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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Cornejo-Moreno BA, Henríquez-García MA, Ramos-Aleman SL, Romero XP, Lazo-Mena E, de Pleitez M, Vullo CM, Ge J, Budowle B. Population data for 21 STRs for the Salvadoran population using GlobalFiler Express and GlobalFiler STR Amplification Kits. Int J Legal Med 2021. [PMID: 34613462 DOI: 10.1007/s00414-021-02709-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
With the advent of expanded STR (short tandem repeats) typing kits, it was necessary to determine allele frequencies and other appropriate population data parameters for El Salvador. Samples were collected from the central, east, and west regions of the country and typed for 21 forensically relevant STR loci. The data indicate that all loci are highly polymorphic, the three regions are genetically similar, and the population data are similar to those of US Hispanics. The results of this study support that the allele frequency data described herein can be used for statistical calculations for human identity testing in El Salvador.
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3
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Manabe S, Fukagawa T, Fujii K, Mizuno N, Sekiguchi K, Akane A, Tamaki K. Development and validation of Kongoh ver. 3.0.1: Open-source software for DNA mixture interpretation in the GlobalFiler system based on a quantitative continuous model. Leg Med (Tokyo) 2021; 54:101972. [PMID: 34629243 DOI: 10.1016/j.legalmed.2021.101972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/27/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022]
Abstract
Probabilistic genotyping software based on continuous models is effective for interpreting DNA profiles derived from DNA mixtures and small DNA samples. In this study, we updated our previously developed Kongoh software (to ver. 3.0.1) to interpret DNA profiles typed using the GlobalFiler™ PCR Amplification Kit. Recently, highly sensitive typing systems such as the GlobalFiler system have facilitated the detection of forward, double-back, and minus 2-nt stutters; therefore, we implemented statistical models for these stutters in Kongoh. In addition, we validated the new version of Kongoh using 2-4-person mixtures and DNA profiles with degradation in the GlobalFiler system. The likelihood ratios (LRs) for true contributors and non-contributors were well separated as the information increased (i.e., larger peak height and fewer contributors), and these LRs tended to neutrality as the information decreased. These trends were observed even in profiles with DNA degradation. The LR values were highly reproducible, and the accuracy of the calculation was also confirmed. Therefore, Kongoh ver. 3.0.1 is useful for interpreting DNA mixtures and degraded DNA samples in the GlobalFiler system.
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Affiliation(s)
- Sho Manabe
- Department of Legal Medicine, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010, Japan.
| | - Takashi Fukagawa
- Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Koji Fujii
- Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Natsuko Mizuno
- Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Kazumasa Sekiguchi
- Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Atsushi Akane
- Department of Legal Medicine, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010, Japan
| | - Keiji Tamaki
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Ghiani ME, Mameli A, Vecchio C, Francalacci P, Robledo R, Calò CM. Estimating population genetics and forensic efficiency of the GlobalFiler PCR amplification kit in the population of Sardinia (Italy). Gene 2021; 794:145775. [PMID: 34126198 DOI: 10.1016/j.gene.2021.145775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/16/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
GlobalFiler is a new PCR amplification kit that includes 21 autosomal short tandem repeats and three sex-determining loci. In the present research, for the first time, the GlobalFiler kit was tested to analyze a sample of 500 unrelated individuals from 18 villages encompassing the entire area of Sardinia (Italy). We tested if the kit, which is a powerful tool in forensic studies, may also find application in the field of population genetics. In agreement with data from the literature on forensic parameters values, marker SE33 showed the highest degree of polymorphism, whereas TPOX was the least informative locus. Seventeen out of twenty-one autosomal markers included in the kit resulted highly polymorphic, and therefore Globalfiler turned out to be highly useful for forensic analysis in the Sardinian population. Moreover, our data suggest developing different STR databases in different populations, like Sardinians, to increase the statistical power of autosomal STR profiling. On the other hand, due to the presence of some very highly polymorphic markers, the efficiency of Globalfiler in detecting geographical variability is affected. Indeed, the differentiation previously observed between the Sardinian and Italian populations appeared greatly reduced and even the presence of genetic isolates, previously recorded when uniparental markers was not revealed.
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Affiliation(s)
- Maria Elena Ghiani
- Reparto Investigazioni Scientifiche Carabinieri di Cagliari, 09100 Cagliari, Italy
| | - Alessandro Mameli
- Reparto Investigazioni Scientifiche Carabinieri di Cagliari, 09100 Cagliari, Italy
| | - Cesare Vecchio
- Reparto Investigazioni Scientifiche Carabinieri di Cagliari, 09100 Cagliari, Italy
| | - Paolo Francalacci
- Dept. of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato (Ca), Italy
| | - Renato Robledo
- Dept. of Biomedical Sciences, University of Cagliari, 09042 Monserrato (Ca), Italy.
| | - Carla Maria Calò
- Dept. of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato (Ca), Italy
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Manabe S, Fujii K, Fukagawa T, Mizuno N, Sekiguchi K, Inoue K, Hashiyada M, Akane A, Tamaki K. Evaluation of probability distribution models for stutter ratios in the typing system of GlobalFiler and 3500xL Genetic Analyzer. Leg Med (Tokyo) 2021; 52:101906. [PMID: 34015722 DOI: 10.1016/j.legalmed.2021.101906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/06/2021] [Accepted: 05/07/2021] [Indexed: 11/19/2022]
Abstract
As DNA typing systems have become increasingly sensitive in recent years, probability distribution models for back, forward, double-back, and minus 2-nt stutter ratios have been desired to be considered in DNA evidence interpretation using specific software programs. However, experimental investigations have been insufficient, especially for forward, double-back, and minus 2-nt stutters. In this study, we experimentally reevaluated the probability distribution models for each stutter ratio in the typing systems of GlobalFiler™ PCR Amplification Kit and 3500xL Genetic Analyzer from Thermo Fisher Scientific. In addition, to enhance the reliability of longest uninterrupted stretch (LUS) values and corrected allele numbers used in previously developed models for stutter ratios using sequence information (i.e., LUS model and multi-seq model), we propose the weighted average of LUS values and corrected allele numbers based on the number of observations in sequence-based population data. Back stutter ratios demonstrated a positive correlation with allele numbers (allele model) in eight loci, LUS values (LUS model) in eight loci, and corrected allele numbers (multi-seq model) in five loci. The forward stutter ratios (FSRs) of D22S1045 followed the LUS model. FSRs other than D22S1045 and double-back stutter ratios followed the LUS model by considering multiple loci together. Minus 2-nt stutter ratios observed in SE33 and D1S1656 did not increase with the increase in the allele numbers. The adopted models for each stutter ratio can be implemented in software programs for DNA evidence interpretation and enable a reliable interpretation of crime stain profiles in forensic caseworks.
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Affiliation(s)
- Sho Manabe
- Department of Legal Medicine, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010, Japan.
| | - Koji Fujii
- Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Takashi Fukagawa
- Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Natsuko Mizuno
- Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Kazumasa Sekiguchi
- Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Kana Inoue
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masaki Hashiyada
- Department of Legal Medicine, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010, Japan
| | - Atsushi Akane
- Department of Legal Medicine, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010, Japan
| | - Keiji Tamaki
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Muinde JM, Chandra Bhanu DR, Neumann R, Oduor RO, Kanja W, Kimani JK, Mutugi MW, Smith L, Jobling MA, Wetton JH. Geographical and linguistic structure in the people of Kenya demonstrated using 21 autosomal STRs. Forensic Sci Int Genet 2021; 53:102535. [PMID: 34051692 DOI: 10.1016/j.fsigen.2021.102535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/11/2021] [Accepted: 05/16/2021] [Indexed: 11/15/2022]
Abstract
Kenya is a diverse and populous nation that employs DNA evidence in its criminal justice system, and therefore requires reliable information on autosomal STR allele frequency variation across the country and in its many ethnic groups. In order to provide reference data and to assess population structure, we analysed the 21 autosomal STRs in the GlobalFiler multiplex in a sample of 510 indigenous Kenyans representing the country's eight former provinces, 43 of its 47 counties, three main linguistic families and all 29 ethnic groups that each comprise >0.5% of the 2019 census population. The indigenous population originated from successive migrations of Cushitic, Nilotic and Bantu speaking groups who settled in regions that suited their distinctive sustenance lifestyles. Consequently, they now largely reside in a patchwork of communities with strong associations with particular counties and provinces and limited degrees of inter-group marriage, as shown by DNA donors' ancestry details. We found significant genetic differentiation between the three Nilotic language sub-families, with Western Nilotes (the Luo ethnic group) showing greater similarity to the Bantu than the Southern and Eastern Nilotes which themselves showed closer affinity to the Cushitic speakers. This concurs with previous genetic, linguistic and social studies. Comparisons with other African populations also showed that linguistic affiliation is a stronger factor than geography. This study revealed several rare off-ladder alleles whose structure was determined by Sanger sequencing. Among the unusual features that could affect profile interpretation were a deletion of Amelogenin Y but no other forensic marker (autosomal or Y-chromosomal), a triallelic pattern at TPOX and an extremely short SE33 allele falling within the expected size range of D7S820. Compared with the currently implemented Identifiler multiplex, Random Match Probabilities decreased from 6.4 × 10-19 to 3.9 × 10-27. The appreciation of local population structure provided by the geographically and ethnically representative sample in this study highlights the structured genetic landscape of Kenya.
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Affiliation(s)
- Jane Mbithe Muinde
- Department of Biochemistry, Microbiology & Biotechnology, Kenyatta University, Nairobi, Kenya
| | | | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK
| | - Richard Okoth Oduor
- Department of Biochemistry, Microbiology & Biotechnology, Kenyatta University, Nairobi, Kenya
| | | | | | | | - Lisa Smith
- Department of Criminology, University of Leicester, Leicester, UK
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
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7
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Romsos EL, French JL, Smith M, Figarelli V, Harran F, Vandegrift G, Moreno LI, Callaghan TF, Brocato J, Vaidyanathan J, Pedroso JC, Amy A, Stoiloff S, Morillo VH, Czetyrko K, Johnson ED, de Tagyos J, Murray A, Vallone PM. Results of the 2018 Rapid DNA Maturity Assessment. J Forensic Sci 2020; 65:953-959. [PMID: 31985834 PMCID: PMC11034630 DOI: 10.1111/1556-4029.14267] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/25/2019] [Accepted: 12/12/2019] [Indexed: 01/27/2023]
Abstract
Three commercially available integrated rapid DNA instruments were tested as a part of a rapid DNA maturity assessment in July of 2018. The assessment was conducted with sets of blinded single-source reference samples provided to participants for testing on the individual rapid platforms within their laboratories. The data were returned to the National Institute of Standards and Technology (NIST) for review and analysis. Both FBI-defined automated review (Rapid DNA Analysis) and manual review (Modified Rapid DNA Analysis) of the datasets were conducted to assess the success of genotyping the 20 Combined DNA Index System (CODIS) core STR loci and full profiles generated by the instruments. Genotype results from the multiple platforms, participating laboratories, and STR typing chemistries were combined into a single analysis. The Rapid DNA Analysis resulted in a success rate of 80% for full profiles (85% for the 20 CODIS core loci) with automated analysis. Modified Rapid DNA Analysis resulted in a success rate of 90% for both the CODIS 20 core loci and full profiles (all attempted loci per chemistry). An analysis of the peak height ratios demonstrated that 95% of all heterozygous alleles were above 59% heterozygote balance. For base-pair sizing precision, the precision was below the standard 0.5 bp deviation for both the ANDE 6C System and the RapidHIT 200.
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Affiliation(s)
- Erica L Romsos
- Applied Genetics Group, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899-8314
| | | | - Mark Smith
- Arizona Department Public Safety, 2102 West Encanto Blvd, Phoenix, AZ, 85009
| | - Vincent Figarelli
- Arizona Department Public Safety, 2102 West Encanto Blvd, Phoenix, AZ, 85009
| | - Frederick Harran
- Bensalem Township Police Department, 2400 Byberry Road, Bensalem, PA, 19020
| | - Glenn Vandegrift
- Bensalem Township Police Department, 2400 Byberry Road, Bensalem, PA, 19020
| | - Lilliana I Moreno
- Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135
| | - Thomas F Callaghan
- Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135
| | - Joanie Brocato
- Louisiana State Police Crime Laboratory, 376 East Airport Drive, Baton Rouge, LA, 70806
| | - Janaki Vaidyanathan
- Louisiana State Police Crime Laboratory, 376 East Airport Drive, Baton Rouge, LA, 70806
| | - Juan C Pedroso
- Miami Beach Police Department, 1100 Washington Ave, Miami Beach, FL, 33139
| | - Andrea Amy
- Miami Beach Police Department, 1100 Washington Ave, Miami Beach, FL, 33139
| | - Stephanie Stoiloff
- Miami-Dade Police Department, Forensic Services Bureau, 9105 NW 25th Street, Doral, FL, 33172
| | - Victor H Morillo
- Miami-Dade Police Department, Forensic Services Bureau, 9105 NW 25th Street, Doral, FL, 33172
| | - Karina Czetyrko
- Miami-Dade Police Department, Forensic Services Bureau, 9105 NW 25th Street, Doral, FL, 33172
| | - Elizabeth D Johnson
- United States Army Criminal Investigation Laboratory Defense Forensic Science Center, 4930 North 31st Street, Forest Park, GA, 30297
| | - Jessica de Tagyos
- United States Army Criminal Investigation Laboratory Defense Forensic Science Center, 4930 North 31st Street, Forest Park, GA, 30297
| | - Ashley Murray
- United States Army Criminal Investigation Laboratory Defense Forensic Science Center, 4930 North 31st Street, Forest Park, GA, 30297
| | - Peter M Vallone
- Applied Genetics Group, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899-8314
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8
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Al-Eitan LN, Darwish NN, Hakooz NM, Dajani RB. Investigation of the forensic GlobalFiler loci in the genetically isolated Circassian subpopulation in Jordan. Gene 2019; 733:144269. [PMID: 31809845 DOI: 10.1016/j.gene.2019.144269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 10/25/2022]
Abstract
Circassians are a Caucasian ethnic group who make up a significant minority in Jordan. Although other ethnic groups have been the subject of forensic genetic analysis, no published study has investigated the forensic genetic efficiency of short tandem repeats (STRs) in Circassians, neither in Jordan nor in any other country. The main objective of the current study is to determine the allelic frequencies and evaluate the forensic efficiency parameters of 21 highly polymorphic autosomal STR loci among the Circassian subpopulation in Jordan. The GlobalFiler loci were amplified using DNA extracted from the whole blood samples of 150 Jordanian Circassians. The SE33 locus was found to be the most informative and polymorphic STR marker while TPOX was the least informative. However, allele 8 of TPOX was the most common across all of the investigated 21 loci in Jordanian Circassians. The combined matching probability (CMP) and combined power of discrimination (CPD) were 5.02E-24 and 0.9999999, respectively.
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Affiliation(s)
- Laith N Al-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan; Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Nizar N Darwish
- Department of Legal Medicine, Toxicology and Forensic Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Nancy M Hakooz
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, University of Jordan, Amman 11942, Jordan
| | - Rana B Dajani
- Department of Biology and Biotechnology, Hashemite University, Zarqa 13133, Jordan; Radcliffe Institute for Advanced Studies, Harvard University, Cambridge, 02138 MA, USA; Jepson School of Leadership, Richmond University, 221 Richmond Way, Richmond, VA 23173, USA
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9
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Hayden DD, Wallin JM. A comparative study for the isolation of exogenous trace DNA from fingernails. Forensic Sci Int Genet 2019; 39:119-128. [PMID: 30640083 DOI: 10.1016/j.fsigen.2018.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/19/2018] [Accepted: 12/19/2018] [Indexed: 11/15/2022]
Abstract
Often fingernails from a victim or suspect involved in a physical assault, such as murder or sexual assault, are submitted to crime laboratories for DNA testing of foreign/exogenous biological material; however, very few studies have been conducted comparing the effectiveness of different sampling methods on the removal of foreign/exogenous DNA while minimizing the fingernail endogenous DNA. In this study three different sampling methods (swabbing, PBS soak, and PrepFiler® lysis buffer soak) were compared in order to identify one that minimizes the amount of endogenous DNA removed and maximizes the amount of foreign/exogenous male DNA removed. The samples were processed using the Tecan HIDEVO150 robot in order to reduce analyst time and the DNA mixtures were interpreted using the probabilistic genotyping software STRmix™. For each sampling method the quantity of male DNA, the mixture proportions, the number of foreign/exogenous male alleles detected, the amount of DNA degradation, and the discrimination power via the likelihood ratio obtained for the foreign/exogenous male DNA donor were determined and compared. The PrepFiler® lysis buffer soak and swabbing sampling methods appear to be equally effective at removing foreign/exogenous DNA from fingernails; however, the lysis buffer soak sampling method extracts more female endogenous DNA from the fingernail and the female DNA is degraded. Marginally higher likelihood ratios were obtained for the swab samples versus the PrepFiler® lysis buffer soak samples; therefore, it was determined that the swabbing sampling method was the best sampling method for the recovery of foreign exogenous DNA from fingernails while minimizing the amount of endogenous DNA removed.
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Affiliation(s)
- Deanna D Hayden
- State of California, Department of Justice, Bureau of Forensic Services, 1001 West Cutting Boulevard, Richmond, CA 94804, United States.
| | - Jeanette M Wallin
- State of California, Department of Justice, Bureau of Forensic Services, 1001 West Cutting Boulevard, Richmond, CA 94804, United States
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10
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Fujii K, Fukagawa T, Watahiki H, Mita Y, Kitayama T, Mizuno N. Ratios and distances of pull-up peaks observed in GlobalFiler kit data. Leg Med (Tokyo) 2018; 34:58-63. [PMID: 30193238 DOI: 10.1016/j.legalmed.2018.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 07/12/2018] [Accepted: 08/22/2018] [Indexed: 10/28/2022]
Abstract
Short tandem repeat (STR) analysis is widely used for forensic examinations with a capillary electrophoresis instrument such as the 3500xL Genetic Analyzer. This instrument adapts multi-locus STR kits to examine up to 27 loci using a 6-fluorescent dye system and corrects the spectral overlap between each dye. However, inaccurate spectral correction can cause pull-up peaks. Here, we examined the pull-up peaks observed in GlobalFiler kit data in terms of their peak height ratios and distances from their parent allele peaks when using the 3500xL and the 3130xl Genetic Analyzers. With the 3500xL, 546 pull-up peaks were observed, and their pull-up ratios averaged 1.03 ± 0.32% (range 0.260-2.80%). Of the 546 pull-up peaks, 534 peaks (97.8%) were within ±1 bp from their parent allele peaks. Overall, the pull-up peaks toward adjacent shorter wavelength channels (e.g., from yellow to green) tended to be observed in the left side (shorter bp) of the corresponding parent allele peaks, and the opposite side tendency was observed for those pull-up peaks toward adjacent longer wavelength channels. These tendencies were also observed in the GlobalFiler data generated with the 3130xl and in the data obtained by injecting a J6 matrix standard with LIZ 500 or 600 v2 size standard into the 3500xL and 3130xl. Inspection of raw data revealed that the shift of pull-up peaks from their parent allele peaks was derived from sigmoid, pull-down, or slightly shifted pull-up shapes. Based on the obtained data, we propose a standard for assessment of questionable pull-up peaks.
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Affiliation(s)
- Koji Fujii
- Fourth Biology Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan; Identification Center, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.
| | - Takashi Fukagawa
- Fourth Biology Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Haruhiko Watahiki
- Fourth Biology Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan; Identification Center, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Yusuke Mita
- Fourth Biology Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Tetsushi Kitayama
- Fourth Biology Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Natsuko Mizuno
- Fourth Biology Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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11
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Ristow PG, D'Amato ME. Characterization of a null TPOX allele for AmpFℓSTR ® Identifiler ® Plus kit. Forensic Sci Int Genet 2018; 35:e1-3. [PMID: 29631895 DOI: 10.1016/j.fsigen.2018.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/05/2018] [Accepted: 03/29/2018] [Indexed: 11/23/2022]
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Lan Q, Chen J, Guo Y, Xie T, Fang Y, Jin X, Cui W, Zhou Y, Zhu B. Genetic structure and polymorphism analysis of Xinjiang Hui ethnic minority based on 21 STRs. Mol Biol Rep 2018; 45:99-108. [PMID: 29372494 DOI: 10.1007/s11033-018-4143-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/27/2017] [Indexed: 01/23/2023]
Abstract
In the present study, we calculated the allelic frequencies and forensic descriptive parameters of Hui ethnic minority on the basis of 21 short tandem repeat (STR) loci aiming at understanding population structure better and enriching population genetic database. Bloodstain samples of 506 unrelated healthy Hui individuals in Xinjiang Uygur Autonomous Region were collected. Altogether 268 alleles were observed and the allelic frequencies ranged from 0.0010 to 0.5306. The combined power of discrimination and the cumulative probability of exclusion of the 21 STR loci in Hui ethnic minority were 0.9999999999999999999999998697 and 0.9999999968, respectively. Population data obtained manifested that the panel of 21 STR loci could provide robust genetic information for individual identification and paternity testing involved in forensic applications for Huis of Xinjiang Region. Furthermore, the present results of interpopulation differentiations, phylogenetic trees and principal component analysis which were conducted based on the overlapping 16 STR loci revealed that Hui group was genetically close to Xibe ethnic group and Han populations from different regions.
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Affiliation(s)
- Qiong Lan
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Jiangang Chen
- Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, People's Republic of China
| | - Yuxin Guo
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, People's Republic of China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, People's Republic of China
| | - Tong Xie
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Yating Fang
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Xiaoye Jin
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, People's Republic of China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, People's Republic of China
| | - Wei Cui
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, People's Republic of China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, People's Republic of China
| | - Yongsong Zhou
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Bofeng Zhu
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China.
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, People's Republic of China.
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, People's Republic of China.
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Fujii K, Watahiki H, Mita Y, Iwashima Y, Miyaguchi H, Kitayama T, Nakahara H, Mizuno N, Sekiguchi K. Next-generation sequencing analysis of off-ladder alleles due to migration shift caused by sequence variation at D12S391 locus. Leg Med (Tokyo) 2016; 22:62-7. [PMID: 27591542 DOI: 10.1016/j.legalmed.2016.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 08/03/2016] [Accepted: 08/10/2016] [Indexed: 10/21/2022]
Abstract
In short tandem repeat (STR) analysis, length polymorphisms are detected by capillary electrophoresis (CE). At most STR loci, mobility shift due to sequence variation in the repeat region was thought not to affect the typing results. In our recent population studies of 1501 Japanese individuals, off-ladder calls were observed at the D12S391 locus using PowerPlex Fusion in nine samples for allele 22, one sample for allele 25, and one sample for allele 26. However, these samples were typed as ordinary alleles within the bins using GlobalFiler. In this study, next-generation sequencing analysis using MiSeq was performed for the D12S391 locus from the 11 off-ladder samples and 33 other samples, as well as the allelic ladders of PowerPlex Fusion and GlobalFiler. All off-ladder allele 22 in the nine samples had [AGAT]11[AGAC]11 as a repeat structure, while the corresponding allele was [AGAT]15[AGAC]6[AGAT] for the PowerPlex Fusion ladder, and [AGAT]13[AGAC]9 for the GlobalFiler ladder. Overall, as the number of [AGAT] in the repeat structure decreased at the D12S391 locus, the peak migrated more slowly using PowerPlex Fusion, the reverse strand of which was labeled, and it migrated more rapidly using GlobalFiler, the forward strand of which was labeled. The allelic ladders of both STR kits were reamplified with our small amplicon D12S391 primers and their mobility was also examined. In conclusion, off-ladder observations of allele 22 at the D12S391 locus using PowerPlex Fusion were mainly attributed to a relatively large difference of the repeat structure between its allelic ladder and off-ladder allele 22.
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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; Identification Center, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, 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
| | - Yasuki Iwashima
- Forensic Science Laboratory, Kyoto Prefectural Police Headquarters, 85-3, 85-4 Shimodachiuri-dori, Kamanza-higashiiru, Yabunouchi-cho, Kamigyo-ku, Kyoto 602-8550, Japan
| | - Hajime Miyaguchi
- Identification Center, 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; Identification Center, 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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Zhang H, Yang S, Guo W, Ren B, Pu L, Ma T, Xia M, Jin L, Li L, Li S. Population genetic analysis of the GlobalFiler STR loci in 748 individuals from the Kazakh population of Xinjiang in northwest China. Int J Legal Med 2016; 130:1187-9. [PMID: 26846763 DOI: 10.1007/s00414-016-1319-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/15/2016] [Indexed: 01/19/2023]
Abstract
The six-dye GlobalFiler™ Express PCR amplification kit incorporates 21 commonly used autosomal short tandem repeat (STR) loci and three gender determination loci. In this study, we analyzed the GlobalFiler STR loci on 748 unrelated individuals from a Chinese Kazakh population of Xinjiang, China. No significant deviations from Hardy-Weinberg equilibrium and linkage disequilibrium were observed within and between 21 autosomal STR loci. SE33 showed the greatest power of discrimination in Kazakh population. The combined power of discrimination of Kazakh was 99.999999999999999999999996797 %. No significant differences of allele frequencies were observed between Kazakh and Uyghur at all 15 tested STR loci, as well as Mongolian. Significant differences were only observed between Kazakh and the other Chinese populations at TH01. Multiple STR loci showed significant differences between Kazakh and Arab, as well as South Portuguese. The multidimensional scaling plot (MDS) plot and neighbor-joining tree also showed Kazakh is genetically close to Uyghur.
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Affiliation(s)
- Honghua Zhang
- Criminal Science & Technology Institute, Bureau of Public Security, Urumqi, China
| | - Shuping Yang
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, China
| | - Wei Guo
- Criminal Science & Technology Institute, Bureau of Public Security, Urumqi, China
| | - Bo Ren
- Criminal Science & Technology Institute, Bureau of Public Security, Urumqi, China
| | - Liwen Pu
- Criminal Science & Technology Institute, Bureau of Public Security, Urumqi, China
| | - Teng Ma
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, China
| | - Mingying Xia
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, China
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, China
| | - Liming Li
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, China.
| | - Shilin Li
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, China.
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Ramos-González B, Aguilar-Velázquez JA, Chávez-Briones MDL, Delgado-Chavarría JR, Alfaro-Lopez E, Rangel-Villalobos H. Population data of 24 STRs in Mexican-Mestizo population from Monterrey, Nuevo Leon (Northeast, Mexico) based on Powerplex(®) Fusion and GlobalFiler(®) kits. Forensic Sci Int Genet 2015; 21:e15-7. [PMID: 26747399 DOI: 10.1016/j.fsigen.2015.12.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 12/02/2015] [Accepted: 12/09/2015] [Indexed: 11/16/2022]
Abstract
The STR loci included into new commercial human identification kits compels geneticists estimating forensic parameters for interpretation purposes in forensic casework. Therefore, we studied for the first time in Mexico the GlobalFiler(®) and Powerplex(®) Fusion systems in 326 and 682 unrelated individuals, respectively. These individuals are resident of the Monterrey City of the Nuevo Leon state (Northeast, Mexico). Population data from 23 autosomal STRs and the Y-STR locus DYS391 are reported and compared against available STR data from American ethnic groups and the unique Mexican population studied with Powerplex(®) Fusion.
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Affiliation(s)
- Benito Ramos-González
- Laboratorio de Genética Forense, Instituto de Criminalística y Servicios Periciales, Procuraduría General de Justicia, Nuevo León, Mexico.
| | | | - María de Lourdes Chávez-Briones
- Laboratorio de Genética Forense, Instituto de Criminalística y Servicios Periciales, Procuraduría General de Justicia, Nuevo León, Mexico; Departamento de Patología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Juan Ramón Delgado-Chavarría
- Laboratorio de Genética Forense, Instituto de Criminalística y Servicios Periciales, Procuraduría General de Justicia, Nuevo León, Mexico
| | - Elizabeth Alfaro-Lopez
- Laboratorio de Genética Forense, Instituto de Criminalística y Servicios Periciales, Procuraduría General de Justicia, Nuevo León, Mexico
| | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Universidad de Guadalajara (CUCI-UdeG), Ocotlán, Jalisco, Mexico.
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