araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

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: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

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: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

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: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Prospective Observational Study of 1st and 2nd Line Vectibix® Use in RAS-wt mCRC Pts to Evaluate Pattern of Use and ORR

Summary: The study will shed additional light on the impact of Vectibix® under the current, standard clinical conditions of mCRC treatment in Greece. It will provide data on the duration and the outcomes of Vectibix® treatment in real-life setting.

Detailed description: This is a single-arm, multi-center, prospective, observational, descriptive, noninterventional study in patients with mCRC in Greece who receive Vectibix®in 1st or 2nd line according to approved indication. The aim of the study is to obtain a clear understanding of the current practices concerning real-life treatment of mCRC patients with Vectibix® in first-line in combination with chemotherapy or second-line in combination with chemotherapy in Greece. This setting will also provide the opportunity to observe in a non-selected patient population with RAS WT mCRC the real-life habits of mCRC treatment, and in particular the duration and the outcomes of Vectibix® treatment. The data generated by this study may be used for reimbursement purposes, as it becomes an increasingly common need in Greece to provide locally generated data for use of drugs in the real-life setting to regulatory agencies and/or payors. Furthermore, this study could address the existing data gap in the treatment of anti-EGFR therapy beyond progression in the real-life setting.
  Primary Objective(s): To describe the pattern of use of Vectibix® in combination with chemotherapy in 1st line or in 2nd line mCRC treatments as per approved Vectibix® indication.
  Secondary Objective(s): To investigate the rate of objective response (ORR, defined as either a Complete Response or a Partial Response) and the rate of stable disease as best response in 1st line or in 2nd line chemotherapy regimens of mCRC including Vectibix®.

Eligibility: Inclusion Criteria:
  -  Adult patient (age ≥18 years) at enrollment
  -  Histological documentation of mCRC diagnosis
  -  RAS WT tumor documented before study enrolment as per routine laboratory finding
  -  Subjects whose care will be managed primarily by the enrolling physician and/or all records will be available
  -  Measurable disease at baseline (preferably according to the Response Evaluation Criteria in Solid Tumors version 1.1 (RECIST v1.1) if routinely used)
  -  Currently under (begin up to 8 weeks before informed consent) a 1st or 2nd line treatment regimen, including Vectibix® as per indication
  -  Tumor assessment (i.e. CT/MRI) within 16 weeks prior to first Vectibix® infusion
  -  Signed informed consent
  Exclusion Criteria:
  -  Participation in any interventional clinical study (currently or during the three previous months from enrollment).
  -  Compromised ability to give informed consent (defined per clinical judgment).
  -  Unknown or mutant RAS tumor type

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

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
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Quality of Life and Surgical Late Effects of Melanoma Treatment

Summary: Health-related Quality of life in Danish stage IB-III cutaneous melanoma patients.

Detailed description: The aim of the PhD-study is to evaluate, in a large cohort of Danish melanoma patients:
  1. Health-related quality of life assessing psychological, physical and social well-being
  2. Physical long term side effects (lymphoedema, scarring and neuropathic pain)
  3. Lymphoedema assessed by clinical examination and DXA scans

Eligibility: Inclusion Criteria:
  -  AJCC stage IB-III cutaneous melanoma patients
  -  At least one year follow-up after melanoma surgery
  Exclusion Criteria:
  -  Pregnancy
  -  Bilateral axilla or groin melanoma surgery

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

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
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Treatment After Irinotecan-based Frontline Therapy: Maintenance With Erbitux (in Patients wtRAS mCRC)

Summary: National multicentric phase II trial evaluating whether single agent cetuximab is effective as maintenance therapy after 8 cycles of first line FOLFIRI plus cetuximab in mCRC patients with KRAS and NRAS wild-type genes, assessed by progression-free survival at 6 months after start of maintenance therapy.


Eligibility: Inclusion Criteria:
  1. Histologically confirmed colorectal cancer
  2. KRAS and NRAS wild-type genes after analysis of mutation status from the primary tumour or metastasis
  3. Non resectable metastatic disease in a curative intent
  4. No prior chemotherapy except for fluoropyrimidines with or without oxaliplatin-based adjuvant treatment, at least 6 months before inclusion
  5. At least one measurable tumour target (higher than 20 mm) according to RECIST criteria, which has never been irradiated
  6. Life expectancy above 3 months
  7. Performance Status ≤2 (WHO)
  8. Patient ≥18 years-old
  9. Acceptable blood test
  10. Patient having signed a written informed consent form
  Exclusion Criteria:
  1. Known and/or symptomatic brain metastases
  2. Known allergy to one of treatment components
  3. Neurological or psychiatric condition which could interfere with good treatment compliance
  4. Current anti-tumour treatment : chemotherapy or targeted therapy or radiotherapy ≤ 14 days before randomisation
  5. Other severe conditions such as: respiratory failure. History of interstitial lung disease e.g. pneumonitis or pulmonary fibrosis or evidence of interstitial lung disease on baseline chest CT scan
  6. Clinically significant cardiovascular disease (including myocardial infarction, unstable angina, symptomatic congestive heart failure, serious uncontrolled cardiac arrhythmia) 6 months before enrollment/randomization
  7. Concomitant severe infection
  8. History of cancer (except skin cancer other than melanoma or an in situ cervical epithelioma or other solid tumour treated for curative purposes without signs of the condition and with no treatment administered in the 5 years before randomisation.)
  9. Patient already included in another clinical trial with an investigational molecule
  10. Prior treatment with anti-EGFr antibodies (e.g. panitumumab (Vectibix® or cetuximab / Erbitux® ) or treatment with small EGFr inhibitor molecules (e.g., erlotinib / Tarceva®)
  11. Pregnant female, likely to be or currently breastfeeding, or planning to become pregnant within 6 months after the end of treatment or absence of effective contraception for males and females of childbearing age during treatment and for 6 months (male or female) after the end of treatment
  12. Those deprived of their freedom or under guardianship
  13. Impossibility of undergoing trial's medical follow-up for geographical, social or psychological reasons

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Sym004 in Combination With FOLFIRI in Metastatic Colorectal Cancer Patients

Summary: This is a Phase 1b/2a study investigating the safety and efficacy of Sym004, an investigational medicinal product (IMP), in combination with FOLFIRI (chemotherapy) when administered every second week (Q2W).

Detailed description: In the Phase 1b (Dose-Escalation) portion of the trial, patients will be sequentially enrolled to dose-escalation cohorts until establishment of the Maximum Tolerated Dose (MTD) and/or Recommended Phase 2 Dose (RP2D) of Sym004 in combination with FOLFIRI.
  The Phase 2a (Dose-Expansion) portion of the trial is expected to begin after establishing the RP2D.
  Note: In January 2017, the trial was terminated during Phase 1b and enrollment was prematurely discontinued. The primary objective changed to assess the safety of the treatment combination; collection of data for secondary and exploratory objectives was omitted.

Eligibility: Main inclusion Criteria:
  1. Male or female, at least 18 years of age at the time of informed consent
  2. Eastern Cooperative Oncology Group (ECOG) performance status (PS) of 0 or 1
  3. Histologically or cytologically confirmed, locally advanced or metastatic colorectal cancer (CRC) that is documented to be without Kirsten rat sarcoma (KRAS) or neuroblastoma rat sarcoma (NRAS) gene mutations (i.e., tumors must express the KRAS and NRAS wild type [WT], exon 2, 3 and 4).
  4. Failed (defined as radiologic progression) treatment for locally advanced or metastatic disease with first-line combination therapy of oxaliplatin and a fluoropyrimidine, with or without bevacizumab, during treatment or < 3 months after the last dose of first-line therapy and within < 3 months of C1/D1. Patients who discontinued first-line therapy due to toxicity may be enrolled provided progression occurred < 6 months after the last dose of the first-line therapy regimen.
  or Failed (defined as radiologic progression) adjuvant therapy with combination therapy of oxaliplatin and a fluoropyrimidine during treatment or within < 6 months after the last dose of oxaliplatin and within < 6 months of C1/D1.
  5. Eligible for FOLFIRI
  6. Measurable disease according to RECIST v1.1
  Main exclusion Criteria:
  1. Prior therapy with anti-EGFR antibodies, anti-EGFR small molecule inhibitors or irinotecan (CPT-11)
  2. Any antineoplastic agent (standard or investigational) within 4 weeks prior to C1/D1
  3. Significant gastrointestinal abnormalities
  4. Patients with a significant cardiovascular disease or condition
  5. Abnormal hematologic, renal or hepatic function

Relevance to patient case: not relevant