Applications and efficiencies of the first cat 63K DNA array
The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats. The properties of feline 62,897 SNPs Illumina Infinium iSelect DNA array are described using a dataset of over 2,000 feline samples, the mos...
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| creator | Gandolfi, Barbara Alhaddad, Hasan Abdi, Mona Bach, Leslie H. Creighton, Erica K. Davis, Brian W. Decker, Jared E. Dodman, Nicholas H. Ginns, Edward I. Grahn, Jennifer C. Grahn, Robert A. Haase, Bianca Haggstrom, Jens Hamilton, Michael J. Helps, Christopher R. Kurushima, Jennifer D. Lohi, Hannes Longeri, Maria Malik, Richard Meurs, Kathryn M. Montague, Michael J. Mullikin, James C. Murphy, William J. Nilson, Sara M. Pedersen, Niels C. Peterson, Carlyn B. Rusbridge, Clare Saif, Rashid Shelton, G. Diane Warren, Wesley C. Wasim, Muhammad Lyons, Leslie A. |
| description | The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats. The properties of feline 62,897 SNPs Illumina Infinium iSelect DNA array are described using a dataset of over 2,000 feline samples, the most extensive to date, representing 41 cat breeds, a random bred population, and four wild felid species. Accuracy and efficiency of the array’s genotypes and its utility in performing population-based analyses were evaluated. Average marker distance across the array was 37,741 Kb, and across the dataset, only 1% (625) of the markers exhibited poor genotyping and only 0.35% (221) showed Mendelian errors. Marker polymorphism varied across cat breeds and the average minor allele frequency (MAF) of all markers across domestic cats was 0.21. Population structure analysis confirmed a Western to Eastern structural continuum of cat breeds. Genome-wide linkage disequilibrium ranged from 50–1,500 Kb for domestic cats and 750 Kb for European wildcats (
Felis silvestris silvestris
). Array use in trait association mapping was investigated under different modes of inheritance, selection and population sizes. The efficient array design and cat genotype dataset continues to advance the understanding of cat breeds and will support monogenic health studies across feline breeds and populations. |
| doi_str_mv | 10.1038/s41598-018-25438-0 |
| format | Article |
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Felis silvestris silvestris
). Array use in trait association mapping was investigated under different modes of inheritance, selection and population sizes. 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Average marker distance across the array was 37,741 Kb, and across the dataset, only 1% (625) of the markers exhibited poor genotyping and only 0.35% (221) showed Mendelian errors. Marker polymorphism varied across cat breeds and the average minor allele frequency (MAF) of all markers across domestic cats was 0.21. Population structure analysis confirmed a Western to Eastern structural continuum of cat breeds. Genome-wide linkage disequilibrium ranged from 50–1,500 Kb for domestic cats and 750 Kb for European wildcats (
Felis silvestris silvestris
). Array use in trait association mapping was investigated under different modes of inheritance, selection and population sizes. The efficient array design and cat genotype dataset continues to advance the understanding of cat breeds and will support monogenic health studies across feline breeds and populations.</description><subject>45</subject><subject>45/43</subject><subject>631/208/212</subject><subject>631/208/727</subject><subject>Cats</subject><subject>Datasets</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Domestic animals</subject><subject>Gene frequency</subject><subject>Gene mapping</subject><subject>Gene polymorphism</subject><subject>Genetics</subject><subject>Genetik</subject><subject>Genotypes</subject><subject>Genotyping</subject><subject>Heredity</subject><subject>Humanities and Social Sciences</subject><subject>Linkage disequilibrium</subject><subject>multidisciplinary</subject><subject>Population</subject><subject>Population structure</subject><subject>Science</subject><subject>Science (multidisciplinary)</subject><subject>Single-nucleotide polymorphism</subject><subject>Wildcats</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>BENPR</sourceid><recordid>eNp9kU1LxDAQhoMoKrp_wIMEvHipppOkTUCExW8Uveg5pGmikW67Jq3ivzfrruvHwUCYgXnyZmZehHZycpATKg4jy7kUGclFBpzRlK2gTSCMZ0ABVn_kG2gU4zNJh4NkuVxHGyBLEIWkm-hoPJ023ujed23Euq2xdc4bb9t0I-4c7p8sdj7EHicKF_Qan96OsQ5Bv2-jNaebaEeLuIUezs_uTy6zm7uLq5PxTWY4k33GKQjhmAEqKskrXpVlKYtKCClMzUmKmrhKcFrlDhwjogZr61JLaaQEXdMtlM1145udDpWaBj_R4V112qvYDJUOs6CiVZIDLxJ_POcTPLG1sW0fdPPr2e9K65_UY_equKS8BJIE9hcCoXsZbOzVxEdjm0a3thuiSggHVqQ5Err3B33uhtCmdcwoVggKOU0UzCkTuhiDdctmcqJmfqq5nyr5qT79VLMudn-OsXzy5V4C6GIvqdQ-2vD99z-yH90lqhA</recordid><startdate>20180504</startdate><enddate>20180504</enddate><creator>Gandolfi, Barbara</creator><creator>Alhaddad, Hasan</creator><creator>Abdi, Mona</creator><creator>Bach, Leslie H.</creator><creator>Creighton, Erica K.</creator><creator>Davis, Brian W.</creator><creator>Decker, Jared E.</creator><creator>Dodman, Nicholas H.</creator><creator>Ginns, Edward I.</creator><creator>Grahn, Jennifer C.</creator><creator>Grahn, Robert A.</creator><creator>Haase, Bianca</creator><creator>Haggstrom, Jens</creator><creator>Hamilton, Michael J.</creator><creator>Helps, Christopher R.</creator><creator>Kurushima, Jennifer D.</creator><creator>Lohi, Hannes</creator><creator>Longeri, Maria</creator><creator>Malik, Richard</creator><creator>Meurs, Kathryn M.</creator><creator>Montague, Michael J.</creator><creator>Mullikin, James C.</creator><creator>Murphy, William J.</creator><creator>Nilson, Sara M.</creator><creator>Pedersen, Niels C.</creator><creator>Peterson, Carlyn B.</creator><creator>Rusbridge, Clare</creator><creator>Saif, Rashid</creator><creator>Shelton, G. 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Diane</au><au>Warren, Wesley C.</au><au>Wasim, Muhammad</au><au>Lyons, Leslie A.</au><aucorp>Sveriges lantbruksuniversitet</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Applications and efficiencies of the first cat 63K DNA array</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2018-05-04</date><risdate>2018</risdate><volume>8</volume><issue>1</issue><spage>7024</spage><epage>15</epage><pages>7024-15</pages><artnum>7024</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats. The properties of feline 62,897 SNPs Illumina Infinium iSelect DNA array are described using a dataset of over 2,000 feline samples, the most extensive to date, representing 41 cat breeds, a random bred population, and four wild felid species. Accuracy and efficiency of the array’s genotypes and its utility in performing population-based analyses were evaluated. Average marker distance across the array was 37,741 Kb, and across the dataset, only 1% (625) of the markers exhibited poor genotyping and only 0.35% (221) showed Mendelian errors. Marker polymorphism varied across cat breeds and the average minor allele frequency (MAF) of all markers across domestic cats was 0.21. Population structure analysis confirmed a Western to Eastern structural continuum of cat breeds. Genome-wide linkage disequilibrium ranged from 50–1,500 Kb for domestic cats and 750 Kb for European wildcats (
Felis silvestris silvestris
). Array use in trait association mapping was investigated under different modes of inheritance, selection and population sizes. The efficient array design and cat genotype dataset continues to advance the understanding of cat breeds and will support monogenic health studies across feline breeds and populations.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>29728693</pmid><doi>10.1038/s41598-018-25438-0</doi><tpages>15</tpages><orcidid>https://orcid.org/0000-0002-6121-135X</orcidid><orcidid>https://orcid.org/0000-0001-5685-7343</orcidid><orcidid>https://orcid.org/0000-0003-0825-3750</orcidid><orcidid>https://orcid.org/0000-0003-0253-4404</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 2045-2322 |
| ispartof | Scientific reports, 2018-05, Vol.8 (1), p.7024-15, Article 7024 |
| issn | 2045-2322 2045-2322 |
| language | eng |
| recordid | cdi_swepub_primary_oai_slubar_slu_se_95256 |
| source | Nature Free; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Alma/SFX Local Collection; Free Full-Text Journals in Chemistry; Springer Nature OA Free Journals |
| subjects | 45 45/43 631/208/212 631/208/727 Cats Datasets Deoxyribonucleic acid DNA Domestic animals Gene frequency Gene mapping Gene polymorphism Genetics Genetik Genotypes Genotyping Heredity Humanities and Social Sciences Linkage disequilibrium multidisciplinary Population Population structure Science Science (multidisciplinary) Single-nucleotide polymorphism Wildcats |
| title | Applications and efficiencies of the first cat 63K DNA array |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-02T18%3A06%3A42IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_swepu&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Applications%20and%20efficiencies%20of%20the%20first%20cat%2063K%20DNA%20array&rft.jtitle=Scientific%20reports&rft.au=Gandolfi,%20Barbara&rft.aucorp=Sveriges%20lantbruksuniversitet&rft.date=2018-05-04&rft.volume=8&rft.issue=1&rft.spage=7024&rft.epage=15&rft.pages=7024-15&rft.artnum=7024&rft.issn=2045-2322&rft.eissn=2045-2322&rft_id=info:doi/10.1038/s41598-018-25438-0&rft_dat=%3Cproquest_swepu%3E2035246777%3C/proquest_swepu%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2034683213&rft_id=info:pmid/29728693&rfr_iscdi=true |