araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: INST 1204: PIK3CA Mutations as Biomarkers for Metastasis in Colon Cancer

Summary: This proposal seeks to further understand the contribution of the PIK3CA mutations in colon cancer, by correlating the type of hotspot mutation with the development of metastases in stage II and stage Ill patients.
  In order to do this, DNA will be extracted from either frozen or paraffin embedded colon cancer tissues to sequence PIK3CA, KRAS and BRAF. Clinical outcome data will be gathered to include metastases and survival to correlate with PIK3CA, KRAS and BRAF mutational status. Patients with stage II and stage Ill colon cancers will be identified in the University of New Mexico Human Tissue Repository and the NIH PLCO prevention trial biorepository.
  Existing banked tissues of stage II and Ill colon cancers will be collected. There will be no direct contact with living individuals. Epidemiological factors such as age, race, gender and outcome data of metastases and survival will be collected.

Detailed description: This proposal aims to identify PIK3CA mutations as a biomarker for metastasis.
  In order to do this, DNA will be extracted from either frozen or paraffin embedded colon cancer tissues to sequence PIK3CA, KRAS and BRAF. Clinical outcome data will be gathered to include metastases and survival to correlate with PIK3CA, KRAS and BRAF mutational status. Patients with stage II and stage Ill colon cancers will be identified in the University of New Mexico Human Tissue Repository and the NIH PLCO prevention trial biorepository.
  Existing banked tissues of stage II and Ill colon cancers will be collected. There will be no direct contact with living individuals. Epidemiological factors such as age, race, gender and outcome data of metastases and survival will be collected.
  Specific Aims:
  1. To develop and standardize methods for high throughput DNA extraction and analysis from colon tumors of patients with stage II and stage III disease harboring PIK3CA exon 9 and exon 20 mutations.
  2. To determine the correlation between wild type and PIK3CA, PIK3CA exon 9 and PIK3CA exon 20 mutations and development of metastatic disease and overall survival in stage II and stage III patients with colorectal cancer.

Eligibility: Inclusion Criteria:
  -  Specimen from patients with stage II and stage III colon cancer.
  Exclusion Criteria:
  -  Any other stage or type of disease outside of stage II and stage III colon cancer.

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Immunization of HLA-A201 Patients With Metastatic Melanoma Using a Combination of Immunodominant Peptides From Three Melanoma Antigens, MART-1, GP100 and Tyrosinase

Summary: This is a study of a melanoma tumor antigen peptide vaccine. Peptides representing HLA-A201 restricted T cell epitopes of the melanoma antigens, MART-1, gp100 and tyrosinase will be administered emulsified in Incomplete Freund's Adjuvant, (IFA) to HLA-A201 patients with melanoma. The study is designed to evaluate the potential therapeutic role, immunologic effects and toxicity of repeated doses of this peptide vaccine administered subcutaneously.
  Immune reactivity to the peptide epitope will be monitored in all patients by analysis of melanoma-specific T cell precursors prior to and after immunization.

Detailed description: This is a study of a melanoma tumor antigen peptide vaccine. Peptides representing HLA-A201 restricted T cell epitopes of the melanoma antigens, MART-1, gp100 and tyrosinase will be administered emulsified in Incomplete Freund's Adjuvant, (IFA) to HLA-A201 patients with melanoma. The study is designed to evaluate the potential therapeutic role, immunologic effects and toxicity of repeated doses of this peptide vaccine administered subcutaneously.
  Immune reactivity to the peptide epitope will be monitored in all patients by analysis of melanoma-specific T cell precursors prior to and after immunization.

Eligibility: Any patient 16 years of age or older with measurable metastatic melanoma who has failed standard treatment and has an expected survival of greater than three months.
  Must be HLA-A0201.
  Serum creatinine of 2.0 mg/dl or less.
  Bilirubin 1.6 mg/dl or less.
  WBC 3000/mm(3) or greater.
  Platelet count 90,000 mm(3) or greater.
  Serum AST/ALT less then two times normal.
  ECOG performance status of 0 or 1.
  Patients of both genders must be willing to practice effective birth control during the trial.
  Must not be undergoing or have undergone in the past 3 weeks any other form of therapy except surgery for their cancer.
  Must not have active systemic infections, coagulation disorders, or other major medical illnesses of the cardiovascular or respiratory systems or any known immunodeficiency disease.
  Must not require steroid therapy.
  Must not be pregnant.
  Must not be positive for hepatitis B(s)AG or HIV antibody.
  Must not have had a known allergic reaction to Incomplete Freund's Adjuvant (IFA).

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: SWOG-9430: Surgery in Treating Patients With Metastatic Melanoma

Summary: RATIONALE: Surgery may be effective therapy in treating patients with metastatic melanoma.
  PURPOSE: This phase II trial is studying how well surgery works in treating patients with metastatic melanoma.

Detailed description: OBJECTIVES:
  -  Assess overall and progression-free survival in patients with metastatic melanoma (beyond the draining lymph nodes) after complete surgical resection of all known disease.
  -  Determine the ability of the Southwest Oncology Group Melanoma Committee to enroll patients with metastatic melanoma who can be resected to a disease-free state.
  OUTLINE: This is a multicenter study.
  All patients undergo gross total resection of all known disease. Patients whose disease cannot be completely resected or who have disease recurrence after surgery are removed from study. Patients found to have microscopic residual disease after surgery are considered completely resected. Resected tissue is submitted for analysis on protocol SWOG-9431.
  Patients may receive any adjuvant therapy (e.g., radiotherapy, interferon, and/or vaccines) deemed clinically appropriate by the treating physician.
  Patients are followed periodically for 5 years after study entry.
  PROJECTED ACCRUAL: A total of 100 eligible patients with completely surgically resected disease will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically confirmed metastatic melanoma that is deemed grossly surgically resectable
  -  Multiple resected sites or metastatic melanoma of unknown primary allowed provided all known disease can be grossly resected
  -  Recurrence in iliac lymph nodes after inguinal lymph dissection allowed
  -  No metastatic disease beyond the lesions planned for resection
  -  Confirmed by CT scan of chest, abdomen, pelvis, and CT or MRI of brain within 42 days of study
  -  Concurrent registration on protocol SWOG-9431 required
  PATIENT CHARACTERISTICS:
  Age:
  -  18 and over
  Performance status:
  -  SWOG 0-2
  Hematopoietic:
  -  Not specified
  Hepatic:
  -  Not specified
  Renal:
  -  Not specified
  Other:
  -  No other malignancy within the past 5 years except adequately treated basal cell or squamous cell skin cancer, carcinoma in situ of the cervix, or adequately treated stage I or II cancer from which patient is currently disease free
  -  Not pregnant
  PRIOR CONCURRENT THERAPY:
  Biologic therapy:
  -  Prior immunotherapy in the adjuvant or metastatic setting allowed
  Chemotherapy:
  -  Prior chemotherapy in the adjuvant or metastatic setting allowed
  Endocrine therapy:
  -  Prior hormonal therapy in the adjuvant or metastatic setting allowed
  Radiotherapy:
  -  Prior radiotherapy in the adjuvant or metastatic setting allowed
  Surgery:
  -  See Disease Characteristics
  -  At least 14 days since prior surgery in the adjuvant or metastatic setting
  Other:
  -  Recovered from prior therapy

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Detection of Melanoma Markers in Lymph Nodes or Peripheral Blood of Patients With Melanoma

Summary: RATIONALE: Diagnostic procedures may improve the ability to detect the presence or recurrence of disease.
  PURPOSE: Diagnostic trial to detect melanoma markers in the lymph nodes or peripheral blood of patients who have melanoma.

Detailed description: OBJECTIVES:
  -  Determine the feasibility of performing reverse transcriptase-polymerase chain reaction (RT-PCR) for five different tumor antigen genes using lymph node samples or peripheral blood from patients with melanoma.
  -  Determine the ability of PCR-positive lymph nodes or peripheral blood to predict relapse of disease in these patients.
  -  Determine the correlation of positive PCR results from peripheral blood with disease stage.
  OUTLINE: Lymph node biopsies or peripheral blood are obtained from patients. These specimens are examined by nested reverse transcriptase-polymerase chain reaction (RT-PCR) and analyzed for various tumor antigens.
  Patients may choose to be told the results of this testing, but the results do not influence or change the planned therapy. Brief counseling is required to discuss the results and their potential implications.
  Patients are followed for at least 2 years.
  PROJECTED ACCRUAL: A total of 30 patients for the lymph node portion and 80 patients (20 per stage of disease) for the peripheral blood portion will be accrued for this study within 3 years.

Eligibility: DISEASE CHARACTERISTICS:
  -  Clinically proven melanoma with indication to perform sentinel lymph node biopsy or elective lymph node dissection OR
  -  Histologically proven or diagnosis highly suspicious for melanoma
  PATIENT CHARACTERISTICS:
  Age:
  -  Any age
  Performance status:
  -  Not specified
  Life expectancy:
  -  Not specified
  Hematopoietic:
  -  Platelet count greater than 50,000/mm^3
  -  Hemoglobin greater than 7 g/dL
  Hepatic:
  -  PT less than 15 sec
  -  PTT less than 30 sec
  Renal:
  -  Not specified
  Other:
  -  No psychiatric illness that precludes compliance
  -  No other concurrent malignancy
  PRIOR CONCURRENT THERAPY:
  Biologic therapy
  -  Not specified
  Chemotherapy
  -  Not specified
  Endocrine therapy
  -  Not specified
  Radiotherapy
  -  Not specified
  Surgery
  -  Not specified

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Comparison of Dendritic Cells Versus Montanide as Adjuvants in a Melanoma Vaccine

Summary: In this study, a melanoma vaccine (5 melanoma peptides) is given with either Montanide or dendritic cells as adjuvants. This randomized trial will establish the safety of both vaccines and compare the 2 vaccine adjuvants in their efficacy to induce immune responses.

Detailed description: In this study, we will examine whether DCs pulsed with candidate melanoma-specific peptides and KLH can boost CTL responses to melanoma antigens in melanoma patients who are clinically free of disease but at high risk for recurrence. This vaccine will be compared to direct injection of the same peptides with KLH and Montanide as adjuvant.

Eligibility: Inclusion Criteria:
  -  Resected stage IIB, IIC, or stage III melanoma.
  -  Fully recovered from surgery
  -  Human leukocyte antigen (HLA) A*0201 positive.
  -  Age >18 years.
  -  Karnofsky performance status: >80% and normal labs.
  Exclusion Criteria:
  -  Prior chemotherapy.
  -  Known chronic infection with HIV, hepatitis B or C.
  -  Patients with known autoimmune disease [e.g. systemic lupus erythematosus (SLE), rheumatoid arthritis (RA)]. Patients with vitiligo are not excluded.
  -  Pregnant women.
  -  Patients with known allergy to gentamicin, tobramycin, streptomycin and amikacin (risk of cross-reaction between aminoglycosides).
  -  Patients who have known retinal or choroidal eye disease.
  -  Patients previously treated with one of the peptides used in this trial, melanoma protein vaccine, melanoma whole cell vaccines, or with Montanide are not eligible.
  -  Allergy to shellfish.

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Vaccine Therapy in Treating Patients With Malignant Melanoma

Summary: RATIONALE: Vaccines made from tumor cells may help the body build an effective immune response to kill tumor cells.
  PURPOSE: This phase II trial is studying vaccine therapy to see how well it works in treating patients with malignant melanoma.

Detailed description: OBJECTIVES:
  -  Determine the response in patients with in-transit cutaneous malignant melanoma treated with active immunotherapy comprising polyvalent melanoma vaccine (Canvaxin™).
  OUTLINE: This is an open-label, multicenter study.
  Patients receive polyvalent melanoma vaccine (Canvaxin™) subcutaneously to the armpit and groin areas every 2 weeks for approximately 10 weeks (5 doses) and then every 4 weeks for up to approximately 1 year of total treatment (total of 15 doses). Patients with no evidence of response at week 24 receive no further treatment. Patients whose disease continues to respond after completion of study treatment are eligible for a new study in which they will continue treatment with polyvalent melanoma vaccine (Canvaxin™).
  After completion of study treatment, patients are followed at 30 days.
  PROJECTED ACCRUAL: A total of 100 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically confirmed malignant melanoma
  -  At least 1 in-transit skin lesion measuring 3-10 mm in the longest diameter
  PATIENT CHARACTERISTICS:
  Age
  -  18 to 80
  Performance status
  -  Not specified
  Life expectancy
  -  Not specified
  Hematopoietic
  -  Not specified
  Hepatic
  -  Not specified
  Renal
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  Biologic therapy
  -  Not specified
  Chemotherapy
  -  Not specified
  Endocrine therapy
  -  Not specified
  Radiotherapy
  -  Not specified
  Surgery
  -  Not specified

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Study of Metastatic Ocular Melanoma

Summary: This study evaluates treatment with combination versus monotherapy for patients with metastatic ocular melanoma.

Detailed description: Treatment of patients with metastatic ocular melanoma with combination chemotherapy Gemcitabine and Treosulfan versus monotherapy with Treosulfan as first-line chemotherapy.

Eligibility: Inclusion Criteria:
  -  Metastatic ocular melanoma
  Exclusion Criteria:
  -  Prior treatment with chemotherapy
  -  Active 2nd malignancy
  -  Cerebral metastasis

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Study of NY-ESO-1 ISCOMATRIX® in Patients With High-risk, Resected Melanoma

Summary: The purpose of this trial is to assess whether treatment with NY-ESO-1 ISCOMATRIX® vaccine improves outcomes for people with Malignant Melanoma which has been removed, but is at high risk of relapse.

Detailed description: NY-ESO-1 protein is an immune target found in many cancers including melanoma. ISCOMATRIX® adjuvant enhances immune responses. This trial compares NY-ESO-1 ISCOMATRIX® vaccine with ISCOMATRIX® adjuvant alone to assess whether treatment with NY-ESO-1 ISCOMATRIX® vaccine improves outcomes for participants with Malignant Melanoma which has been removed, but is at high risk of recurrence.
  Eligible participants are randomly allocated to a treatment arm. Treatment involves four intramuscular (into a muscle) injections (1 injection every 4 weeks x 3, plus 1 injection at 6 months).
  Participants are assessed for recurrence of melanoma, safety and immune responses (by blood test) over the 18 month study period. Off study, their own doctor will follow them for melanoma recurrence and survival.

Eligibility: Inclusion Criteria:
  -  Histologically proven malignant melanoma.
  -  Tumor expression of NY-ESO-1 antigen by immunohistochemistry.
  -  Fully resected AJCC stage IIc, IIIb, IIIc or IV melanoma.
  -  Within six months of surgery for melanoma.
  -  Full recovery from surgery.
  -  No immunotherapy or systemic adjuvant therapy for melanoma since most recent relapse and/or resection. (Previous adjuvant therapy accepted providing pt relapsed and resected after this.)
  -  Age 18 years or older.
  -  Able to give written informed consent.
  -  Vital laboratory parameters within normal range, or protocol specified ranges.
  Exclusion Criteria:
  -  Other serious or significant illnesses.
  -  Resected cerebral metastases.
  -  Ocular melanoma.
  -  Other malignancy within last 3 years, except for treated non-melanoma skin cancer and cervical cancer in situ.
  -  Using immunosuppressive drugs.
  -  Anticoagulation.
  -  Known HIV positivity.
  -  Chemotherapy or radiation therapy in last four weeks (6 weeks for nitrosourea drugs).
  -  Not available for immunological and clinical follow-up assessments.
  -  Participation in prior clinical trial involving an investigational agent within last 4 weeks.
  -  Previous isolated limb perfusion (ILP).
  -  Pregnancy or breastfeeding.
  -  Refusal or inability to use effective means of contraception for women of childbearing potential.
  -  Mental impairment that may compromise ability to give informed consent and to comply with study requirements.

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Vaccination With Tumor mRNA in Metastatic Melanoma - Fixed Combination Versus Individual Selection of Targeted Antigens

Summary: The purpose of the vaccination protocol is to induce specific immune responses against melanoma associated antigens by intradermal injections of mRNA coding for the corresponding antigen.

Detailed description: vaccination protocol to induce clinically specific immune responses against melanoma associated antigens by intradermal injections of mRNA coding for the corresponding antigens. Half of patients is treated with mRNA coding for Melan-A, Mage-A1, Mage-A3, Survivin, GP100 and Tyrosinase. The other half of patients is treated with an individualized selection of mRNAs after analysis of overexpressed melanoma antigens in autologous tumor tissue. GM-CSF is used as an adjuvants. Phase I/II clinical trial to analyse safety and immune responses in stage III/IV melanoma patients.

Eligibility: Inclusion Criteria:
  -  malignant melanoma stage III/IV
  -  fresh frozen tumor tissue available
  -  informed consent given
  -  Karnofsky >= 70%
  Exclusion Criteria:
  -  brain metastasis
  -  parallel chemotherapy
  -  systemic treatment with glucocorticoids
  -  other malignancies

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: A Study to Evaluate RAF265, an Oral Drug Administered to Subjects With Locally Advanced or Metastatic Melanoma

Summary: The purpose of this study is to determine the safety profile, pharmacokinetics, pharmacodynamics and maximum tolerated dose of RAF265 in patients with locally advanced and metastatic melanoma.
  Phase II portion of study (dose expansion) has been cancelled with Amendment 7 as of Dec 2011.

Detailed description: The Ras/Raf/MEK/ERK pathway plays a prominent role in controlling several key cellular functions including growth, proliferation and survival. B-Raf is a member of the Ras/Raf/MEK/ERK pathway and is frequently mutated in melanoma resulting in activation of the MAPK pathway. RAF265 is a novel, orally active, small molecule with potent inhibitory activity against B-Raf kinase and additional antiangiogenic activity through inhibition of vascular endothelial growth factor receptor type 2 (VEGFR-2) in non-clinical studies.
  The primary objectives of this study are to determine the maximum tolerated dose (MTD), dose limiting toxicities (DLTs), and the safety profile of RAF265 when administered orally to subjects with locally advanced or metastatic melanoma; to determine the plasma pharmacokinetics (PKs) of orally administered RAF265; and to evaluate potential pharmacodynamic effects of RAF265 using tumor biopsies, peripheral blood samples, and tumor imaging.

Eligibility: Inclusion Criteria:
  1. Confirmed diagnosis of melanoma, locally advanced AJCC Stage IIIB to metastatic Stage IV
  2. Measurable disease - at least one lesion measured in at least one dimension as ≥ 20 mm with conventional techniques or ≥ 10 mm with spiral computed tomography (CT) scan
  3. ECOG performance status of 0 or 1
  4. No concurrent anticancer or investigational therapy for at least 4 weeks prior to enrollment
  5. No major surgery for at least 4 weeks prior to enrollment
  Exclusion Criteria:
  1. Significant cardiac disease or other significant medical/psychiatric disease
  2. History of primary central nervous system tumor or brain metastases onths
  3. History of melena, hematemesis, or hemoptysis within the last 3 months
  4. Previous therapy with certain molecularly targeted agents

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Genetic Analysis of Familial Melanoma

Summary: In collaboration with members of The International Melanoma Consortium, we propose to study melanoma in families lacking mutations in the cyclin-dependent kinase inhibitor 2 (CDKN2 or p16) gene, or the cyclin-dependant kinase 4 (CDK4). CDKN2 and CDK4 are both genes that encode presumed tumor suppressor genes, mutant forms of which are known to cause increased susceptibility to melanoma. The purpose of the present study then is to confirm the existence of and to identify additional gene(s) involved in heritable melanoma (cutaneous and ocular) and their precursor lesions (atypical nevi) by linkage analysis and gene mapping strategies. It is clear that the risk to develop atypical nevi and/or melanoma is strongly influenced by genetic and environmental factors (e.g. sun exposure). Characterization of such genes could provide important insights into the inheritance, pathogenesis, and treatment of this increasingly important disease.

Detailed description: In collaboration with members of The International Melanoma Genetics Consortium, we propose to study melanoma in families lacking mutations in the cyclin-dependent kinase inhibitor 2 (CDKN2A), or the cyclin-dependant kinase 4 (CDK4) genes. CDKN2 and CDK4 are both genes that encode presumed tumor suppressor genes, mutant forms of which are known to cause increased susceptibility to melanoma. The purpose of the present study then is to confirm the existence of and to identify additional gene(s) involved in heritable melanoma (cutaneous and ocular) and their precursor lesions (atypical nevi) by linkage analysis and gene mapping strategies. It is clear that the risk to develop atypical nevi and/or melanoma is strongly influenced by genetic and environmental factors (e.g. sun exposure). Characterization of such genes could provide important insights into the inheritance, pathogenesis, and treatment of this increasingly important disease.

Eligibility: -  INCLUSION CRITERIA:
  Inclusion into this study was restricted to families containing at least three CMM cases with DNA available for genotyping, and CDKN2A and CDK4 involvement and had been excluded.
  All families must be mutation negative for both CDKN2A and CDK4.
  This study will also include families with at least one case of ocular and two cases of other cutaneous melanomas, or at least 2 ocular melanomas (except where they occur in parent and child).
  EXCLUSION CRITERIA:
  Any family showing evidence of haplotype sharing in the 9p21-p22 region, where CDKN2A is located, was also excluded.

Relevance to patient case: not relevant