araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 63-year-old female with melanoma; genetic feature: NRAS (Q61R)

Clinical trial: Study of Tumor Tissue Samples From Patients With Stage I, Stage II, or Stage III Malignant Melanoma

Summary: RATIONALE: Studying the genes expressed in samples of tumor tissue from patients with cancer may help doctors identify biomarkers related to cancer.
  PURPOSE: This research study is looking at tumor tissue samples from patients with stage I, stage II, or stage III malignant melanoma.

Detailed description: OBJECTIVES:
  -  Determine the genetic profile of primary melanomas with and without synchronous regional nodal involvement by examining for 1) activating mutations B-Raf and N-Ras associated with melanoma development, and 2) allelic imbalances across the genome.
  -  Compare the genetic profile of primary melanomas from patients with and without lymph node involvement.
  -  Determine the combinations of genetic lesions that correlate with nodal metastasis by adopting a statistical machine learning approach to build a lesion-based classifier for nodal metastasis.
  OUTLINE: Laser capture microdissection is performed on the archived tissue samples to isolate melanoma cells. DNA is then purified from the samples and amplified using PCR. Matrix-assisted laser desorption/ionization (MALDI)-time of flight mass spectrometry technology is used to detect mutations of B-Raf and N-Ras. Single nucleotide polymorphism arrays are also performed.
  Information about the patient's demographics (e.g., TNM staging, sex, age, and tissue collection dates) will be gathered by chart review or from the Multidisciplinary Melanoma Conference at University Hospitals tumor conference report in order to match cases.

Eligibility: Inclusion Criteria:
  -  Node positive Group (experimental group)
  -  Primary melanoma > 2 mm in depth
  -  Metastasis must be > 0.1 mm and detectable by IHC or hematoxylin and eosin (H&E) to be considered node positive
  -  Slides and block for primary and node must be archived in UH dermatopathology
  -  Node Negative Group (control group)
  -  Primary melanoma > 2 mm in depth
  -  A negative sentinel lymph node must be negative by IHC and H&E
  -  No stage IV disease
  -  No acral and mucosal histology
  -  No history of prior invasive melanoma
  -  Underwent primary excision and sentinel lymph node biopsy within 3 months of each other
  -  Archived tissue available
  -  Slides and block for primary tumor and node biopsy must be archived in University Hospitals Case Medical Center (UH) dermatopathology
  Exclusion Criteria:
  -  Acral and mucosal histology
  -  Previous diagnosis of invasive melanoma
  -  previous chemotherapy or immunotherapy
  -  patients who are found to have stage IV disease during workup

Relevance to patient case: definitely relevant
Patient case: 63-year-old female with melanoma; genetic feature: NRAS (Q61R)

Clinical trial: Efficacy and Safety Study of PEG-rIL-29 Plus Ribavirin to Treat Chronic Hepatitis C Virus Infection

Summary: Interleukin 29 (IL-29) is a substance that is produced in the body to help fight viral infections. The purpose of this study is to evaluate the safety and antiviral effects of several different doses of PEG-rIL-29 (a man-made form of IL-29) when it is given in combination with daily oral doses of ribavirin (an antiviral drug) to subjects with hepatitis C infection who have received no prior treatment for this disease.

Detailed description: PEG-rIL-29 (also known as PEG-interferon lambda) is a unique Type III interferon molecule that has demonstrated antiviral activity when administered weekly for 4 weeks to treatment-relapsed and treatment-naive subjects with genotype 1 hepatitis C virus (HCV) infection. Because PEG-rIL-29 binds to a unique receptor with a more limited distribution than the receptor for interferon (IFN)-α, it may have the potential to treat HCV without some of the treatment-limiting side effects associated with IFN-α-based therapies. The purpose of this Phase 2a/b randomized, controlled, multicenter study is to compare the safety and efficacy of PEG-rIL-29 and peginterferon alfa-2a, both administered subcutaneously weekly for up to 48 weeks in combination with daily oral ribavirin, in treatment-naive subjects with chronic genotype 1, 2, 3, or 4 HCV infection. The initial part of the study (Phase 2a) will be conducted as an open-label study; the second part of the study (Phase 2b) will be conducted as a blinded study. The above information provided in this listing is specific to the Phase 2b portion of the study. In addition, two small open-label substudies will be conducted to evaluate the efficacy of 24-week treatment with PEG-rIL-29 and ribavirin in subjects with HCV genotype 1 who have a particular genetic polymorphism associated with favorable response (n=60) and to evaluate the efficacy of 16-week treatment with PEG-rIL-29 and ribavirin in subjects with HCV genotype 2 or 3 (n=30).

Eligibility: Inclusion Criteria:
  -  No prior therapy for chronic HCV, other than up to 2 weeks of single-agent therapy with a direct-acting antiviral agent, including but not limited to, a protease or polymerase inhibitor
  -  HCV genotype 1, 2, 3, or 4
  -  HCV RNA ≥100,000 IU/mL
  -  ALT and AST ≤5.0 × ULN
  -  Documented absence of cirrhosis
  -  Able to comprehend the investigational nature of this study and sign an informed consent form
  Exclusion Criteria:
  -  Mixed genotype HCV infection
  -  Current or prior history of decompensated liver disease
  -  Received any investigational drug, including a direct-acting antiviral agent, within 60 days prior to receiving study drug
  -  Positive test for hepatitis B surface antigen, human immunodeficiency virus (HIV)-1, or HIV2 antibody at screening
  -  Active substance abuse, such as alcohol, or inhaled or injected drugs, within 6 months
  Additional inclusion and exclusion criteria are specified in the protocol.

Relevance to patient case: not relevant
Patient case: 63-year-old female with melanoma; genetic feature: NRAS (Q61R)

Clinical trial: Neoadjuvant Treatment of Colon Cancer

Summary: This study will investigate
  -  the effect of preoperative combination chemotherapy in patients with locally advanced colon cancer with mutation in the KRAS, BRAF or PIK3CA gene
  -  the effect of preoperative combination chemotherapy in combination with biological treatment in patients without mutation in the KRAS, BRAF or PIK3CA gene.


Eligibility: Inclusion Criteria:
  -  Histologically verified locally advanced T3 or T4 colon cancer assessed by CT scan
  -  Analysis of KRAS, BRAF, PIK3CA
  -  Age ≥18 år
  -  Performance status ≤ 2
  -  Hematology
  -  ANC ≥ 1.5x10^9/l. Thrombocytes ≥ 100x10^9/l.
  -  Biochemistry
  -  Bilirubinaemia ≤ 3 x UNL. ALAT ≤ 5 x UNL
  -  Consent to translational research
  -  Fertile women must present a negative pregnancy test and use secure birth control during and 3 months after treatment.
  -  Written and orally informed consent.
  Exclusion Criteria:
  -  Clinically significant cardiovascular disease (including myocardial infarction, unstable angina, symptomatic congestive heart failure, serious uncontrolled cardiac arrhythmia) ≤ 1 year before enrollment, active severe infections or other concurrent disease.
  -  Peripheral neuropathy NCI grade >1
  -  Other malignant disease within 5 years prior to enrollment, except basal cell squamous carcinoma of the skin and cervical carcinoma-in-situ
  -  Other investigational treatment within 30 days prior to treatment start
  -  History of interstitial lung disease e.g. pneumonitis or pulmonary fibrosis or evidence of interstitial lung disease on baseline chest CT scan.
  -  Bleeding tumors
  -  Hypersensitivity to one or more of the substances

Relevance to patient case: not relevant
Patient case: 63-year-old female with melanoma; genetic feature: NRAS (Q61R)

Clinical trial: Using High Resolution Function Imaging To Detect Melanoma and Dysplastic Nevi

Summary: A novel infrared imaging tool to aid in the clinical detection of atypical pigmented lesions and melanoma is developed. Goals include evaluation of the utility of high-resolution infrared scanning of cutaneous lesions in the diagnosis of pigmented lesions and the identification of high-risk lesions and melanomas.


Eligibility: Inclusion Criteria:
  -  Patients seen in the high-risk pigmented lesion clinic, who posses a pigmented lesion with a clinical indication for biopsy
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 63-year-old female with melanoma; genetic feature: NRAS (Q61R)

Clinical trial: Comparison of Predictive Factors Related to Coronary Artery Disease Among Different Menopausal Status and Effect of a Life Style Management Program on Risk Factors Modification Among Middle-aged Women

Summary: In Taiwan, heart disease and cerebrovascular disease ranked the second and third of ten leading causes of death in female in 2007; half of these deaths is due to coronary artery disease (CAD). Postmenopausal status is an independent risk factor for CAD. Early assessment and proper management of risk factors may reduce the prevalence rate of CAD. In the past decade, despite increased attention to CAD in women, most studies focused on certain menopausal status instead of all phases of menopause or on risk factors limited to related metabolic syndrome. Because the prevalence of risk factors related to CAD is influenced by various physiological and lifestyle status in different menopausal statuses, the purpose of this study, at the first stage, is to explore respectively the risk factors of CAD among middle-aged women in three menopausal statuses. At the second stage, the influence of a lifestyle management program on risk factors modification among pre-menopausal women is examined in this study.


Eligibility: Inclusion Criteria:
  -  diagnosis of CAD by coroangiography
  -  LVEF >30%
  Exclusion Criteria:
  -  impairment of physical activity
  -  history of psychiatric disorder, vital arrhythmia

Relevance to patient case: not relevant
Patient case: 63-year-old female with melanoma; genetic feature: NRAS (Q61R)

Clinical trial: Early Diagnosis of Malignant Transformation of Pigmentary Skin Lesions

Summary: Malignant Melanoma is a deadly skin cancer that can be cured if diagnosed early. To date atypical pigmented skin lesions are diagnosed by appearance alone and many moles and lesions are excised unnecessarily and on the other hand malignant lesions are missed and diagnosed too late. In this study a protein conjugated to a florescent dye is spread on a suspicious pigmented lesion, the hypothesis is that this protein binds to malignant cells only and thus with a special camera that picks up the dye we can find pigmented lesions with early malignant transformation.


Eligibility: Inclusion Criteria:
  -  pigmented lesion indicated for surgical excision
  -  over 18 years of age
  Exclusion Criteria:
  -  pregnancy

Relevance to patient case: not relevant
Patient case: 63-year-old female with melanoma; genetic feature: NRAS (Q61R)

Clinical trial: A Safety and MORAb-028 Dose Determination Study in Subjects With Metastatic Melanoma

Summary: The purpose of this study is to evaluate whether therapy with MORAb-028 is safe, effective, and to determine the appropriate dose of MORAb-028 in the treatment of metastatic melanoma.

Detailed description: Melanoma is a serious form of skin cancer. If untreated, the melanoma can spread beyond the original affected tissue and invade distant tissue and organs. Treatment for metastatic melanoma includes medical treatments (chemotherapy or immunotherapy), surgery, or radiation therapy. MORAb-028 is a recombinant human immunoglobulin M (IgM) monoclonal antibody that recognizes a cell surface diacyl ganglioside named disialoganglioside (GD2). GD2 is overexpressed in tumors of neuro-ectodermal origin such as melanomas, neuroblastomas, small-cell lung carcinomas, and many sarcomas, while absent in most normal tissues. GD2 expression has been demonstrated in human melanoma and small cell lung cancer by thin layer chromatography and radiolabeled anti-GD2 antibody detection. It is hypothesized that one mode of action of MORAb-028 is complement-dependent cytotoxicity. Complement-dependent cytotoxicity is a mechanism for killing tumor cells in which an antibody bound to the target cell surface fixes complement, which results in assembly of the complement membrane attack complex that punches holes in the target cell membrane resulting in subsequent cell lysis. IgMs strongly bind to C1Q and robustly activate complement-dependent cytotoxicity. MORAb-028 is being developed as a potential therapy for GD2-positive tumors.

Eligibility: Inclusion Criteria:
  -  Measurable metastatic melanoma that has failed standard therapy
  -  Males and females greater than or equal to 18 years of age
  -  Life expectancy of greater than or equal to 3 months
  Exclusion Criteria:
  -  Significant cardiovascular impairment
  -  Clinically significant illness, medical condition, surgical history, or laboratory abnormality that could affect the safety of the subject or negatively impact the study results
  -  Chemotherapy, radiotherapy, or immunotherapy within 3 weeks prior to administration to MORAb-028

Relevance to patient case: not relevant
Patient case: 63-year-old female with melanoma; genetic feature: NRAS (Q61R)

Clinical trial: A Phase II Study of Single Agent MEK162 in Patients With Advanced Melanoma

Summary: The study will assess the safety and efficacy of single-agent MEK162 in adult patients with locally advanced and unresectable or metastatic malignant cutaneous melanoma, harboring BRAFV600E or NRAS mutations.


Eligibility: Inclusion Criteria:
  -  Locally advanced or metastatic cutaneous melanoma AJCC Stage IIIB to IV, not potentially curable with surgery
  -  BRAF or NRAS mutation in tumor tissue
  -  All patients enrolled should provide sufficient fresh or archival tumor sample at baseline to enable confirmation of BRAF or NRAS mutations and the additional analyses described in the protocol
  -  Evidence of measurable tumor disease as per RECIST
  -  WHO performance status of 0-2
  -  Adequate organ function and laboratory parameters
  Exclusion Criteria:
  -  History or evidence of central serous retinopathy (CSR), retinal vein occlusion (RVO) or any eye condition that would be considered a risk factor for CSR or RVO
  -  Patients with unstable CNS metastasis
  -  Prior treatment with a MEK- inhibitor
  -  Impaired cardiovascular function
  -  HIV, active Hepatitis B, and/or active Hepatitis C infection
  -  Pregnant or nursing (lactating) women
  -  Women of child-bearing potential UNLESS they comply with protocol contraceptive requirements
  Other protocol-defined inclusion/exclusion criteria may apply.

Relevance to patient case: possibly relevant
Patient case: 63-year-old female with melanoma; genetic feature: NRAS (Q61R)

Clinical trial: Detection of Choroidal Nevus Cells in Vitrectomy Fluid

Summary: The purpose of this study is to determine if the investigators can detect the presence of choroidal nevi cells in the vitreous fluid of humans, as this may improve the diagnosis and classification of choroidal nevi and melanomas in the future.

Detailed description: Approximately 7% of the population has a choroidal nevus, or "freckle," in the back of the eye. Like a nevus on the skin, there is potential for malignant change to a melanoma. Dermatologists have the ability to quickly and easily biopsy suspicious skin lesions while ophthalmologists currently have no way of determining the malignant potential of choroidal nevi other than a fine needle aspiration (which is invasive and has the potential complications of bleeding and retinal detachment). This study's sole aim is to see if choroidal nevi cells are present in the inside fluid of the eye. The investigators plan to analyze the fluid of the eye, which is routinely removed during retina surgery, to detect any nevus cells. If the investigators are able to detect these cells, then future studies may allow us to better classify choroidal nevi for potential malignant change.

Eligibility: Inclusion Criteria:
  -  Patients with a choroidal nevus who are undergoing routine vitrectomy surgery for another indication (such as epiretinal membrane or macular hole repair).
  Exclusion Criteria:
  -  Patients without a choroidal nevus
  -  Children under the age of 18
  -  Pregnant and nursing females

Relevance to patient case: not relevant
Patient case: 63-year-old female with melanoma; genetic feature: NRAS (Q61R)

Clinical trial: Characterisation of T Lymphocytes, NK Cells and Macrophages in Melanoma Patients

Summary: Melanoma tumor tissue ( in particular regressive areas) present a lymphocytic infiltrate with an anti-tumoral specificity. The aim of the study is to analyse at different stages of the disease, tumor samples and to characterise the cellular infiltrate in situ ( in particular T lymphocytes, NK cells and macrophages), the role of inhibitor receptors on in situ immunosuppression, and potential modulation by medical treatments such as dacarbazine.

Detailed description: The study is divided in 4 parts:
  Part 1: study of cellular infiltrate (lymphocytes) performed on large primary melanoma and cutaneous metastasis ( fresh samples) Part 2: NK cells study on metastatic regional lymph nodes ( fresh samples) and blood samples Part 3: a retrospective study of macrophages in sentinel lymph nodes and in corresponding primary melanomas Part 4: study of the cellular modulation by the chemotherapy (DTIC or cisplatin or inhibitor of B-raf) which(who) will be made on two cutaneous metastases by patient (one taken before the treatment(processing) and one taken during the evaluation after 2 or 3 cycles of treatment(processing))

Eligibility: Inclusion Criteria:
  -  Patients with confirmed melanoma-patients informed of the aims of the study , the modalities
  -  Patients who signed the consent form ou a non opposition form signed by the patient or by a relative
  According to study part:
  Part 1: patients with a melanoma larger than 10mm or with cutaneous metastasis Part 2: stage IV melanoma patients who shall undergo a regional lymph node dissection Part 3: retrospective study of patients who underwent a sentinel node procedure Part 4: Patients achieves of inoperable melanomas the stage(stadium) III or IV that must receive in treatment (processing) a chemotherapy (by the dacarbazine or by the cisplatin or by the inhibitor of B-raf) and carrier of at least two cutaneous metastases
  Exclusion Criteria:
  -  Refusal to take part in the study (patient or relative)
  -  Contraindications known to the xylocaine (groups 1,2, and 4)
  -  No affiliated to the social security system (groups 1, 2, and 4)

Relevance to patient case: not relevant
Patient case: 63-year-old female with melanoma; genetic feature: NRAS (Q61R)

Clinical trial: Safety, Pharmacokinetics and Pharmacodynamics of BEZ235 Plus MEK162 in Selected Advanced Solid Tumor Patients

Summary: This is an open label, dose finding, phase Ib clinical trial to determine the maximum tolerated dose (MTD) and/or RP2D of the orally administered PI3K/mTOR inhibitor BEZ235 in combination with the MEK1/2 inhibitor MEK162. This combination will be explored in patients with EGFR mutant NSCLC which has progressed on EGFR inhibitors and triple negative breast cancer, as well as pancreatic cancer, colorectal cancer, malignant melanoma, NSCLC, and other advanced solid tumors with KRAS, NRAS, and/or BRAF mutations. Dose escalation will be guided by a Bayesian logistic regression model with overdose control. At MTD or RP2D, two expansion arms will be opened in order to further assess safety and preliminary anti-tumor activity of the combination of BEZ235 and MEK162.
  Study drugs will be administered orally on a continuous schedule, MEK162 bid and BEZ235 qd, a treatment cycle is defined as 28 days.


Eligibility: Inclusion Criteria:
  -  histologically/cytologically confirmed, advanced non resectable solid tumors
  -  Measurable or non-measurable, but evaluable disease as determined by RECIST 1.0
  Exclusion Criteria:
  -  Patients with primary CNS tumor or CNS tumor involvement
  -  Diabetes mellitus - Unacceptable ocular/retinal conditions
  Other protocol-defined inclusion/exclusion criteria may apply

Relevance to patient case: definitely relevant
Patient case: 63-year-old female with melanoma; genetic feature: NRAS (Q61R)

Clinical trial: MEK162 and RAF265 in Adult Patients With Advanced Solid Tumors Harboring RAS or BRAFV600E Mutations

Summary: This is a multi- center, open-label, dose finding, Phase Ib study to be conducted in two stages: a dose escalation part to determine the maximum tolerated dose (MTD) safety and tolerability of concurrent administration of MEK162 and RAF265, followed by an expansion part to further assess the safety and preliminary anti-tumor efficacy of this oral combination within two separate patient populations: i) patients with advanced solid tumors harboring BRAFV600E mutations or ii) patients with advanced solid tumors harboring RAS mutations.


Eligibility: Inclusion Criteria:
  Patients with histologically or cytologically confirmed and non-resectable advanced solid tumors for which no further effective standard therapy exists.
  -  The patients' tumors must contain documented activating somatic BRAFV600E* , NRAS or KRAS mutations (except for pancreatic cancer)
  -  All patients enrolled MUST provide fresh or archival tumor samples at baseline to enable central confirmation of BRAF or KRAS/NRAS mutations
  -  Measurable, or non-measurable but evaluable disease as determined by RECIST
  -  Adequate bone marrow function
  -  Adequate hepatic and renal function
  -  Adequate cardiovascular function
  -  Negative serum β HCG test (female patients of childbearing potential only) within 72 hrs prior to first dose
  Exclusion Criteria:
  -  Patients with a history of primary central nervous system tumors or brain metastases or who have signs/symptoms attributable to brain metastases and have not been assessed with radiologic imaging to rule out the presence of brain metastases
  -  Current evidence of retinal disease; or ophthalmopathy as assessed by ophthalmologic examination at baseline that would be considered a risk factor for CSR/RVO (e.g., optic disc cupping, visual field defects, IOP > 21 mm Hg)
  -  Impaired cardio-/vascular function or clinically significant cardiovascular diseases, including any of the following:
  -  History/evidence of acute coronary syndromes (including MI, unstable angina, CABG, coronary angioplasty, or stenting) ≤ 6 months prior to starting study drugs
  -  Thromboembolic event (DVT, CVA, PE) ≤ 6 months prior to starting study
  -  Symptomatic CHF, history or current evidence of clinically significant cardiac arrhythmia and/or conduction abnormality
  -  Uncontrolled arterial hypertension, defined as BP > 140/100 mmHg (average of 3 consecutive readings)
  -  History of melena, hematemesis or hemoptysis within the last 3 months
  -  Pregnant or nursing (lactating) women, where pregnancy is defined as the state of a female after conception and until the termination of gestation, confirmed by a positive hCG laboratory test (> 5 mIU/mL)
  Other protocol-defined inclusion/exclusion criteria may apply

Relevance to patient case: possibly relevant