GÖNÜL FİLOĞLU TÜFEK, Irmak SAH, Muhammed DOĞAN, Sila Bulut NALCAOGLU, ÖZLEM BÜLBÜL, Ilksen TAVACİ, TUĞBA ÜNSAL SAPAN

Application of next generation sequencing in forensic science

Yeni nesil dizileme teknolojileri (Next Generation Sequencing; NGS) genetik araştırmalarda 2000'li yıllardan itibaren kullanılmaya başlanmıştır. Günümüze kadar daha hızlı, verimli ve düşük maliyetli çeşitli yöntemler geliştirilmiştir. NGS yöntemleri ve platformları gelişerek dizilerin kalitesi artmış ve son yıllarda adli genetik laboratuvarları da bu teknolojiye yönelmiştir. NGS teknolojisi adli genetikte kullanılan birçok sistemin (STRs, SNPs, mRNA) aynı anda tek bir analizle çalışılmasına olanak sağlamaktadır. Ayrıca bu teknoloji ile adli alanda DNA veri tabanı oluşturma, soy ve fenotip belirleme, tek yumurta ikizlerinin ayırt edilmesi, vücut sıvısı ve türlerin tanımlanması ve mikrobiyoloji analizleri yapılabilmektedir. Bu derleme NGS teknolojilerinin adli genetikte olası kullanım alanları üzerine dikkat çekmek ve gelecekteki adli çalışmalar için referans sağlamak amacıyla hazırlanmıştır

Yeni nesil dizilemenin adli bilimlerde kullanımı

Next Generation Sequencing (NGS) Technology has been emerged and started to use in genetic research since the 2000s. Until today, various methods which are faster, high throughput and low cost have been developed. NGS Technologies have been gradually developed and the quality of sequencing has been reached the high level and forensic genetics labs have moved to this technology for recent years. NGS Technologies provide new opportunities for forensic genetics research. NGS Technologies enable to analysis of many forensic genetic markers (as STRs, SNPs, mRNA) in only one experiment. Besides, NGS technologies are applicable for different practices which are essential in forensic researches. Among these, create of a DNA database, ancestry and phenotype studies, monozygotic twin studies, identification of body fluids and species, forensic microbiology studies can be considered. This review has been written to focus on NGS technologies in forensic genetics applications and to be a reference study for next forensic researchers

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1. Olsvik O, Wahlberg J, Petterson B, Uhlen M, Popovic T, Wachsmuth KI, Fields PI. Use of Automated Sequencing of Polymetase Chain Reaction-generated Amplicons To Identify Three Types of Cgolera Toxin Subunit b in Vibrio cholerae O1 Strains. J Clin Microbiol. 1993;31(1):22-5.
2. Petterson E, Lundeberg J, Ahmadian A. Generations of Sequencing Technologies. Genomics, 2009;93(2):105-11.
3. Filho JS. Next-generation Sequencing. Breast Cancer Research. 2009;11:12-9.
4. Üstek D, Abacı N, Sırma S, Çakiris A. Yeni Nesil DNA Dizileme. DETAE. 2011;1:11-8.
5. Børsting C, Fordyce SL, Olofsson J, Mogensen HS, Morling N. Evaluation of the Ion Torrent™ HID SNP 169-plex: A SNP typing assay developed for human identification by second generation sequencing. Forensic Sci Int Genet 2014;12:144-54.
6. Yang Y, Xie B, Yan J. Application of next-generation sequencing technology in forensic science. Genomics Proteomics Bioinformatics. 2014;12(5):190-7.
7. Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. Ten Years of NextGeneration Sequencing Technology. Trends Genet. 2014;30(9):418- 26.
8. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF. New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogrouptree. Genome Res. 2008;18(5):830-8.
9. Pakstis AJ, Speed WC, Fang R, Hyland FC, Furtado MR, Kidd JR, Kidd KK. SNPs for a universal individual identification panel.Hum Genet. 2010;127(3):315-24.
10. Phillips C, Fang R, Ballard D, Fondevila M, Harrison C, Hyland F. Evaluation of the Genplex SNP typing system and a 49plex forensic marker panel. Forensic Sci Int Genet. 2007;1(2):180-5.
11. Kosoy R, Nassir R, Tian C, White PA, Butler LM, Silva G, Kittles R, Alarcon-Riquelme ME, Gregersen PK, Belmont JW. Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Hum Mutat. 2009;30(1):69-78.
12. Kidd KK, Speed WC, Pakstis AJ, Furtado MR, Fang R, Madbouly A, Maiers M, Middha M, Friedlaender FR, Kidd JR. Progress toward an efficient panel of SNPs for ancestry inference. Forensic sci Int Genet. 2014;(10):23-32.
13. Nievergelt, CM, Maihofer AX, Shekhtman T, Libiger O, Wang X, Kidd KK, Kidd JR. Inference of human continental origin and admixture proportions using a highly discriminative ancestry informative 41-SNP panel. Investig Genet. 2013(4):13.
14. Seo SB, King J, Warshauer DH, Davis CP, Ge J, Budowle B. Single nucleotide polymorphism typing with massively parallel sequencing for human identification. Int J Legal Med. 2013;127(6):1079-86.
15. Grandell I, Samara R, Green H, Tillmar A. A SNP panel for identity and kinship testing using massive parallel sequencing. J Legal Med. 2016;130(4):905-14.
16. Churchill J, Schmedes SE, King J, Budowle B. Evaluation of the Illumina® Beta Version ForenSeq™ DNA Signature Prep Kit for use in genetic profiling. Forensic Sci Int Genet. 2015;20:20-9.
17. Kim H, Erlich HA, Calloway CD. Analysis of mixtures using next generation sequencingof mitochondrial DNA hypervariable regions. Croat Med J. 2015;56:208-17.
18. Van der Gaag KJ, de Leeuw RH, Hoogenboom J, Patel J, Storts DR, Laros JF, de Knijff P. Massively parallel sequencing of short tandem repeats-Population data and mixture analysis results for the PowerSeq™ system.Forensic Sci Int Genet. 2016;24:86-96.
19. Dalsgaard S, Rockenbauer E, Buchard A, Mogensen HS, FrankHansen R, Børsting C, Morling N. Non-Uniform Phenotyping of D12S391 Resolved by Second Generation Sequencing. Forensic Sci Int Genet. 2014;8:195-9.
20. Gelardi C, Rockenbauer E, Dalsgaard S, Børsting C, Morling N. Second Generation Sequencing of Three STRs D3S1358, D12S391 and D21S11 in Danes and a New Nomenclature for Sequenced STR Alleles”, Forensic Sci Int Genet. 2014;12:38-41.
21. Fordyce SL, Mogensen HS, Borsting C, Lagace RE, Chang CW, Rajagopalan N, Morling N. Second-generation sequencing of forensic STRs using the ion torrent HID STR 10-Plex and the ion PGM. Forensic Sci Int Genet. 2015;(14):132-40.
22. Xue Y, Wang Q, Long Q, Ng BL, Swerdlow H, Burton J. Skuce C, Taylor R, Abdellah Z, Zhao Y; Asan, MacArthur DG, Quail MA, Carter NP, Yang H, Tyler-Smith C. Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree. Curr Biol. 2009;19(17):1453-7.
23. Coble MD. Mystery solved: The identification of the two missing Romanov children using DNA analysis.ploS One 2009;4(3):e4838. 24. Coble M.D. The identification of the Romanovs: Can we (finally) put the controversies to rest? Investigative Genetics, Coble Investigative Genetics. 2011;2(20):1-7.
25. Demircan K. Rusya İmparatorluğu’nu 300 Yıl Yöneten Romanov Ailesi’nin 100 Yıllık Efsanesi: ANASTASYA, Bilim Teknik, 2013;58:61.
26. Parson W, Strobl C, Huber G, Zimmermann B, Gomes SM, Souto L, Fendt L, Delport R, Langit R, Wooton S, Lagace R, Irwin J. Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM), See comment in PubMed Commons Below Forensic Sci Int Genet. 2013;7(5):543-9.
27. Turi E, King et all. Identification of the remains of King Richard III, Nature Comminations. 2014;5(5631):1-8.
28. Magalhaes S, Marques SL, Alves C, Amorim A, Alvarez L, Goios A. Evaluation of Heteroplasmy Detection in the Ion Torrent PGM. Forensic Sci Int Genet Suppl. 2015;5:e13-e15.
29. McElhoe JA, Holland MM, Makova KD, Shu-Wei Su M, Paul IM, Baker CH, Faith SA, Young B. Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq. Forensic Sci Int Genet. 2014;13:20-9.
30. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schübeler D. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells Nat Genet. 2005;37(8):853-62.
31. Hanson E, Ingold S, Haas C, Ballantyne J. Targeted Multiplexed Next Generation RNA Sequencing Assay for Tissue Source Determination of Forensic Samples. Forensic Sci Int Genet Suppl. 2015;5:e441-e443.
32. Vidaki A, Ballard D, Barron L, Syndercombe Court D. DNA Methylation-Based Age Prediction Usin Artificial Nural Networks and Next Generation Sequencing. 26th Congress of The International Society for Forensic Genetics. Krakow, Polonya. 31 Ağustos-5 Eylül.2015;80-1.
33. Weber-Lehmann J, Schilling E, Gradl G, Richte DC, Wiehler J, B Rolf. Finding the needle in the haystack: Differentiating ‘‘identical’’ twins in paternity testing and forensics by ultra-deep next generation sequencing Forensic Sci Int Genet. 2014;9:42-6.
34. Cummings C.A, Bormann Chung CA, Fang R, Barker M, Brzoska P, Williamson PC. Accurate, rapid and high-throughput detection of strain-specific polymorphisms in Bacillus anthracis and Yersinia pestis by next-generation sequencing. Investig Genet. 2010;1(5):1-14.
35. Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, Knight R. Forensic identification using skin bacterial communities. Proc Natl Acad Sci USA. 2010;107(64):77-81.
36. Borsting C, Morling N. Next generation Sequencing and Its Applications in Forensic Genetics. Forensic Sci Int Genet. 2015;(18):78-9.