Development of a multiplex panel with 36 insertion/deletion markers (InDel) for individual identification.
Degraded DNA snalysis
Forensic genetics
Human identification
Insertion/Deletion (InDel) polymorphism
Optimization
Panel development
Population genetics
Validation
Journal
Forensic science, medicine, and pathology
ISSN: 1556-2891
Titre abrégé: Forensic Sci Med Pathol
Pays: United States
ID NLM: 101236111
Informations de publication
Date de publication:
02 Jun 2023
02 Jun 2023
Historique:
accepted:
10
05
2023
medline:
2
6
2023
pubmed:
2
6
2023
entrez:
2
6
2023
Statut:
aheadofprint
Résumé
In recent years, the insertion/deletion (InDel) polymorphism has become a preferred genetic marker in forensic genetics due to its low mutation rates and small amplicon sizes. In this study, a 36-InDelplex identification panel, consisting of autosomal 34 InDel loci, 1 Y InDel locus, and amelogenin, was developed, and gene frequencies in the Turkish population were determined. The loci of the InDel panel with global minimum allele frequencies (MAF) ≥ 0.4 were selected from the 1000 Genomes Project Phase 3 data. The amplicon sizes of the loci were designed in the range of 69-252 bp. In the validation study of the developed panel, analysis threshold, dynamic range, sensitivity, stochastic threshold, inhibitor tolerance, and reproducibility parameters were studied by following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. The sensitivity studies indicated that complete and reliable InDel profiles could be obtained with 0.25 ng of DNA. A population study was evaluated using 250 samples from Turkey. The mean observed heterozygosity ratio (Ho) of all loci was 0.48. The combined discrimination power (CPD) is 0.999999999990867 and the combined exclusion probability (CPE) was 0.9930. The population comparison was also made using Turkish and the five major populations from the 1000 Genomes Phase 3 populations' data (Africa, Europe, East Asia, South Asia, and America). In conclusion, the results showed that the 36-InDelplex panel is a reliable, sensitive, and accurate system that is suitable for human identification and population genetics purposes.
Identifiants
pubmed: 37266863
doi: 10.1007/s12024-023-00652-z
pii: 10.1007/s12024-023-00652-z
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : TUBITAK
ID : 217S586
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Thompson R, Zoppis S, McCord B. An overview of DNA typing methods for human identification: past, present, and future. DNA Electrophoresis Protocols Forensic Genetics. 2012;3–16. https://doi.org/10.1007/978-1-61779-461-2_1 .
Schneider PM. Beyond STRs: the role of diallelic markers in forensic genetics. Transfusion Med Hemotherapy. 2012;39(3):176–80. https://doi.org/10.1159/000339139 .
doi: 10.1159/000339139
Kayser M, De Knijff P. Improving human forensics through advances in genetics, genomics, and molecular biology. Nat Rev Genet. 2011;12(3):179–92. https://doi.org/10.1038/nrg2952 .
doi: 10.1038/nrg2952
pubmed: 21331090
Romanini C, Catelli ML, Borosky A, Pereira R, Romero M, Puerto MS, Phillips C, Fondevila M, Freire A, Santose C, Carracedo A, Lareue MV, Gusmao L, Vullo CM. Typing short amplicon binary polymorphisms: supplementary SNP and Indel genetic information in the analysis of highly degraded skeletal remains. Forensic Sci Int Genetics. 2012;6(4):469–76. https://doi.org/10.1016/j.fsigen.2011.10.006 .
doi: 10.1016/j.fsigen.2011.10.006
Pereira R, Gusmão L. Capillary Electrophoresis of 38 Noncoding Biallelic Mini-Indels for Degraded Samples and as Complementary Tool in Paternity Testing. DNA Electrophoresis Protocols Forensic Genetics, Humana Press. 2012;141–157. https://doi.org/10.1007/978-1-61779-461-2_10 .
LaRue BL, Ge J, King JL, Budowle B. A validation study of the Qiagen Investigator DIPplex® kit; an INDEL-based assay for human identification. Int J Leg Med. 2012;126(4):533–40. https://doi.org/10.1007/s00414-012-0667-9 .
doi: 10.1007/s00414-012-0667-9
Yang Q, Yu H, Qu Y, Zhang X, Xia R, Wang Z, Tan R, Xiong L, Xi S, Wu J, Gao Y, Zhang S, Li C. Developmental validation of the novel six-dye GoldeneyeTM DNA ID System 35InDel kit for forensic application. Forensic Sci Res C. 2021;1–12. https://doi.org/10.1080/20961790.2021.1945723 .
Pereira R, Phillips C, Alves C, Amorim A, Carracedo A, Gusmao L. A new multiplex for human identification using insertion/deletion polymorphisms. Electrophoresis. 2009;30(21):3682–90. https://doi.org/10.1002/elps.200900274 .
doi: 10.1002/elps.200900274
pubmed: 19862748
Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson J, Davis DG, MacArthur A, Sidow L, Duret M, Gerstein KD, Makova J, Marchini G, McVean G. Lunter and 1000 Genomes Project Consortium, The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Res. 2013;23(5):749–761. https://doi.org/10.1101/gr.148718.112 .
Weber JL, David D, Heil J, Fan Y, Zhao C, Marth G. Human diallelic insertion/deletion polymorphisms. Am J Human Genetics. 2002;71(4):854–62. https://doi.org/10.1086/342727 .
doi: 10.1086/342727
Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, Devine SE. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 2006;16(9):1182–90. https://doi.org/10.1101/gr.4565806 .
doi: 10.1101/gr.4565806
pubmed: 16902084
Wendt FR, Warshauer DH, Zeng X, Churchill JD, Novroski NM, Song B, King JL, Larue BL, Budowle B. Massively parallel sequencing of 68 insertion/deletion markers identifies novel microhaplotypes for utility in human identity testing. Forensic Sci Int Genetics. 2016;25:198–209. https://doi.org/10.1016/j.fsigen.2016.09.005 .
doi: 10.1016/j.fsigen.2016.09.005
Jin R, Cui W, Fang Y, Jin X, Wang H, Lan Q, Guo Y, Chen C, Zhang X, Zhu B. A Novel Panel of 43 Insertion/Deletion Loci for Human Identifications of Forensic Degraded DNA Samples: Development and Validation. Front Genet. 2021;12:210. https://doi.org/10.3389/fgene.2021.610540 .
doi: 10.3389/fgene.2021.610540
Pimenta JR, Pena SDJ. Efficient human paternity testing with a panel of 40 short insertion-deletion polymorphisms. Genetics Mol Res GMR. 2010;9(1):601–7. https://doi.org/10.4238/vol9-1gmr838 .
doi: 10.4238/vol9-1gmr838
pubmed: 20391344
Li C, Zhang S, Li L, Chen J, Liu Y, Zhao S. Selection of 29 highly informative InDel markers for human identification and paternity analysis in Chinese Han population by the SNPlex genotyping system. Mol Biol Rep. 2012;39(3):3143–3152. https://doi.org/10.1007/s11033-011-1080-z .
Huang J, Luo H, Wei W, Hou Y. A novel method for the analysis of 20 multi-Indel polymorphisms and its forensic application. Electrophoresis. 2014;35(4):487–93. https://doi.org/10.1002/elps.201300346 .
doi: 10.1002/elps.201300346
pubmed: 24242919
Zhang S, Zhu Q, Chen X, Zhao Y, Zhao X, Yang Y, Gao Z, Fang T, Wang Y, Zhang J. Forensic applicability of multi-allelic InDels with mononucleotide homopolymer structures. Electrophoresis. 2018;39(16):2136–43. https://doi.org/10.1002/elps.201700468 .
doi: 10.1002/elps.201700468
pubmed: 29704251
Chen L, Du W, Wu W, Yu A, Pan X, Feng P, Feng C, Li C, Xy L, Liu C, Liu C. Developmental validation of a novel six-dye typing system with 47 A-InDels and 2 Y-InDels. Forensic Science International: Genetics. 2019;40:64–73. https://doi.org/10.1016/j.fsigen.2019.02.009 .
doi: 10.1016/j.fsigen.2019.02.009
pubmed: 30776773
YHuang Y, Liu C, Xiao C, Chen X, Yi S, Huang D. Development of a new 32-plex InDels panel for forensic purposes. Forensic Sci Int Genetics. 2020;44:102171. https://doi.org/10.1016/j.fsigen.2019.102171 .
Scientific Working Group on DNA Analysis Methods. Interpretation Guidelines for Autosomal STR Typing by Forensic DNA Testing Laboratories. 2017. https://1ecb9588ea6f4feb971a73265dbf079c.filesusr.com/ugd/4344b0_50e2749756a242528e6285a5bb478f4c.pdf . Aaccessed 23 March 2022.
Excoffier L, Lischer HEL. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resources. 2010;10:564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x .
Murthy V, Jia LF, Samuel VP, Kademane K. Forensic Identification by Using Insertion-deletion Polymorphisms. Int J Hum Genet. 2015;15(2):55–9. https://doi.org/10.1080/09723757.2015.11886253 .
doi: 10.1080/09723757.2015.11886253
Bender K, Farfán MJ, Schneider PM. Preparation of degraded human DNA under controlled conditions. Forensic Sci Int Genetics. 2004;139(2–3):135–40. https://doi.org/10.1016/j.forsciint.2003.10.003 .
doi: 10.1016/j.forsciint.2003.10.003
Machida M, Taki T, Kibayashi K. Screening for single nucleotide polymorphisms in highly degraded DNA by using the amplified fragment length polymorphism technique. Forensic Sci Int Genetics. 2017;31:5–11. https://doi.org/10.1016/j.fsigen.2017.08.007 .
Li J, Lin L, Jiang B, Wang C, Zeye MM, Wen D, He W, Qu W, Liu Y, Zha L. An 18 Multi‐InDels panel for analysis of highly degraded forensic biological samples. Electrophoresis. 2021;42(9–10):1143–1152. https://doi.org/10.1002/elps.202000245 .
Machida M, Taki T, Shimada R, Kibayashi K. Investigation of single nucleotide polymorphism loci susceptible to degradation by ultraviolet light. J Forensic Leg Med. 2016;43:120–5. https://doi.org/10.1016/j.jflm.2016.08.002 .
doi: 10.1016/j.jflm.2016.08.002
pubmed: 27570235
Bender K, Farfán MJ, Schneider PM. Preparation of degraded human DNA under controlled conditions. Forensic Sci Int. 2004;139(2–3):135–40. https://doi.org/10.1016/j.forsciint.2003.10.003 .
doi: 10.1016/j.forsciint.2003.10.003
pubmed: 15040906
Freire-Aradas A, Fondevila M, Kriegel AK, Phillips C, Gill P, Prieto L, Schneider PM, Carracedo Á, Lareu MV. A new SNP assay for identification of highly degraded human DNA. Forensic Sci Int Genetics. 2012;6(3):341–9. https://doi.org/10.1016/j.fsigen.2011.07.010 .
doi: 10.1016/j.fsigen.2011.07.010
Romanini C, Catelli ML, Borosky A, Pereira R, Romero M, Puerto MS, Phillips C, Fondevila M, Freire A, Santos C, Carracedo A,Lareu MV, Gusmao L, Vullo CM. Typing short amplicon binary polymorphisms: supplementary SNP and Indel genetic information in the analysis of highly degraded skeletal remains. Forensic Sci Int Genetics. 2012;6.4:469–476. https://doi.org/10.1016/j.fsigen.2011.10.006 .
Børsting C, Mogensen HS, Morling N. Forensic genetic SNP typing of low-template DNA and highly degraded DNA from crime case samples. Forensic Sci Int Genetics. 2013;7(3):345–52. https://doi.org/10.1016/j.fsigen.2013.02.004 .
doi: 10.1016/j.fsigen.2013.02.004
Wei YL, Qin CJ, Dong H, Jia J, Li CX. A validation study of a multiplex INDEL assay for forensic use in four Chinese populations. Forensic Sci Int Genetics. 2014;9:e22–5. https://doi.org/10.1016/j.fsigen.2013.09.002 .
doi: 10.1016/j.fsigen.2013.09.002
Pinell TL. A comparison of the Powerplex® 16 HS System and Identifiler® Plus Kit for forensic casework samples. University of North Texas Health Science Center at Fort Worth. 2011.
Duvenci A, Bulbul O, Filoglu G. Evaluation of population data and forensic parameters of Turkish population on 30 autosomal insertion and deletion polymorphisms. Russian J Genetics. 2019;55(2):246–252. https://doi.org/10.1134/S1022795419020042 .
Li C, Zhao S, Zhang S, Li L, Liu Y, Chen J, Xue J. Genetic polymorphism of 29 highly informative InDel markers for forensic use in the Chinese Han population. Forensic Sci Int Genetics. 2011;5(1):e27–e30. https://doi.org/10.1016/j.fsigen.2010.03.004 .