Characterizing partial AZFc deletions of the Y chromosome with amplicon-specific sequence markers

The amplicon content of partial AZFc deletion products was characterized with novel amplicon-specific sequence markers. Data indicate that partial AZFc deletions are a male infertility risk [odds ratio: 5.6 (95% CI: 1.6–30.1)] and although high diversity of partial deletion products and sequence conversion profiles were recorded, the AZFc marker profiles detected in fertile men were also observed in infertile men. Additionally, the assessment of rearrangement recurrence by Y-lineage analysis indicated that while partial AZFc deletions occurred in highly diverse samples, haplotype diversity was minimal in fertile men sharing identical marker profiles.Although partial AZFc deletion products are highly heterogeneous in terms of amplicon content, this plasticity is not sufficient to account for the observed phenotypical variance. The lack of causative association between the deletion of specific gene copies and infertility suggests that AZFc gene content might be part of a multifactorial network, with Y-lineage evolution emerging as a possible phenotype modulator.The human Y chromosome contains relatively few genes but exhibits remarkable functional coherence since many of them are directly or indirectly related to sex determination and fertility [1]. Approximately 10 megabases (Mb) of the Y consists of complex arrays of individual repeating units (designated as amplicons), each spanning up to 700 kilobases (kb) [2]. Amplicons are divided in different families, each one possessing very high sequence identity between member copies (99.8%) [2,3]. It has been established that all genes with testis-specific or predominant expression, except SRY, locate to these units and are consequently arranged in multi-copy gene families [2]. Yet, genome architectures based on repetitive units favour the occurrence of nonallelic homologous recombination (NAHR), leading to both chromosome duplications and corresponding deletions [4]. Accordingly, both Y duplications and deletions have bee