araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 34-year-old female with melanoma; genetic feature: NRAS (Q61L)

Clinical trial: Lavage of the Uterine Cavity for the Diagnosis of Ovarian and Tubal Carcinoma and Their Premalignant Changes.

Summary: Epithelial Ovarian cancer (EOC) is the leading cause of death among gynaecologic malignancies in western civilized countries, with an estimated prevalence in Europe and the US of 752,600 in 2007 and 59,828 deaths annually.
  State-of-the-art diagnostic tests for EOC include transvaginal ultrasonography and serum cancer antigen (CA-125) measurements; the specificity of these diagnostic tools however is low, and both tests are not effective enough at detecting EOC early enough to improve clinical outcomes. Definitive diagnosis of EOC still relies on histological or cytological confirmation. These findings underline the importance for an effective test for early detection of EOC.
  In the current project we will obtain a lavage of the uterine cavity. It will be investigated whether cells from EOCs or genetic material from those cells can be detected in the lavage fluid.
  Aim of this study:
  There is a clear clinical need for a diagnosis test to detect EOC at an earlier stage.

Detailed description: Epithelial Ovarian cancer is the leading cause of death among gynaecologic malignancies in western civilized countries, with an estimated prevalence in Europe and the US of 752,600 in 2007 and 59,828 deaths annually. Treatment and survival of the patients depend primarily on the stage of the disease. Of all EOC patients only 25% are diagnosed at an early stage while the tumour is confined to the pelvis. In these cases the five-year survival rate is 80% to 90% and the disease can often be cured by the combination of surgery and chemotherapy. Unfortunately, almost 75% of women affected have advanced stage disease with metastatic spread throughout the abdominal cavity or to retroperitoneal lymph nodes at the time of diagnosis; five-year survival rates drop to 10%-30% for advanced disease, despite maximum surgical effort and combination chemotherapy.
  State-of-the-art diagnostic tests for EOC include transvaginal ultrasonography and serum cancer antigen (CA-125) measurements; the specificity of these diagnostic tools however is low, and both tests are not effective enough at detecting EOC early enough to improve clinical outcomes. Definitive diagnosis of EOC still relies on histological or cytological confirmation. These findings underline the importance for an effective test for early detection of EOC.
  In the current project we will obtain a lavage of the uterine cavity. It will be investigated whether cells from EOCs or genetic material from those cells can be detected in the lavage fluid.
  Aim of this study:
  There is a clear clinical need for a diagnosis test to detect EOC at an earlier stage.

Eligibility: Inclusion Criteria:
  -  suspected ovarian cancer
  -  verified ovarian cancer
  Exclusion Criteria:
  -  pregnant
  -  incapacitated persons

Relevance to patient case: not relevant
Patient case: 34-year-old female with melanoma; genetic feature: NRAS (Q61L)

Clinical trial: Circulating Cell-free DNA in Metastatic Melanoma Patient: Mutational Analyses in Consecutive Measurement Before and After Chemotherapy

Summary: Therapies that target specific molecules markedly inhibit cancer growth in several malignancies, and provide valuable strategies for the treatment of advanced melanoma. In recent years, BRAF and KIT have become established therapeutic targets in melanoma patients showing activating mutations in these oncogenes. However, it is crucial that genetic mutations present in the melanoma lesions are identified if the investigators are to design tailormade therapies for individual patients. The tumour genotypes that determine the selection of molecular-targeted therapies are usually identified in primary tumours; however, primary tumours are not always representative of metastases. Circulating free DNA may be a source of valuable information because it can be obtained via routine blood sampling, it provides real-time information about a patient's current disease state, and it allows monitoring and molecular characterization before and after chemotherapy. The aim of the study is to determine the mutational status in circulating DNA in melanoma metastatic patients, with the Sequenom Mass Array, a next generation sequencing technology. Results obtained before and after treatment will be compared with the primary tumor genotype.


Eligibility: Inclusion Criteria:
  -  Age>18 years
  -  Surgical biopsy for histologic diagnostic
  -  All melanoma subtypes
  -  Known genotype BRAF V600
  -  Affiliation social security
  -  Consent form signed
  Exclusion Criteria:
  -  Patient with histories of cancer or the other synchronous cancer
  -  Pregnant women
  -  Breast-feeding women
  -  Vulnerable patients: major under guardianship; patient deprived of its rights

Relevance to patient case: not relevant
Patient case: 34-year-old female with melanoma; genetic feature: NRAS (Q61L)

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: 34-year-old female with melanoma; genetic feature: NRAS (Q61L)

Clinical trial: A Single-Arm, Open-Label, Multicenter Clinical Trial With Nivolumab (BMS-936558) for Subjects With Histologically Confirmed Stage III (Unresectable) or Stage IV Melanoma Progressing Post Prior Treatment Containing an Anti-CTLA4 Monoclonal Antibody (CheckMate 172)

Summary: The purpose of this study is to determine the rate and frequency of high-grade (CTCAE v4.0 Grade 3 or higher), treatment-related, select adverse events in subjects with histologically confirmed stage III (unresectable) or stage IV melanoma and progression post prior treatment containing an anti-Cytotoxic T Lymphocyte Antigen (CTLA-4) monoclonal antibody, treated with Nivolumab (BMS-936558) at a dose of 3 mg/kg every two weeks.


Eligibility: For more information regarding BMS clinical trial participation, please visit www.BMSStudyConnect.com
  Inclusion Criteria:
  -  Subjects with histologically confirmed malignant melanoma
  -  Eastern Cooperative Oncology Group (ECOG) Performance Status (PS):
  -  PS 0 to 1
  -  PS 2
  -  Previously treated unresectable stage III or stage IV melanoma as per the American Joint Committee on Cancer 2010 Guidelines regardless of BRAF mutation status
  -  Subjects must have experienced evaluable Response Evaluation Criteria In Solid Tumors (RECIST 1.1)-defined disease progression
  -  Prior treatment with chemotherapy, interferon (adjuvant setting), Interleukin (IL-2), BRAF/MEK inhibitors for subjects with known BRAF mutations, Mitogen-activated or extracellular signal- regulated protein kinase (MEK) inhibitors for Neuroblastoma Ras Viral (v-ras) oncogene homolog (NRAS) mutations, and cKIT inhibitor subjects with known cKIT mutations are allowed
  -  Patients with CNS metastases are eligible:
  -  if CNS metastases are treated, patients are asymptomatic or neurologically returned to baseline
  -  if they have previously untreated CNS metastases and are asymptomatic
  -  if they have leptomeningeal metastases, are treated and asymptomatic or neurologically returned to baseline with life expectancy > 3 months
  -  Patients with a known history of Grades 3-4 immune-related adverse reactions during/after anti-CTLA-4 therapy if all toxicities have resolved at least to Grade 1
  Exclusion Criteria:
  -  Subjects with untreated, active Central Nervous System (CNS) metastases are excluded

Relevance to patient case: not relevant
Patient case: 34-year-old female with melanoma; genetic feature: NRAS (Q61L)

Clinical trial: Study to Determine the Feasibility of Sentinel Node Biopsy in Patients With Anal Cancer

Summary: The purpose of this study is assess the technical and operational feasibility of a specialised biopsy technique, sentinel lymph node biopsy (SLNB), in patients with anal cancer.

Detailed description: SLNB is based on the premise that lymphatic dissemination from a tumour occurs in a stepwise fashion, with initial involvement of a primary node, called the sentinel node, before dissemination to the remainder of the lymphatic chain. If the sentinel node is histologically negative, then the remainder of the nodes in the same anatomic region will be at a lower (assumed to be minimal) risk of containing metastases. SLNB is part of standard care for patients with malignant melanoma and with breast cancer but has yet to be prospectively evaluated in patients with anal cancer.
  Currently, the standard way to treat patients with anal cancer is to deliver a combination of chemotherapy and radiation to the tumour at the anus together with 'preventative' (prophylactic) radiotherapy to the lymph glands of the groin and pelvis. There is a growing perception for the need to reduce the morbidity of radiotherapy i.e. current regimens over-treat the patient and one approach is to reduce radiotherapy volume and/or dose where there is an absence or very low risk of nodal metastases.
  This feasibility study is a vital first step in informing the design of a larger study examining the role of SLNB in clinical decision-making and outcomes for patients with anal cancer. In this trial eligible patients will attend for lymphoscintigraphy, to locate the lymph node, before sentinel lymph node removal by surgery. Detection rate of the sentinel node(s) will be the key outcome for the study.

Eligibility: Inclusion Criteria:
  -  Patients with squamous cell carcinoma (SCC) of the anus (any T size and/or those with recurrent disease)
  -  Equivocal lymph node involvement on standard CT staging or magnetic resonance (MR) staging or PET-CT scan, as determined by the anal cancer multidisciplinary team (MDT)
  -  Age >= 18 years
  -  Written informed consent provided by the patient
  Exclusion Criteria:
  -  Patients with unequivocal lymph node involvement on standard CT staging or MR staging, as determined by the anal cancer MDT.
  -  Unfit for surgical biopsy
  -  Patients undergoing palliative treatment
  -  Previous pelvic or inguinal area radiotherapy
  -  Other coincident cancers
  -  Previous inguinal surgery (e.g. hernia repair) with mesh insertion

Relevance to patient case: not relevant
Patient case: 34-year-old female with melanoma; genetic feature: NRAS (Q61L)

Clinical trial: The Oncopanel Pilot (TOP) Study

Summary: The BCCA Oncopanel is a clinical assay being developed to determine genotype status of a prospectively defined set of genes.
  The purpose of this pilot study is to assess the feasibility and effect on clinical-decision-making of the Oncopanel test. Eligible patients are those with advanced lung, colorectal, melanoma and GIST cancers and patients with diagnosed malignancies being considered for clinical trials.

Detailed description: Somatic mutations in solid tumors represent an established means of characterizing malignancies for prognostic, diagnostic and therapeutic purposes. Mutations in EGFR, KRAS, BRAF, and KIT and PDGFRA genes direct therapy in patients with advanced lung, colorectal, melanoma, and GIST tumors, respectively. Known or novel mutations in other genes may also be of clinical significance but are not identified by current genotyping offered to BC Cancer Agency (BCCA) patients. Furthermore, numerous candidate genes have been implicated as potential prognostic and predictive biomarkers in patients with solid tumours. As such, the Oncopanel is a clinical assay being developed to determine genotype status of a prospectively defined set of genes. The following clinically relevant set of genes and exons are included in the Oncpanel: KRAS, EGFR, BRAF, NRAS and HRAS, PIK3CA Signal Transduction Pathway Genes, RAS-RAF-MEK-MAPK Pathway, HER2, IDH1 and IDH2, ALK, TP53, c-KIT, STAT1&3 and PDGFRA. Additional testing on the tumour material will also include analysis of specific gene variants associated with adverse events or response to therapy.
  Numerous studies have documented the presence of circulating tumour DNA (ctDNA) among patients with advanced and early stage malignancies (20-22). The ability to diagnose standard cancer mutations with a blood-based assay (a "liquid biopsy") has not yet been established but presents obvious advantages. The emergence of "resistance" mutations arising in the metastatic tumor or throughout the course of therapy is well documented (21, 22). A blood biopsy may represent more accurate determination of the tumor's genetic features than archival DNA specimen. Adequate tissue specimens can be difficult to obtain from some patients with diagnosed malignancies, particularly lung cancer. A blood biopsy may represent a less invasive and timelier means of diagnosing both standard and translational cancer mutations.

Eligibility: Patients with archival tumor tissue and a known history of invasive malignancies are eligible if they meet one or more of the following criteria:
  -  Advanced colorectal cancer and eligible for standard KRAS testing,
  -  Advanced non-small cell lung cancer and eligible for standard EGFR testing,
  -  Advanced melanoma and eligible for standard BRAF testing,
  -  Gastrointestinal stromal tumors (GISTs) eligible for standard c-KIT and PDGFRA testing,
  -  Being considered for potential eligibility in clinical trial.

Relevance to patient case: not relevant
Patient case: 34-year-old female with melanoma; genetic feature: NRAS (Q61L)

Clinical trial: Pancreatic Cancer Early Detection Program

Summary: Early detection testing is recommended for individuals at elevated risk for the development of Pancreatic Cancer. This Protocol will define sufficiently elevated risk as either equal to or greater than five times the general population risk, or five times the average risk (1.5%) of developing pancreatic cancer by age 70; that is a 7.5% lifetime risk. Our inclusion criteria has a strong focus on the risk for pancreatic cancer imparted by the presence of hereditary cancer genes, as well as by family history. Enrolled subjects will undergo Endoscopic Ultrasound (EUS) alternating with Magnetic Resonance Imaging (MRI), every six to 12 months, for up to 5 years.

Detailed description: Interested individuals can be referred by physicians, or by family or friends.
  Individuals are informed that the purpose of this study is to collect outcome data following early detection testing based upon our criteria for elevated risk.
  Consent is obtained by any of the co-investigators. Consent is obtained for the primary PCEDP, and also obtained to allow for data to be used by our Cancer Program.
  We have a weekly review of all calls made and of all enrollments.
  We have a monthly meeting to review all proceeding regarding the study.
  Our IRB routinely reviews the proceedings of the study
  Our institution has a monthly Clinical research Committee meeting.

Eligibility: Inclusion Criteria: Any of the following:
  1. Known carrier of either the BRCA2 or CDKN2A mutation;
  2. Known carrier of any of the following mutations (BRCA1, MLH1, MSH2, PMS2, MSH6, EPCAM , P53, PALB2, APC, or ATM) PLUS first or second degree relative affected with pancreatic cancer;
  3. Individual with Peutz-Jeghers Syndrome;
  4. Familial Pancreatic Cancer, defined as at least two affected relatives with Pancreatic Cancer, who are first degree relatives with each other, and at least one of those affected must be first degree relative to the study subject;
  5. Both parents affected, any age:
  6. Any first degree relative diagnosed with pancreatic cancer under age 50;
  7. Chronic Pancreatitis Syndrome, defined by either PRSS1 or SPINK1 mutations AND appropriate clinical and family history
  Exclusion Criteria:
  1. Any medical condition that contraindicates endoscopy or biopsy
  2. Any medical condition that contraindicates MRI
  3. Status post partial or complete resection of the pancreas
  4. History of pancreatic cancer, either endocrine or exocrine
  5. Clinical suspicion of pancreatic cancer, or any previous radiographic or histologic diagnosis of a pre-malignant finding, including IPMN (Intraductal papillary mucinous neoplasm) and PanIN (Pancreatic intraepithelial Neoplasm).
  6. diagnosis of dementia
  7. Uncontrolled, current illness
  8. Renal insufficiency with serum creatinine greater than 2.0 mg/dl

Relevance to patient case: not relevant
Patient case: 34-year-old female with melanoma; genetic feature: NRAS (Q61L)

Clinical trial: Use of Exome Sequence Analysis and Circulating Tumour in Assessing Tumour Heterogeneity in BRAF Mutant Melanoma

Summary: Despite recent advances in cancer treatment, little impact has been made on curing as opposed to controlling cancers over the last several decades. Part of the problem is that investigators have an incomplete understanding of how tumours behave as they evolve and in response to treatment. In this trial, the investigators hope to better understand the evolution of BRAF melanoma in response to drugs a patient may have received such as vemurafenib or dabrafenib. Importantly, the investigators want to understand how the tumours evolve resistance to these drugs and whether this can be predicted through blood tests, in particular of the circulating tumour DNA.

Detailed description: Study population: BRAF mutant melanoma patients
  Pre-mortem bloods will be taken from the patient on three occasions at one to thirty days apart from each other, with the first blood draw taking place on the patient's first clinic visit. Six 7 ml EDTA and one 6 ml SST vacutainers of blood (a total of approx. 50 ml of blood) will be taken from the patient.
  When death is expected within the next 48-72 hours, the Medical Oncologist/ Radiation Oncologist/ Hematologist OR delegate will revisit the RAP process with the patient and/or family/substitute decision maker to ensure that they are still in agreement. The patient and the families will also be provided with an additional consent form for participation including blood sampling.

Eligibility: Inclusion Criteria:
  UHN adult patient with BRAF mutant melanoma
  Exclusion Criteria:
  Non BRAF mutant melanoma patient Pediatric patient Non-UHN patient

Relevance to patient case: not relevant
Patient case: 34-year-old female with melanoma; genetic feature: NRAS (Q61L)

Clinical trial: Pancreatic Cancer Screening of High-Risk Individuals in Arkansas

Summary: 100 subjects who have a family history of pancreatic cancer (PC), or known genetic syndromes associated with increased risk of pancreatic cancer, will be followed for five years. This data will be used to determine the pancreatic cancer and precancerous lesion detection rate in High Risk Individuals (HRIs). Subjects may agree to annual imaging and annual biomarkers or to biomarkers only.


Eligibility: Inclusion Criteria:
  -  Have a family history of PC as listed below or who have one of the following syndromes: Peutz-Jeghers syndrome - STK11; BRCA 1 and 2; PALB2; ATM; FAMMM / P16; HNPCC (Lynch) / MMR genes; Hereditary pancreatitis - PRSS1
  -  Individuals with three or more affected blood relatives (1st, 2nd or 3rd degree)
  -  Individuals with two or more affected blood relatives with PC, with at least one affected FDR, should be considered for screening.
  -  Patients with a history of Peutz-Jeghers syndrome should be screened, regardless of family history of PC.
  -  Patients with a known p16 (FAMMM syndrome) with one affected 1st or 2nd degree relative will be considered for screening.
  -  Patients with a known BRCA1 or BRCA2 mutation with one affected 1st or 2nd degree relative should be considered for screening.
  -  Patients with a known PALB2 mutation with one affected family member should be considered for screening.
  -  Patients with a known Mismatch-repair gene-mutation carriers (Lynch syndrome) with one affected family member should be considered for screening.
  Exclusion Criteria:
  -  Not candidates for surgery

Relevance to patient case: not relevant
Patient case: 34-year-old female with melanoma; genetic feature: NRAS (Q61L)

Clinical trial: Automatic Early Melanoma Detection by Ultrahigh Resolution Three Dimensional Optical Coherence Tomography

Summary: The investigators will use optical coherence tomography to detect the ex-vivo tissue image of surgical removed melanoma or other benign pigmented lesions of skin.

Detailed description: The investigators will use an advanced high resolution 3D optical coherence tomography (OCT) technology to observe skin tissue images in ex vivo culture. Parts of melanoma or benign pigmented lesions specimens derived from biopsy or surgical excision specimen will be observed by 3D optical tomography. A tiny tissue fragment of melanoma or benign pigmented lesions will be taken from surgical specimen without interference normal pathological evaluation. The location of melanocytic cells in melanoma or benign tissue fragments will be mapped by the 3D optical coherence tomography (OCT). The 3D optic tomography system utilize a Ce:YAG optical fiber as light source and also combined with confocal microscopy. Taken together, these features made the 3D optic tomography system have very high resolution and suitable for single cell imaging. This study will not interfere with the normal medical practice and had no impact on patient's safety and health. All of the materials will be destroyed once the experiments are done. The enrollment criteria will be dermatological patients who need to surgical intervention.

Eligibility: Inclusion Criteria:
  -  Patients aged older than 20 years old
  -  Patients who had melanoma, melanoma in situ, and/or other benign pigmented lesions,
  -  Patients who had non-melanoma skin cancers (basal cell carcinoma, or squamous cell carcinoma).
  -  Patients who had precancerous skin lesions (Bowen's disease, actinicc keratosis)
  Exclusion Criteria:
  • Pregnant women.

Relevance to patient case: not relevant