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dbGaP phs000730 Genomics of Brain Metastases - pht005058.v1.p1

- 28/12/22 - 4 formularios, 1 itemgroup, 2 items, 1 idioma

Itemgroup: pht005058

Principal Investigator: Priscilla Brastianos, Broad Institute, Cambridge, MA, USA MeSH: Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000730 Brain metastases are the most frequently occurring intracranial tumors in adults. Median survival after the diagnosis of a brain metastasis is in the order of a few months. Despite its large burden of disease and devastating clinical sequelae, we continue to have a limited understanding of the molecular mechanisms driving brain metastasis. We subjected 86 trios consisting of primary tumor, brain metastasis, and matched normal tissue to whole exome sequencing (WES). To analyze the data, we developed novel computational tools to perform an integrative analysis of somatic single nucleotide variants (SSNVs) and somatic copy-number alterations (SCNAs). This analysis allowed us to estimate the clonal architecture of the primary and metastatic samples of each patient, and to reconstruct a phylogenetic tree relating all of the subclones.

Neoplasms

pht005059.v1.p1

1 itemgroup 3 items

pht005060.v1.p1

1 itemgroup 15 items

pht005061.v1.p1

1 itemgroup 4 items

dbGaP phs000495 The Gene Partnership (TGP) - eMERGE Data - Eligibility

- 13/12/22 - 5 formularios, 1 itemgroup, 7 items, 1 idioma

Itemgroup: IG.elig

Principal Investigator: Isaac S. Kohane, MD, PhD, Boston Children's Hospital, Boston, MA, USA MeSH: Autistic Disorder,Heart Defects, Congenital,Asthma,Attention Deficit Disorders,Diabetes Mellitus, Type 1,Diabetes Mellitus, Type 2,Epilepsy,Gastrointestinal Diseases,Hypersensitivity,Autoimmune Diseases,Hematologic Diseases,Neoplasms,Arrhythmias, Cardiac,Chromosome Aberrations,Congenital Abnormalities,Dermatology,Developmental Disabilities,Endocrine System,Otolaryngology,Syndrome,Urogenital System,Hearing Loss,Immune System Diseases,Musculoskeletal Abnormalities,Nervous System Diseases,Neuromuscular Diseases,Metabolic Diseases,Nutrition Disorders,Vision Disorders,Mouth Diseases,Mental Disorders,Kidney Diseases,Respiration Disorders,Thyroid Diseases,Vascular Diseases https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000495 The Gene Partnership (TGP) is a prospective longitudinal registry at Boston Children's Hospital (BCH) to study the genetic and environmental contributions to childhood health and disease, collect genetic information on a large number of children who have been phenotyped, and implement the Informed Cohort and the Informed Cohort Oversight Board (ICOB). The term "*The Gene Partnership*" reflects a partnership between researchers and participants. Children seen at BCH are offered enrollment, as are their parents and siblings. DNA is collected on all enrollees. BCH has a comprehensive EMR system, and virtually all inpatient and outpatient data are captured electronically. Clinical data in the BCH EMR is loaded in the i2b2 data warehouse which is available to investigators. Cases, phenotypes, and covariates are ascertained using the i2b2 database. Participants at BCH in TGP have consented to receive any research result and/or incidental finding that arises from studies using TGP that is approved by the Informed Cohort Oversight Board (ICOB) and is in accordance with the participants' preferences; results are returned through the Personally Controlled Health Record (PCHR). BCH and Cincinnati Children's Hospital Medical Center (CCHMC) have partnered as the *P*ediatric *A*lliance for *G*enomic and *E*lectronic Medical Record (EMR) *R*esearch (*PAGER*) site for the eMERGE Phase II network for pediatric institutions, and the cohort for eMERGE at BCH is TGP.

pht002864.v1.p1

1 itemgroup 4 items

pht002865.v1.p1

1 itemgroup 5 items

pht002866.v1.p1

1 itemgroup 42 items

pht002867.v1.p1

1 itemgroup 4 items

dbGaP phs000559 PAGE: Epidemiologic Architecture for Genes Linked to Environment (EAGLE) - BioVU Cancer Project - Eligibility

- 12/12/22 - 5 formularios, 1 itemgroup, 20 items, 1 idioma

Itemgroup: IG.elig

Principal Investigator: Dana Crawford, PhD, Vanderbilt University, Nashville, TN, USA MeSH: Neoplasms,Breast Neoplasms,Colorectal Neoplasms,Endometrial Neoplasms,Lung Neoplasms,Lymphoma, Non-Hodgkin,Ovarian Neoplasms,Melanoma,Prostatic Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000559 As part of Population Architecture using Genomics and Epidemiology PAGE study (Phase I), the Epidemiologic Architecture using Genomics and Epidemiology (EAGLE I) project accessed both epidemiologic- and clinic-based collections. The epidemiologic-based collection of EAGLE I included the National Health and Nutritional Examination Surveys (NHANES), ascertained between 1991-1994 (NHANES III), 1999-2002, and 2007-2008. NHANES is a population-based cross-sectional survey now conducted every year in the United States to assess the health status of Americans at the time of ascertainment and to assess trends over the years of survey. Genetic NHANES consists of 19,613 DNA samples linked to thousands of variables including demographics, health and lifestyle variables, physical examination variables, laboratory variables, and exposures. NHANES is diverse with almost one-half of the samples (46.4%) coming from self-reported Mexican Americans and non-Hispanic blacks. In contrast to NHANES, BioVU is a clinic-based collection of 150,000 DNA samples from Vanderbilt University Medical Center linked to de-identified electronic medical records (EMRs). Approximately 12% of BioVU's overall DNA sample collection is from African American, Hispanic, and Asian patients. The overall goals of PAGE I and EAGLE I were broad and several-fold:- Replicate genome-wide association study (GWAS)- identified variants in European Americans; - Identify population-specific and trans-population genotype-phenotype associations; - Identify genetic and environmental modifiers of these associations. NHANES is an excellent resource for the study of quantitative traits associated with common human diseases. However, given that the age range of NHANES spans childhood to late adulthood and not all diseases are surveyed, NHANES is less useful for the study of adult-onset diseases such as major cancers. Therefore, under American Recovery and Reinvestment Act (ARRA) funding, EAGLE as part of PAGE I defined eight major cancers sites for genetic analysis in BioVU, Vanderbilt's biorepository linked to de-identified EMRs. The eight major cancers defined for this study included melanoma, breast, ovarian, prostate, colorectal, lung, endometrial, and Non-Hodgkin's lymphoma (NHL). Cancer cases were defined using a combination of ICD-9 codes and tumor registry entries. Controls include BioVU participants without cancer and encompassing the age and gender distributions of cancer cases. Targeted genotyping of GWAS-identified variants for these diseases (124 SNPs) and ancestry informative markers (128 AIMs) was performed by the Center for Human Genetics Research Vanderbilt DNA Resources Core. After quality control, a total of 116 cancer-associated SNPs and 122 AIMs were available for downstream analyses.

pht003614.v1.p1

1 itemgroup 2 items

pht003615.v1.p1

1 itemgroup 3 items

pht003616.v1.p1

1 itemgroup 58 items

pht003617.v1.p1

1 itemgroup 5 items

dbGaP phs000612 The mutational characterization of adenoid cystic carcinoma - pht003526.v1.p1

- 25/11/22 - 5 formularios, 1 itemgroup, 4 items, 1 idioma

Itemgroup: pht003526

Principal Investigator: Timothy A. Chan, MD, PhD, Memorial Sloan-Kettering Cancer Center, New York, NY MeSH: Cancer,Carcinoma, Adenoid Cystic https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000612 Adenoid cystic carcinoma (ACC) typically emanate from the major and minor salivary glands of the head and neck. ACCs have high rates of perineural invasion, locoregional recurrence, and distant metastasis. Here we report sequencing of 60 tumor/normal pairs and find substantial mutational diversity. On pathway analysis, a significant percentage of mutations involved chromatin remodeling, DNA damage, protein kinase A signaling, and FGF/IGF/PI3K signaling. Whole genome sequencing and FISH confirmed the MYB-NFIB translocation as the main structural variant in ACC. Evaluation of potential driver mutations KDM6A and PIK3CA reveal that specific, observed alterations impart functional consequences. Collectively, our data delineate the ACC mutational landscape and establish a molecular foundation for investigating new therapies for this disease.

pht003527.v1.p1

1 itemgroup 3 items

pht003528.v1.p1

1 itemgroup 13 items

pht003529.v1.p1

1 itemgroup 14 items

Eligibility

1 itemgroup 2 items

dbGaP phs000646 Breakpoint Detection Using Long Insert Whole Genome Sequencing - pht003434.v1.p1

- 25/11/22 - 4 formularios, 1 itemgroup, 3 items, 1 idioma

Itemgroup: pht003434

Principal Investigator: Winnie S. Liang, PhD, Translational Genomics Research Institute, Phoenix, AZ, USA MeSH: Chromosome Breakpoints,Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000646 In this study, we hypothesize that shallow long insert whole genome sequencing (LI-WGS) increases our power for detecting breakpoints compared to shallow short insert WGS. We performed a priori analyses to demonstrate the benefits of LI-WGS, developed a long insert library preparation protocol based off Illumina's protocol, and compared LI-WGS against short insert WGS on test samples. We then used long insert WGS to identify translocations and copy number changes in tumor and germline samples collected from cancer patients with different malignancies.

pht003435.v1.p1

1 itemgroup 3 items

pht003436.v1.p1

1 itemgroup 3 items

pht003437.v1.p1

1 itemgroup 7 items

dbGaP phs000525 Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers - pht002933.v1.p1

- 15/11/22 - 3 formularios, 1 itemgroup, 5 items, 1 idioma

Itemgroup: pht002933

Principal Investigator: Arul M. Chinnaiyan, MD, PhD, University of Michigan, MI, USA MeSH: Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000525 In this study, we describe a systematic analysis of pseudogene 'transcription' from an RNA-Seq resource of 293 samples, from 13 cancer and normal tissue types. We observed a highly prevalent, genome-wide expression of pseudogenes that could be categorized as universally expressed or lineage- and/or cancer-specific. We also explored disease subtype specificity and functions of selected expressed pseudogenes. We provide evidence that transcribed pseudogenes are a significant contributor to the transcriptional landscape of cells and are positioned to play significant roles in cellular differentiation and cancer progression. Our work provides a transcriptome resource that enables high-throughput analyses of pseudogene expression.

Neoplasms

pht002934.v1.p1

1 itemgroup 5 items

pht002935.v1.p1

1 itemgroup 5 items

dbGaP phs000602 Identification of Targetable FGFR Gene Fusions in Diverse Cancers - Eligibility

- 11/11/22 - 4 formularios, 1 itemgroup, 19 items, 1 idioma

Itemgroup: IG.elig

Principal Investigator: Arul M. Chinnaiyan, MD, PhD, University of Michigan, MI, USA MeSH: Neoplasms,Cholangiocarcinoma,Breast Neoplasms,Prostatic Neoplasms,Urinary Bladder Neoplasms,Mouth Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000602 In this study, patients with advanced cancer across all histologies were enrolled in our IRB approved clinical sequencing program, called MI-ONCOSEQ, to go through an integrative sequencing which includes whole exome sequencing of the tumor and matched normal, and transcriptome sequencing. Four index cases were identified which harbor gene rearrangements of FGFR2 including two cholangiocarcinoma cases, a metastatic breast cancer case, and a metastatic prostate cancer case. After extending our assessment of FGFR rearrangements across multiple tumor cohorts, including TCGA, we identified FGFR gene fusions with intact kinase domains of FGFR1, FGFR2, or FGFR3 in cholangiocarcinoma, breast cancer, prostate cancer, lung squamous cell cancer, bladder cancer, thyroid cancer, oral cancer, glioblastoma, and head and neck squamous cell cancer. All FGFR fusion partners tested exhibit oligomerization capability, suggesting a shared mode of kinase activation. Overexpression of FGFR fusion proteins in vitro induced cell proliferation, and bladder cancer cell lines that harbors FGFR3 fusion proteins exhibited enhanced susceptibility to pharmacologic inhibition in vitro and in vivo. Due to the combinatorial possibilities of FGFR family fusion to a variety of oligomerization partners, clinical sequencing efforts which incorporate transcriptome analysis for gene fusions are poised to identify rare, targetable FGFR fusions across diverse cancer types.

pht003221.v1.p1

1 itemgroup 5 items

pht003222.v1.p1

1 itemgroup 6 items

pht003220.v1.p1

1 itemgroup 5 items

dbGaP phs000397 NIA Long Life Family Study (LLFS) - Eligibility

- 12/10/22 - 6 formularios, 1 itemgroup, 3 items, 1 idioma

Itemgroup: IG.elig

Principal Investigator: Michael A. Province, PhD, Washington University School of Medicine, St. Louis, MO, USA MeSH: Longevity,Aging,Cardiovascular Diseases,Neoplasms,Stroke,Inflammation,Immune System,Diabetes Mellitus,Hypertension,Dyslipidemias,Lipids,Osteoporosis,Pulmonary Function Tests,Kidney Function Tests,Alzheimer Disease,Depression,Personality,Executive Function,Reproductive History https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000397 The Long Life Family Study (LLFS) is an international collaborative study of the genetics and familial components of exceptional survival, longevity, and healthy aging. Families were recruited through elderly probands (generally in their 90s) who self-reported on the survival history of their parents and siblings, and on the basis of this information, families which showed clustering of exceptional survival were recruited. [Specifically, a Family Longevity Selection Score (FLOSS) ≥7 was required. The FLOSS measures the average excess Observed lifespan over that Expected based upon lifetables, while adding a bonus term for still-living individuals. Thus FLOSS is a useful tool for scoring and selecting families for inclusion in a research study of exceptional survival (Sebastiani et al., 2009, PMID: 19910380)]. Probands resided in the catchment areas of four Field Centers (Boston University, Columbia University, University of Pittsburgh, and University of Southern Denmark). Recruited family members were phenotyped through extensive in-home visits by teams of technicians who traveled all over the USA and Denmark. Blood assays were centrally processed at a Laboratory Core (University of Minnesota) and protocols were standardized, monitored and coordinated through a Data Management Coordinating Center (Washington University). We examined and extensively phenotyped in all major domains of healthy aging, 4,953 individuals in 539 families through comprehensive in-home visits. Of these, 4,815 gave dbGaP sharing permission and had sufficient quantity/quality of DNA for GWAS genotyping. This large collection of families, selected on the basis of clustering for exceptional survival, is a unique resource for the study of human longevity and healthy aging. We estimate that less than 1% of the Framingham Heart Study (FHS) families (a roughly random population family sample) would meet the minimal entrance criteria for exceptional survival required in the LLFS (Sebastiani et al., 2009, PMID: 19910380). Thus, the least exceptional LLFS families show more clustering for exceptional longevity than 99% of the FHS families. Although the LLFS pedigrees were selected on the basis of longevity per se in the upper generation (and the generation above that), the children's generation have significantly lower rates of many major diseases and have better healthy aging profiles for many disease phenotypes (Newman et al., 2011, PMID: 21258136). The participants had their first in-person visit between 2006 and 2009. After that visit, they were contacted annually by telephone to update vital status, medical history, and general health. Between 2014 and 2017, willing participants completed a second in-person visit. The second visit followed the same protocols and centralized training as the first visit. During the second visit, a portable carotid ultrasound exam was added. Again, participants were continuously contacted annually for telephone follow-up during the period of the second in-person visit and after that. Annual telephone follow-ups currently ongoing, and plans for a third in-person visit are in progress.

pht002407.v3.p3

1 itemgroup 4 items

pht002408.v3.p3

1 itemgroup 6 items

pht002410.v3.p3

1 itemgroup 106 items

pht003356.v3.p3

1 itemgroup 4 items

pht002409.v3.p3

1 itemgroup 3 items

A Phase II Study of AZD4877 (a Novel Anti-mitotic DRKS00004052 - Eligibility Bladder Cancer NCT00661609

- 27/9/21 - 1 formulario, 2 itemgroups, 8 items, 1 idioma

Itemgroups: Inclusion Criteria, Exclusion Criteria

The purpose of this Phase II study is to determine if AZD4877, an experimental drug that is a novel anti-mitotic agent (Eg5 or Kinesin Spindle Protein inhibitor that interferes with tumor cell division leading to tumor growth), can reduce tumor sizes in patients with bladder cancer see http://clinicaltrials.gov/ct2/show/study/NCT00661609

Pharmacokinetic Study of Doxorubicin in Children With Cancer DRKS00003787 NCT01095926 - 1st Sampling period

- 27/9/21 - 2 formularios, 20 itemgroups, 113 items, 1 idioma

Itemgroups: Physical Examination, Determination of cardiac function (before sampling period), Clinical chemistry, Haematology, Agents that are known to interact with doxorubicin according to SmPCs administered?, Antiemetic agents administered?, Cardioprotective agents administered?, Systemic antimycotic agents, Other agents administered?, Actual protocol block, Start of actual protocol block, Chemotherapy in actual protocol block administered ?, Previous anthracycline treatment, Doxorubicin treatment in 1st sampling period, Haematological toxicity of actual protocol block, Transfusions, Determination of cardiac function (end of sampling period), Adverse events, Start of next protocol block, Footer module

Official Title: Phase II Pharmacokinetic Study to Assess the Age-dependency in the Clearance of Doxorubicin in Paediatric Patients With Solid Tumours and Leukaemia Analyze pharmacokinetics of doxorubicin in children with cancer. Furthermore investigate the predictive role of troponin and natriuretic peptides for anthracycline-induced cardiotoxicity. https://clinicaltrials.gov/ct2/show/NCT01095926 NCT01095926

Registration

6 itemgroups 25 items

quality management ADT-dataset breast cancer breast cancer - quality management

- 27/9/21 - 1 formulario, 7 itemgroups, 32 items, 2 idiomas

Itemgroups: Patientendaten, Patientenadresse, Breast, Hormonrezeptoren, MammaCa, Tumorproteasen, MammaCa

ADT - specific dataset for breast cancer, add for base-dataset, ODM derived from http://www.tumorzentren.de/tl_files/dokumente/Module%20zum%20Basisdatensatz/Anlage_2_Organspezifischer_DS_Mamma_Aufnahme%20BIRADS_24.04.2012.pdf

quality management ADT-autopsy cancer - quality management

- 27/9/21 - 1 formulario, 9 itemgroups, 50 items, 2 idiomas

Itemgroups: Patientendaten, Patientenadresse, Autopsie, TNM-Klassifikation, Tumorhistologie, Lymphgefäßinvasion, Veneninvasion, Tumorausbreitung, Fernmetastasen

base-dataset from ADT - autopsy, ODM derived from http://www.tumorzentren.de/tl_files/dokumente/adt_basis.pdf

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