Use of ethnicity-specific sequence tag site markers for Y chromosome microdeletion studies

Microdeletions in the azoospermia factor region on the long arm of Y chromosome are associated with spermatogenic failure. There are many markers for the diagnosis of Y chromosome microdeletion analysis, but in routine practice only a limited set of markers can be tested.

The objectives of this study were to determine the frequency of Y chromosome microdeletion in idiopathic cases of male infertility in India, to attempt genotype-phenotype correlation, and to evaluate whether markers to be tested for diagnosis of Y chromosome microdeletion should be ethnicity specific.

Microdeletions in the Y chromosome were analyzed in 200 infertile males. The six sequence tag site (STS) markers prescribed by the European Academy of Andrology (EAA) were used initially. Patients in whom no deletions were detected by use of these markers were tested by markers selected from other studies from India.

The STS markers prescribed by EAA detected deletions in only 6 (3%) of 200 infertile males. However, markers selected from previous Indian studies showed deletions in an additional 15 (7.5%) of infertile males. Overall, Y chromosome microdeletions were observed in 21 (10.5%) of 200 patients. Of these, 13 were cases of azoospermia and 8 were cases of severe oligospermia.

The markers prescribed by EAA alone are not suitable for the diagnosis of Y chromosome microdeletions in infertile males. The protocol for identification of Y chromosome microdeletions in cases of nonobstructive azoospermia/severe oligospermia would have to include a different set of STS markers.