Efficiency of genotype imputation in buffalo's metacentric chromosomes rearranged from bovine reference
The assembly of a reference genome is essential for genome-wide studies, which requires the exact position of SNPs in any species. Buffalo specie has only scaffolds and annotated genes available, but the ordination of they are still not assembled. Previous studies carried out by our group observed t...
Gespeichert in:
| Veröffentlicht in: | CES medicina veterinaria y zootecnia 2016-09, Vol.11 (3), p.187 |
|---|---|
| Hauptverfasser: | , , , , , , |
| Format: | Artikel |
| Sprache: | spa |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | |
|---|---|
| container_issue | 3 |
| container_start_page | 187 |
| container_title | CES medicina veterinaria y zootecnia |
| container_volume | 11 |
| creator | Abreu dos Santos, Daniel Jordan Francisco Cardoso, Diercles Ferreira de Camargo, Gregório Miguel Aspilcueta- Borquis, Rusbel Raul Buzanskas, Marcos Eli Hurtado-Lugo, Naudin Alejandro Tonhati, Humberto |
| description | The assembly of a reference genome is essential for genome-wide studies, which requires the exact position of SNPs in any species. Buffalo specie has only scaffolds and annotated genes available, but the ordination of they are still not assembled. Previous studies carried out by our group observed the possibility of rearranging the buffalo's chromosomes using bovine reference map, by linkage disequilibrium between chromosomal structures. Thus, the aim of this study was to evaluate the imputation efficiency on five buffalo's chromosomes with (R_BBU) and without (NR_BBU) rearrangement. A total of 352 buffaloes were genotyped with 90K Axiom Buffalo Genotyping (Affymetrix). A total of 46,378 SNPs passed in the genotype quality control (call rate [greater than or equal to]0.95, MAF [greater than or equal to]0.05, P-HWE |
| format | Article |
| fullrecord | <record><control><sourceid>gale</sourceid><recordid>TN_cdi_gale_infotracmisc_A596403161</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A596403161</galeid><sourcerecordid>A596403161</sourcerecordid><originalsourceid>FETCH-gale_infotracmisc_A5964031613</originalsourceid><addsrcrecordid>eNqNjMEKwjAQRIMoKNp_WPDgSUhprfYoUvEDvEuMm7rSZEuSCv17c_Dg0bnM8BjeRCzyWsptXcn99GfPRRbCS6ZUsijLw0K0jTGkCZ0egQ206DiOPQLZfogqEjsgB_fBGNXxJoDFqDS66EmDfnq2HNhiAI_Ke-VafIBJFO78JocJG_RJjisxS4aA2beXYn1urqfLtlUd3sgZjl5pS0Hfjru6KmWRV3nx3-sDQVhJ8g</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype></control><display><type>article</type><title>Efficiency of genotype imputation in buffalo's metacentric chromosomes rearranged from bovine reference</title><source>Alma/SFX Local Collection</source><creator>Abreu dos Santos, Daniel Jordan ; Francisco Cardoso, Diercles ; Ferreira de Camargo, Gregório Miguel ; Aspilcueta- Borquis, Rusbel Raul ; Buzanskas, Marcos Eli ; Hurtado-Lugo, Naudin Alejandro ; Tonhati, Humberto</creator><creatorcontrib>Abreu dos Santos, Daniel Jordan ; Francisco Cardoso, Diercles ; Ferreira de Camargo, Gregório Miguel ; Aspilcueta- Borquis, Rusbel Raul ; Buzanskas, Marcos Eli ; Hurtado-Lugo, Naudin Alejandro ; Tonhati, Humberto</creatorcontrib><description>The assembly of a reference genome is essential for genome-wide studies, which requires the exact position of SNPs in any species. Buffalo specie has only scaffolds and annotated genes available, but the ordination of they are still not assembled. Previous studies carried out by our group observed the possibility of rearranging the buffalo's chromosomes using bovine reference map, by linkage disequilibrium between chromosomal structures. Thus, the aim of this study was to evaluate the imputation efficiency on five buffalo's chromosomes with (R_BBU) and without (NR_BBU) rearrangement. A total of 352 buffaloes were genotyped with 90K Axiom Buffalo Genotyping (Affymetrix). A total of 46,378 SNPs passed in the genotype quality control (call rate [greater than or equal to]0.95, MAF [greater than or equal to]0.05, P-HWE <[10.sup.-6]). Only autosomal markers with known position (UMD3.1) were used. The software Beagle v.4 was used for genotype imputation. Scenarios that considered 10%, 15%, 20%, 25%, and 30% of the markers were used to calculate the allelic concordance rate (CR) and allelic R- square ([r.sup.2]). The analyses were performed dividing the animals into reference and 88 imputation sets in a 4-fold cross-validation scheme. Considering full chromosomes, the average of accuracy was similar between R_BBU and NR_BBU but varied between scenarios, ranging from 0.87 to 0.91 ([r.sup.2]) and 0.92 to 0.96 (CR). Only for R_BBU1 (scenario 10%) and R_BBU4 (scenario 30%) a significant increase (P<0.05, t-test) in the CR was observed. However, considering one Megabase window to either side of the centromere, we found a more evident difference in the imputation accuracy for all five chromosomes in most scenarios. An increase of 11% and 9% in the [r.sup.2] and CR, respectively, was observed on R_BBU1. Therefore, the rearrangement was appropriate for increase imputation efficiency due to a better construction of haplotypes.</description><identifier>ISSN: 1900-9607</identifier><identifier>EISSN: 1900-9607</identifier><language>spa</language><publisher>Universidad del CES</publisher><subject>Analysis ; Chromosomes ; Genes ; Genetic aspects ; Genomes ; Genomics</subject><ispartof>CES medicina veterinaria y zootecnia, 2016-09, Vol.11 (3), p.187</ispartof><rights>COPYRIGHT 2016 Universidad del CES</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780</link.rule.ids></links><search><creatorcontrib>Abreu dos Santos, Daniel Jordan</creatorcontrib><creatorcontrib>Francisco Cardoso, Diercles</creatorcontrib><creatorcontrib>Ferreira de Camargo, Gregório Miguel</creatorcontrib><creatorcontrib>Aspilcueta- Borquis, Rusbel Raul</creatorcontrib><creatorcontrib>Buzanskas, Marcos Eli</creatorcontrib><creatorcontrib>Hurtado-Lugo, Naudin Alejandro</creatorcontrib><creatorcontrib>Tonhati, Humberto</creatorcontrib><title>Efficiency of genotype imputation in buffalo's metacentric chromosomes rearranged from bovine reference</title><title>CES medicina veterinaria y zootecnia</title><description>The assembly of a reference genome is essential for genome-wide studies, which requires the exact position of SNPs in any species. Buffalo specie has only scaffolds and annotated genes available, but the ordination of they are still not assembled. Previous studies carried out by our group observed the possibility of rearranging the buffalo's chromosomes using bovine reference map, by linkage disequilibrium between chromosomal structures. Thus, the aim of this study was to evaluate the imputation efficiency on five buffalo's chromosomes with (R_BBU) and without (NR_BBU) rearrangement. A total of 352 buffaloes were genotyped with 90K Axiom Buffalo Genotyping (Affymetrix). A total of 46,378 SNPs passed in the genotype quality control (call rate [greater than or equal to]0.95, MAF [greater than or equal to]0.05, P-HWE <[10.sup.-6]). Only autosomal markers with known position (UMD3.1) were used. The software Beagle v.4 was used for genotype imputation. Scenarios that considered 10%, 15%, 20%, 25%, and 30% of the markers were used to calculate the allelic concordance rate (CR) and allelic R- square ([r.sup.2]). The analyses were performed dividing the animals into reference and 88 imputation sets in a 4-fold cross-validation scheme. Considering full chromosomes, the average of accuracy was similar between R_BBU and NR_BBU but varied between scenarios, ranging from 0.87 to 0.91 ([r.sup.2]) and 0.92 to 0.96 (CR). Only for R_BBU1 (scenario 10%) and R_BBU4 (scenario 30%) a significant increase (P<0.05, t-test) in the CR was observed. However, considering one Megabase window to either side of the centromere, we found a more evident difference in the imputation accuracy for all five chromosomes in most scenarios. An increase of 11% and 9% in the [r.sup.2] and CR, respectively, was observed on R_BBU1. Therefore, the rearrangement was appropriate for increase imputation efficiency due to a better construction of haplotypes.</description><subject>Analysis</subject><subject>Chromosomes</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Genomics</subject><issn>1900-9607</issn><issn>1900-9607</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><recordid>eNqNjMEKwjAQRIMoKNp_WPDgSUhprfYoUvEDvEuMm7rSZEuSCv17c_Dg0bnM8BjeRCzyWsptXcn99GfPRRbCS6ZUsijLw0K0jTGkCZ0egQ206DiOPQLZfogqEjsgB_fBGNXxJoDFqDS66EmDfnq2HNhiAI_Ke-VafIBJFO78JocJG_RJjisxS4aA2beXYn1urqfLtlUd3sgZjl5pS0Hfjru6KmWRV3nx3-sDQVhJ8g</recordid><startdate>20160901</startdate><enddate>20160901</enddate><creator>Abreu dos Santos, Daniel Jordan</creator><creator>Francisco Cardoso, Diercles</creator><creator>Ferreira de Camargo, Gregório Miguel</creator><creator>Aspilcueta- Borquis, Rusbel Raul</creator><creator>Buzanskas, Marcos Eli</creator><creator>Hurtado-Lugo, Naudin Alejandro</creator><creator>Tonhati, Humberto</creator><general>Universidad del CES</general><scope>INF</scope></search><sort><creationdate>20160901</creationdate><title>Efficiency of genotype imputation in buffalo's metacentric chromosomes rearranged from bovine reference</title><author>Abreu dos Santos, Daniel Jordan ; Francisco Cardoso, Diercles ; Ferreira de Camargo, Gregório Miguel ; Aspilcueta- Borquis, Rusbel Raul ; Buzanskas, Marcos Eli ; Hurtado-Lugo, Naudin Alejandro ; Tonhati, Humberto</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-gale_infotracmisc_A5964031613</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>spa</language><creationdate>2016</creationdate><topic>Analysis</topic><topic>Chromosomes</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genomes</topic><topic>Genomics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Abreu dos Santos, Daniel Jordan</creatorcontrib><creatorcontrib>Francisco Cardoso, Diercles</creatorcontrib><creatorcontrib>Ferreira de Camargo, Gregório Miguel</creatorcontrib><creatorcontrib>Aspilcueta- Borquis, Rusbel Raul</creatorcontrib><creatorcontrib>Buzanskas, Marcos Eli</creatorcontrib><creatorcontrib>Hurtado-Lugo, Naudin Alejandro</creatorcontrib><creatorcontrib>Tonhati, Humberto</creatorcontrib><collection>Gale OneFile: Informe Academico</collection><jtitle>CES medicina veterinaria y zootecnia</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Abreu dos Santos, Daniel Jordan</au><au>Francisco Cardoso, Diercles</au><au>Ferreira de Camargo, Gregório Miguel</au><au>Aspilcueta- Borquis, Rusbel Raul</au><au>Buzanskas, Marcos Eli</au><au>Hurtado-Lugo, Naudin Alejandro</au><au>Tonhati, Humberto</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Efficiency of genotype imputation in buffalo's metacentric chromosomes rearranged from bovine reference</atitle><jtitle>CES medicina veterinaria y zootecnia</jtitle><date>2016-09-01</date><risdate>2016</risdate><volume>11</volume><issue>3</issue><spage>187</spage><pages>187-</pages><issn>1900-9607</issn><eissn>1900-9607</eissn><abstract>The assembly of a reference genome is essential for genome-wide studies, which requires the exact position of SNPs in any species. Buffalo specie has only scaffolds and annotated genes available, but the ordination of they are still not assembled. Previous studies carried out by our group observed the possibility of rearranging the buffalo's chromosomes using bovine reference map, by linkage disequilibrium between chromosomal structures. Thus, the aim of this study was to evaluate the imputation efficiency on five buffalo's chromosomes with (R_BBU) and without (NR_BBU) rearrangement. A total of 352 buffaloes were genotyped with 90K Axiom Buffalo Genotyping (Affymetrix). A total of 46,378 SNPs passed in the genotype quality control (call rate [greater than or equal to]0.95, MAF [greater than or equal to]0.05, P-HWE <[10.sup.-6]). Only autosomal markers with known position (UMD3.1) were used. The software Beagle v.4 was used for genotype imputation. Scenarios that considered 10%, 15%, 20%, 25%, and 30% of the markers were used to calculate the allelic concordance rate (CR) and allelic R- square ([r.sup.2]). The analyses were performed dividing the animals into reference and 88 imputation sets in a 4-fold cross-validation scheme. Considering full chromosomes, the average of accuracy was similar between R_BBU and NR_BBU but varied between scenarios, ranging from 0.87 to 0.91 ([r.sup.2]) and 0.92 to 0.96 (CR). Only for R_BBU1 (scenario 10%) and R_BBU4 (scenario 30%) a significant increase (P<0.05, t-test) in the CR was observed. However, considering one Megabase window to either side of the centromere, we found a more evident difference in the imputation accuracy for all five chromosomes in most scenarios. An increase of 11% and 9% in the [r.sup.2] and CR, respectively, was observed on R_BBU1. Therefore, the rearrangement was appropriate for increase imputation efficiency due to a better construction of haplotypes.</abstract><pub>Universidad del CES</pub></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1900-9607 |
| ispartof | CES medicina veterinaria y zootecnia, 2016-09, Vol.11 (3), p.187 |
| issn | 1900-9607 1900-9607 |
| language | spa |
| recordid | cdi_gale_infotracmisc_A596403161 |
| source | Alma/SFX Local Collection |
| subjects | Analysis Chromosomes Genes Genetic aspects Genomes Genomics |
| title | Efficiency of genotype imputation in buffalo's metacentric chromosomes rearranged from bovine reference |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-30T15%3A59%3A38IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Efficiency%20of%20genotype%20imputation%20in%20buffalo's%20metacentric%20chromosomes%20rearranged%20from%20bovine%20reference&rft.jtitle=CES%20medicina%20veterinaria%20y%20zootecnia&rft.au=Abreu%20dos%20Santos,%20Daniel%20Jordan&rft.date=2016-09-01&rft.volume=11&rft.issue=3&rft.spage=187&rft.pages=187-&rft.issn=1900-9607&rft.eissn=1900-9607&rft_id=info:doi/&rft_dat=%3Cgale%3EA596403161%3C/gale%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_id=info:pmid/&rft_galeid=A596403161&rfr_iscdi=true |