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Characterization of sequence variations in the extended flanking regions using massively parallel sequencing in 21 A-STRs and 21 Y-STRs.
Li, Hui; Li, Beixu; Liu, Yanan; Yang, Fan; Cao, Yu; Xie, Jianhui; Liu, Xiling; Zhao, Zhenmin; Li, Chengtao.
Afiliación
  • Li H; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Key Laboratory of Forensic Science, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, China.
  • Li B; Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
  • Liu Y; School of Policing Studies, Shanghai University of Political Science and Law, Shanghai, 201701, China.
  • Yang F; Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai, 200083, China.
  • Cao Y; Ministry of Education's Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China.
  • Xie J; Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai, 200083, China.
  • Liu X; Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai, 200083, China.
  • Zhao Z; Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
  • Li C; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Key Laboratory of Forensic Science, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, China.
BMC Genomics ; 25(1): 841, 2024 Sep 07.
Article en En | MEDLINE | ID: mdl-39244600
ABSTRACT
In forensic genetics, utilizing massively parallel sequencing (MPS) to analyze short tandem repeats (STRs) has demonstrated several advantages compared to conventional capillary electrophoresis (CE). Due to the current technical limitations, although flanking region polymorphisms had been mentioned in several previous studies, most studies focused on the core repeat regions of STRs or the variations in the adjacent flanking regions. In this study, we developed an MPS system consisting of two sets of multiplex PCR systems to detect not only the STR core repeat regions but also to observe variants located at relatively distant positions in the flanking regions. The system contained 42 commonly used forensic STRs, including 21 autosomal STRs (A-STRs) and 21 Y-chromosomal STRs (Y-STRs), and a total of 350 male individuals from a Chinese Han population were genotyped. The length and sequence variants per locus were tallied and categorized based on length (length-based, LB), sequence without flanking region (core repeat regions sequence-based, RSB), and sequence with flanking region (core repeat and flanking regions sequence-based, FSB), respectively. Allele frequencies, Y-haplotype frequencies, and forensic parameters were calculated based on LB, RSB, and FSB, respectively, to evaluate the improvement in discrimination power, heterozygosity, and effectiveness of forensic systems. The results suggested the sequence variations have more influence on A-STRs and could improve the identification ability of MPS-STR genotyping. Concordance between MPS and CE methods was confirmed by using commercial CE-based STR kits. The impact of flanking region variations on STR genotype analysis and potential factors contributing to discordances were discussed. A total of 58 variations in the flanking regions (53 SNPs/SNVs and 5 InDels) were observed and most variations (48/58) were distributed in A-STRs. In summary, this study delved deeper into the genetic information of forensic commonly used STR and advanced the application of massively parallel sequencing in forensic genetics.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Repeticiones de Microsatélite / Cromosomas Humanos Y / Secuenciación de Nucleótidos de Alto Rendimiento / Frecuencia de los Genes Límite: Humans / Male Idioma: En Revista: BMC Genomics Asunto de la revista: GENETICA Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Repeticiones de Microsatélite / Cromosomas Humanos Y / Secuenciación de Nucleótidos de Alto Rendimiento / Frecuencia de los Genes Límite: Humans / Male Idioma: En Revista: BMC Genomics Asunto de la revista: GENETICA Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Reino Unido