araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Phase I/Ib Study of NIS793 in Combination With PDR001 in Patients With Advanced Malignancies.

Summary: To characterize the safety and tolerability of NIS793 as single agent and in combination with PDR001 and to identify recommended doses for future studies.


Eligibility: Inclusion Criteria:
  1. Written informed consent must be obtained prior to any screening procedures.
  2. Patient (male or female) ≥ 18 years of age.
  3. Escalation: Patients with advanced/metastatic solid tumors, with measurable or non-measurable disease as determined by RECIST version 1.1 who have progressed despite standard therapy or are intolerant of standard therapy, or for whom no standard therapy exists.
  4. Expansion: Patients with advanced/metastatic solid tumors, with at least one measurable lesion as determined by RECIST version 1.1, who have progressed despite standard therapy following their last prior therapy or are intolerant to standard therapy and fit into one of the following groups: Group 1: NSCLC; Group 2: TNBC; Group 3: HCC; Group 4: MSS-CRC; Group 5: pancreatic, prostate and ccRCC.
  5. ECOG Performance Status ≤ 2.
  6. Patients must have a site of disease amenable to biopsy, and be a candidate for tumor biopsy. Patient must be willing to undergo a new tumor biopsy at screening, and during therapy on this study. Exceptions may be made on a case by case basis after documented discussion with Novartis.
  Exclusion Criteria:
  1. History of severe hypersensitivity reactions to study treatment ingredients or other monoclonal antibodies and components of study drug.
  2. Patients with active, known or suspected autoimmune disease. Note: Patients with vitiligo, type I diabetes mellitus, residual hypothyroidism only requiring hormone replacement, psoriasis not requiring systemic treatment, or conditions not expected to recur in the absence of an external trigger are permitted to enroll.
  3. HIV infection.
  4. Active HBV or HCV infection.
  Other protocol-defined inclusion/exclusion criteria may apply.

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Elevated LDH Serum Levels and FDG-PET in Metastatic Melanoma Patients

Summary: A retrospective study investigating the relationship between FDG-PET uptake and LDH levels.

Detailed description: Patient characteristics, tumour characteristics including the BRAF mutation status and baseline serum S100B and LDH levels of each patient will be retrospectively determined from the electronical patient file. In each patient, tumour burden and 18F-FDG uptake of the tumour lesions will be measured using multiple standard quantification parameters of the baseline 18F-FDG-PET scan. Tumour burden will also be measured on the baseline contrast enhanced CT scan. The correlation of each FDG-PET parameter with baseline LDH and S100B levels, respectively, will be analyzed using univariate and multivariate regression analysis.

Eligibility: Inclusion Criteria:
  - All patients >18 years with histologically proven metastatic melanoma (American Joint Committee on Cancer [AJCC] stage IV melanoma) treated in the UMCG between May 2014 and December 2015.
  Exclusion Criteria:
  -  participation in interventional studies
  -  missing baseline 18F-FDG PET scan and/or baseline contrast enhanced CT scan
  -  missing baseline serum LDH level
  -  missing BRAF mutation status, concurrent malignancies or a history of previous malignancies.

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Trial of Hu5F9-G4 in Combination With Cetuximab in Patients With Solid Tumors and Advanced Colorectal Cancer

Summary: This trial will evaluate Hu5F9-G4 in combination with cetuximab. Hu5F9-G4 is a monoclonal antibody which is designed to block a protein called CD47, which is widely expressed on human cancer cells. Blocking CD47 with Hu5F9-G4 may enable the body's immune system to find and destroy the cancer cells. Cetuximab is a monoclonal antibody drug that is used for treatment of certain types of colorectal cancer as well as head and neck cancer.
  The major aims of the study are: (Phase 1b) to define the safety profile and to determine a recommended Phase 2 dose for Hu5F9-G4 in combination with cetuximab, and (Phase 2) to evaluate the objective response rate of Hu5F9-G4 in combination with cetuximab in patients with advanced colorectal cancer.


Eligibility: Inclusion Criteria:
  -  Histological Diagnosis
  -  Phase 1b only: Advanced solid malignancy with an emphasis on colorectal, head and neck, breast, pancreatic and ovarian cancers who have been treated with at least one regimen of prior systemic therapy, or who refuse systemic therapy, and for which there is no curative therapy available.
  -  Phase 2:
  -  KRAS Mutant CRC: Advanced KRAS mutant CRC who have progressed or are ineligible for both irinotecan and oxaliplatin based chemotherapy
  -  KRAS Wild Type CRC: Advanced KRAS wild type CRC who have progressed or are ineligible for both irinotecan and oxaliplatin based chemotherapy and who are relapsed or refractory to at least 1 prior systemic therapy that included an anti-EGFR antibody, such as cetuximab, panitumumab or others.
  -  Adequate performance status and hematological, liver, and kidney function
  -  Phase 2 only: Willing to consent to 1 mandatory pre-treatment and 1 on-treatment tumor biopsy
  Exclusion Criteria:
  -  Active brain metastases
  -  Prior treatment with CD47 or signal regulatory protein alpha (SIRPα) targeting agents.
  -  Phase 2 only: second malignancy within the last 3 years.
  -  Known active or chronic hepatitis B or C infection or HIV
  -  Pregnancy or active breastfeeding

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: BRCA 1/2 Mutation in Korean Patients With Epithelial Ovarian Cancer

Summary: PURPOSE: To investigate the prevalence and clinical correlation of the germline BRCA 1/2 mutation in Korean patients with high grade(HG) serous and/or endometrioid epithelial ovarian cancer (EOC).
  PATIENTS AND METHODS: In a nationwide case-control study on EOC conducted in Korea between 2010 and 2015, 298 Korean women with HG serous and/or endometrioid EOC were tested for gBRCA 1/2 mutation, regardless of the family history. Mutation screening was performed using the Ion AmpliSeq BRCA 1/2 Panel (Life Technologies, Carlsbad, CA, USA) and Ion PGM platform according to the manufacturer's instructions. Clinical characteristics including survival outcome was assessed in gBRCAm carriers.


Eligibility: Inclusion Criteria:
  -  women 18 years of age and older with previously untreated, HG serous and/or endometrioid EOC, fallopian tube or primary peritoneal carcinoma who consented to genetic testing between 2010 and 2015
  Exclusion Criteria:
  -  women with mucinous , clear cell, low-grade serous or endometrioid, mixed epithelial adenocarcinoma, undiffereniated carcinoma or malignant brenner's tumor

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: A Study of PLX3397 in Patients With Unresectable or Metastatic KIT-mutated Melanoma

Summary: The purpose of this Phase I/II study is to evaluate safety, pharmacokinetics, and preliminary efficacy of the investigational drug PLX3397 in subjects with unresectable or metastatic KIT-mutated melanoma.


Eligibility: Inclusion Criteria:
  -  Age ≥ 18 years
  -  Unresectable stage III or stage IV melanoma which is histologically confirmed at the treating institution with KIT mutation(s) not known to be resistant to PLX3397
  -  Presence of measurable lesions by Response Evaluation Criteria in Solid Tumors
  -  Eastern Cooperative Oncology Group (ECOG) performance Status (PS) 0-2
  -  Life expectancy ≥ 3 months
  -  Adequate organ and bone marrow function
  -  Women of child-bearing potential must have a negative serum pregnancy test at Screening and must agree to use an effective form of contraception from the time of the negative pregnancy test up to 3 months after the last dose of study drug. Women of non-child-bearing potential must have been postmenopausal for ≥ 1 year or surgically sterile.
  -  Fertile men must agree to use an effective method of birth control during the study and for up to 3 months after the last dose of study drug.
  -  Willingness and ability to provide written informed consent prior to any study-related procedures and to comply with all study requirements
  Exclusion Criteria:
  -  Prior treatment with a KIT inhibitor for melanoma
  -  Presence of NRAS or BRAF mutation
  -  Exposure to any investigational drug within 28 days or unresolved adverse effects from previous therapy
  -  Symptomatic brain metastases.
  -  Active secondary malignancy unless the malignancy is not expected to interfere with the evaluation of safety and is approved by the Sponsor
  -  Concomitant treatment with other anti-neoplastic agents (hormonal therapy acceptable)
  -  Uncontrolled intercurrent or infectious illness
  -  Major surgical procedure or significant traumatic injury within 14 days of initiating study drug or anticipation of the need for major surgery during the study
  -  Previous radiotherapy to 25% or more of the bone marrow and/or radiation therapy within 28 days prior to study entry
  -  Inability to swallow capsules, or refractory nausea and vomiting, malabsorption, an external biliary shunt, or significant bowel resection that would preclude adequate absorption
  -  Congestive heart failure (CHF) New York (NY) Heart Association class III or IV; unstable coronary artery disease (myocardial infarction [MI] more than 6 months prior to study entry is permitted); or serious cardiac arrhythmia
  -  Baseline QTcF ≥ 450 msec (for males) or ≥ 470 msec (for females) at Screening
  -  Active or chronic infection with human immunodeficiency virus (HIV), hepatitis C virus (HCV), or hepatitis B virus (HBV)
  -  Known chronic liver disease
  -  Women who are breast-feeding or pregnant

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Imaging Multiparametric/Multimodality for Lungcancer

Summary: 1. To build an imaging biobank of 200 patients with lungcancer, including pathologic and molecular characteristics of the tumor (mutational status, circulating DeoxyriboNucleic Acid (DNA) from serum biobank…), staging of the cancer (according to the new 2016 Tumor Node Metastasis (TNM) status, the table that classify non-small cell lungcancer) and follow-up informations (Response to first-line treatment (Response Evaluation Criteria in Solid Tumors (RECIST)), disease-free survival, 1-3 years survival).
  2. To propose a simple severity scoring system based on tumor features such as size, doubling time (if available), location, amount of enhancement and necrosis. Such approach has been proposed for glioma evaluation (Visually Accessible Rembrandt Images (VASARI)) but is not available for the lung. The objective is to do better than the Tumor Node Metastasis (TNM) staging.
  3. To develop and evaluate an IntraVoxel Incoherent Motion (IVIM) protocol for lungcancer evaluation.


Eligibility: Inclusion Criteria:
  -  Adults over 18 years
  -  High suspicion of lungcancer confirmed
  -  Tumor > 2 cm
  -  Incomplete cerebral staging or not yet realized in the initial consultation of screening
  Exclusion Criteria:
  -  Lungcancer medical history
  -  During Pregnancy
  -  Contraindications to MRI
  -  Patient not able to understand the information of the protocol, taking into account the state of the brain
  -  Patient unable to keep lying in MRI the necessary time

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Real-Life Efficacy and Safety of Nivolumab Monotherapy or in Combination With Ipilimumab in Patients With Advanced (Unresectable or Metastatic) Melanoma

Summary: Real-Life Efficacy and Safety of Nivolumab monotherapy or in combination with Ipilimumab in Patients with Advanced (Unresectable or Metastatic) Melanoma


Eligibility: Inclusion Criteria:
  -  ≥ 18 years
  -  advanced melanoma (Stage III/Stage IV)
  -  histologically confirmed diagnosis
  -  treatment decision for nivolumab mono- or combination therapy already taken
  -  signed informed consent
  Exclusion Criteria:
  -  current primary diagnosis of a cancer other than advanced melanoma, that requires systemic or other treatment
  -  previous treatment with nivolumab
  -  current active participation in an interventional clinical trial for treatment of advanced melanoma

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Cambridge Liquid Biopsy and Tumour Profiling Study for Patients on Experimental Therapeutics Trials

Summary: This study will explore the potential of the circulating tumour DNA (ctDNA) as predictive factor of response/resistance to anticancer treatment. The project will involve the collection and study of the archived tumour tissue where available (mandatory), serial blood samples (mandatory) and fresh tumour biopsies (optional) from patients taking part in an early phase clinical trial.

Detailed description: Some patients respond to anti-cancer drugs whilst others do not, despite having tumours with, apparently, similar characteristics such as site of origin. This variability in response can in some cases be explained by the genetic profile of the tumour. Therefore, studying the relationship between the molecular profiles of individual cancers and the response to therapy over time is of crucial importance in drug development. However, this endeavour is hampered by the difficulty in accessing suitable tumour material for analysis. Many patients' tumours are at anatomical sites which make biopsy difficult / hazardous which is in addition to the discomfort of a biopsy procedure. Therefore, this study will explore the potential of the circulating tumour DNA as a predictive factor of response/resistance to anticancer treatment.
  For patients recruited to early phase clinical trials of experimental therapies, archival tumour tissue (mandatory), serial blood samples (mandatory) and fresh tumour biopsies (optional) will be collected according to the individual schedule of each clinical trial.
  Blood plasma samples will be tested for cell-free and ctDNA levels and genomic profiles, which may include analyses of mutational profiles, copy number variations, translocations, chromosomal rearrangements and/or epigenetic profiles.
  Molecular profiling of archival and fresh tumour biopsies will also be carried out to study the correlation with cell-free and ctDNA samples and investigate the potential predictor response/resistance to treatment.

Eligibility: Inclusion criteria:
  -  Histological or cytological confirmation of cancer
  -  Patient being considered for participation in an experimental therapeutic trials
  -  Absence of any psychological, familial, sociological or geographical condition potentially hampering compliance with the study protocol and follow up schedule (such conditions should be discussed with the patient before registration in the study)
  Exclusion criteria:
  -  Age below 18 years old
  -  Patient not physically and mentally able to give informed consent.

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Study of 1cm Versus 2cm Margins for the Surgical Treatment of cT2N0M0 Melanoma

Summary: This is a randomized non-blinded pilot study for patients with melanoma staging cT2N0M0 who are candidates for surgical resection. The primary objective is to determine the feasibility of randomizing participants with cT2N0M0 malignant melanoma to surgical treatment with 1cm versus 2cm margins. Study will try to determine overall survival for cT2N0M0 malignant melanoma after surgical treatment with 1cm versus 2cm margins.

Detailed description: After randomization, participants will undergo surgery with wide local excision with either 1cm or 2cm margins. The margin will be based upon the previous biopsy site or area of pigmentation. The skin and subcutaneous tissue (down to fascia) will be resected. Closure considerations may require removal of additional tissue for non-oncologic purposes. As per standard of care, sentinel lymph node biopsy will be performed using a dual tracer technique (technetium radiolabeled sulfur colloid and isosulfan blue) with or without lymphoscintigraphy.

Eligibility: Inclusion Criteria:
  -  Biopsy proven T2 malignant melanoma.
  -  Eastern Cooperative Oncology Group (ECOG) score of 0-2.
  Exclusion Criteria:
  -  Visible additional disease that suggests a greater than T2 malignant melanoma
  -  Unable to tolerate general anesthesia
  -  Evidence of distant metastatic disease
  -  Melanoma located on face or digits

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Study of Stereotactic Radiotherapy for Breast Cancer

Summary: This is a Phase II trial of preoperative stereotactic radiation to the breast for low risk breast cancer.

Detailed description: This is a single arm phase II study design, evaluating the pathologic response (primary endpoint) as well as toxicity, cosmetic outcome, quality of life, and translational correlates (secondary endpoints) to pre-operative stereotactic body radiotherapy (SBRT) to intact breast tumors in patients with hormone-receptor positive early stage breast cancer.

Eligibility: Inclusion Criteria:
  -  Female sex
  -  Age > or = to 50 years of age
  -  Invasive ductal carcinoma
  -  Clinically and radiographically T1 tumor
  -  Clinically node negative
  -  Clearly demarcated tumor on magnetic resonance imaging (MRI), as determined by treating physician (MRI may be done after enrollment if not done prior)
  -  Planning breast conserving surgery including sentinel node biopsy
  -  ≥10% expression of ER and/or PR
  -  HER2- using the current College of American Pathologists guidelines
  -  Post-menopausal
  -  Willing and able to provide informed consent
  Exclusion Criteria:
  -  Medical conditions that may increase risk for poor cosmetic outcome (i.e. Lupus, rheumatoid arthritis, scleroderma
  -  Pure DCIS without invasive cancer
  -  Patients who have received or will be receiving neoadjuvant systemic therapy, endocrine therapy, or targeted agents
  -  Breast implant in the involved breast unless the implant will be removed prior to initiation of study treatment
  -  Positive pregnancy test
  -  Subjects without placement of a biopsy clip at the diagnostic procedure who are unwilling to undergo clip placement.
  -  Unable to meet dosimetric constraints due to tumor location and/or patient anatomy
  -  Planning mastectomy
  -  Unable to tolerate prone positioning

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Detection of Tumor DNA in Blood Samples From Patients With Early Stage Cancer and "Healthy Controls"

Summary: The aim of this study is to employ genomic detection methodologies to measure the relative amount of tumor-derived nucleic acids in the blood of patients diagnosed with an early stage solid tumor who are either commencing, currently undergoing or have completed treatment. This approach will allow the investigators to develop a quantitative measure of therapy efficacy via the counting of the relative changes in tumor molecules over the course of treatment.

Detailed description: The aim of this study is to employ genomic detection methodologies to measure the relative amount of tumor-derived nucleic acids in the blood of patients diagnosed with an early stage solid tumor who are either commencing, currently undergoing or have completed treatment. This approach will allow the investigators to develop a quantitative measure of therapy efficacy via the counting of the relative changes in tumor molecules over the course of treatment.
  The presence of circulating tumor-derived cfDNA in the plasma of patients can potentially enable a non-invasive means of detecting the presence or absence of tumor, assessing tumor burden and characterizing tumor biology in patients with cancer. The ability to measure the distribution of circulating tumor DNA may allow determination of a quantitative tumor load score in plasma that correlates to clinical tumor load. Clinical tumor load is a measure of disease burden, and the investigators propose to test in this study whether the tumor load score can measure this disease burden. A simple, reliable measure of disease burden would have diverse utility during patient therapy.

Eligibility: Inclusion Criteria:
  1. For all participants:
  -  Age 18 years or older
  -  Able to understand and grant informed consent
  -  Able to have their blood drawn at enrollment before surgery and 7 to 28 days after surgery
  For participants with early stage solid tumors:
  -  Diagnosed with an early stage (I-III) solid tumor with curative intent surgery without neoadjuvant therapy planned
  For "healthy control" subgroup:
  -  No prior or current diagnosis of any cancer. Participants with prior in situ cancer or non-melanoma skin cancer will be allowed to participate but will not be included in the "healthy control" cohort and will be analyzed separately.
  Exclusion Criteria:
  -  Unable to grant informed consent or comply with all study procedures
  -  Diagnosed with a hematological malignancy (acute or chronic leukemia, myelodysplastic syndrome, myeloproliferative neoplasm, myeloma or lymphoma).

Relevance to patient case: not relevant