Sequence family variant loss from the AZFc interval of the human Y chromosome, but not gene copy loss, is strongly associated with male infertility

Abstract

Background: Complete deletion of the complete AZFc interval of the Y chromosome is the most common known genetic cause of human male infertility. Two partial AZFc deletions (gr/gr and b1/b3) that remove some copies of all AZFc genes have recently been identified in infertile and fertile populations, and an association study indicates that the resulting gene dose reduction represents a risk factor for spermatogenic failure. Methods: To determine the incidence of various partial AZFc deletions and their effect on fertility, we combined quantitative and qualitative analyses of the AZFc interval at the DAZ and CDY1 loci in 300 infertile men and 399 control men. Results: We detected 34 partial AZFc deletions (32 gr/gr deletions), arising from at least 19 independent deletion events, and found gr/gr deletion in 6% of infertile and 3.5% of control men (p.0.05). Our data provide evidence for two large AZFc inversion polymorphisms, and for relative hot and cold spots of unequal crossing over within the blocks of homology that mediate gr/gr deletion. Using SFVs (sequence family variants), we discriminate DAZ1/2, DAZ3/4, CDY1a (proximal), and CDY1b (distal) and define four types of DAZ-CDY1 gr/gr deletion. Conclusions:The only deletion type to show an association with infertility was DAZ3/4-CDY1a (p = 0.042), suggesting that most gr/gr deletions are neutral variants. We see a stronger association, however, between loss of the CDY1a SFV and infertility (p = 0.002). Thus, loss of this SFV through deletion or gene conversion could be a major risk factor for male infertility.

Clinical data for 185 infertile Iranian men with Y-chromosome microdeletion

“…Some studies suggested a link between a partial deletion in the AZFc region and spermatogenic failure [35,36]. However other studies have disagreed, proposing it to be simply a polymorphic deletion with no clinical ramification [37].…”

Susceptibility of gr/gr rearrangements to azoospermia or oligozoospermia is dependent on DAZ and CDY1 gene copy deletions

“…Deletions of DAZ and CDY1 gene copies were analysed using sequence family variant (SFV) analysis [41,42]. Briefly for DAZ gene copy deletions, sY581 and sY587 were amplified and digested overnight using Sau3AI and DraI restriction enzyme (Thermo Fisher Scientific Inc., Waltham, Massachusetts, USA), respectively.…”

Quantitative PCR technique for the identification of microrearrangements of the AZFc region

“…Fourteen controls were selected according to their molecular and cytogenetic characteristics : -DNA from a patient with a complete AZFb deletion (P5 -proximal P1; AZFb -del) as a partial deletion control (lack of DAZ1-DAZ2 cluster) [4,16] -DNA from a man carrying a t(X;Y)(qter->p22::q11->qter) as a duplication control [19] -DNA from a 47,XYY male was also included to valid the Q-PCR technique -DNA from 8 patients previously studied and characterized with FISH and quantitative techniques: 2 "b2-b3" partial deletion, 1 "gr-gr" partial deletion, 2 deletions followed by duplication and 3 with no AZFc rearrangements [11]. DNA from a man with proven fertility was chosen as a positive control and as a reference for Q-PCR, and female DNA as well as DNA from a man with an AZFc microdeletion (AZFc-del) were used as a negative control.…”

“…Contrary to "complete" AZF deletions, the clinical relevance of partial deletion is still discussed. Indeed, several studies have shown the existence of partial AZFc deletions responsible for the loss of one cluster of the DAZ genes in fertile men [10][11][12]. In addition to deletion, duplication events and deletion followed by duplication events were identified, but their consequence in male infertility are unknown [3,5,11,[13][14][15].…”

“…Previous papers reporting the detection of AZFc partial deletions used several different techniques, namely FISH (fluorescence in situ hybridisation) on leukocytes or spermatozoa, Southern blotting or similar quantitative gene copy deletion assays associated with SNP (single nucleotide polymorphism) or SFV (sequence family variant) analyses [3,11,13,[16][17][18]. However, a major drawback of the PCR digest assays is that the variants studied appear to be polymorphic, making interpretation of the results difficult, and STS analysis alone does not allow the detection of duplications.…”