Partial-AZFc deletions in Chilean men with primary spermatogenic impairment: gene dosage and Y-chromosome haplogroups

J Assist Reprod Genet. 2020 Dec;37(12):3109-3119. doi: 10.1007/s10815-020-01957-6. Epub 2020 Oct 9.


Purpose: To investigate the association of partial-AZFc deletions in Chilean men with primary spermatogenic failure and their testicular histopathological phenotypes, analyzing the contribution of DAZ dosage, CDY1 copies, and Y-chromosome haplogroups.

Subjects and methods: We studied 479 Chilean men: 334 infertile patients with histological examination (233 cases with spermatogenic defects and 101 normal spermatogenesis, obstructive controls, OC), and 145 normozoospermic controls (NC). AZFc subdeletions were detected by single-tagged sequences and single nucleotide variants analysis. DAZ-copy number was quantified by real-time qPCR. Y-chromosome haplogroups (Y-hg) were hierarchically genotyped through 16 biallelic-markers.

Results: The prevalence of AZFc-partial deletions was increased in cases (6%) compared with NC (1.4%) (P = 0.035). There was no difference between 143 Sertoli-cell only syndrome, 35 maturation arrest, or 35 mix atrophy patients and controls. However, gr/gr deletions were more frequent in 16 subjects with hypospermatogenesis compared with NC (P = 0.003) and OC (P = 0.013). Y-hg R was the most prevalent (~ 50%), but decreased among gr/gr deletions (21%, P = 0.03). The prevalence of Y-hg M increased in cases versus controls, both in total and non-deleted men (3.9 and 3.7% versus 0.4%, P = 0.009 and P = 0.016, respectively). Among gr/gr deletions, Y-hg H increased compared with non-deleted men (14.3% versus 0.4%, P = 0.0047).

Conclusion: Partial-AZFc deletions in a Chilean admixed population are associated with secretory azo/oligozoospermia and might have a role in the development of hypospermatogenesis. Low represented haplogroups, Y-hg M and Y-hg H, show an association with the occurrence of spermatogenic failure and gr/gr deletions respectively; however, additional studies are required.

Keywords: AZFc subdeletions; DAZ duplications; Male infertility; Spermatogenic failure; Y-chromosome haplogroups.

MeSH terms

  • Adult
  • Case-Control Studies
  • Chromosome Deletion*
  • Chromosomes, Human, Y / genetics*
  • Deleted in Azoospermia 1 Protein / genetics*
  • Gene Dosage*
  • Genetic Loci
  • Haplotypes*
  • Humans
  • Infertility, Male / etiology
  • Infertility, Male / pathology*
  • Male
  • Oligospermia / genetics
  • Oligospermia / pathology*
  • Spermatogenesis
  • Spermatozoa / metabolism
  • Spermatozoa / pathology


  • DAZ1 protein, human
  • Deleted in Azoospermia 1 Protein