RESUMEN
Genomic relationships based on markers capture the actual instead of the expected (based on pedigree) proportion of genome shared identical by descent (IBD). Several methods exist to estimate genomic relationships. In this research, we compare four such methods that were tested looking at the empirical distribution of the estimated relationships across 6704 pairs of half-sibs from a cross-bred pig population. The first method based on multiple marker linkage analysis displayed a mean and standard deviation (SD) in close agreement with the expected ones and was robust to changes in the minor allele frequencies (MAF). A single marker method that accounts for linkage disequilibrium (LD) and inbreeding came second, showing more sensitivity to changes in the MAF. Another single marker method that considers neither inbreeding nor LD showed the smallest empirical SD and was the most sensible to changes in MAF. A higher mean and SD were displayed by VanRaden's method, which was not sensitive to changes in MAF. Therefore, the method based on multiple marker linkage analysis and the single marker method that considers LD and inbreeding performed closer to theoretical values and were consistent with the estimates reported in literature for human half-sibs.
Asunto(s)
Sus scrofa/genética , Animales , Cruzamientos Genéticos , Femenino , Genotipo , Masculino , Linaje , Polimorfismo de Nucleótido Simple , HermanosRESUMEN
Accurate prediction of breeding values depends on capturing the variability in genome sharing of relatives with the same pedigree relationship. Here, we compare two approaches to set up genomic relationship matrices for precision of genomic relationships (GR) and accuracy of estimated breeding values (GEBV). Real and simulated data (pigs, 60k SNP) were analysed, and GR were estimated using two approaches: (i) identity by state, corrected with either the observed (GVR-O ) or the base population (GVR-B ) allele frequencies and (ii) identity by descent using linkage analysis (GIBD-L ). Estimators were evaluated for precision and empirical bias with respect to true pedigree IBD GR. All three estimators had very low bias. GIBD-L displayed the lowest sampling error and the highest correlation with true genome-shared values. GVR-B approximated GIBD-L 's correlation and had lower error than GVR-O . Accuracy of GEBV for selection candidates was significantly higher when GIBD-L was used and identical between GVR-O and GVR-B . In real data, GIBD-L 's sampling standard deviation was the closest to the theoretical value for each pedigree relationship. Use of pedigree to calculate GR improved the precision of estimates and the accuracy of GEBV.
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Simulación por Computador , Sus scrofa/genética , Animales , Biomarcadores/análisis , Femenino , Genotipo , Masculino , Linaje , Polimorfismo de Nucleótido SimpleRESUMEN
Genome-wide association (GWA) studies based on GBLUP models are a common practice in animal breeding. However, effect sizes of GWA tests are small, requiring larger sample sizes to enhance power of detection of rare variants. Because of difficulties in increasing sample size in animal populations, one alternative is to implement a meta-analysis (MA), combining information and results from independent GWA studies. Although this methodology has been used widely in human genetics, implementation in animal breeding has been limited. Thus, we present methods to implement a MA of GWA, describing the proper approach to compute weights derived from multiple genomic evaluations based on animal-centric GBLUP models. Application to real datasets shows that MA increases power of detection of associations in comparison with population-level GWA, allowing for population structure and heterogeneity of variance components across populations to be accounted for. Another advantage of MA is that it does not require access to genotype data that is required for a joint analysis. Scripts related to the implementation of this approach, which consider the strength of association as well as the sign, are distributed and thus account for heterogeneity in association phase between QTL and SNPs. Thus, MA of GWA is an attractive alternative to summarizing results from multiple genomic studies, avoiding restrictions with genotype data sharing, definition of fixed effects and different scales of measurement of evaluated traits.
Asunto(s)
Cruzamiento , Estudio de Asociación del Genoma Completo/veterinaria , Genómica/métodos , Modelos Genéticos , Animales , Femenino , Genética de Población , Genotipo , Masculino , Fenotipo , Polimorfismo de Nucleótido Simple , Sitios de Carácter Cuantitativo , Carne Roja , Sus scrofa/genéticaRESUMEN
Eleven patients with advanced gastrointestinal (GI) carcinoma were entered in Phase I initial clinical trials with IgG2a antiGI carcinoma monoclonal antibodies (MAbs) GA733 (five patients) or CO19-9 (six patients). Infusion of MAb GA733 in doses greater than 30 mg was accompanied by mild and short-lasting GI toxicity. Infused MAb GA733 was bound to each patient's tumor tissue in vivo. MAb circulated in the blood for 10-25 days. All patients developed anti-mouse antibodies between 15 and 60 days post infusion. Furthermore, all but one patient raised anti-idiotypic antibodies against MAb GA733. Following administration of 10-600 mg of MAb CO19-9, no immediate or delayed toxicity symptoms were noted. Binding of infused MAb CO19-9 to tumor cells in vivo could not be detected in any of the six patients studied. The MAb circulated in the bloodstream between 5 and 12 days. Human anti-mouse antibody was detected in sera of three patients. None of the eleven patients treated with either MAb had anti-tumor responses in this Phase I clinical trial. The strong binding reactivity of MAb GA733 to tumors in vivo suggests the use of this MAb in cancer patients with less tumor burden to determine the tumoricidal efficacy of this antibody.