title: Pseudoautosomal abnormalities in terminal AZFb+c deletions are associated with isochromosomes Yp and may lead to abnormal growth and neuropsychiatric function.
abstract: Are copy number variations (CNVs) in the pseudoautosomal regions (PARs) frequent in subjects with Y-chromosome microdeletions and can they lead to abnormal stature and/or neuropsychiatric disorders?
  
  
  
  Only subjects diagnosed with azoospermia factor (AZF)b+c deletions spanning to the end of the Y chromosome (i.e. terminal deletions) harbor Y isochromosomes and/or cells 45,X that lead to pseudoautosomal gene CNVs, which were associated with abnormal stature and/or neuropsychiatric disorders.
  
  
  
  The microdeletions in the long arm of the Y chromosome (Yq) that include the loss of one to three AZF regions, referred to as Yq microdeletions, constitute the most important known etiological factor for primary spermatogenic failure. Recently, controversy has arisen about whether Yq microdeletions are associated with gain or loss of PAR genes, which are implicated in skeletal development and neuropsychiatric function.
  
  
  
  We studied a cohort of 42 Chilean patients with complete AZF deletions (4 AZFa, 4 AZFb, 23 AZFc, 11 AZFb+c) from a university medical center, diagnosed over a period of 15 years. The subjects underwent complete medical examinations with special attention to their stature and neuropsychiatric function.
  
  
  
  All subjects were characterized for Yq breakpoints by PCR, and for CNVs in PARs by multiplex ligation-dependent probe amplification (MLPA), followed by qPCR analysis for genes in PAR1 (SHOX and ZBED1), PAR2 (IL9R) and two single copy genes (SRY and DDX3Y, respectively located in Yp11.3 and AZFa). In addition, karyotypes revision and fluorescence in situ hybridization (FISH) for SRY and centromeric probes for X (DXZ1) and Y (DYZ3) chromosomes were performed in males affected with CNVs.
  
  
  
  We did not detect CNVs in any of the 35 AZF-deleted men with interstitial deletions (AZFa, AZFb, AZFc or AZFb+c). However, six of the seven patients with terminal AZFb+c deletions showed CNVs: two patients showed a loss and four patients showed a gain of PAR1 genes, with the expected loss of VAMP-7 in PAR2. In these patients, the Yq breakpoints localized to the palindromes P8, P5 or P4. In the four cases with gain of PAR1, qPCR analysis showed duplicated signals for SRY and DDX3Y and one copy of IL9R, indicating isodicentric Yp chromosomes [idic(Y)] with breakpoint in Yq11.22. The two patients who had loss of PAR1, as shown by MLPA, had an additional reduction for SRY and DDX3Y, as shown by qPCR, associated with a high proportion of 45,X cells, as determined by FISH and karyotype. In agreement with the karyotype analysis, we detected DYZ3++ and DYZ3+ cells by FISH in the six patients, confirming idic(Y) and revealing additional monocentric Y chromosome [i(Y)]. Five patients had a history of major depressive disorders or bipolar disorder, and three had language impairment, whereas two patients showed severe short stature (Z score: -2.75 and -2.62), while a man with bipolar disorder was very tall (Z score: +2.56).
  
  
  
  N/A.
  
  
  
  The number of males studied with Y-chromosome microdeletions and normozoospermic controls with normal karyotypes may not be enough to rule out an association between AZF deletions and PAR abnormalities. The prevalence of Y isochromosomes and/or 45,X cells detected in peripheral blood does not necessarily reflect the variations of PAR genes in target tissues.
  
  
  
  This study shows that CNVs in PARs were present exclusively in patients with terminal AZFb+c deletions associated with the presence of Y isochromosomes and 45,X cells, and may lead to neuropsychiatric and growth disorders. In contrast, we show that men with interstitial Yq microdeletions with normal karyotypes do not have an increased risk of PAR abnormalities and of phenotypical consequences. Moreover, our results highlight the importance of performing molecular studies, which are not considered in the usual screening for patients with Yq microdeletions.
  
  
  
  This work was supported by the National Fund for Scientific and Technological Development of Chile (FONDECYT), grant no. 1120176 (A.C.). The authors declare that no conflicting interests exist.
authors.affiliation: Institute of Maternal and Child Research, School of Medicine, University of Chile, Hospital San Borja Arriarán, Santiago 8360160, Chile acastro@med.uchile.cl.
authors.forename: A
authors.initials: A
authors.lastname: Castro
authors.affiliation: Institute of Maternal and Child Research, School of Medicine, University of Chile, Hospital San Borja Arriarán, Santiago 8360160, Chile.
authors.forename: F
authors.initials: F
authors.lastname: Rodríguez
authors.affiliation: Institute of Maternal and Child Research, School of Medicine, University of Chile, Hospital San Borja Arriarán, Santiago 8360160, Chile.
authors.forename: M
authors.initials: M
authors.lastname: Flórez
authors.affiliation: Institute of Maternal and Child Research, School of Medicine, University of Chile, Hospital San Borja Arriarán, Santiago 8360160, Chile.
authors.forename: P
authors.initials: P
authors.lastname: López
authors.affiliation: Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile.
authors.forename: B
authors.initials: B
authors.lastname: Curotto
authors.affiliation: Institute of Maternal and Child Research, School of Medicine, University of Chile, Hospital San Borja Arriarán, Santiago 8360160, Chile.
authors.forename: D
authors.initials: D
authors.lastname: Martínez
authors.affiliation: Psychiatric Unit, Clínica Las Condes, Santiago 7591046, Chile.
authors.forename: A
authors.initials: A
authors.lastname: Maturana
authors.affiliation: Institute of Maternal and Child Research, School of Medicine, University of Chile, Hospital San Borja Arriarán, Santiago 8360160, Chile.
authors.forename: M C
authors.initials: MC
authors.lastname: Lardone
authors.affiliation: Department of Urology, José Joaquín Aguirre Clinical Hospital, School of Medicine, University of Chile, Santiago 8380453, Chile.|Department of Urology, Clínica Las Condes, Santiago 7591046, Chile.
authors.forename: C
authors.initials: C
authors.lastname: Palma
authors.affiliation: Institute of Maternal and Child Research, School of Medicine, University of Chile, Hospital San Borja Arriarán, Santiago 8360160, Chile.
authors.forename: V
authors.initials: V
authors.lastname: Mericq
authors.affiliation: Institute of Maternal and Child Research, School of Medicine, University of Chile, Hospital San Borja Arriarán, Santiago 8360160, Chile.
authors.forename: M
authors.initials: M
authors.lastname: Ebensperger
authors.affiliation: Institute of Maternal and Child Research, School of Medicine, University of Chile, Hospital San Borja Arriarán, Santiago 8360160, Chile.
authors.forename: F
authors.initials: F
authors.lastname: Cassorla
mesh_terms: D000293:Adolescent; D000328:Adult; D001827:Body Height / Q000235:genetics; D002872:Chromosome Deletion; D041322:Chromosomes, Human, Y; D056915:DNA Copy Number Variations; D006130:Growth Disorders / Q000523:psychology*; D006801:Humans; D018404:Isochromosomes; D008297:Male; D001523:Mental Disorders / Q000235:genetics*; D009845:Oligospermia / Q000235:genetics*; D000071439:Pseudoautosomal Regions / Q000235:genetics*; D055815:Young Adult
keywords: Y chromosome microdeletion; male infertility; neuropsychiatric disorders; pseudoautosomal region; short, tall stature