The Role and İmportance of Next Generation Sequencing Technologies in Forensic Applications

Öz

The use of autosomal STR (short tandem repeat) analysis is now accepted as the gold standard in forensic identification worldwide. STR typing provides sufficient discrimination power for many forensic cases. Furthermore, additional markers, such as X and Y chromosome STR markers (X-STR and Y-STR) and mitochondrial DNA analysis, are employed in the identification of disaster victims, particularly in instances where there is a considerable loss of life, compromised body integrity, and a paucity of DNA samples, or when the samples are fragmented or mixed. The evaluation of epigenetic changes, such as DNA methylation patterns and miRNA analyses, is employed in the identification of body fluids, the separation of monozygotic twins and the determination of the time of death. In instances where the aforementioned forensic markers prove inadequate, next-generation sequencing (NGS) technologies have been employed in recent years. NGS is a technology that rapidly sequences the entire exome or genome, thereby enabling the acquisition of a comprehensive range of genomic data. In addition to forensic identification and body fluid identification, forensic entomological studies, chimerism detection, ancestry research and phenotypic inference studies can be carried out rapidly and reliably thanks to NGS technologies. The objective of this review is to examine the role and importance of NGS technologies in the context of forensic identification and other related forensic applications.

Anahtar Kelimeler

• Next Generation Sequencing
• Forensic Identification
• DNA Sequencing

Adli Uygulamalarda Yeni Nesil Dizileme Teknolojilerinin Yeri ve Önemi

Öz

Günümüzde tüm dünyada adli kimliklendirmede otozomal STR (Short Tandem Repeat; Kısa Ardışık Tekrarlar) analizi altın standart olarak kabul edilmektedir ve birçok adli vaka için STR tiplemesi yeterli ayrım gücü sağlamaktadır. Özellikle can kaybının çok olduğu, vücut bütünlüğünün bozulduğu ve DNA örneğinin az ya da karışmış veya parçalanmış olduğu felaket kurbanlarının kimliklendirilmesinde X ve Y kromozomu STR belirteçleri (X-STR ve Y-STR) ve mitokondriyal DNA analizi gibi ilave belirteçlerden de yararlanılmaktadır. Vücut sıvılarının kimliklendirilmesi, monozigotik ikizlerin ayrılması ve ölüm zamanının belirlenmesinde ise DNA metilasyon kalıpları ve miRNA analizleri gibi epigenetik değişiklikler değerlendirilmektedir. Tüm bu adli belirteçlerin yetersiz kaldığı vakalarda son yıllarda Yeni nesil dizileme (YND) teknolojilerinden de yararlanılmaktadır. YND tüm ekzom ya da tüm genomu hızlı bir şekilde dizileyen ve genom hakkında geniş çaplı bilgi edinmemizi sağlayan bir teknolojidir. Adli kimliklendirme ve vücut sıvılarını kimliklendirmenin yanı sıra adli entomolojik çalışmalar, kimerizm tespiti, soy ve fenotipik çıkarım araştırmaları da YND teknolojileri sayesinde hızlı ve güvenilir bir şekilde yapılabilmektedir. Bu derleme YND teknolojilerinin adli kimliklendirme ve diğer adli uygulamalardaki yeri ve önemine odaklanmaktadır.

Anahtar Kelimeler

• Yeni Nesil Dizileme
• Adli Kimliklendirme
• DNA Dizileme

Kaynakça

1. Görmez Ö, Yılmaz H. Kimliklendirmede dental değerlendirmenin önemi. Med J SDU 2014;21(1):29-34.
2. Sultana GNN, Sultan MZ. Mitochondrial DNA and methods for forensic identification. J Forensic Sci Crimin Inves 2018;9(1):555755.
3. Al-Koofee DAF, Mubarak SMH. Genetic polymorphisms. The Recent Topics in Genetic Polymorphisms. eds: Çalışkan M, Erol O, Öz GC. BoD–Books on Demand; 2020:1-15
4. Banday MZ, Nissar S, Aga SS. Genetic Polymorphism and Disease 1st Edition. eds Aga SS, Banday MZ, Nissar S. CRC Press; 2022.
5. Subaşıoğlu A. Afetlerde Kimliklendirme ve Genetik Yaklaşımlar. İKÇÜSBFD 2023;8(2):717-20.
6. Tekcan E, Tural Ş. AdliDNA Analizlerinde Güncel Moleküler Genetik Gelişmeler. Van Med J 2023;30(2):217-22.
7. Yang Y, Xie B, Yan J. Application of next-generation sequencing technology in forensic science. Genomics Proteomics Bioinformatics 2014;12(5):190-7.
8. Filoglu G, Sah I, Dogan M, Nalcaoglu SB, Bulbul ITO, Unsal T. Application of next generation sequencing in forensic science Yeni nesil dizilemenin adli bilimlerde kullanımı. Med 2017;6(1):157-62.

9. Clarke TH, Gomez A, Singh H, Nelson KE, Brinkac LM. Integrating the microbiome as a resource in the forensics toolkit. Forensic Sci Int Genet 2017;30:141-7.
10. Wong L-P, Ong RT-H, Poh W-T, Liu X, Chen P, Li R, et al. Deep whole-genome sequencing of 100 southeast Asian Malays. Am J Hum Genet 2013;92(1):52-66.
11. 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 Supp Ser 2015;5:e441-e3.
12. Darcan C, Türkyılmaz O. Yeni Nesil Dizileme Teknolojisine Genel Bakış. Bilecik Şeyh Edebali Üniversitesi Fen Bilimleri Dergisi 2018;5(1):41-9.
13. Hu T, Chitnis N, Monos D, Dinh A. Next-generation sequencing technologies: An overview. Hum Immunol 2021;82(11):801-11.
14. Tytgat O, Van Nieuwerburgh F. Applications of nanopore sequencing for forensic analysis. Next Generation Sequencing (NGS) Technology in DNA Analysis: Academic Press; 2024. p. 85-98.
15. Yang TT, Zhang JR, Xie ZH, Ren ZL, Yan JW, Ni M. Nanopore sequencing of forensic short tandem repeats using QNome of Qitan Technology. Electrophoresis 2024;45:1535-45
16. Bruijns B, Tiggelaar R, Gardeniers H. Massively parallel sequencing techniques for forensics: A review. Electrophoresis 2018;39(21):2642-54.
17. Børsting C, Morling N. Next generation sequencing and its applications in forensic genetics. Forensic Sci Int Genet 2015;18:78-89.
18. Hunter P. Uncharted waters: Next-generation sequencing and machine learning software allow forensic science to expand into phenotype prediction from DNA samples. EMBO Rep 2018;19(3):e45810
19. Cusick MF, Clark L, Tu T, Goforth J, Zhang X, LaRue B, et al. Performance characteristics of chimerism testing by next generation sequencing. Hum Immunol 2022;83(1):61-9.
20. Topaloğlu T, Şener EF, Canatan H. Nöropsikiyatrik Hatalıklarda Yeni Nesil Sekans Teknolojisinin Kullanımı ve Güncel Yaklaşımlar. Sağlık Bilimleri Dergisi 2016;25(2):92-9.
21. Gettings KB, Kiesler KM, Faith SA, Montano E, Baker CH, Young BA, et al. Sequence variation of 22 autosomal STR loci detected by next generation sequencing. Forensic Sci Int Genet 2016;21:15-21.
22. Çağlayan AO. Yeni Nesil Dizileme Teknolojisinin Tıpta Kullanımı: Örnek Hastalık Grubu Olarak Nöregelişimsel Hastalıklar. Turkiye Klinikleri J Med Genet-Special Topics 2016;1(1):155-60.
23. Bredemeyer S, Roewer L, Willuweit S. Next generation sequencing of Y-STRs in father-son pairs and comparison with traditional capillary electrophoresis. Forensic Sci Res 2022;7(3):484-9.
24. Van Neste C, Vandewoestyne M, Van Criekinge W, Deforce D, Van Nieuwerburgh F. My-Forensic-Loci-queries (MyFLq) framework for analysis of forensic STR data generated by massive parallel sequencing. Forensic Sci Int Genet 2014;9:1-8.
25. Senst A, Caliebe A, Scheurer E, Schulz I. Validation and beyond: Next generation sequencing of forensic casework samples including challenging tissue samples from altered human corpses using the MiSeq FGx system. J Forensic Sci 2022;67(4):1382-98.
26. Shih SY, Bose N, Gonçalves ABR, Erlich HA, Calloway CD. Applications of probe capture enrichment next generation sequencing for whole mitochondrial genome and 426 nuclear SNPs for forensically challenging samples. Genes 2018;9(1):49.
27. Warshauer DH, Lin D, Hari K, Jain R, Davis C, LaRue B, et al. STRait Razor: a length-based forensic STR allele calling tool for use with second generation sequencing data. Forensic Sci Int Genet 2013;7(4):409-17.
28. Hertz CL, Christiansen SL, Ferrero-Miliani L, Fordyce SL, Dahl M, Holst AG, et al. Next-generation sequencing of 34 genes in sudden unexplained death victims in forensics and in patients with channelopathic cardiac diseases. Int J Legal Med 2015;129(4):793-800.
29. Proceedings of the 4th national symposium on forensic DNA inspection technology. International symposium on new advances in forensic genetics; China 2012. p. 9-12.
30. Dash HR, Ranga A. Sequence analysis and secondary structure prediction of autosomal STR alleles using next generation sequencing (NGS) data. Human Gene 2024;40:201274.
31. Hall CL, Kesharwani RK, Phillips NR, Planz JV, Sedlazeck FJ, Zascavage RR. Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device. Forensic Sci Int Genet 2022;56:102629.
32. Poethe S-S, Holtel J, Biermann J-P, Riemer T, Grabmüller M, Madea B, et al. Cost-Effective Next Generation Sequencing- Based STR Typing with Improved Analysis of Minor, Degraded and Inhibitor-Containing DNA Samples. Int J Mol Sci 2023;24(4):3382.
33. Bülbül Ö, Argaç D, Shahzad MS, Filoğlu G, Altunçul H. Kimliklendirme ve Nesep Tayini İçint oOzomal SNP Lokuslarının Belirlenmesi. Turkiye Klinikleri J Foren Sci Leg Med 2013;10(1):7-13.
34. Fondevila M, Børsting C, Phillips C, De La Puente M, Carracedo A, Morling N, et al. Forensic SNP genotyping with SNaPshot: technical considerations for the development and optimization of multiplexed SNP assays. Forensic Sci Rev 2017;29(1):57-76.
35. Gorden EM, Greytak EM, Sturk-Andreaggi K, Cady J, McMahon TP, Armentrout S, et al. Extended kinship analysis of historical remains using SNP capture. Forensic Sci Int Genet 2022;57:102636.
36. Kokotas S, Budowle B, Papatheodorou A, Bolanaki E, Kondili A, Metheniti A, et al. Comparison of Next Generation Sequencing (NGS)-(SNPs) and Capillary Electrophoresis (CE)-(STRs) in the genetic analysis of human remains. Forensic Sci Int Genet 2024:103131.
37. Sapan V, Simsek SZ, Filoğlu G, BulbOul. Forensic DNA phenotyping using Oxford Nanopore Sequencing system. Electrophoresis 2024:1-14
38. Ren Z-L, Zhang J-R, Zhang X-M, Liu X, Lin Y-F, Bai H, et al. Forensic nanopore sequencing of STRs and SNPs using Verogen’s ForenSeq DNA signature prep kit and MinION. Int J Legal Med 2021;135(5):1685-93.
39. Tytgat O, Škevin S, Deforce D, Van Nieuwerburgh F. Nanopore sequencing of a forensic combined STR and SNP multiplex. Forensic Sci Int Genet 2022;56:102621.
40. Bülbül Ö, Filoğlu G. Biyocoğrafik Soy Tahmini ve Adli Bilimlerde Kullanımı. Bull Leg Med 2019;24(2):131-40.
41. Larmuseau MH, Van Geystelen A, Kayser M, van Oven M, Decorte R. Towards a consensus Y-chromosomal phylogeny and Y-SNP set in forensics in the next-generation sequencing era. Forensic Sci Int Genet 2015;15:39-42.
42. Xue Y, Wang Q, Long Q, Ng BL, Swerdlow H, Burton J, et al. Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree. Curr Biol 2009;19(17):1453-7.
43. Qian X, Hou J, Wang Z, Ye Y, Lang M, Gao T, et al. Next generation sequencing plus (NGS+) with Y-chromosomal markers for forensic pedigree searches. Sci Rep 2017;7(1):11324.
44. Abatay Sel F, Savran Oğuz F. Moleküler Kimerizm Metotları: Geçmiş ve Günümüz. Akd Tıp D 2022;8(1):82-90.
45. Serin A, Canan H, Alper B. Adli Amaçlı Kimliklendirmede Mitokondriyal DNA. Turkiye Klinikleri J Foren Sci Leg Med 2013;10(2):51-8.
46. Syndercombe Court D. Mitochondrial DNA in forensic use. Emerg Top Life Sci 2021;5(3):415-26.
47. Szibor R, Michael M, Plate I, Krause D. Efficiency of forensic mtDNA analysis: Case examples demonstrating the identification of traces. Forensic Sci Int 2000;113(1-3):71-8.
48. del Mar González M, Ramos A, Aluja MP, Santos C. Sensitivity of mitochondrial DNA heteroplasmy detection using Next Generation Sequencing. Mitochondrion 2020;50:88-93.
49. Mikkelsen M, Rockenbauer E, Wächter A, Fendt L, Zimmermann B, Parson W, et al. Application of full mitochondrial genome sequencing using 454 GS FLX pyrosequencing. Forensic Sci Int Suppl Ser 2009;2(1):518-9.
50. Stewart JE, Fisher CL, Aagaard PJ, Wilson MR, Isenberg AR, Polanskey D, et al. Length variation in HV2 of the human mitochondrial DNA control region. J Forensic Sci 2001;46(4):862-70.
51. Coble MD, Just RS, O’Callaghan JE, Letmanyi IH, Peterson CT, Irwin JA, et al. Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians. Int J Legal Med 2004;118(3):137-46.
52. Parsons TJ, Coble MD. Increasing the forensic discrimination of mitochondrial DNA testing through analysis of the entire mitochondrial DNA genome. Croat Med J 2001;42(3):304-9.
53. Forsythe B, Melia L, Harbison S. Methods for the analysis of mitochondrial DNA. Wiley Interdisciplinary Reviews: Forensic Sci 2021;3(1):e1388.
54. Weber-Lehmann J, Schilling E, Gradl G, Richter DC, Wiehler J, Rolf B. Finding the needle in the haystack: differentiating “identical” twins in paternity testing and forensics by ultradeep next generation sequencing. Forensic Sci Int Genet 2014;9:42-6.
55. Çeppioğlu SK, Yurdun T. Adli Bilimlerde Epigenetik: Yeri ve Geleceği. Turkiye Klinikleri Forensic Med-Special Topics 2015;1(3):38-47.
56. Yanar K, Aksungur S. Adli Bilimlerde DNA Metilasyonları Kullanılarak Bireysel Yaş Tahmini. ABSAD 2024;6(1):42-57.
57. Forat S, Huettel B, Reinhardt R, Fimmers R, Haidl G, Denschlag D, et al. Correction: Methylation Markers for the Identification of Body Fluids and Tissues from Forensic Trace Evidence. PLoS One 2016;11(5):e0156472.
58. Li C, Zhao S, Zhang N, Zhang S, Hou Y. Differences of DNA methylation profiles between monozygotic twins’ blood samples. Mol Biol Rep 2013;40:5275-80.
59. Cai Y, Yu X, Hu S, Yu J. A brief review on the mechanisms of miRNA regulation. Genomics Proteomics Bioinformatics 2009;7(4):147-54.
60. Courts C, Madea B. Specific micro‐RNA signatures for the detection of saliva and blood in forensic body‐fluid identification. J Forensic Sci 2011;56(6):1464-70.
61. Holumen N. Usage areas of microRNA (miRNA) in forensic genetics. NOFOR 2022;1(1):7-14.
62. Silva SS, Lopes C, Teixeira A, De Sousa MC, Medeiros R. Forensic miRNA: potential biomarker for body fluids? Forensic Sci Int Genet 2015;14:1-10.
63. Glynn CL. Potential applications of microRNA profiling to forensic investigations. RNA. 2020;26(1):1-9.
64. Wang Z, Luo H, Pan X, Liao M, Hou Y. A model for data analysis of microRNA expression in forensic body fluid identification. Forensic Sci Int Genet 2012;6(3):419-23.
65. Tam S, De Borja R, Tsao M-S, McPherson JD. Robust global microRNA expression profiling using next-generation sequencing technologies. Lab Invest 2014;94(3):350-8.
66. Noren Hooten N, Abdelmohsen K, Gorospe M, Ejiogu N, Zonderman AB, Evans MK. microRNA expression patterns reveal differential expression of target genes with age. PLoS One 2010;5(5):e10724.
67. Aslan FG, Altındiş M. İnsan mikrobiyom projesi, mikrobiyotanın geleceği ve kişiye özel tıp uygulamaları. Journal of Biotechnology and Strategic Health Research 2017;1:1-6.
68. Wilkins D, Leung MH, Lee PK. Microbiota fingerprints lose individually identifying features over time. Microbiome 2017;5(1):1.
69. Neckovic A, van Oorschot RA, Szkuta B, Durdle A. Investigation of direct and indirect transfer of microbiomes between individuals. Forensic Sci Int Genet 2020;45:102212.
70. Zhang J, Liu W, Simayijiang H, Hu P, Yan J. Application of microbiome in forensics. Genomics Proteomics Bioinformatics 2023;21(1):97-107.
71. Kuiper I. Microbial forensics: next‐generation sequencing as catalyst: The use of new sequencing technologies to analyze whole microbial communities could become a powerful tool for forensic and criminal investigations. EMBO reports 2016;17(8):1085-7.
72. Benschop CC, Quaak FC, Boon ME, Sijen T, Kuiper I. Vaginal microbial flora analysis by next generation sequencing and microarrays; can microbes indicate vaginal origin in a forensic context? Int J Legal Med 2012;126(2):303-10.
73. Cardinali I, Tancredi D, Lancioni H. The revolution of animal genomics in forensic sciences. International Journal of Molecular Sciences 2023;24(10):8821.
74. Mitra I, Roy S, Haque I. Application of molecular markers in wildlife DNA forensic investigations. J. Forensic Med 2018;4(3):156-60.
75. Lyons LA, Grahn RA, Kun TJ, Netzel LR, Wictum EE, Halverson JL. Acceptance of domestic cat mitochondrial DNA in a criminal proceeding. Forensic Sci Int Genet 2014;13:61-7.
76. Ali M, Hashim U, Kashif M, Mustafa S, Che Man Y, Abd Hamid S. Development of swine-specific DNA markers for biosensor-based halal authentication. Genet Mol Res 2012;11(2):1762-72.
77. Malmström H, Storå J, Dalén L, Holmlund G, Götherström A. Extensive human DNA contamination in extracts from ancient dog bones and teeth. MBE 2005;22(10):2040-7. 281
78. Hajibabaei M, Shokralla S, Zhou X, Singer GA, Baird DJ. Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS One 2011;6(4):e17497.
79. Hancock-Hanser BL, Frey A, Leslie MS, Dutton PH, Archer FI, Morin PA. Targeted multiplex next-generation sequencing: advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics. Mol Ecol Resour 2013;13(2):254-68.
80. Cheng X, Chen X, Su X, Zhao H, Han M, Bo C, et al. DNA extraction protocol for biological ingredient analysis of Liuwei Dihuang Wan. Genomics Proteomics Bioinformatics 2014;12(3):137-43.
81. Phillips C, Prieto L, Fondevila M, Salas A, Gómez-Tato A, Álvarez-Dios J, et al. Ancestry analysis in the 11-M Madrid bomb attack investigation. PLoS One 2009;4(8):e6583.
82. Koops B-J, Schellekens M. Forensic DNA phenotyping: regulatory issues. Colum Sci & Tech L Rev 2008;9:158.
83. Budowle B, Van Daal A. Forensically relevant SNP classes. Biotechniques 2008;44(5):603-10.
84. Haidar M, Abbas FA, Alsaleh H, Haddrill PR. Population genetics and forensic utility of 23 autosomal PowerPlex Fusion 6C STR loci in the Kuwaiti population. Sci Rep 2021;11(1):1865.
85. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 2006;38(8):904-9.
86. Walsh S, Liu F, Ballantyne KN, van Oven M, Lao O, Kayser M. IrisPlex: a sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information. Forensic Sci Int Genet 2011;5(3):170-80.
87. Walsh S, Liu F, Wollstein A, Kovatsi L, Ralf A, Kosiniak- Kamysz A, et al. The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA. Forensic Sci Int Genet 2013;7(1):98-115.
88. Breslin K, Wills B, Ralf A, Garcia MV, Kukla-Bartoszek M, Pospiech E, et al. HIrisPlex-S system for eye, hair, and skin color prediction from DNA: Massively parallel sequencing solutions for two common forensically used platforms. Forensic Sci Int Genet 2019;43:102152.
89. Gill P. An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. Int J Legal Med 2001;114(4):204-10.
90. Pakstis AJ, Speed WC, Fang R, Hyland FC, Furtado MR, Kidd JR, et al. SNPs for a universal individual identification panel. Hum gen 2010;127:315-24.
91. Redler S, Brockschmidt F, Tazi-Ahnini R, Drichel D, Birch M, Dobson K, et al. Investigation of the male pattern baldness major genetic susceptibility loci AR/EDA2R and 20p11 in female pattern hair loss. Br J Dermatol 2012;166(6):1314-8.
92. Haidar M, Mousawi F, Al-Matrouk AK. Forensic DNA phenotyping using next-generation sequencing. Next Generation Sequencing (NGS) Technology in DNA Analysis: Elsevier; 2024. p. 289-310.
93. Carratto TMT, de Oliveira MLG, Mendes-Junior CT. Forensic DNA phenotyping in the next-generation sequencing era. Next Generation Sequencing (NGS) Technology in DNA Analysis: Elsevier; 2024. p. 311-36.
94. Budowle B, Arnette A, Sajantila A. A cost–benefit analysis for use of large SNP panels and high throughput typing for forensic investigative genetic genealogy. Int J Legal Med 2023;137(5):1595-614.
95. Vidaki A, Kayser M. Recent progress, methods and perspectives in forensic epigenetics. Forensic Sci Int Genet 2018;37:180-95.
96. Akıncıoğlu NU, Aslan İ, Doğan Y. Afet Kurbanlarının Kimliklendirilmesinde Kullanılan Yöntemler ve Ülkemizdeki Durum. Güvenlik Bilimleri Dergisi 2021;10(1):217-38.