Turkiye Klinikleri Journal of Forensic Medicine and Forensic Sciences

.: ORIGINAL RESEARCH
Assessing Population Structure Using 46 AIM-Indel (Ancestry Informative Marker-Insertion/Deletion) Panel in Türkiye: Experimental Research (Population Study)
46 AIM-InDel (Soy Bilgilendirici Belirteçler-İnsersiyon/Delesyon) Paneli Kullanılarak Türkiye Popülasyon Yapısının Değerlendirilmesi: Deneysel Araştırma (Popülasyon Çalışması)
Cemaleddin ARSLANa, Özlem BÜLBÜLa, Gönül FİLOĞLUa
aDepartment of Science, Institute of Forensic Science and Legal Medicine, İstanbul University-Cerrahpaşa, Istanbul, Türkiye
Turkiye Klinikleri J Foren Sci Leg Med. 2022;19(2):129-37
doi: 10.5336/forensic.2022-89115
Article Language: EN
Full Text
ABSTRACT
Objective: Insertion/deletion (InDels), also known as 'new generation genetic markers' can be an alternative to short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). Identification and inference of biogeographical ancestry analysis can be more accurate when InDels are used with STRs and SNPs. The aim of this study is to determine the allele frequencies of 46 AIM-InDel loci in Turkish population which can be used to infer biogeographical ancestry. We also compare our population results with other populations. Material and Methods: 46 AIM-InDel loci were typed in 148 Turkish volunteers. Allele frequencies, Hardy Weinberg equilibrium and pairwise FST values were calculated using Arlequin ver.3.5. Biogeographic ancestry was analyzed using Structure 2.3.4. Snipper program was used for individual based inference of biogeographical ancestry. Results: The lowest genetic distance was observed between Turkish population and European, Middle Eastern and Central South Asian populations. When the genetic distance are longer, we observed clearer differences between Turkish and African and East Asian populations. Conclusion: The study provides new InDel data on understanding population structure of Türkiye. This could be useful in forensic investigations and as well as molecular anthropology.

Keywords: Ancestry informative markers (AIMs); InDel; Turkish population; biogeographical ancestry (BGA); forensic genetics
ÖZET
Amaç: 'Yeni nesil genetik belirteçler' olarak da bilinen insersiyon/delesyonlar (InDel), kısa tekrar dizilerilerine [short tandem repeats (STRs)] ve tek nükleotid polimorfizmlerine [single nucleotide polymorphisms (SNP)] alternatif bir belirteç olabilir. InDel belirteçleri, STR'ler ve SNP'ler ile birlikte kullanıldığında, daha doğru bir biyocoğrafik soy analizi yapılabilir. Bu çalışmanın amacı, Türkiye popülasyonundaki 46 AIM-InDel lokusunun biyocoğrafik soy tahmini yapmak için kullanılabilecek alel frekanslarını belirlemektir. Bunun yanı sıra Türkiye popülasyonu sonuçlarını diğer popülasyonlarla da karşılaştırılmaktır. Gereç ve Yöntemler: 148 Türkiyeli gönüllüde 46 AIM-InDel lokusu çalışıldı. Alel frekansları, Hardy Weinberg dengesi ve ikili FST değerleri Arlequin ver.3.5 kullanılarak hesaplandı. Biyocoğrafik soy, Structure 2.3.4 kullanılarak analiz edildi. Snipper Programı ile de bireysel bazda biyocoğrasif soy tahmini yapıldı. Bulgular: En düşük genetik uzaklık Türkiye popülasyonu ile Avrupa, Orta Doğu ve Orta Güney Asya popülasyonları arasında gözlendi. Genetik mesafe arttıkça Türkiye ile Afrika ve Doğu Asya popülasyonları arasında daha net genetik farklılıklar gözlemlendi. Sonuç: Çalışma, Türkiye'nin popülasyon yapısını anlama konusunda yeni InDel verileri sunmaktadır. Bu, adli araştırmalarda ve moleküler antropolojide faydalı olabilir.

Anahtar Kelimeler: Soy bilgilendirici markırlar (AIMs); InDel; Türkiye popülasyonu; biyocoğrafik soy (BGA); adli genetik
REFERENCES:
  1. Pereira R, Phillips C, Pinto N, Santos C, dos Santos SE, Amorim A, et al. Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing. PLoS One. 2012;7(1):e29684. [Crossref]  [PubMed]  [PMC] 
  2. Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, et al. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 2006;16(9):1182-90. [Crossref]  [PubMed]  [PMC] 
  3. Mullaney JM, Mills RE, Pittard WS, Devine SE. Small insertions and deletions (INDELs) in human genomes. Hum Mol Genet. 2010;19(R2):R131-6. [Crossref]  [PubMed]  [PMC] 
  4. Weber JL, David D, Heil J, Fan Y, Zhao C, Marth G. Human diallelic insertion/deletion polymorphisms. Am J Hum Genet. 2002;71(4):854-62. [Crossref]  [PubMed]  [PMC] 
  5. Phillips C. Application of autosomal SNPs and indels in forensic analysis. Forensic Sci Rev. 2012;24(1):43-62. [PubMed] 
  6. Pereira R, Phillips C, Alves C, Amorim A, Carracedo A, Gusmão L. A new multiplex for human identification using insertion/deletion polymorphisms. Electrophoresis. 2009;30(21):3682-90. [Crossref]  [PubMed] 
  7. Friis SL, Børsting C, Rockenbauer E, Poulsen L, Fredslund SF, Tomas C, et al. Typing of 30 insertion/deletions in Danes using the first commercial indel kit--Mentype® DIPplex. Forensic Sci Int Genet. 2012;6(2):e72-4. [Crossref]  [PubMed] 
  8. Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, et al. Intraspecific phylogeography: the mitochondrial dna bridge between population genetics and systematics. Annu Rev Ecol Syst. 1987;18(1):489-522. [Crossref] 
  9. Tishkoff SA, Kidd KK. Implications of biogeography of human populations for 'race' and medicine. Nat Genet. 2004;36(11 Suppl):S21-7. [Crossref]  [PubMed] 
  10. Kidd JM, Gravel S, Byrnes J, Moreno-Estrada A, Musharoff S, Bryc K, et al. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am J Hum Genet. 2012;91(4):660-71. [Crossref]  [PubMed]  [PMC] 
  11. Gross TE, Zaumsegel D, Rothschild MA, Schneider PM. Combined analysis of two different ancestry informative assays using SNPs and Indels in Eurasian populations. Forensic Science International: Genetics Supplement Series. 2013;4(1):e25-6. [Crossref] 
  12. Pereira R, Gusmão L. Capillary electrophoresis of 38 noncoding biallelic mini-Indels for degraded samples and as complementary tool in paternity testing. Methods Mol Biol. 2012;830:141-57. [Crossref]  [PubMed] 
  13. Pereira R, Pereira V, Gomes I, Tomas C, Morling N, Amorim A, et al. A method for the analysis of 32 X chromosome insertion deletion polymorphisms in a single PCR. Int J Legal Med. 2012;126(1):97-105. [Crossref]  [PubMed] 
  14. Ünsal T, Filoğlu G, Aşıcıoğlu F, Bülbül Ö. Population data of new 21 mini-InDels from Turkey. Forensic Sci Int Genet Suppl Ser. 2017;6:e189-91. [Crossref] 
  15. Santos NP, Ribeiro-Rodrigues EM, Ribeiro-Dos-Santos AK, Pereira R, Gusmão L, Amorim A, et al. Assessing individual interethnic admixture and population substructure using a 48-insertion-deletion (INSEL) ancestry-informative marker (AIM) panel. Hum Mutat. 2010;31(2):184-90. [Crossref]  [PubMed] 
  16. Santos C, Phillips C, Oldoni F, Amigo J, Fondevila M, Pereira R, et al. Completion of a worldwide reference panel of samples for an ancestry informative Indel assay. Forensic Sci Int Genet. 2015;17:75-80. [Crossref]  [PubMed] 
  17. Amigo J, Salas A, Phillips C, Carracedo A. SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access. BMC Bioinformatics. 2008;9:428. [Crossref]  [PubMed]  [PMC] 
  18. Excoffier L, Lischer HE. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 2010;10(3):564-7. [Crossref]  [PubMed] 
  19. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, et al. Genetic structure of human populations. Science. 2002;298(5602):2381-5. [Crossref]  [PubMed] 
  20. Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I. Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Resour. 2015;15(5):1179-91. [Crossref]  [PubMed]  [PMC] 
  21. Wright S. The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution. 1965;19(3):395-420. [Crossref] 
  22. Bulbul O, Duvenci A, Zorlu T, Gurkan C, Santos C, Phillips C, et al. Studies of East European populations with a 46-plex ancestry-informative indel set. Forensic Sci Int Genet Suppl Ser. 2015;e16-8. [Crossref] 
  23. Phillips C, Freire Aradas A, Kriegel AK, Fondevila M, Bulbul O, Santos C, et al. Eurasiaplex: a forensic SNP assay for differentiating European and South Asian ancestries. Forensic Sci Int Genet. 2013;7(3):359-66. [Crossref]  [PubMed] 
  24. Yun LB, Gao TZ, Sun K, Gu Y, Hou YP. Comparison of two online algorithm methods for forensic ancestry inference. Forensic Sci Int Genet Suppl Ser. 2015;5:e559-60. [Crossref] 
  25. Phillips C, Salas A, Sánchez JJ, Fondevila M, Gómez-Tato A, Alvarez-Dios J, et al; SNPforID Consortium. Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci Int Genet. 2007;1(3-4):273-80. [Crossref]  [PubMed] 
  26. Rosenberg NA, Li LM, Ward R, Pritchard JK. Informativeness of genetic markers for inference of ancestry. Am J Hum Genet. 2003;73(6):1402-22. [Crossref]  [PubMed]  [PMC] 

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