1
|
Vašek J, Čílová D, Melounová M, Svoboda P, Zdeňková K, Čermáková E, Ovesná J. OpiumPlex is a novel microsatellite system for profiling opium poppy (Papaver somniferum L.). Sci Rep 2021; 11:12799. [PMID: 34140548 PMCID: PMC8211840 DOI: 10.1038/s41598-021-91962-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/01/2021] [Indexed: 02/05/2023] Open
Abstract
Opium poppy (Papaver somniferum L.) is a versatile plant exploited by the pharmaceutical and food industries. Unfortunately, it is also infamously known as a source of highly addictive narcotics, primarily heroin. Drug abuse has devastating consequences for users and also has many direct or indirect negative impacts on human society as a whole. Therefore, developing a molecular genetic tool for the individualization of opium poppy, raw opium or heroin samples could help in the fight against the drug trade by retrieving more information about the source of narcotics and linking isolated criminal cases. Bioinformatic analysis provided insight into the distribution, density and other characteristics of roughly 150 thousand microsatellite loci within the poppy genome and indicated underrepresentation of microsatellites with the desired attributes. Despite this fact, 27 polymorphic STR markers, divided into three multiplexed assays, were developed in this work. Internal validation confirmed species-specific amplification, showed that the optimal amount of DNA is within the range of 0.625-1.25 ng per reaction, and indicate relatively well balanced assays according to the metrics used. Moreover, the stutter ratio (mean + 3 SD 2.28-15.59%) and allele-specific stutters were described. The analysis of 187 individual samples led to the identification of 158 alleles in total, with a mean of 5.85 alleles and a range of 3-14 alleles per locus. Most of the alleles (151) were sequenced by the Sanger method, which enabled us to propose standardized nomenclature and create three allelic ladders. The OpiumPlex system discriminates most of the varieties from each other and pharmaceutical varieties from the others (culinary, dual and ornamental).
Collapse
Affiliation(s)
- Jakub Vašek
- grid.15866.3c0000 0001 2238 631XDepartment of Genetics and Breeding, FAFNR, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Daniela Čílová
- grid.15866.3c0000 0001 2238 631XDepartment of Genetics and Breeding, FAFNR, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Martina Melounová
- grid.15866.3c0000 0001 2238 631XDepartment of Genetics and Breeding, FAFNR, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Pavel Svoboda
- grid.417626.00000 0001 2187 627XDivision of Crop Genetics and Breeding, Crop Research Institute, Prague, Czech Republic
| | - Kamila Zdeňková
- grid.448072.d0000 0004 0635 6059Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Eliška Čermáková
- grid.448072.d0000 0004 0635 6059Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Jaroslava Ovesná
- grid.417626.00000 0001 2187 627XDivision of Crop Genetics and Breeding, Crop Research Institute, Prague, Czech Republic
| |
Collapse
|
2
|
Lozano-Peral D, Rubio L, Santos I, Gaitán MJ, Viguera E, Martín-de-Las-Heras S. DNA degradation in human teeth exposed to thermal stress. Sci Rep 2021; 11:12118. [PMID: 34108558 PMCID: PMC8190102 DOI: 10.1038/s41598-021-91505-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 05/26/2021] [Indexed: 11/09/2022] Open
Abstract
Human identification from burned remains poses a challenge to forensic laboratories, and DNA profiling is widely used for this purpose. Our aim was to evaluate the effect of temperature on DNA degradation in human teeth. Thirty teeth were exposed to temperatures of 100, 200, or 400 °C for 60 min. DNA was quantified by Real-Time qPCR (Quantifiler Human DNA Quantification Kit) and fluorescence spectroscopy (Qubit 3.0 Fluorometer). DNA degradation was evaluated by using STR markers (AmpFLSTR Identifiler Plus PCR Amplification Kit) to determine the allele and locus dropout, inter-locus balance, and degradation slope (observed (Oa) to expected (Ea) locus peak height ratio against the molecular weight). Most of the genomic DNA was degraded between 100 °C and 200 °C. At 100 °C, locus dropout ratios showed significant differences between the largest loci (FGA, D7S820, D18S51, D16S539, D2S1338 and CSF1PO) and amelogenin. Inter-locus balance values significantly differed between all dye channels except between NED and PET. The dropout ratio between D18S51 (NED) and amelogenin (PET) can be recommended for the evaluation of DNA degradation. The Oa/Ea regression model can predict locus peak heights in DNA degradation (R2 = 0.7881). These findings may be useful to assess the reliability of DNA typing for human identification in teeth subjected to prolonged incineration.
Collapse
Affiliation(s)
- Diego Lozano-Peral
- Department of Forensic Dentistry and Medicine, Instituto de Investigación Biomédica de Málaga-IBIMA (CE-18), School of Medicine, University of Malaga, 29071, Malaga, Spain
- Supercomputing and Bioinnovation Center, Servicios Centrales de Apoyo a la Investigación, University of Malaga, 29590, Malaga, Spain
| | - Leticia Rubio
- Department of Forensic Dentistry and Medicine, Instituto de Investigación Biomédica de Málaga-IBIMA (CE-18), School of Medicine, University of Malaga, 29071, Malaga, Spain.
| | - Ignacio Santos
- Department of Forensic Dentistry and Medicine, Instituto de Investigación Biomédica de Málaga-IBIMA (CE-18), School of Medicine, University of Malaga, 29071, Malaga, Spain
| | - María Jesús Gaitán
- Department of Forensic Dentistry and Medicine, Instituto de Investigación Biomédica de Málaga-IBIMA (CE-18), School of Medicine, University of Malaga, 29071, Malaga, Spain
| | - Enrique Viguera
- Department of Cellular Biology, Genetics and Physiology, University of Malaga, 29071, Malaga, Spain
| | - Stella Martín-de-Las-Heras
- Department of Forensic Dentistry and Medicine, Instituto de Investigación Biomédica de Málaga-IBIMA (CE-18), School of Medicine, University of Malaga, 29071, Malaga, Spain
| |
Collapse
|
3
|
Dash HR, Rawat N, Vajpayee K, Shrivastava P, Das S. Useful autosomal STR marker sets for forensic and paternity applications in the Central Indian population. Ann Hum Biol 2021; 48:37-48. [PMID: 33470866 DOI: 10.1080/03014460.2021.1877353] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
BACKGROUND Many countries have developed their core set of STR loci for forensic application and database generation, which India lacks. AIM To assess the usefulness of various combinations of autosomal STR marker sets for their superior use in the central Indian population for forensic and paternity applications. SUBJECTS AND METHODS 19 STR marker sets were analysed on 200 central Indian populations and 20 paternity cases to assess their usefulness. RESULTS Two marker sets each comprising 19 STR markers are found to be superior to 20 expanded CODIS loci in the studied population. These marker sets also showed their effectiveness in 20 paternity cases having CPI values of 7.62 × 1011 and 7.16 × 1011. Three non-CODIS STR markers Penta E, Penta D, and SE33 showed amplification in 50 challenging samples with >0.80 heterozygosity. CONCLUSION Population-specific STR marker sets are useful in forensic and paternity applications, as well as database generation, and it is envisioned that Penta E, Penta D, and SE33 markers will be included in the list of core STR loci in the central Indian population.
Collapse
Affiliation(s)
| | - Neha Rawat
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, India.,Department of Forensic Science, Banaras Hindu University, Varanasi, India
| | | | | | - Surajit Das
- Department of Life Science, National Institute of Technology, Rourkela, India
| |
Collapse
|
4
|
Oldoni F, Podini D. Forensic molecular biomarkers for mixture analysis. Forensic Sci Int Genet 2019; 41:107-119. [DOI: 10.1016/j.fsigen.2019.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/06/2019] [Accepted: 04/17/2019] [Indexed: 01/10/2023]
|
5
|
Inter-laboratory validation study of the ForenSeq™ DNA Signature Prep Kit. Forensic Sci Int Genet 2018; 36:77-85. [DOI: 10.1016/j.fsigen.2018.05.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 11/19/2022]
|
6
|
Application of DNA-based forensic analysis for the detection of homologous transfusion of whole blood and of red blood cell concentrates in doping control. Forensic Sci Int 2016; 265:204-10. [DOI: 10.1016/j.forsciint.2016.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 04/06/2016] [Accepted: 04/15/2016] [Indexed: 01/09/2023]
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Hedman J, Knutsson R, Ansell R, Rådström P, Rasmusson B. Pre-PCR processing in bioterrorism preparedness: improved diagnostic capabilities for laboratory response networks. Biosecur Bioterror 2014; 11 Suppl 1:S87-101. [PMID: 23971826 DOI: 10.1089/bsp.2012.0090] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Diagnostic DNA analysis using polymerase chain reaction (PCR) has become a valuable tool for rapid detection of biothreat agents. However, analysis is often challenging because of the limited size, quality, and purity of the biological target. Pre-PCR processing is an integrated concept in which the issues of analytical limit of detection and simplicity for automation are addressed in all steps leading up to PCR amplification--that is, sampling, sample treatment, and the chemical composition of PCR. The sampling method should maximize target uptake and minimize uptake of extraneous substances that could impair the analysis--so-called PCR inhibitors. In sample treatment, there is a trade-off between yield and purity, as extensive purification leads to DNA loss. A cornerstone of pre-PCR processing is to apply DNA polymerase-buffer systems that are tolerant to specific sample impurities, thereby lowering the need for expensive purification steps and maximizing DNA recovery. Improved awareness among Laboratory Response Networks (LRNs) regarding pre-PCR processing is important, as ineffective sample processing leads to increased cost and possibly false-negative or ambiguous results, hindering the decision-making process in a bioterrorism crisis. This article covers the nature and mechanisms of PCR-inhibitory substances relevant for agroterrorism and bioterrorism preparedness, methods for quality control of PCR reactions, and applications of pre-PCR processing to optimize and simplify the analysis of various biothreat agents. Knowledge about pre-PCR processing will improve diagnostic capabilities of LRNs involved in the response to bioterrorism incidents.
Collapse
Affiliation(s)
- Johannes Hedman
- Johannes Hedman, PhD, is employed as a specialist at the Swedish National Laboratory of Forensic Science (SKL) and holds a research position at Applied Microbiology, Lund University. Rickard Knutsson, PhD, is Director of Security Department, National Veterinary Institute (SVA), Uppsala, Sweden . Ricky Ansell, PhD, is employed as forensic advisor and senior reporting officer at the Swedish National Laboratory of Forensic Science (SKL). Birgitta Rasmusson, PhD, is employed as research director at the Swedish National Laboratory of Forensic Science (SKL) and holds a position as adjunct professor at Applied Microbiology, Lund University. Peter Rådström, PhD, is employed as professor Applied Microbiology, Lund University
| | | | | | | | | |
Collapse
|
9
|
Hu N, Cong B, Gao T, Hu R, Chen Y, Tang H, Xue L, Li S, Ma C. Evaluation of parameters in mixed male DNA profiles for the Identifiler® multiplex system. Int J Mol Med 2014; 34:43-52. [PMID: 24821391 PMCID: PMC4072395 DOI: 10.3892/ijmm.2014.1779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 05/07/2014] [Indexed: 11/06/2022] Open
Abstract
The analysis of complex DNA mixtures is challenging for forensic DNA testing. Accurate and sensitive methods for profiling these samples are urgently required. In this study, we developed 11 groups of mixed male DNA samples (n=297) with scientific validation of D‑value [>95% of D‑values ≤0.1 with average peak height (APH) of the active alleles ≤2,500 rfu]. A strong linear correlation was detected between the peak height (PH) and peak area (PA) in the curve fit using the least squares method (P<2e-16). The Kruskal-Wallis rank-sum test revealed significant differences in the heterozygote balance ratio (H(b)) at 16 short tandem repeat (STR) loci (P=0.0063) and 9 mixed gradients (P=0.02257). Locally weighted regression fitting of APH and Hb (inflection point at APH = 1,250 rfu) showed 92.74% of H(b) >0.6 with the APH ≥1,250. The variation of H(b) distribution in the different STR loci suggested the different forensic efficiencies of these loci. Allelic drop-out (ADO) correlated with the APH and mixed gradient. All ADOs had an APH of <1,000 rfu, and the number of ADO increased when the APH of mixed DNA profiles gradually decreased. These results strongly suggest that calibration parameters should be introduced to correct the deviation in the APH at each STR locus during the analysis of mixed DNA samples.
Collapse
Affiliation(s)
- Na Hu
- Hebei Key Laboratory of Forensic Medicine, Department of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Bin Cong
- Hebei Key Laboratory of Forensic Medicine, Department of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Tao Gao
- Institute of Statistics, Renmin University of China, Beijing 100872, P.R. China
| | - Rong Hu
- Hebei Key Laboratory of Forensic Medicine, Department of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Yi Chen
- Institute of Statistics, Renmin University of China, Beijing 100872, P.R. China
| | - Hui Tang
- DNA Laboratory, Forensic Science Service of Beijing Public Security Bureau, Beijing 100085, P.R. China
| | - Luyan Xue
- DNA Laboratory, Forensic Science Service of Beijing Public Security Bureau, Beijing 100085, P.R. China
| | - Shujin Li
- Hebei Key Laboratory of Forensic Medicine, Department of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Chunling Ma
- Hebei Key Laboratory of Forensic Medicine, Department of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| |
Collapse
|
10
|
Timken MD, Klein SB, Buoncristiani MR. Stochastic sampling effects in STR typing: Implications for analysis and interpretation. Forensic Sci Int Genet 2014; 11:195-204. [PMID: 24799164 DOI: 10.1016/j.fsigen.2014.03.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 02/20/2014] [Accepted: 03/27/2014] [Indexed: 11/28/2022]
Abstract
The analysis and interpretation of forensic STR typing results can become more complicated when reduced template amounts are used for PCR amplification due to increased stochastic effects. These effects are typically observed as reduced heterozygous peak-height balance and increased frequency of undetected alleles (allelic "dropout"). To investigate the origins of these effects, a study was performed using the AmpFlSTR(®) Identifiler Plus(®) and MiniFiler(®) kits to amplify replicates from a dilution series of NIST Human DNA Quantitation Standard (SRM(®) 2372A). The resulting amplicons were resolved and detected on two different genetic analyzer platforms, the Applied Biosystems 3130xL and 3500 analyzers. Results from our study show that the four different STR/genetic analyzer combinations exhibited very similar peak-height ratio statistics when normalized for the amount of template DNA in the PCR. Peak-height ratio statistics were successfully modeled using the Poisson distribution to simulate pre-PCR stochastic sampling of the alleles, confirming earlier explanations that sampling is the primary source for peak-height imbalance in reduced template dilutions. In addition, template-based pre-PCR sampling simulations also successfully predicted allelic dropout frequencies, as modeled by logistic regression methods, for the low-template DNA dilutions. We discuss the possibility that an accurately quantified DNA template might be used to characterize the linear signal response for data collected using different STR kits or genetic analyzer platforms, so as to provide a standardized approach for comparing results obtained from different STR/CE combinations and to aid in validation studies.
Collapse
Affiliation(s)
- Mark D Timken
- State of California, Department of Justice, Jan Bashinski DNA Laboratory, 1001 W. Cutting Blvd., Richmond, CA 94804, USA.
| | - Sonja B Klein
- State of California, Department of Justice, Jan Bashinski DNA Laboratory, 1001 W. Cutting Blvd., Richmond, CA 94804, USA.
| | - Martin R Buoncristiani
- State of California, Department of Justice, Jan Bashinski DNA Laboratory, 1001 W. Cutting Blvd., Richmond, CA 94804, USA.
| |
Collapse
|
11
|
Murigneux V, Dufour AB, Lobry JR, Pène L. Analysis of Positive Control STR Experiments Reveals that Results Obtained for FGA, D3S1358, and D13S317 Condition the Success Rate of the Analysis of Routine Reference Samples. J Forensic Sci 2014; 59:1074-9. [DOI: 10.1111/1556-4029.12360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 01/21/2013] [Accepted: 02/09/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Valentine Murigneux
- Laboratoire de Police Scientifique de Lyon; Institut National de Police Scientifique; F-69134 Ecully France
| | - Anne-Béatrice Dufour
- Université de Lyon; F-69000 Lyon France
- Université Lyon 1; F-69622 Villeurbanne France
- Laboratoire de Biométrie et Biologie Evolutive; CNRS, UMR5558; F-69622 Villeurbanne France
| | - Jean R. Lobry
- Laboratoire de Police Scientifique de Lyon; Institut National de Police Scientifique; F-69134 Ecully France
| | - Laurent Pène
- Laboratoire de Police Scientifique de Lyon; Institut National de Police Scientifique; F-69134 Ecully France
| |
Collapse
|
12
|
Kelly H, Bright JA, Curran JM, Buckleton J. Modelling heterozygote balance in forensic DNA profiles. Forensic Sci Int Genet 2012; 6:729-34. [DOI: 10.1016/j.fsigen.2012.08.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Revised: 08/02/2012] [Accepted: 08/02/2012] [Indexed: 11/17/2022]
|
13
|
Andreassen R, Schregel J, Kopatz A, Tobiassen C, Knappskog PM, Hagen SB, Kleven O, Schneider M, Kojola I, Aspi J, Rykov A, Tirronen KF, Danilov PI, Eiken HG. A forensic DNA profiling system for Northern European brown bears (Ursus arctos). Forensic Sci Int Genet 2012; 6:798-809. [PMID: 22483764 DOI: 10.1016/j.fsigen.2012.03.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 02/10/2012] [Accepted: 03/11/2012] [Indexed: 11/29/2022]
Abstract
A set of 13 dinucleotide STR loci (G1A, G10B, G1D, G10L, MU05, MU09, MU10, MU15, MU23, MU26, MU50, MU51, MU59) were selected as candidate markers for a DNA forensic profiling system for Northern European brown bear (Ursus arctos). We present results from validation of the markers with respect to their sensitivity, species specificity and performance (precision, heterozygote balance and stutter ratios). All STRs were amplified with 0.6ng template input, and there were no false bear genotypes in the cross-species amplification tests. The validation experiments showed that stutter ratios and heterozygote balance was more pronounced than in the tetranucleotide loci used in human forensics. The elevated ratios of stutter and heterozygote balance at the loci validated indicate that these dinucleotide STRs are not well suited for interpretation of individual genotypes in mixtures. Based on the results from the experimental validations we discuss the challenges related to genotyping dinucleotide STRs in single source samples. Sequence studies of common alleles showed that, in general, the size variation of alleles corresponded with the variation in number of repeats. The samples characterized by sequence analysis may serve as standard DNA samples for inter laboratory calibration. A total of 479 individuals from eight Northern European brown bear populations were analyzed in the 13 candidate STRs. Locus MU26 was excluded as a putative forensic marker after revealing large deviations from expected heterozygosity likely to be caused by null-alleles at this locus. The remaining STRs did not reveal significant deviations from Hardy-Weinberg equilibrium expectations except for loci G10B and MU10 that showed significant deviations in one population each, respectively. There were 9 pairwise locus comparisons that showed significant deviation from linkage equilibrium in one or two out of the eight populations. Substantial genetic differentiation was detected in some of the pairwise population comparisons and the average estimate of population substructure (F(ST)) was 0.09. The average estimate of inbreeding (F(IS)) was 0.005. Accounting for population substructure and inbreeding the total average probability of identity in each of the eight populations was lower than 1.1×10(-9) and the total average probability of sibling identity was lower than 1.3×10(-4). The magnitude of these measurements indicates that if applying these twelve STRs in a DNA profiling system this would provide individual specific evidence.
Collapse
Affiliation(s)
- R Andreassen
- Faculty of Health Sciences, Oslo and Akershus University College, Oslo, Norway.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|