Reevaluation of azoospermic factor c microdeletions using sequence-tagged site markers with confirmed physical positions from the GenBank database

ObjectiveTo investigate microdeletions and palindrome complexes in the azoospermic factor (AZF) c regions of the Y chromosome, by polymerase chain reaction (PCR) with sequence-tagged site (STS) markers with known physical positions, after verification of the exact physical locations of candidate STSs and exclusion of those that would give ambiguous results on PCR.DesignRetrospective STS deletion study in infertile Japanese men.SettingUniversity hospital and reproductive clinic.Patient(s)A total of 410 men with nonobstructive azoospermia and severe oligospermia (sperm concentrations of <5 × 106/mL).Intervention(s)Polymerase chain reaction was performed for all STS markers confirmed to be physically located in the partial AZFb and AZFc regions of the Y chromosome. All STSs were retrieved from the University of California at Santa Cruz database, and their location and specificity were verified.Main Outcome Measure(s)Presence or absence of appropriately sized PCR products.Result(s)Sixty-nine markers were retrieved, 32 of which were not specific to the long arm of the Y chromosome (Yq). The markers retained for test use were contiguous deletions classified as P1+P2 (AZFc) or P3 proximal/P1 (AZFb+c). The prevalence of accurately mapped microdeletions was 5.1% (21 of 410) in this patient population.Conclusion(s)Although noncontiguous deletions were observed, considerable confusion remained until the genome sequence was finally determined because many of the STSs were either repetitive sequences or polymorphic between individuals or races.