Fecha/hora: 16/06/2024 02:09:26

Biblioteca(s): | INIA Las Brujas.
Fecha corriente: | 26/11/2015
Fecha de la última actualización: | 18/06/2019
Autoria: | FORNERIS, N. S.; LEGARRA, A.; VITEZICA, Z. G.; TSURUTA, S.; AGUILAR, I.; MISZTAL, I.; CANTET, R. J. C.
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).
Título: | Quality control of genotypes using heritability estimates of gene content at the marker.
Año de publicación: | 2015
Fuente/Imprenta: | Genetics, 2015, v. 199, p. 675-681. OPEN ACCESS.
DOI: | 10.1534/genetics.114.173559
Idioma: | Inglés
Notas: | Manuscript received September 26, 2014; accepted for publication December 18, 2014; published Early Online January 6, 2015.

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

Palabras-Clave: | GENE CONTENT; GENOMIC SELECTION; GENPRED; QUALITY CONTROL; REML; SHARED DATA RESOURCE; SNP.
Thesagro: | MEJORAMIENTO GENETICO ANIMAL.
Categoría del tema: | L10 Genética y mejoramiento animal
URL: | http://www.ainfo.inia.uy/digital/bitstream/item/5302/1/Forneris-et-al-2015-Genetics.pdf
Registro original: | INIA Las Brujas (LB)
Ejemplares: | LB - (100868-1) - PXI - AP - DD -  -  -  - DIS