Turkiye Klinikleri Journal of Forensic Medicine and Forensic Sciences

.: ORIGINAL RESEARCH
X Kromozomunda Bulunan 15 SNP Lokusunun Türkiye Populasyonundaki Polimorfizmi
Polymorphism of 15 X-Chromosome SNPs in the Turkish Population
İlksen TAVACIa, Özlem BÜLBÜLa, Gönül FİLOĞLUa, Havva ALTUNÇULa
aİstanbul Üniversitesi-Cerrahpaşa Adli Tıp ve Adli Bilimler Enstitüsü, Fen Bilimleri ABD, İstanbul, TÜRKİYE
Turkiye Klinikleri J Foren Sci Leg Med. 2020;17(3):238-44
doi: 10.5336/forensic.2020-75487
Article Language: TR
Full Text
ÖZET
 Amaç: Adli bilimlerde genetik kimliklendirmede sıklıkla otozomal belirteçler kullanılsa da bazı olgularda, gonozomal belirteçlere ihtiyaç duyulmaktadır. X kromozomu üzerinde bulunan tek nükleotid polimorfizmi [single nucleotide polymorhism (SNP)] belirteçleri, baba olduğu düşünülen kişinin bulunmadığı olguların çözümünde, uzak akrabalık ilişkilerinin belirlenmesinde, savaşlar ve göçler nedeni ile ayrı düşen ailelerin birleşmesi gibi olgularda kullanılmaktadır. Bu çalışmanın amacı, X kromozomu üzerinde bulunan 15 SNP lokusundan oluşan bir multipleks oluşturmak ve bu X-SNP lokuslarının Türkiye popülasyonundaki polimorfizmini belirlemektir. Gereç ve Yöntemler: Bu araştırmada, sağlıklı ve aralarında akrabalık ilişkisi bulunmayan 150 (75 kadın, 75 erkek) gönüllü bireyden alınan kan örnekleri kullanıldı. On beş X-SNP lokusu, mini sekanlama yöntemine dayalı SNaPshot' Multiplex Kit (Thermo Fisher Scientific) tekniği kullanılarak tetkik edildi. Örnekler, ABI 3130 genetik analizör cihazında yürütüldü ve analiz edildi. Popülasyonlar arası karşılaştırma için NCBI (www.ncbi.nlm.nih.gov/) veri bankasındaki Asya, Avrupa ve Afrika popülasyonlarına ait veriler kullanıldı. Allel frekansları, popülasyonlar arasındaki farklılaşma değerleri (Fst), ayrım gücü, Arlequin v.3.5.1.2, MEGA 5.1, SNP Analyzer v2.0, PowerStats V12 yazılım programları kullanılarak hesaplandı. Bulgular: 15 X-SNP lokusu, tek bir multipleks reaksiyonda optimize edildi. Türkiye popülasyonu çalışması sonucunda, 4 lokus dışında (X122, X165, X109 ve X143) HardyWeinberg dengesinden sapma görülmedi. On beş X-SNP lokusuna ait elde edilen gen sıklıkları diğer popülasyonların sonuçları ile karşılaştırıldığında, Türkiye popülasyonun Avrupa (Fst=0,0307) popülasyonuna daha yakın olduğu; Asya (Fst=0,06978) ve Afrika (Fst=0,10547) popülasyonlarına ise daha uzak olduğu belirlendi. Sonuç: Sonuç olarak Türkiye popülasyonu için 15 X-SNP lokusunun adli istatistik ve popülasyon verileri belirlenmiş olup, bu multipleks adli bilimlerde özel olgularda tamamlayıcı/ek bilgi verici olarak kullanılabilir.

Anahtar Kelimeler: X kromozomu; SNP; Türkiye popülasyonu
ABSTRACT
 Objective: Autosomal markers are frequently used in genetic identification in forensic sciences, however gonosomal markers are needed in some cases. The SNP (single nucleotide polymorphism) markers on the X chromosome are used in the solution of the cases where the person considered to be a father is not present, in the determination of distant kinship relations, in the merging of families separated by wars and migrations. The aim of this study is to develop a multiplex consisting of the X chromosome 15 SNP loci and to determine these X-SNP loci polymorphisms in the population of Turkish Republic. Material and Methods: In this study, we collected blood samples which taken from 150 (75 women, 75 men) healthy and nonrelative volunteers. 15 X-SNP loci were detected by using SNaPshot' Multiplex Kit (Thermo Fisher Scientific) based on minisequencing method. Samples were run and analyzed on the ABI 3130 genetic analyzer device. For population comparison, we used data from Asian, European and African populations in the NCBI (www.ncbi.nlm.nih.gov/) database. Allele frequencies, differentiation between populations (Fst), and power of discrimination (PD) were calculated using Arlequin v.3.5.1.2, MEGA 5.1, SNP Analyzer v2.0, PowerStats V12 softwares. Results: 15 X-SNP loci were optimized in a single multiplex reaction. No deviation from Hardy-Weinberg equilibrium is observed except four loci (X122, X165, X109 and X143). Gene frequencies obtained from 15 X-SNP loci were compared with the results of other populations. We determined that Turkish population is closer to European populations (Fst=0.0307) and Turkish population is more distant to Asian (Fst=0,06978) and African (Fst=0,10547) populations. Conclusion: As a result, forensic statistics and population data of the Turkish population is deternmined for 15 X-SNP loci and this multiplex can be used as complementary/supplementary tool in special cases in forensic sciences.

Keywords: X-chromosome; SNP; Turkish population
REFERENCES:
  1. Butler JM. X-chromosome analysis. Advanced Topics in Forensic DNA Typing: Methodology. 3rd eds. San Diego, USA: Academic Press-Elsevier Science; 2011. p.457-72. [Crossref]  [PMC] 
  2. Tomas C, Sanchez JJ, Barbaro A, Brandt-Casadevall C, Hernandez A, Dhiab MB, et al. X-chromosome SNP analyses in 11 human mediterranean populations show a high overall genetic homogeneity except in North-West Africans (Moroccans). BMC Evol Biol. 2008;8:75. [Crossref]  [PubMed]  [PMC] 
  3. Pereira V, Tomas C, Amorim A, Morling N, Gusmão L, Prata MJ. Study of 25 X-chromosome SNPs in the Portuguese. Forensic Sci Int Genet. 2011;5(4):336-8. [Crossref]  [PubMed] 
  4. Szibor R. X-chromosomal markers: past, present and future. Forensic Sci Int Genet. 2007;1(2):93-9. [Crossref]  [PubMed] 
  5. Li L, Li C, Zhang S, Zhao S, Liu Y, Lin Y. Analysis of 14 highly informative SNP markers on X chromosome by TaqMan SNP genotyping assay. Forensic Sci Int Genet. 2010;4(5):e145-8. [Crossref]  [PubMed] 
  6. Szibor R, Krawczak M, Hering S, Edelmann J, Kuhlish E, Krause D. Use of X-linked markers for forensic purposes. Int J Legal Med. 2003;117(2):67-74. [Crossref]  [PubMed] 
  7. Oki T, Hayashi T, Ota M, Asamura H. Development of multiplex assay with 16 SNPs on X chromosome for degraded samples. Leg Med (Tokyo). 2012;14(1):11-6. [Crossref]  [PubMed] 
  8. Senge T, Madea B, Junge A, Rothschild MA, Schneider PM. STRs, miniSTRs and SNPs--a comparative study for typing degraded DNA. Leg Med (Tokyo). 2011;13(2):68-74. [Crossref]  [PubMed] 
  9. Lai E. Application of SNP technologies in medicine: lessons learnd and features challenges. Genome Res. 2001;11(6):927-9. [Crossref]  [PubMed] 
  10. Senge T, Junge A, Madea B. The development of three SNP assays for forensic caseworks. International Congress Series. 2006;1288:46-8. [Crossref] 
  11. Phillips C. Application of autosomal SNPs and indels in forensic analysis. Forensic Sci Rev. 2012;24(1):43-62. [PubMed] 
  12. Sobrino B, Brión M, Carracedo A. SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int. 2005;154(2-3):181-94. [Crossref]  [PubMed] 
  13. Butler JM, Coble MD, Vallone PM. STRs vs. SNPs: thoughts on the future of forensic DNA testing. Forensic Sci Med Pathol. 2007;3(3):200-5. [Crossref]  [PubMed] 
  14. Pereira V, Tomas C, Pietroni C, Andersen JD, Fordyce SL, Pinto N, et al. Assessing the potential application of X-chromosomal haploblocks in population genetics and forensic studies. Forensic Science International: Genetics Supplement Series. 2013;4(1):e9-e10. [Crossref] 
  15. Zar MS, Shahid AA, Shahzad MS, Shin KJ, Lee HY, Lee SS, et al. Forensic SNP genotyping with SNaPshot: development of a novel in-house SBE multiplex SNP assay. J Forensic Sci. 2018;63(6):1824-9. [Crossref]  [PubMed] 
  16. Bulbul O, Fernandez-Formoso L, Phillips C, Altuncul H, Filoglu G, Lareu MV, et al. Allele frequencies of the five new European standard set (ESS) STRs and 15 established STRs in a Turkish population. Forensic Sci Int Genet. 2014;9:e26. [Crossref]  [PubMed] 
  17. Canturk KM, Gurkan C, Sevay H, Emre R. Evaluation of the genetic parameters for 10 common and five new ESS core autosomal STR loci in seven major geographic regions and the largest metropolitan province of Turkey. Ann Hum Biol. 2017;44(2):149-63. [Crossref]  [PubMed] 
  18. Acar E, Filoglu G, Bulbul O. Polymorphism of 8 X-chromosomal STR loci in Turkish population. Med Science. 2018;7(3):672-6. [Crossref] 
  19. Duvenci A, Bulbul O, Filoglu G. Evaluation of population data and forensic parameters of Turkish population on 30 autosomal insertion and deletion polymorphisms. Russian Journal of Genetics. 2019;55(2):246-52. [Crossref] 

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