Human Molecular Genetics Advance Access published online on December 22, 2006
Human Molecular Genetics, doi:10.1093/hmg/ddl465
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural variation on the short arm of the human Y chromosome: recurrent multigene deletions encompassing Amelogenin Y
1 Department of Genetics, University of Leicester, University Road, Leicester, UK 2 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK 3 Malaysian Forensic DNA Laboratory, Department of Chemistry, Jalan Sultan, Selangor, Malaysia 4 MGC-Department of Human and Clinical Genetics, Leiden University Medical Centre, The Netherlands 5 Institut für Blutgruppenforschung LGC GmbH, Köln, Germany 6 Cattedra di Genetica Medica, Policlinico, Piazza Giulio Cesare, Bari, Italy 7 Orchid Cellmark Ltd, Blacklands Way, Abingdon, UK 8 Victoria Police Forensic Services Department, Melbourne, Victoria, Australia 9 Department of Genetics and Human Variation, School of Molecular Sciences, La Trobe University, Melbourne, Australia
* Corresponding author: Prof Mark A. Jobling, Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK Tel.: +44 (0)116 252 3427 Fax: +44 (0)116 252 3378 Email: maj4{at}le.ac.uk
Received October 20, 2006; Revised December 8, 2006; Accepted December 8, 2006
Structural polymorphism is increasingly recognised as a major form of human genome variation, and is particularly prevalent on the Y chromosome. Assay of the Amelogenin Y gene (AMELY) on Yp is widely used in DNA-based sex testing, and sometimes reveals males who have interstitial deletions. In a collection of 45 deletion males from 12 populations, we used a combination of STS (sequence-tagged site) mapping, and binary-marker and Y-STR (short tandem repeat) haplotyping to understand the structural basis of this variation. 41/45 males carry indistinguishable deletions, 3.0-3.8Mb in size. Breakpoint mapping strongly implicates a mechanism of non-allelic homologous recombination between the proximal major array of TSPY-gene-containing repeats, and a single distal copy of TSPY; this is supported by estimation of TSPY copy number in deleted and non-deleted males. The remaining four males carry three distinct non-recurrent deletions (2.5-4.0Mb) which may be due to non-homologous mechanisms. Haplotyping shows that TSPY-mediated deletions have arisen seven times independently in the sample. One instance, represented by 30 chromosomes mostly of Indian origin within haplogroup J2e1*/M241, has a time-to-most-recent-common-ancestor of 
7700±1300 years. In addition to AMELY, deletion males all lack the genes PRKY and TBL1Y, and the rarer deletion classes also lack PCDH11Y. The persistence and expansion of deletion lineages, together with direct phenotypic evidence, suggests that absence of these genes has no major deleterious effects.
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