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Watahiki H, Fujii K, Fukagawa T, Mita Y, Kitayama T, Mizuno N. Frequencies of D19S433 silent alleles in a Japanese population of 1501 individuals and their effect on likelihood ratios calculated in kinship tests. Leg Med (Tokyo) 2022; 54:102008. [PMID: 34974234 DOI: 10.1016/j.legalmed.2021.102008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/02/2021] [Accepted: 12/23/2021] [Indexed: 11/15/2022]
Abstract
Although silent alleles in D19S433 typing using the GlobalFiler PCR Amplification Kit have been reported, the exact frequency of the D19S433 silent alleles in population data of 1501 Japanese individuals, which are widely used for the assessment of Japanese STR typing results, is unclear. In this study, we examined the exact D19S433 silent allele frequency in this population data. We newly observed the G32A variant causing silent alleles at D19S433 in five samples. Combining them with data including 30 samples with the variant reported previously, we determined that the total frequency of the silent alleles (i.e. the frequency of the G32A variant) in the 1501 Japanese samples was 0.0117 (35/3002). Using the D19S433 allele frequency data, we evaluated the effect of presence/absence information for the D19S433 silent allele on kinship tests. Likelihood ratios (LRs) were calculated for both simulated parent-child and full sibling cases, revealing that the LR may change by approximately 10-2 to 103 fold when the presence/absence of the D19S433 silent allele is revealed in a kinship test. Therefore, if a sufficiently large or small LR is obtained, there is little need to determine the presence/absence of the D19S433 silent allele in Japanese kinship tests using GlobalFiler. This study will be beneficial for the assessment of Japanese human identification and kinship test results using GlobalFiler.
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Affiliation(s)
- Haruhiko Watahiki
- National Research Institute of Police Science, 6-3-1 Kashiwanoha Kashiwa, Chiba 277-0882, Japan.
| | - Koji Fujii
- National Research Institute of Police Science, 6-3-1 Kashiwanoha Kashiwa, Chiba 277-0882, Japan
| | - Takashi Fukagawa
- National Research Institute of Police Science, 6-3-1 Kashiwanoha Kashiwa, Chiba 277-0882, Japan
| | - Yusuke Mita
- National Research Institute of Police Science, 6-3-1 Kashiwanoha Kashiwa, Chiba 277-0882, Japan
| | - Tetsushi Kitayama
- National Research Institute of Police Science, 6-3-1 Kashiwanoha Kashiwa, Chiba 277-0882, Japan
| | - Natsuko Mizuno
- National Research Institute of Police Science, 6-3-1 Kashiwanoha Kashiwa, Chiba 277-0882, Japan
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2
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Comparative analysis of allele variation using allele frequencies according to sample size in Korean population. Genes Genomics 2021; 43:1301-1305. [PMID: 34432235 PMCID: PMC8478755 DOI: 10.1007/s13258-021-01159-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/19/2021] [Indexed: 11/18/2022]
Abstract
Background Allele frequency using short tandem repeats (STRs) is used to calculate likelihood ratio for database match, to interpret DNA mixture and to estimate ethnic groups in forensic genetics. In Korea, three population studies for 23 STR loci have been conducted with different sample size for forensic purposes. Objective We performed comparative analysis to determine how the difference of sample size affects the allele frequency and allele variation within same ethnic population (i.e. Korean). Furthermore, this study was conducted to check how the sampling group and multiplex kit also affect allele variation such as rare alleles and population specific alleles. Methods To compare allele variation, we used allele frequencies of three population data published from three Korean forensic research groups. Allele frequencies were calculated using different sample sizes and multiplex kits: 526, 1000, and 2000 individuals, respectively. Results The results showed the different distribution of allele frequencies in some loci. There was also a difference in the number of rare alleles observed by the sample size and sampling bias. In particular, an allele of 9.1 in the D2S441 locus was not observed in population study with 526 individuals due to multiplex kits. Conclusion Because the allele frequencies play an important role in forensic genetics, even if the samples are derived from the same population, it is important to consider the effects of sample size, sampling bias, and selection of multiplex kits in population studies.
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3
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Shao C, Yao Y, Pan X, Wu M, Zhang B, Xu H, Xie J, Sun K. Variants in linkage status at D5S818 detected by multiple STR kits comparison and Sanger sequencing. Mol Genet Genomic Med 2021; 9:e1765. [PMID: 34302451 PMCID: PMC8457698 DOI: 10.1002/mgg3.1765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/16/2021] [Accepted: 07/08/2021] [Indexed: 11/17/2022] Open
Abstract
Background D5S818 discrepancies have been reported in forensic parental testing due to null alleles. However, more cases may be ignored since proportional null alleles were missed without detection of heredity discrepancy between parents and offspring. Results In this study, null allele 12 at D5S818 was detected by the PowerPlex® 21 System with a higher occurrence rate on the basis of review on 2824 samples from the 1282 routine cases in Chinese Han population. Sequencing results revealed novel variant of guanine (G) into adenine (A) in the 7th [AGAT] repeats in the core repeat region accompanied by rs1187948322 in the samples with null allele 12. Conclusions Forensic STR typing may benefit from this discovery: (1) primer design of CE profiling system could be improved for sensitive population and (2) polymorphic information could be enriched for the accuracy and precision of NGS genotyping system. Peak area of D5S818 was also analyzed through different commercial STR kits. It is suggested that more attention should be paid on observed homozygosity with reduced peak area, especially for the samples from Chinese Han population.
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Affiliation(s)
- Chengchen Shao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yining Yao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xinwei Pan
- Shanghai Hengping Judicial Expertise Center, Shanghai, 200070, China
| | - Mengde Wu
- Shanghai Hengping Judicial Expertise Center, Shanghai, 200070, China
| | - Beilei Zhang
- Fujian Zhengtai Judicial Expertise Center, Xiamen, Fujian, 361000, China
| | - Hongmei Xu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jianhui Xie
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Kuan Sun
- Shanghai Key Laboratory of Forensic Medicine (Academy of Forensic Science), Shanghai, 200063, China.,Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
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4
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Schayek H, Waiskopf O, Rashkovski K, Amiel M, Wolf E, Avlas O. Concordance testing between Powerplex ESI 16 Fast System and VeriFiler Express. J Forensic Sci 2020; 66:1013-1016. [PMID: 33315267 DOI: 10.1111/1556-4029.14642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 11/30/2022]
Abstract
DNA profiles generated by different STR kits may show different alleles for identical amplified loci. This well-known phenomenon affects the smooth transition of data generated by new STR kits to a database or casework laboratory or cross-laboratory comparison of STR profiles. As in other DNA databases throughout the world, it has become clear that the number of the analyzed loci should be expanded for a variety of reasons, such as partial profiles resulting from low copy-number DNA template or degraded samples, working with mixtures or when prevalence of familial inbreeding. In the course of introducing a new STR kit, VeriFiler™ Express (Applied Biosystems, Foster City, CA, USA), we compared genotyping data of 1568 samples amplified by the VeriFiler™ Express with the data generated on the same samples by the Powerplex™ ESI FAST (Promega, Madison WI, USA) kit. Discordance was noted in 20 samples (1.27%), 14 (0.89%) of them showing allele dropout mismatch and six (0.38%) showing an additional fixed-size third allele. These rates are well above the reported rates of 0.4% for this kit. Since correct genotyping and accurate consistent allele assignment is of paramount importance, it seems timely to recommend for DNA laboratories and genetic-match search systems to take these possible inconsistencies into account.
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Affiliation(s)
- Hagit Schayek
- DNA Database Laboratory, Division of Identification and Forensic Science (DIFS), Israel Police, Jerusalem, Israel
| | - Ortal Waiskopf
- DNA and Biology Laboratory, Division of Identification and Forensic Science (DIFS), Israel Police, Jerusalem, Israel
| | - Ksenia Rashkovski
- DNA Database Laboratory, Division of Identification and Forensic Science (DIFS), Israel Police, Jerusalem, Israel
| | - Merav Amiel
- DNA and Biology Laboratory, Division of Identification and Forensic Science (DIFS), Israel Police, Jerusalem, Israel
| | - Ehud Wolf
- DNA Database Laboratory, Division of Identification and Forensic Science (DIFS), Israel Police, Jerusalem, Israel
| | - Orna Avlas
- DNA Database Laboratory, Division of Identification and Forensic Science (DIFS), Israel Police, Jerusalem, Israel
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5
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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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6
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Inokuchi S, Yamashita Y, Nishimura K, Nakanishi H, Saito K. Identification of a common single nucleotide polymorphism at the primer binding site of D2S1360 that causes heterozygote peak imbalance when using the Investigator HDplex Kit. Int J Legal Med 2017; 131:1531-1535. [PMID: 28386691 DOI: 10.1007/s00414-017-1571-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/06/2017] [Indexed: 10/19/2022]
Abstract
Phenomena known as null alleles and peak imbalance can occur because of mutations in the primer binding sites used for DNA typing. In these cases, an accurate statistical evaluation of DNA typing is difficult. The estimated likelihood ratio is incorrectly calculated because of the null allele and allele dropout caused by mutation-induced peak imbalance. Although a number of studies have attempted to uncover examples of these phenomena, few reports are available on the human identification kit manufactured by Qiagen. In this study, 196 Japanese individuals who were heterozygous at D2S1360 were genotyped using an Investigator HDplex Kit with optimal amounts of DNA. A peak imbalance was frequently observed at the D2S1360 locus. We performed a sequencing analysis of the area surrounding the D2S1360 repeat motif to identify the cause for peak imbalance. A point mutation (G>A transition) 136 nucleotides upstream from the D2S1360 repeat motif was discovered in a number of samples. The allele frequency of the mutation was 0.0566 in the Japanese population. Therefore, human identification or kinship testing using the Investigator HDplex Kit requires caution because of the higher frequency of single nucleotide polymorphisms at the primer binding site of D2S1360 locus in the Japanese population.
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Affiliation(s)
- Shota Inokuchi
- Department of Forensic Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan. .,Criminal Scientific Investigation Laboratory, Metropolitan Police Department of Tokyo, 3-35-21, Shakujiidai, Nerima, Tokyo, 177-0045, Japan.
| | - Yasuhiro Yamashita
- Criminal Scientific Investigation Laboratory, Metropolitan Police Department of Tokyo, 3-35-21, Shakujiidai, Nerima, Tokyo, 177-0045, Japan
| | - Kazuma Nishimura
- Criminal Scientific Investigation Laboratory, Metropolitan Police Department of Tokyo, 3-35-21, Shakujiidai, Nerima, Tokyo, 177-0045, Japan
| | - Hiroaki Nakanishi
- Department of Forensic Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan
| | - Kazuyuki Saito
- Department of Forensic Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan
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7
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Fujii K, Watahiki H, Mita Y, Iwashima Y, Kitayama T, Nakahara H, Mizuno N, Sekiguchi K. Typing concordance between PowerPlex ® Fusion and GlobalFiler ® based on 1501 Japanese individuals and the causes of typing discrepancies. Forensic Sci Int Genet 2016; 25:e12-e13. [DOI: 10.1016/j.fsigen.2016.07.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 07/27/2016] [Accepted: 07/30/2016] [Indexed: 10/21/2022]
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8
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Park HC, Kim K, Nam Y, Park J, Lee J, Lee H, Kwon H, Jin H, Kim W, Kim W, Lim S. Population genetic study for 24 STR loci and Y indel (GlobalFiler™ PCR Amplification kit and PowerPlex® Fusion system) in 1000 Korean individuals. Leg Med (Tokyo) 2016; 21:53-7. [DOI: 10.1016/j.legalmed.2016.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 06/16/2016] [Accepted: 06/21/2016] [Indexed: 11/15/2022]
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9
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Fujii K, Watahiki H, Mita Y, Kitayama T, Nakahara H, Mizuno N, Sekiguchi K. Validation of STR typing method using the GlobalFiler kit for forensic purposes. ACTA ACUST UNITED AC 2016. [DOI: 10.3408/jafst.700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Koji Fujii
- National Research Institute of Police Science
| | | | - Yusuke Mita
- National Research Institute of Police Science
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10
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Effects of using the GlobalFiler™ multiplex system on parent–child analyses of cases with single locus inconsistency. Leg Med (Tokyo) 2016; 18:72-4. [DOI: 10.1016/j.legalmed.2015.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 11/25/2015] [Accepted: 12/25/2015] [Indexed: 11/20/2022]
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11
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Chen L, Tai Y, Qiu P, Du W, Liu C. A silent allele in the locus D5S818 contained within the PowerPlex®21 PCR Amplification Kit. Leg Med (Tokyo) 2015; 17:509-11. [PMID: 26593999 DOI: 10.1016/j.legalmed.2015.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/06/2015] [Accepted: 10/30/2015] [Indexed: 02/06/2023]
Abstract
Three paternity tests cases were found with a single locus mismatch at the locus D5S818 with PowerPlex®21 PCR Amplification Kit (Promega). Forward and reverse primers were redesigned to type the samples again and to evaluate if there were alleles dropped out. The results showed the existence of a silent allele 12 in all the three families, due to a point mutation that changed cytosine to adenine at 90 nucleotides upstream from the 5' end of the AGAT repeat sequences in all the six individuals. A single locus mismatch due to a silent allele may occur in any locus using any kit. Therefore, we recommend using multiple kits to confirm the results in paternity testing cases with mismatches, especially when there is a single locus mismatch with homozygote involved.
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Affiliation(s)
- Ling Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, PR China
| | - Yunchun Tai
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, PR China
| | - Pingming Qiu
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, PR China
| | - Weian Du
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, PR China
| | - Chao Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, PR China; Guangzhou Forensic Science Institute, Guangzhou, Guangdong Province 510030, PR China.
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12
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Asari M, Okuda K, Hoshina C, Omura T, Tasaki Y, Shiono H, Matsubara K, Shimizu K. Multicolor-based discrimination of 21 short tandem repeats and amelogenin using four fluorescent universal primers. Anal Biochem 2015; 494:16-22. [PMID: 26505528 DOI: 10.1016/j.ab.2015.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 10/06/2015] [Accepted: 10/14/2015] [Indexed: 01/20/2023]
Abstract
The aim of this study was to develop a cost-effective genotyping method using high-quality DNA for human identification. A total of 21 short tandem repeats (STRs) and amelogenin were selected, and fluorescent fragments at 22 loci were simultaneously amplified in a single-tube reaction using locus-specific primers with 24-base universal tails and four fluorescent universal primers. Several nucleotide substitutions in universal tails and fluorescent universal primers enabled the detection of specific fluorescent fragments from the 22 loci. Multiplex polymerase chain reaction (PCR) produced intense FAM-, VIC-, NED-, and PET-labeled fragments ranging from 90 to 400 bp, and these fragments were discriminated using standard capillary electrophoretic analysis. The selected 22 loci were also analyzed using two commercial kits (the AmpFLSTR Identifiler Kit and the PowerPlex ESX 17 System), and results for two loci (D19S433 and D16S539) were discordant between these kits due to mutations at the primer binding sites. All genotypes from the 100 samples were determined using 2.5 ng of DNA by our method, and the expected alleles were completely recovered. Multiplex 22-locus genotyping using four fluorescent universal primers effectively reduces the costs to less than 20% of genotyping using commercial kits, and our method would be useful to detect silent alleles from commercial kit analysis.
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Affiliation(s)
- Masaru Asari
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan.
| | - Katsuhiro Okuda
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Chisato Hoshina
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Tomohiro Omura
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto 606-8507, Japan
| | - Yoshikazu Tasaki
- Department of Hospital Pharmacy and Pharmacology, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Hiroshi Shiono
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Kazuo Matsubara
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto 606-8507, Japan
| | - Keiko Shimizu
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
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Hiroshige Y, Ohtaki H, Yoshimoto T, Ogawa H, Ishii A, Yamamoto T. Species specificities among primates probed with commercially available fluorescence-based multiplex PCR typing kits. Leg Med (Tokyo) 2015; 17:326-33. [PMID: 25899252 DOI: 10.1016/j.legalmed.2015.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/04/2015] [Accepted: 03/26/2015] [Indexed: 11/26/2022]
Abstract
To assess species specificities among primates of signals from short tandem repeat (STR) loci included in two commercially available kits, mainly the AmpFlSTR Identifiler kit and additionally the GenePrint PowerPlex 16 system, we analyzed 69 DNA samples from 22 nonhuman primate species representing apes, Old World Monkeys (OWMs), New World Monkeys (NWMs), and prosimians. Each prosimian species and the NWM cotton-top tamarin apparently lacked all STR loci probed. Only one peak, the amelogenin-X peak, was evident in samples from all other NWMs, except the owl monkey. In contrast, several loci, including the amelogenin-X peak, was evident in samples from each OWM species. Notably, for each ape sample, the amelogenin peaks were concordant with morphological gender of the individual. Among the primates, especially in apes, the numbers of alleles for STR loci were increasing according to their phylogenetic order: prosimians<NWMs<OWNs<apes, and so among apes: agile gibbons<white handed gibbons<orangutans<gorillas/common chimpanzees/bonobos. The species specificities among primates for a few commercially released multiplex STR kits examined in this study would contribute to forensic examinations.
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Affiliation(s)
- Yuuji Hiroshige
- Department of Legal Medicine and Bioethics, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Hiroyuki Ohtaki
- Department of Legal Medicine and Bioethics, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Takashi Yoshimoto
- Department of Legal Medicine and Bioethics, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Hisae Ogawa
- Department of Legal Medicine and Bioethics, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Akira Ishii
- Department of Legal Medicine and Bioethics, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Toshimichi Yamamoto
- Department of Legal Medicine and Bioethics, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan.
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14
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False deletion of the D15S986 maternal allele in a suspected case of Angelman syndrome. Clin Chim Acta 2015; 439:191-4. [DOI: 10.1016/j.cca.2014.10.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/09/2014] [Accepted: 10/12/2014] [Indexed: 12/14/2022]
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15
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Tomas C, Mogensen HS, Friis SL, Hallenberg C, Stene MC, Morling N. Concordance study and population frequencies for 16 autosomal STRs analyzed with PowerPlex® ESI 17 and AmpFℓSTR® NGM SElect™ in Somalis, Danes and Greenlanders. Forensic Sci Int Genet 2014; 11:e18-21. [PMID: 24810256 DOI: 10.1016/j.fsigen.2014.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 04/08/2014] [Accepted: 04/10/2014] [Indexed: 12/01/2022]
Abstract
A concordance study of the results of PowerPlex(®) ESI 17 and AmpFℓSTR(®) NGM SElect™ kits obtained from 591 individuals from Somalia (N=198), Denmark (N=199) and Greenland (N=194) was performed. Among 9456 STR types, seven discordant results were found with the two kits: one observed in the D19S433 system in an individual from Denmark and six in the SE33 system in six individuals from Somalia. Sequencing of SE33 in the six samples with discordant results showed G>A transition 15bp downstream of the repeat unit in three of the individuals, and G>A transition 68bp downstream of the repeat unit in the other three individuals. Population data for 16 autosomal STR systems analyzed in 989 individuals from Somalia, Denmark and Greenland are also presented. The highest mean heterozygosity was observed in Danes (82.5%). With the exception of D8S1179 in Danes, no significant deviations from Hardy-Weinberg expectations were observed. Only one pair of systems (D12S391 and D18S51) showed significant allelic association in Greenlanders (after Holm-Šidák correction). A MDS plot drawn from pairwise FST values calculated between 21 populations showed a clear displacement of the Greenlandic population versus the other ones included in the analyses. The highest combined chance of exclusion and power of discrimination was observed for Danes reaching values of 99.9999987% and 1 in 1.8×10(21), respectively.
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Affiliation(s)
- C Tomas
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark.
| | - H S Mogensen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark
| | - S L Friis
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark
| | - C Hallenberg
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark
| | - M C Stene
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark
| | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark
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16
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Chen W, Cheng J, Ou X, Chen Y, Tong D, Sun H. Identification of the sequence variations of 15 autosomal STR loci in a Chinese population. Ann Hum Biol 2014; 41:524-30. [PMID: 24654839 DOI: 10.3109/03014460.2014.897754] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND DNA sequence variation including base(s) changes and insertion or deletion in the primer binding region may cause a null allele and, if this changes the length of the amplified fragment out of the allelic ladder, off-ladder (OL) alleles may be detected. AIM In order to provide accurate and reliable DNA evidence for forensic DNA analysis, it is essential to clarify sequence variations in prevalently used STR loci. SUBJECTS AND METHODS Suspected null alleles and OL alleles of PlowerPlex16® System from 21,934 unrelated Chinese individuals were verified by alternative systems and sequenced. RESULTS A total of 17 cases with null alleles were identified, including 12 kinds of point mutations in 16 cases and a 19-base deletion in one case. The total frequency of null alleles was 7.751 × 10(-4). Eight hundred and forty-four OL alleles classified as being of 97 different kinds were observed at 15 STR loci of the PowerPlex®16 system except vWA. All the frequencies of OL alleles were under 0.01. CONCLUSION Null alleles should be confirmed by alternative primers and OL alleles should be named appropriately. Particular attention should be paid to sequence variation, since incorrect designation could lead to false conclusions.
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Affiliation(s)
- Wenjing Chen
- Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University , Guangzhou , PR China
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17
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Mizuno N, Inokuchi S, Kitayama T, Fujii K, Kasai K, Sekiguchi K. A method to determine the 5' end of the binding site of primers included in a commercially available forensic human identification kit. Forensic Sci Int Genet 2013; 9:76-80. [PMID: 24528584 DOI: 10.1016/j.fsigen.2013.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 11/10/2013] [Accepted: 11/18/2013] [Indexed: 11/18/2022]
Abstract
Analysis for short tandem repeat (STR) loci is widely performed in forensic laboratories for human identification that utilizes commercially available kits that employ fluorescently labeled primers and capillary electrophoresis. With only a few exceptions, the sequences of the primers included in a kit are not disclosed by the kit manufacturers. Therefore, we developed a simple method to determine the 5' end of the binding site of the primers included in commercial kits. Our method requires only custom primers and human genome sequence data and routinely used equipment and consumables. One or two custom primers are added to the PCR reaction mixture containing kit primers and input human DNA prior to amplification, and PCR products are separated by capillary electrophoresis after amplification. With this method we can determine which primer of the pair is fluorescently labeled and the 5' end of the binding site of primers based on the changes in an electropherogram that are caused by the addition of the custom primer(s), and the human genome sequence data. This method is also useful for the determination of the shortest possible lengths of labeled kit primers.
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Affiliation(s)
- Natsuko Mizuno
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa 277-0882, Japan.
| | - Shota Inokuchi
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa 277-0882, Japan
| | - Tetsushi Kitayama
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa 277-0882, Japan
| | - Koji Fujii
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa 277-0882, Japan
| | - Kentaro Kasai
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa 277-0882, Japan
| | - Kazumasa Sekiguchi
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa 277-0882, Japan
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18
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Allele frequencies of 37 short tandem repeat loci in a Japanese population. Leg Med (Tokyo) 2013; 15:342-6. [DOI: 10.1016/j.legalmed.2013.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 08/30/2013] [Indexed: 11/23/2022]
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19
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Lin X, Wu J, Li H, Wang Z, Lin JM. Determination of mini-short tandem repeat (miniSTR) loci by using the combination of polymerase chain reaction (PCR) and microchip electrophoresis. Talanta 2013; 114:131-7. [DOI: 10.1016/j.talanta.2013.04.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 03/26/2013] [Accepted: 04/04/2013] [Indexed: 11/27/2022]
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20
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Rohlfs RV, Fullerton SM, Weir BS. Familial identification: population structure and relationship distinguishability. PLoS Genet 2012; 8:e1002469. [PMID: 22346758 PMCID: PMC3276546 DOI: 10.1371/journal.pgen.1002469] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 11/22/2011] [Indexed: 11/18/2022] Open
Abstract
With the expansion of offender/arrestee DNA profile databases, genetic forensic identification has become commonplace in the United States criminal justice system. Implementation of familial searching has been proposed to extend forensic identification to family members of individuals with profiles in offender/arrestee DNA databases. In familial searching, a partial genetic profile match between a database entrant and a crime scene sample is used to implicate genetic relatives of the database entrant as potential sources of the crime scene sample. In addition to concerns regarding civil liberties, familial searching poses unanswered statistical questions. In this study, we define confidence intervals on estimated likelihood ratios for familial identification. Using these confidence intervals, we consider familial searching in a structured population. We show that relatives and unrelated individuals from population samples with lower gene diversity over the loci considered are less distinguishable. We also consider cases where the most appropriate population sample for individuals considered is unknown. We find that as a less appropriate population sample, and thus allele frequency distribution, is assumed, relatives and unrelated individuals become more difficult to distinguish. In addition, we show that relationship distinguishability increases with the number of markers considered, but decreases for more distant genetic familial relationships. All of these results indicate that caution is warranted in the application of familial searching in structured populations, such as in the United States.
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Affiliation(s)
- Rori V Rohlfs
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA.
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21
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Yoshida K, Yayama K, Hatanaka A, Tamaki K. Efficacy of extended kinship analyses utilizing commercial STR kit in establishing personal identification. Leg Med (Tokyo) 2010; 13:12-5. [PMID: 20952240 DOI: 10.1016/j.legalmed.2010.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 08/31/2010] [Accepted: 09/01/2010] [Indexed: 10/18/2022]
Abstract
Unprecedented fidelity and specificity have afforded DNA testing its long reigning status as the gold standard for establishing personal identification. While the method itself is flawless, forensic experts have undoubtedly stumbled across challenging cases in which no reference samples for an unknown person (UP) are available for comparison. In such cases, experts often must resort to an assortment of kinship analyses-primarily those involving alleged parents or children of a UP-to establish personal identification. The present study derives likelihood ratio (LR) distributions from an extensive series of kinship simulations and places actual data, obtained from 120 cases in which personal identification of a UP was established via kinship analyses, to a comprehensive comparison in order to evaluate the efficacy of kinship assessments in establishing personal identification. A commercially available AmpFlSTR Identifiler kit was used to obtain DNA profiles. UP DNAs were extracted and isolated from fingernail (n=87), cardiac blood (24), carpal bone (7) and tooth (2). Buccal cells were procured from alleged kin (AK) for subsequent kinship analyses. In 72 cases 1-3 alleged children were available for comparison; in 46 cases, one or both alleged parents were available; and in the final 2 cases (involving a pair of bodies discovered together in a dwelling), their alleged children were typed for comparison. For each case a LR was calculated based on the DNA typing results. Interestingly, we found that the median LR observed in the actual cases virtually mirrored those of the simulations. With exception to 2 cases in which a silent allele was observed at D19S433, biological relatives showed a LR greater than 100 and in these cases, kinship between the UP and AK were further supported by additional forms of evidence. We show here that in the vast majority of identification cases where direct reference samples are unavailable for a UP, kinship analyses referring to alleged parents/children and using 15 standard loci is more than capable of establishing the identification of a UP. However, discretion should be advised for silent alleles which-albeit rare-are known to occur at loci such as D19S433, along with other mutations which could render a deceivingly reduced LR.
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Affiliation(s)
- Koichi Yoshida
- Forensic Science Laboratory, Kyoto Prefectural Police Headquarters, Kyoto 602-8550, Japan
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22
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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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23
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Tsuji A, Ishiko A, Umehara T, Usumoto Y, Hikiji W, Kudo K, Ikeda N. A silent allele in the locus D19S433 contained within the AmpFlSTR Identifiler PCR Amplification Kit. Leg Med (Tokyo) 2010; 12:94-6. [PMID: 20110189 DOI: 10.1016/j.legalmed.2009.12.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Revised: 12/11/2009] [Accepted: 12/11/2009] [Indexed: 11/30/2022]
Abstract
We present two cases where a single locus mismatch was found in the locus D19S433 using the AmpFlSTR Identifiler PCR Amplification Kit (Applied Biosystems) (Identifiler Kit) during paternity and maternity tests. This mismatch differed from the mismatch pattern where there is usually a one repeat difference. We designed forward and reverse primers so that they were positioned further away from the primer set contained in the Identifiler Kit. The results showed the existence of a silent allele 13 in both families, due to a point mutation that changed guanine to adenine at 32 nucleotides downstream from the 3' end of the AAGG repeat sequences in all four members. A single locus mismatch due to a silent allele may occur in any locus using any kit. Accordingly, we should pay attention to this silent allele when carrying out human identification and parentage analysis.
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Affiliation(s)
- Akiko Tsuji
- Department of Forensic Pathology and Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.
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