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

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: 63-year-old female with melanoma; genetic feature: NRAS (Q61R)

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

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: 63-year-old female with melanoma; genetic feature: NRAS (Q61R)

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

Clinical trial: Moletest Clinical Study in Scotland

Summary: To evaluate an iPad based photoimage analysis system (Moletest) for improving discrimination of benign from malignant suspicious skin lesions or moles. Specifically the objective is to demonstrate that the Moletest system is able with a sufficient degree of confidence (95%) to identify lesions which are benign


Eligibility: Inclusion Criteria:
  All patients referred to the Dermatology Department, Lanarkshire Hospitals during a period to be defined for assessment of suspicious skin lesions (cutaneous moles) will be eligible for inclusion in the study. There are no age limits but patients under the age of 18 years will also have their inclusion subject to parental/guardian consent
  Exclusion Criteria:
  There is no exclsion criteria

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

Clinical trial: FDG-PET in Advanced Melanoma

Summary: This clinical trial studies how well FDG-PET/CT measures early response in patients with stage III-IV melanoma who are receiving chemotherapy. Positron emission tomography (PET)/computed tomography (CT) uses a metabolic imaging radiotracer, [18F]fluorodeoxyglucose (FDG), which selectively accumulates in tumors. FDG-PET/CT of advanced melanoma before, during, and after treatment may improve methods for predicting which patients may benefit from therapy.

Detailed description: PRIMARY OBJECTIVES:
  I. To correlate treatment-induced changes in FDG uptake with changes in tumor size and progression-free survival (PFS) in patients receiving therapy for advanced melanoma.
  II. To correlate treatment-induced changes in FDG uptake with changes in the activity and/or expression of available molecular biomarkers from patients receiving therapy for advanced melanoma.
  OUTLINE:
  Patients undergo FDG-PET/CT up to 2 weeks prior to first dose of therapy, after completion of the first treatment course (day 21), and after completion of the fourth treatment course (day 84).

Eligibility: Inclusion Criteria:
  -  Subjects must have signed Institutional Review Board (IRB)-approved informed consent documentation
  -  Subjects must be diagnosed with histologically proven stage IV (metastatic) melanoma or stage III with bulky disease which may or may not be amenable for surgery and are receiving therapy at present
  -  Subjects must be scheduled to begin treatment through the Vanderbilt-Ingram Cancer Center (VICC) Melanoma Program; this will include patients receiving standard-of-care chemotherapy, targeted therapy, and/or immunotherapy, as well as patients accrued to VICC clinical trials for the study of investigational agents
  -  Subjects must have measurable disease by CT or magnetic resonance imaging (MRI) per Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 criteria; to comply with PET Response Criteria in Solid Tumors (PERCIST) criteria, subjects should have at least one lesion measuring at least 2 cm in the longest diameter
  Exclusion Criteria:
  -  Subjects who are pregnant or nursing; urine pregnancy test/or serum human chorionic gonadotropin (HCG) will be performed on women of child bearing potential
  -  Subjects who have experienced allergic or other adverse reactions in response to intravenous injection of fluorinated radiotracers and other contrast media used in PET/CT
  -  Subjects incapable of giving informed written consent, for the following reasons:
  -  Inability to adhere to the experimental protocols for any reason
  -  Inability to communicate with the research team
  -  Limited ability to give informed consent due to mental disability, altered mental status, confusion, or psychiatric disorders
  -  Prisoners or other individuals deemed to be susceptible to coercion

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

Clinical trial: Mohs and Immunofluorescence for Malignant Melanoma In Situ

Summary: The purpose of this study is to determine if immunofluorescence (IF) can effectively identify features of malignant melanoma in situ, on sun-damaged skin, in the setting of Mohs Micrographic Surgery.

Detailed description: The aim of this study is to
  1. Determine the feasibility of using melanocytic markers such as Melanoma antigen recognized by T cells 1 (MART-1) with fluorescence to clear surgical margins when compared to conventional MART-1 immunohistochemistry (IHC) in the setting of MMS for LM (lentigo maligna type melanoma in situ).
  2. Compare the use of a cocktail of immunofluorescent markers such as, but not limited to, Sex-determining Region Y (SRY)-box 10 (SOX10), human melanoma black 45 (HMB-45), and Kiel-67 (Ki-67) to sections only stained with fluorescent MART-1 alone.
  3. Explore the value of using other combinations of immunofluorescent markers such as S-100 with Microphthalmia-associated transcription factor (MiTF), Nestin with Ki-67, and HMB-45 with Lamin.

Eligibility: Inclusion Criteria:
  1. Male or female of any race and at least 18 years of age
  2. Patient with biopsied proven Lentigo maligna (LM) in situ
  3. Patient meets criteria for Mohs Micrographic Surgery (MMS)
  1. The cancer is large
  2. The edges of the cancer (clinical margins) cannot be clearly defined
  3. Prior treatment has failed, i.e. recurrent tumor
  4. The cancer is located in a cosmetically sensitive or functionally critical area of the body (such as eyelids, nose, ears, lips, fingers, toes, and genitals)
  5. The histologic pattern of the cancer is aggressive
  6. The patient is immunosuppressed
  4. Patient with biopsied proven LM in situ located on an anatomic areas appropriate for MMS:
  1. Area H: ''Mask areas'' of face (central face, eyelids [including inner/outer canthi], eyebrows, nose, lips [cutaneous/mucosal/vermillion], chin, ear and periauricular skin/sulci, temple), genitalia (including perineal and perianal), hands, feet, nail units, ankles, and nipples/areola.
  2. Area M: Cheeks, forehead, scalp, neck, jawline, pretibial surface.
  3. Area L: Trunk and extremities (excluding pretibial surface, hands, feet, nail units, and ankles).
  5. Patient able to tolerate surgery
  6. Patient is able to comply with appointments including follow-up appointments
  7. Ability to understand and willingness to sign a written informed consent document
  Exclusion Criteria:
  1. Patients under the age of 18
  2. Patient does not meet criteria for MMS or has LM located in areas that are not accessible with MMS
  3. Patient with previously diagnosed invasive LM
  4. Patients unable to comply with follow-up
  5. Adults unable to consent
  6. Pregnant women
  7. Prisoners

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

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: 63-year-old female with melanoma; genetic feature: NRAS (Q61R)

Clinical trial: A Trial of Trametinib and Panitumumab in RAS/RAF Wild Type Advanced Colorectal Cancer

Summary: This is a phase 2 study (the second phase in testing a new drug or drug combination) to see how useful the combination of two drugs, panitumumab and trametinib, are in patients with advanced colorectal cancer with KRAS, NRAS, or BRAF wild type (genes that are not mutated).
  Panitumumab is a drug that is approved by Health Canada for the treatment of advanced colorectal cancer with KRAS wild type. Panitumumab works by binding to and blocking the protein, epidermal growth factor receptor (EGFR) from working.
  Trametinib is a drug that is approved by Health Canada for the treatment of melanoma with a mutation in the BRAF gene. Trametinib works by binding to and blocking mitogen-activated protein kinase kinase (MEK) 1 and MEK2 from working.
  Previous studies have shown that the combination of panitumumab and trametinib may be more useful in KRAS, NRAS, or BRAF wild type colorectal cancer.


Eligibility: Inclusion Criteria:
  -  18 years of age or older
  -  KRAS/NRAS/BRAF wild type colorectal cancer, not responsive to standard therapies, no approved or curative therapy, refuse standard therapy
  -  Prior 5-FU, oxaliplatin and irinotecan
  -  ECOG Performance Status of 0 or 1
  -  Able to swallow/retain oral drugs
  -  Able and agree to have provide tumor tissue/have biopsies
  -  Agree to use contraception
  -  Not pregnant
  -  Adequate organ system function
  Exclusion Criteria:
  -  Chemotherapy, radiotherapy, immunotherapy, or other anti-cancer therapies <28 days or 5 half lives
  -  Prior EGFR, MEK, or RAF inhibitor or regorafenib
  -  Current use of prohibited medications
  -  Unresolved side effects
  -  GI disease or other condition affecting GI absorption
  -  Mucosal or internal bleeding
  -  Any major surgery <four weeks
  -  HIV, HBV, or HCV positive
  -  Active infection
  -  Leptomeningeal disease
  -  Brain metastases
  -  Unacceptable QTcF interval
  -  Significant uncontrolled arrhythmias
  -  Acute coronary syndromes, myocardial infarction, coronary angioplasty, or stenting or bypass grafting < 6 mos.
  -  Class II, III, or IV heart failure
  -  Other clinically significant ECGs
  -  Intra - cardiac defibrillators
  -  Cardiac metastases
  -  Condition that may interfere with patient safety
  -  Hypersensitivity to study drugs
  -  Severe or uncontrolled systemic diseases
  -  Pregnant or lactating
  -  Retinal vein occlusion
  -  Interstitial lung disease or pneumonitis
  -  Active liver or biliary disease

Relevance to patient case: not relevant