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

Clinical trial: To Study the Effect of Fursultiamine in Esophageal Squamous Cell Carcinoma Patients Who Receive Concurrent Chemoradiotherapy

Summary: Esophageal cancer is a common and fatal malignancy. It is the eighth most common incident cancer and the sixth leading cause of cancer death in the world. In Taiwan, esophageal cancer was newly diagnosed in 2199 patients and was the cause of 1507 deaths in 2011. Squamous cell carcinoma is the predominant histological tumor type, accounting for about 90% of the cases. Esophageal squamous cell carcinoma (ESCC) is an aggressive disease, characterized with extensive local growth and frequent metastases. Concurrent chemoradiotherapy (CCRT) with or without surgery is the treatment option for locally advanced ESCC. Further, target therapy is used in conjunction with CCRT and surgery in ESCC since several years ago. However, the therapeutic outcomes are not satisfactory due to the emergence of chemo-radioresistance. It is imperative to investigate new biomarkers and to find novel treatment targets in ESCC.
  A small population of tumor-initiating cells or cancer stem cells (CSCs) possess some biological functions like normal stem cells, including self-renewal, asymmetric cell division, slowly proliferation rate and drug-resistance. CSCs from many primary tumors and cell lines express specific stem cell markers, including Oct4, Sox2, Nanog, CD133 (promimin-1), Nestin, CD44 ,CD24, ALDH (Aldehyde dehydrogenase) and c-Kit. There are many evidences that CSCs are responsible for tumor initiation, progression and metastasis. CSCs are also believed to have important roles in cancer recurrence due to their resistance to anti-cancer drugs and radiation. CSCs express high levels of ATP-binding cassette (ABC) transporters. ABC transporter can pump cytotoxic drugs out of cells and is one important mechanism of multidrug resistance in CSCs. In addition, CSCs have high reactive oxygen species (ROS) scavenger expression to remove ROS produced from irradiation therapy.
  Fursultiamine (also known as thiamine tetrahydrofurfuryl disulfide, TTFD) is a derivative of vitamin B and currently used for nutrition supplement. The investigators have identified that Fursultiamine suppressed OCT-4, SOX-2, NANOG expression and decreased ABCB1 and ABCG2 in tumor sphere of ESCC cell lines. In this project, the investigators will conduct a prospective phase II study to investigate the effect of Fursultiamine combined with CCRT in ESCC patients. Stem cell markers in clinical specimens collected before and after CCRT will be evaluated.


Eligibility: Inclusion Criteria:
  -  newly diagnosed stage II and III esophageal squamous cell carcinoma
  Exclusion Criteria:
  -  ECOG≧2;
  -  impaired function of lung, liver, kidney or bone marrow

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

Clinical trial: Re-Examination of Tumor Material and Re-Evaluation of Patient Data From Patients Treated With Neo-adjuvant Therapy

Summary: This is a prospective examination of ribonucleic acid (RNA) extracted from tumor material of breast cancer patients treated with a neo-adjuvant therapy. The RNA will be analysed for expression of estrogen receptor (ER 1), progesterone receptor (PgR), HER2 and Ki-67 with MammaTyper™.
  According to the determined values for the individual parameters at least 4 subtypes can be distinguished to date
  -  Luminal A-type
  -  Luminal B-type
  -  HER2-type
  -  Triple-negative-type As non-clinical endpoint, the agreement of new subtyping with Immunohistochemical methods will be evaluated.
  As clinical objective, the 5 year Distant metastasis free survival (DMFS) and Overall survival (OS) will be reevaluated according to the new subtyping.

Detailed description: Tumor material collected from patients who received neoadjuvant therapy either with four cycles of doxorubicin 60 mg/m² plus pemetrexed 500 mg/m² on day 1 every 21 days followed by four cycles of docetaxel 100 mg/m² on day 1 every 21 days or four cycles of doxorubicin 60 mg/m² plus cyclophosphamide 600 mg/m² on day 1 every 21 days followed by four cycles of docetaxel 100 mg/m² on day 1 every 21 days will be re-analyzed with the MammaTyper Kit. The Kit is an in-vitro molecular diagnostic test for molecular subtyping of breast cancers into Luminal A & B, HER2 and Triple negative. It allows quantitative detection of the RNA expression status of the genes for estrogen receptor (ESR1), PgR, HER2 and Ki-67 on the basis of their mRNA present in the samples. This prospective diagnostic study will investigate the subtyping-results of the MammaTyper™ analysis and will compare them to the subtyping of the former immunohistochemical analysis performed. Based on the MammaTyper™-subtypes the efficiency of the therapy regimen and the outcome will be re-evaluated from the patient data.

Eligibility: Inclusion Criteria:
  -  Women aged 18-70 years with histologically confirmed primary invasive breast cancer stages T2-T4/N0-N2/M0 with a tumor size of ≥ 2 cm as measured by ultrasound
  -  The patient provides a written informed consent for analysis of tumor material
  Exclusion Criteria:
  -  Prior anticancer therapy with an anthracycline or other prior antitumor therapy for breast cancer
  -  Inflammatory or exulcerating breast cancer
  -  A second primary malignancy [except carcinoma in situ (CIS) of the cervix or adequately treated nonmelanoma skin cancer] unless diagnosed and treated ≥ 5 years ago with no evidence of recurrence
  -  Any serious concomitant systemic disorder

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

Clinical trial: HPV Self-Test Intervention in Ohio Appalachia

Summary: This study will pilot test a culturally appropriate human papillomavirus (HPV) self-test intervention among women from Ohio Appalachia in order to determine the feasibility of HPV self-testing as a potential cervical cancer screening strategy. The intervention group will receive culturally appropriate materials and the control group will receive standard materials with their HPV self-test device.

Detailed description: PRIMARY OBJECTIVES:
  I. To determine the feasibility of HPV self-testing as a potential cervical cancer screening strategy and obtain preliminary efficacy data of culturally appropriate materials on self-test use.
  OUTLINE:
  Participants are randomized to 1 of 2 arms.
  ARM I: Participants receive a study kit that includes culturally appropriate instructions for using and returning the HPV self-test device and a photo story information sheet about HPV and HPV self-testing. Participants are asked to complete the HPV self-test and return the test for HPV testing.
  ARM II: Participants receive a study kit that includes standard instructions for using and returning the HPV self-test device and a standard information sheet about HPV and cervical cancer. Participants are asked to complete the HPV self-test and return the test for HPV testing.
  Participants are followed up at 4 weeks for return of their HPV self-test device and then for 2 months after notification letters are sent.

Eligibility: Inclusion Criteria:
  -  Ages 30-65
  -  No Pap test in the last 3 years
  -  Resident of an Ohio Appalachia county
  -  Not currently pregnant or was not pregnant in the last 3 months
  -  No history of invasive cervical cancer
  -  No history of hysterectomy; women will not be eligible for the pilot randomized controlled trial (RCT) if they participated in the focus groups that helped develop this study (focus groups were institutional review board [IRB] approved as Protocol 2014C0086) or the preliminary device test; we will also require women to read and understand English and have the ability to provide informed consent, which will be inferred upon completion and return of the study eligibility, consent, and Health Insurance Portability and Accountability Act (HIPAA) forms

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

Clinical trial: Patients With Refractory, Metastatic Cancer Harboring KIT Mutation or Amplification to Investigate the Clinical Efficacy and Safety of Imatinib Therapy

Summary: KIT is a receptor tyrosine kinase that binds to stem-cell factor (SCF), activating a series of downstream effector pathways. KIT is an established therapeutic target in cancer with activating mutations of KIT, such as gastrointestinal stromal tumors (GIST), and significant benefit is achieved with various small molecule inhibitors of KIT such as imatinib mesylate. Moreover, there is increasing evidence implicating KIT mutations as tractable therapeutic targets in melanoma. Additional information is required to characterize the functional role of low-frequency mutations in KIT and to determine whether amplification of wild type KIT is a real driver that can be targeted therapeutically. Except GIST and melanoma, other solid cancers were reported to have KIT mutation even in low frequency. A molecular profiling of the tumors of patients referred to the phase I clinic at the M.D. Anderson Cancer Center showed KIT mutation in 7 patients in total of 431 patients (2%).
  Hence, the investigators planned this study to apply the molecularly targeted agent, imatinib to various types of cancers harboring KIT mutation or amplification.


Eligibility: Inclusion Criteria:
  1. age ≥ 20
  2. advanced, refractory cancer patients who failed standard of care (SOC)
  3. KIT aberration: defined as mutation in exons 9, 11, 13, 17 or 18, or nanostring CNV by quantitative PCR (greater than 3 copies) or subject with specific sensitivity (Z-score<-1) to imatinib by Avatar scan whose disease has progressed following standard therapy or that has not responded to standard therapy or for which there is no standard therapy
  4. ECOG performance status of 0~2
  5. measurable or evaluable lesion per RECIST 1.1 criteria
  6. adequate marrow, hepatic, renal and cardiac functions
  -  Serum aspartate transaminase (AST) and serum alanine transaminase (ALT) ≤ 2.5 x upper limit of normal (ULN), or AST and ALT ≤ 5 x ULN if liver function abnormalities are due to underlying malignancy
  -  Total serum bilirubin ≤ 1.5 x ULN
  -  Absolute neutrophil count(ANC) ≥ 1,500/uL
  -  Platelets ≥ 100,0000/uL
  -  Hemoglobin ≥ 9.0 g/dL
  7. provision of a signed written informed consent
  Exclusion Criteria:
  1. severe co-morbid illness and/or active infections
  2. pregnant or lactating women
  3. history of major surgery or radiotherapy within 4 weeks
  4. active CNS metastases not controllable with radiotherapy or corticosteroids (however, CNS metastases (except for leptomeningeal seeding) are allowed if controlled by gamma knife surgery or surgery or radiotherapy or steroid)
  5. known history of hypersensitivity to study drugs

Relevance to patient case: possibly relevant
Patient case: 58-year-old female with adenoid cystic carcinoma; genetic feature: KIT

Clinical trial: A Study of BIND-014 in Patients With Urothelial Carcinoma, Cholangiocarcinoma, Cervical Cancer and Squamous Cell Carcinoma of the Head and Neck

Summary: BIND-014 (docetaxel nanoparticles for injectable suspension) is being studied in patients with advanced urothelial carcinoma, cervical cancer, cholangiocarcinoma or carcinomas of the biliary tree and squamous cell carcinoma of the head and neck.
  Ferumoxytol imaging will also be investigated at US sites as an exploratory endpoint.


Eligibility: Inclusion Criteria:
  1. Diagnosis of advanced urothelial carcinoma, cervical cancer, cholangiocarcinoma or carcinomas of the biliary tree or squamous cell carcinoma of the head and neck.
  2. Progressive disease after ≥ 1 prior chemotherapy regimen.
  3. Patients with brain metastases are eligible if asymptomatic and neurologically stable for at least 4 weeks and are not taking any medications contraindicated
  4. Chemotherapy must have been completed at least 4 weeks prior to initiation of study medication
  5. ECOG performance status 0-1
  6. Tumors must have measurable disease as per RECIST (version 1.1);
  7. Female or male, 18 years of age or older
  8. Adequate organ function
  9. Life expectancy of > 3 months
  Exclusion Criteria:
  1. Current treatment on another therapeutic clinical trial
  2. Prior treatment with docetaxel within 6 months of enrollment
  3. Stage II, III or IV cardiac failure
  4. Carcinomatous meningitis
  5. Ongoing cardiac dysrhythmias
  6. Peripheral neuropathy
  7. Serious concomitant conditions
  8. Pregnant or breast feeding
  9. Known sensitivity to ferumoxytol
  10. Hypersensitivity to polysorbate 80

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

Clinical trial: Phase 1 Study of BLU-285 in Patients With Gastrointestinal Stromal Tumors (GIST) and Other Relapsed and Refractory Solid Tumors

Summary: This is a Phase 1, open-label, first-in-human (FIH) study designed to evaluate the safety, tolerability, pharmacokinetics (PK), pharmacodynamics (PD) and antineoplastic activity of BLU-285, administered orally (PO), in adult patients with unresectable GIST or other relapsed or refractory solid tumors. The study consists of 2 parts, a dose-escalation part (Part 1) and an expansion part (Part 2).


Eligibility: Inclusion Criteria:
  -  For Part 1: Histologically- or cytologically-confirmed diagnosis of unresectable GIST or another advanced solid tumor. Patients with unresectable GIST must have disease that has progressed following imatinib and at least 1 of the following: sunitinib, regorafenib, sorafenib, dasatinib, pazopanib or an experimental agent that targets KIT, or disease with a D842 mutation in the PDGFRα gene. Patients with an advanced solid tumor other than GIST must have relapsed or refractory disease without an available effective therapy.
  OR For Part 2:
  -  Group 1: Patients must have a confirmed diagnosis of unresectable GIST that has progressed following imatinib and at least 1 of the following: sunitinib, regorafenib, sorafenib, dasatinib, pazopanib, or an experimental agent that targets KIT, and the patient does not have a D842V mutation in PDGFRα.
  -  Group 2: Patients must have a confirmed diagnosis of unresectable GIST with a D842V mutation in the PDGFRα gene. The PDGFRα mutation will be identified by local or central assessment, either in an archival tissue sample or a new tumor biopsy obtained prior to treatment with BLU-285.
  -  Groups 1 and 2: A tumor sample (archival tissue or a new tumor biopsy) has been submitted for mutational testing.
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0-2
  Exclusion Criteria:
  -  QT interval corrected using Fridericia's formula (QTcF) >450 milliseconds
  -  Platelet count <90,000/mL
  -  Absolute neutrophil count <1000/mL
  -  Hemoglobin <9 g/dL
  -  Aspartate aminotransferase (AST) or alanine aminotransferase (ALT) >3 x the upper limit of normal (ULN) if no hepatic metastases are present; >5 × ULN if hepatic metastases are present
  -  Total bilirubin >1.5 × ULN; >3 × ULN with direct bilirubin, >1.5 × ULN in the presence of Gilbert's Disease
  -  Estimated (Cockroft-Gault formula) or measured creatinine clearance <40 mL/min Brain malignancy or metastases to the brain
  -  History of a seizure disorder or requirement for anti-seizure medication

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

Clinical trial: Study of Intravenous RXDX-107 in Patients With Solid Tumors

Summary: This is an open-label, Phase I/Ib, dose escalation study of intravenous RXDX-107 administered to subjects with advanced solid tumors. The study is designed to explore the safety, maximum tolerated dose (MTD), pharmacokinetics, pharmacodynamics, and preliminary clinical activity of RXDX-107 and to define a recommended Phase 2 dose (RP2D)


Eligibility: Inclusion Criteria:
  1. Confirmed relapsed or refractory locally advanced or metastatic solid cancer for whom no standard therapy is considered appropriate, or for whom standard therapy is considered intolerable.
  2. >18 years of age.
  3. ECOG performance status of 0 or 1.
  4. Life expectancy of at least 3 months.
  5. Received the last dose of previous treatment / therapy before Day 1 of cycle 1:
  -  28 days for cytotoxic chemotherapy, immunotherapy, whole brain radiotherapy, anticonvulsive therapy, stereotactic radiosurgery and major surgery
  -  42 days for nitrosureas, mitomycin C, and liposomal anthracycline
  -  14 days for non-cytotoxic cancer therapies and radiotherapy
  6. Recovered from all toxic effects (excluding alopecia) of any prior anti-cancer therapy to Grade ≤ 1 or to the baseline laboratory values.
  7. Adequate organ function and baseline laboratory values
  8. Women of childbearing potential must have a negative serum pregnancy
  Phase 1b: Patient must have measurable disease
  Exclusion Criteria:
  1. Receiving other experimental therapy
  2. Known symptomatic brain mets or leptomeningeal involvement
  3. Myocardial infarction in the previous 12 weeks. Active ischemia or any other uncontrolled cardiac condition such as angina pectoris, significant cardiac arrhythmia requiring therapy, uncontrolled hypertension, or CHF.
  4. Another concurrent illness which would preclude study conduct and assessment, uncontrolled: medical condition, active infection, risk of bleeding, diabetes mellitus, or pulmonary disease, or alcoholic liver disease, or primary biliary cirrhosis.
  5. Malignancy within 3 years or active disease requiring treatment other than the target cancer. The exceptions are prostate cancer (Gleason grade < 6 with normalized PSA levels), treated in situ cervical, breast carcinoma, squamous or basal cell skin cancer.
  6. Any condition that may compromise the ability to give written informed consent or to comply with the study protocol.

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

Clinical trial: Vitamin D and Microbiota in Cystic Fibrosis

Summary: The objective of this study is to assess the effects of a high-dose vitamin D3 on the composition of gut and lung microbiota in adolescents and adults with cystic fibrosis who are vitamin D deficient.

Detailed description: Monocentric, double-blind, randomized, placebo-controlled, interventional pilot study to investigate the beneficial effects of high dose vitamin D supplementation on gut and lung microbiota in patients with cystic fibrosis who are vitamin D insufficient.

Eligibility: Inclusion Criteria:
  -  Presenting to the Cystic fibrosis clinic for routine follow up of cystic fibrosis
  -  Serum 25(OH)D concentrations obtained within 2 months of enrollment
  -  Able to tolerate oral medications
  Exclusion Criteria:
  -  Inability to obtain or declined informed consent from the subject and/or legally authorized representative
  -  Pregnancy or plans to become pregnant in the next 3 months
  -  History of disorders associated with hypercalcemia including parathyroid disease
  -  Current hypercalcemia (albumin-corrected serum calcium >10.8 mg/dL or ionized calcium >5.2 mg/dL)
  -  History of nephrolithiasis with active symptoms within the past two years
  -  Chronic kidney disease worse than stage III (<60 ml/min)
  -  Current significant hepatic dysfunction total bilirubin > 2.5 mg/dL with direct bilirubin > 1.0 mg/dL
  -  Current use of cytotoxic or immunosuppressive drugs
  -  History of AIDS
  -  History of illicit drug abuse (defined as history of enrollment into a drug rehabilitation program or hospital visits due to drug use within the past 3 years or any use of the following drugs in the past 6 months (cocaine, opiates, amphetamines, marijuana) or any positive toxicology screen for (cocaine, opiates, amphetamines, marijuana)
  -  Too ill to participate in study based on investigator's or study team's opinion
  -  Current enrollment in another intervention trial

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

Clinical trial: nSTRIDE APS in Females With Primary Patellofemoral Osteoarthritis

Summary: The purpose of this study is to evaluate clinical outcomes following a single injection of nSTRIDE Autologous Protein Solution in females with isolated patellofemoral osteoarthritis. A secondary objective of this study is to document the duration of treatment effect following nSTRIDE injection.

Detailed description: Clinical trials have, in general, formally demonstrated the effectiveness and safety of various autologous therapies for the treatment of knee OA. Differences in the processing of autologous therapies can yield substantial differences in the resulting output. Thus, making generalizations regarding the effectiveness across these autologous therapies is more complicated. Each autologous therapy requires independent efficacy evaluation. nSTRIDE APS has been shown to decrease pain, increase function and have a favorable safety profile in a pilot trial. Further, demonstration of the treatment effects in patellofemoral osteoarthritis, an important subset of knee osteoarthritis is lacking. This study will evaluate a population of female patients with patellofemoral osteoarthritis in which treatment with other modalities provides limited/short lived relief with the hope that APS treatment will provide and extend relief to these patients. The study will document the treatment effects and timeline of treatment effects for nSTRIDE APS following a single injection (per symptomatic knee).

Eligibility: Inclusion Criteria:
  -  Patient must be female
  -  Isolated patellofemoral osteoarthritis (PFOA) in one or both knees as diagnosed by the treating physician
  -  Objective evidence of PFOA on one or both of a radiograph or MRI taken within 3 months of treatment
  -  From 40-65 years of age, inclusive at time of injection
  -  Symptoms return such that there is a need for further treatment within 3 months of a corticosteroid or hyaluronic acid injection
  -  Willing and able to comply with the study procedures
  -  Sign informed consent form
  Exclusion Criteria:
  -  Any systematic inflammatory condition (e.g. rheumatoid arthritis)
  -  Active malignancy at time of injection
  -  Pregnant at time of injection
  -  Lactating at time of injection
  -  Knee joint infections or skin diseases or infections in the area of the injection site
  -  Leukemia, metastatic malignant cells, or who are receiving chemotherapeutic treatment
  -  Participation in another device, biologic or drug study

Relevance to patient case: not relevant