Improved detection of disease-associated variation by sex-specific characterization and prediction of genes required for fertility

N. R.Y. Ho, N. Huang, Don Conrad

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Despite its great potential, high-throughput functional genomic data are rarely integrated and applied to characterizing the genomic basis of fertility. We obtained and reprocessed over 30 functional genomics datasets from human and mouse germ cells to perform genome-wide prediction of genes underlying various reproductive phenotypes in both species. Genes involved in male fertility are easier to predict than their female analogs. Of the multiple genomic data types examined, protein-protein interactions are by far the most informative for gene prediction, followed by gene expression, and then epigenetic marks. As an application of our predictions, we show that copy number variants (CNVs) disrupting predicted fertility genes are more strongly associated with gonadal dysfunction in male and female case-control cohorts when compared to all gene-disrupting CNVs (OR = 1.64, p < 1.64 × 10-8 vs. OR = 1.25, p < 4 × 10-6). Using gender-specific fertility gene annotations further increased the observed associations (OR = 2.31, p < 2.2 × 10-16). We provide our gene predictions as a resource with this article. Andrology

Original languageEnglish (US)
Pages (from-to)1140-1149
Number of pages10
JournalAndrology
Volume3
Issue number6
DOIs
StatePublished - Nov 1 2015
Externally publishedYes

Fingerprint

Fertility
Genes
Andrology
Molecular Sequence Annotation
Gene Dosage
Genomics
Epigenomics
Germ Cells
Proteins
Genome
Phenotype
Gene Expression

Keywords

  • Fertility genes
  • Machine learning
  • Ovary
  • Systems biology
  • Testis

ASJC Scopus subject areas

  • Endocrinology, Diabetes and Metabolism
  • Reproductive Medicine
  • Endocrinology
  • Urology

Cite this

Improved detection of disease-associated variation by sex-specific characterization and prediction of genes required for fertility. / Ho, N. R.Y.; Huang, N.; Conrad, Don.

In: Andrology, Vol. 3, No. 6, 01.11.2015, p. 1140-1149.

Research output: Contribution to journalArticle

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