Quality control of genotypes using heritability estimates of gene content.
Resumen:
ABSTRACT.Quality control filtering of single nucleotide polymorphisms (SNP) is a key step when analyzing genomic data. Here, we present a practical method to identify poorly genotyped SNPs by detecting those for which gene content deviates from the pedigree-based expectation. This can be achieved by estimating the heritability of gene content at each marker, defined as the number of copies of a particular reference allele in a genotype of an animal (0, 1 or 2). The method uses Restricted Maximum Likelihood (REML) to estimate heritability of gene content at each SNP and also builds a likelihood ratio test statistic to test for zero error variance in genotyping. The proposed method is illustrated with a real dataset with genotypes from Illumina PorcineSNP60 chip.
| 2014 | |
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Quality Control Gene Content Heritability Likelihood Ratio |
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| Inglés | |
| Instituto Nacional de Investigación Agropecuaria | |
| AINFO | |
| http://www.ainfo.inia.uy/consulta/busca?b=pc&id=61920&biblioteca=vazio&busca=61920&qFacets=61920 | |
| Acceso abierto |
| _version_ | 1805580526541602816 |
|---|---|
| author | FORNERIS, N. S. |
| author2 | LEGARRA, A. VITEZICA, Z. G. TSURUTA, S. AGUILAR, I. CANTET, R.J.C. MISZTAL, I. |
| author2_role | author author author author author author |
| author_facet | FORNERIS, N. S. LEGARRA, A. VITEZICA, Z. G. TSURUTA, S. AGUILAR, I. CANTET, R.J.C. MISZTAL, I. |
| author_role | author |
| bitstream.checksum.fl_str_mv | f7cb5505d9593672487546f3f24fbcbb |
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| bitstream.url.fl_str_mv | https://redi.anii.org.uy/jspui/bitstream/20.500.12381/1729/1/sword-2022-10-20T22%3a48%3a56.original.xml |
| collection | AINFO |
| dc.creator.none.fl_str_mv | FORNERIS, N. S. LEGARRA, A. VITEZICA, Z. G. TSURUTA, S. AGUILAR, I. CANTET, R.J.C. MISZTAL, I. |
| dc.date.accessioned.none.fl_str_mv | 2022-10-21T01:48:56Z |
| dc.date.available.none.fl_str_mv | 2022-10-21T01:48:56Z |
| dc.date.issued.none.fl_str_mv | 2014 |
| dc.date.updated.none.fl_str_mv | 2022-10-21T01:48:56Z |
| dc.description.abstract.none.fl_txt_mv | ABSTRACT.Quality control filtering of single nucleotide polymorphisms (SNP) is a key step when analyzing genomic data. Here, we present a practical method to identify poorly genotyped SNPs by detecting those for which gene content deviates from the pedigree-based expectation. This can be achieved by estimating the heritability of gene content at each marker, defined as the number of copies of a particular reference allele in a genotype of an animal (0, 1 or 2). The method uses Restricted Maximum Likelihood (REML) to estimate heritability of gene content at each SNP and also builds a likelihood ratio test statistic to test for zero error variance in genotyping. The proposed method is illustrated with a real dataset with genotypes from Illumina PorcineSNP60 chip. |
| dc.identifier.none.fl_str_mv | http://www.ainfo.inia.uy/consulta/busca?b=pc&id=61920&biblioteca=vazio&busca=61920&qFacets=61920 |
| dc.language.iso.none.fl_str_mv | en eng |
| dc.rights.es.fl_str_mv | Acceso abierto |
| dc.rights.none.fl_str_mv | info:eu-repo/semantics/openAccess |
| dc.source.none.fl_str_mv | reponame:AINFO instname:Instituto Nacional de Investigación Agropecuaria instacron:Instituto Nacional de Investigación Agropecuaria |
| dc.subject.none.fl_str_mv | Quality Control Gene Content Heritability Likelihood Ratio |
| dc.title.none.fl_str_mv | Quality control of genotypes using heritability estimates of gene content. |
| dc.type.none.fl_str_mv | ConferenceObject PublishedVersion info:eu-repo/semantics/conferenceObject |
| dc.type.version.none.fl_str_mv | info:eu-repo/semantics/publishedVersion |
| description | ABSTRACT.Quality control filtering of single nucleotide polymorphisms (SNP) is a key step when analyzing genomic data. Here, we present a practical method to identify poorly genotyped SNPs by detecting those for which gene content deviates from the pedigree-based expectation. This can be achieved by estimating the heritability of gene content at each marker, defined as the number of copies of a particular reference allele in a genotype of an animal (0, 1 or 2). The method uses Restricted Maximum Likelihood (REML) to estimate heritability of gene content at each SNP and also builds a likelihood ratio test statistic to test for zero error variance in genotyping. The proposed method is illustrated with a real dataset with genotypes from Illumina PorcineSNP60 chip. |
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| instacron_str | Instituto Nacional de Investigación Agropecuaria |
| institution | Instituto Nacional de Investigación Agropecuaria |
| instname_str | Instituto Nacional de Investigación Agropecuaria |
| language | eng |
| language_invalid_str_mv | en |
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| oai_identifier_str | oai:redi.anii.org.uy:20.500.12381/1729 |
| publishDate | 2014 |
| reponame_str | AINFO |
| repository.mail.fl_str_mv | lorrego@inia.org.uy |
| repository.name.fl_str_mv | AINFO - Instituto Nacional de Investigación Agropecuaria |
| repository_id_str | |
| rights_invalid_str_mv | Acceso abierto |
| spelling | 2022-10-21T01:48:56Z2022-10-21T01:48:56Z20142022-10-21T01:48:56Zhttp://www.ainfo.inia.uy/consulta/busca?b=pc&id=61920&biblioteca=vazio&busca=61920&qFacets=61920ABSTRACT.Quality control filtering of single nucleotide polymorphisms (SNP) is a key step when analyzing genomic data. Here, we present a practical method to identify poorly genotyped SNPs by detecting those for which gene content deviates from the pedigree-based expectation. This can be achieved by estimating the heritability of gene content at each marker, defined as the number of copies of a particular reference allele in a genotype of an animal (0, 1 or 2). The method uses Restricted Maximum Likelihood (REML) to estimate heritability of gene content at each SNP and also builds a likelihood ratio test statistic to test for zero error variance in genotyping. The proposed method is illustrated with a real dataset with genotypes from Illumina PorcineSNP60 chip.https://hdl.handle.net/20.500.12381/1729enenginfo:eu-repo/semantics/openAccessAcceso abiertoQuality ControlGene ContentHeritabilityLikelihood RatioQuality control of genotypes using heritability estimates of gene content.ConferenceObjectPublishedVersioninfo:eu-repo/semantics/conferenceObjectinfo:eu-repo/semantics/publishedVersionreponame:AINFOinstname:Instituto Nacional de Investigación Agropecuariainstacron:Instituto Nacional de Investigación AgropecuariaFORNERIS, N. S.LEGARRA, A.VITEZICA, Z. G.TSURUTA, S.AGUILAR, I.CANTET, R.J.C.MISZTAL, I.SWORDsword-2022-10-20T22:48:56.original.xmlOriginal SWORD entry documentapplication/octet-stream1976https://redi.anii.org.uy/jspui/bitstream/20.500.12381/1729/1/sword-2022-10-20T22%3a48%3a56.original.xmlf7cb5505d9593672487546f3f24fbcbbMD5120.500.12381/17292022-10-20 22:48:56.693oai:redi.anii.org.uy:20.500.12381/1729Gobiernohttp://inia.uyhttps://redi.anii.org.uy/oai/requestlorrego@inia.org.uyUruguayopendoar:2022-10-21T01:48:56AINFO - Instituto Nacional de Investigación Agropecuariafalse |
| spellingShingle | Quality control of genotypes using heritability estimates of gene content. FORNERIS, N. S. Quality Control Gene Content Heritability Likelihood Ratio |
| status_str | publishedVersion |
| title | Quality control of genotypes using heritability estimates of gene content. |
| title_full | Quality control of genotypes using heritability estimates of gene content. |
| title_fullStr | Quality control of genotypes using heritability estimates of gene content. |
| title_full_unstemmed | Quality control of genotypes using heritability estimates of gene content. |
| title_short | Quality control of genotypes using heritability estimates of gene content. |
| title_sort | Quality control of genotypes using heritability estimates of gene content. |
| topic | Quality Control Gene Content Heritability Likelihood Ratio |
| url | http://www.ainfo.inia.uy/consulta/busca?b=pc&id=61920&biblioteca=vazio&busca=61920&qFacets=61920 |
