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

Clinical trial: Patients With Refractory, Metastatic Cancer Harboring KIT Mutation or Amplification to Investigate the Clinical Efficacy and Safety of Imatinib Therapy

Summary: KIT is a receptor tyrosine kinase that binds to stem-cell factor (SCF), activating a series of downstream effector pathways. KIT is an established therapeutic target in cancer with activating mutations of KIT, such as gastrointestinal stromal tumors (GIST), and significant benefit is achieved with various small molecule inhibitors of KIT such as imatinib mesylate. Moreover, there is increasing evidence implicating KIT mutations as tractable therapeutic targets in melanoma. Additional information is required to characterize the functional role of low-frequency mutations in KIT and to determine whether amplification of wild type KIT is a real driver that can be targeted therapeutically. Except GIST and melanoma, other solid cancers were reported to have KIT mutation even in low frequency. A molecular profiling of the tumors of patients referred to the phase I clinic at the M.D. Anderson Cancer Center showed KIT mutation in 7 patients in total of 431 patients (2%).
  Hence, the investigators planned this study to apply the molecularly targeted agent, imatinib to various types of cancers harboring KIT mutation or amplification.


Eligibility: Inclusion Criteria:
  1. age ≥ 20
  2. advanced, refractory cancer patients who failed standard of care (SOC)
  3. KIT aberration: defined as mutation in exons 9, 11, 13, 17 or 18, or nanostring CNV by quantitative PCR (greater than 3 copies) or subject with specific sensitivity (Z-score<-1) to imatinib by Avatar scan whose disease has progressed following standard therapy or that has not responded to standard therapy or for which there is no standard therapy
  4. ECOG performance status of 0~2
  5. measurable or evaluable lesion per RECIST 1.1 criteria
  6. adequate marrow, hepatic, renal and cardiac functions
  -  Serum aspartate transaminase (AST) and serum alanine transaminase (ALT) ≤ 2.5 x upper limit of normal (ULN), or AST and ALT ≤ 5 x ULN if liver function abnormalities are due to underlying malignancy
  -  Total serum bilirubin ≤ 1.5 x ULN
  -  Absolute neutrophil count(ANC) ≥ 1,500/uL
  -  Platelets ≥ 100,0000/uL
  -  Hemoglobin ≥ 9.0 g/dL
  7. provision of a signed written informed consent
  Exclusion Criteria:
  1. severe co-morbid illness and/or active infections
  2. pregnant or lactating women
  3. history of major surgery or radiotherapy within 4 weeks
  4. active CNS metastases not controllable with radiotherapy or corticosteroids (however, CNS metastases (except for leptomeningeal seeding) are allowed if controlled by gamma knife surgery or surgery or radiotherapy or steroid)
  5. known history of hypersensitivity to study drugs

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

Clinical trial: Videoscopic Ilioinguinal Lymphadenectomy for Melanoma

Summary: Groin lymph node dissection for melanoma patients is burdened by high post-operative morbidity, mainly related to wound. This is a prospective pilot trial investigated feasibility and postoperative outcomes of videoscopic ilioinguinal lymphadenectomy in patients with inguinal lymph node melanoma metastases.

Detailed description: Videoscopic ilioinguinal dissection is a two-stage procedure. Dissection is performed using an ultrasound dissector. The inguinal step is performed via three ports (one 3-5 cm above the apex of the femoral triangle, a second 5 cm medial to the adductors, and the third 5 cm lateral to the Sartorius muscle). After subcutaneous inflation, a formal inguinal lymph node (LN) dissection is performed, removing the contents of the femoral triangle, with incision and removal of the femoral fascia and proximal and distal ligation of the saphenous vein with vascular endostaplers and endoclips. The specimen is extracted using an endobag from the incision of SLNB, which is systematically removed, or through a small enlargement of the incision of the apex trocar for patients with clinically positive LNs. The iliac step starts with open insertion in the pro-peritoneal space of a Hasson trocar, followed by positioning of two additional trocars (5 and 10 mm respectively) just laterally of the umbilical pubic line. After creation of pneumo-pelvis, the iliac femoral vessels are identified, isolated and all the external iliac LNs removed. Afterwards, the obturator LNs are dissected off the obturator nerve. LNs are retrieved with an endobag or directly through the 10mm trocar after insertion of protective endotrocar. Two drains are positioned at the end of procedure in the obturator fossa and in the inguinal space, respectively. Intra-operative and early post-operative outcome (lenght of stay, complications, number of LNs) is recorded. Follow-up consists in detection of any recurrence, measurement of lymphedema of the leg and evaluation of quality of life

Eligibility: Inclusion Criteria:
  Melanoma patients without distant metastasis and either positive SLNB or clinically positive inguinal lymph nodes
  Exclusion Criteria:
  American Society of Anaesthesiologists (ASA) classification III-IV Severe chronic obstructive pulmonary disease (COPD) and other restrictive lung disease, Severe ischemic heart disease and chronic heart failure Previous cerebral abnormalities (aneurysm/arteriovenous malformations, ischemic/hemorrhagic stroke, primary or secondary tumors), History of deep vein thrombosis (DVT) Childbearing state Severe hip functional limitation Previous hip/knee arthroplasty. Previous surgery in the groin region (e.g., hernia repair, great saphenous vein surgery, iliac-femoral bypass) was considered a contraindication only for the iliac stage of lymphadenectomy.

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

Clinical trial: Impact of Duration Of Absolute Voice Rest on Voice Outcome After Phonomicrosurgery

Summary: Absolute voice rest is commonly prescribed after vocal fold surgery, also known as phonomicrosurgery, for benign vocal fold lesions. This is thought to decrease scarring of vocal folds, which could result in increasing tissue stiffness and limitations in optimal vocal outcome. Unfortunately there is no standardized protocol as to how long patients should rest their voice after phonomicrosurgery. To date, there are no studies in the literature directly comparing the impact of short-term and long-term voice rest on vocal fold healing and voice outcome after phonomicrosurgery.

Detailed description: The purpose of this study is to determine whether 3 days versus 7 days of absolute voice rest will result in different voice outcomes in patients who have undergone phonomicrosurgery for benign vocal fold lesions.

Eligibility: Inclusion Criteria:
  1. Patients with benign mid membranous vocal fold lesions such as the following:
  1. Polyps
  2. Cysts
  3. Sub-epithelial fibrous mass
  2. Undergoing elective phonomicrosurgery for vocal fold lesions, which involves microflap excision +/- truncation +/- steroid injection into the vocal folds.
  3. Age 18 and older
  Exclusion Criteria:
  Patients with any of the following will be excluded from the study:
  1. Reinke's edema
  2. Active smokers
  3. Ligamentous mid membranous vocal fold lesions
  4. RRP (Recurrent Respiratory Papillomatosis)
  5. Dysplasia
  6. CIS (Carcinoma-in-situ)
  7. SCC (squamous cell carcinoma)
  8. Extent of surgery exceeds what is mentioned in the inclusion criteria (e.g., CO2 laser, balloon dilatation, vocal fold augmentation in addition to phonomicrosurgery)
  9. Previous vocal fold surgery
  10. Systemic steroids
  11. History of systemic illness that could affect wound healing

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

Clinical trial: iMATRIXcobi: Safety and Pharmacokinetics of Cobimetinib in Pediatric and Young Adult Patients With Previously Treated Solid Tumors

Summary: This open-label, dose-escalation study is designed to evaluate the safety, tolerability, pharmacokinetics, and preliminary efficacy of cobimetinib in pediatric and young adult participants with solid tumors with known or potential kinase pathway activation for which standard therapy has proven to be ineffective or intolerable and for which no curative standard-of-care treatment options exist. The study will be conducted in two stages: a dose-escalation stage and an expansion stage at the recommended dose.


Eligibility: Inclusion Criteria:
  -  For dose-escalation stage: age at study entry to be greater than (>) 6 years to less than (<) 18 years and weighing >= 20 kilograms
  -  For expansion stage: age at study entry to be >6 years to <30 years
  -  Histologically or cytologically confirmed tumors for which prior treatment has proven to be ineffective or intolerable or for which no standard therapy exists
  -  Tumor with known or expected RAS/RAF/MEK/ERK pathway involvement. Diagnosis MUST be one of the following tumor types:
  Central nervous system gliomas, including high- and low-grade gliomas, and DIPG Embryonal rhabdomyosarcoma and other non-rhabdomyosarcoma soft tissue sarcomas Neuroblastoma Melanoma Malignant peripheral nerve sheath tumor Rhabdoid tumors, including ATRT NF1-associated tumor (including plexiform neurofibroma), schwannoma, or RASopathy-associated tumor that in the judgment of the investigator is life threatening, results in severe symptoms (including severe pain), or is in close proximity to vital structures;
  -  Measurable disease as defined by International Neuroblastoma Response Criteria, Response Assessment in Neuro-Oncology Criteria, Response Evaluation Criteria in Solid Tumors (RECIST) v1.1, or evaluable by nuclear medicine techniques, immunocytochemistry, tumor markers or other reliable measures
  -  Availability of tumor tissue at study enrollment
  -  Lansky performance status or Karnofsky performance status of at least 50 percent
  -  Life expectancy of at least 3 months
  -  Adequate hematologic, cardiac, and end-organ function
  -  Body weight must be greater than or equal to 20 kg
  Exclusion Criteria:
  -  Pregnant or lactating women
  -  Close proximity in time to treatment with high dose chemotherapy, differentiation therapy, immunotherapy, autologous stem cell transplant, radiotherapy, hormonal therapy, hematopoietic growth factor, or investigational therapy according to protocol-defined criteria prior to initiation of study drug
  -  Inability to swallow tablets
  -  Impaired gastrointestinal absorption
  -  History or evidence of retinal pathology according to protocol-defined criteria, including serous retinopathy

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

Clinical trial: Biomarkers for the Activity of Immune Checkpoint Inhibitor Therapy in Patients With Advanced Melanoma

Summary: 1. Screen and recruitment: patients will be screened based on their prior history and intention to initiate treatment with an immune checkpoint inhibitor.
  2. Study phase:
  -  Collection of baseline demographic data, prior disease history, nature of ICI therapy, outcome data of ICI therapy (treatment disposition, toxicity, tumor response and survival).
  -  Collection of blood samples will be performed every 3 to 4 weeks for the first year on ICI therapy and every 6 to 12 weeks thereafter until the end of ICI therapy, disease progression, death or loss to follow-up. Collection of blood samples will be aligned with the visits necessary for the administration of the ICI therapy.
  -  Collection of archival melanoma metastasis tissues will be performed on a continuous basis and be triggered by availability of such tissue following therapeutic resections of melanoma metastases.
  3. Follow-up phase

Detailed description: 1. Screen and recruitment: patients will be screened based on their prior history and intention to initiate treatment with an immune checkpoint inhibitor. This screening of candidate patients by the investigators will be non-interventional. Patients that are considered eligible candidates will be invited to participate in this study and to Page 3/18 provide written informed consent.
  2. Study phase:
  -  Collection of baseline demographic data, prior disease history, nature of ICI therapy, outcome data of ICI therapy (treatment disposition, toxicity, tumor response and survival).
  -  Collection of blood samples will be performed every 3 to 4 weeks for the first year on ICI therapy and every 6 to 12 weeks thereafter until the end of ICI therapy, disease progression, death or loss to follow-up. Collection of blood samples will be aligned with the visits necessary for the administration of the ICI therapy.
  -  Collection of archival melanoma metastasis tissues will be performed on a continuous basis and be triggered by availability of such tissue following therapeutic resections of melanoma metastases.
  3. Follow-up phase: patients who stop treatment with the immune checkpoint inhibitor will be followed-up for

Eligibility: Inclusion Criteria:
  1. Histologically confirmed malignant melanoma;
  2. AJCC Stage IIIC or IV melanoma with evaluable disease;
  3. Treatment with an immune checkpoint inhibitor;
  4. Willing and able to give written informed consent;
  5. Accessible for treatment and follow-up;
  Exclusion Criteria:
  -  non

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

Clinical trial: Analysis of Plasma for Diagnosis and Follow-up of Neurofibromatosis Type 1

Summary: The purpose of this study is to find blood plasma based biomarkers of disease progression in neurofibromatosis type 1 (NF1). NF1 is associated with the development of benign cutaneous tumors as well as a variety of malignancies. Analysis of plasma DNA and chemical composition may provide tools for diagnosis and follow-up of NF1. The hypothesis of the study is that NF1-associated tumor burden and malignant transformation of tumors can be detected in plasma. To test this hypothesis, Finnish patients with NF1 are recruited and blood sample is taken. Blood plasma is separated and analyzed chemically. DNA is then also extracted and quantified.

Detailed description: Neurofibromatosis type 1 (NF1) is a dominant hereditary multiorgan disease that causes both benign cutaneous neurofibromas and malignant tumors. Timely detection of malignant transformation in NF1 tumors is of great clinical importance. Also methods to easily monitor individual's overall tumor burden would be useful. Blood plasma is collected from NF1 patients and age- and gender-matched controls. The samples are stored at -80 C until analysis. Free circulating plasma DNA is extracted and quantified using commercial reagents. Also a previously described chemical detection method to observe overall changes in plasma composition is utilized. The analysis results are compared between NF1 patients and healthy controls, and also correlated with NF1 tumor burden and diagnosis of malignancy during five-year follow-up.

Eligibility: Inclusion Criteria:
  -  Finnish-speaking
  -  18-85 years old
  -  For NF1 group: Diagnosis of type 1 neurofibromatosis and visit to Turku Neurofibromatosis Centre
  -  For control group: Suitable as an age- and gender-matched control for some of the NF1 patients
  Exclusion Criteria:
  -  Non-Finnish-speaking
  -  For control group: diagnosis of neurofibromatosis type 1 or cancer

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

Clinical trial: Targeting the Mechanisms Underlying Cutaneous Neurofibroma Formation in NF1: A Clinical Translational Approach.

Summary: The purpose of the research study is intended to use specimens (such as tissue) and medical information in the Laboratory of Musculoskeletal Oncology at the Van Andel Research Institute for laboratory research in Grand Rapids, Michigan. Small tissue samples of cutaneous neurofibromas will be collected as part of this research. The samples will help researchers learn more about cutaneous neurofibroma and help them better understand NF1. There are many different types of studies, both now and in the future, that can be done using the specimens they receive. These include using the specimens and information to look for new ways to diagnose and treat Neurofibromatosis Type 1 (NF1). The specimens may be used to study how genes affect health and disease, or how genes affect the way a disease or condition responds to treatment. Some of these studies may lead to new products, such as treatments or tests for diseases. Through this study, we hope to find better ways to understand and treat NF1 in the future.

Detailed description: Skin tumors in Neurofibromatosis Type 1 (NF1) are very common and diminish quality of life. Apart from surgery, very few treatment options exist. In comparison to other types of tumors in NF1, skin tumors receive less attention in the research world because they almost never turn into cancer. Under the microscope, skin tumors and plexiform tumors look similar, however they do not share the same growth potential, nor do they appear at the same time during development. These differences suggest that skin tumors are driven by different factors than plexiform tumors.
  In this study we will be harvesting CNFs from 3 groups of subjects in order to obtain a minimum of 18 tumors in three size categories: <5mm, 5-10mm, and >1cm. These sizes were selected based on the variable natural history of CNF progression where incipient lesions (typically <5mm) are more numerous and demonstrate a less aggressive growth pattern, whereas the intermediate group (5-10mm) represent a transition state towards growth to larger (>1cm) lesions. Interestingly, CNF growth tends to stall out at 3cm. We plan to do experiments that identify which factors are important to CNF progression, and then find matching drugs that can shrink the tumors.

Eligibility: Inclusion Criteria:
  1. Any subject with an established diagnosis NF1 and CNFs. The diagnosis may be based on clinical criteria or genetic testing.
  2. Age >18 years.
  3. Specific Vulnerable Populations:Pregnant women and Adults with diminished decision-making capacity with defined legal guardian.
  Exclusion Criteria:
  1. Adults with diminished decision-making capacity with no defined legal guardian.
  2. Prisoners.
  3. Breastfeeding mothers.

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

Clinical trial: Deformable Registration of Multi-parametric MRI to Intra-operative Transrectal Ultrasound for Prostate Brachytherapy

Summary: Objective:
  To focus the high dose radiation to the gross tumor in the prostate while maintaining adequate dose for control of microscopic disease elsewhere in the prostate.
  In order to test the incorporation of the robust MRI and TRUS fusion algorithm in the clinical setting the investigators planned a study of Focused therapy with a primary endpoint of accurate localization of the high risk region. This is a pilot study of dose painted permanent I-125 seed implant to verify absence of tumor cells outside a high risk region using multi-parametric MRI and deformable TRUS registration. The high risk region will be dose painted to 160 Gy and the rest of the prostate will receive the normal prescription dose.

Detailed description: Primary end-point:
  Feasibility of dose painting will be determined by the absence of tumor outside the high-risk region on an intra-operative trans-perineal biopsy.
  Frozen sections will not be obtained, however on receipt of the final pathology 2-4 weeks after the procedure 2 possible scenarios arise:
  1. There is no evidence of cancer: this confirms the accuracy of the TRUS MRI registration.
  2. There is evidence of tumor on the stereotactic biopsy: In this case a regular dosimetric check (this is performed in the Standard of care procedure and is known as post-operative dosimetry) will be performed to determine whether adequate dose was delivered. If not, as the involved needle position was recorded in the treatment plan and labeled with co-ordinates, the regular possibility of accurately adding radioactive seeds is possible.

Eligibility: Inclusion Criteria:
  -  Men suitable for monotherapy with permanent Iodine 125 implant
  -  Age > 50 yrs
  -  PS 0-2 (WHO)
  -  Histologic diagnosis of prostate adenocarcinoma made on transrectal guided prostate biopsy with no fewer than 12 cores taken
  -  No more than 50% of cores involved (summary)
  -  MRI of Prostate with Diffusion Weighted Imaging and Dynamic Contrast Enhancement with demonstrable lesion compatible with biopsy result
  -  Gleason sum no greater than 3+4 =7 in any core
  -  Clinical T stage no higher than T T (tumor) 2A
  -  Prostate volume ≤60 cc
  -  Serum prostate-specific antigen (PSA) no higher than 15 ng/mL
  -  No prior history of malignancy except non-melanoma skin cancer
  -  Must be suitable for general or spinal anesthesia
  Exclusion Criteria:
  Have anesthesia surgical assignment category IV or greater
  -  Cannot cease anti-coagulant therapy
  -  Had a malignancy, other than prostate or skin cancer (except malignant melanoma), within 5 years
  -  urethral stricture
  -  Prior prostate cancer therapies

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

Clinical trial: Evaluation Interest of the Circulating Tumor DNA Dosage in Patient With Hepatic Metastatic Uveal Melanoma Candidate to Complete Resection (ct DNA R0)

Summary: Prospective, open labelled, monocentric trial to evaluation of the circulating tumor DNA rate in the blood, before and after curative resection of hepatic metastasis of uveal melanoma (HMUM) and during post-surgery follow-up

Detailed description: The ct DNA R0 study is a prospective, open labelled, monocentric trial. The aim is to evaluate the circulating tumor DNA rate in the blood, before and after curative resection of hepatic metastasis of uveal melanoma (HMUM) and during post-surgery follow-up.
  The patient will have a blood sample before and after the surgery and during the post-surgery follow-up. The patient will have a maximum of 10 blood samples during the 2 years of his follow-up of the study.

Eligibility: Inclusion Criteria:
  1. Aged 18 years old or more
  2. Patient with hepatic injury of metastatic uveal melanoma eligible for curative surgery (R0).
  3. No other distant metastasis (CT thoracic -abdomino -pelvic, bone scan).Measurable metastatic disease (echography, CT and/or MRI, FDG-PET, (fluoro- D-glucose integrated with computed tomography)).
  4. Patient able to stand a blood collection.
  5. Patient explanation given and consent information signed or by legal representative.
  Exclusion Criteria:
  6. Patient without social protection / insurance..
  7. Patient with hepatic metastasis unresectable by surgery
  8. Patient with extra-hepatic metastasis.
  9. Person deprived of liberty or under guardianship
  10. Inability to submit to medical monitoring of the trial for reasons of geography, social or psychological.

Relevance to patient case: not relevant