Development and validation of an MPS-based 513-Plex SNP identity panel for degraded forensic samples

Alketbi SK (2023) The role of DNA in forensic science: a comprehensive review. Int J Sci Res Archive 9(02):814–829

Article  Google Scholar 

Bender K, Farfán M, Schneider PM (2004) Preparation of degraded human DNA under controlled conditions. Forens Sci Int 139(2):135–140. https://doi.org/10.1016/j.forsciint.2003.10.003

Article  CAS  Google Scholar 

Bhoyar L, Mehar P, Chavali K (2024) An overview of DNA degradation and its implications in forensic caseworks. Egypt J Forensic Sci 14(1):15. https://doi.org/10.1186/s41935-024-00389-y

Article  Google Scholar 

Børsting C, Mogensen HS, Morling N (2013) Forensic genetic SNP typing of low-template DNA and highly degraded DNA from crime case samples. Forensic Sci Int Genet 7(3):345–352. https://doi.org/10.1016/j.fsigen.2013.02.004

Article  PubMed  CAS  Google Scholar 

Browne TN, Freeman M (2024) Next generation sequencing: forensic applications and policy considerations. WIREs Forensic Sci 6(6):e1531

Article  CAS  Google Scholar 

Bustin SA, Mueller R, Nolan T (2020) Parameters for successful PCR primer design. Quantitative Real-Time PCR: Methods and Protocols, 5–22

Carratto TMT, Moraes VMS, Recalde TSF, Oliveira MLGd, Teixeira C (2022) Applications of massively parallel sequencing in forensic genetics. Genet Mol Biol 45(3 Suppl 1):e20220077

Article  PubMed  PubMed Central  CAS  Google Scholar 

Chen M, Lan Q, Nie S, Hu L, Fang Y, Cui W, Bai X, Liu L, Zhu B (2023) Forensic efficiencies of individual identification, kinship testing and ancestral inference in three Yunnan groups based on a self-developed multiple DIP panel. Front Genet 13:1057231

Article  PubMed  PubMed Central  Google Scholar 

Chen J, Chen A, Tao R, Zhu R, Zhang H, You X, Li C, Zhang S (2024) Solution to a case involving the interpretation of trace degraded DNA mixtures. Int J Legal Med 138(6):2325–2330

Article  PubMed  PubMed Central  Google Scholar 

Cuesta-Aguirre DR, Malgosa A, Santos C (2024) An easy-to-use pipeline to analyze amplicon-based next generation sequencing results of human mitochondrial DNA from degraded samples. PLoS ONE 19(11):e0311115

Article  PubMed  PubMed Central  CAS  Google Scholar 

Dash HR, Avila E, Jena SR, Kaitholia K, Agarwal R, Alho CS, Srivastava A, Singh AK (2022) Forensic characterization of 124 SNPs in the central Indian population using precision ID identity panel through next-generation sequencing. Int J Legal Med. https://doi.org/10.1007/s00414-021-02742-5

Article  PubMed  Google Scholar 

Dash HR, Elkins KM, Al-Snan NR (2023) Applications of NGS technology in forensic DNA analysis. Advancements in forensic DNA analysis. Springer, Berlin, pp 91–104

Chapter  Google Scholar 

Davenport L, Devesse L, Court DS, Ballard D (2023) Forensic identity snps: characterisation of flanking region variation using massively parallel sequencing. Forensic Sci Int Genet 64:102847

Article  PubMed  CAS  Google Scholar 

De Cario R, Kura A, Suraci S, Magi A, Volta A, Marcucci R, Gori AM, Pepe G, Giusti B, Sticchi E (2020) Sanger validation of high-throughput sequencing in genetic diagnosis: still the best practice? Front Genet 11:592588

Article  PubMed  PubMed Central  Google Scholar 

Devyatkin V, Shklyar A, Fursova A, Rumyantseva Y, Kozhevnikova O (2024) Allele-specific pcr with fluorescently labeled probes: criteria for selecting primers for genotyping. Vavilov J Genet Breed 28(3):351

Article  CAS  Google Scholar 

Emery MV, Bolhofner K, Spake L, Ghafoor S, Versoza CJ, Rawls EM, Winingear S, Buikstra JE, Loreille O, Fulginiti LC (2024) Targeted enrichment of whole-genome SNPs from highly burned skeletal remains. J Forensic Sci. https://doi.org/10.1111/1556-4029.15482

Article  PubMed  Google Scholar 

Fan H, Wang L, Liu C, Lu X, Xu X, Ru K, Qiu P, Liu C, Wen S-Q (2022a) Development and validation of a novel 133-plex forensic STR panel (52 STRs and 81 Y-STRs) using single-end 400 bp massive parallel sequencing. Int J Legal Med 136(2):447–464

Article  PubMed  Google Scholar 

Fan H, Xie Q, Wang L, Ru K, Tan X, Ding J, Wang X, Huang J, Wang Z, Li Y, Wang X, He Y, Gu C, Liu M, Ma S, Wen S, Qiu P (2022b) Microhaplotype and Y-SNP/STR (MY): a novel MPS-based system for genotype pattern recognition in two-person DNA mixtures. Forensic Sci Int Genet 59:102705. https://doi.org/10.1016/j.fsigen.2022.102705

Article  PubMed  CAS  Google Scholar 

Fan H, Xu Y, Zhao Y, Feng K, Hong L, Zhao Q, Lu X, Shi M, Li H, Wang L, Wen S (2024) Development and validation of YARN: a novel SE-400 MPS kit for East Asian paternal lineage analysis. Forensic Sci Int Genet. https://doi.org/10.1016/j.fsigen.2024.103029

Article  PubMed  Google Scholar 

Flores M, Ho E, Ly C, Ceberio N, Guardado M, Felix K, Thorner HM, Paunovich M, Godek C, Kalaydjian C (2024) Decreased accuracy of forensic DNA mixture analysis for groups with lower genetic diversity. iScience. https://doi.org/10.1016/j.isci.2024.111067

Article  PubMed  PubMed Central  Google Scholar 

Gouveia N, Brito P, Bogas V, Serra A, Bento A, Lopes V, Balsa F, Sampaio L, São Bento M, Cunha P (2017) The effect of different levels of degradation and DNA concentrations on the quality of genetic profiles. Forensic Sci Int Genet Suppl Ser 6:e428–e429

Article  Google Scholar 

Guo F, Yu J, Zhang L, Li J (2017) Massively parallel sequencing of forensic STRs and SNPs using the Illumina® ForenSeq™ DNA signature prep kit on the miseq FGx™ forensic genomics system. Forensic Sci Int Genet 31:135–148

Article  PubMed  CAS  Google Scholar 

Guo F, Liu Z, Long G, Zhang B, Liu D, Yu S (2024) Performance and characterization of 94 identity-informative SNPs in Northern Han Chinese using ForenSeq™ DNA signature prep kit. J Forensic Leg Med 103:102678

Article  PubMed  Google Scholar 

Hares DR, Kneppers A, Onorato AJ, Kahn S (2020) Rapid DNA for crime scene use: enhancements and data needed to consider use on forensic evidence for state and National DNA Databasing–An agreed position statement by ENFSI, SWGDAM and the rapid DNA crime scene technology advancement task group. Forensic Science International, p 48

Herrick NC (2023) Exploring the effects of ancestry on inference and identity using bioinformatics. Purdue University Graduate School, Purdue

Google Scholar 

Holmes JB, Moyer E, Phan L, Maglott D, Kattman B (2020) SPDI: data model for variants and applications at NCBI. Bioinformatics 36(6):1902–1907

Article  PubMed  CAS  Google Scholar 

Hwa H-L, Wu M-Y, Chung W-C, Ko T-M, Lin C-P, Yin H-I, Lee T-T, Lee JC-I (2018) Massively parallel sequencing analysis of nondegraded and degraded DNA mixtures using the ForenSeq™ system in combination with EuroForMix software. Int J Legal Med 133(1):25–37. https://doi.org/10.1007/s00414-018-1961-y

Article  PubMed  Google Scholar 

Ji X, Tang J, Zhang J (2022) Effects of salt stress on the morphology, growth and physiological parameters of Juglansmicrocarpa L. seedlings. Plants. https://doi.org/10.3390/plants11182381

Article  PubMed  PubMed Central  Google Scholar 

Jiang X, Xiang J, Wang R, Wan Q (2020) A development strategy to fast establish the Taqman qPCR based method to detect SNP mutations. Hum Cell 33(4):1331–1333

Article  PubMed  PubMed Central  CAS  Google Scholar 

Knight KL, Mauriello A, Williams G (2023) Quantitation of DNA using the applied biosystems quantifiler® Trio DNA quantification kit. Forensic DNA Analysis: methods and protocols. Springer, Berlin, pp 175–188

Chapter  Google Scholar 

Larguinho M, Santos HM, Doria G, Scholz H, Baptista PV, Capelo JL (2010) Development of a fast and efficient ultrasonic-based strategy for DNA fragmentation. Talanta 81(3):881–886

Article  PubMed  CAS  Google Scholar 

Li R, Shen X, Chen H, Peng D, Wu R, Sun H (2021) Developmental validation of the MGIEasy signature identification library prep kit, an all-in-one multiplex system for forensic applications. Int J Legal Med 135:739–753

Article  PubMed  Google Scholar 

Liu X, Yang C, Chen X, Han X, Liu H, Zhang X, Xu Q, Yang X, Liu C, Chen L (2024) A novel 193-plex MPS panel integrating STRs and SNPs highlights the application value of forensic genetics in individual identification and paternity testing. Hum Genet 143(3):371–383

Article  PubMed  CAS  Google Scholar 

Mathieson W, Thomas G (2019) Using FFPE tissue in genomic analyses: advantages, disadvantages and the role of biospecimen science. Curr Pathobiol Rep 7:35–40

Article  CAS 

Comments (0)

No login
gif