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Haplotype analysis of two X-chromosome STR clusters in the Pakistani population

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Abstract

Haplotype analysis of closely associated markers has proven to be a powerful tool in kinship analysis especially when X-chromosome short tandem repeats fail to resolve uncertainty in relationship analysis. Microsatellites located on the X chromosome show stronger linkage disequilibrium compared with autosomal microsatellites; hence, it is necessary to estimate the haplotype frequencies directly from population studies as linkage disequilibrium is population-specific. Here, we describe five markers residing in two clusters; cluster I harboring three STR markers DXS6801–DXS6809–DXS6789 and cluster II harboring two STR markers DXS7424–DXS101. A total of 302 male DNA samples of Pakistani descent were analyzed. Theoretically, 847 and 160 different combinations of haplotypes are possible in clusters I and II, but genotyping identified only 129 and 75 haplotypes, respectively. No evidence of linkage disequilibrium was detected, except for the pair (DXS6801–DXS6789), consistent with results obtained with the cluster I in a German population. Our results demonstrate that 83% haplotypes of cluster I and 65% haplotypes of cluster II show <1% frequency in the Pakistani population. This strongly suggests that haplotypes of these two clusters provide a powerful tool for kinship testing and relationship investigations.

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Acknowledgements

The authors are grateful to all individuals for their participation in this study. This work was supported in part by Higher Education Commission, Islamabad, Pakistan and Ministry of Science and Technology, Islamabad, Pakistan.

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Authors and Affiliations

  1. National Centre of Excellence in Molecular Biology, University of the Punjab, 87 West Canal Bank Road, Lahore, 53700, Pakistan

    Muhammad Akram Tariq, Muhammad Farooq Sabir, S. Amer Riazuddin & Sheikh Riazuddin

Authors
  1. Muhammad Akram Tariq
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  2. Muhammad Farooq Sabir
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  3. S. Amer Riazuddin
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  4. Sheikh Riazuddin
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Corresponding authors

Correspondence to S. Amer Riazuddin or Sheikh Riazuddin.

Additional information

This study was supported in part by Higher Education Commission and Ministry of Science and Technology Islamabad, Pakistan.

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Supplementary Table 1

Sequencing Results of DXS6801, DXS6809, DXS6789, DXS7424, and DXS101. (XLS 29.0 KB)

Supplementary Table 2

Haplotype analysis of DXS6801–DXS6809–DXS6789 cluster in 302 Pakistani males. Footnote: Count represents the number of appearances of a particular haplotype in the 302 DNA samples. MLE maximum likelihood estimate of haplotype frequency, UCL upper 95% confidence limit. (XLS 30.5 KB)

Supplementary Table 3

Haplotype analysis of DXS7424–DXS101 cluster in 302 Pakistani males. Footnote: Count represents the number of appearances of a particular haplotype in the 302 DNA samples. MLE maximum likelihood estimate of haplotype frequency, UCL upper 95% confidence limit. (XLS 25.5 KB)

Supplementary Table 4

Allelic frequencies of 5 X-linked markers. Footnote: MEC T mean exclusion chance in trios involving daughter, MEC D mean exclusion chance in duos father/daughter, PD F power of discrimination for females, PD M power of discrimination for males. (XLS 31.0 KB)

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Tariq, M.A., Sabir, M.F., Riazuddin, S.A. et al. Haplotype analysis of two X-chromosome STR clusters in the Pakistani population. Int J Legal Med 123, 85–87 (2009). https://doi.org/10.1007/s00414-008-0294-7

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  • DOI: https://doi.org/10.1007/s00414-008-0294-7

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