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Construction of a library of cloned short tandem repeat (STR) alleles as universal templates for allelic ladder preparation.
Forensic Sci Int Genet. 2014 Sep; 12:136-43.FS

Abstract

Short tandem repeat (STR) genotyping methods are widely used for human identity testing applications, including forensic DNA analysis. Samples of DNA containing the length-variant STR alleles are typically separated and genotyped by comparison to an allelic ladder. Here, we describe a newly devised library of cloned STR alleles. The library covers alleles X and Y for the sex-determining locus Amelogenin and 259 other alleles for 22 autosomal STR loci (TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, vWA, D13S317, D16S539, D18S51, D21S11, D2S1338, D6S1043, D12S391, Penta E, D19S433, D11S4463, D17S974, D3S4529 and D12ATA63). New primers were designed for all these loci to construct recombinant plasmids so that the library retains core repeat elements of STR as well as 5'- and 3'-flanking sequences of ∼500 base pairs. Since amplicons of commercial STR genotyping kits and systems developed in laboratories are usually distributed from 50 to <500 base pairs, this library could provide universal templates for allelic ladder preparation. We prepared three different sets of allelic ladders for this locus TH01 and an updated version of an allelic ladder for the DNATyper(®)19 multiplex system using these plasmids to confirm the suitability of the library as a good source for allelic ladder preparation. Importantly, the authenticity of each construct was confirmed by bidirectional nucleotide sequencing and we report the repeat structures of the 259 STR alleles. The sequencing results showed all repeat structures we obtained for TPOX, CSF1PO, D7S820, TH01, D16S539, D18S51 and Penta E were the same as reported. However, we identified 102 unreported repeat structures from the other 15 STR loci, supplementing our current knowledge of repeat structures and leading to further understanding of these widely used loci.

Authors+Show Affiliations

Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China. Electronic address: wangle_02@163.com.Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China. Electronic address: zhaoxchun@sina.com.Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China. Electronic address: yejian77@126.com.School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, PR China.School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, PR China.Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China.Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China.Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China.Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China.The First Research Institute of the Ministry of Public Security, Beijing 100048, PR China.Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

24997318

Citation

Wang, Le, et al. "Construction of a Library of Cloned Short Tandem Repeat (STR) Alleles as Universal Templates for Allelic Ladder Preparation." Forensic Science International. Genetics, vol. 12, 2014, pp. 136-43.
Wang L, Zhao XC, Ye J, et al. Construction of a library of cloned short tandem repeat (STR) alleles as universal templates for allelic ladder preparation. Forensic Sci Int Genet. 2014;12:136-43.
Wang, L., Zhao, X. C., Ye, J., Liu, J. J., Chen, T., Bai, X., Zhang, J., Ou, Y., Hu, L., Jiang, B. W., & Wang, F. (2014). Construction of a library of cloned short tandem repeat (STR) alleles as universal templates for allelic ladder preparation. Forensic Science International. Genetics, 12, 136-43. https://doi.org/10.1016/j.fsigen.2014.06.005
Wang L, et al. Construction of a Library of Cloned Short Tandem Repeat (STR) Alleles as Universal Templates for Allelic Ladder Preparation. Forensic Sci Int Genet. 2014;12:136-43. PubMed PMID: 24997318.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Construction of a library of cloned short tandem repeat (STR) alleles as universal templates for allelic ladder preparation. AU - Wang,Le, AU - Zhao,Xing-Chun, AU - Ye,Jian, AU - Liu,Jin-Jie, AU - Chen,Ting, AU - Bai,Xue, AU - Zhang,Jian, AU - Ou,Yuan, AU - Hu,Lan, AU - Jiang,Bo-Wei, AU - Wang,Feng, Y1 - 2014/06/17/ PY - 2014/02/23/received PY - 2014/06/07/revised PY - 2014/06/11/accepted PY - 2014/7/6/entrez PY - 2014/7/6/pubmed PY - 2015/4/4/medline KW - Allelic ladder KW - Forensic science KW - Recombinant plasmid KW - Repeat structure KW - Short tandem repeat (STR) SP - 136 EP - 43 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 12 N2 - Short tandem repeat (STR) genotyping methods are widely used for human identity testing applications, including forensic DNA analysis. Samples of DNA containing the length-variant STR alleles are typically separated and genotyped by comparison to an allelic ladder. Here, we describe a newly devised library of cloned STR alleles. The library covers alleles X and Y for the sex-determining locus Amelogenin and 259 other alleles for 22 autosomal STR loci (TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, vWA, D13S317, D16S539, D18S51, D21S11, D2S1338, D6S1043, D12S391, Penta E, D19S433, D11S4463, D17S974, D3S4529 and D12ATA63). New primers were designed for all these loci to construct recombinant plasmids so that the library retains core repeat elements of STR as well as 5'- and 3'-flanking sequences of ∼500 base pairs. Since amplicons of commercial STR genotyping kits and systems developed in laboratories are usually distributed from 50 to <500 base pairs, this library could provide universal templates for allelic ladder preparation. We prepared three different sets of allelic ladders for this locus TH01 and an updated version of an allelic ladder for the DNATyper(®)19 multiplex system using these plasmids to confirm the suitability of the library as a good source for allelic ladder preparation. Importantly, the authenticity of each construct was confirmed by bidirectional nucleotide sequencing and we report the repeat structures of the 259 STR alleles. The sequencing results showed all repeat structures we obtained for TPOX, CSF1PO, D7S820, TH01, D16S539, D18S51 and Penta E were the same as reported. However, we identified 102 unreported repeat structures from the other 15 STR loci, supplementing our current knowledge of repeat structures and leading to further understanding of these widely used loci. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/24997318/Construction_of_a_library_of_cloned_short_tandem_repeat__STR__alleles_as_universal_templates_for_allelic_ladder_preparation_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(14)00123-9 DB - PRIME DP - Unbound Medicine ER -