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Yao Y, Yang Q, Shao C, Liu B, Zhou Y, Xu H, Zhou Y, Tang Q, Xie J. Null alleles and sequence variations at primer binding sites of STR loci within multiplex typing systems. Leg Med (Tokyo) 2017; 30:10-13. [PMID: 29125964 DOI: 10.1016/j.legalmed.2017.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 10/22/2017] [Accepted: 10/27/2017] [Indexed: 10/18/2022]
Abstract
Rare variants are widely observed in human genome and sequence variations at primer binding sites might impair the process of PCR amplification resulting in dropouts of alleles, named as null alleles. In this study, 5 cases from routine paternity testing using PowerPlex®21 System for STR genotyping were considered to harbor null alleles at TH01, FGA, D5S818, D8S1179, and D16S539, respectively. The dropout of alleles was confirmed by using alternative commercial kits AGCU Expressmarker 22 PCR amplification kit and AmpFℓSTR®. Identifiler® Plus Kit, and sequencing results revealed a single base variation at the primer binding site of each STR locus. Results from the collection of previous reports show that null alleles at D5S818 were frequently observed in population detected by two PowerPlex® typing systems and null alleles at D19S433 were mostly observed in Japanese population detected by two AmpFℓSTR™ typing systems. Furthermore, the most popular mutation type appeared the transition from C to T with G to A, which might have a potential relationship with DNA methylation. Altogether, these results can provide helpful information in forensic practice to the elimination of genotyping discrepancy and the development of primer sets.
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Affiliation(s)
- Yining Yao
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Qinrui Yang
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Chengchen Shao
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Baonian Liu
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yuxiang Zhou
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Hongmei Xu
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yueqin Zhou
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Qiqun Tang
- Department of Biochemistry and Molecular Biology, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jianhui Xie
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China.
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Fujii K, Iwashima Y, Watahiki H, Mita Y, Kitayama T, Nakahara H, Mizuno N, Sekiguchi K. D5S818 Typing Discrepancy Between PowerPlex(®) Fusion and Other STR Kits Including GlobalFiler(®) Caused by a One-base Deletion in 31 Nucleotides Upstream of the Repeat Region. J Forensic Sci 2016; 61:752-8. [PMID: 27122415 DOI: 10.1111/1556-4029.13039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/10/2015] [Accepted: 07/11/2015] [Indexed: 12/01/2022]
Abstract
Short tandem repeat (STR) typing is widely used in forensic investigation. When the same DNA sample is analyzed with different STR typing kits, a typing discrepancy is occasionally observed. In this study, we examined the cause of a typing discrepancy in a sample at D5S818 locus. This sample was designated as 10, 12 using Identifiler(®) , Identifiler(®) Plus, GlobalFiler(®) , PowerPlex(®) 16HS, and PowerPlex(®) 18D, but as 9.3, 12 using PowerPlex(®) Fusion. Sequencing results indicated that the shorter allele in the sample had a deletion (U31Tdel) at 31 nucleotides upstream of the repeat region (AGAT)10 . This deletion was located in the binding site of the published D5S818 forward primer in PowerPlex(®) 16 and was only 9 and 11 nucleotides downstream of our estimated 5' end position of D5S818 forward primer in GlobalFiler(®) and PowerPlex(®) 18D, respectively. We also examined the effect of primer length on the heterozygous peak balance in this sample.
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Affiliation(s)
- Koji Fujii
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Yasuki Iwashima
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan.,Forensic Science Laboratory, Kyoto Prefectural Police HQ, 85-3, 85-4, Shimodachiuri-dori, Kamanza-higashiiru, Yabunouchi-cho, Kamigyo-ku, Kyoto, 602-8550, Japan
| | - Haruhiko Watahiki
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Yusuke Mita
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Tetsushi Kitayama
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Hiroaki Nakahara
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Natsuko Mizuno
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Kazumasa Sekiguchi
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
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Jiang W, Kline M, Hu P, Wang Y. Identification of dual false indirect exclusions on the D5S818 and FGA loci. Leg Med (Tokyo) 2011; 13:30-4. [DOI: 10.1016/j.legalmed.2010.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2010] [Revised: 08/17/2010] [Accepted: 08/24/2010] [Indexed: 11/28/2022]
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Kline MC, Hill CR, Decker AE, Butler JM. STR sequence analysis for characterizing normal, variant, and null alleles. Forensic Sci Int Genet 2010; 5:329-32. [PMID: 20932816 DOI: 10.1016/j.fsigen.2010.09.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Revised: 07/23/2010] [Accepted: 09/08/2010] [Indexed: 11/16/2022]
Abstract
DNA sequence variation is known to exist in and around the repeat region of short tandem repeat (STR) loci used in human identity testing. While the vast majority of STR alleles measured in forensic DNA laboratories worldwide type as "normal" alleles compared with STR kit allelic ladders, a number of variant alleles have been reported. In addition, a sequence difference at a polymerase chain reaction (PCR) primer binding site in the DNA template can cause allele drop-out (i.e., a "null" or "silent" allele) with one set of primers and not with another. Our group at the National Institute of Standards and Technology (NIST) has been sequencing variant and null alleles supplied by forensic labs and cataloging this information on the NIST STRBase website for the past decade. The PCR primer sequences and strategy used for our STR allele sequencing work involving 23 autosomal STRs and 17 Y-chromosome STRs are described along with the results from 111 variant and 17 null alleles.
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Affiliation(s)
- Margaret C Kline
- National Institute of Standards and Technology, 100 Bureau Drive, M/S 8312, Gaithersburg, MD 20899, USA.
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Toscanini U, Gusmão L, Berardi G, Amorim A, Carracedo A, Salas A, Raimondi E. Testing for genetic structure in different urban Argentinian populations. Forensic Sci Int 2007; 165:35-40. [PMID: 16846710 DOI: 10.1016/j.forsciint.2006.02.042] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Revised: 02/14/2006] [Accepted: 02/14/2006] [Indexed: 11/19/2022]
Abstract
Fifteen autosomal short tandem repeat (STR) markers (D3S1358, HUMTH01, D21S11, D18S51, PENTA E, D5S818, D13S317, D7S820, D16S539, CSF1PO, PENTA D, HUMvWA, D8S1179, HUMTPOX, FGA) were analyzed in 1734 individuals living in urban areas of cities from six different Argentinian provinces (Buenos Aires, Neuquén, Tucumán, La Pampa, San Luis, Santa Cruz) in order to determine if a common urban database could be used in Argentina for forensic purposes. Frequencies estimates, Hardy-Weinberg equilibrium (HWE), and other parameters of forensic interest were computed. Comparisons between the six populations, and with published data from one Native American population from Argentina and other urban populations from Argentina and Europe were also performed. Our results reveal evidences for population structure, both when testing for genetic differentiation and when comparing frequencies distributions between different pairs of populations. Therefore, caution should be taken when using a common pooled database with general forensic purposes in Argentina.
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Affiliation(s)
- Ulises Toscanini
- PRICAI-Fundacion Favaloro, Av. Belgrano 1782, 1er Subsuelo, 1093 Capital Federal, Buenos Aires, Argentina
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Abstract
Over the past decade, the human identity testing community has settled on a set of core short tandem repeat (STR) loci that are widely used for DNA typing applications. A variety of commercial kits enable robust amplification of these core STR loci. A brief history is presented regarding the selection of core autosomal and Y-chromosomal STR markers. The physical location of each STR locus in the human genome is delineated and allele ranges and variants observed in human populations are summarized as are mutation rates observed from parentage testing. Internet resources for additional information on core STR loci are reviewed. Additional topics are also discussed, including potential linkage of STR loci to genetic disease-causing genes, probabilistic predictions of sample ethnicity, and desirable characteristics for additional STR loci that may be added in the future to the current core loci. These core STR loci, which form the basis for DNA databases worldwide, will continue to play an important role in forensic science for many years to come.
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Affiliation(s)
- John M Butler
- National Institute of Standards and Technology, Gaithersburg, MD 20899-8311, USA.
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Delamoye M, Duverneuil C, Riva K, Leterreux M, Taieb S, De Mazancourt P. False homozygosities at various loci revealed by discrepancies between commercial kits: implications for genetic databases. Forensic Sci Int 2004; 143:47-52. [PMID: 15177629 DOI: 10.1016/j.forsciint.2004.02.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Indexed: 10/26/2022]
Abstract
Routine control of 2055 consecutive genotypes revealed discrepancies between the profiles established with the SGM plus and/or Profiler plus kits on one hand, and the profiles established with the Powerplex16 kit on the other hand. Furthermore, five discrepancies for vWA, three for D8S1179, two for FGA and three for D18S51 loci were found. In 10 cases (loci vWA, FGA, D18S51, D8S1179), the SGM plus and/or Profiler plus profiles showed homozygosity and the Powerplex16 genotype revealed heterozygosities which were confirmed to be true, both by typing with individual primer pairs and DNA sequencing. In four cases (two discrepancies at locus FGA, one at D18S51 and an abnormal paternity pattern for D5S818), the Powerplex16 kit showed apparent homozygosity and the SGM plus and/or Profiler plus kits showed heterozygosity. Mutation analysis could be performed for some of these individuals and evidenced variants, presumably leading to an annealing failure of one primer; the identified mutations are reported. It is suggested that databases should include information about the kits used to determine the profiles while ensuring that the primer sequences are made available.
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Affiliation(s)
- Magali Delamoye
- Service de Biochimie, Faculté de Médecine Paris-Ouest, 104 Boulevard Raymond Poincaré, 92380 Garches, France
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Alves C, Gusmão L, Damasceno A, Soares B, Amorim A. Contribution for an African autosomic STR database (AmpF/STR Identifiler and Powerplex 16 System) and a report on genotypic variations. Forensic Sci Int 2004; 139:201-5. [PMID: 15040917 DOI: 10.1016/j.forsciint.2003.11.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2003] [Revised: 10/27/2003] [Accepted: 11/06/2003] [Indexed: 11/16/2022]
Abstract
Allele frequencies, together with some parameters of forensic interest, for 17 STRs included in the AmpF/STR Identifiler (CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPO and VWA) and Powerplex 16 System (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, Penta D, Penta E, TH01, TPO and VWA) were estimated from a sample of 135-144 unrelated individuals from Mozambique. No deviations from Hardy-Weinberg equilibrium were observed with the exception of the FGA locus (using the Bonferroni correction for the number of loci analysed, the departure observed at this locus was not significant). Comparative analyses between our population data and other African databases, namely Promega's African-Americans, AB Applied Biosystems African-Americans and two other population samples from Mozambique and Guiné Bissau, are presented and discussed. Genotype inconsistencies between both commercial kits (for D16S539 and D8S1179) and other genotypic variations (three-banded allele patterns for TPO) are also reported.
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Affiliation(s)
- Cíntia Alves
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
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