dbGaPapplication/xmlftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000942/phs000942.v1.p1/manifest/Study_Report.phs000942.CancerGeneticsClinic.v1.p1.MULTI.pdfftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000942/phs000942.v1.p1/manifest/manifest_phs000942.CancerGeneticsClinic.v1.p1.c1.GRU-PUB-MDS.pdfftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000942/phs000942.v1.p1/release_notes/Release_Notes.phs000942.CancerGeneticsClinic.v1.p1.MULTI.pdfftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000942/phs000942.v1.p1/pheno_variable_summaries/phs000942.v1.pht004835.v1.Cancer_Genetics_Clinic_Sample.data_dict.xmlftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000942/phs000942.v1.p1/pheno_variable_summaries/phs000942.v1.pht004837.v1.p1.Cancer_Genetics_Clinic_Sample_Attributes.var_report.xmlftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000942/phs000942.v1.p1/pheno_variable_summaries/phs000942.v1.pht004836.v1.p1.Cancer_Genetics_Clinic_Subject_Phenotypes.var_report.xmlftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000942/phs000942.v1.p1/pheno_variable_summaries/phs000942.v1.pht004837.v1.Cancer_Genetics_Clinic_Sample_Attributes.data_dict.xmlftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000942/phs000942.v1.p1/pheno_variable_summaries/phs000942.v1.pht004835.v1.p1.Cancer_Genetics_Clinic_Sample.var_report.xmlftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000942/phs000942.v1.p1/pheno_variable_summaries/phs000942.v1.pht004836.v1.Cancer_Genetics_Clinic_Subject_Phenotypes.data_dict.xmlftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000942/phs000942.v1.p1/GapExchange_phs000942.v1.p1.xmlftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000942/phs000942.v1.p1/pheno_variable_summaries/phs000942.v1.pht004834.v1.p1.Cancer_Genetics_Clinic_Subject.var_report.xmlftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000942/phs000942.v1.p1/pheno_variable_summaries/phs000942.v1.pht004834.v1.Cancer_Genetics_Clinic_Subject.data_dict.xmlftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000942/phs000942.v1.p1/pheno_variable_summaries/varreports_v3.xslftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000942/phs000942.v1.p1/pheno_variable_summaries/datadict_v2.xslftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000942/phs000942.v1.p1/dbGaPEx2.1.5.xsdprimary200OKGenomicCohortDiagnoses and Examination, WGS, Antemortem Diagnoses, screening, heredity., Postmortem Diagnoses, primary cancer, Antemortem Diagnosis, findings, Malignant Neoplasm, Malignancy, Neoplasms, Benign Neoplasm, signs, Benign Neoplasms, Cancers, Diagnoses and Examinations, Tumor, Diagnosis, Malignant, malignant tumor, Examination and Diagnoses, Diagnoses, Malignant Neoplasms, Neoplasias, Postmortem, Screenings, MT, Benign, malignant neoplasm, Mass Screenings, Examinations and Diagnoses, Mass, symptoms, Neoplasm, Screening, Malignancies, Antemortem, Postmortem Diagnosis, Neoplasia, Diagnose, Cancer, Tumors<p>Individuals from the cancer genetics clinics of the University of Texas Southwestern Medical Center (UTSW) and the Ohio State University (OSU) cancer genetics programs were recruited to the study following informed consent approved by the Institutional Review Boards of both institutions. Only unrelated individuals were included in this study. Blood samples were obtained and de-identified. Subsequent genetic results were not returned to participants.</p>https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000942<p>First samples collected March 2003. Additional patients recruited at Ohio State University, Columbus, OH, and University of Texas Southwestern Medical Center, Dallas, TX, continued through 2013. First samples submitted to Complete Genomics, Inc. in December 2012. Study ended October 2014.</p>Institute - Heather L. Hampel - Department of Human Genetics, Ohio State University, Columbus, OH, USAFunding Source - Jeanne Ann Plitt Professorship in Breast Cancer Research, Dallas, TX, USA - UT Southwestern Medical Center, Dallas, TX, USAInstitute - Jonathan J. Rios - Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA. Department of Pediatrics, McDermott Center for Human Growth and Development, and Department of Orthopaedic Surgery, UT Southwestern Medical Center, Dallas, TX, USAInstitute - Victoria E. Mgbemena - Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USAFunding Source - UL1TR001105 - National Institutes of Health, Bethesda, MD, USAInstitute - Leslie Durham - Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USAFunding Source - H. Ben and Isabelle T. Decherd Chair in Internal Medicine, Dallas, TX, USA - UT Southwestern Medical Center, Dallas, TX, USAInstitute - Samantha B. Foley - Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USAInstitute - Amanda E. Toland - Department of Human Genetics, Ohio State University, Columbus, OH, USAInstitute - Linda S. Robinson - Department of Cancer Genetics, UT Southwestern Medical Center, Dallas, TX, USAFunding Source - Clinical Scientist Award ID# 1007448 - Burroughs Wellcome Fund, Research Triangle Park, NC, USAPrincipal 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, USAdbGaPRNF53, Allele Frequencies, other disease, scale tissue, Antemortem Diagnosis, Materials, determination, acetylglucosaminyltransferase-like protein, P62, Neoplasms, peltate hair, Benign Neoplasm, Mbp1, Gene, sci, Tumor, PPP1R53, Diagnosis, Malignant, LARGE1, froggy, Gyltl1a, DOI, Mutations, Relative, Allele Frequency, diseases, reduced, heredity, Equilibrium, Mass, symptoms, Familiar breast and Ovarian cancer syndrome, Screening, IRIS, disease or disorder, HOW, How, diseases and disorders, BROVCA1, tiny, Antemortem, myd, l(3)j5D5, 24B, FACT80, human disease, Genetic, l(3)s2612, BRCC1, like-acetylglucosaminyltransferase, Genomes, Malignancy, FACT, MDDGB6, plant peltate hair, hypoplasia, stru, PNCA4, Mbp-1, LARGE, l(3)S053606, Diagnoses and Examinations, FANCS, CG10293, non-neoplastic, genetic, Neoplasias, BPFD#36, l(3)j5B5, malignant neoplasm, Clients, DmelCG10293, Allele, disorder, Homo sapiens disease, Malignancies, Frequency, constitutitional genetic, Genetic Equilibrium, Diagnose, Cancer, Tumors, small, WGS, Antemortem Diagnoses, screening, hereditary breast ovarian cancer, 0904/17, findings, Malignant Neoplasm, BRCA1, gyltl1b-b, BRCA2, clone 2.39, disorders, familial, BRCAI, PSCP, medical condition, function, qkr, Cistrons, l(3)S090417, Client, Examination and Diagnoses, results, predicted, Diagnoses, doi., Postmortem, Screenings, MT, Benign, Mass Screenings, Frequencies, SZ1, MDDGA6, Examinations and Diagnoses, mKIAA0609, KH93F, chemical analysis, 163, Relative Risks, Diseases, Neoplasm, BRCA, Genetic Materials, condition, rare (European definition), scales, Postmortem Diagnosis, KIAA0609, Genetic Material, acetylglucosaminyltransferase-like 1A, Relative Risk, who, Diagnoses and Examination, fg, Postmortem Diagnoses, primary cancer, Gene Frequencies, gyltl1b, scale, Risk, underdeveloped, Risks, mdc1d, signs, Benign Neoplasms, patient, whole genome, Cancers, Who/How, LARGE_HUMAN, malignant tumor, Malignant Neoplasms, disease, MDC1D, like-glycosyltransferase, enr, Patient, Material, T160, qkr[93F], Cistron, anon-EST:Liang-2.39, inherited genetic, assay, hereditary, Neoplasia, glycosyltransferase-like protein LARGE1falseUse of WGS for Diagnosis and Discovery in the Cancer Genetics Clinic<p>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 &#60; 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&#39; cancer genetic risks. "Reprinted from doi:10.1016/j.ebiom.2014.12.003, with permission from EBioMedicine."</p>2015-06-292015-06-24phs000942Oncocytoma, renal25318351249411822117370023788249198929422167720022344227230350472509957516021471179420082269914324896178932249824733792126456482494117910213508227038792448727624319668125451652405511326023681242513832362213923460708245106522071986110.1016/j.ebiom.2014.12.003