araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 14-year-old female with Li-Fraumeni syndrome; genetic feature: TP53

Clinical trial: Genetics of EGFR (Epidermal Growth Factor Receptor) Mutation Study

Summary: The investigators wish to document the distribution of EGFR somatic mutations, and assess the relationship between specific genotype, clinical demographic, therapy, and survival, in a large cohort of EGFR mutant NSCLC.
  The investigators also wish to comprehensively investigate the relationship between germline DNA and risk of EGFR mutant NSCLC developing, through a GWAS (Genome-Wide Association Studies) and candidate gene approach, and explore the relationship between germline DNA and clinical outcome, in order to potentially identify germline genetic modifiers of EGFR TKI (Tyrosine Kinase Inhibitor) outcome.

Detailed description: Objective 1: To identify germline allelic DNA variation associated with somatic EGFR mutation in NSCLC, Objective 2: Correlation between germline allelic variants and survival in EGFR somatic mutant NSCLC.
  Objective 3: Study germline allelic DNA variation associated with never /ex light smoking NSCLC.
  Objective 4: Catalogue distribution of somatic EGFR mutant genotypes in 1,000 EGFR mutant NSCLC cases and describe their relationship to clinical outcome.

Eligibility: -  Histologically or cytologically diagnosed NSCLC, all histologies are acceptable.
  -  Patients can be included in the study with any disease stage and at any time during the disease course.
  -  Any type (surgery, RadioTherapy, chemotherapy, targeted agents) of previous treatment and any line of treatment are eligible.
  -  Age ≥18 years.
  Absence of any psychological, familial, sociological or geographical condition potentially hampering compliance with the study protocol; those conditions should be discussed with the patient before registration in the trial.
  Before patient registration, written informed consent must be given according to ICH/GCP (International Conference on Harmonisation/Good Clinical Practice), and national/local regulations.

Relevance to patient case: not relevant
Patient case: 14-year-old female with Li-Fraumeni syndrome; genetic feature: TP53

Clinical trial: Phase I Endovenous Administration of Oncolytic Adenovirus ICOVIR-5 in Patients With Advanced or Metastatic Melanoma

Summary: The investigators will evaluate the safety of a single endovenous infusion of ICOVIR5 in adults with locally advanced and metastatic melanoma. ICOVIR5 consists in a conditionally replicative or oncolytic adenovirus.


Eligibility: Inclusion Criteria:
  -  Malignant melanoma advanced or metastatic.
  -  Other than 18 years
  -  Karnofsky index > 60 %
  -  Life expectancy > 3 months
  -  ALT/AST <=2.5 times the upper normal limit
  -  Creatinine clearance >= 50 ml/min.
  -  Bilirubin <25 umol/l
  -  Alkaline phosphatase <= 2.5 time upper normal limit
  -  Normal bone marrow function: Neutrophils >=1.5 E9/L, platelets >= 1E11/L, hemoglobin >= 100 g/l, Normal prothrombin time and thromboplastin time,
  -  HIV negative
  -  Measurable disease
  -  Signed informed consent.
  Exclusion Criteria:
  -  Geographical, social or psychological conditions that may impair the protocol compliance.
  -  Active infections or other severe medical status.
  -  History of liver disease.
  -  Other or concomitant treatments for melanoma or investigational product.
  -  Previous participation in studies with adenovirus.
  -  Virus diseases diagnosed two weeks before inclusion.
  -  Immunosuppressive concomitant treatments
  -  Concomitant malignant haematological disease.
  -  Patients having family members with immunodeficient status or disease
  -  Patients with Li Fraumeni syndrome or germinal retinoblastoma gene defects.

Relevance to patient case: not relevant
Patient case: 14-year-old female with Li-Fraumeni syndrome; genetic feature: TP53

Clinical trial: Periperal Blood Lymphocytes During Prostate RT

Summary: Right now it is not possible to predict which patients are going to react more to RT. Many things could affect patient's response to radiation. One of the factors is whether the person can repair damage to the genetic material (DNA/RNA) caused by the RT. There is some evidence that a certain protein called Gamma H2AX is involved in DNA damage and repair and this can be used to predict the sensitivity of individual patients. The investigators will be studying this protein: Gamma H2AX) in the blood samples of prostate cancer patients exposed to both computed tomography (CT) scan and RT treatment. This will help us to understand why different individuals show differences in side effects following RT.


Eligibility: Inclusion Criteria:
  -  Intermediate-risk prostate cancer patients (T1/T2N0M0 with either GS < 7 and PSA between 10-20 ng/ml or GS 7 and PSA less than 20 ng/ml).
  -  Planned for radical RT to the prostate with IMRT planning (79Gy/39fractions or 60 Gy/20 fractions).
  -  No contraindications to diagnostic CT scanning.
  -  Prostate volumes will be less than 80 cc to control the planning dose volume histogram (DVH) as much as possible in terms of rectal and bladder volumes.
  -  No known DNA repair disorders (e.g. family history of AT, BRCA1/2 or Li Fraumeni syndrome) or contraindications to radical pelvic RT.
  Exclusion Criteria:
  -  Inability to provide informed consent.
  -  Patient having contraindications to diagnostic CT scan.
  -  Patients who have unobtainable data regarding previous therapy and their clinical outcome.
  -  Patients should not have any diagnostic X-rays or CAT scans 2 weeks prior to their enrollment into the study.

Relevance to patient case: not relevant
Patient case: 14-year-old female with Li-Fraumeni syndrome; genetic feature: TP53

Clinical trial: Tissue Banking Study - Polycythemia Vera or Essential Thrombocythemia (PV & ET) Patients

Summary: The purpose of the study is to isolate and characterize stem cells of patients with Polycythemia Vera (PV) and Essential Thrombocythemia (ET) to find out why these cells are not working the way they should be and why they seem to be sensitive to regulatory factors in the blood, such as clotting.

Detailed description: Specific Aim 1: Assess the effects of RG7112 on MPN HSC/HPC p53 levels and study how it affects MPN stem cell function.
  Specific Aim 2. Assess the effects of a combination of low doses of IFNα and RG7112 on MPN HSC/HPC.

Eligibility: Inclusion Criteria:
  -  polycythemia vera or essential thrombocythemia
  -  agree to give blood for study
  Exclusion Criteria:
  -  none

Relevance to patient case: not relevant
Patient case: 14-year-old female with Li-Fraumeni syndrome; genetic feature: TP53

Clinical trial: Mitochondrial Dysfunction in Phelan-McDermid Syndrome: Explaining Clinical Variation and Providing a Path Towards Treatment

Summary: The purpose of this study is to determine whether a relationship exists between gene deletion(s) specific to the mitochondrial electron transport chain and presentation of clinical characteristics in patients with Phelan-McDermid Syndrome (PMS).

Detailed description: Phelan-McDermid Syndrome (PMS) results from a deletion within the 22q13 chromosome region. Most children have specific physical morphology and developmental delays with many displaying characteristics of autism spectrum disorder (ASD) including abnormalities in social development. The behavioral aspect of PMS that parallels ASD has raised particular interest as the SHANK3 gene, which lies in the 22q13 region, is important for synaptic development, and animal SHANK3 knockout models demonstrate ASD characteristics thereby confirming the importance of this gene in PMS. However, despite the importance of the SHANK3 gene, individuals with PMS have variations in their development, behavior and medical characteristics that cannot be fully explained by the SHANK3 deletion.
  Recently, Frye (2012) has noted the existence of 6 mitochondrial genes that lie slightly proximal to the SHANK3 gene within the 22q13 region. These include genes important electron transport change function (SCO2, NDUFA6), mitochondrial DNA (TYMP) and RNA (TRMU) metabolism, fatty acid metabolism (CPT1B) and tricarboxylic acid cycle function (ACO2). Since most Individuals with PMS have deletions that include chromosomal deletion outside of the SHANK3 region, it is very likely that many, if not most, of children with PMS may have deletions in these mitochondrial genes. Many of these genes have been linked to mitochondrial disease, even in the heterozygous state. Even if recognized, mitochondrial disease is only linked to a homozygous abnormal state (autosomal recessive), the loss of one gene (heterozygous state) could result in symptomatology when associated with deletions in other mitochondrial or non-mitochondrial genes. Abnormalities in mitochondrial pathways can result in neurologic and non-neurologic symptoms including those sometimes seen in children with PMS. Added with the SHANK3 deletion, abnormalities in these mitochondrial genes could explain variations in patterns of development and the eventual cognitive potential.
  References: Frye RE. Mitochondrial disease in 22q13 duplication syndrome. J Child Neurol. 2012; 27(7):942-9.

Eligibility: Inclusion Criteria:
  -  1-21 years of age
  -  Diagnosed with Phelan-McDermid Syndrome AND diagnosed with Mitochondrial Disorder
  -  Diagnosed with Phelan-McDermid Syndrome
  Exclusion Criteria:
  -  none

Relevance to patient case: not relevant
Patient case: 14-year-old female with Li-Fraumeni syndrome; genetic feature: TP53

Clinical trial: Assessment of Adverse Events in a Naive Pediatric Population Treated With an Antipsychotic

Summary: We propose a prospective multicenter study, whose originality lies in the inclusion of the naive child and adolescent population. Its purpose is to evaluate the incidence of adverse events related to the use of l antipsychotic drugs in children and adolescents with no history of taking such drugs.
  The inclusion criteria will be: (1) male or female inpatients, (2) aged from 6 to 18 years, (3) requiring antipsychotic treatment, (4) receiving antipsychotic drug for less than 28 days without taking antipsychotic before or with a history of antipsychotic over a maximum period of three consecutive months and discontinued for at least 6 months.
  Therapeutic monitoring during the 12 month study period will include clinical assessments and laboratory testing. These assessments will be performed before treatment (at inclusion), and at 1, 3, 6, 9, 12 months after the introduction of the antipsychotic drug.

Detailed description: a prospective multicenter study, whose originality lies in the inclusion of the naive child and adolescent population

Eligibility: Inclusion Criteria:
  -  Male or female patients
  -  Aged from 6 to 18 years
  -  In whom antipsychotic treatment is indicated
  -  Who have never been treated with antipsychotic medication (other than metoclopramide (Primperan®) for pediatric indications) or with a history of antipsychotic over a maximum period of three consecutive months and discontinued for at least 6 months. .
  The non-inclusion criteria:
  -  Any
  The exclusion criteria:
  -  Refusal or withdrawal of consent by the patient or his/her parents.

Relevance to patient case: not relevant
Patient case: 14-year-old female with Li-Fraumeni syndrome; genetic feature: TP53

Clinical trial: Phase I Dose Escalation Study of Intravenous VCN-01 With or Without Gemcitabine and Abraxane® in Patients With Advanced Solid Tumors

Summary: The purpose of this study is to determine the safety and tolerability of VCN-01 either administered alone or in combination with Abraxane®/Gemcitabine, and to determine the recommended phase II dose of VCN-01 alone or in combination with Abraxane®/Gemcitabine.

Detailed description: The study consists of three parts:
  -  Part I is a dose escalation study to determine the safety and tolerability of a single intravenous injection of VCN-01 alone
  -  In Part II the safety and tolerability of the two highest VCN-01 tolerable doses from part I will be evaluated in combination with Abraxane®/Gemcitabine.
  -  In Part III the safety and tolerability of the two highest VCN-01 tolerable doses from part I will be evaluated in combination with Abraxane®/Gemcitabine in a "delayed" schedule compared with Part II.

Eligibility: Inclusion Criteria:
  -  Male/Female patients aged 18 years or over
  -  Patients must provide written informed consent
  -  Part I: Patients with histologically confirmed, locally advanced or metastatic solid tumors. Part II and Part III: Patients with histologically confirmed, pancreatic adenocarcinoma for which the established therapy is Abraxane®/Gemcitabine (clinical standard of care)
  -  Life expectancy above 3 months
  -  Patients willing to comply with treatment follow-up
  -  ECOG Performance status 0 or 1
  -  Adequate baseline organ function (hematologic, liver, renal and nutritional)
  -  Use a reliable method of contraception in fertile men and women
  Exclusion Criteria:
  -  Active infection or other serious illness or autoimmune disease
  -  Treatment with live attenuated vaccines in the last three weeks
  -  Known chronic liver disease (liver cirrhosis, chronic hepatitis)
  -  Treatment with another investigational agent within its five half-lives prior to VCN-01 infusion
  -  Viral syndrome diagnosed during the two weeks before inclusion
  -  Chronic immunosuppressive therapy
  -  Concurrent malignant hematologic or solid disease
  -  Pregnancy or lactation. Patients must agree to use effective contraception or be surgically sterile.
  -  Patients receiving full-dose anticoagulant / antiplatelet therapy
  -  Adequate levels of neutralizing antibodies against adenovirus
  -  Patients with Li Fraumeni syndrome or with previous known retinoblastoma protein pathway germinal deficiency

Relevance to patient case: not relevant
Patient case: 14-year-old female with Li-Fraumeni syndrome; genetic feature: TP53

Clinical trial: Panitumumab for Intravenous Infusion 100 mg and 400 mg Special Drug Use Surveillance "Survey on Unresectable, Advanced or Recurrent Colorectal Cancer With Wild-type KRAS Gene" (All-patient Surveillance)

Summary: The efficacy and safety of panitumumab (Vectibix) in the routine clinical setting will be studied.
  Specifically, information will be collected on the following as events of interest: skin disorders, interstitial lung disease, infusion reactions, electrolyte abnormalities, and cardiac disorders.

Detailed description: The efficacy and safety of panitumumab (Vectibix) in the routine clinical setting will be studied.
  Participants of this surveillance will be patients with unresectable, advanced or recurrent colorectal cancer with the wild-type KRAS gene. The planned sample size is 2,000 patients.
  The usual adult dosage is 6 mg/kg of panitumumab given by intravenous drip infusion over a 60-minute period once every 2 weeks. The dosage may also be reduced as needed, depending on the patient's condition.

Eligibility: Inclusion Criteria:
  -  Unresectable, advanced or recurrent colorectal cancer with wild-type KRAS gene
  Exclusion Criteria:
  -  Patients with a medical history of severe hypersensitivity to any of the ingredients of Vectibix

Relevance to patient case: not relevant
Patient case: 14-year-old female with Li-Fraumeni syndrome; genetic feature: TP53

Clinical trial: Study of the Impact of Indacaterol (Onbrez®) on the Individual Lives and Health Status of Patients With COPD

Summary: A prospective observational multi centre research study in GP practices clustered within up to 10 UK Primary care trusts.


Eligibility: Inclusion Criteria:
  -  Patients with active diagnosis of COPD, confirmed by spirometry documented in medical notes
  Exclusion Criteria:
  -  Patients who are currently receiving other maintenance therapy (except LAMA) for COPD.
  -  Patients previously prescribed Indacaterol.

Relevance to patient case: not relevant
Patient case: 14-year-old female with Li-Fraumeni syndrome; genetic feature: TP53

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: 14-year-old female with Li-Fraumeni syndrome; genetic feature: TP53

Clinical trial: Triple Negative Breast Cancer and Germline Hereditary Breast and Ovarian Cancer Mutation Carrier Registry

Summary: PROGECT is a registry for patients with Triple Negative breast cancer (TNBC) or patients who have an identified germline mutations (such as a mutation on the BRCA1 or BRCA2 genes).

Detailed description: This study is being done to collect cancer-related information from patients with triple negative breast cancer and patients with hereditary genetic mutations. This information will help us better understand the link between genetic changes and cancer outcome in patients with triple negative breast cancer.

Eligibility: Inclusion criteria include:
  Triple Negative Breast Cancer
  -  ER/PR <10% and HER negative per current ASCO/CAP guidelines
  -  Stages I-IV
  -  Any age at diagnosis
  -  Patient must be within 5 years of diagnosis
  -  Eligible regardless of genetic testing status
  -  Genetic testing recommended for patients meeting NCCN and Medicare guidelines
  AND/OR
  Germline mutation Carriers
  -  Patients with deleterious or uncertain mutations in HBOC genes (BRCA, PTEN, P53, -PALB2 etc) are eligible regardless of type/site of cancer
  -  Healthy patients harboring mutations also eligible
  -  There is no time limit from the time of diagnosis of cancer and enrollment.
  -  Eligible regardless of personal history of cancer
  Exclusion Criteria include:
  Triple Negative Breast Cancer -Patient is not within five years of diagnosis
  Germline mutation Carriers:
  -Patient only carries a HBOC mutation that is classified as "polymorphism" of "favor polymorphism"

Relevance to patient case: not relevant
Patient case: 14-year-old female with Li-Fraumeni syndrome; genetic feature: TP53

Clinical trial: Is There Any Relation Between Serum Anti-p53 Antibody and TLG, MTV and SUV as PET Parameters in Lung Cancer Patients?

Summary: p53 is a tumor suppressor gene which plays an important role in controlling normal cell proliferation regulation that is located on the chromosome 17 (17p13.1). It is the most common goal of genetic alteration in many tumors. Serum p53 protein is presence in normal healthy individuals. However p53 antibody is extremely rare. Mutations in this gene cause an accumulation of non-functional proteins and development of anti-p53 antibodies, which can be detectable in tissues, slouhed cells, blood and other body fluids. Some studies have reported that, p53 mutations are highly common in leukemia, lymphoma, lung, esophagus, stomach, liver, bone, bladder, ovarian, and brain cancers. Lung cancer is the most common cause of cancer-related deaths and the survey is low after the initial diagnosis. Accurate staging is important for determine the choice of treatment and predict prognosis. 18F-FDG PET/BT has important value for initial staging and it is the most advanced imaging technique developed all over the world for determine of the characterization of the metabolic tumor volume. Maksimum Standardized Uptake Value (SUVmax) which was acquired by PET imaging is commonly used in clinical practice as a criterion for malignancy. Due to the development of new software programs recently studies have shown that metabolic tumor volume (MTV) and total lesion glycolysis (TLG) may be useful quantitative parameters for the prognostic evaluation. Viable tumor volume could be estimate with this programs.The purpose of this study was to assess the relation between serum anti-p53 antibody level and quantitative PET parameters as SUVmax, SUVave, MTV and TLG.


Eligibility: Inclusion Criteria:
  -  patients who were referred to our department with the purpose of 18F-FDG PET/CT imaging for staging due to lung cancer diagnosis
  -  patients who were performed 18F-FDG PET/CT for diagnosis in the cause of the suspected pulmonary nodule/lesion in thorax CT but not detected pathologic FDG accumulation
  -  In the control group, healthy subjects with no history of cancer and without any complaint
  Exclusion Criteria:
  -  Patients had operated for lung cancer, received prior chemotherapy or radiotherapy for lung cancer, with no definitive histological diagnosis, and a blood glucose level greater than 150 mg/dL

Relevance to patient case: not relevant