Evaluation of pooled whole genome sequencing (Pool-Seq) to recover known GWAS signals (gene effects)

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Esmail, Amin; Porto Neto, Laercio ORCID ID icon; Reverter-Gomez, Toni; Kijas, James


2017-07-05


Conference Material


The Association for the Advancement of Animal Breeding and Genetics, Townsville, Qld, 2-5 July 2017


4


Whole-genome sequencing (WGS) of pools of individuals (Pool-Seq) provides a cost-effective method for genome-wide association studies (GWAS), and offers an alternative to sequencing of individuals that remains cost prohibitive. Pool-Seq is being increasingly used in population genomic studies in both model and non-model organisms. In this paper, the ability of Pool-Seq to recover known GWAS signals was evaluated. Existing GWAS data for 2,112 animals with 729K SNPs were obtained and pooled to simulate data obtained from a pooled WGS approach. Traditional GWAS results was compared with the absolute allele frequency difference (dAF) metric suitable for use with Pool-Seq data. Specifically, we tested the ability of dAF scans to recover known GWAS signals for two different traits with large and moderate gene effects. Pools of different sizes (50, 100 and 200 individuals per pool) were also compared. The results showed the ability of the absolute allele frequency difference (dAF) approach to recover known GWAS peaks obtained by traditional SNP association and recommended the use of a pool size of 100 individuals for DNA pooling.


The Association for the Advancement of Animal Breeding and Genetics


Genomics


EP173772


Conference Paper - Refereed


English


Esmail, Amin; Porto Neto, Laercio; Reverter-Gomez, Toni; Kijas, James. Evaluation of pooled whole genome sequencing (Pool-Seq) to recover known GWAS signals (gene effects). In: The Association for the Advancement of Animal Breeding and Genetics; 2-5 July 2017; Townsville, Qld. The Association for the Advancement of Animal Breeding and Genetics; 2017. 4. http://hdl.handle.net/102.100.100/88346?index=1



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