araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Impact of Methylation Alterations in Colon Cancer: Epidemiology and Prognosis

Summary: We conducted a preliminary study in 2010 using the innovative Illumina GoldenGate (methylation assay) which has enabled us to characterize the level of methylation of 807 potential markers on a series of 200 adenocarcinomas of the colon (C18) and rectosigmoid junction (C19) resected between 1998 and 2001. The results, validated by pyrosequencing, allowed us to establish a panel of 12 markers to assess the level of methylation. The aim of this project is to validate the prognostic value of this panel in a second cohort of patients with adenocarcinomas (stage I to IV) resected between 2002 and 2006 in public and private hospitals (n=685).
  This study relies on an original collection of surgical specimens of colorectal cancers resected in public and private hospitals among patients resident in the département of Côte-d'Or and followed by the cancer registry of Burgundy. Samples obtained from each cancer and from adjacent normal mucosa are stored in liquid nitrogen in the Ferdinand Cabane Biological Resources Centre(certified S 96900). Annotations are collected by the cancer registry staff from multiple sources (pathologists, gastroenterologists, oncologists and radiotherapists).
  Pyrosequencing will be used to quantify the level of methylation. The percentage of methylated allele for each marker on cancerous DNA and the ratio of methylated markers to the number of markers analyzed will be determined. The molecular status of MSI, BRAF, KRAS, and PI3K will be taken into consideration.
  To study the prognosis, relative and relapse free-survival will be calculated. A multivariate relative survival analysis will be performed to determine independent prognostic factors taking into account the characteristics of patients and tumours and epigenetic and molecular alterations. Epigenetic alterations will be described according to age group, sex and subsite. The epigenetic phenotypes will be evaluated according to already known molecular status using logistic regression models.


Eligibility: Inclusion Criteria:
  -  Adenocarcinomas of the colon (C18) and rectosigmoid junction (C19)
  -  Resident in Côte-d'Or
  -  Treated by surgical resection
  Exclusion Criteria:
  -  Rectal cancer
  -  Cancer on Crohn's disease and ulcerate colitis
  -  Hereditary colon cancer (HNPCC, familial polyposis)

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: New Biopsy Technique for Uveal Melanoma

Summary: This pilot study intends to investigate a new biopsy technique that will decrease the incidence of tumor cells in the biopsy tract.

Detailed description: Uveal melanoma is the most common primary malignancy of the eye and is one of the few fatal diseases that are detected initially through an eye examination. For many years, clinical decision-making regarding which patient with uveal melanoma required treatment has been based solely on clinical features observed at the time of diagnosis. These features include: tumor size as measured by ultrasound, associated subretinal fluid, presence of orange lipofuscin pigment, lack of drusen, posterior location, and ciliary body involvement. All of these clinical features have been demonstrated to be associated with tumor growth which is associated with the eventual development of metastases. However, these clinical features are not adequately sensitive or specific enough to predict which patients will develop metastases.
  More recently, researchers studying the genomics of uveal melanoma have focused on identifying genetic abnormalities present in tumor tissue in order to characterize these lesions more fully. Several landmark papers over the past 15 years have reported cytogenic and genomic abnormalities in uveal melanoma tumor tissue that are associated with a poorer prognosis. Although rare, there have been at least five cases in which patients undergoing biopsy of these lesions have developed extraocular spread of melanoma from the biopsy sites. With this new technique, the possible rate of extraocular spread should be lower, making the biopsy a safer technique than what is currently in practice.

Eligibility: Inclusion Criteria:
  -  Diagnosed with uveal melanoma
  -  Scheduled for enucleation surgery
  Exclusion Criteria:
  -  Patients under 21 years old
  -  Patients unable to undergo surgery
  -  Patients with known metastatic uveal melanoma or other cancer.

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: HPV Serum DNA Levels Predicting Outcome in p16+ Squamous Cell Head and Neck Cancer

Summary: To assess in an exploratory manner, the pronostic utility for locoregional control, progression-free and distant metastasis-free survival of a pre-therapy and post-therapy blood DNA test of HPV E6 and E7 DNA for subtypes 16 and 18 in p16+ and/or HPV+ oropharyngeal cancer patients. This will entail analysis of both initial pre-therapy HPV level as a continuous variable and initial post-therapy HPV level as a dichotomous variable.


Eligibility: Inclusion Criteria:
  -  Histoloically proven primary cancer of the oropharynx, p16(+) and/or HPV (+), who are planned for treatment with resection, radiation and/or chemotherapy.
  -  Subsites of oropharynx:include tonsil, base of tongue, vallecula, oropharyngeal wall, soft palate, glossotonsillar sulcus.
  -  No or minimal smoking history (</= 10 pack-year, no smoking in the past 12 months last 10 years based on documented history and/or subject report)
  -  Age 18 years or older
  -  Subjects are capable of giving informed consent or have an acceptabl;e surrogate capable of giving consent on the subjects behalf.
  -  Enrollment on any other study, regardless of therapy is allowed.
  -  Enrollment on any other tumor or tissue banking study is allowed.
  -  Patients who have had blood drawn as part of another study, including the IRB-approved ENT Tumor Bank Study, may be included in this study even if the patient has already had surgery.
  Exclusion Criteria:
  -  Previous chemotherapy or radiation therapy to the head and neck unrelated to current disease.
  -  Previous surgery for head and neck cancer unrelated to current disease.
  -  Widespread , biopsy-proven metastatic disease (stage IVC disease) at time of presentation (small indeterminate lung or mediastinal nodules are allowed)
  -  Patients who have started induction chemotherapy prior to consideration for study eligibility.
  -  Another active cancer except nonmelanomatous skin cancer.
  -  History of cervical penile or anal cancer.
  -  Patient treated with surgery, adjuvant radiation therapy or chemotherapy outside of the University of Pennsylvania.
  -  History of smoking in the past last 12 months 10 years
  -  History of 10 pack-years of cigarette smoking based on documented history and/or subject report
  -  Presence of sidespread leukoplakia or erythroplakia.

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Phase 2 Study of Ipilimumab in Japanese Advanced Melanoma Patients

Summary: The purpose of this study is to assess the safety of Ipilimumab monotherapy in Japanese subjects with advanced melanoma


Eligibility: For more information regarding BMS clinical trial participation, please visit www.BMSStudyConnect.com.
  Inclusion Criteria:
  -  Histologically or cytologically confirmed diagnosis of malignant melanoma
  -  Previously-treated or untreated unresectable Stage III or Stage IV melanoma
  -  Measurable/evaluable disease per modified World Health Organization (mWHO) criteria, within 28 days of first dose of study drug
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1
  Exclusion Criteria:
  -  Active brain metastases
  -  Primary ocular or mucosal melanoma
  -  History of or current active autoimmune disease

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Mitochondrial Dysfunction in Phelan-McDermid Syndrome: Explaining Clinical Variation and Providing a Path Towards Treatment

Summary: The purpose of this study is to determine whether a relationship exists between gene deletion(s) specific to the mitochondrial electron transport chain and presentation of clinical characteristics in patients with Phelan-McDermid Syndrome (PMS).

Detailed description: Phelan-McDermid Syndrome (PMS) results from a deletion within the 22q13 chromosome region. Most children have specific physical morphology and developmental delays with many displaying characteristics of autism spectrum disorder (ASD) including abnormalities in social development. The behavioral aspect of PMS that parallels ASD has raised particular interest as the SHANK3 gene, which lies in the 22q13 region, is important for synaptic development, and animal SHANK3 knockout models demonstrate ASD characteristics thereby confirming the importance of this gene in PMS. However, despite the importance of the SHANK3 gene, individuals with PMS have variations in their development, behavior and medical characteristics that cannot be fully explained by the SHANK3 deletion.
  Recently, Frye (2012) has noted the existence of 6 mitochondrial genes that lie slightly proximal to the SHANK3 gene within the 22q13 region. These include genes important electron transport change function (SCO2, NDUFA6), mitochondrial DNA (TYMP) and RNA (TRMU) metabolism, fatty acid metabolism (CPT1B) and tricarboxylic acid cycle function (ACO2). Since most Individuals with PMS have deletions that include chromosomal deletion outside of the SHANK3 region, it is very likely that many, if not most, of children with PMS may have deletions in these mitochondrial genes. Many of these genes have been linked to mitochondrial disease, even in the heterozygous state. Even if recognized, mitochondrial disease is only linked to a homozygous abnormal state (autosomal recessive), the loss of one gene (heterozygous state) could result in symptomatology when associated with deletions in other mitochondrial or non-mitochondrial genes. Abnormalities in mitochondrial pathways can result in neurologic and non-neurologic symptoms including those sometimes seen in children with PMS. Added with the SHANK3 deletion, abnormalities in these mitochondrial genes could explain variations in patterns of development and the eventual cognitive potential.
  References: Frye RE. Mitochondrial disease in 22q13 duplication syndrome. J Child Neurol. 2012; 27(7):942-9.

Eligibility: Inclusion Criteria:
  -  1-21 years of age
  -  Diagnosed with Phelan-McDermid Syndrome AND diagnosed with Mitochondrial Disorder
  -  Diagnosed with Phelan-McDermid Syndrome
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Bevacizumab Combined With Carboplatin Plus Paclitaxel Chemotherapy to Treat Metastatic Mucosal Melanoma

Summary: Mucosal melanoma is rare and associated with extremely poor prognosis.No effective treatment for advanced mucosal melanoma patients.Investigators conducted a randomized phase II study in patients with previously untreated metastatic mucosal melanoma to characterize the efficacy and safety of bevacizumab when combined with carboplatin plus paclitaxel.

Detailed description: Mucosal melanoma is rare and associated with extremely poor prognosis.It is the second most common subtype in Asians.No effective treatment for advanced mucosal melanoma patients.Malignant melanoma is a highly vascular tumor in which vascular endothelial growth factor(VEGF) is strongly expressed and seems to play an important role in disease progression.A randomized phase II study evaluated the activity of Bevacizumab in combination with carboplatin plus paclitaxel(CPB arm) in patients with previously untreated advanced melanoma.Overall response rates was 25.5%,median overall survival time(OS) was 12.3 months in the CPB arm. Investigators conducted a randomized phase II study in patients with previously untreated metastatic mucosal melanoma to characterize the efficacy and safety of bevacizumab when combined with carboplatin plus paclitaxel.

Eligibility: Inclusion Criteria:
  1. Histologically confirmed mucosal melanoma with metastases and has no received any systemic treatment.
  2. ECOG performance status 0, 1
  3. Estimated life expectancy of 12 weeks or greater
  4. Age 18 years or older, male or female
  5. At least one measurable site (diameter≥1cm) of disease (RECIST 1.1).
  6. Adequate organ function
  7. Without symptoms of brain metastases and stable in neuro-functions.
  8. Willingness and ability to comply with scheduled visits, treatment plans, laboratory tests, and other study procedures
  Exclusion Criteria:
  1. Mutations in C-KIT or BRAF-V600E, asked for other target treatments
  2. Pregnant or lactation women
  3. Acute infections without control.
  4. Heart disease history, cardiac function class≥NYHA II.
  5. HIV positive or chronic HBV/HCV in active stage.
  6. Brain metastases or primary tumor with positive symptoms
  7. Need anti-epileptic treatments
  8. Organ transplantation history
  9. Hemorrhagic tendency or related history
  10. Renal dialysis patients
  11. Diagnosis of any second malignancy within the last 3 years, except for adequately treated.
  12. Current treatment on another clinical trial
  13. The other improper situations which investigator judged.

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Phase 1 Safety and Tolerability of MEDI4736 in Combination With Dabrafenib and Trametinib or With Trametinib Alone

Summary: The purpose of this study is to determine the maximum tolerated dose and the safety profile of MEDI4736 in combination with dabrafenib and trametinib or with trametinib alone in subjects with metastatic or unresectable melanoma with BRAF-mutation positive or Wild Type BRAF, respectively.


Eligibility: Inclusion Criteria:
  -  Adults >/= 18 years old
  -  Histologically confirmed cutaneous melanoma that is either Stage IIIc (unresectable) or Stage IV (metastatic) and determined to be BRAF V600E or V600K mutation-positive (cohort A) or mutation-negative (cohorts B and C)
  -  ECOG performance status of 0 or 1
  -  Measurable disease by radiographic or physical examination
  -  Adequate organ and marrow function
  -  Willingness to provide consent for biopsies positive or BRAF WT measurable disease, Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1, and adequate organ and marrow function
  Exclusion Criteria:
  -  Prior treatment with a BRAF inhibitor or MEK inhibitor
  -  Any prior Grade ≥ 3 immune-related adverse event while receiving immunotherapy
  -  Active or prior documented autoimmune disease within the past 2 years
  -  History of or current risk for retinal vein occlusion (RVO) or central serous retinopathy (CSR)
  -  History of or current cardiovascular risk including myocardial infarction, ≥ Class II congestive heart failure, uncontrolled arrhythmias, or refractory hypertension
  -  Active, untreated CNS metastases
  -  Women who are pregnant or lactating

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Study to Evaluate Treatment of Dabrafenib Plus Trametinib in Subjects With BRAF Mutation-Positive Melanoma That Has Metastasized to the Brain

Summary: This is a multi-cohort, open label, Phase II study with Dabrafenib (GSK2118436) and Trametinib (GSK1120212) combination therapy in subject with BRAF mutation-positive melanoma that has metastasized to the brain. This study will evaluate the safety and efficacy of 4 cohorts. Cohorts will consist of; V600 E, D, K, R mutations, metastases to the brain, symptomatic and asymptomatic, with or without prior local (brain) therapy, with or without prior local (brain) therapy, and range of ECOG scores from 0-2.


Eligibility: Inclusion Criteria:
  -  ECOG Performance Status range of 0-2
  -  Histologically confirmed cutaneous metastatic melanoma of V600 E, K, D or R.
  -  May be systemic naïve or received up to two previous systemic treatment regimens for metastatic melanoma.
  -  Must be able to undergo MRI and have at least one measurable intracranial lesion for which specific criteria have to be met.
  Exclusion Criteria:
  -  Prior treatment with any BRAF inhibitor or any mitogen-activated protein/extracellular signal-regulated kinase inhibitor.
  -  Anti-cancer therapy or investigational anti-cancer therapy or chemotherapy without delayed toxicity within treatment specific timeframe.
  -  Treatment with stereotactic radiosurgery or treatment with whole-brain radiation within treatment specific timeframe.
  -  Any presence of leptomeningeal disease or any parenchymal brain metastasis
  -  History of another malignancy, some exceptions may apply.
  -  A history or evidence of cardiovascular risk- specific criteria have to be met
  -  A history or current evidence/risk of retinal vein occlusion or retinal pigment epithelial detachment - specific criteria have to be met.

Relevance to patient case: definitely relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: An Observational Study of BRAF Inhibitors Effectiveness in Patients With Newly Diagnosed Metastatic Melanoma

Summary: This observational study will evaluate the effectiveness of BRAF inhibitors and current therapies in patients with newly diagnosed metastatic melanoma with or without BRAF V600 mutation. Patients will be treated per the locally approved therapeutic options in clinical practice. The observation period for each patient will be up to 24 months.


Eligibility: Inclusion Criteria:
  -  Adult patients, >/= 18 years of age at diagnosis
  -  Histologically confirmed new diagnosis of unresectable or metastatic melanoma
  -  Patients with tumor samples available for assessment of BRAF V600 mutation
  Exclusion Criteria:
  -  Prior systemic therapy for metastatic disease
  -  Participation in interventional clinical trials

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: A Phase II Study of Pegylated Interferon Alfa-2b for the Adjuvant Treatment of Melanoma Subjects in Russia (MK-4031-400)

Summary: This study will assess the safety of Pegylated Interferon Alfa-2b (PEG-IFN) as an adjuvant treatment for melanoma.


Eligibility: Inclusion Criteria:
  -  Competent to self-administer the subcutaneous injections of PEG-IFN
  -  Histologically documented involved regional lymph nodes of a primary cutaneous melanoma or unknown primary, meeting the study's staging criteria
  -  Had the primary melanoma completely resected with adequate surgical margins and undergone operation for positive regional lymph nodes within 84 days of study start
  -  Eastern Cooperative Oncology Group Performance Status (ECOG PS) score of 0 or 1
  -  Adequate hepatic, renal and bone marrow function as defined by study parameters obtained within 4 weeks prior to study start
  -  For a female subject who is of childbearing potential or male participant with female sexual partner who is of childbearing potential, agree to use acceptable methods of contraception for at least 2 weeks prior to study start and continue until at least 6 months after last dose of study medication, or longer if dictated by local regulations
  Exclusion Criteria:
  -  Mucous membrane melanoma or ocular melanoma
  -  Known hypersensitivity to the components of study drug (including acetaminophen), or its analogs
  -  Evidence of distant or non-regional lymph node metastases or in-transit metastases
  -  Disease that cannot be completely surgically resected
  -  Prior malignancy within the past 5 years other than surgically cured non-melanoma skin cancer or cervical carcinoma in situ
  -  Severe cardiovascular disease, i.e. arrhythmias, requiring chronic treatment, congestive heart failure or symptomatic ischemic heart disease
  -  Hepatic decompensation
  -  Thyroid dysfunction not responsive to therapy
  -  Uncontrolled diabetes mellitus
  -  Clinically active autoimmune disease
  -  Clinically active and/or uncontrolled infection, including active hepatitis
  -  Human immunodeficiency virus (HIV)
  -  History of neuropsychiatric disorder requiring hospitalization
  -  Actively abusing alcohol or drugs
  -  Pregnant, lactating, or of reproductive potential and not using an effective means of contraception
  -  Medical condition requiring chronic systemic corticosteroids
  -  Received any experimental therapy within 30 days prior to enrolling in this study
  -  Received any prior chemotherapy, immunotherapy, hormonal or radiation therapy for melanoma
  -  Previously received interferon-α for any reason
  -  Known serious hypersensitivity reaction to PEG-IFN or interferon alfa-2b

Relevance to patient case: not relevant