The effects of Asian population substructure on Y STR forensic analyses

Bruce Budowle, Jianye Ge, Joyce Low, Crystal Lai, Wong Hang Yee, Grace Law, Wai Fun Tan, Yuet Meng Chang, Revathi Perumal, Phoon Yoong Keat, Natsuko Mizuno, Kentaro Kasai, Kazumasa Sekiguchi, Ranajit Chakraborty

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A total of 3046 males of Chinese, Malay, Thai, Japanese, and Indian population affinity were previously typed for the Y STR loci DYS19, DYS385 (counted as two loci), DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS456, DYS458, DYS635, DYS448, and Y GATA H4 using the AmpFlSTR® Yfiler™ kit. These samples were assessed for population genetic parameters that impact forensic statistical calculations. All population samples were highly polymorphic for the 16 Y STR markers with the marker DYS385 being the most polymorphic, because it is comprised of two loci. Most (2677 out of a total of 2806 distinct haplotypes) of the 16 marker haplotypes observed in the sample populations were represented only once in the data set. Haplotype diversities were greater than 99.57% for the Chinese, Malay, Thai, Japanese, and Indian sample populations. For the Y STR markers, population substructure correction was considered when calculating the rarity of a Y STR profile. An FST value, rather than a RST value, is more appropriate under a forensic model. Because the FST values are very small within the Asian populations, the estimate of the rarity of a haplotype comprised of 10-16 markers does not need substructure correction. However haplotypes with fewer markers may require FST corrections when calculating the rarity of the profile.

Original languageEnglish
Pages (from-to)64-69
Number of pages6
JournalLegal Medicine
Issue number2
StatePublished - Mar 2009


  • DNA typing
  • F
  • Forensic science
  • Haplotype
  • Partial profile
  • Population substructure
  • Statistics
  • Y chromosome
  • Y short tandem repeat (Y STR)


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