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Evaluation of the genetic basis of primary hypoadrenocorticism in Standard Poodles using SNP array genotyping and whole-genome sequencing

Abstract

Primary hypoadrenocorticism, also known as Addison’s disease, is an autoimmune disorder leading to the destruction of the adrenal cortex and subsequent loss of glucocorticoid and mineralocorticoid hormones. The disease is prevalent in Standard Poodles and is believed to be highly heritable in the breed. Using genotypes derived from the Illumina Canine HD SNP array, we performed a genome-wide association study of 133 carefully phenotyped Standard Poodles (61 affected, 72 unaffected) and found no markers significantly associated with the disease. We also sequenced the entire genomes of 20 Standard Poodles (13 affected, 7 unaffected) and analyzed the data to identify common variants (including SNPs, indels, structural variants, and copy number variants) across affected dogs and variants segregating within a single pedigree of highly affected dogs. We identified several candidate genes that may be fixed in both Standard Poodles and a small population of dogs of related breeds. Further studies are required to confirm these findings more broadly, as well as additional gene-mapping efforts aimed at fully understanding the genetic basis of what is likely a complex inherited disorder.

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Notes

  1. 1.

    We are aware of one unpublished report of a genome-wide association study of 120 affected and 120 unaffected Standard Poodles performed at the Broad Institute that failed to identify any genetic differences between these two groups (The Broad Institute).

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Acknowledgements

SGF is supported by a National Institutes of Health T32 training award (5T32OD011130-07). Funding for whole-genome sequencing was provided in part by the Poodle Club of America Foundation and the Morris Animal Foundation. Seed funding for this project was provided by the North Carolina State University Comparative Medicine Institute. Some whole-genome sequencing data were graciously contributed by Drs. Leigh Anne-Clark (13 dogs), Natasha J. Olby and Theirry Olivry (11 dogs), and Joshua A. Stern (two dogs).

Author contributions

SGF collected samples, designed the study, analyzed the data, and wrote the manuscript. KFL collected samples and provided guidance regarding phenotyping of dogs. KMM collected samples and supervised the study. All authors have read and edited the manuscript.

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Correspondence to Steven G. Friedenberg.

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The authors declare no conflict of interest.

Electronic supplementary material

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335_2016_9671_MOESM1_ESM.tiff

Supplemental figure 1—Scoring algorithm and follow-up criterial used to evaluate genetic variants for Addison’s disease. Each variant was allocated one point for meeting criteria in each of three categories: variant consequence, GERP++ conservation score, or biological function (top). Scoring was carried out using custom scripting/filtering in R. A maximum of 3 points was allocated to each variant. After each variant was scored, specific follow-up criteria were applied by manual curation (bottom). Variants flagged for follow-up were evaluated in additional population of dogs as described in the Methods section of the text. See http://useast.ensembl.org/info/genome/variation/predicted_data.html#consequences for a complete listing of VEP variant consequences. (TIFF 1848 kb)

335_2016_9671_MOESM2_ESM.tiff

Supplemental figure 2—Principal components plots of the first and second eigenvalues for 175 Standard Poodles passing initial filtering criteria. Individual dogs are colored to indicate (A) MDS outliers, (B) phenotype, and (C) gender. In (A), gray squares represent the 42 dogs that were removed from from downstream GWAS analysis based upon MDS outlier detection. (TIFF 36918 kb)

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Supplementary material 5 (XLSX 169 kb)

Supplementary material 6 (XLSX 30 kb)

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Friedenberg, S.G., Lunn, K.F. & Meurs, K.M. Evaluation of the genetic basis of primary hypoadrenocorticism in Standard Poodles using SNP array genotyping and whole-genome sequencing. Mamm Genome 28, 56–65 (2017). https://doi.org/10.1007/s00335-016-9671-6

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Keywords

  • Validation Cohort
  • Impute Genotype
  • Variant Effect Predictor
  • Standard Poodle
  • Cavalier King Charles Spaniel