International Journal of Legal Medicine

, Volume 132, Issue 4, pp 967–973 | Cite as

Establishment of 11 linked X-STR loci within 1.1 Mb to assist with kinship testing

  • James Chun-I Lee
  • Chun-Yen Lin
  • Li-Chin Tsai
  • Yu-Jen Yu
  • Keng-Hsien Liao
  • Adrian Linacre
  • Hsing-Mei Hsieh
Original Article


This report identifies and characterizes 10 novel short tandem repeat (STR) loci on the human X chromosome, all of which are within a range of 1.1 Mb. These newly characterized loci were developed to aid in kinship assignment when the X chromosome is specifically required. The repeat DNA sequences were identified initially using data in GenBank and are located immediately upstream and downstream from the previously described locus DXS6807. Only those loci with seven or more observed alleles were used for further study resulting in the identification of 10 new loci. The distance between each pair of loci ranged from 24,998 to 244,701 bp with an average of approximately 110.8 kb. The number of observed alleles ranged from 7 to 30 for these 10 loci with a polymorphic information content ranging from 0.593 to 0.930. The LOD score from a pairwise linkage study ranged from 4.40 to 23.73, indicating that these 11 loci were highly linked, as expected. In line with standard forensic practice, all 11 loci can be amplified in one multiplex reaction, and comprehensive allelic ladders for all the loci have been constructed. These newly established 11 linked STR loci on the human X chromosome were found to be highly polymorphic and have the potential to aid in kinship testing where the X chromosome loci currently plays a role.


X-STR Kinship testing Linkage disequilibrium LOD score test Haplotype 



We thank the Ministry of Science and Technology of Taiwan who supported the study by the grant NSC97-2320-B-002-037-MY3 and the Department of Medical Research at the National Taiwan University Hospital (Taipei, Taiwan) for assistance with capillary electrophoresis.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

Human oral swabs used in this study were collected with informed consent after approval from the Institutional Review Board of National Taiwan University Hospital (IRB No. 201212148RIND). The studies have been performed in accordance with the ethical standards as laid down in the 1964 Declaration of Helsinki and its later amendments or comparable ethical standards.

Informed consent

Informed consent was obtained from all individual participants included in the study.


This study was funded by the Ministry of Science and Technology in Taiwan (Grant No. NSC97-2320-B-002-037-MY3).

Supplementary material

414_2017_1637_MOESM1_ESM.docx (17 kb)
Online Resource 1 (DOCX 17 kb)
414_2017_1637_MOESM2_ESM.docx (79 kb)
Online Resource 2 (DOCX 78 kb)
414_2017_1637_MOESM3_ESM.docx (36 kb)
Online Resource 3 (DOCX 36 kb)
414_2017_1637_MOESM4_ESM.docx (278 kb)
Online Resource 4 (DOCX 277 kb)
414_2017_1637_MOESM5_ESM.docx (32 kb)
Online Resource 5 (DOCX 32 kb)
414_2017_1637_MOESM6_ESM.docx (18 kb)
Online Resource 6 (DOCX 17 kb)
414_2017_1637_MOESM7_ESM.doc (38 kb)
Online Resource 7 (DOC 38 kb)
414_2017_1637_MOESM8_ESM.docx (18 kb)
Online Resource 8 (DOCX 17 kb)
414_2017_1637_MOESM9_ESM.docx (14 kb)
Online Resource 9 (DOCX 14 kb)


  1. 1.
    Pinto N, Gusmão L, Amorim A (2011) X-chromosome markers in kinship testing: a generalisation of the IBD approach identifying situations where their contribution is crucial. Forensic Sci Int Genet 5:27–32. doi: 10.1016/j.fsigen.2010.01.011 CrossRefPubMedGoogle Scholar
  2. 2.
    Hering S, Augustin C, Edelmann J, Heidel M, Dressler J, Rodig H, Kuhlisch E, Szibor R (2006) DXS10079, DXS10074 and DXS10075 are STRs located within a 280-kb region of Xq12 and provide stable haplotypes useful for complex kinship cases. Int J Legal Med 120:337–345. doi: 10.1007/s00414-005-0061-y CrossRefPubMedGoogle Scholar
  3. 3.
    Hundertmark T, Hering S, Edelmann J, Augustin C, Plate I, Szibor R (2008) The STR cluster DXS10148-DXS8378-DXS10135 provides a powerful tool for X-chrosomal haplotyping at Xp22. Int J Legal Med 122:489–492. doi: 10.1007/s00414-008-0277-8 CrossRefPubMedGoogle Scholar
  4. 4.
    Nothnagel M et al (2012) Collaborative genetic mapping of 12 forensic short tandem repeat (STR) loci on the human X chromosome. Forensic Sci Int Genet 6:778–784. doi: 10.1016/j.fsigen.2012.02.015 CrossRefPubMedGoogle Scholar
  5. 5.
    Hedman M, Palo JU, Sajantila A (2009) X-STR diversity patterns in the Finnish and the Somali population. Forensic Sci Int Genet 3:173–178. doi: 10.1016/j.fsigen.2009.02.005 CrossRefPubMedGoogle Scholar
  6. 6.
    Hwa HL, Chang YY, Lee JC, Yin HY, Chen YH, Tseng LH, Su YN, Ko TM (2009) Thirteen X-chromosomal short tandem repeat loci multiplex data from Taiwanese. Int J Legal Med 123:263–269. doi: 10.1007/s00414-008-0310-y CrossRefPubMedGoogle Scholar
  7. 7.
    Luo HB, Ye Y, Wang YY, Liang WB, Yun LB, Liao M, Yan J, Wu J, Li YB, Hou YP (2011) Characteristics of eight X-STR loci for forensic purposes in the Chinese population. Int J Legal Med 125:127–131. doi: 10.1007/s00414-009-0386-z CrossRefPubMedGoogle Scholar
  8. 8.
    Tomas C, Pereira V, Morling N (2012) Analysis of 12 X-STRs in Greenlanders, Danes and Somalis using Argus X-12. Int J Legal Med 126:121–128. doi: 10.1007/s00414-011-0609-y CrossRefPubMedGoogle Scholar
  9. 9.
    Liu QL, Lu DJ, Quan L, Chen YF, Shen M, Zhao H (2012) Development of multiplex PCR system with 15 X-STR loci and genetic analysis in three nationality populations from China. Electrophoresis 33:1299–1305. doi: 10.1002/elps.201100558 CrossRefPubMedGoogle Scholar
  10. 10.
    Diegoli TM, Linacre A, Coble MD (2014) Population genetic data for 15 X chromosomal short tandem repeat markers in three U.S. populations. Forensic Sci Int Genet 8:64–67. doi: 10.1016/j.fsigen.2013.07.008 CrossRefPubMedGoogle Scholar
  11. 11.
    Rębała K, Kotova SA, Rybakova VI, Zabauskaya TV, Shyla AA, Spivak AA, Tsybovsky IS, Szczerkowska Z (2015) Variation of X-chromosomal microsatellites in Belarus within the context of their genetic diversity in Europe. Forensic Sci Int Genet 16:105–111. doi: 10.1016/j.fsigen.2014.12.011 CrossRefPubMedGoogle Scholar
  12. 12.
    Prieto-Fernández E, Núñez C, Baeta M, Jiménez-Moreno S, Martínez-Jarreta B, de Pancorbo MM (2016) Forensic Spanish allele and haplotype database for a 17 X-STR panel. Forensic Sci Int Genet 24:120–123. doi: 10.1016/j.fsigen.2016.06.016 CrossRefPubMedGoogle Scholar
  13. 13.
    Tillmar AO, Mostad P, Egeland T, Lindblom B, Holmlund G, Montelius K (2008) Analysis of linkage and linkage disequilibrium for eight X-STR markers. Forensic Sci Int Genet 3:37–41. doi: 10.1016/j.fsigen.2008.09.006 CrossRefPubMedGoogle Scholar
  14. 14.
    Inturri S, Menegon S, Amoroso A, Torre C, Robino C (2011) Linkage and linkage disequilibrium analysis of X-STRs in Italian families. Forensic Sci Int Genet 5:152–154. doi: 10.1016/j.fsigen.2010.10.012 CrossRefPubMedGoogle Scholar
  15. 15.
    Hering S, Edelmann J, Augustin C, Kuhlisch E, Szibor R (2010) X chromosomal recombination—a family study analysing 39 STR markers in German three-generation pedigrees. Int J Legal Med 124:483–491. doi: 10.1007/s00414-009-0387-y CrossRefPubMedGoogle Scholar
  16. 16.
    Liu QL, Li ZD, Li CT, Zhao H, Wu YD, Li Q, Lu DJ (2013) X chromosomal recombination—a family study analyzing 26 X-STR loci in Chinese Han three-generation pedigrees. Electrophoresis 34:3016–3022. doi: 10.1002/elps.201300204 PubMedCrossRefGoogle Scholar
  17. 17.
    Ross MT et al (2005) The DNA sequence of the human X chromosome. Nature 434:325–337. doi: 10.1038/nature03440 CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Weir BS (1996) Genetic data analysis II. Sinauer Associates Inc, U S AGoogle Scholar
  20. 20.
    Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129. doi: 10.1093/bioinformatics/bti282 CrossRefPubMedGoogle Scholar
  21. 21.
    Lathrop GM, Lalouel JM, Julier C, Ott J (1984) Strategies for multilocus linkage analysis in humans. Proc Natl Acad Sci U S A 81:3443–3446CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Excoffier L, Laval G, Schneider S (2007) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinformatics Online 1:47–50Google Scholar
  23. 23.
    Trejaut JA, Poloni ES, Yen JC, Lai YH, Loo JH, Lee CL, He CL, Lin M (2014) Taiwan Y-chromosomal DNA variation and its relationship with island Southeast Asia. BMC Genet 15:77–99. doi: 10.1186/1471-2156-15-77 CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Szibor R, Krawczak M, Hering S, Edelmann J, Kuhlisch E, Krause D (2003) Use of X-linked markers for forensic purposes. Int J Legal Med 117:67–74. doi: 10.1007/s00414-002-0352-5 PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  • James Chun-I Lee
    • 1
  • Chun-Yen Lin
    • 2
  • Li-Chin Tsai
    • 3
  • Yu-Jen Yu
    • 1
  • Keng-Hsien Liao
    • 1
  • Adrian Linacre
    • 4
  • Hsing-Mei Hsieh
    • 3
  1. 1.Department of Forensic Medicine, College of MedicineNational Taiwan UniversityTaipeiTaiwan
  2. 2.Institute of Forensic Medicine, Ministry of JusticeNew Taipei CityTaiwan
  3. 3.Department of Forensic ScienceCentral Police UniversityTaoyuanTaiwan
  4. 4.School of Biological SciencesFlinders UniversityAdelaideAustralia

Personalised recommendations