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dbGaP phs000942 Use of WGS for Diagnosis and Discovery in the Cancer Genetics Clinic - Eligibility

- 27/11/2024 - 5 Formulär, 1 Item-grupp, 1 Dataelement, 1 Språk
Item-grupp: IG.elig
Principal Investigator: Theodora S. Ross, MD, PhD, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA, and Department of Cancer Genetics, UT Southwestern Medical Center, Dallas, TX, USA MeSH: Neoplasms,Breast Neoplasms,Ovarian Neoplasms,Peritoneal Neoplasms,Skin Neoplasms,Esophageal Neoplasms,Thyroid Neoplasms,Urinary Bladder Neoplasms,Endometrial Neoplasms,Fallopian Tube Neoplasms,Melanoma,Testicular Neoplasms,Bile Duct Neoplasms,Lung Neoplasms,Colonic Neoplasms,Adrenocortical Carcinoma,Carcinoma, Renal Cell,Colonic Polyps,Adenomatous Polyposis Coli,Lymphoma, Large B-Cell, Diffuse,Pheochromocytoma,Paraganglioma,Leiomyoma,Hemangioblastoma,Hyperparathyroidism,Pancreatic Neoplasms,Vulvar Neoplasms,Brain Neoplasms,Liver Neoplasms,Kidney Neoplasms,Prostatic Neoplasms,Glioblastoma,Oncocytoma, renal https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000942 Despite the potential of whole-genome sequencing (WGS) to improve patient diagnosis and care, the empirical value of WGS in the cancer genetics clinic is unknown. We performed WGS on members of two cohorts of cancer genetics patients: those with BRCA1/2 mutations (n = 176) and those without (n = 82). Initial analysis of potentially pathogenic variants (PPVs, defined as nonsynonymous variants with allele frequency 1% in ESP6500) in 163 clinically-relevant genes suggested that WGS will provide useful clinical results. This is despite the fact that a majority of PPVs were novel missense variants likely to be classified as variants of unknown significance (VUS). Furthermore, previously reported pathogenic missense variants did not always associate with their predicted diseases in our patients. This suggests that the clinical use of WGS will require large-scale efforts to consolidate WGS and patient data to improve accuracy of interpretation of rare variants. While loss-of-function (LoF) variants represented only a small fraction of PPVs, WGS identified additional cancer risk LoF PPVs in patients with known BRCA1/2 mutations and led to cancer risk diagnoses in 21% of non-BRCA cancer genetics patients after expanding our analysis to 3209 ClinVar genes. These data illustrate how WGS can be used to improve our ability to discover patients' cancer genetic risks. "Reprinted from doi:10.1016/j.ebiom.2014.12.003, with permission from EBioMedicine."

pht004834.v1.p1

1 Item-grupp 5 Dataelement

pht004835.v1.p1

1 Item-grupp 5 Dataelement

pht004836.v1.p1

1 Item-grupp 16 Dataelement

pht004837.v1.p1

1 Item-grupp 5 Dataelement

dbGaP phs000863 NCI GWAS of Renal Cell Carcinoma in African Americans - Eligibility

- 16/03/2024 - 5 Formulär, 1 Item-grupp, 1 Dataelement, 1 Språk
Item-grupp: IG.elig
Principal Investigator: Jonathan Hofmann, PhD, MPH, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA MeSH: Carcinoma, Renal Cell https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000863 The NCI GWAS of renal cell carcinoma (RCC) in African Americans was undertaken to provide insight into genetic loci affecting susceptibility to this malignancy in a racial group known to be at elevated risk. We genotyped 1,136,723 single-nucleotide polymorphisms (SNPs) among 255 cases and 375 controls of African ancestry from the NCI Kidney Cancer Study, and further investigated 16 SNPs in a replication set consisting of 140 cases and 543 controls from a case-control study conducted at the University of Texas MD Anderson Cancer Center. The variant rs10771279 located on 12p11, 77kb from a European-ancestry RCC risk marker, was associated with RCC risk in the GWAS (P=1.2 x 10-7) but did not replicate (P=0.99). The variant 7105934 on 11q13.3, previously associated with RCC in a GWAS using European-ancestry samples, was associated with risk in both studies [meta-analysis odds ratio (OR)=0.76, 95% confidence interval (CI)=0.64-0.91; P=0.0022]. The frequency of this allele was higher than that observed in the European-ancestry GWAS (0.56 and 0.07 respectively among controls). The rs7105934 association was stronger for clear cell RCC (ccRCC: OR=0.56; P=7.4 x 10-7) and absent for cases of other or unknown histology (OR=1.02; P=0.86). In conclusion, this study provides evidence that rs7105934 is a susceptibility locus for RCC, and clear-cell RCC in particular, among African Americans.

pht004742.v1.p1

1 Item-grupp 3 Dataelement

pht004744.v1.p1

1 Item-grupp 6 Dataelement

pht004745.v1.p1

1 Item-grupp 5 Dataelement

pht004743.v1.p1

1 Item-grupp 3 Dataelement

dbGaP phs001175 CTSP: Clinical Trial Sequencing Project - pht007755.v2.p2

- 02/06/2023 - 2 Formulär, 1 Item-grupp, 3 Dataelement, 1 Språk
Item-grupp: pht007755
Principal Investigator: Jean Claude Zenklusen, PhD, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA MeSH: Breast,Carcinoma, Renal Cell,Lymphoma, Large B-Cell, Diffuse https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001175 For the Clinical Trials Sequencing Project (CTSP), National Cancer Institute (NCI) will utilize whole genome sequencing and/or whole exome sequencing in conjunction with transcriptome sequencing to try to identify recurrent genetic alterations (mutations, deletions, amplifications, rearrangements) and/or gene expression signatures that would be important to the hypothesis(es) submitted by the investigators. The samples will be processed and submitted for genomic characterization using pipelines and procedures established within The Cancer Genome Analysis (TCGA) project. Data analysis will be performed as a collaboration between the National Clinical Trials Network (NCTN) Group and its investigators submitting the proposal. The investigators at the NCI-sponsored Genomic Data Analysis Center (GDAC) will characterize the samples. The NCTN Group will be responsible for providing the clinical data needed for the proposal to the open clinical system maintained by NCI CCG's Biospecimen Core Resource (BCR) at Nationwide Children's Hospital in Columbus, Ohio. The project team (Network Group/investigators and GDAC) will analyze the data together. Additionally, clinical and genomic data related to the analyses will also need to be registered by NCI and will be made available to qualified researchers via a controlled-access database (e.g., dbGaP) upon publication of the primary analysis described in the study proposal. A substudy description and its molecular data information are provided under its own page: phs001184 CTSP Diffuse Large B-Cell Lymphoma (DLBCL) CALGB 50303

pht007756.v2.p2

1 Item-grupp 3 Dataelement

dbGaP phs001271 Pooled Genome-Wide Analysis of Kidney Cancer Risk (KIDRISK) - pht006116.v1.p1

- 20/03/2023 - 5 Formulär, 1 Item-grupp, 4 Dataelement, 1 Språk
Item-grupp: pht006116
Principal Investigator: Ghislaine Scélo, PhD, International Agency for Research on Cancer (IARC), Lyon, France MeSH: Carcinoma, Renal Cell,Kidney Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001271 Incidence rates of renal cell carcinoma (RCC) are rising and the latest estimates show that it accounts for over 300,000 cases and 120,000 deaths worldwide each year. Mechanisms underlying RCC occurrence are not fully understood and a large part of the disease heritability remains unexplained. The study aimed at augmenting the size of available RCC genome-wide association studies to increase the statistical power to detect genetic variants associated with the disease. The study includes genome-wide genotyping data from RCC cases (n=2,781) and controls (n=2,526) recruited in Western Europe, Central and Eastern Europe, and Australia.

pht006117.v1.p1

1 Item-grupp 3 Dataelement

pht006118.v1.p1

1 Item-grupp 4 Dataelement

pht006119.v1.p1

1 Item-grupp 6 Dataelement

Eligibility

1 Item-grupp 1 Dataelement

dbGaP phs000744 Yale Center for Mendelian Genomics (Y CMG) - pht003977.v4.p2

- 11/12/2022 - 5 Formulär, 1 Item-grupp, 5 Dataelement, 1 Språk
Item-grupp: pht003977
Principal Investigator: Richard Lifton, Yale University, New Haven, CT, USA MeSH: Familial Idiopathic Pulmonary Fibrosis,Aortic Coarctation,Aortic Stenosis, Supravalvular,Aortic Valve, Bicuspid,Arteries,Blepharophimosis,Bronchiectasis,Carcinoma, Renal Cell,Cardiomyopathies,Ciliary Motility Disorders,Cleft Palate,Congenital Abnormalities,Diaphragmatic Hernia,Ductus Arteriosus, Patent,Gastroschisis,Heart Defects, Congenital,Heart Septal Defects, Atrial,Heart Valve Diseases,Hemangioma,Hereditary Sensory and Autonomic Neuropathies,Hydrocephalus,Hyper-IgM Immunodeficiency Syndrome,Hyperaldosteronism,Hypertension,Ichthyosiform Erythroderma, Congenital,Idiopathic Pulmonary Fibrosis,Lung Diseases, Interstitial,Muscular Atrophy, Spinal,Neuroblastoma,Pneumothorax,Pulmonary Atresia,Pulmonary Valve Stenosis,Rett Syndrome,Spina Bifida,Tetralogy of Fallot,Transposition of Great Vessels,Tricuspid Atresia https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000744 Yale University is home to one of three national centers created by the NIH to study the genetics of rare inherited diseases. Researchers at Yale, the University of Washington, and a center operated jointly by Baylor and Johns Hopkins University will analyze the genomes of thousands of patients who suffer from more than 6,000 rare Mendelian disorders affecting more than 25 million individuals in US. The Centers for Mendelian Genomics will apply next-generation sequencing and computational approaches to discover the genes and variants that underlie Mendelian disorders. The discovery of new genes that cause Mendelian conditions will expand our understanding about their biology to facilitate their diagnosis, and potentially indicate new treatments. The Centers for Mendelian Genomics will provide free exome sequencing and analysis to collaborating investigators for qualified phenotypes. If you are interested in working with the CMG to discover the genetic basis of a Mendelian condition, please contact Yale Center (shrikant.mane@yale.edu) for further information.

pht003978.v4.p2

1 Item-grupp 3 Dataelement

pht003979.v4.p2

1 Item-grupp 7 Dataelement

pht003980.v4.p2

1 Item-grupp 2 Dataelement

pht003976.v4.p2

1 Item-grupp 2 Dataelement

dbGaP phs000491 Whole-Genome and Exome Sequencing in Clear-Cell Renal Cell Carcinoma - pht002697.v1.p1

- 17/10/2022 - 5 Formulär, 1 Item-grupp, 3 Dataelement, 1 Språk
Item-grupp: pht002697
Principal Investigator: James Brugarolas, MD, PhD, UT Southwestern Medical Center, Dallas, TX, USA MeSH: Carcinoma, Renal Cell,Urogenital Neoplasms,Urologic Diseases https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000491 Study to evaluate the molecular genetics of ccRCC through integrative analyses of tumors and tumorgrafts using multiple platforms in clinically annotated samples. Genome and exome data for patients giving consent to have the information available on a public, secure, database is being submitted.

pht002698.v1.p1

1 Item-grupp 3 Dataelement

pht002699.v1.p1

1 Item-grupp 12 Dataelement

pht002700.v1.p1

1 Item-grupp 10 Dataelement

pht002706.v1.p1

1 Item-grupp 2 Dataelement

dbGaP phs000351 NCI Genome-Wide Association Study of Renal Cell Carcinoma - pht002205.v1.p1

- 12/10/2022 - 4 Formulär, 1 Item-grupp, 2 Dataelement, 1 Språk
Item-grupp: pht002205
Principal Investigator: Mark Purdue, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA MeSH: Carcinoma, Renal Cell,Kidney Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000351 The National Cancer Institute (NCI) genome-wide association study (GWAS) of renal cell carcinoma (RCC) was conducted to investigate common genetic variants associated with RCC risk. The GWAS includes 1,453 RCC cases and 3,531 controls of European background from 4 studies (3 cohort, 1 case-control), scanned using the Illumina InfiniumHumanHap 550, 610 and 660W chips. This project was supported by the Intramural Research Program of the National Institutes of Health and NCI. Data from this GWAS were pooled with those from another GWAS of RCC (2,639 cases and 5,392 controls) conducted in Europe by the International Agency for Research on Cancer and the Centre National de Gènotypage. Findings from this collaboration are described in an upcoming report (Purdue et al. Nature Genetics 2011;43(1):60-65; PMID: 21131975). Only data from the NCI scan are included in this dbGaP submission.

pht002206.v1.p1

1 Item-grupp 4 Dataelement

Eligibility

1 Item-grupp 4 Dataelement

pht002204.v1.p1

1 Item-grupp 3 Dataelement

Eligibility Carcinoma, Renal Cell NCT02454478

- 20/09/2021 - 1 Formulär, 2 Item-grupper, 35 Dataelement, 1 Språk
Item-grupper: Inclusion Criteria, Exclusion Criteria
Study of Lenvatinib in Combination With Everolimus in Patients With Unresectable Advanced or Metastatic Renal Cell Carcinoma (RCC); ODM derived from: https://clinicaltrials.gov/show/NCT02454478

Eligibility Carcinoma, Renal Cell NCT01441388

- 20/09/2021 - 1 Formulär, 2 Item-grupper, 10 Dataelement, 1 Språk
Item-grupper: Inclusion Criteria, Exclusion Criteria
A Study Of Crizotinib Plus VEGF Inhibitor Combinations In Patients With Advanced Solid Tumors.; ODM derived from: https://clinicaltrials.gov/show/NCT01441388

Eligibility DRKS00004096 NCT00688753 Carcinoma - Eligibility

- 20/09/2021 - 1 Formulär, 2 Item-grupper, 23 Dataelement, 2 Språk
Item-grupper: Inclusion Criteria, Exclusion Criteria
ODM derived from http://clinicaltrials.gov/show/NCT00688753

Eligibility Criteria NCT00044564 - Eligibility

- 17/09/2021 - 1 Formulär, 2 Item-grupper, 7 Dataelement, 1 Språk
Item-grupper: Inclusion criteria, Exclusion criteria

Eligibility Carcinoma, Renal Cell NCT01107509

- 17/10/2019 - 1 Formulär, 2 Item-grupper, 17 Dataelement, 1 Språk
Item-grupper: Inclusion Criteria, Exclusion Criteria
Pilot Study of Neo-Adjuvant Everolimus to Treat Advanced Renal Cell Carcinoma - Analysis of Biomarkers; ODM derived from: https://clinicaltrials.gov/show/NCT01107509

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