{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["N/A"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001004088"],"sample_count":["81"],"description":["EGA dataset EGAD00001004088"],"repository":["EGA"],"title":["Comprehensive cancer predisposition gene testing in an adult multiple primary tumor series shows a broad range of deleterious variants and atypical tumor phenotypes"],"name_synonyms":["Vasp, VASP, DmelCG15112, ENHANCER OF ATNSI ACTIVITY, Data Set, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, 2018., ENA/VASP"],"description_synonyms":["cluster, MGC130048, Materials, PhrB photolyase activity, syndrome associated with disease or disorder, determination, A4, Tumor, pigmented epithelium, prevention, Relative, School-Age, \"syndrome, symptom, Genetic Predictive Testing, 3, NUP96, epithelium, prevention and control, gamma sarcoglycan, Predictive Genetic, Genetic Predisposition, reference sample, proportionality to, Moods, pigmented retina, DNA cyclobutane dipyrimidine photolyase activity, SUPPRESSOR OF AUXIN RESISTANCE 3, genetic, preventive measures, malignant neoplasm, syndromic disease, Symptom Clusters, gamma-sarcoglycan, Malignancies, Long-Term Cancer Survivors, infrequent, Tumors, Genetic Predictive, PRE, Genetic Testing, preventive therapy, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, frequency, familial, SG-gamma, Genome Sequencing, Clusters, Genetic Screenings, results, Benign, Screenings, Complete Genome, symptom cluster, retinal pigment, School Age, RENBP, Relative Risks, Long-Term Cancer, Childhood Cancer Survivors, dipyrimidine photolyase (photosensitive), Genetic Materials, sarcoglycan, retinal pigment layer, Genetic Material, region, Populations, Risk, Predisposition Testing, Long-Term Cancer Survivor, proportionality, Benign Neoplasms, rate, INSDC_feature:gene, gamma (35kDa dystrophin-associated glycoprotein), surveillance, morbidity, clusters, Malignant Neoplasms, AGE, Phenotypes, phr A photolyase activity, DMDA, DNA-photoreactivating enzyme, Syndromes, Cluster, Material, 35kD dystrophin-associated glycoprotein, Survivorship, Cistron, inherited genetic, School-Age Population, other neoplasm, SGCG_HUMAN, Neoplasms, low frequency, MPT, Benign Neoplasm, Gene, photoreactivating enzyme activity, Malignant, syndromic disease or disorder, TYPE, DAGA4, Childhood Cancer Survivor, heredity, \"syndrome\" EXACT [MTH:NOCODE], 35DAG, symptom clusters, Screening, Mood, stratum pigmentosa retinae, MAM, gamma-SG, Survivors of Childhood Cancer, SCG3, Long Term Cancer Survivors, School-Age Populations, proportion, MOS3, Complete, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, Whole Genome, Genetic, Malignancy, PRECOCIOUS, occurrence, Complete Genome Sequencing, prevalence, F23A5.3, syndrome, Long-Term, Population, syndromes, Sequencing, Symptom, Neoplasias, Survivor, NOS\" EXACT [SNOMEDCT_2005_07_31:64572001], Cancer Survivorship, Whole, site, Predictive, School Age Population, constitutitional genetic, F23A5_3, incidence, Controlled, Cancer, WGS, Controlling, Malignant Neoplasm, 35 kDa dystrophin-associated glycoprotein, RnBP, Affects, Predictive Testing, GlcNAc 2-epimerase, Cistrons, Genetic Screening, mitochondrial membrane permeabilization., SGCG, Testing, LGMD2C, MODIFIER OF SNC1, N-acetyl-D-glucosamine 2-epimerase, MT, Symptom Cluster, chemical analysis, deoxyribonucleic photolyase activity, Neoplasm, outbreaks, Relative Risk, mitochondrial membrane permeabilization, Cancer Survivors, Predictive Genetic Testing, primary cancer, RPE, DMDA1, photolyase activity, prophylaxis, Risks, Cancers, Childhood, malignant tumor, School Age Populations, endemics, Genetic Predisposition Testing, p. pigmentosa retinae, Survivors, mitochondrial permeability transition, control, SCARMD2, quotient, Cancer Survivor, renin-binding protein, epidemics, deoxyribonucleate pyrimidine dimer lyase (photosensitive), assay, mitochondrial membrane permeability transition, hereditary, Neoplasia"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-UCAM-GEL-19-04-2018-15:13:08:207-299 - samples","description":"Multiple primary tumors (MPT) affect a substantial proportion of cancer survivors and may result from various causes including inherited predisposition. Currently, germline genetic testing of MPT cases for cancer predisposition gene (CPG) variants is mostly targeted by tumor type. We ascertained pre-assessed MPT cases from genetics centers (defined as ≥2 primaries by age 60 years or ≥3 by 70) and performed whole genome sequencing (WGS) on 460 individuals from 440 families. Despite previous negative genetic assessment/molecular investigations, pathogenic variants in moderate and high-risk CPGs were detected in 67/440 (15.2%) of probands. WGS detected variants that would not be (or were not) detected by targeted resequencing strategies including structural variants at low frequency (6/440 (1.4%) of probands). In most individuals with a germline variant assessed as pathogenic or likely pathogenic (P/LP), at least one of their tumor types was characteristic of variants in the relevant CPG. However, in 29 probands (42.2% of those with a P/LP variant) the tumor phenotype appeared discordant. The frequency of individuals with truncating or splice site CPG variants and at least one discordant tumor type was significantly higher than a control population (Ç2=43.642 P=<0.0001). 2/67 (3%) of probands with P/LP variants had evidence of multiple inherited neoplasia allele syndrome (MINAS) with deleterious variants in two CPGs. Summing together variant detection rates from a similarly ascertained previous MPT case series, the present results suggest that first-line comprehensive CPG analysis in a clinical genetics referral-based MPT cohort would detect a deleterious variant in about a third of cases.","dates":{"updated":"2024-07-18 13:55:40"},"accession":"EGAD00001004088","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAC00001000259","EGAS00001001012"]}}