araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 78-year-old female with sarcoma; genetic feature: MDM2

Clinical trial: Elucidating the Genetic Basis of the Pleuropulmonary Blastoma (PPB) Familial Cancer Syndrome

Summary: Pleuropulmonary Blastoma (PPB) is a rare lung tumor which develops in childhood. The underlying genetic factors which contribute to the development and progression of PPB are not defined. We are working to identify the genetic factors which may contribute to the development of this rare tumor.

Detailed description: Studies of inherited cancer syndromes have provided unique opportunities to uncover and explain important cellular pathways with broad relevance to both sporadic cancers and human development. This proposal studies the cancer predisposition syndrome originally described as a familial form of pleuropulmonary blastoma (PPB). PPB is a rare, aggressive lung cancer that affects young children. Children with PPB and/or their family members are at increased risk for a number of rare conditions, including Wilms tumor, rhabdomyosarcoma, brain tumors, ovarian tumors and nodular hyperplasia of the thyroid gland. In 2009, we mapped a PPB locus and identified germline, loss of function mutations in one copy of DICER1 as the genetic basis of this syndrome. DICER1 encodes a protein that performs the final critical step in maturation of microRNAs (miRNAs). miRNAs are an important form of gene regulation. The syndrome's varied nature is likely attributable to the various roles of miRNAs during different developmental and/or functional circumstances. This study focuses on defining the full phenotype of this cancer predisposition syndrome including penetrance, expressivity in children and adults, pathologic classification of disease and spectrum of predisposing DICER1 mutations. Improved understanding of the clinical and genetic features of this cancer predisposition syndrome is essential to facilitate early diagnosis when the diseases are most curable, and to create genetic counseling and educational materials to guide medical care.

Eligibility: Inclusion Criteria:
  -  Child or adult diagnosed with pleuropulmonary blastoma, cystic nephroma, embryonal rhabdomyosarcoma of uterine cervix, ovarian Sertoli-Leydig tumor or gynandroblastoma, pineoblastoma, pituitary blastoma, nasal chondromesenchymal hamartoma, medulloepithelioma, Wilms tumor, germline or mosaic DICER1 mutation
  Exclusion Criteria:
  -  child or adult who does not fit inclusion criteria as listed above

Relevance to patient case: not relevant
Patient case: 78-year-old female with sarcoma; genetic feature: MDM2

Clinical trial: Novel Biochemical and Molecular Determinants for Soft Tissue Sarcoma

Summary: The purpose of this study is to study normal and sarcoma cells. To study these cells we need to have human tissue. You will be having or have already had a procedure to remove tissue. We would like to use some of this tissue. We will use it for laboratory studies on the diagnosis,behavior and treatment of sarcoma. We will perform an extensive analysis of your samples. We will only use extra tissue left over after all needed testing has been done or remove an additional small amount of tissue if you are having a biopsy. We will also take blood samples before and/or after your procedure to measure biochemical factors that may help us predict the behavior of sarcoma.

Detailed description: In this protocol, we plan to identify specific markers from biochemical, proteomic, epigenetic and molecular genetic analyses that predict clinical outcome, responsiveness to therapy and might serve as promising therapeutic targets in patients with soft tissue sarcoma.

Eligibility: Inclusion Criteria:
  -  All patients with known or suspected sarcoma who will have or have had tissue removed for therapeutic or diagnostic purposes.
  -  Patients will be entered without preference for any particular racial/ethnic group or gender.
  -  Patients may have received prior hormonal therapy, cytotoxic chemotherapy, irradiation, immunotherapy or surgical therapy.
  -  Tissue specimens must be large enough in quantity to allow routine pathologic analysis, with the research laboratory specimen removed from the residual specimen, which would otherwise be discarded. Optimal tissue amounts for snap freeze: Core biopsy - 2 tissue cores Incisional biopsy- 0.5 to 1.5 grams Resected sarcoma specimen- 1.0 to 50 grams depending on size of specimen Normal fat or muscle tissue - 0.5 to 4.0 grams (if available from resected sarcoma specimen) Optimal tissue amounts for RNA later Core biopsy - 2 tissue cores Incisional biopsy- 30 mg (three 3 x 3 x 3 mm cubes) Resected sarcoma specimen - 30 mg (three 3 x 3 x 3 mm cubes) Normal fat or muscle tissue - 30 mg (three 3 x 3 x 3 mm cube
  Exclusion Criteria:
  - None

Relevance to patient case: not relevant
Patient case: 78-year-old female with sarcoma; genetic feature: MDM2

Clinical trial: High-Dose Proton/Photon RT + Surgery of Sarcomas of the Thoracic, Lumbar Spine/Sacrum

Summary: The purpose of this study is to test the effectiveness of high dose radiation administered by both proton and photon therapy. Radiation is an effective treatment for many types of tumors and it is thought that radiation alone, when given in much higher doses over a shorter period of time, may be more effective in controlling recurrence of sarcoma.

Detailed description: -  In this study three types of radiation will be used: standard radiation (called photon); alternative form of radiation called proton beam therapy; and a localized radiation applicator plaque that can be applied to the surface of the dura (the fibrous outer envelope that surrounds the spinal cord and fluid surrounding the spinal cord) at time of surgical removal of the tumor.
  -  Radiation treatments (photon and proton) and possibly surgical removal of portions of the tumor with intraoperative radiation delivery to the surface dura with intraoperative radiation delivery will be performed over a period of 12 weeks. As part of the treatment planning process, participants will need two treatment planning CT scans and 2-3 treatment planning sessions.
  -  Participants will receive, in total, 39-43 photon/proton treatments.

Eligibility: Inclusion Criteria:
  -  Pathological diagnosis of malignant mesenchymal tumor of the thoracic/lumbar/spine/sacrum or paraspinal soft tissues involving nerve roots or extending into spinal canal. Inter-osseous bone sarcomas are to be managed by wide resectional surgery for patients that are medically operable.
  -  Patient tumor status: 1) post biopsy or post resection with gross residual disease 2) post grossly complete resection but with margins positive or very close or tumor spill or cut through
  -  Lesion may be primary or recurrent after prior surgery
  -  No clinical, radiographic or other evidence of distant metastasis
  -  Fit for the exposure of the affected vertebral segment
  -  Life expectancy of greater than 36 months
  -  KPS equal to or greater than 70
  -  18 years of age or older
  -  Declines radical surgery
  -  No prior radiation treatment to the affected spine region
  Exclusion Criteria:
  -  Pregnancy
  -  Disease/conditions characterized by high radiation sensitivity. These include genetic diseases, such as ataxia telangiectasia. Major local conditions which are the local tolerance viz., multiple surgical procedures, serious local injuries.
  -  No evident cord/cauda malfunction for causes other than effects of local tumor growth or due to metabolic effects of tumor

Relevance to patient case: not relevant
Patient case: 78-year-old female with sarcoma; genetic feature: MDM2

Clinical trial: Environmental Pollutants and the Risk of Soft Tissue Sarcoma: A Pilot Study

Summary: The purpose of this study is to assess the feasibility of conducting a large hospital based case control study of the role of dioxins and dioxinlike polychlorinated dibenzofurans (PCDFs) and polychlorinated biphenyls (PCBs).


Eligibility: Inclusion Criteria:
  -  Patients with Soft tissue sarcoma at MSKCC are eligible for this study if they meet the following criteria:
  -  Between 18 and 79 years of age
  -  were diagnosed within the previous 6 months with primary soft tissue sarcoma of one of the following histologic subtypes: liposarcoma, leiomyoscaroma, MFH, or synovial sarcoma
  -  are enrolled in protocol 02-060 ("Novel Biochemical and Molecularr Determinants for Soft Tissue Sarcoma"; PI, Dr. Samuel Singer)
  -  controls will be eligibile for this study if they meet the following criteria
  -  are b/w 18-79 years of age
  -  have no prior history of cancer (other than non melanoma skin cancer)
  Exclusion Criteria:
  -  Individuals will be excluded if they
  -  are unable to sign informed consent for medical or other reasons
  -  do not speak english

Relevance to patient case: not relevant
Patient case: 78-year-old female with sarcoma; genetic feature: MDM2

Clinical trial: Huntsman Biopsy Study

Summary: Bone and soft tissue sarcomas are currently classified based upon light microscopy supplemented by immunohistochemistry, but within many if not all of these tumor histologic types, considerable heterogeneity exists not only in microscopic appearance but also in biologic behavior and prognosis. Progress in the directed treatment of these tumors, particularly the sarcomas, awaits characterization of the gene profiles for these tumors. Orthopedic oncology researchers at Huntsman Cancer Institute at the University of Utah are establishing a tumor bank for this purpose. The long term objectives of this work include:
  1. creating tumor specific gene profiles to improve diagnostic accuracy
  2. performing gene set validation for diagnostic predictive power
  3. defining a discriminate gene list implicated in pathogenesis
  The tissue procured under this protocol at SUNY Upstate Medical University will be limited to excess soft tissue and bone tumor tissue from patients otherwise undergoing clinically indicated procedures for diagnosis or treatment under the care of the local principal investigator (PI) and will be forwarded to the central investigator, R. Lor Randall, MD at Huntsman Cancer Institute for use in the characterization of the gene profiles of these tumors.

Detailed description: as stated in brief summary

Eligibility: Inclusion Criteria:
  -  Bone or soft tissue tumor that has been established to be or is suspected to possibly be a sarcoma AND who will require a diagnostic or therapeutic surgical procedure which will result in procurement of tissue for histologic review
  Exclusion Criteria:
  -  Non cancer patients

Relevance to patient case: not relevant
Patient case: 78-year-old female with sarcoma; genetic feature: MDM2

Clinical trial: A Study of R1507 in Participants With Recurrent or Refractory Sarcoma

Summary: This study will evaluate the efficacy and safety of R1507 in participants with recurrent or refractory sarcoma. Eight cohorts of sarcoma participants will be studied in parallel. Cohort 1: Ewing's sarcoma primary cohort defined as participants who have relapsed less than or equal to (<=) 24 months from diagnosis, received at least two prior chemotherapy programs and are unresectable. Cohort 2: Ewing's sarcoma non-primary (secondary) cohort defined as participants who have relapsed greater than or equal to (>=) 24 months from diagnosis or have only received one prior chemotherapy program. Cohort 3: Expanded Ewing's sarcoma defined as participants with recurrent or relapse regardless of prior number of salvage regimens and regardless of time of relapse. Cohort 4: participants with osteosarcoma. Cohort 5: Participants with synovial sarcoma. Cohort 6: Participants with rhabdomyosarcoma Cohort 7: Participants with alveolar soft part sarcoma (7a), desmoplastic small round cell tumors (7b), extraskeletal myxoid chondrosarcoma (7c), clear cell sarcoma (7d), myxoid liposarcoma (7e). Cohort 8: Participants with unspecified sarcoma diagnosis. Participants in the expanded Ewing's sarcoma Cohort 3 will receive 27 milligrams (mg)/kilogram (kg) every 3 weeks intravenously (IV). All other participants will receive R1507 9 mg/kg IV weekly. The anticipated time on study treatment is until disease progression or unacceptable adverse events, withdrawal or death.


Eligibility: Inclusion Criteria:
  -  progressive, recurrent or refractory Ewing's sarcoma, or recurrent or refractory osteosarcoma, synovial sarcoma, rhabdomyosarcoma, or other sarcomas of the following sub-types: alveolar soft part sarcoma, desmoplastic small round cell tumor, extraskeletal myxoid chondrosarcoma, clear cell sarcoma and myxoid liposarcoma;
  -  Cohort 3 only: age must be >= 2 and <= 21 years
  Exclusion Criteria:
  -  clinically significant unrelated systemic illness which would compromise the participant's ability to tolerate the investigational agent, or interfere with the study procedures or results;
  -  known hypersensitivity to any of the components of R1507 or prior hypersensitivity reactions to monoclonal antibodies;
  -  treatment (within the past 2 weeks) with pharmacologic doses of corticosteroids or other immunosuppressive agents;
  -  current or prior therapy with insulin-like growth factor (IGF) inhibitor (monoclonal or specific kinase inhibitor);
  -  history of solid organ transplant;
  -  other malignant disease diagnosed within the previous 5 years, excluding intra-epithelial cervical neoplasia or non-melanoma skin cancer;
  -  active central nervous system disease

Relevance to patient case: not relevant
Patient case: 78-year-old female with sarcoma; genetic feature: MDM2

Clinical trial: Functional and Clinical Long-Term Outcome of Ewing Sarcoma Treatment

Summary: The purpose of the study is to assess the functional outcome, quality of life and late sequelae in a representative sample of 600 long-term survivors of Ewing sarcoma and to build a unique clinical and functional data pool of the underlying cohort of 3000 Ewing sarcoma patients with a follow-up of 3 decades.

Detailed description: Trial objective: As survival rates of bone sarcoma patients have been raised owing to improved treatment strategies the focus of investigations is now on the medical, social, and economic sequelae of intensive multimodal treatment. This study aims to assess the functional outcome, quality of life and late sequelae in a representative sample of long-term survivors of Ewing sarcoma. The data recorded combined with standardized treatment data covering a 30-year period will produce a data pool that is unique for its magnitude and will be used for the development of guidelines for further improvements of future bone sarcoma treatment.
  Working plan: The working plan provides for the assessment of functional outcome and quality of life by means of validated tools (TESS, SF36, PEDQOL) and objectively measuring daily activity patterns by using the Step Activity Monitor (SAM) in 600 long-term Ewing sarcoma survivors and a control group of 300 matched healthy subjects. Information on sarcoma treatment and follow-up is obtained by re-structuring and complementing the database of the relevant patient cohort (n=3000) from four consecutive nationwide and international clinical trials between 1980 and 2008. Procedures of local treatment will be evaluated regarding functional outcome, quality of life, and survival probability and prognostic factors predicting long-term outcome will be identified.
  Exploitation of results: The results will be presented at scientific meetings and will be published in international journals. Guidelines will be developed regarding improvements in the treatment, rehabilitation, and social integration of bone sarcoma patients to be utilized in guiding patients and in the decision process of medical professionals regarding their treatment. In the long run, the evidence based guidelines on treatment and follow-up are to be transferred into the health system.

Eligibility: Inclusion Criteria:
  -  CESS81/CESS86/EICESS92/EURO-E.W.I.N.G.99 trials participants of the German Society of Pediatric Hematology and Oncology (GPOH)
  Exclusion Criteria:
  -  no complete remission (CR)
  -  any kind of paralysis
  -  <3y after diagnosis

Relevance to patient case: not relevant
Patient case: 78-year-old female with sarcoma; genetic feature: MDM2

Clinical trial: Anterior Mediastinum Teratoma: A Case Report

Summary: The investigators report a case of a 39-year-old man who presented an anterior mediastinal cystic mature teratoma. Those kind of tumor contain elements derived from more than one of the three primary germ layers (ectoderm, mesoderm, endoderm), frequently arranged in a haphazard manner. They arise from totipotent cells and, therefore, are primarily found in gonads, and more rarely in primitive cells kidnapped in other parts of the body. The tissues are immature to well differentiated and foreign to the anatomic site. Mature teratomas are either cystic or solid, although the cystic presentation predominates in gonadal sites. Benign teratomas are the most common mediastinal germ cell tumor, accounting 70% of the mediastinal germ cell tumors in children and 60% of those in adults. Immature teratomas are potentially malignant tumors; their prognosis is influenced by the anatomic site of the tumor, patient age, and the fraction of the tumor that is immature. Treatment of benign mediastinal teratoma includes complete surgical resection, with results in a excellent long-term cure rates. Complete resection of teratomas should be the goal of treatment.


Eligibility: Inclusion Criteria:
  -  Clinical diagnosis of mediastinum teratoma
  Exclusion Criteria:
  -  Tumor absent

Relevance to patient case: not relevant
Patient case: 78-year-old female with sarcoma; genetic feature: MDM2

Clinical trial: Observation Versus Post-surgery Radiotherapy After Complete Exeresis in Soft Tissues Members Sarcoma

Summary: Soft tissue sarcomas represent less than 1% of malignant tumors in adults and sarcomas members represent 60% of them.
  These rare tumors involve complex multidisciplinary care better in centers having expertise.
  Loco-regional therapy strategies have evaluated over time for tumors of members leading to propose more often the combination of a large conservative tumor excision with radiotherapy. Results have been demonstrated equivalent to those of an amputation in terms of local control and survival.
  The local recurrence rate for sarcomas of the members of any kind after surgery with or without radiotherapy in the literature varies from 10 to 30%.
  The main objective is to achieve a low recurrence rate while maintaining the function. The question remains the possibility of an absence of irradiation in selected cases in a de-escalation therapy order.


Eligibility: Inclusion Criteria:
  -  Soft tissue sarcoma members histologically confirmed
  -  Tumor primitive complete excision with margins greater than or equal to 10 mm in the soft tissue in all directions during the initial surgery.
  A sub-centimeter margin is authorized under an anatomic barrier (fascia, fascia, inter-osseous membrane, periosteum), if surgery is R0 a margin sub-centimeter depth is allowed for superficial tumors if the underlying fascia RESECTED is not invaded.
  -  Primitive tumors without breaking initial tumor and without tumor residue in the systematic recovery in case of incomplete initial excision margins or doubtful
  -  WHO less than or equal to 2
  -  Age greater than or equal to 18 years
  -  Review extension negative (normal chest CT)
  -  Information and monitoring possible
  -  Patient affiliated to social security
  Exclusion Criteria:
  -  Previously treated local sarcoma relapse
  -  Visceral or lymph node metastases
  -  pre-operative treatment (chemotherapy or radiotherapy)
  -  PNET, alveolar rhabdomyosarcoma, Darrier-Ferrand sarcoma
  -  excision margins of less than 10 mm in one direction or doubtful or unspecified, except under an anatomic barrier (fascia, fascia, inter-osseous membrane, periosteum), if surgery is R0 and tumors if the superficial fascia underlying RESECTED is not invaded.
  -  Break-tumor during the initial surgery, or residual tumor at second surgery
  -  Chemotherapy
  -  Delay between surgery R0 margins greater than or equal to 1 cm (initial surgery or recovery) and the start of radiotherapy exceeding 8 weeks
  -  History of radiation on the Member
  -  History of cancer (except carcinoma in situ of the cervix and basal cell skin cancer or in complete remission for over 5 years)
  -  Pregnant Women
  -  Patients under guardianship or curatorship

Relevance to patient case: not relevant
Patient case: 78-year-old female with sarcoma; genetic feature: MDM2

Clinical trial: Tissue Sample Collection From Patients With Soft Tissue Sarcoma of the Arms, Hands, Legs, or Feet Treated on Clinial Trial CRUK-VORTEX

Summary: RATIONALE: Collecting and storing samples of tumor tissue from patients with soft tissue sarcoma to test in the laboratory may help the study of cancer in the future.
  PURPOSE: This laboratory is collecting tissue samples from patients with soft tissue sarcoma of the arms, hands, legs, or feet treated on clinical trial CRUK-VORTEX.

Detailed description: OBJECTIVES:
  -  Determine early in the course of treatment which patients treated on clinical trial CRUK-VORTEX have an increased likelihood of distant metastases so as to highlight individuals who might benefit from early adjuvant systemic therapy.
  OUTLINE: This is a multicenter study.
  Tumour and normal tissue samples will be taken at the time of surgery during treatment on clinical trial CRUK-VORTEXand preserved for future microarray analyses. Tissue microarrays will be produced from both tumor and normal tissues. Blood samples will be collected for future DNA analysis.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically confirmed soft tissue sarcoma
  -  Receiving treatment on clinical trial CRUK-VORTEX
  -  Underwent surgery to remove the tumor no more than 3 months ago
  PATIENT CHARACTERISTICS:
  -  Not pregnant or nursing
  -  Negative pregnancy test
  -  Fertile patients must use effective contraception during and for 3 months after completion of study treatment
  -  No other major medical illness that would preclude study treatment
  -  No other prior or concurrent malignancy except adequately treated nonmelanoma carcinoma of the skin or in situ carcinoma of the cervix
  PRIOR CONCURRENT THERAPY:
  -  No prior radiotherapy to the local site
  -  No prior neoadjuvant or adjuvant chemotherapy

Relevance to patient case: not relevant
Patient case: 78-year-old female with sarcoma; genetic feature: MDM2

Clinical trial: Studying Tumor Tissue Samples From Patients With Soft Tissue Sarcoma

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.
  PURPOSE: This research study is looking at tumor tissue samples from patients with soft tissue sarcoma.

Detailed description: OBJECTIVES:
  -  To develop a pilot program for the collection, archiving, and experimental analyses of soft tissue sarcomas (STS).
  -  To obtain STS tumors from cancer patients undergoing tumor removal or core needle biopsies.
  -  To evaluate cellular and molecular factors involved in STS oncogenesis by studying samples derived from human tumor specimens.
  -  To develop an accompanying bioinformatics database of the demographics of STS patients from which tumor specimens are derived for experimental study.
  OUTLINE: Tumor tissue samples are analyzed for gene and protein expression by cDNA microarray analysis, RT-PCR, immunohistochemistry, in vitro transformation assays, RNA interference, and Western blot or immunoprecipitation.

Eligibility: DISEASE CHARACTERISTICS:
  -  Meets one of the following criteria:
  -  Patients with soft tissue sarcoma (STS) undergoing evaluation, treatment, and/or follow-up at the Arizona Cancer Center or University Medical Center
  -  Patients undergoing surgical treatment for STS removal or core needle biopsy for medically indicated diagnostic or therapeutic purposes
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant