Open Access Research article

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

Paulo Navarro-Costa12, Luísa Pereira34, Cíntia Alves3, Leonor Gusmão3, Carmen Proença1, Pedro Marques-Vidal5, Tiago Rocha6, Sónia C Correia6, Sónia Jorge6, António Neves6, Ana P Soares7, Joaquim Nunes7, Carlos Calhaz-Jorge7, António Amorim38, Carlos E Plancha2 and João Gonçalves1*

Author Affiliations

1 Centro de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, 1649-016 Lisboa, Portugal

2 Unidade de Biologia da Reprodução, Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, 1649-028 Lisboa, Portugal

3 IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-465 Porto, Portugal

4 Faculdade de Medicina da Universidade do Porto, 4200-319 Porto, Portugal

5 Unidade de Nutrição e Metabolismo, Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, 1649-028 Lisboa, Portugal

6 Unidade de Medicina da Reprodução, Maternidade Dr. Alfredo da Costa, 1069-089 Lisboa, Portugal

7 Unidade Pluridisciplinar de Reprodução Humana, Hospital de Santa Maria, 1649-028 Lisboa, Portugal

8 Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal

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BMC Genomics 2007, 8:342  doi:10.1186/1471-2164-8-342

Published: 28 September 2007



The AZFc region of the human Y chromosome is a highly recombinogenic locus containing multi-copy male fertility genes located in repeated DNA blocks (amplicons). These AZFc gene families exhibit slight sequence variations between copies which are considered to have functional relevance. Yet, partial AZFc deletions yield phenotypes ranging from normospermia to azoospermia, thwarting definite conclusions on their real impact on fertility.


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.