araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Trial With Telomerase Peptide Vaccine In Combination With Temozolomide in Patients With Advanced Malignant Melanoma

Summary: Primary objective: Determination of safety and tolerability of GV1001 administration combined with Temozolomide (based on blood samples and adverse events).
  Feasibility of combining active immunisation with Temozolomide treatment. Determination of immunological response after administration of GV1001 and Temozolomide as measured by presence of DTH skin test reaction and specific T-cell responses.
  Secondary: Evaluation of objective tumour response
  The trial is an exploratory study which main objective is to estimate safety and feasibility of combining active immunisation with chemotherapy. However, the trial may also indicate the efficacy of the combination.


Eligibility: Inclusion Criteria:
  -  Histologically confirmed diagnosis of malignant melanoma.
  -  Previously untreated and non-resectable disease
  -  Measurable or evaluable tumour.
  -  Age ≥ 18 and ≤ 75 years.
  -  Performance status ECOG-WHO 0, 1 and 2 (Appendix III)
  -  Written informed consent (Appendix II)
  -  Adequate bone marrow liver, heart and renal function:
  -  WBC count >3.0 x 109/L and platelets count >100 x 109/L.
  -  ASAT, ALAT <2 x upper normal laboratory value.
  -  Serum creatinine <2 x upper normal laboratory value.
  Exclusion Criteria:
  -  Previous treatment with chemotherapy.
  -  Clinical signs of brain metastases.
  -  Severe cardiac insufficiency (NYHA III or IV) with uncontrolled and/or unstable cardiac or coronary artery disease.
  -  Severe active infections such as HIV or hepatitis B or Hepatitis C.
  -  Medication for severe intercurrent disease which might affect immunocompetence (e.g. immunosuppressants, systemic corticosteroids).
  -  Pregnancy, breast-feeding or absence of adequate contraception for fertile patients.
  -  Simultaneously participation in other clinical studies.
  -  Any reason why, in the opinion of the investigator, the patient should not participate.

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Interferon Alfa Sensitivity in HIV/HCV Persons Before and After HIV Meds

Summary: The chief purpose of this research is to evaluate interferon alpha sensitivity and cell type specific levels of interferon receptor and interferon stimulated genes and proteins in HIV/ HCV (hepatitis C virus) coinfected persons before and after administration of HIV medications (antiretroviral therapy).

Detailed description: We plan to perform liver biopsy by microlaparoscopy on previously untreated HIV/HCV coinfected persons, then give them a dose of peginterferon alfa 2b. HCV and HIV kinetics will be studied. Afterward, HIV will be treated using antiretroviral therapy and the procedure will be repeated.

Eligibility: Inclusion Criteria:
  -  Adult Human
  -  Able to provide written informed consent
  -  HIV antibody positive
  -  HIV viral load positive
  -  HIV treatment naive
  -  Hepatitis C antibody positive
  -  Hepatitis C viral load positive
  -  Hepatitis C treatment naive
  -  Approved to take HIV medications for minimum 9 months
  -  Willing to use contraception, Life expectancy greater than 2 years
  Exclusion Criteria:
  -  Significant opportunistic infections within 12 month
  -  Hepatitis B positive
  -  Evidence of liver cirrhosis
  -  Decompensated liver disease
  -  Chronic alcohol abuse
  -  Allergy to raltegravir, tenofovir, and/or emtricitabine
  -  Active or suspected malignancy
  -  Sarcoidosis
  -  Active TB
  -  Coronary artery disease
  -  Uncontrolled seizures
  -  Untreated thyroid disease
  -  Untreated diabetes
  -  Weight greater than 125 kg
  -  Severe depression or severe psychiatric disorder
  -  Ongoing alcohol or illicit drug use
  -  Pregnant, nursing, pr planning to become pregnant
  -  Allergy to interferon

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: BEZ235 Trial in Patients With HER2-(Human Epidermal Growth Factor Receptor 2 Negative) /HR+ (Hormonal Receptor Positive) Metastatic Breast Cancer

Summary: This is a prospective, multi-center, open-label, single arm, phase II study with a 2-stage design and Bayesian interim monitoring to investigate the safety and efficacy of BEZ235 in patients with progressive metastatic HR+ HER2- breast cancer who have received at least one prior line of endocrine therapy and two to three prior lines of chemotherapy for metastatic disease. Patients will be stratified into 3 groups according to their PI3K (phosphatidylinositol 3-Kinase) pathway activation status.


Eligibility: Inclusion Criteria:
  -  Female ≥ 18 years
  -  ECOG performance status ≤ 2
  -  Histologically and/or cytologically confirmed diagnosis of breast cancer presenting with metastatic disease (hormone receptor positive and HER2 negative)
  -  Known PI3K activation status (defined by PIK3CA (Phosphoinositide-3-kinase, catalytic, alpha polypeptide) mutation and PTEN PTEN (Phosphatase and Tensin Homolog) mutation/expression)
  -  Prior treatment with at least one prior line of endocrine therapy and at least two and no more than three prior lines of chemotherapy for metastatic breast cancer
  -  Objective and radiologically confirmed progression of disease after prior treatment and at least one measurable lesion as per RECIST
  -  Adequate bone marrow and organ function
  Exclusion Criteria:
  -  Previous treatment with PI3K and/or mTOR inhibitors
  -  Symptomatic Central Nervous System (CNS) metastases
  -  Concurrent malignancy or malignancy in the last 5 years prior to start of study treatment
  -  Wide field radiotherapy ≤ 28 days or limited field radiation for palliation ≤ 14 days prior to starting study drug
  -  Active cardiac disease (e.g. Left Ventricular Ejection Fraction (LVEF) < 50%, QTcF > 480 msec on screening ECGelectrocardiogram (ECG), unstable angina pectoris, ventricular, supraventricular or nodal arrhythmias)
  -  Inadequately controlled hypertension
  -  Impairment of gastrointestinal (GI) function or GI disease that may significantly alter the absorption of BEZ235
  -  Treatment at start of study treatment with drugs with a known risk to induce Torsades de Pointes, moderate and strong inhibitors or inducers of isoenzyme CYP3A4, warfarin and coumadin analogues, LHRH agonists
  -  History of photosensitivity reactions to other drugs
  -  Pregnant or nursing (lactating) woman
  Other protocol-defined inclusion/exclusion criteria may apply

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Pharmacokinetic, Safety and Tolerability Study of SPARC1028

Summary: Evaluation of pharmacokinetic profile of SPARC1028

Detailed description: This is a phase I study of SPARC1028 and recommend phase II dose of SPARC1028 administered once a week for 3 weeks, followed by 1 week of rest.

Eligibility: Inclusion Criteria:
  -  Histologically or cytologically confirmed diagnosis of solid tumor in advanced stage which taxane-based therapy is a rational treatment option.
  -  Age ≥18 years
  -  ECOG Performance Status ≤ 1.
  -  Estimated life expectancy of at least 12-weeks;
  Exclusion Criteria:
  -  Any malignancy within past 5-years, except non-melanoma skin cancer, cervical intraepithelial neoplasia, or in situ cervical cancer
  -  Known hypersensitivity to the study drugs
  -  Treatment with any anti-cancer agents within 28 days of study entry
  -  Presence of clinically evident active CNS metastases, including leptomeningeal involvement, requiring steroid or radiation therapy

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Detection of Choroidal Nevus Cells in Vitrectomy Fluid

Summary: The purpose of this study is to determine if the investigators can detect the presence of choroidal nevi cells in the vitreous fluid of humans, as this may improve the diagnosis and classification of choroidal nevi and melanomas in the future.

Detailed description: Approximately 7% of the population has a choroidal nevus, or "freckle," in the back of the eye. Like a nevus on the skin, there is potential for malignant change to a melanoma. Dermatologists have the ability to quickly and easily biopsy suspicious skin lesions while ophthalmologists currently have no way of determining the malignant potential of choroidal nevi other than a fine needle aspiration (which is invasive and has the potential complications of bleeding and retinal detachment). This study's sole aim is to see if choroidal nevi cells are present in the inside fluid of the eye. The investigators plan to analyze the fluid of the eye, which is routinely removed during retina surgery, to detect any nevus cells. If the investigators are able to detect these cells, then future studies may allow us to better classify choroidal nevi for potential malignant change.

Eligibility: Inclusion Criteria:
  -  Patients with a choroidal nevus who are undergoing routine vitrectomy surgery for another indication (such as epiretinal membrane or macular hole repair).
  Exclusion Criteria:
  -  Patients without a choroidal nevus
  -  Children under the age of 18
  -  Pregnant and nursing females

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Characterisation of T Lymphocytes, NK Cells and Macrophages in Melanoma Patients

Summary: Melanoma tumor tissue ( in particular regressive areas) present a lymphocytic infiltrate with an anti-tumoral specificity. The aim of the study is to analyse at different stages of the disease, tumor samples and to characterise the cellular infiltrate in situ ( in particular T lymphocytes, NK cells and macrophages), the role of inhibitor receptors on in situ immunosuppression, and potential modulation by medical treatments such as dacarbazine.

Detailed description: The study is divided in 4 parts:
  Part 1: study of cellular infiltrate (lymphocytes) performed on large primary melanoma and cutaneous metastasis ( fresh samples) Part 2: NK cells study on metastatic regional lymph nodes ( fresh samples) and blood samples Part 3: a retrospective study of macrophages in sentinel lymph nodes and in corresponding primary melanomas Part 4: study of the cellular modulation by the chemotherapy (DTIC or cisplatin or inhibitor of B-raf) which(who) will be made on two cutaneous metastases by patient (one taken before the treatment(processing) and one taken during the evaluation after 2 or 3 cycles of treatment(processing))

Eligibility: Inclusion Criteria:
  -  Patients with confirmed melanoma-patients informed of the aims of the study , the modalities
  -  Patients who signed the consent form ou a non opposition form signed by the patient or by a relative
  According to study part:
  Part 1: patients with a melanoma larger than 10mm or with cutaneous metastasis Part 2: stage IV melanoma patients who shall undergo a regional lymph node dissection Part 3: retrospective study of patients who underwent a sentinel node procedure Part 4: Patients achieves of inoperable melanomas the stage(stadium) III or IV that must receive in treatment (processing) a chemotherapy (by the dacarbazine or by the cisplatin or by the inhibitor of B-raf) and carrier of at least two cutaneous metastases
  Exclusion Criteria:
  -  Refusal to take part in the study (patient or relative)
  -  Contraindications known to the xylocaine (groups 1,2, and 4)
  -  No affiliated to the social security system (groups 1, 2, and 4)

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Assessing DNA Changes in High Risk Prostate Cancer to Determine Prognosis

Summary: One of the biggest problems facing prostate cancer patients and their treating physicians is who needs to be treated and when. Common clinical and pathological parameters are useful (PSA, Gleason score, etc.) but do not clearly predict who will benefit from treatment and who will fail. Genetic markers for tumor aggressivity would be of greater value. The finding that the TMPRSS2-ERG gene fusion is associated with an increase risk of cancer progression is important. TMPRSS2 is controlled by androgen (testosterone) and ERG is part of a family of proteins which have a role in controlling cell growth, cell specialization and producing tumors. As a consequence of this gene fusion, production of the ERG protein increases in the presence of testosterone and could be key to the development of prostate cancer, resistance to treatment and poor outcome. The PTEN gene is known to have a role as a tumor suppressor. Its deletion is a contributing factor in the development of prostate cancers and poor outcome. The coexistence of the two markers could be associated with a higher risk of recurrence.
  To date there have been no studies regarding the presence of either of these two markers or their coexistence in high risk prostate cancer patients who, despite radiation therapy and androgen suppression, develop biochemical failure (their PSA levels rise once again). Patients participating in the PCS IV study (high risk prostate cancer treated with radiation therapy plus either 18 or 36 months of hormonal suppression) who have had biochemical failure or 3 years of follow-up post hormonal therapy will be approached.
  Tumor blocks from consenting patients will be collected and analyzed for the presence of the TMPRSS2-ERG gene fusion and the PTEN deletion at the Pathology Department of the Jewish General Hospital. Statistical analysis will be carried out to see whether either or both markers are present, whether they are associated with certain clinical and pathological high risk factors, and whether they can be used to predict which patients will fail treatment.


Eligibility: Inclusion Criteria:
  -  patients with prostate cancer post radical radiation therapy and LHRH agonist treated in PCSIV clinical trial
  -  biochemical failure (PSA nadir + 2) or minimum follow-up of 3 years post completion of hormonal therapy
  -  high risk group
  1. gleason score 8-10
  2. PSA ≥ 20 ng/ml
  3. T3 or T4

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Safety Study of a Melanoma Vaccine (GVAX) With or Without Cyclophosphamide in Patients With Surgically Resected Melanoma

Summary: The primary objective of this study is to evaluate the safety and feasibility of administering an allogeneic GM-CSF-secreting lethally irradiated whole melanoma cell vaccine ("melanoma GVAX"), alone or in combination with low dose cyclophosphamide (CPM), for the adjuvant treatment of patients with surgically resected stage IIB-IV melanoma. Secondarily, the investigators will assess in vitro correlates of anti-melanoma immunization by melanoma GVAX, including serological and cellular immune responses in patients treated with either the vaccine alone or the vaccine given with low dose CPM.


Eligibility: Inclusion Criteria:
  -  Any patient age ≥18 years with melanoma of cutaneous or mucosal origin, and with clinicopathologic stage IIB, IIC, III or IV that has been completely resected
  -  Patients must be able to provide informed consent.
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1.
  -  Life expectancy of at least 6 months.
  -  Adequate hematologic function.
  -  Adequate renal function
  -  Adequate hepatic function
  -  Patients of both genders must agree to practice effective birth control during the study period and for at least 4 weeks after the last treatment.
  Exclusion Criteria:
  -  Patients whose primary site of melanoma is ocular.
  -  Are undergoing or have undergone in the past 4 weeks any systemic treatment for melanoma.
  -  Are undergoing or have undergone in the past 2 weeks any surgery or focal radiation therapy.
  -  Have active systemic infections, coagulation disorders (including therapeutic anticoagulation), or other major medical or psychiatric illnesses.
  -  Are known to be positive for hepatitis B surface antigen, anti-Hepatitis C Virus or anti-Human Immunodeficiency Virus (HIV) antibody (because of possible immune effects of these conditions).
  -  Documented history of autoimmune disease, for example, systemic lupus erythematosus, sarcoidosis, rheumatoid arthritis, glomerulonephritis, or vasculitis.
  -  Any form of primary or secondary immunodeficiency. This would include hereditary disorders such as ataxia-telangiectasia or Wiskott-Aldrich syndrome, or acquired immune deficiencies such as following bone marrow transplantation.
  -  Requirement for systemic steroid therapy or immunosuppressive therapy.
  -  Have received any type of cancer immunotherapy, including but not limited to interleukin-2, interferon alfa or melanoma vaccines.
  -  Have been diagnosed with another invasive cancer within the past 3 years.
  -  Radiographic evidence of melanoma recurrence.
  -  Pregnant or lactating women.
  -  Known or suspected hypersensitivity to GM-CSF, pentastarch, hetastarch, corn, Dimethyl sulfoxide, fetal bovine serum or trypsin (porcine origin).

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: A Phase I Study of Oral LGX818 in Adult Patients With Advanced or Metastatic BRAF Mutant Melanoma

Summary: CLGX818X2101 is a first-time in-human, phase I study to establish the maximum tolerated dose (MTD) and/or recommended phase 2 dose (RP2D) of daily administered LGX818 (daily, twice daily and/or every-other-day), a RAF kinase inhibitor. Patients with locally advanced or metastatic melanoma harboring the BRAF V600 mutation (during dose escalation phase and expansion phase) and patients with metastatic colorectal cancer harboring the BRAF V600 mutation (during the expansion phase) will be enrolled. The study consists of a dose escalation part were cohorts of patients will receive escalating oral doses of LGX818, followed by a safety dose expansion part were patients will be treated with oral dose of LGX818 given at the MTD or RP2D.


Eligibility: Inclusion Criteria:
  For the dose escalation phase:
  1. Histologically confirmed diagnosis of locally advanced or metastatic melanoma (stage IIIB to IV per American Joint Committee on Cancer [AJCC]). For the dose expansion phase: (i) Histologically confirmed diagnosis of locally advanced or metastatic melanoma (stage IIIB to IV per American Joint Committee on Cancer [AJCC]), or (ii) confirmed diagnosis and non-resectable advanced metastatic colorectal cancer (mCRC) for which no further effective standard therapy exists.
  2. Written documentation of BRAF V600E mutation, or any other BRAF V600 mutation.
  3. Evidence of measurable disease
  Exclusion Criteria:
  1. Previous therapy with a MEK inhibitor.
  2. Symptomatic or untreated leptomeningeal disease.
  3. Symptomatic or untreated brain metastasis.Patients previously treated for these conditions that are asymptomatic in the absence of corticosteroid therapy are allowed to enroll. Brain metastasis must be stable with verification by imaging.
  4. Known acute or chronic pancreatitis.
  5. Clinically significant cardiac disease
  6. Impairment of gastrointestinal (GI) function or GI disease that may significantly alter the absorption of oral LGX818
  7. Previous or concurrent malignancy. Exceptions to this exclusion criteria include: adequately treated basal cell or squamous cell skin cancer; in situ carcinoma of the cervix, treated curatively and without evidence of recurrence for at least 3 years prior to study entry; or other solid tumor treated curatively, and without evidence of recurrence for at least 3 years prior to study entry.
  8. Pregnant or nursing (lactating) women, where pregnancy is defined as the state of a female after conception and until the termination of gestation, confirmed by a positive hCG laboratory test (> 5 mIU/mL).
  9. History of thromboembolic or cerebrovascular events within the last 6 months
  Other protocol-defined inclusion/exclusion criteria may apply

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Genetics, Brain Structure and Thinking Skills in Autism

Summary: The purpose of this research is to better understand the genetic, biochemical, cognitive and behavioral symptom abnormalities that contribute to autism spectrum disorders. The investigators anticipate recruiting at least 100 participants with autism spectrum disorder and large head size, at least 100 participants with autism spectrum disorder without large head size and at least 40 healthy siblings. Biological parents are expected to be recruited only as genetic changes are identified in individuals with autism spectrum disorders to better understand the nature of these genetic changes. Participants are asked to complete cognitive testing, a blood draw, urine collection and measurement of his/her height, weight and head circumference. Parents or caregivers may be asked to complete a diagnostic evaluation and will complete questionnaires that examine the participant's medical and family history as well as his/her current symptoms, functioning, and quality of life. A brief report simply listing and giving a basic description of any behavioral diagnostic information, autism symptoms, adaptive functioning, and a listing of results from cognitive testing will be provided as part of this study.


Eligibility: Inclusion Criteria:
  -  Clinical diagnosis of autism
  -  Consent from parents or guardians or an adult with or suspected of having an autism spectrum disorder that does not require a legal guardian or an adult who is the healthy sibling of an individual with an autism spectrum disorder.
  -  Youth ages 2-17 and adults ages 18-50. Youths and adults who are able (some young or severely impaired participants may not be able to provide assent) will be asked to provide assent.
  -  Families with multiple children who meet the above inclusion criteria will be permitted to have as many children participate as they wish.
  -  Youth ages 2-17 and adults ages 18-50 who do not have an autism spectrum disorder or are not suspected of having an autism spectrum disorder and who have a sibling with an autism spectrum disorder who has participated in the present study.
  Exclusion Criteria:
  -  Clinically significant medical disease that would prohibit participation in the study procedures.
  -  Children younger than 2 years old and adults older than 50 years old.

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Comparative Microarray Analysis in Primary Cutaneous Malignant Melanoma

Summary: Perturbations in microRNA (miRNA) expression profiles has been reported for cutaneous malignant melanoma (CMM). This study will be an exploratory analysis by miRNA expression profiling using microarrays.

Detailed description: Perturbations in microRNA (miRNA) expression profiles has been reported for cutaneous malignant melanoma (CMM). With regards to a rapidly growing number of newly discovered miRNA sequences, the availability of up-to-date miRNA expression profiles for primary cutaneous malignant melanoma (PCMM), cutaneous malignant melanoma metastases (CMMM) and benign melanocytic naevi (BMN) is limited. Patients with PCMM, CMMM and BMN are included in the study to perform an exploratory analysis by miRNA expression profiling using microarrays. Expression levels of miRNA candidates will be validated by TaqMan real-time quantitative polymerase chain reaction (RT-PCR).

Eligibility: Inclusion Criteria:
  -  Primary Cutaneous Malignant Melanoma
  -  Cutaneous Malignant Melanoma Metastases
  -  Benign Melanocytic Naevi
  Exclusion Criteria:
  - Other Skin Cancer than Primary Cutaneous Malignant Melanoma

Relevance to patient case: not relevant