araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: Characterization of the Melanoma-Specific Immune Response

Summary: The aim of this study is to study T-cells. Blood will be collected and the samples will be used to generate T cell clones. Two separate blood draws will be required at the maximum.

Detailed description: The aim of the study is to in-vitro characterize and expand T cells specific for melanoma-derived antigens. Peripheral blood with be collected from 20 volunteers with biopsy proven melanoma and 10 age matched controls. Blood will be collected prior to the initiation of chemotherapy. There will be no more than two blood draws per patient. Most patients will receive a single blood draw; however, some participants may be asked to return for a single additional blood draw if investigators were unable to isolate melanoma-specific immune cells after the first blood draw. Two separate blood draws will be the maximum. The interval between these blood draws will be a minimum of 3 months apart. Blood samples will be used to determine the patient's HLA haplotype via PCR and DNA sequencing. After the patient's haplotype has been established melanoma-specific T cell clones will be generated from the peripheral blood samples and expanded in-vitro. These clones will then be assayed for specificity against commercially available melanoma cell lines. The T cell clones will also be assayed for reactivity to melanocyte differentiation antigens such as MART-1 and gp100. If the volunteer requires a palliative resection of a melanoma tumor then the patient's own tumor cells may also be used to test the specificity of the isolated T cell clones. All experiments will be conducted in-vitro.

Eligibility: Inclusion Criteria:
  -  Biopsy diagnosis of malignant melanoma
  -  Have had a biopsy diagnosis of malignant melanoma in the past
  Exclusion Criteria:
  -  Patients taking immunosuppressive medications

Relevance to patient case: not relevant
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: Efficacy of Albumin Interferon Alfa-2b With Ribavirin Compared With Peg-IFN Alfa-2a With Ribavirin in IFN Naive Patients

Summary: This is a phase 3, randomized, multi-center study to evaluate the efficacy and safety of albumin interferon alfa 2b (alb-IFN)in combination with ribavirin compared with peginterferon alfa-2a (PEGASYS or PEG-IFNa2a) in combination with ribavirin in subjects with chronic hepatitis C, genotype 1 who are IFNa treatment naive.


Eligibility: Key Inclusion Criteria:
  -  Diagnosis of chronic hepatitis C.
  -  Liver biopsy performed within 2 years of Day 0 or during screening.
  -  Infected with hepatitis C virus genotype 1.
  -  Interferon alfa treatment naïve (ie, have never been treated with an interferon product).
  -  Subjects are eligible to enter the study if they (or their partners) are not pregnant or nursing, are sterile, or of non childbearing potential, or are willing to practice abstinence or use appropriate birth control methods during the study and for 7 months after the last dose of ribavirin.
  -  Have compensated liver disease.
  Key Exclusion Criteria:
  -  Decompensated liver disease including those subjects with a past history or presence of ascites, bleeding varices or hepatic encephalopathy.
  -  History of moderate, severe or uncontrolled psychiatric disease, especially depression, including a history of hospitalization or prior suicidal attempt.
  -  Positive for human immunodeficiency virus (HIV-1) or hepatitis B surface antigen (HBsAG).
  -  Clinical diagnosis of other causes of chronic liver disease including but not limited to hepatitis B, autoimmune hepatitis, primary biliary cirrhosis, alcoholic liver disease, hemochromatosis, Wilson's Disease, or alpha 1-antitrypsin deficiency.
  -  A history of immunologically mediated disease (eg, rheumatoid arthritis, inflammatory bowel disease, moderate/severe psoriasis, sarcoidosis, systemic lupus erythematosus).
  -  Active seizure disorder within the last 2 years.
  -  Organ transplant other than cornea and hair transplant.
  -  Clinically significant hemoglobinopathy (eg, thalassemia, sickle cell anemia).
  -  Cancer within the last 5 years(with the exception of adequately treated basal cell carcinoma of the skin or in situ carcinoma of the uterine cervix).
  -  Drug or alcohol addiction within the last 6 months. Subjects in a supervised methadone treatment program may be enrolled in the study.
  -  Received any experimental agent within 28 days prior to Day 0.

Relevance to patient case: not relevant
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: Melanoma Inhibitory Activity (MIA): A Serological Marker for Metastatic Uveal Melanoma

Summary: Uveal Melanoma is the most common primary intraocular tumor in adults. Most tumors metastasize to the liver. So far no sensitive or specific serological tumor marker is routinely used. The marker "Melanoma inhibitory activity" is a promising marker. Study hypothesis is to detect metastatic lesions in an early stage. This would increase life expectance of our patients

Detailed description: Serum is taken from each melanoma patient at every follow up after signed concent. With ELISA the marker MIA is evaluated. An increase of MIA serum level will lead to search for metastasis by oncologists.

Eligibility: Inclusion Criteria:
  -  uveal melanoma (With/without overt metastatic disease)

Relevance to patient case: not relevant
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: The DANTE Trial. A Randomized Study on Lung Cancer Screening With Low-Dose Spiral Computed Tomography

Summary: High survival rates have been reported for screen-detected Stage I lung cancer patients, but there are concerns about the potential biases of uncontrolled studies. DANTE is a prospective randomized controlled trial exploring the effects of screening with LDCT on lung-cancer-specific mortality, and on the prevalence and incidence rates of lung cancer, stage distribution and resectability rates in a selected high-risk population. The prevalence of a set of biomarkers in sputum and blood samples is also being determined.


Eligibility: Inclusion Criteria:
  -  Male sex
  -  Age 60-74 years
  -  smokers of more than 20 cigarettes/day for at least 20 years (actual smokers or ex-smokers from no more than 10 years)
  Exclusion Criteria:
  -  severe cardiopathy
  -  advanced BPCO with chronic hypoxaemia (rest SatO2 < 94%)
  -  chronic severe renal insufficiency
  -  hypertension not controlled with drugs
  -  type 2 diabetes or other severe systemic disease
  -  severe previous cerebrovascular lesions with permanent invalidity (not self-sufficient).
  -  severe vascular lesions with repeated ictus, trophic lesions, or limb loss, if actual smoker
  -  Dementia, psychosis, severe depression or maniac-depressive syndrome
  -  actual or precedent neoplasia, excepted skin tumor not-melanoma or scaly cells laryngeal and buccal cavity tumor, N0, recovered from more than 10 years or other tumors recovered from more than 10 years
  -  transplantation less than 5 years or with rejection episodes in the last 2 years
  -  unable subjects

Relevance to patient case: not relevant
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

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: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: Study of Families With Melanoma

Summary: RATIONALE: A study that evaluates patients' lifestyle, skin, and blood and tissue samples may help doctors understand the risk factors for melanoma relapse.
  PURPOSE: This clinical trial is studying the risk factors for melanoma in families with melanoma.

Detailed description: OBJECTIVES:
  Primary
  -  Determine what lifestyle factors and which genes govern relapse from melanoma.
  Secondary
  -  Compare sun exposure and genes that cause melanoma in patients with melanoma vs healthy participants.
  -  Assess how unusual moles relate to sun exposure and genes that cause melanoma.
  OUTLINE: This is a multicenter, cohort study.
  Patients and healthy participants complete lifestyle questionnaires by mail and telephone. Some patients* and healthy participants undergo a skin examination to count moles and classify skin type (e.g., degree of freckling and wrinkling indicative of sun damage).
  NOTE: *Patients diagnosed with primary invasive melanoma after September 2005 do not need to consent to a skin examination.
  Patients and healthy participants also undergo blood collection for lymphocyte analysis, DNA extraction, and the measurement of minerals, vitamins, and beta carotene. Tissue samples from original diagnosis are examined by immunohistochemistry for gene expression and mutations, including CDKN2A and CDK4.
  Patients and healthy participants are followed annually.
  Peer reviewed and funded or endorsed by Cancer Research UK
  PROJECTED ACCRUAL: A total of 3,700 patients and healthy participants will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Meets 1 of the following criteria:
  -  Newly diagnosed primary invasive melanoma (patient group)
  -  Lentigo maligna malignant melanoma allowed
  -  Rare variants of melanoma allowed, including any of the following:
  -  Acral lentiginous
  -  Subungual
  -  Ear, nose, and throat
  -  Oropharyngeal
  -  Perineal
  -  Vaginal
  -  Vulval
  -  Rectal
  -  Nodal with no known primary
  -  Patients undergoing sentinel node biopsy are eligible
  -  No in situ melanoma, melanocytic intraepidermal neoplasia, or ocular melanoma
  -  Healthy participant meeting either of the following criteria (control group):
  -  Relative of a patient who was diagnosed with melanoma after September 2005
  -  Healthy volunteer who is age- and sex-matched for patients who were diagnosed with melanoma before October 2005
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: Clinical Outcomes of Patients With Clostridium Difficile Associated Disease Attributable to Diverse tcdC Genotypes

Summary: The purpose of the study is to establish the clinical disease outcomes and features of CDAD associated with variant tcdC genotypes. Two hypotheses are to be tested in this study:
  1. Severe CDAD and tcdC truncation:
  Severe CDAD (defined by death and/or colectomy or secondary endpoints) is associated with severe truncations (> 6 amino acid residues) in TcdC, a negative regulator of toxin A/B production.
  2. Disease in low risk populations (patients never exposed to health care facilities and/or patients who never received antibiotics) of any severity is attributable to strains of C. difficile with severe tcdC truncation.

Detailed description: The following information will be collected: age, sex, occupation, hospital location at the time of positive culture (ER, medical ward, ICU etc), prior hospitalization, receipt of outpatient dialysis, home care or other regular medical care (eg, outpatient chemotherapy), date of specimen collection, presence of invasive devices, receipt of antibiotics, including their type and whether they were adequate for the resistance profile of the organism, prior positive microbiologic cultures, time and location of positive cultures, underlying diseases and severity of illness, presence of urinary or intravascular devices, recent immunomodulative therapies or radiation therapy, physical exam findings, laboratory and radiographical data, antimicrobial usage within 6 months of onset of the infection, microbiological data and resistance patterns, choice of antibiotics once organism identified, bacteriological outcomes, laboratory results, demographic information, medications, clinical outcome,gender, height, weight, ethnicity, past medical history and outcomes. We will collect information retrospectively.

Eligibility: Inclusion Criteria:
  -  All patients who have confirmed CDAD, confirmed by testing at UPMC's clinical microbiology lab in March 1, 2001- December 31, 2005 for C. difficile by stool toxin test with subsequent positive culture for the organism from inpatients/outpatients at UPMC Presbyterian-Montefiore, from WPIC inpatient units, from ER visits at the Presbyterian University Hospital emergency department, and from clinics closely affiliated with UPMC Presbyterian (medical and surgical clinics in Falk Clinic, the 9 South Montefiore internal medicine clinic, the geriatrics clinic in Montefiore, and the digestive disorders center (GI clinic on 3rd floor of PUH).

Relevance to patient case: not relevant
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: The Chinese Mutation Hotspot of ENaC Causing Liddle's Syndrome and the Association of ENaC Variations and Hypertension

Summary: The variations of ENaC have an impact on the degradation of epithelial sodium channels and sodium reabsorption, and thus are associated with hypertension and hypokalemia.
  Liddle's syndrome is a rare monogenic form of autosomal-dominant hypertension caused by truncating or missense mutations in the C-termini of epithelial sodium channel β- or γ-subunit encoded by SCNN1B or SCNN1G. Our purpose is to determine the hotspot of mutation causing Chinese Liddle's syndrome.
  The second purpose is to determine wether the polymorphisms of ENaC are associated with hypertension in Chinese. Some polymorphisms of ENaC associated with hypertension may be genetic risk factors for Chinese hypertension.


Eligibility: Inclusion Criteria:
  -  Clinical diagnosis of hypertension and Liddle's syndrome
  -  Clinical diagnosis of normal controls with no cardiovascular disease
  Exclusion Criteria:
  -  Hypertension caused by other single gene mutation

Relevance to patient case: not relevant
Patient case: 70-year-old male with melanoma; genetic feature: NF1 truncation

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: 70-year-old male with melanoma; genetic feature: NF1 truncation

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: 70-year-old male with melanoma; genetic feature: NF1 truncation

Clinical trial: Phase I/II Study of Chemo-Immunotherapy Combination in Melanoma Patients

Summary: This phase I/II study is directed at evaluating safety and immunogenicity of a melanoma peptide vaccine in combination or not with Dacarbazine administration in melanoma patients

Detailed description: Recently, it is becoming increasingly accepted that, in order to induce a clinically effective antitumor response, immunotherapy needs to be combined with chemotherapy. Thus, the traditional perception that chemotherapy and immunotherapy act through unrelated mechanisms which may be antagonistic is challenged on the premises that a selected panel of drugs can induce an immunogenic cell death producing specific danger signals. Furthermore, chemotherapy combined to immunotherapy may affect antigen cross-presentation, induce a "cytokine storm", reduce the number of regulatory T cells and activate homeostatic lymphoid proliferation. Our previous results obtained in a mouse model, demonstrated that drug-induced cytokines can favour antitumor immunity. Based on this observation, we explored whether the administration of dacarbazine (DTIC) in disease-free melanoma patients in combination with peptide vaccination could result into an improved anti tumor immune response.
  Patients included in the study were assigned to two treatment arms either receiving anti-tumor vaccination with Melan-A and gp100 analog peptides alone (arm 1) or in combination with DTIC pre-treatment (arm 2).
  Arm 1, vaccine alone: patients received i.d. injections of Melan-A: 26-35 (A27L) and gp100: 209-217 (210M) peptides (250 µg each) formulated in Montanide ISA-51 plus s.c. injection of 3MU IFN-α, as an adjuvant on day 1 and 8 every 21 days for a total of 5 courses (10 vaccinations). Both peptides and IFN-α were injected in close but separate sites next to local lymph nodes.
  Arm 2, DTIC plus vaccine: the same vaccination schedule was combined with DTIC (800 mg/mq i.v.) administered one day before each vaccine administration according to the standard treatment.

Eligibility: Inclusion Criteria:
  -  histologically proven diagnosis of melanoma stage II, III, and IV without clinical/radiological evidence of disease
  -  Age >18 years
  -  life expectancy of more than 6 months
  -  ECOG performance status of 0-2
  -  adequate blood cell counts and kidney-liver function
  -  use of adequate contraceptive methods
  -  signed informed consent
  Exclusion Criteria:
  -  concomitant or previous history of malignant disease, except for in situ cervical carcinoma or non melanomatous skin cancer
  -  severe cardiovascular disease
  -  clinically active infections and/or significant autoimmune diseases
  -  concomitant or previous (within 6 weeks) treatment with immunosuppressive drugs
  -  previous treatments with chemotherapy and/or interferon alpha or beta within 4 weeks and/or radiotherapy within 6 weeks an/or biological therapy within 8 weeks before starting vaccination
  -  psychiatric illness interfering with patient compliance, pregnancy or lactation

Relevance to patient case: not relevant