{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HiSeq 2000;ILLUMINA"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001002715"],"sample_count":["1027"],"description":["EGA dataset EGAD00001002715"],"repository":["EGA"],"title":["Exome sequencing of isolate populations and Generation Scotland"],"pubmed_abstract":["Homozygous loss of function (HLOF) variants provide a valuable window on gene function in humans, as well as an inventory of the human genes that are not essential for survival and reproduction. All humans carry at least a few HLOF variants, but the exact number of inactivated genes that can be tolerated is currently unknown—as are the phenotypic effects of losing function for most human genes. Here, we make use of 1432 whole exome sequences from five European populations to expand the catalogue of known human HLOF mutations; after stringent filtering of variants in our dataset, we identify a total of 173 HLOF mutations, 76 (44%) of which have not been observed previously. We find that population isolates are particularly well suited to surveys of novel HLOF genes because individuals in such populations carry extensive runs of homozygosity, which we show are enriched for novel, rare HLOF variants. Further, we make use of extensive phenotypic data to show that most HLOFs, ascertained in population-based samples, appear to have little detectable effect on the phenotype. On the contrary, we document several genes directly implicated in disease that seem to tolerate HLOF variants. Overall HLOF genes are enriched for olfactory receptor function and are expressed in testes more often than expected, consistent with reduced purifying selection and incipient pseudogenisation."],"pubmed_title":["Homozygous loss-of-function variants in European cosmopolitan and isolate populations."],"pubmed_authors":["Kaiser Vera B VB, Svinti Victoria V, Prendergast James G JG, Chau You-Ying YY, Campbell Archie A, Patarcic Inga I, Barroso Inês I, Joshi Peter K PK, Hastie Nicholas D ND, Miljkovic Ana A, Taylor Martin S MS, Enroth Stefan S, Memari Yasin Y, Kolb-Kokocinski Anja A, Wright Alan F AF, Gyllensten Ulf U, Durbin Richard R, Rudan Igor I, Campbell Harry H, Polašek Ozren O, Johansson Åsa Å, Sauer Sascha S, Porteous David J DJ, Fraser Ross M RM, Drake Camilla C, Vitart Veronique V, Hayward Caroline C, Semple Colin A CA, Wilson James F JF"],"description_synonyms":["WES, Complete Transcriptome, Exome Sequencing, Whole Exome, Complete, Complete Transcriptome Sequencing, Exome Sequencings, Complete Exome Sequencings, Whole, Complete Exome Sequencing, Whole Transcriptome Sequencing, Whole Exome Sequencing, Exome, Whole Transcriptome, Transcriptome Sequencing, Transcriptome Sequencings, Sequencing, Complete Exome."],"name_synonyms":["Vasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"pubmed_title_synonyms":["White, white, function, Occidental, Caucasian, Whites, Caucasians., Caucasoid, European"],"pubmed_abstract_synonyms":["small, Reproductive, whole exome, other disease, Materials, human being, Indices, Data Set, Index, testicle, Modern, Reproductive Period, number, disorders, Gene, white, Human Reproductive Indexes, function, medical condition, Cistrons, Human, Mutations, Reproductive Index, gonad of male reproductive system, School-Age, survival, Caucasian, Homo sapiens, Period, diseases, reduced, Human Reproductive Indices, European, School Age, Diseases, gonad of male genitalia, disease or disorder, Genetic Materials, condition, diseases and disorders, rare (European definition), testiculus, tiny, selection process., Reproductive Periods, Man, Genetic Material, Caucasoid, Caucasians, Human Reproductive Index, School-Age Populations, Populations, human disease, Occidental, Genetic, Man (Taxonomy), death rate, underdeveloped, Testicle, hypoplasia, male gonad, INSDC_feature:gene, Population, School Age Populations, human, Reproductive Indices, loss of, non-neoplastic, Phenotypes, disease, Material, Whites, time of survival, Indexes, orchis, Modern Man, cardinality, Testicles, reproductive physiological process, Periods, disorder, Cistron, White, Homo sapiens disease, School-Age Population, School Age Population, testes, Human Reproductive, Testes, humans"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-IGMM-28-09-2016-11:49:17:763-561 - samples","description":"Exome sequencing of isolate populations and Generation Scotland","dates":{"updated":"2017-07-26 15:39:29"},"accession":"EGAD00001002715","cross_references":{"TAXONOMY":["9606"],"pubmed":["26173456"],"EGA":["EGAC00001000063","EGAS00001001606"]}}