ID
46133
Description
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."
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- 11/27/24 11/27/24 - Dr. Christian Niklas
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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
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November 27, 2024
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Creative Commons BY 4.0
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dbGaP phs000942 Use of WGS for Diagnosis and Discovery in the Cancer Genetics Clinic
Subject ID, consent group, subject source, source subject ID, and affection status of participants with or without different types of cancer and involved in the "Use of Whole Genome Sequencing for Diagnosis and Discovery in the Cancer Genetics Clinic" project.
- StudyEvent: Use of Whole Genome Sequencing for Diagnosis and Discovery in the Cancer Genetics Clinic
- Eligibility Criteria
- Subject ID, consent group, subject source, source subject ID, and affection status of participants with or without different types of cancer and involved in the "Use of Whole Genome Sequencing for Diagnosis and Discovery in the Cancer Genetics Clinic" project.
- Subject ID, sample ID, sample source, source sample ID, and sample use variable of participants with or without different types of cancer and involved in the "Use of Whole Genome Sequencing for Diagnosis and Discovery in the Cancer Genetics Clinic" project.
- Subject ID, gender, year of birth, life status, race, medical history of participant with cancer #1, #2, #3, #4, medical history of other diagnosis, onset of cancer #1, #2, #3, #4, age at other diagnosis, and current age of participant with or without different types of cancer and involved in the "Use of Whole Genome Sequencing for Diagnosis and Discovery in the Cancer Genetics Clinic" project.
- Sample ID, body site where sample was obtained, analyte type, tumor status of sample, and sequencing center of participants with or without different types of cancer and involved in the "Use of Whole Genome Sequencing for Diagnosis and Discovery in the Cancer Genetics Clinic" project.
Similar models
Subject ID, consent group, subject source, source subject ID, and affection status of participants with or without different types of cancer and involved in the "Use of Whole Genome Sequencing for Diagnosis and Discovery in the Cancer Genetics Clinic" project.
- StudyEvent: Use of Whole Genome Sequencing for Diagnosis and Discovery in the Cancer Genetics Clinic
- Eligibility Criteria
- Subject ID, consent group, subject source, source subject ID, and affection status of participants with or without different types of cancer and involved in the "Use of Whole Genome Sequencing for Diagnosis and Discovery in the Cancer Genetics Clinic" project.
- Subject ID, sample ID, sample source, source sample ID, and sample use variable of participants with or without different types of cancer and involved in the "Use of Whole Genome Sequencing for Diagnosis and Discovery in the Cancer Genetics Clinic" project.
- Subject ID, gender, year of birth, life status, race, medical history of participant with cancer #1, #2, #3, #4, medical history of other diagnosis, onset of cancer #1, #2, #3, #4, age at other diagnosis, and current age of participant with or without different types of cancer and involved in the "Use of Whole Genome Sequencing for Diagnosis and Discovery in the Cancer Genetics Clinic" project.
- Sample ID, body site where sample was obtained, analyte type, tumor status of sample, and sequencing center of participants with or without different types of cancer and involved in the "Use of Whole Genome Sequencing for Diagnosis and Discovery in the Cancer Genetics Clinic" project.
C0441833 (UMLS CUI [1,2])
C0242481 (UMLS CUI [1,2])
C0449416 (UMLS CUI [1,2])
C0681850 (UMLS CUI [1,3])
C3847505 (UMLS CUI [1,2])
C0449416 (UMLS CUI [1,3])
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