Forensic Science International: Genetics
Volume 5, Issue 3 , Pages 155-169 , June 2011

Analysis of global variability in 15 established and 5 new European Standard Set (ESS) STRs using the CEPH human genome diversity panel

  • C. Phillips

      Affiliations

    • Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
    • Genomics Medicine Group, CIBERER, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
    • Corresponding Author InformationCorresponding author at: Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain. Tel.: +34 981 582 327; fax: +34 981 580 336.
    • ,
  • L. Fernandez-Formoso

      Affiliations

    • Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
    • ,
  • M. Garcia-Magariños

      Affiliations

    • Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
    • ,
  • L. Porras

      Affiliations

    • Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
    • ,
  • T. Tvedebrink

      Affiliations

    • Department of Mathematical Sciences, Aalborg University, Aalborg, Denmark
    • ,
  • J. Amigo

      Affiliations

    • Genomics Medicine Group, CIBERER, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
    • ,
  • M. Fondevila

      Affiliations

    • Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
    • ,
  • A. Gomez-Tato

      Affiliations

    • Faculty of Mathematics, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
    • ,
  • J. Alvarez-Dios

      Affiliations

    • Faculty of Mathematics, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
    • ,
  • A. Freire-Aradas

      Affiliations

    • Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
    • ,
  • A. Gomez-Carballa

      Affiliations

    • Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
    • ,
  • A. Mosquera-Miguel

      Affiliations

    • Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
    • ,
  • Á. Carracedo

      Affiliations

    • Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
    • Genomics Medicine Group, CIBERER, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
    • ,
  • M.V. Lareu

      Affiliations

    • Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain

Received 10 December 2009 ,Revised 2 February 2010 ,Accepted 6 February 2010.

References 

  1. ALFRED allele frequency database: http://alfred.med.yale.edu/alfred/.
  2. Cann HM, de Tomas C, Cazes L, Legrand MF, Morel V, Piouffre L, et al A human genome diversity cell line panel. Science. 2002;296:261–262
  3. Rosenberg NA. Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives. Ann. Hum. Genet. 2006;70:841–847
  4. Gill P, Fereday L, Morling N, Schneider PM. New multiplexes for Europe-Amendments and clarification of strategic development. Forensic Sci. Int. 2006;163:155–157
  5. Lareu MV, Pestoni C, Schurenkamp M, Rand S, Brinkmann B, Carracedo Á. A highly variable STR at the D12S391 locus. Int. J. Legal Med. 1996;109:134–138
  6. Lareu MV, Barral S, Salas A, Pestoni C, Carracedo Á. Sequence variation of a hypervariable short tandem repeat at the D1S1656 locus. Int. J. Legal Med. 1998;111:244–247
  7. Butler JM, Shen Y, McCord BR. The development of reduced size STR amplicons as tools for analysis of degraded DNA. J. Forensic Sci. 2003;48:1054–1064
  8. Phillips C, Barbaro A, Fernandez Formoso L, Ballard D, Syndercombe Court D, Carracedo Á, et al. Development and validation of a next generation STR ESS-pentaplex. Forensic Sci. Int. Genet. Suppl. 2009;2:25–26
  9. Amigo J, Salas A, Phillips C, Carracedo Á. SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access. BMC Bioinformatics. 2008;9:428
  10. Amigo J, Phillips C, Salas A, Fernandez Formoso L, Carracedo Á, Lareu M. pop.STR—an online population frequency browser for established and new. Forensic Sci. Int. Genet. Suppl. 2009;2:361–362
  11. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, et al. Genetic structure of human populations. Science. 2002;298:2381–2385
  12. Promega Powerstats download page: http://www.promega.com/geneticidtools/powerstats/.
  13. Lowe AL, Urquhart A, Foreman LA, Evett IW. Inferring ethnic origin by means of an STR profile. Forensic Sci. Int. 2001;119:17–22
  14. Graydon M, Cholette F, Ng LK. Inferring ethnicity using 15 autosomal STR loci – comparisons among populations of similar and distinctly different physical traits. Forensic Sci. Int. Genet. 2009;3:251–254
  15. Halder I, Yang BZ, Kranzler HR, Stein MB, Shriver MD, Gelernter J. Measurement of admixture proportions and description of admixture structure in different U.S. populations. Hum. Mutat. 2009;30:1299–1309
  16. Goldstein DB, Ruiz-Linares A, Cavalli-Sforza LL, Feldman MW. An evaluation of genetic distances for use with microsatellite loci. Genetics. 1995;92:6723–6727
  17. Goldstein DB, Ruiz-Linares A, Cavalli-Sforza LL, Feldman MW. Genetic absolute dating based on microsatellites and the origin of modern humans. Proc. Natl. Acad. Sci. U.S.A. 1995;92:6723–6727
  18. Rosenberg NA, Li LM, Ward R, Pritchard JK. Informativeness of genetic markers for inference of ancestry. Am. J. Hum. Genet. 2003;73:1402–1422
  19. Phillips C, Salas A, Sánchez JJ, Fondevila M, Gómez-Tato A, Álvarez-Dios J, et al. Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci. Int. Genet. 2007;1:273–280
  20. vWA data: http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=240641; D12 data: http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=2703.
  21. Balding DJ, Nichols RA. A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica. 1995;96:3–12
  22. Weir BS. The rarity of DNA profiles. Ann. Appl. Stat. 2007;1:358–370
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  24. Weir BS, Hill WG. Estimating F-statistics. Ann. Rev. Genet. 2002;36:721–750
  25. ALFRED population descriptions: The Karitianas make up a very small Amazonian basin population that is composed of less than 200 people (1994 est.) who live in a single village on a reservation in Brazil's Rondonia Province. The approximately 800 Rondonian Surui, or Paiter, live in several small villages scattered along the border between the Brazilian provinces of Mato Grosso and Rondonia which was in isolation from the outside world until 1969.
  26. T. Tverdebrink, Overdispersion in allelic counts and θ-correction in forensic genetics, Ann. Appl. Stat., 2010, submitted for publication.
  27. Schmid D, Anslinger K, Rolf B. Allele frequencies of the ACTBP2, D18S51, D8S1132, D12S391, D2S1360, D3S1744, D5S2500, D7S1517, D10S2325 and D21S2055 loci in a German population sample. Forensic Sci. Int. 2005;151:303–305
  28. Oberacher H, Pitterl F, Huber G, Niederstätter H, Steinlechner M, Parson W. Increased forensic efficiency of DNA fingerprints through simultaneous resolution of length and nucleotide variability by high-performance mass spectrometry. Hum. Mutat. 2008;29:427–432
  29. Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL. Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc. Natl. Acad. Sci. U.S.A. 2005;102:15942–15947
  30. Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, et al. Worldwide human relationships inferred from genome-wide patterns of variation. Science. 2008;319:1100–1104
  31. Walsh SJ, Mitchell RJ, Torpy F, Buckleton JS. Use of subpopulation data in Australian forensic DNA casework. Forensic Sci. Int. Genet. 2007;1:238–246
  32. Buckleton JS, Curran JM, Walsh SJ. How reliable is the subpopulation model in DNA testimony?. Forensic Sci. Int. 2006;157:144–148
  33. Phillips C, Fondevila M, García-Magariños M, Rodriguez A, Salas A, Carracedo Á, et al. Resolving relationship tests that show ambiguous STR results using autosomal SNPs as supplementary markers. Forensic Sci. Int. Genet. 2008;2:198–204

PII: S1872-4973(10)00031-1

doi: 10.1016/j.fsigen.2010.02.003

Forensic Science International: Genetics
Volume 5, Issue 3 , Pages 155-169 , June 2011

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