02951naa a2200313 a 450000100080000000500110000800800410001902400370006010000200009724501160011726000090023350001280024252019630037065000330233365300170236665300220238365300120240565300200241765300090243765300250244665300080247170000160247970000200249570000160251570000160253170000160254770000210256377300530258410540042019-06-18       2015    bl uuuu     u00u1 u    #d7 a10.1534/genetics.114.1735592DOI1 aFORNERIS, N. S.  aQuality control of genotypes using heritability estimates of gene content at the marker.h[electronic resource]  c2015  aManuscript received September 26, 2014; accepted for publication December 18, 2014; published Early Online January 6, 2015.  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  aMEJORAMIENTO GENETICO ANIMAL  aGENE CONTENT  aGENOMIC SELECTION  aGENPRED  aQUALITY CONTROL  aREML  aSHARED DATA RESOURCE  aSNP1 aLEGARRA, A.1 aVITEZICA, Z. G.1 aTSURUTA, S.1 aAGUILAR, I.1 aMISZTAL, I.1 aCANTET, R. J. C.  tGenetics, 2015gv. 199, p. 675-681. OPEN ACCESS.