Human Genetics

, Volume 122, Issue 3, pp 237–249

Molecular characterization of a polymorphic 3-Mb deletion at chromosome Yp11.2 containing the AMELY locus in Singapore and Malaysia populations


  • Rita Y. Y. Yong
    • Defence Medical and Environmental Research InstituteDSO National Laboratories
  • Linda S. H. Gan
    • Defence Medical and Environmental Research InstituteDSO National Laboratories
  • Yuet Meng Chang
    • Department of ChemistryForensic DNA Laboratory
    • Defence Medical and Environmental Research InstituteDSO National Laboratories
Original Investigation

DOI: 10.1007/s00439-007-0389-0

Cite this article as:
Yong, R.Y.Y., Gan, L.S.H., Chang, Y.M. et al. Hum Genet (2007) 122: 237. doi:10.1007/s00439-007-0389-0


Amelogenin paralogs on Chromosome X (AMELX) and Y (AMELY) are commonly used sexing markers. Interstitial deletion of Yp involving the AMELY locus has previously been reported. The combined frequency of the AMELY null allele in Singapore and Malaysia populations is 2.7%, 0.6% in Indian and Malay ethnic groups respectively. It is absent among 541 Chinese screened. The null allele in this study belongs to 3 Y haplogroups; J2e1 (85.7%), F* (9.5%) and D* (4.8%). Low and high-resolution STS mapping, followed by sequence analysis of breakpoint junction confirmed a large deletion of 3 to 3.7-Mb located at the Yp11.2 region. Both breakpoints were located in TSPY repeat arrays, suggesting a non-allelic homologous recombination (NAHR) mechanism of deletion. All regional null samples shared identical breakpoint sequences according to their haplogroup affiliation, providing molecular evidence of a common ancestry origin for each haplogroup, and at least 3 independent deletion events recurred in history. The estimated ages based on Y-SNP and STR analysis were ∼13.5 ± 3.1 kyears and ∼0.9 ± 0.9 kyears for the J2e1 and F* mutations, respectively. A novel polymorphism G > A at Y-GATA-H4 locus in complete linkage disequilibrium with J2e1 null mutations is a more recent event. This work re-emphasizes the need to include other sexing markers for gender determination in certain regional populations. The frequency difference among global populations suggests it constitutes another structural variation locus of human chromosome Y. The breakpoint sequences provide further information to a better understanding of the NAHR mechanism and DNA rearrangements due to higher order genomic architecture.

Supplementary material

439_2007_389_MOESM1_ESM.doc (51 kb)
ESM1 (DOC 51 kb)

Copyright information

© Springer-Verlag 2007