Display options
Cite
Porras-Hurtado L, Ruiz Y, Santos C, et al. An overview of STRUCTURE: applications, parameter settings, and supporting software. Front Genet. 2013;4:98doi: 10.3389/fgene.2013.00098.
Porras-Hurtado, L., Ruiz, Y., Santos, C., Phillips, C., Carracedo, A., & Lareu, M. V. (2013). An overview of STRUCTURE: applications, parameter settings, and supporting software. Frontiers in genetics, 498. https://doi.org/10.3389/fgene.2013.00098
Porras-Hurtado, Liliana, et al. "An overview of STRUCTURE: applications, parameter settings, and supporting software." Frontiers in genetics vol. 4 (2013): 98. doi: https://doi.org/10.3389/fgene.2013.00098
Porras-Hurtado L, Ruiz Y, Santos C, Phillips C, Carracedo A, Lareu MV. An overview of STRUCTURE: applications, parameter settings, and supporting software. Front Genet. 2013 May 29;4:98. doi: 10.3389/fgene.2013.00098. eCollection 2013. PMID: 23755071; PMCID: PMC3665925.
Copy Download .nbib Format: NLM
Share it on

Front Genet. 2013 May 29;4:98. doi: 10.3389/fgene.2013.00098. eCollection 2013.

An overview of STRUCTURE: applications, parameter settings, and supporting software.

Frontiers in genetics

Liliana Porras-Hurtado, Yarimar Ruiz, Carla Santos, Christopher Phillips, Angel Carracedo, Maria V Lareu

Affiliations

  1. Universidad Tecnológica de Pereira Pereira, Colombia ; Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela Santiago de Compostela, Spain.

PMID: 23755071 PMCID: PMC3665925 DOI: 10.3389/fgene.2013.00098

Abstract

OBJECTIVES: We present an up-to-date review of STRUCTURE software: one of the most widely used population analysis tools that allows researchers to assess patterns of genetic structure in a set of samples. STRUCTURE can identify subsets of the whole sample by detecting allele frequency differences within the data and can assign individuals to those sub-populations based on analysis of likelihoods. The review covers STRUCTURE's most commonly used ancestry and frequency models, plus an overview of the main applications of the software in human genetics including case-control association studies (CCAS), population genetics, and forensic analysis. The review is accompanied by supplementary material providing a step-by-step guide to running STRUCTURE.

METHODS: With reference to a worked example, we explore the effects of changing the principal analysis parameters on STRUCTURE results when analyzing a uniform set of human genetic data. Use of the supporting software: CLUMPP and distruct is detailed and we provide an overview and worked example of STRAT software, applicable to CCAS.

CONCLUSION: The guide offers a simplified view of how STRUCTURE, CLUMPP, distruct, and STRAT can be applied to provide researchers with an informed choice of parameter settings and supporting software when analyzing their own genetic data.

Keywords: CLUMPP; STRAT; STRUCTURE; case-control association studies; distruct; population structure; stratification

References

  1. Genet Epidemiol. 2004 May;26(4):305-15 - PubMed
  2. Ann Hum Genet. 2000 Mar;64(Pt 2):171-86 - PubMed
  3. Ann Hum Genet. 2006 Nov;70(Pt 6):841-7 - PubMed
  4. Forensic Sci Int Genet. 2013 Jan;7(1):28-40 - PubMed
  5. Int J Legal Med. 2006 May;120(3):188-9; author reply 190 - PubMed
  6. Mol Biol Evol. 2010 Feb;27(2):385-93 - PubMed
  7. BMC Genet. 2009 Jul 24;10:39 - PubMed
  8. Am J Hum Genet. 2008 Feb;82(2):290-303 - PubMed
  9. PLoS One. 2010 Oct 15;5(10):e13443 - PubMed
  10. Forensic Sci Int Genet. 2013 Jan;7(1):98-115 - PubMed
  11. Science. 2008 Feb 22;319(5866):1100-4 - PubMed
  12. PLoS One. 2012;7(10):e46519 - PubMed
  13. Nat Genet. 2005 Aug;37(8):868-72 - PubMed
  14. BMC Genomics. 2007 Mar 10;8:68 - PubMed
  15. Bioinformatics. 2012 May 15;28(10):1359-67 - PubMed
  16. Nat Rev Genet. 2010 Jul;11(7):459-63 - PubMed
  17. Science. 2002 Apr 12;296(5566):261-2 - PubMed
  18. PLoS Genet. 2005 Sep;1(3):e32 - PubMed
  19. Mol Ecol Resour. 2009 Sep;9(5):1322-32 - PubMed
  20. PLoS One. 2009 Aug 11;4(8):e6583 - PubMed
  21. Forensic Sci Int Genet. 2011 Jun;5(3):155-69 - PubMed
  22. Genome Res. 2006 Feb;16(2):290-6 - PubMed
  23. Am J Hum Genet. 2006 Apr;78(4):680-90 - PubMed
  24. Electrophoresis. 1999 Jun;20(8):1682-96 - PubMed
  25. BMC Bioinformatics. 2011 Jun 18;12:246 - PubMed
  26. Theor Popul Biol. 2001 Nov;60(3):227-37 - PubMed
  27. Mol Ecol. 2006 May;15(6):1419-39 - PubMed
  28. Nat Genet. 2012 Feb 05;44(3):243-6 - PubMed
  29. Genetics. 2003 Jan;163(1):367-74 - PubMed
  30. Heredity (Edinb). 2011 Apr;106(4):625-32 - PubMed
  31. Hum Genet. 2006 Oct;120(3):431-45 - PubMed
  32. PLoS Genet. 2008 Jan;4(1):e236 - PubMed
  33. Bioinformatics. 2009 Jun 15;25(12):i213-21 - PubMed
  34. Forensic Sci Int. 2001 Jun 1;119(1):17-22 - PubMed
  35. Nature. 1994 Mar 31;368(6470):455-7 - PubMed
  36. Hum Genet. 2005 Dec;118(3-4):382-92 - PubMed
  37. PLoS Genet. 2009 Jun;5(6):e1000519 - PubMed
  38. Am J Hum Genet. 2003 Dec;73(6):1402-22 - PubMed
  39. Mol Ecol. 2006 Sep;15(10):2833-43 - PubMed
  40. Am J Hum Genet. 2000 Jul;67(1):170-81 - PubMed
  41. PLoS Genet. 2006 Dec;2(12):e190 - PubMed
  42. Hum Genomics. 2013 Jan 05;7:1 - PubMed
  43. Forensic Sci Int Genet. 2007 Dec;1(3-4):273-80 - PubMed
  44. Stat Comput. 2011 Jan 4;21(2):261-273 - PubMed
  45. Science. 2002 Dec 20;298(5602):2381-5 - PubMed
  46. Am J Hum Genet. 2007 Sep;81(3):559-75 - PubMed
  47. Hum Mutat. 2008 May;29(5):648-58 - PubMed
  48. Nat Genet. 2006 Aug;38(8):904-9 - PubMed
  49. Int J Mol Epidemiol Genet. 2011 Jan 1;2(1):30-5 - PubMed
  50. Genetics. 2000 Jun;155(2):945-59 - PubMed
  51. BMC Genet. 2007 Jun 25;8:34 - PubMed
  52. Genome Res. 2009 Sep;19(9):1655-64 - PubMed
  53. Nat Genet. 2010 Apr;42(4):355-60 - PubMed
  54. Forensic Sci Int Genet. 2013 Feb;7(2):217-20 - PubMed
  55. Am J Hum Genet. 2010 May 14;86(5):661-73 - PubMed
  56. Genet Epidemiol. 2005 May;28(4):289-301 - PubMed
  57. PLoS One. 2008 Mar 12;3(3):e0001757 - PubMed
  58. Science. 2009 Dec 11;326(5959):1541-5 - PubMed
  59. BMC Bioinformatics. 2008 Oct 10;9:428 - PubMed
  60. J Psychopharmacol. 2006 Jul;20(4 Suppl):19-26 - PubMed
  61. Mol Ecol Notes. 2007 Jul 1;7(4):574-578 - PubMed
  62. Forensic Sci Int Genet. 2009 Sep;3(4):251-4 - PubMed
  63. Ann Hum Genet. 2012 Nov;76(6):510-23 - PubMed
  64. PLoS Genet. 2008 Jan;4(1):e4 - PubMed
  65. Bioinformatics. 2007 Jul 15;23(14):1801-6 - PubMed
  66. Genetics. 2003 Aug;164(4):1567-87 - PubMed

Publication Types