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

Clinical trial: Study of Tumor Tissue From Patients With Melanoma Treated on Clinical Trial EST-1690

Summary: RATIONALE: Studying samples of tumor tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer. It may also help doctors predict how patients will respond to treatment.
  PURPOSE: This research study is looking at tumor tissue samples from patients with melanoma treated on clinical trial EST-1690.

Detailed description: OBJECTIVES:
  -  To validate the prognostic role of several biomarkers suggested by gene expression profiling and tissue microarray (TMA) studies (e.g., NCOA3, SPP1, and RGS1) on the outcome associated with melanoma in the EST-1690 cohort using IHC analysis.
  -  To examine the potential predictive role of such biomarkers in patients undergoing adjuvant interferon alfa therapy.
  -  To analyze the correlation between the intensity of biomarker expression and survival of this cohort both in the observation and in the interferon-treated groups.
  -  To examine the prognostic role of these biomarkers on the outcome associated with melanoma in the EST-1690 cohort using quantitative-PCR.
  -  To isolate RNA from the primary specimens from patients enrolled in the EST-1690 cohort to assess the expression of genes suggested by cDNA microarray and IHC analyses (e.g., NCOA3, SPP1, and RGS1) as prognostic or predictive markers.
  OUTLINE: Samples from the EST-1690 cohort are obtained and analyzed for several biomarkers (i.e., NCOA3, SPP1, and RGS1) via immunohistochemistry and quantitative PCR. RNA is isolated from the specimens to assess gene expression via quantitative PCR.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of melanoma
  -  No metastatic disease at diagnosis
  -  Treated on protocol EST-1690
  -  Primary tumor tissue specimens available
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

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

Clinical trial: Ultraviolet Light Exposure and Immunosuppression in Cutaneous Melanoma

Summary: This project seeks to understand differences in the serum vitamin D levels and immune status in cutaneous malignant melanoma patients with different UV exposure histories in New Mexico.

Detailed description: It is well established that ultraviolet radiation (UV) exposure is related to the development of melanoma. There is also evidence that immune reactions are altered after UV exposure in the skin (locally) and perhaps throughout the body (systemically). Additionally, while the role of vitamin D and melanoma development has not been fully established, UV-B exposure is essential for vitamin D production in the skin. Increased sun exposure is also related to the presence of solar elastosis, which might protect (1) or improve survival from melanoma. Thus, melanoma represents a unique model for studying UV exposure, the immune system, and vitamin D. Malignant melanoma is an antigenic cancer; therefore, the role of UV exposure-induced immunosuppression and vitamin D production in the recognition, destruction and growth inhibition of cancerous melanocytes is worth further study.
  To underscore the importance of this project, the Scientific Advisory Committee of the Melanoma Research Foundation and the Steering Committee of the Society of Melanoma Research have indicated a need to collect more human data on the host immune response mechanisms in melanoma and also to focus on the skin as a whole microenvironment, moving away from only in vitro experiments.

Eligibility: Inclusion Criteria:
  -  Resident of New Mexico
  -  Age between the 1 and 95
  -  Newly diagnosed with cutaneous invasive melanoma; any stage permitted (ICDO C44.0-9) between September 1, 2008 and December 31, 2011.
  -  SSM (superficial spreading melanoma) and NM (nodular melanoma) histological subtypes are allowed
  -  Access to a telephone or be able to participate in a personal interview at the clinic
  -  Physically and mentally competent to complete a 1-hour telephone or personal interview
  Exclusion Criteria:
  -  Ocular melanoma, LMM (lentigo maligna melanoma) or ALM (acral lentigo melanoma), and mucosal melanoma cases.
  -  No access to a telephone or is not able to meet with the interviewer.

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

Clinical trial: Efficacy and Safety Study of PEG-rIL-29 Plus Ribavirin to Treat Chronic Hepatitis C Virus Infection

Summary: Interleukin 29 (IL-29) is a substance that is produced in the body to help fight viral infections. The purpose of this study is to evaluate the safety and antiviral effects of several different doses of PEG-rIL-29 (a man-made form of IL-29) when it is given in combination with daily oral doses of ribavirin (an antiviral drug) to subjects with hepatitis C infection who have received no prior treatment for this disease.

Detailed description: PEG-rIL-29 (also known as PEG-interferon lambda) is a unique Type III interferon molecule that has demonstrated antiviral activity when administered weekly for 4 weeks to treatment-relapsed and treatment-naive subjects with genotype 1 hepatitis C virus (HCV) infection. Because PEG-rIL-29 binds to a unique receptor with a more limited distribution than the receptor for interferon (IFN)-α, it may have the potential to treat HCV without some of the treatment-limiting side effects associated with IFN-α-based therapies. The purpose of this Phase 2a/b randomized, controlled, multicenter study is to compare the safety and efficacy of PEG-rIL-29 and peginterferon alfa-2a, both administered subcutaneously weekly for up to 48 weeks in combination with daily oral ribavirin, in treatment-naive subjects with chronic genotype 1, 2, 3, or 4 HCV infection. The initial part of the study (Phase 2a) will be conducted as an open-label study; the second part of the study (Phase 2b) will be conducted as a blinded study. The above information provided in this listing is specific to the Phase 2b portion of the study. In addition, two small open-label substudies will be conducted to evaluate the efficacy of 24-week treatment with PEG-rIL-29 and ribavirin in subjects with HCV genotype 1 who have a particular genetic polymorphism associated with favorable response (n=60) and to evaluate the efficacy of 16-week treatment with PEG-rIL-29 and ribavirin in subjects with HCV genotype 2 or 3 (n=30).

Eligibility: Inclusion Criteria:
  -  No prior therapy for chronic HCV, other than up to 2 weeks of single-agent therapy with a direct-acting antiviral agent, including but not limited to, a protease or polymerase inhibitor
  -  HCV genotype 1, 2, 3, or 4
  -  HCV RNA ≥100,000 IU/mL
  -  ALT and AST ≤5.0 × ULN
  -  Documented absence of cirrhosis
  -  Able to comprehend the investigational nature of this study and sign an informed consent form
  Exclusion Criteria:
  -  Mixed genotype HCV infection
  -  Current or prior history of decompensated liver disease
  -  Received any investigational drug, including a direct-acting antiviral agent, within 60 days prior to receiving study drug
  -  Positive test for hepatitis B surface antigen, human immunodeficiency virus (HIV)-1, or HIV2 antibody at screening
  -  Active substance abuse, such as alcohol, or inhaled or injected drugs, within 6 months
  Additional inclusion and exclusion criteria are specified in the protocol.

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

Clinical trial: The Expression of PTEN Protein and mRNA in Malignant Cells of Chronic Myelomonocytic Leukemia

Summary: The purpose of this study is to evaluate the level of a specific protein (PTEN) in the cancer cells of chronic myelomonocytic leukemia (CMML) patients. This protein might be involved in the transformation from normal blood cells to leukemia cells. The PTEN protein has not been investigated in CMML specifically but it has been discovered in closely related cancers. If this study demonstrates an abnormality in this protein, future testing will be designed to evaluate the genetic abnormality that resulted in lack of the normal presence of this protein. The goal is that the results of this study will help to develop new drugs and strategies to treat the future patients with CMML by understanding the abnormality of the disease at the cellular and molecular levels. The results of this study can also be utilized by future studies to develop individualized treatment to patients who have abnormal levels of this protein.


Eligibility: Inclusion Criteria:
  -  Subject must be at least 18 years or older.
  -  Subject must sign informed consent.
  -  For study population only, the subject must have a CMML diagnosis based on the WHO 2009 criteria.
  -  For control population only, the subject must be deemed healthy with no hematologic disorders.

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

Clinical trial: Study of BMS-650032 With Peginterferon Alfa-2a Plus Ribavirin

Summary: The purpose of this study is to identify one or more doses of BMS-650032 that, when used in combination with pegylated-interferon alpha and ribavirin are safe and demonstrate sufficient activity against hepatitis C virus (Genotypes 1 and 4).


Eligibility: Inclusion Criteria:
  -  Subjects chronically infected with HCV genotype 1 (Phase 2a and Phase 2b)
  -  Subjects chronically infected with HCV genotype 4 (Phase 2b only)
  -  HCV RNA viral load of ≥ 10*5* IU/mL at screening
  -  BMI of 18 - 35 kg/m² at screening
  Exclusion Criteria:
  -  Cirrhosis (Phase 2a only)
  -  Decompensated cirrhosis (Phase 2b)
  -  Co-infection with HBV or HIV
  -  Hepatocellular carcinoma
  -  Prior treatment with anti-HCV drugs

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

Clinical trial: A Retrospective Study of Biomarkers in Non-Small Cell Lung Cancer

Summary: The purpose of this study is:
  1. To characterize the types and frequency of molecular alterations to the epidermal growth factor receptor (EGFR) pathway, FGFR4 and EML-ALK in Asian patients with non-small cell lung cancer
  2. To identify candidate biomarkers of importance in the EGFR and estrogen pathways
  Most, if not all, human malignancies including lung cancer are caused by somatic alterations of the genome, leading to activation of oncogenes or inactivation of tumor suppressor genes and their resultant oncogenic effects. In addition to mutations, increased chromosomal copy number (by amplification or polysomy) and DNA methylation are other mechanisms of oncogene activation and tumour suppressor gene inactivation respectively.
  Little is known about the relationship between these oncogenes of the EGFR family and the recently described oncogenes FGFR4 and fusion gene EML4-ALK. Recent data suggests molecularly defined subgroups of non-small cell lung cancer (NSCLC) exist and can be used to predict for sensitivity to targeted agents (erlotinib or gefitinib) or cytotoxic chemotherapy (pemetrexate, gemcitabine, platinum agents). The findings that estrogen receptors are present in lung tumours and that estrogen can stimulate growth and proliferation of lung cancers in vitro and in vivo are provocative. Further studies to evaluate the role of estrogens and other sex hormones in lung cancer are warranted.
  A further understanding of the molecular indicators of lung cancer prognosis and treatment prediction would improve drug development and patient treatment selection.
  Archived paraffin-embedded and fresh frozen NSCLC tumor tissue will be obtained via the Department of Pathology and the National University Tissue Repository respectively. Clinico-pathological characteristics will be obtained from the case records, Pathology and Tissue Repository. DNA will be isolated using standard techniques. Sequencing of genes in the EGFR signaling pathway: EGFR, KRAS, ErbB2, ErbB3, MET, PI3K, and BRAF as well as FGFR4. Unstained slides from the paraffin-embedded tissue will be obtained and subjected to fluoresce in vitro hybridization (FISH) for breakpoints in the EML4 and ALK genes as previously described. For cases that have been snap-frozen, RNA will be extracted and EML4-ALK fusions will be confirmed using RT-PCR and pre-specified primers. To analyse the expression of proteins of putative relevance to EGFR function (such as EGFR, ErbB2, ErbB3, AKT, MET, STAT, ERK, MAPK, cyclin D1, C/EBPa), downstream effects of EGFR: cell proliferation (Ki-67), angiogenesis (CD34, VEGF-A), apoptosis (bcl-2), metastasis, and hormonal influence (oestrogen and progesterone receptors, aromatase), TMA technology will be utilised. The status of the tumor suppressor genes PTEN and C/EBPa will be analysed.


Eligibility: Inclusion Criteria:
  Exclusion Criteria:

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

Clinical trial: Early Diagnosis of Malignant Transformation of Pigmentary Skin Lesions

Summary: Malignant Melanoma is a deadly skin cancer that can be cured if diagnosed early. To date atypical pigmented skin lesions are diagnosed by appearance alone and many moles and lesions are excised unnecessarily and on the other hand malignant lesions are missed and diagnosed too late. In this study a protein conjugated to a florescent dye is spread on a suspicious pigmented lesion, the hypothesis is that this protein binds to malignant cells only and thus with a special camera that picks up the dye we can find pigmented lesions with early malignant transformation.


Eligibility: Inclusion Criteria:
  -  pigmented lesion indicated for surgical excision
  -  over 18 years of age
  Exclusion Criteria:
  -  pregnancy

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

Clinical trial: A Study of BEZ235 in Adult Japanese Patients With Advanced Solid Tumors

Summary: In this study, BEZ235 will be administered to adult patients with advanced solid tumors whose disease has progressed despite standard therapy or for whom no standard therapy exists. The trial will confirmed the safety and tolerability and determine the MTD of BEZ235 in Japanese patients.


Eligibility: Inclusion Criteria:
  1. Patients with histologically-confirmed, advanced unresectable solid tumors who have progressed on (or not been able to tolerate) standard therapy or for whom no standard anticancer therapy exists.
  2. At least one measurable lesion as defined by RECIST criteria for solid tumors.
  3. Age ≥ 20
  4. Eastern Cooperative Oncology Group Performance Status (ECOG P.S.) of ≤ 2
  5. Life expectancy of ≥ 12 weeks
  6. Patients must have the laboratory values Patients in the expansion part of this study have to meet the following criteria in addition to the criteria described above.
  7. Availability of a representative tumor tissue specimen (either archival tumor or fresh tumor biopsy) for pre-screening.
  8. Patients whose molecular status proved to meet the criteria (PIK3CA mutation/amplification and/or PTEN mutation and/or low/null PTEN expression) during pre-screening.
  Exclusion Criteria:
  1. Patients who have brain metastases or who have signs/symptoms attributable and have not been assessed with radiologic imaging to rule out the presence of brain metastases
  2. Patients with any peripheral neuropathy ≥ CTCAE grade 2
  3. Patients with unresolved diarrhea ≥ CTCAE grade 2
  4. Patients with a history of photosensitivity reactions to other drugs
  5. Women of child-bearing potential who are pregnant or breast feeding or adults of reproductive potential not employing an effective method of birth control. Barrier contraceptives must be used throughout the trial in both sexes. Women of child-bearing potential, defined as sexually mature women who have not undergone a hysterectomy or who have not been naturally postmenopausal for at least consecutive 1 years (i.e., who has had menses any time in the preceding consecutive 2 years), must have a negative serum pregnancy test ≤ 7 days prior to starting BEZ235.
  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: Differences in Evoked Intracellular Interferon Signaling Pathways Using Single Cell Phosphoprotein Profiling

Summary: Purpose:
  The purpose of this exploratory study is to evaluate phosphoprotein profiling to determine differences in the intracellular actions of interferon or interferon stimulated genes among people with different treatment outcomes to interferon based therapy for hepatitis C (HCV). Participants: Patients with genotype 1 HCV who have had interferon based therapy at the University of North Carolina (UNC). Procedures: Thirty patients with varied responses to treatment will be given a single subcutaneous injection of interferon alpha 2b. Prior to the injection and at 30 minutes, 1,2,4,6,12 and 20 hours after injection, blood will be drawn for analysis of phosphoprotein profiling and changes in serum cytokines.


Eligibility: Inclusion Criteria:
  To be eligible for this study, subjects must meet the following inclusion criteria:
  -  Willing and able to provide informed consent
  -  Males or females age 18 - 65 years
  -  For women of childbearing potential, negative blood pregnancy test documented within the 24-hour period prior to IFN-α administration
  -  History of genotype 1 HCV infection previously treated with peginterferon and ribavirin and with a virological response that can be determined from retrospective review of medical records
  -  A washout period of >12 weeks between the last dose of prescribed peginterferon and ribavirin and the screening visit
  Exclusion Criteria
  Subjects with any of the following will not be eligible for participation:
  -  Neutrophil count <1500 cells/mm3, Hgb <12 g/dL in women or 13 g/dL in men, or platelet count <75,000 cells/mm3 at screening
  -  Serum creatinine level >1.5 times the upper limit of normal at screening
  -  Poorly controlled psychiatric illness, as determined by the study physician, which can be exacerbated by interferon therapy
  -  Infection requiring antibiotics, symptomatic viral infection, inflammatory process requiring therapy, or allergic reactions in the week immediately preceding the inpatient study visit
  -  Use of medications that affect the immune system (e.g. glucocorticoids, chronic NSAIDs daily) in the week immediately preceding the inpatient study visit
  -  History of immunologically mediated disease (e.g., inflammatory bowel disease, idiopathic thrombocytopenic purpura, lupus erythematosus, autoimmune hemolytic anemia, psoriasis, rheumatoid arthritis)
  -  Women with ongoing pregnancy or breast-feeding
  -  History or other evidence of bleeding from esophageal varices or other conditions consistent with decompensated liver disease
  -  History of a seizure disorder or current anticonvulsant use
  -  History of major organ transplantation with an existing functional graft
  -  History of thyroid disease poorly controlled on prescribed medications
  -  History or other evidence of severe illness or any other conditions which would make the patient, in the opinion of the investigator, unsuitable for the study

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

Clinical trial: Safety, Tolerability & Potential Anti-cancer Activity of Increasing Doses of AZD5363 in Different Treatment Schedules

Summary: This study is designed to investigate the safety and tolerability of a new drug, AZD5363, in patients with advanced cancer - and to identify a dose and schedule that can be used in the future. This study will also investigate how the body handles AZD5363 (ie, how quickly the body absorbs and removes the drug). This study will also investigate anti-tumour activity of AZD5363 in patients with advanced / metastatic breast, gynaecological cancers or other solid cancers bearing either AKT1 / PIK3CA or PTEN mutation.

Detailed description: A Phase I, Open-Label, Multicentre Study to Assess the Safety, Tolerability, Pharmacokinetics and Preliminary Anti-tumour Activity of Ascending Doses of AZD5363 under Adaptable Dosing Schedules in Patients with Advanced Solid Malignancies.

Eligibility: Inclusion Criteria:
  -  Aged at least 18 years.
  -  Parts A,B: The presence of a solid, malignant tumour, excluding lymphoma, that is resistance to standard therapies or for which no standard therapies exist.
  -  ER+/HER2+ breast, ovarian, cervical, endometrial cancer, or other solid cancers, resistance to standard therapies with a PIK3CA gene mutation (Part C), AKT1 gene mutation (Part D) or a dysregulatory aberration on the PIK/AKT pathway (Part D), advanced or metastatic ER+ positive breast cancer that has an AKT1 gene mutation (Part E) or advanced or metastatic ER+ positive breast cancer that has a PTEN gene mutation (Part F).
  -  The presence of at least one lesion that can be accurately assessed at baseline by CT, MRI or plain X-ray and is suitable for repeated assessment. Estimated life expectancy of more than 12 weeks.
  -  Estimated life expectancy of more than 12 weeks.
  Exclusion Criteria:
  -  Clinically significant abnormalities of glucose metabolism.
  -  Spinal cord compression or brain metastases unless asymptomatic, treated and stable (not requiring steroids).
  -  Evidence of severe or uncontrolled systemic diseases, including active bleeding diatheses or active infections including hepatitis B, C and HIV.
  -  Evidence of clinically significant cardiac abnormalities, uncontrolled hypotension, left ventricular ejection fraction below the lower limit of normal for the site or experience of significant cardiac interventional procedures.
  -  A bad reaction to AZD5363 or any drugs similar to it in structure or class.

Relevance to patient case: possibly relevant