Reply: Y-chromosome microdeletions are not associated with SHOX haploinsufficiency

This letter addresses the debate between our recently published paper (Chianese et al., 2013) and the earlier publication of Jorgez et al. (2011). Overall, we feel that Jorgez et al. missed the main objective of our study, which was SHOX gene dosage and not pseudoautosomal region-1 (PAR1)-related copy number variations (CNVs). We investigated this specific aspect, as the alarming finding of SHOX haploinsufficiency in 5.4% of azoospermia factor (AZF) deletion carriers with normal karyotype (Jorgez et al., 2011) raised much concern for the genetic counselling of Y-chromosome deletion carriers. Our conclusion was completely different and analytical issues have been proposed to explain the differences.