Ontology type: schema:ScholarlyArticle Open Access: True
2018-12
AUTHORSNaim Panjwani, Bowei Xiao, Lizhen Xu, Jiafen Gong, Katherine Keenan, Fan Lin, Gengming He, Zeynep Baskurt, Sangook Kim, Lin Zhang, Mohsen Esmaeili, Scott Blackman, Stephen W. Scherer, Harriet Corvol, Mitchell Drumm, Michael Knowles, Garry Cutting, Johanna M. Rommens, Lei Sun, Lisa J. Strug
ABSTRACTDoes genotype imputation with public reference panels identify variants contributing to disease? Genotype imputation using the 1000 Genomes Project (1KG; 2504 individuals) displayed poor coverage at the causal cystic fibrosis (CF) transmembrane conductance regulator (CFTR) locus for the International CF Gene Modifier Consortium. Imputation with the larger Haplotype Reference Consortium (HRC; 32,470 individuals) displayed improved coverage but low sensitivity of variants clinically relevant for CF. A hybrid reference that combined whole genome sequencing (WGS) from 101 CF individuals with the 1KG imputed a greater number of single-nucleotide variants (SNVs) that would be analyzed in a genetic association study (r2 ≥ 0.3 and MAF ≥ 0.5%) than imputation with the HRC, while the HRC excelled in the lower frequency spectrum. Using the 1KG or HRC as reference panels missed the most common CF-causing variants or displayed low imputation accuracy. Designs that incorporate population-specific WGS can improve imputation accuracy at disease-specific loci, while imputation using public data sets can omit disease-relevant genotypes. More... »
PAGES8
http://scigraph.springernature.com/pub.10.1038/s41525-018-0047-6
DOIhttp://dx.doi.org/10.1038/s41525-018-0047-6
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1101582153
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/29581887
JSON-LD is the canonical representation for SciGraph data.
TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT
[
{
"@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json",
"about": [
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Genetics",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biological Sciences",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "Hospital for Sick Children",
"id": "https://www.grid.ac/institutes/grid.42327.30",
"name": [
"Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada"
],
"type": "Organization"
},
"familyName": "Panjwani",
"givenName": "Naim",
"id": "sg:person.0666605447.40",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0666605447.40"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Hospital for Sick Children",
"id": "https://www.grid.ac/institutes/grid.42327.30",
"name": [
"Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada"
],
"type": "Organization"
},
"familyName": "Xiao",
"givenName": "Bowei",
"id": "sg:person.010155710631.24",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010155710631.24"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Hospital for Sick Children",
"id": "https://www.grid.ac/institutes/grid.42327.30",
"name": [
"The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada"
],
"type": "Organization"
},
"familyName": "Xu",
"givenName": "Lizhen",
"id": "sg:person.01236655170.74",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01236655170.74"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Hospital for Sick Children",
"id": "https://www.grid.ac/institutes/grid.42327.30",
"name": [
"Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada"
],
"type": "Organization"
},
"familyName": "Gong",
"givenName": "Jiafen",
"id": "sg:person.0721564744.75",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0721564744.75"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Hospital for Sick Children",
"id": "https://www.grid.ac/institutes/grid.42327.30",
"name": [
"Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Toronto, ON, Canada"
],
"type": "Organization"
},
"familyName": "Keenan",
"givenName": "Katherine",
"id": "sg:person.01071207725.26",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01071207725.26"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Hospital for Sick Children",
"id": "https://www.grid.ac/institutes/grid.42327.30",
"name": [
"Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada"
],
"type": "Organization"
},
"familyName": "Lin",
"givenName": "Fan",
"id": "sg:person.01030306662.33",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01030306662.33"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Hospital for Sick Children",
"id": "https://www.grid.ac/institutes/grid.42327.30",
"name": [
"Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada"
],
"type": "Organization"
},
"familyName": "He",
"givenName": "Gengming",
"id": "sg:person.011476675331.15",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011476675331.15"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Hospital for Sick Children",
"id": "https://www.grid.ac/institutes/grid.42327.30",
"name": [
"Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada"
],
"type": "Organization"
},
"familyName": "Baskurt",
"givenName": "Zeynep",
"id": "sg:person.0637046071.51",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0637046071.51"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Toronto",
"id": "https://www.grid.ac/institutes/grid.17063.33",
"name": [
"Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada"
],
"type": "Organization"
},
"familyName": "Kim",
"givenName": "Sangook",
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Toronto",
"id": "https://www.grid.ac/institutes/grid.17063.33",
"name": [
"Department of Statistics, University of Toronto, Toronto, ON, Canada"
],
"type": "Organization"
},
"familyName": "Zhang",
"givenName": "Lin",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Hospital for Sick Children",
"id": "https://www.grid.ac/institutes/grid.42327.30",
"name": [
"Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada"
],
"type": "Organization"
},
"familyName": "Esmaeili",
"givenName": "Mohsen",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Johns Hopkins University",
"id": "https://www.grid.ac/institutes/grid.21107.35",
"name": [
"Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MA, USA"
],
"type": "Organization"
},
"familyName": "Blackman",
"givenName": "Scott",
"id": "sg:person.07636650254.30",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.07636650254.30"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Toronto",
"id": "https://www.grid.ac/institutes/grid.17063.33",
"name": [
"The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada",
"McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada"
],
"type": "Organization"
},
"familyName": "Scherer",
"givenName": "Stephen W.",
"id": "sg:person.011066475117.55",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011066475117.55"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "French Institute of Health and Medical Research",
"id": "https://www.grid.ac/institutes/grid.7429.8",
"name": [
"Pediatric Pulmonary Department, Hospital Trousseau, Assistance Publique-H\u00f4pitaux de Paris (AP-HP), Paris, France",
"Sorbonne Universit\u00e9s, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint-Antoine (CRSA), Paris, France"
],
"type": "Organization"
},
"familyName": "Corvol",
"givenName": "Harriet",
"id": "sg:person.01115423145.99",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01115423145.99"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Case Western Reserve University",
"id": "https://www.grid.ac/institutes/grid.67105.35",
"name": [
"Department of Pediatrics, Case Western Reserve University, Cleveland, OH, USA",
"Department of Genetics, Case Western Reserve University, Cleveland, OH, USA"
],
"type": "Organization"
},
"familyName": "Drumm",
"givenName": "Mitchell",
"id": "sg:person.01101417301.47",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01101417301.47"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of North Carolina System",
"id": "https://www.grid.ac/institutes/grid.410711.2",
"name": [
"Cystic Fibrosis Pulmonary Research and Treatment Center, University of North Carolina, Chapel Hill, NC, USA"
],
"type": "Organization"
},
"familyName": "Knowles",
"givenName": "Michael",
"id": "sg:person.015517451472.41",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015517451472.41"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Johns Hopkins University",
"id": "https://www.grid.ac/institutes/grid.21107.35",
"name": [
"Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MA, USA",
"McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA"
],
"type": "Organization"
},
"familyName": "Cutting",
"givenName": "Garry",
"id": "sg:person.0752157206.07",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0752157206.07"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Toronto",
"id": "https://www.grid.ac/institutes/grid.17063.33",
"name": [
"Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada",
"Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada"
],
"type": "Organization"
},
"familyName": "Rommens",
"givenName": "Johanna M.",
"id": "sg:person.01355172356.46",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01355172356.46"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Toronto",
"id": "https://www.grid.ac/institutes/grid.17063.33",
"name": [
"Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada",
"Department of Statistics, University of Toronto, Toronto, ON, Canada"
],
"type": "Organization"
},
"familyName": "Sun",
"givenName": "Lei",
"id": "sg:person.01270376351.10",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01270376351.10"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Toronto",
"id": "https://www.grid.ac/institutes/grid.17063.33",
"name": [
"Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada",
"The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada",
"Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada"
],
"type": "Organization"
},
"familyName": "Strug",
"givenName": "Lisa J.",
"id": "sg:person.0776774476.26",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0776774476.26"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1038/ng.3656",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1006258085",
"https://doi.org/10.1038/ng.3656"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/978-1-61779-120-8_21",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1008460822",
"https://doi.org/10.1007/978-1-61779-120-8_21"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/978-1-61779-120-8_21",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1008460822",
"https://doi.org/10.1007/978-1-61779-120-8_21"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature15393",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1021812064",
"https://doi.org/10.1038/nature15393"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ncomms9382",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023757952",
"https://doi.org/10.1038/ncomms9382"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature02168",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1033654326",
"https://doi.org/10.1038/nature02168"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature02168",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1033654326",
"https://doi.org/10.1038/nature02168"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ng.3620",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1037284658",
"https://doi.org/10.1038/ng.3620"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pgen.1004129",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1042472911"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ng.3643",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1050700099",
"https://doi.org/10.1038/ng.3643"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ng.3643",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1050700099",
"https://doi.org/10.1038/ng.3643"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1101/cshperspect.a009480",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1053057222"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ncomms15606",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1085591931",
"https://doi.org/10.1038/ncomms15606"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.ajhg.2017.04.014",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1085601700"
],
"type": "CreativeWork"
}
],
"datePublished": "2018-12",
"datePublishedReg": "2018-12-01",
"description": "Does genotype imputation with public reference panels identify variants contributing to disease? Genotype imputation using the 1000 Genomes Project (1KG; 2504 individuals) displayed poor coverage at the causal cystic fibrosis (CF) transmembrane conductance regulator (CFTR) locus for the International CF Gene Modifier Consortium. Imputation with the larger Haplotype Reference Consortium (HRC; 32,470 individuals) displayed improved coverage but low sensitivity of variants clinically relevant for CF. A hybrid reference that combined whole genome sequencing (WGS) from 101 CF individuals with the 1KG imputed a greater number of single-nucleotide variants (SNVs) that would be analyzed in a genetic association study (r2\u2009\u2265\u20090.3 and MAF\u2009\u2265\u20090.5%) than imputation with the HRC, while the HRC excelled in the lower frequency spectrum. Using the 1KG or HRC as reference panels missed the most common CF-causing variants or displayed low imputation accuracy. Designs that incorporate population-specific WGS can improve imputation accuracy at disease-specific loci, while imputation using public data sets can omit disease-relevant genotypes.",
"genre": "research_article",
"id": "sg:pub.10.1038/s41525-018-0047-6",
"inLanguage": [
"en"
],
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.2494517",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.2859417",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1053748",
"issn": [
"2056-7944"
],
"name": "npj Genomic Medicine",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "3"
}
],
"name": "Improving imputation in disease-relevant regions: lessons from cystic fibrosis",
"pagination": "8",
"productId": [
{
"name": "readcube_id",
"type": "PropertyValue",
"value": [
"84efd2dbdae2fff7e1a130e6a3e98066b553911fb7b183076e054e3322bc2a94"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"29581887"
]
},
{
"name": "nlm_unique_id",
"type": "PropertyValue",
"value": [
"101685193"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1038/s41525-018-0047-6"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1101582153"
]
}
],
"sameAs": [
"https://doi.org/10.1038/s41525-018-0047-6",
"https://app.dimensions.ai/details/publication/pub.1101582153"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-11T13:20",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000368_0000000368/records_78972_00000000.jsonl",
"type": "ScholarlyArticle",
"url": "https://www.nature.com/articles/s41525-018-0047-6"
}
]Download the RDF metadata as: json-ld nt turtle xml License info
JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/s41525-018-0047-6'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41525-018-0047-6'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41525-018-0047-6'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41525-018-0047-6'
This table displays all metadata directly associated to this object as RDF triples.
268 TRIPLES
21 PREDICATES
40 URIs
21 LITERALS
9 BLANK NODES