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Genetic factors play important role in the causation of human disease, including male infertility. The objective was to study copy number variations in testicular maturation arrest using single nucleotide polymorphism (<jats:styled-content style=\"fixed-case\">SNP<\/jats:styled-content>) microarray technique. Conventional cytogenetics, targeted fluorescence in\u00a0situ hybridization (<jats:styled-content style=\"fixed-case\">FISH<\/jats:styled-content>) and sequence\u2010tagged site (<jats:styled-content style=\"fixed-case\">STS<\/jats:styled-content>) polymerase chain reaction (<jats:styled-content style=\"fixed-case\">PCR<\/jats:styled-content>) were used to confirm some of the <jats:styled-content style=\"fixed-case\">SNP<\/jats:styled-content> microarray findings. <jats:styled-content style=\"fixed-case\">SNP<\/jats:styled-content> microarray on 68 cases of testicular maturation arrest detected copy number variations (<jats:styled-content style=\"fixed-case\">CNV<\/jats:styled-content>s) mostly on sex chromosomes involving pseudoautosomal regions (<jats:styled-content style=\"fixed-case\">PAR<\/jats:styled-content>) 1, 2 and 3 as well as azoospermic factors (<jats:styled-content style=\"fixed-case\">AZF<\/jats:styled-content>s) besides three cases of chromosomal abnormalities (two Klinefelter syndromes and one case of dicentric Y). The <jats:styled-content style=\"fixed-case\">AZF<\/jats:styled-content> deletion was observed in 14 (20.6%) cases and the <jats:styled-content style=\"fixed-case\">AZF<\/jats:styled-content>c gain was observed in 6 (8.8%) cases. <jats:styled-content style=\"fixed-case\">PAR<\/jats:styled-content> 1 and 2 <jats:styled-content style=\"fixed-case\">CNV<\/jats:styled-content>s was observed in 5 (7.3%) cases. <jats:styled-content style=\"fixed-case\">PAR<\/jats:styled-content> 3 <jats:styled-content style=\"fixed-case\">CNV<\/jats:styled-content>s was detected in 19 cases and 2 controls. The <jats:italic>TSPY2<\/jats:italic> gene gain (within <jats:styled-content style=\"fixed-case\">PAR<\/jats:styled-content> 3 <jats:styled-content style=\"fixed-case\">CNV<\/jats:styled-content>s) was observed in 16 cases and 1 control. <jats:styled-content style=\"fixed-case\">CNV<\/jats:styled-content> containing autosomal genes possibly associated with male infertility in this study was <jats:italic>SPATA31A2\u2010A5<\/jats:italic> (9p12) in five cases. In this study, <jats:styled-content style=\"fixed-case\">SNP<\/jats:styled-content> microarray identified possible underlying aetiology in 55.9% (38\/68) cases besides identifying minimal critical region of <jats:styled-content style=\"fixed-case\">AZF<\/jats:styled-content>c deletion as 0.51\u00a0mb (Y:24356128\u201324873665) involving <jats:italic>TTY5, RBMY2FP, RBMY1F, RBMY1J, TTY6<\/jats:italic> and <jats:italic>PRY<\/jats:italic> genes. <jats:styled-content style=\"fixed-case\">SNP<\/jats:styled-content> microarray seems superior, sensitive, specific as well as cost\u2010effective method and has potential to be the first tier investigations to explore underlying genomic factors of testicular maturation arrest. The present study is an attempt to find out probable genomic factors with idiopathic testicular maturation arrest.<\/jats:p>","DOI":"10.1111\/andr.12330","type":"journal-article","created":{"date-parts":[[2017,2,20]],"date-time":"2017-02-20T04:36:53Z","timestamp":1487565413000},"page":"460-472","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Copy number variations in testicular maturation arrest"],"prefix":"10.1111","volume":"5","author":[{"given":"A.","family":"Halder","sequence":"first","affiliation":[{"name":"Department of Reproductive Biology All India Institute of Medical Sciences New Delhi India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P.","family":"Kumar","sequence":"additional","affiliation":[{"name":"Department of Reproductive Biology All India Institute of Medical Sciences New Delhi India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M.","family":"Jain","sequence":"additional","affiliation":[{"name":"Department of Reproductive Biology All India Institute of Medical Sciences New Delhi India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"V. 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