araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

Clinical trial: Evaluation of Pigmented Skin Lesions With MelaFind(R) System

Summary: The purpose of this clinical trial is to demonstrate that MelaFind®, a new instrument that uses machine vision for non-invasive early detection of cutaneous pigmented malignant melanoma, is safe and effective. MelaFind® acquires digital images of the lesion with illumination in different spectral bands, from visible to near infrared, and automatically analyzes these images. Diagnostic accuracy of MelaFind® and that of study dermatologists will be evaluated. The reference standard will be final interpretation of lesions by central dermatohistopathology.


Eligibility: Inclusion Criteria:
  -  The lesion is pigmented (i.e., melanin, keratin, blood)
  -  Clinical management of the lesion by the examining dermatologist is either biopsy of the lesion in toto, or 3-month follow-up of the lesion
  -  The diameter of the pigmented area is between 2 and 22 millimeters
  -  The lesion is accessible to the MelaFind hand-held imaging device
  -  The patient, or a legally authorized representative, has consented to participate in the study and has signed the Informed Consent Form
  Exclusion Criteria:
  -  The patient has a known allergy to isopropyl alcohol
  -  The lesion has been previously biopsied, excised, or traumatized
  -  The skin is not intact (e.g., open sores, ulcers, bleeding)
  -  The lesion is within 1 cm of the eye
  -  The lesion is on mucosal surfaces (e.g., lips, genitals)
  -  The lesion is on palmar hands
  -  The lesion is on plantar feet
  -  The lesion is on or under nails
  -  The lesion is located on or in an area of visible scarring
  -  The lesion contains foreign matter (e.g., tattoo, splinter, marker)

Relevance to patient case: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

Clinical trial: High-resolution Magnetic Resonance Imaging (MRI) Scans to Look for Spread of Melanoma to Nearby Lymph Nodes

Summary: The study is designed to see if a high-resolution MRI scan of lymph node areas near where a melanoma has been removed from the skin can pick up the spread of melanoma to those lymph nodes with a high degree of accuracy.

Detailed description: When a melanoma of the skin is diagnosed, there is some chance it can spread to nearby lymph nodes, and from there to other parts of the body. Currently, patients with melanoma at low risk for spreading to lymph nodes do not get the lymph nodes assessed except by a physical exam. Those at high risk for spreading to lymph nodes get one or more lymph nodes removed surgically to check for melanoma spread. But physical exam alone will often miss small areas of melanoma in lymph nodes; removal of lymph nodes by surgery is painful and can cause complications. Neither assessment tool is optimal.
  This study is designed to see if use of very high-resolution contrast-enhanced MRI scans of lymph node areas near the primary melanoma site in the skin can accurately detect small areas of melanoma spread to those lymph nodes. If this turns out to be the case, in the future, MRI scans could potentially be an alternative for assessing lymph nodes, compared to physical exams alone or surgical removal of the lymph nodes.
  In this study, patients with low risk melanoma will receive very high-resolution MRI scans of nearby lymph nodes every 6 months for 5 years of follow-up. If the MRI looks abnormal, the lymph nodes will be biopsied, and results from the biopsy compared to the results from the MRI.
  Patients with high risk melanoma will get a baseline MRI of the nearby lymph nodes, and then one or more lymph nodes will be removed (usually by sentinel lymph node biopsy) regardless of the MRI results. Again, results from the biopsy will be compared to the results from the MRI. MRI's will still be repeated every 6 months to assess whether lymph nodes not removed at surgery develop any changes.
  We plan to enroll 200 patients on this study and by the end of the study will have a measure of the sensitivity and specificity of high-resolution MRI scans in the detection of melanoma involvement of regional lymph nodes.

Eligibility: Inclusion Criteria:
  -  history of invasive cutaneous melanoma stages 1-3 within 2 years of treatment of the melanoma by primary excision
  -  eligible whether or not a sentinel lymph node biopsy or regional lymph node dissection has been performed
  -  adequate renal function (creatinine 2 or less)
  -  life expectancy 2 years of more
  Exclusion Criteria:
  -  history of severe claustrophobia precluding MRI scans
  -  known hypersensitivity or other contraindication to gadolinium contrast
  -  known presence of metastatic melanoma at sites beyond regional lymph nodes (stage 4)

Relevance to patient case: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

Clinical trial: Changes in Semen or Sperm Caused by Temozolomide in Patients With Newly Diagnosed, Progressive, or Recurrent Primary Malignant Brain Tumors

Summary: RATIONALE: Learning whether temozolomide changes semen or sperm in patients with brain tumors may help doctors learn about the long-term effects of treatment and plan the best treatment.
  PURPOSE: This clinical trial is studying changes in semen or sperm caused by temozolomide in patients with newly diagnosed, progressive, or recurrent primary malignant brain tumors.

Detailed description: OBJECTIVES:
  Primary
  -  Assess if temozolomide induces any changes in standard semen or sperm analysis parameters (i.e., volume, viscosity, pH, forward progression, total count, total motile count, motility, presence of round cells, agglutination, and morphology) in patients with newly diagnosed, recurrent, or progressive primary malignant brain tumors.
  OUTLINE: This is a pilot study.
  During treatment with temozolomide, patients undergo semen or sperm sample collection at baseline, 3 months, and 6 months for semen analysis. Samples are analyzed for volume, viscosity, pH, forward progression, total count, total motile count, motility, presence of round cells, agglutination, and morphology.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically confirmed primary malignant brain tumor
  -  Newly diagnosed, progressive, or recurrent disease
  -  May have received prior radiotherapy with or without chemotherapy
  -  Scheduled to begin single-agent temozolomide chemotherapy
  -  Must be able to ejaculate
  -  Must abstain from ejaculating (e.g., not have sex or masturbate) for 2-7 days prior to study
  -  No known abnormal sperm motility and/or morphology
  PATIENT CHARACTERISTICS:
  -  Karnofsky performance status 60-100%
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

Clinical trial: MicroRNA Expression and Function in Cutaneous Malignant Melanoma

Summary: Spectrophotometric intracutaneous analysis (SIAscopy) is a new technique for imaging pigmented skin lesions and for diagnosing melanoma and non-melanoma skin cancer. The SIAscope is a portable system comprising of a laptop computer connected to a small handheld skin probe equipped with a light source. The skin lesion is interrogated with light of different wavelengths and the reflection spectra analysed by proprietary algorithms showing distribution, position and quantity of melanin, blood and collagen within the papillary dermis (the SIAgraphs). Earlier studies generated promising results and documented >80% specificity and sensitivity of SIAscopy for melanoma diagnosis. It has been suggested that this technique could be used for the initial screening and selection of pigmented lesion for excision. In this work we addressed the usefulness of SIAscopy for the clinical diagnosis of pigmented malignant melanoma in a prospective, blinded design.


Eligibility: Inclusion Criteria:
  -  Pigmented lesion
  Exclusion Criteria:
  -  No pigmented lesion

Relevance to patient case: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

Clinical trial: A Pilot Study to Evaluate Optical Spectroscopy of Pigmented Skin Lesions

Summary: The incidence of malignant melanoma has increased dramatically in recent decades. In 1930, the lifetime risk of an individual in the United States developing melanoma was 1 in 1,500. This has been exponentially increasing over the years with the risk estimated to be 1 in 75 in 2000 . According to the American Cancer Society, approximately 59,580 new cases of melanoma will be diagnosed in the United States in 2005 and about 7,770 people are expected to die of the disease.

Detailed description: The researcher ucan use special imaging devices to obtain information about a typical mole and melanoma and use this information to determine the different between malignant and benign melanized lesions. The imaging devices are, Modified Two Layer Diffuse Optical Spectroscopy,multi-spectral imaging, and Spatially Modulated Quantitative Spectroscopy can use to measure atypical moles and melanoma and correlate the results of the biopsy tissue histology.
  The imaging devices can quantify melanin, oxy and deoxy hemoglobin concentration, water, lipid and reduced scattering coefficients and can compare results to histopathologic. Atypical moles and melanoma have a different optical profile based on physiological parameters compared to benign nevus.

Eligibility: Inclusion Criteria:
  -  18 years or older.
  -  Have atypical mole/s and melanoma
  Exclusion Criteria:
  -  Age less than 18 years old.
  -  have NO atypical mole/s and melanoma

Relevance to patient case: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

Clinical trial: Feasibility and Functionality of fPAM Imaging in Melanoma

Summary: Melanoma is a cutaneous malignancy that has the potential for local (skin) and regional (lymph node) recurrence. These recurrences may be difficult to detect in their earliest stages. We are attempting to use novel form of skin imaging that uses ultrasound combined with laser to identify these recurrences early, when they may be most amenable to treatment. This imaging will detect melanoma pigment below the surface of the skin and in the draining lymph nodes, as well as new blood vessel formation that occurs with these loco-regional metastases.

Detailed description: recruiting healthy individuals with pigmented lesions and individuals with melanoma and pigmented lesions

Eligibility: Inclusion Criteria:
  -  Adult patients (> 18 yrs of age) with recently diagnosed or a history of, Stage I - III melanoma who are able to give informed consent.
  Exclusion Criteria:
  -  Patients with melanomas < 1mm.
  -  Pregnant females.
  -  Children and young adults < 18 yrs of age and patients who are unable to give informed consent.

Relevance to patient case: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

Clinical trial: Haploidentical NK Cell Infusion in Malignant Melanoma

Summary: We hypothesized that haploidentical NK cells kill tumor cells more efficiently than autologous NK cells, based on the missing-self hypothesis. Therefore, we performed this study to investigate the role of haploidentical NK cell therapy in patients with refractory or relapsed malignant melanoma.

Detailed description: Human NK cells recognize and kill transformed cells in a MHC-unrestricted fashion, suggesting the role of cancer immunotherapy. However, autologous NK cells showed the lack of significant clinical effects, because they are inhibited by self MHC class I molecules, based on the missing-self hypothesis. Contrarily, haploidentical NK cells with KIR-ligand incompatibility can mediate graft-versus-leukemia effect and protect patients with acute myelogenous leukemia (AML) from graft-versus-host disease. In addition, adoptive transfer of haploidentical NK cells following high-intensity conditioning induced complete remission (26%) in poor-prognosis AML patients. Thus, this study was designed to investigate the role of adoptive NK cell therapy in patients with refractory or relapsed malignant melanoma using CD3+ depleting CliniMACS® system.

Eligibility: Inclusion Criteria:
  -  Histologically confirmed metastatic or relapsed malignant melanoma
  -  Patients who received prior chemotherapy or immunotherapy
  -  Patients who have at least one haploidentical donor willing to donate
  -  ECOG performance status 0 or 1
  -  18 - 75 years
  -  At least one measurable disease according to the RECIST criteria
  -  Patients with 45% or more left ventricular ejection fraction
  -  Patients with 50% or more predicted DLCO
  -  Adequate bone marrow function: absolute neutrophil count ≥ 1.5 x 109/L; platelet count ≥ 100 x 109/L; and hemoglobin ≥ 9 g/dL
  -  Adequate liver function: total bilirubin ≤ 1.0 x upper limit of the normal range (ULN); AST/ALT ≤ 2.5 x ULN; and alkaline phosphatase ≤ 2.5 x ULN
  -  Adequate renal function: serum creatinine ≤ 1.0 x ULN or creatinine clearance ≥ 60 mL/min/1.73m2
  -  At least 3 months of expected survival
  -  Patients who signed informed consent
  Exclusion Criteria:
  -  Patients who received other chemotherapeutic agents within 30 days prior to study enrollment
  -  Patients who received adoptive cell therapy including hematopoietic stem cell transplantation
  -  Patients infected with HIV, HBV, or HCV
  -  Hypersensitivity to cyclophosphamide or interleukin-2
  -  Patients who received organ transplantation
  -  Patients who had arrhythmia or ischemic heart disease
  -  Pregnant or lactating women
  -  Patients with uncontrolled infection who did not respond to appropriate antimicrobial agents

Relevance to patient case: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

Clinical trial: Studying Tumor Tissue Samples From Patients With Melanoma Who Have Undergone Sentinel Lymph Node Biopsy

Summary: RATIONALE: Studying samples of tumor tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer. It may also help the study of cancer in the future.
  PURPOSE: This laboratory study is looking at tumor tissue samples from patients with melanoma who have undergone sentinel lymph node biopsy.

Detailed description: OBJECTIVES:
  -  Develop a predictive model for sentinel lymph node biopsy positivity in patients with melanoma who have undergone sentinel lymph node biopsy.
  -  Develop a survival model for relapse based on sentinel lymph node biopsy positivity.
  -  Assess the genetic determinants in primary melanomas that predict a metastatic phenotype and thereby improve understanding of the biology of the metastases in melanoma.
  OUTLINE: This is a retrospective, case-controlled, multicenter study. Patients are stratified according to Breslow thickness of the tumor (0.75-1.50 mm vs 1.51- 4 mm vs > 4 mm) and gender.
  Archived tumor tissue is analyzed by immunohistochemistry (IHC) for AP2, vascular endothelial growth factor, MMP 2, MCM4, and others, if feasible. Sentinel node biopsies are analyzed by IHC for CD31, LYVE-1, and D2-40 expression. RNA and DNA are also extracted for genetic expression studies and mutation analysis (e.g., BRAF, NRAS, PTEN, CDKN2A).
  Patient data related to relapse and recurrence is collected, if available.
  Peer reviewed and funded or endorsed by Cancer Research UK
  PROJECTED ACCRUAL: A total of 1,000 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Confirmed diagnosis of cutaneous melanoma
  -  Breslow thickness > 0.75 mm
  -  Has undergone sentinel lymph node biopsy
  -  No primary melanoma that has not originated in the skin
  -  No multiple primary melanomas
  -  Currently under clinical followup OR discharged from follow up within the past 3 months
  PATIENT CHARACTERISTICS:
  -  No other malignancy except for nonmelanoma skin cancer or cervical carcinoma in situ
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: possibly relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

Clinical trial: Efficacy of Methylene Blue for Malaria Treatment in Adults of Burkina Faso: Proof of Principle Study in Semi-Immune Adults of Burkina Faso in the Frame of the A8 Project of the SFB 544

Summary: Design: Single-centre, controlled study in adults with uncomplicated falciparum malaria in the Nouna Health District, north-western Burkina Faso
  Phase: Phase II
  Objectives: The primary objective of this trial is to study the efficacy of different methylene blue regimens given to adults with uncomplicated falciparum malaria in an African area of high malaria transmission intensity.
  Population: Male adults with uncomplicated malaria from Nouna town.
  Sample size: N= 60 (n=20 for each group; three different dosing regimens of MB).
  Treatment: The participants in the three different MB regimens will receive orally twice daily 390 mg MB (total daily dose 780mg) over 7,5 or 3 days respectively. Treatment with the five (three) day regimen will only start after all patients of the seven (five) days regimen have been followed up until day 3.
  Endpoints: The primary endpoint is the adequate clinical and parasitological response (ACPR) rate on day 28. Secondary endpoints are the number of adverse events (AE) after drug intake until day 28, clinical and parasitological failure rates on day 14 and 28, changes in haemoglobin/haematocrit until day 28, and fever and parasite clearance time.


Eligibility: Inclusion Criteria:
  -  Male adults (>17 years;<55 years)
  -  Uncomplicated malaria caused by P. falciparum
  -  Asexual parasites ≥ 1000/µl and ≤ 200 000/µl
  -  Axillary temperatures ≥ 37.5°C or history of fever during 48 hours
  -  Living in nouna Health District
  -  Informed consent
  Exclusion Criteria:
  -  Complicated or severe malaria
  -  Any apparent significant disease
  -  Anaemia (haematocrit < 21%)
  -  Antimalarial treatment prior to inclusion (last three days)
  -  Increased creatinine blood levels

Relevance to patient case: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

Clinical trial: Comparison of AZD6244 in Combination With Dacarbazine Versus (vs) Dacarbazine Alone in BRAF Mutation Positive Melanoma Patients

Summary: To assess the efficacy in terms of overall survival of AZD6244 in combination with dacarbazine, compared with dacarbazine alone, in first line patients with BRAF mutation positive advanced cutaneous or unknown primary melanoma


Eligibility: Inclusion Criteria:
  -  Histological or cytological confirmation of advanced (inoperable stage III and stage IV) cutaneous or unknown primary melanoma
  -  Tumor sample confirmed as BRAF mutation positive
  Exclusion Criteria:
  -  Diagnosis of uveal or mucosal melanoma
  -  Any prior Investigational therapy comprising inhibitors of Ras, Raf or MEK
  -  Having received an investigational drug within 30 days of starting treatment, or have not recovered from side effects of an investigational drug

Relevance to patient case: possibly relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

Clinical trial: A Study of Vemurafenib in Previously Treated Patients With Metastatic Melanoma

Summary: This open-label single arm study will assess the efficacy, safety and tolerability of Vemurafenib in previously treated patients with metastatic melanoma. Patients will receive oral Vemurafenib [RG7204; PLEXXIKON: PLX4032] at a dose of 960 mg b.i.d. continuously until disease progression or withdrawal from study and will be assessed at regular intervals for tumour response and tolerability. Target sample size is <100 patients.


Eligibility: Inclusion Criteria:
  -  adult patients >/=18 years of age
  -  histologically confirmed metastatic melanoma (Stage IV, AJCC)
  -  patients must have completed and failed at least one prior standard of care regimen (e.g. DTIC, temozolomide, etc.)
  -  BRAF V600E positive mutation (by Roche CoDx BRAF mutation assay)
  -  measurable disease by RECIST criteria
  -  negative pregnancy test and, for fertile men and women, effective contraception during treatment and for 6 months after completion
  Exclusion Criteria:
  -  active CNS metastases on CT/MRI within 28 days prior to enrollment
  -  history of or known carcinomatous meningitis
  -  previous treatment with BRAF (sorafenib allowed) or MEK inhibitor
  -  cardiac dysrhythmias >2 NCI CTCAE or treatment with drugs with dysrhythmic potential
  -  uncontrolled hypertension(>150/100mmHg) despite optimal medical therapy
  -  infectious disease including HIV, HBV and HCV

Relevance to patient case: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

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: not relevant