNA testing) and to improve the screening test (HPV DNA testing, computer-assisted cytology). Self-collected vaginal samples (SCVS) for HPV DNA testing could be a relevant screening option: this technique appears reliable and it could allow to reach women who are never or seldom screened. The performance of the SCVS to detect cervical HPV infection has been assessed by the first part of the whole study: APACHE-1.
  The goal of this study is to compare the attitudes of women not attending organized cervical cancer screening face to different strategies: further invitation to make a cervical smear or kit for self-collected vaginal sample sent at home.
  Description of the project :
  Nine months after a primary invitation to make a cervical smear, a random sample of 6000 women not attending organized cervical cancer screening will be randomly assigned to one of the following arms:
  -  Intervention arm 1:
  Women will receive a further invitation to make a cervical smear
  -  Intervention arm 2:
  Women will be directly sent the kit for self-collected vaginal sample at home. The women who will send the self-sample to the laboratory for analyse will receive their results at home as well as their general practitioner if the HPV DNA test is positive (infection by a high-risk HPV).
  For them who will have a HPV DNA test positive, it will be necessary to complete the screening action with a cervical smear. That's why those women will receive an invitation to make a cervical smear if they won't do it during the 9 months following the first mail.
  -  Control arm: Those women will receive complete information about the study, the main results and the screening recommendations at the end of the study.


Eligibility: Inclusion Criteria :
  -  Women from 30 to 65 years
  -  Living in Indre-et-Loire (french territorial division 37)
  Exclusion Criteria :
  -  Women who attend organized cervical cancer screening or who answer to the invitation
  -  Cervical smear made in the three last years
  -  HPV linked cervical condition undergoing treatment
  -  Hysterectomy (including cervix)

Relevance to patient case: not relevant
Patient case: 58-year-old female with adenoid cystic carcinoma; genetic feature: KIT

Clinical trial: An Observational Pilot Study Evaluating the Feasibility of Conducting Genome-Wide Association Studies Utilizing Subject Provided Information in Subjects With Locally Recurrent or MBC, MCRC, MNSCLC, RGBM or MRCC Treated With Avastin (Bevacizumab) (InVite)

Summary: This pilot, non-interventional, observational, Web-based, prospective cohort study is designed to collect self-reported safety and effectiveness and genetic data from subjects with locally recurrent breast cancer (BC) or metastatic breast cancer (MBC), metastatic colorectal cancer (MCRC), metastatic non-squamous non-small cell lung cancer (MNSCLC), recurrent glioblastoma (RGBM), or metastatic renal cell cancer (MRCC) in the United States who have been previously treated with Avastin (bevacizumab). The cohort will be composed of male and female subjects who have been diagnosed with locally recurrent BC or MBC, MCRC, MNSCLC, RGBM, or MRCC who have received treatment with bevacizumab in combination with chemotherapy, which started prior to or up to 31 December 2012. Participants will be self-referred to this study. They will be recruited online via a number of sources, including through the involvement of patient advocacy groups, social media tools, traditional media, physicians, and events to raise awareness of this study. After appropriate informed consent and authorization are obtained, data will be collected directly from subjects in an online survey. Participants will be contacted electronically to complete quarterly follow-up surveys. The follow-up period will be 1 year from responding to the baseline survey. DNA collection will be performed as part of this study. DNA will be extracted from saliva, which will be provided by the subject utilizing a collection kit sent to the participants for at-home use.


Eligibility: Inclusion Criteria:
  -  Locally recurrent BC or MBC, MCRC, MNSCLC, RGBM, or MRCC in patients treated or on treatment with bevacizumab, which started prior to or up to 31 December 2012
  -  Ability to read and understand English
  -  Ability to access and use a computer connected to the Internet
  -  Signed informed consent and authorization form
  -  Residence in the United States
  -  At least 18 years of age
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 58-year-old female with adenoid cystic carcinoma; genetic feature: KIT

Clinical trial: The Effect of Epidural Fentanyl on Immune Function

Summary: Background: For cancer to grow and metastasize, inflammatory and immunologic conditions in the host must be favorable. The perioperative period provides inflammatory and immunologic changes that may be pro-malignant. Anesthetic medications, including the use of opioid medication, may contribute to these changes.
  Hypothesis: The investigators hypothesize that perioperative immunologic changes in patients undergoing resection of hepatic colorectal cancer recurrence, as measured by natural killer cell function and cytokine levels, will undergo less alterations in those who receive only epidural bupivacaine, as compared to those who receive epidural bupivacaine and fentanyl.
  Methods: In this double blind control trial patients with no extra-hepatic evidence of cancer, undergoing a planned curative resection of hepatic recurrence of colorectal cancer, will be randomized to receive an epidural with bupivacaine and fentanyl, or bupivacaine alone. No other perioperative opioid medication will be given, and post-operative analgesia will be supplemented with acetaminophen and gabapentin. Blood samples and pain ratings using a verbal analogue scale will be obtained preoperatively, immediately and 6 hours postoperatively, and then daily until removal of the epidural catheter. Samples will be analyzed for levels of interleukin 2, 6, 8, 10, 12, 16, 17,TNF-α, TGF α and β, MCP-1, CRP, and NK cell activity. Cytokines will be measured using a suspension bead array immunoassay kit, and NK activity will be measured using flow cytometry of isolated peripheral blood mononuclear cells exposed to the K562 cell line and treated with fluorescent antibodies to intracellular markers of activation. Data will be compared between groups using t-tests, or Mann-Whitney tests as appropriate. To demonstrate a 50% smaller decrease of NK cell activity in the bupivacaine group as compared to the bupivacaine and fentanyl group the investigators will need to randomize a total of 30 patients.


Eligibility: Inclusion Criteria:
  We will consider for inclusion any adult patient undergoing a planned curative hepatic resection of a colorectal carcinoma liver recurrence.
  Exclusion Criteria:
  E 3. Patients Excluded Any patient unable to communicate in English or French. Any patient with evidence of extra-hepatic metastasis. Any patient with contra-indications to epidural anesthesia, or any of the medications used in the study.
  Any patient with evidence of coronary artery disease or congestive heart failure, either previously or currently.
  Any patient with insulin treated diabetes. Any patient with a BMI greater than 40. Any patient who has received steroids in the past 2 months. Any patient who has taken any pain medication the week before surgery. Any pregnant or breast feeding patient. Any patient with a chronic inflammatory disease, including but not limited to Lupus, rheumatoid arthritis, and inflammatory bowel disease.

Relevance to patient case: not relevant