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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha : |
26/11/2015 |
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Actualizado : |
18/06/2019 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
FORNERIS, N. S.; LEGARRA, A.; VITEZICA, Z. G.; TSURUTA, S.; AGUILAR, I.; MISZTAL, I.; CANTET, R. J. C. |
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Afiliación : |
NATALIA S. FORNERIS, Universidad de Buenos Aires (UBA)/ Facultad de Agronomía; INRA (Institut National de la Recherche Agronomique); ANDRÉS LEGARRA, INRA (Institut National de la Recherche Agronomique); Université de Toulouse; ZULMA G. VITEZICA, INRA (Institut National de la Recherche Agronomique); Université de Toulouse; SHOGO TSURUTA, Universidad de Georgia (UG); IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; IGNACY MISZTAL, Universidad de Georgia (UG); RODOLFO J. C. CANTET, Universidad de Buenos Aires (UBA)/ Facultad de Agronomía; INRA (Institut National de la Recherche Agronomique). |
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Título : |
Quality control of genotypes using heritability estimates of gene content at the marker. |
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Fecha de publicación : |
2015 |
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Fuente / Imprenta : |
Genetics, 2015, v. 199, p. 675-681. OPEN ACCESS. |
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DOI : |
10.1534/genetics.114.173559 |
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Idioma : |
Inglés |
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Notas : |
Manuscript received September 26, 2014; accepted for publication December 18, 2014; published Early Online January 6, 2015. |
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Contenido : |
ABSTRACT
Quality control filtering of single-nucleotide polymorphisms (SNPs) is a key step when analyzing genomic data. Here we present a practical method to identify low-quality SNPs, meaning markers whose genotypes are wrongly assigned for a large proportion of individuals, by estimating the heritability of gene content at each marker, where gene content is the number of copies of a particular reference allele in a genotype of an animal (0, 1, or 2). If there is no mutation at the marker, gene content has an additive heritability of 1 by construction. 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. As a by-product, estimates of the allele frequencies of markers at the base population are obtained. Using simulated data with 10% permutation error (4% actual error) in genotyping, the method had a specificity of 0.96 (4% of correct markers are rejected) and a sensitivity of 0.99 (1% of wrong markers are accepted) if markers with heritability lower than 0.975 are discarded. Checking of Mendelian errors resulted in a lower sensitivity (0.84) for the same simulation. The proposed method is further illustrated with a real data set with genotypes from 3534 animals genotyped for 50,433 markers from the Illumina PorcineSNP60 chip and a pedigree of 6473 individuals; those markers underwent very little quality control. A total of 4099 markers with P-values lower than 0.01 were discarded based on our method, with associated estimates of heritability as low as 0.12. Contrary to other techniques, our method uses all information in the population simultaneously, can be used in any population with markers and pedigree recordings, and is simple to implement using standard software for REML estimation. Scripts for its use are provided.
Copyright © 2015 by the Genetics Society of America MenosABSTRACT
Quality control filtering of single-nucleotide polymorphisms (SNPs) is a key step when analyzing genomic data. Here we present a practical method to identify low-quality SNPs, meaning markers whose genotypes are wrongly assigned for a large proportion of individuals, by estimating the heritability of gene content at each marker, where gene content is the number of copies of a particular reference allele in a genotype of an animal (0, 1, or 2). If there is no mutation at the marker, gene content has an additive heritability of 1 by construction. 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. As a by-product, estimates of the allele frequencies of markers at the base population are obtained. Using simulated data with 10% permutation error (4% actual error) in genotyping, the method had a specificity of 0.96 (4% of correct markers are rejected) and a sensitivity of 0.99 (1% of wrong markers are accepted) if markers with heritability lower than 0.975 are discarded. Checking of Mendelian errors resulted in a lower sensitivity (0.84) for the same simulation. The proposed method is further illustrated with a real data set with genotypes from 3534 animals genotyped for 50,433 markers from the Illumina PorcineSNP60 chip and a pedigree of 6473 individuals; those markers underwent very little quality control. A total of 4... Presentar Todo |
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Palabras claves : |
GENE CONTENT; GENOMIC SELECTION; GENPRED; QUALITY CONTROL; REML; SHARED DATA RESOURCE; SNP. |
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Thesagro : |
MEJORAMIENTO GENETICO ANIMAL. |
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Asunto categoría : |
L10 Genética y mejoramiento animal |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/5302/1/Forneris-et-al-2015-Genetics.pdf
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Marc : |
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100 1 $aFORNERIS, N. S.
245 $aQuality control of genotypes using heritability estimates of gene content at the marker.$h[electronic resource]
260 $c2015
500 $aManuscript received September 26, 2014; accepted for publication December 18, 2014; published Early Online January 6, 2015.
520 $aABSTRACT Quality control filtering of single-nucleotide polymorphisms (SNPs) is a key step when analyzing genomic data. Here we present a practical method to identify low-quality SNPs, meaning markers whose genotypes are wrongly assigned for a large proportion of individuals, by estimating the heritability of gene content at each marker, where gene content is the number of copies of a particular reference allele in a genotype of an animal (0, 1, or 2). If there is no mutation at the marker, gene content has an additive heritability of 1 by construction. 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. As a by-product, estimates of the allele frequencies of markers at the base population are obtained. Using simulated data with 10% permutation error (4% actual error) in genotyping, the method had a specificity of 0.96 (4% of correct markers are rejected) and a sensitivity of 0.99 (1% of wrong markers are accepted) if markers with heritability lower than 0.975 are discarded. Checking of Mendelian errors resulted in a lower sensitivity (0.84) for the same simulation. The proposed method is further illustrated with a real data set with genotypes from 3534 animals genotyped for 50,433 markers from the Illumina PorcineSNP60 chip and a pedigree of 6473 individuals; those markers underwent very little quality control. A total of 4099 markers with P-values lower than 0.01 were discarded based on our method, with associated estimates of heritability as low as 0.12. Contrary to other techniques, our method uses all information in the population simultaneously, can be used in any population with markers and pedigree recordings, and is simple to implement using standard software for REML estimation. Scripts for its use are provided. Copyright © 2015 by the Genetics Society of America
650 $aMEJORAMIENTO GENETICO ANIMAL
653 $aGENE CONTENT
653 $aGENOMIC SELECTION
653 $aGENPRED
653 $aQUALITY CONTROL
653 $aREML
653 $aSHARED DATA RESOURCE
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700 1 $aLEGARRA, A.
700 1 $aVITEZICA, Z. G.
700 1 $aTSURUTA, S.
700 1 $aAGUILAR, I.
700 1 $aMISZTAL, I.
700 1 $aCANTET, R. J. C.
773 $tGenetics, 2015$gv. 199, p. 675-681. OPEN ACCESS.
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Registro original : |
INIA Las Brujas (LB) |
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Registro completo
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Biblioteca (s) : |
INIA Las Brujas; INIA Tacuarembó. |
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Fecha actual : |
19/07/2015 |
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Actualizado : |
21/10/2019 |
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Tipo de producción científica : |
Revista INIA |
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Autor : |
INIA (INSTITUTO NACIONAL DE INVESTIGACIÓN AGROPECUARIA) |
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Título : |
Revista INIA Uruguay. (No.34, Setiembre 2013). |
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Fecha de publicación : |
2013 |
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Fuente / Imprenta : |
Montevideo (Uruguay): INIA, 2013. |
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Páginas : |
64 p. |
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Serie : |
(Revista INIA; 34) |
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ISSN : |
1510-9011 |
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Idioma : |
Español |
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Thesagro : |
ARROZ; BIOTECNOLOGIA; BOVINOS DE CARNE; CAMBIO CLIMÁTICO; CIENCIA; CITRUS; CLIMA; CLIMATOLOGIA; COMUNICACIÓN; CONTROL DE ENFERMEDADES; CULTIVOS DE GRANO; CULTIVOS DE SECANO; ENTOMOLOGIA; ESPECIES FORRAJERAS; EUCALYPTUS; EXPLOTACION AGRICOLA FAMILIAR; FITOPATOLOGÍA; FORESTALES; FORRAJES; FRUTALES; FRUTICULTURA; GANADO BOVINO; GRANOS; GRAS; HORTALIZAS; HORTICULTURA; INIA; INNOVACION; INVESTIGACIÓN; LECHERÍA; LEGUMINOSAS FORRAJERAS; MANEJO DEL CULTIVO; MEJORAMIENTO ANIMAL; METEOROLOGIA; MICROBIOLOGÍA; OVINOS; PASTURAS; PRODUCCIÓN ANIMAL; PRODUCCION DE LANA; PRODUCCION DE LECHE; PRODUCCION LECHERA; REVISTA INIA 2013; SEMILLAS; SOJA; SUELOS; SUINOS; SUSTENTABILIDAD AMBIENTAL; TECNOLOGÍA; TRANSFERENCIA DE TECNOLOGIA; VARIEDADES; VITICULTURA. |
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Asunto categoría : |
A50 Investigación agraria |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/4849/1/revista-INIA-34.pdf
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Marc : |
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