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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] [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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2
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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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3
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García-Aceves ME, Romero Rentería O, Díaz-Navarro XX, Rangel-Villalobos H. Paternity tests in Mexico: Results obtained in 3005 cases. J Forensic Leg Med 2018; 55:1-7. [PMID: 29433009 DOI: 10.1016/j.jflm.2018.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/25/2018] [Accepted: 02/04/2018] [Indexed: 11/28/2022]
Abstract
National and international reports regarding the paternity testing activity scarcely include information from Mexico and other Latin American countries. Therefore, we report different results from the analysis of 3005 paternity cases analyzed during a period of five years in a Mexican paternity testing laboratory. Motherless tests were the most frequent (77.27%), followed by trio cases (20.70%); the remaining 2.04% included different cases of kinship reconstruction. The paternity exclusion rate was 29.58%, higher but into the range reported by the American Association of Blood Banks (average 24.12%). We detected 65 mutations, most of them involving one-step (93.8% and the remaining were two-step mutations (6.2%) thus, we were able to estimate the paternal mutation rate for 17 different STR loci: 0.0018 (95% CI 0.0005-0.0047). Five triallelic patterns and 12 suspected null alleles were detected during this period; however, re-amplification of these samples with a different Human Identification (HID) kit confirmed the homozygous genotypes, which suggests that most of these exclusions actually are one-step mutations. HID kits with ≥20 STRs detected more exclusions, diminishing the rate of inconclusive results with isolated exclusions (<3 loci), and leading to higher paternity indexes (PI). However, the Powerplex 21 kit (20 STRs) and Powerplex Fusion kit (22 STRs) offered similar PI (p = 0.379) and average number of exclusions (PE) (p = 0.339) when a daughter was involved in motherless tests. In brief, besides to report forensic parameters from paternity tests in Mexico, results describe improvements to solve motherless paternity tests using HID kits with ≥20 STRs instead of one including 15 STRs.
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Affiliation(s)
- M E García-Aceves
- Instituto de Investigación en Genética Molecular, Universidad de Guadalajara (CUCiénega-UdeG), Av Universidad 1115, Paso Blanco, 47810 Ocotlán, Jalisco, Mexico; Doctorado en Genética Humana, Universidad de Guadalajara (CU Ciencias de la Salud), Sierra Mojada 950, Independencia, 44348, Guadalajara, Jalisco, Mexico
| | - O Romero Rentería
- DNA Profile SC, Laboratorio de Genética, Jamaica 90, Col. El Rosario, Ocotlán, Jalisco, Mexico
| | - X X Díaz-Navarro
- DNA Profile SC, Laboratorio de Genética, Jamaica 90, Col. El Rosario, Ocotlán, Jalisco, Mexico
| | - H Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Universidad de Guadalajara (CUCiénega-UdeG), Av Universidad 1115, Paso Blanco, 47810 Ocotlán, Jalisco, Mexico.
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4
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Tschoche J, Lutz-Bonengel S, Anslinger K. Vaterschaftstest: ein „Standard“-Triofall? Rechtsmedizin (Berl) 2017. [DOI: 10.1007/s00194-017-0215-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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5
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Forensic genetic study of 29 Y-STRs in Korean population. Leg Med (Tokyo) 2016; 23:17-20. [DOI: 10.1016/j.legalmed.2016.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/10/2016] [Accepted: 09/01/2016] [Indexed: 11/21/2022]
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6
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Su Q, Jin B, Luo H, Li Y, Wu J, Yan J, Hou Y, Liang W, Zhang L. Population study and mutation analysis for 28 short tandem repeat loci in southwest Chinese Han population. J Forensic Leg Med 2016; 44:10-13. [DOI: 10.1016/j.jflm.2016.08.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 08/08/2016] [Accepted: 08/23/2016] [Indexed: 11/30/2022]
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7
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Jin B, Su Q, Luo H, Li Y, Wu J, Yan J, Hou Y, Liang W, Zhang L. Mutational analysis of 33 autosomal short tandem repeat (STR) loci in southwest Chinese Han population based on trio parentage testing. Forensic Sci Int Genet 2016; 23:86-90. [DOI: 10.1016/j.fsigen.2016.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 02/17/2016] [Accepted: 03/28/2016] [Indexed: 11/27/2022]
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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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Abstract
Determing the sex of a give DNA sample can provide criminal investigators with useful intelligence and can aid the identification of missing persons and disaster victims. Polymerase chain reaction-based systems that amplify regions of the am elogenin gene have become the method of choice for sex determination of biological samples. This system can, however, result in false female sex designation when mutations affect primer binding sites of the Y homolog of this target sequence, causing drop out of the Y amplification product. Erroneous sex determination could have drastic consequences when applied to forensic situations by misdirecting investigators or hindering the identification of deceased individuals. Current methods of sex determination are described and possible alternative approaches to avoid errors are discussed.
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Affiliation(s)
- Eleanor A M Graham
- Forensic Pathology Unit, University of Leicester, Robert Kilpatrick Building Leicester Royal Infirmary, LE2 7LX, Leicester, UK,
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Gill P, Haned H, Bleka O, Hansson O, Dørum G, Egeland T. Genotyping and interpretation of STR-DNA: Low-template, mixtures and database matches-Twenty years of research and development. Forensic Sci Int Genet 2015; 18:100-17. [PMID: 25866376 DOI: 10.1016/j.fsigen.2015.03.014] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 03/19/2015] [Accepted: 03/24/2015] [Indexed: 12/17/2022]
Abstract
The introduction of Short Tandem Repeat (STR) DNA was a revolution within a revolution that transformed forensic DNA profiling into a tool that could be used, for the first time, to create National DNA databases. This transformation would not have been possible without the concurrent development of fluorescent automated sequencers, combined with the ability to multiplex several loci together. Use of the polymerase chain reaction (PCR) increased the sensitivity of the method to enable the analysis of a handful of cells. The first multiplexes were simple: 'the quad', introduced by the defunct UK Forensic Science Service (FSS) in 1994, rapidly followed by a more discriminating 'six-plex' (Second Generation Multiplex) in 1995 that was used to create the world's first national DNA database. The success of the database rapidly outgrew the functionality of the original system - by the year 2000 a new multiplex of ten-loci was introduced to reduce the chance of adventitious matches. The technology was adopted world-wide, albeit with different loci. The political requirement to introduce pan-European databases encouraged standardisation - the development of European Standard Set (ESS) of markers comprising twelve-loci is the latest iteration. Although development has been impressive, the methods used to interpret evidence have lagged behind. For example, the theory to interpret complex DNA profiles (low-level mixtures), had been developed fifteen years ago, but only in the past year or so, are the concepts starting to be widely adopted. A plethora of different models (some commercial and others non-commercial) have appeared. This has led to a confusing 'debate' about the 'best' to use. The different models available are described along with their advantages and disadvantages. A section discusses the development of national DNA databases, along with details of an associated controversy to estimate the strength of evidence of matches. Current methodology is limited to searches of complete profiles - another example where the interpretation of matches has not kept pace with development of theory. STRs have also transformed the area of Disaster Victim Identification (DVI) which frequently requires kinship analysis. However, genotyping efficiency is complicated by complex, degraded DNA profiles. Finally, there is now a detailed understanding of the causes of stochastic effects that cause DNA profiles to exhibit the phenomena of drop-out and drop-in, along with artefacts such as stutters. The phenomena discussed include: heterozygote balance; stutter; degradation; the effect of decreasing quantities of DNA; the dilution effect.
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Affiliation(s)
- Peter Gill
- Norwegian Institute of Public Health, Department of Forensic Biology, PO Box 4404 Nydalen, 0403 Oslo, Norway; Department of Forensic Medicine, Sognsvannsveien 20, Rikshospitalet, 0372 Oslo, Norway.
| | - Hinda Haned
- Netherlands Forensic Institute, Department of Human Biological Traces, The Hague, The Netherlands
| | - Oyvind Bleka
- Norwegian Institute of Public Health, Department of Forensic Biology, PO Box 4404 Nydalen, 0403 Oslo, Norway
| | - Oskar Hansson
- Norwegian Institute of Public Health, Department of Forensic Biology, PO Box 4404 Nydalen, 0403 Oslo, Norway
| | - Guro Dørum
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Aas, Norway
| | - Thore Egeland
- Norwegian Institute of Public Health, Department of Forensic Biology, PO Box 4404 Nydalen, 0403 Oslo, Norway; Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Aas, Norway
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11
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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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12
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Westen AA, Kraaijenbrink T, Robles de Medina EA, Harteveld J, Willemse P, Zuniga SB, van der Gaag KJ, Weiler NE, Warnaar J, Kayser M, Sijen T, de Knijff P. Comparing six commercial autosomal STR kits in a large Dutch population sample. Forensic Sci Int Genet 2014; 10:55-63. [DOI: 10.1016/j.fsigen.2014.01.008] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/21/2014] [Accepted: 01/24/2014] [Indexed: 12/11/2022]
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13
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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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14
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Recognizing the advantage of employing the PowerPlex® ESI and PowerPlex® ESX complementary kits for purposes of clarification in routine casework. Forensic Sci Int Genet 2013; 7:461-6. [DOI: 10.1016/j.fsigen.2013.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/20/2013] [Accepted: 03/27/2013] [Indexed: 11/18/2022]
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15
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Turrina S, Caratti S, De Leo D. Powerplex® Y 23 System: Molecular characterization of a null allele at locus DYS549. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2013. [DOI: 10.1016/j.fsigss.2013.10.060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Davis C, Ge J, Sprecher C, Chidambaram A, Thompson J, Ewing M, Fulmer P, Rabbach D, Storts D, Budowle B. Prototype PowerPlex® Y23 System: A concordance study. Forensic Sci Int Genet 2013; 7:204-8. [DOI: 10.1016/j.fsigen.2012.06.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 06/01/2012] [Accepted: 06/02/2012] [Indexed: 11/15/2022]
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17
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Laurin N, DeMoors A, Frégeau C. Performance of Identifiler Direct and PowerPlex 16 HS on the Applied Biosystems 3730 DNA Analyzer for processing biological samples archived on FTA cards. Forensic Sci Int Genet 2012; 6:621-9. [PMID: 22405517 DOI: 10.1016/j.fsigen.2012.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 01/16/2012] [Accepted: 02/07/2012] [Indexed: 10/28/2022]
Abstract
Direct amplification of STR loci from biological samples collected on FTA cards without prior DNA purification was evaluated using Identifiler Direct and PowerPlex 16 HS in conjunction with the use of a high throughput Applied Biosystems 3730 DNA Analyzer. In order to reduce the overall sample processing cost, reduced PCR volumes combined with various FTA disk sizes were tested. Optimized STR profiles were obtained using a 0.53 mm disk size in 10 μL PCR volume for both STR systems. These protocols proved effective in generating high quality profiles on the 3730 DNA Analyzer from both blood and buccal FTA samples. Reproducibility, concordance, robustness, sample stability and profile quality were assessed using a collection of blood and buccal samples on FTA cards from volunteer donors as well as from convicted offenders. The new developed protocols offer enhanced throughput capability and cost effectiveness without compromising the robustness and quality of the STR profiles obtained. These results support the use of these protocols for processing convicted offender samples submitted to the National DNA Data Bank of Canada. Similar protocols could be applied to the processing of casework reference samples or in paternity or family relationship testing.
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Affiliation(s)
- Nancy Laurin
- Royal Canadian Mounted Police, Forensic Science and Identification Services, National Services and Research, 1200 Vanier Parkway, Ottawa, ON, Canada.
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18
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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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19
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Lu D, Liu Q, Wu W, Zhao H. Mutation analysis of 24 short tandem repeats in Chinese Han population. Int J Legal Med 2011; 126:331-5. [DOI: 10.1007/s00414-011-0630-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 10/04/2011] [Indexed: 10/16/2022]
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20
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Cowell R, Lauritzen S, Mortera J. Probabilistic expert systems for handling artifacts in complex DNA mixtures. Forensic Sci Int Genet 2011; 5:202-9. [DOI: 10.1016/j.fsigen.2010.03.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 02/01/2010] [Accepted: 03/20/2010] [Indexed: 10/19/2022]
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21
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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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22
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Deucher A, Chiang T, Schrijver I. Rare sequence variation in the genome flanking a short tandem repeat locus can lead to a question of "nonmaternity". J Mol Diagn 2010; 12:384-9. [PMID: 20203001 PMCID: PMC2860477 DOI: 10.2353/jmoldx.2010.090201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2009] [Indexed: 11/20/2022] Open
Abstract
Typing of STR (short tandem repeat) alleles is used in a variety of applications in clinical molecular pathology, including evaluations for maternal cell contamination. Using a commercially available STR typing assay for maternal cell contamination performed in conjunction with prenatal diagnostic testing, we were posed with apparent nonmaternity when the two fetal samples did not demonstrate the expected maternal allele at one locus. By designing primers external to the region amplified by the primers from the commercial assay and by performing direct sequencing of the resulting amplicon, we were able to determine that a guanine to adenine sequence variation led to primer mismatch and allele dropout. This explained the apparent null allele shared between the maternal and fetal samples. Therefore, although rare, allele dropout must be considered whenever unexplained homozygosity at an STR locus is observed.
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Affiliation(s)
- Anne Deucher
- Department of Pathology, Stanford University Medical Center, Stanford, California
| | - Tsoyu Chiang
- Department of Molecular Pathology Laboratory, Stanford University Medical Center, Stanford, California
| | - Iris Schrijver
- Department of Pathology, Stanford University Medical Center, Stanford, California
- Department of Pediatrics, Stanford University Medical Center, Stanford, California
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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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24
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Pitterl F, Schmidt K, Huber G, Zimmermann B, Delport R, Amory S, Ludes B, Oberacher H, Parson W. Increasing the discrimination power of forensic STR testing by employing high-performance mass spectrometry, as illustrated in indigenous South African and Central Asian populations. Int J Legal Med 2010; 124:551-8. [DOI: 10.1007/s00414-009-0408-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 12/17/2009] [Indexed: 11/28/2022]
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25
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Bekada A, Benhamamouch S, Boudjema A, Fodil M, Menegon S, Torre C, Robino C. Analysis of 21 X-chromosomal STRs in an Algerian population sample. Int J Legal Med 2009; 124:287-94. [DOI: 10.1007/s00414-009-0397-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 11/18/2009] [Indexed: 11/29/2022]
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26
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False homozygosities at CSF1PO loci revealed by discrepancies between two kits in Chinese population. Int J Legal Med 2009; 124:457-8. [PMID: 19876641 DOI: 10.1007/s00414-009-0381-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 09/29/2009] [Indexed: 10/20/2022]
Abstract
During the course of paternity test, three samples in two cases were apparently homozygous at the CSF1PO locus using AmpFlSTRs Identifiler PCR Amplification kits, but using the PowerPlexs 16 kit, the three individuals were found to be heterozygous. This puzzling problem was solved by using multiple analytical approaches, including the use of different primer pairs and the characterization of the mutation causing the ''null allele.'' Dropout was caused by a single mutation event in the presumptive binding site of the forward primer. While the frequency of these silent alleles remains low (0.5% in our study), it is suggested that appropriate measures should be taken for database comparisons and that allelic dropout should be further investigated by sequence analysis and be reported to the forensic community.
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27
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Alenizi MA, Goodwin W, Hadi S, Alenizi HH, Altamar KA, Alsikel MS. Concordance Between the AmpFℓSTR®MiniFiler™ and AmpFℓSTR®Identifiler®PCR Amplification Kits in the Kuwaiti Population. J Forensic Sci 2009; 54:350-2. [DOI: 10.1111/j.1556-4029.2008.00962.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Gill P, Puch-Solis R, Curran J. The low-template-DNA (stochastic) threshold—Its determination relative to risk analysis for national DNA databases. Forensic Sci Int Genet 2009; 3:104-11. [DOI: 10.1016/j.fsigen.2008.11.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 09/10/2008] [Accepted: 11/03/2008] [Indexed: 10/21/2022]
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29
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An INDEL polymorphism at the X-STR GATA172D05 flanking region. Int J Legal Med 2008; 123:89-94. [PMID: 19048268 DOI: 10.1007/s00414-008-0300-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Accepted: 11/10/2008] [Indexed: 10/21/2022]
Abstract
A new polymorphic INDEL was detected at the X-STR GATA172D05 flanking region, which corresponds to an 18-bp deletion, 141 bp upstream the TAGA repeat motif. This INDEL was found to be polymorphic in different population samples from Native Americans, Africans, and Europeans as well as in an admixed population from the Amazonia (Belém). Gene diversities varied between 37.5% in Native Americans and 49.9% in Africans. Comparison between human and chimpanzee sequences showed that the ancestral state corresponds to the presence of two copies of 18 bp, detected in both species; and the mutated allele has lost one of these two copies. The simultaneous analysis of the short tandem repeat (STR) and INDEL variation showed an association between the INDEL ancestral allele with the shorter STR alleles. High diversities were found in all population groups when combining the information provided by the INDEL and STR variation. Gene diversities varied between 76.7% in Native Americans and 80.6% in both Portugal and Belém.
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30
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Populationsgenetik autosomaler Polymorphismen. MED GENET-BERLIN 2008. [DOI: 10.1007/s11825-008-0127-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Zusammenfassung
Für die Sammlung valider populationsgenetischer Daten zu den in der forensischen Genetik gebräuchlichen autosomalen DNA-Polymorphismen müssen eine Reihe von Kriterien erfüllt werden. Diese umfassen zunächst die untersuchten polymorphen Marker und ihre Typisierungsverfahren, da nur auf der Basis einer gesicherten Unterscheidung der Allele sowie einer verbindlichen Nomenklatur die Vergleichbarkeit und Reproduzierbarkeit der gesammelten Daten gegeben ist. Die genetische Validierung umfasst den Nachweis des Mendel-Erbgangs sowie die Überprüfung der Mutationsrate. Die Selektion der Probanden für die Bestimmung der Allelhäufigkeiten, die für eine Bevölkerungsgruppe repräsentativ sein sollen, muss zufällig erfolgen, und die Daten müssen auf das Vorliegen des Hardy-Weinberg-Gleichgewichts geprüft werden. Eine allgemein anerkannte Definition von Populationen im forensisch-genetischen Kontext ist Gegenstand der aktuellen Diskussion. Daher beruht die Auswahl der Probanden aus pragmatischen Gründen primär auf ihrer geografischen Herkunft. Zusätzlich wird empfohlen, bei der biostatistischen Bewertung populationsgenetische Maßzahlen wie Fst und Θ als Korrekturen für mögliche Inhomogenitäten in der untersuchten Populationsstichprobe zu verwenden.
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31
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Mizuno N, Kitayama T, Fujii K, Nakahara H, Yoshida K, Sekiguchi K, Yonezawa N, Nakano M, Kasai K. A D19S433 primer binding site mutation and the frequency in Japanese of the silent allele it causes. J Forensic Sci 2008; 53:1068-73. [PMID: 18636979 DOI: 10.1111/j.1556-4029.2008.00806.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Short tandem repeat studies are powerful tools for parentage analysis and for identification of missing persons, victims of murder, and victims of mass fatalities when reference samples are unavailable. The primer in the Identifiler kit failed to amplify an allele at the D19S433 locus, producing a silent ("null") allele. The causal mutation is a base change (G>A) 32 nucleotides downstream from the 3' end of the AAGG repeats. The silent alleles are problematical in parentage analysis because when transmitted, they can cause a parent-child inconsistency that is unrelated to Mendelian genetics. The inconsistency is sometimes termed an "apparent opposite homozygosity" and it produces false evidence of nonparentage. Alternative primers were designed to amplify the D19S433 locus alleles and they detect the silent allele. Frequencies of the (no longer) silent allele were determined to be 0.0114 in 176 people from Shizuoka (Honshu) and 0.0128 in 156 people from Okinawa.
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Affiliation(s)
- Natsuko Mizuno
- National Research Institute of Police Science, Kashiwa, Chiba, Japan.
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32
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Takayama T, Takada N, Suzuki R, Nagaoka S, Watanabe Y. Identification of a rare mutation in a TH01 primer binding site. Leg Med (Tokyo) 2007; 9:289-92. [PMID: 17562382 DOI: 10.1016/j.legalmed.2007.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 04/13/2007] [Accepted: 04/14/2007] [Indexed: 10/23/2022]
Abstract
We experienced a difficult case of TH01 typing. Instability of TH01 allele 9.3 was observed using GenePrint STR System TH01. Allele dropout was observed when an AmpFlSTR Profiler Kit was subsequently used for confirmation of the TH01 type. Use of the PowerPlex 16 System made it possible to detect allele 9.3. As a result of sequencing, a single point mutation (G-to-A transition) located 37 bases upstream of the first TCAT motif of the repeat region was identified as the cause of the allele dropout during use of the AmpFlSTR Profiler Kit. This mutation was located at the 3' end of the forward primers of the AmpFlSTR Profiler Kit and GenePrint STR System TH01.
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Affiliation(s)
- Tomohiro Takayama
- Criminal Investigation Laboratory, Gifu Prefectural Police Headquarters, 2-1-1 Yabuta minami, Gifu City, Gifu 500-8501, Japan.
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33
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Becker D, Bender K, Edelmann J, Götz F, Henke L, Hering S, Hohoff C, Hoppe K, Klintschar M, Muche M, Rolf B, Szibor R, Weirich V, Jung M, Brabetz W. New alleles and mutational events at 14 STR loci from different German populations. Forensic Sci Int Genet 2007; 1:232-7. [PMID: 19083767 DOI: 10.1016/j.fsigen.2007.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Revised: 04/10/2007] [Accepted: 04/11/2007] [Indexed: 11/30/2022]
Abstract
The molecular origin of DNA mutations and the mutation rates were analyzed at 14 short tandem repeat (STR) loci with samples from trio cases derived from 10 different German population samples. STR loci comprised of D2S1360, D3S1744, D4S2366, D5S2500, D6S474, D7S1517, D8S1132, D10S2325, D12S391, D18S51, D19S246, D20S480, D21S226, and D22S689. In a total of 488 meioses, 16 isolated genetic inconsistencies in 8 different STRs were observed, whereas no mutations were found at the other loci. The data of five mutations suggested the presence of silent or null alleles due to sequence variation in primer binding site. This could be confirmed for four suspected cases by the use of alternative primer sets and by DNA sequence analyses. Furthermore, this study revealed nine new allelic variants at five different loci.
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Affiliation(s)
- Dorit Becker
- Biotype AG, Moritzburger Weg 67 D, 01109 Dresden, Germany.
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34
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Vanderheyden N, Mai A, Gilissen A, Cassiman JJ, Decorte R. Identification and sequence analysis of discordant phenotypes between AmpFlSTR SGM Plus and PowerPlex 16. Int J Legal Med 2007; 121:297-301. [PMID: 17406881 DOI: 10.1007/s00414-007-0167-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Accepted: 03/15/2007] [Indexed: 10/23/2022]
Abstract
During duplicate analysis of buccal swabs from 1,377 individuals with 2 commercial short tandem repeat (STR) kits, we observed 8 discordant phenotypes with SGM Plus (SGM, second generation multiplex) for the STRs THO1 (2), vWA (4) and D18S51 (2), and 1 discrepancy with PowerPlex 16 for D18S51. One individual even showed two discrepancies (vWA and THO1) for SGM Plus. In each case, the difference observed was due to the non-amplification or allele dropout of the second allele in a heterozygous genotype. Sequence analysis revealed each time the presence of a mutation that probably coincided with the primer-binding site. Primer-binding site mutations for vWA and D18S51 have been reported previously, while the mutation for THO1 (C-to-T substitution at position 1286 of GenBank sequence D00269) is reported here for the first time. While the frequency of these silent alleles remains low (0.58% in our study), it is suggested that appropriate measures should be taken for database comparisons and that allelic dropout should be further investigated by sequence analysis and be reported to the forensic community.
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Affiliation(s)
- Nancy Vanderheyden
- Laboratory of Forensic Genetics and Molecular Archaeology, K.U. Leuven, Campus Gasthuisberg O&N, Herestraat 49-bus 602, 3000 Leuven, Belgium
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35
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Schneider PM. Scientific standards for studies in forensic genetics. Forensic Sci Int 2007; 165:238-43. [PMID: 16875790 DOI: 10.1016/j.forsciint.2006.06.067] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 06/13/2006] [Accepted: 06/19/2006] [Indexed: 11/16/2022]
Abstract
Forensic molecular genetics has evolved from a rapidly developing field with changing technologies into a highly recognized and generally accepted forensic science, leading to the establishment of national DNA databases with DNA profiles from suspects and convicted offenders. DNA evidence has taken a central role by carrying a significant weight for convictions, as well as by excluding innocent suspects early on in a criminal investigation. Due to this impact on the criminal justice system, guidelines for research in forensic genetics have been introduced already since many years. The most important issues regarding the selection and definition of typing systems both for paternity testing and for forensic identification, the criteria for technical and biostatistical validation, as well as the use of mitochondrial DNA analysis are summarized and discussed.
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Affiliation(s)
- Peter M Schneider
- Institute of Legal Medicine, University of Cologne, Melatenguertel 60-62, D-50858 Cologne, Germany.
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36
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Lukka M, Tasa G, Ellonen P, Moilanen K, Vassiljev V, Ulmanen I. Triallelic patterns in STR loci used for paternity analysis: Evidence for a duplication in chromosome 2 containing the TPOX STR locus. Forensic Sci Int 2006; 164:3-9. [PMID: 16337759 DOI: 10.1016/j.forsciint.2005.11.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Revised: 10/17/2005] [Accepted: 11/01/2005] [Indexed: 11/27/2022]
Abstract
We report triallelic patterns in several short tandem repeat (STR) loci revealed by routine paternity testing using the commercial AMPFlSTR Profiler and AMPFlSTR SGMplus kits. One case where the TPOX-locus (2p25.3) produced three peaks from the blood sample of a child was analysed further. Quantitative polymerase chain reaction (QPCR) and STR typing of the DNAs of the family trio revealed a large (>1.59 Mb) duplication flanking the TPOX-locus in chromosome 2 in both the mother and child. The implications of such genetic anomalies for paternity testing are discussed.
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Affiliation(s)
- Matti Lukka
- Paternity Testing Laboratory, Department of Molecular Medicine, National Public Health Institute, Mannerheimintie 166, 00300 Helsinki, Finland
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37
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Dawid AP, Mortera J, Vicard P. Object-oriented Bayesian networks for complex forensic DNA profiling problems. Forensic Sci Int 2006; 169:195-205. [PMID: 17055679 DOI: 10.1016/j.forsciint.2006.08.028] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2005] [Revised: 07/28/2006] [Accepted: 08/29/2006] [Indexed: 10/24/2022]
Abstract
We describe a flexible computational toolkit, based on object-oriented Bayesian networks, that can be used to model and solve a wide variety of complex problems of relationship testing using DNA profiles. In particular this can account for such complicating features as missing individuals, mutation and null alleles. We illustrate the use of this toolkit with several examples, including disputed paternity with missing or additional measurements, and criminal identification. We investigate the effects on likelihood ratios of introducing mutation and/or null alleles, and show that this can be substantial even when the underlying perturbations are small.
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Affiliation(s)
- A P Dawid
- Department of Statistical Science, University College London, London, UK.
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38
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Dawid A, Mortera J, Vicard P. Representing and solving complex DNA identification cases using Bayesian networks. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.ics.2005.09.115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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39
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Abstract
Over the past decade, the human identity testing community has settled on a set of core short tandem repeat (STR) loci that are widely used for DNA typing applications. A variety of commercial kits enable robust amplification of these core STR loci. A brief history is presented regarding the selection of core autosomal and Y-chromosomal STR markers. The physical location of each STR locus in the human genome is delineated and allele ranges and variants observed in human populations are summarized as are mutation rates observed from parentage testing. Internet resources for additional information on core STR loci are reviewed. Additional topics are also discussed, including potential linkage of STR loci to genetic disease-causing genes, probabilistic predictions of sample ethnicity, and desirable characteristics for additional STR loci that may be added in the future to the current core loci. These core STR loci, which form the basis for DNA databases worldwide, will continue to play an important role in forensic science for many years to come.
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Affiliation(s)
- John M Butler
- National Institute of Standards and Technology, Gaithersburg, MD 20899-8311, USA.
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40
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Grgicak CM, Rogers S, Mauterer C. Discovery and identification of new D13S317 primer binding site mutations. Forensic Sci Int 2005; 157:36-9. [PMID: 16098699 DOI: 10.1016/j.forsciint.2005.02.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2004] [Revised: 02/14/2005] [Accepted: 02/17/2005] [Indexed: 10/25/2022]
Abstract
During the course of conventional testing of CODIS standards at the Alabama Department of Forensic Sciences, a sample with a heterozygous null genotype at D13S317 was discovered using the PowerPlex 1.1 kit (Promega, Madison, WI). The loss of both alleles was confirmed when the sample was amplified using PowerPlex 1.2 primers and resulted in a 9, 10 genotype at this locus. To determine the cause of the silent alleles, the ADFS designed D13S317 primers which encompassed the PowerPlex 1.1 D13S317 primer binding sites and sequenced the region. Both alleles showed the presence of two substitutions (T-->A and G-->T) at positions 1 and 5 (5'-->3') of the reverse primer (positions 196 and 200 of the sequence in GenBank accession number ). Since the mutations were identical on both alleles, they may be assumed to be of ancestral origin.
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Affiliation(s)
- Catherine M Grgicak
- Alabama Department of Forensic Sciences, Forensic Biology/DNA Section, Birmingham, AL 35233, USA
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41
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Hering S, Nixdorf R, Dressler J. Identification of more sequence variations in the D8S1179 locus. Forensic Sci Int 2005; 149:275-8. [PMID: 15749373 DOI: 10.1016/j.forsciint.2004.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2004] [Revised: 07/26/2004] [Accepted: 07/28/2004] [Indexed: 11/25/2022]
Abstract
Routine STR-typing of 10,293 buccal swabs using different multiplex kits presented discordant D8S1179 profiles in four cases. Sequencing analysis identified a G-to-A transition upstream to the repeat, and an A-to-T transversion and a G-to-A transition downstream to the repeat. In the fourth case a four-base pair deletion downstream resulted in altered genotypes using different primer pairs. Current searching algorithms of the German DNA database are not capable of matching profiles that are divergent in only one STR-locus. Thus, to accommodate matching requirements and to avoid errors in individual genetic characterization for D8S1179, as described here, it is suggested that alternative primer pairs be used for routine genotyping as a matter of course.
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Affiliation(s)
- Sandra Hering
- Institute of Legal Medicine, Technical University of Dresden, Fetscherstrasse 74, D-01307 Dresden, Germany.
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42
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Abstract
Sherlock Holmes said "it has long been an axiom of mine that the little things are infinitely the most important", but never imagined that such a little thing, the DNA molecule, could become perhaps the most powerful single tool in the multifaceted fight against crime. Twenty years after the development of DNA fingerprinting, forensic DNA analysis is key to the conviction or exoneration of suspects and the identification of victims of crimes, accidents and disasters, driving the development of innovative methods in molecular genetics, statistics and the use of massive intelligence databases.
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Affiliation(s)
- Mark A Jobling
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom.
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43
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Heinrich M, Müller M, Rand S, Brinkmann B, Hohoff C. Allelic drop-out in the STR system ACTBP2 (SE33) as a result of mutations in the primer binding region. Int J Legal Med 2004; 118:361-3. [PMID: 15322828 DOI: 10.1007/s00414-004-0473-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2004] [Accepted: 06/29/2004] [Indexed: 11/28/2022]
Abstract
In the course of routine genotyping of forensic reference samples by multiplex PCR, an allelic drop-out due to mutations in the primer binding regions of the highly polymorphic STR marker ACTBP2 was observed in 17 samples. The variation rate was estimated to be 0.0014 (95% confidence interval: 0.0006-0.003). The most frequently found mutation was an G to A transition in the reverse primer binding region which was present in 14 out of 17 cases. To overcome the problem we have added a modified reverse primer to different multiplex kits that led to the correct genotype.
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Affiliation(s)
- Marielle Heinrich
- Institut für Rechtsmedizin, Universitätsklinikum Münster, Röntgenstrasse 23, 48149 Münster, Germany
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