1
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Liu YY, Cheng K, Just R, Enke S, Bright JA. Sequencing-induced artefacts in NGS STR data. Forensic Sci Int Genet 2024; 72:103086. [PMID: 38897164 DOI: 10.1016/j.fsigen.2024.103086] [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: 01/29/2024] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024]
Abstract
Significant progress has been made in recent years in the development of techniques for Next Generation Sequencing (NGS), or Massively Parallel Sequencing (MPS), of forensically relevant short tandem repeat (STR) loci. However, as these technologies are investigated and adopted by forensic laboratories, new challenges unfold that require further scrutiny. In the analysis of DNA profiles generated using the MiSeq FGx sequencing system, we have observed noise sequences with relatively high readcounts that are challenging to distinguish from genuine alleles. These high read count noise sequences appear as allele sequences with one or a few substituted bases compared to a known allele sequence within the profile. An examination of ForenSeq DNA Signature Prep Kit STR noise sequences revealed that the substituted base of a parent allele can align to the same position on the sequence across noise sequences. This suggests that these substitution events occur at specific positions within the amplicon, resulting in multiple noise reads with substitutions at the same position. Mapping of the noise events onto the original raw read positions revealed a high number of events, or "noise spikes", occurring at specific positions within a given sequencing run. These noise spikes affected reads across the entire run, agnostic of locus or sample, while the position, occurrence, and amplitude of the spikes differed across runs. The majority of noise sequences with high read counts in a DNA profile were generated from base changes at these spike positions, and could be classified as "noise spike artefacts". In this paper we present evidence of the noise spike artefacts and their genesis during the sequencing process in the sequencing-by-synthesis (SBS) cycles, as well as the methods developed to detect them. The information and methods will assist laboratories with detecting noise spikes in MiSeq FGx sequencing runs, differentiating authentic allele sequences from noise spike artefacts, and developing protocols for analyst review and handling of MiSeq FGx data.
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Affiliation(s)
- Yao-Yuan Liu
- ESR Limited, Private Bag 92021, Auckland, New Zealand.
| | - Kevin Cheng
- ESR Limited, Private Bag 92021, Auckland, New Zealand
| | - Rebecca Just
- National Bioforensic Analysis Center, National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD, United States
| | - Sana Enke
- National Bioforensic Analysis Center, National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD, United States
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2
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Grgicak CM, Bhembe Q, Slooten K, Sheth NC, Duffy KR, Lun DS. Single-cell investigative genetics: Single-cell data produces genotype distributions concentrated at the true genotype across all mixture complexities. Forensic Sci Int Genet 2024; 69:103000. [PMID: 38199167 DOI: 10.1016/j.fsigen.2023.103000] [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: 08/21/2023] [Revised: 11/07/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
In the absence of a suspect the forensic aim is investigative, and the focus is one of discerning what genotypes best explain the evidence. In traditional systems, the list of candidate genotypes may become vast if the sample contains DNA from many donors or the information from a minor contributor is swamped by that of major contributors, leading to lower evidential value for a true donor's contribution and, as a result, possibly overlooked or inefficient investigative leads. Recent developments in single-cell analysis offer a way forward, by producing data capable of discriminating genotypes. This is accomplished by first clustering single-cell data by similarity without reference to a known genotype. With good clustering it is reasonable to assume that the scEPGs in a cluster are of a single contributor. With that assumption we determine the probability of a cluster's content given each possible genotype at each locus, which is then used to determine the posterior probability mass distribution for all genotypes by application of Bayes' rule. A decision criterion is then applied such that the sum of the ranked probabilities of all genotypes falling in the set is at least 1-α. This is the credible genotype set and is used to inform database search criteria. Within this work we demonstrate the salience of single-cell analysis by performance testing a set of 630 previously constructed admixtures containing up to 5 donors of balanced and unbalanced contributions. We use scEPGs that were generated by isolating single cells, employing a direct-to-PCR extraction treatment, amplifying STRs that are compliant with existing national databases and applying post-PCR treatments that elicit a detection limit of one DNA copy. We determined that, for these test data, 99.3% of the true genotypes are included in the 99.8% credible set, regardless of the number of donors that comprised the mixture. We also determined that the most probable genotype was the true genotype for 97% of the loci when the number of cells in a cluster was at least two. Since efficient investigative leads will be borne by posterior mass distributions that are narrow and concentrated at the true genotype, we report that, for this test set, 47,900 (86%) loci returned only one credible genotype and of these 47,551 (99%) were the true genotype. When determining the LR for true contributors, 91% of the clusters rendered LR>1018, showing the potential of single-cell data to positively affect investigative reporting.
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Affiliation(s)
- Catherine M Grgicak
- Department of Chemistry, Rutgers University, Camden, NJ 08102, USA; Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; Program in Biomedical Forensic Sciences, Boston University, Boston, MA 02118, USA.
| | - Qhawe Bhembe
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA
| | - Klaas Slooten
- Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, the Netherlands; VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, the Netherlands
| | - Nidhi C Sheth
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA
| | - Ken R Duffy
- Department of Mathematics, Northeastern University, Boston, MA 02115, USA; Department of Electrical and Computer Engineering, Northeastern University, Boston, MA 02115, USA; Hamilton Institute, Maynooth University, Ireland
| | - Desmond S Lun
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; Department of Computer Science, Rutgers University, Camden, NJ 08102, USA
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3
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Dierig L, Kunz SN, Wiegand P. Comparison of massively parallel sequencing to capillary electrophoresis for short tandem repeat genotyping of trace DNA. Electrophoresis 2024; 45:451-462. [PMID: 38085164 DOI: 10.1002/elps.202300145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/08/2023] [Accepted: 10/23/2023] [Indexed: 03/20/2024]
Abstract
In forensic genetics, massively parallel sequencing (MPS) offers several advantages over the current golden standard, capillary electrophoresis (CE): additional sequence information, shorter amplicon lengths, and the simultaneous analysis of many markers. These benefits result in a reduced number of reactions necessary while improving the amount of data obtained, thereby conserving valuable sample extracts. This proves particularly advantageous for the analysis of trace DNA. This study assessed the suitability of MPS for short tandem repeat (STR) typing of low template samples compared with results obtained through CE. The MPS genotypes showed higher concordance to reference genotypes, with donor alleles being more frequently assigned to be the major contributor, meeting the requirements for database entry. However, the MPS workflow is more time-consuming and associated with higher costs.
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Affiliation(s)
- Lisa Dierig
- Institute of Legal Medicine, Ulm University, Ulm, Germany
| | | | - Peter Wiegand
- Institute of Legal Medicine, Ulm University, Ulm, Germany
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4
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Inokuchi S, Nakanishi H, Takada A, Saito K. Effect existence of aging on stutter ratio evaluated via Bayesian inference. Forensic Sci Int Genet 2023; 67:102933. [PMID: 37722181 DOI: 10.1016/j.fsigen.2023.102933] [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: 12/19/2022] [Revised: 07/31/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023]
Abstract
The stochastic behavior of the stutter ratio (SR) in capillary electrophoresis-based DNA typing is currently described and predicted using statistical models in forensic genetics. Clarifying this behavior can help obtain more objective and robust evidence to the court in terms of mixture interpretation. This study aimed to investigate the effect existence of aging on SR via a Bayesian framework. Nail scrapings and clippings were collected from 68 healthy individuals with informed consent. Samples were classified by age-class: young group (0-16 years; n = 36) and older-adult group (>61 years; n = 32). Then, they were compared in terms of their SRs for each simple repeat locus included in GlobalFiler Kit. Bayesian modeling was performed with lognormal distribution model, which implemented multiple linear regression, allele and age-class as explanatory variables. For all simple repeat loci, the median of the posterior distribution of the age-class parameter was a positive value. For CSF1PO and D7S820, the 95% credible interval of the posterior distribution did not include 0. Our data suggested that aging slightly increases the SR. These findings might help elucidate the stochastic behavior of SR.
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Affiliation(s)
- Shota Inokuchi
- Department of Forensic Medicine, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, Japan; Forensic Science Laboratory, Tokyo Metropolitan Police Department, 3-35-21 Shakujiidai, Nerima-ku, Tokyo, Japan.
| | - Hiroaki Nakanishi
- Department of Forensic Medicine, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Aya Takada
- Department of Forensic Medicine, Saitama Medical University, 38 Moroyamamachimorohongo, Saitama, Japan
| | - Kazuyuki Saito
- Department of Forensic Medicine, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, Japan
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5
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Chen YH, Connelly JP, Florian C, Cui X, Pruett-Miller SM. Short tandem repeat profiling via next-generation sequencing for cell line authentication. Dis Model Mech 2023; 16:dmm050150. [PMID: 37712227 PMCID: PMC10618599 DOI: 10.1242/dmm.050150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
Cell lines are indispensable models for modern biomedical research. A large part of their usefulness derives from the ability of a cell line to proliferate over multiple passages (often indefinitely), allowing multiple experiments to be performed. However, over time, cell line identity and purity can be compromised by human errors. Cross-contamination from other cell lines and complete misidentification are both possible. Routine cell line authentication is a necessary preventive measure and has become a requirement for many funding applications and publications. Short tandem repeat (STR) profiling is the most common method for cell line authentication and is usually carried out using standard polymerase chain reaction-capillary electrophoresis analysis (STR-CE). Here, we evaluated next-generation sequencing (NGS)-based STR profiling of human and mouse cell lines at 18 and 15 loci, respectively, in a high-throughput format. Using the Python program STRight, we demonstrate that NGS-based analysis (STR-NGS) is superior to standard STR-CE in terms of the ability to report the sequence context of repeat motifs, sensitivity and flexible multiplexing capability. STR-NGS is thus a valuable alternative for cell line authentication.
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Affiliation(s)
- Yi-Hsien Chen
- Genome Engineering & Stem Cell Center (GESC@MGI), Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Jon P. Connelly
- Center for Advanced Genome Engineering (CAGE), Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Colin Florian
- Genome Engineering & Stem Cell Center (GESC@MGI), Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Xiaoxia Cui
- Genome Engineering & Stem Cell Center (GESC@MGI), Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Shondra M. Pruett-Miller
- Center for Advanced Genome Engineering (CAGE), Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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6
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Using unique molecular identifiers to improve allele calling in low-template mixtures. Forensic Sci Int Genet 2023; 63:102807. [PMID: 36462297 DOI: 10.1016/j.fsigen.2022.102807] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/20/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022]
Abstract
PCR artifacts are an ever-present challenge in sequencing applications. These artifacts can seriously limit the analysis and interpretation of low-template samples and mixtures, especially with respect to a minor contributor. In medicine, molecular barcoding techniques have been employed to decrease the impact of PCR error and to allow the examination of low-abundance somatic variation. In principle, it should be possible to apply the same techniques to the forensic analysis of mixtures. To that end, several short tandem repeat loci were selected for targeted sequencing, and a bioinformatic pipeline for analyzing the sequence data was developed. The pipeline notes the relevant unique molecular identifiers (UMIs) attached to each read and, using machine learning, filters the noise products out of the set of potential alleles. To evaluate this pipeline, DNA from pairs of individuals were mixed at different ratios (1-1, 1-9) and sequenced with different starting amounts of DNA (10, 1 and 0.1 ng). Naïvely using the information in the molecular barcodes led to increased performance, with the machine learning resulting in an additional benefit. In concrete terms, using the UMI data results in less noise for a given amount of drop out. For instance, if thresholds are selected that filter out a quarter of the true alleles, using read counts accepts 2381 noise alleles and using raw UMI counts accepts 1726 noise alleles, while the machine learning approach only accepts 307.
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7
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Cheng K, Bright JA, Kelly H, Liu YY, Lin MH, Kruijver M, Taylor D, Buckleton J. Developmental validation of STRmix™ NGS, a probabilistic genotyping tool for the interpretation of autosomal STRs from forensic profiles generated using NGS. Forensic Sci Int Genet 2023; 62:102804. [PMID: 36370677 DOI: 10.1016/j.fsigen.2022.102804] [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: 08/29/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022]
Abstract
We describe the developmental validation of the probabilistic genotyping software - STRmix™ NGS - developed for the interpretation of forensic DNA profiles containing autosomal STRs generated using next generation sequencing (NGS) also known as massively parallel sequencing (MPS) technologies. Developmental validation was carried out in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) Guidelines for the Validation of Probabilistic Genotyping Systems and the International Society for Forensic Genetics (ISFG) recommendations and included sensitivity and specificity testing, accuracy, precision, and the interpretation of case-types samples. The results of developmental validation demonstrate the appropriateness of the software for the interpretation of profiles developed using NGS technology.
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Affiliation(s)
- Kevin Cheng
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand.
| | - Jo-Anne Bright
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
| | - Hannah Kelly
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
| | - Yao-Yuan Liu
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
| | - Meng-Han Lin
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
| | - Maarten Kruijver
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
| | - Duncan Taylor
- Forensic Science SA, GPO Box 2790, Adelaide, SA 5001, Australia
| | - John Buckleton
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
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8
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Crysup B, Woerner AE. A genotype likelihood function for DNA mixtures. Forensic Sci Int Genet 2022; 61:102776. [PMID: 36152508 DOI: 10.1016/j.fsigen.2022.102776] [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: 06/12/2022] [Revised: 08/10/2022] [Accepted: 09/14/2022] [Indexed: 11/04/2022]
Abstract
The recent advent of genetic genealogy has brought about a renewed interest in genome-scale forensic analyses, of which kinship estimation is a critical component. Most genomic kinship estimators consider SNPs (single nucleotide polymorphisms), often leveraging the co-inheritance of shared alleles to inform their analyses. While current estimators cannot directly evaluate mixed samples, there exist well-established SNP-based kinship estimators tailored to considering challenged samples, including low-pass whole genome sequencing. As an example, several studies have shown remarkable success in imputing genotype posterior probabilities in low template samples when linked sites are considered. Critical to these approaches is the ability to account for genotype uncertainty; the lack of an expression for a genotype likelihood in imbalanced mixtures has prevented direct application. This work develops such an expression. The formulation is fully compatible with genotype imputation software, suggesting a genomic pipeline that estimates genotype likelihoods, performs imputation, and then estimates kinship when the sample is a mixture. Further, when framed as an imbalanced mixture, the problem of mixture deconvolution is reducible to the problem of genotyping mixed samples. Herein, the ability to genotype two-person mixtures is assessed through example and in silico settings. While certain mixture scenarios and classes of sites are inherently inseparable, simulations of read depths between 60 and 190 appear to produce likelihoods of sufficient magnitude to deconvolve two-person mixtures whenever the mixture fraction is moderately imbalanced. The described approach and results suggest a path forward for estimating the kinship coefficient (and similar inferences on relatedness) when the sample is a mixture.
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Affiliation(s)
- Benjamin Crysup
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - August E Woerner
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science, USA.
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9
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A New String Edit Distance and Applications. ALGORITHMS 2022. [DOI: 10.3390/a15070242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only single-character edits. In forensic applications polymorphic genetic markers such as short tandem repeats (STRs) are used. At these repetitive motifs the DNA copying errors consist of more than just single base differences. More often the phenomenon of “stutter” is observed, where the number of repeated units differs (by whole units) from the template. To adapt the Levenshtein distance to be suitable for forensic applications where DNA sequence similarity is of interest, a generalized string edit distance is defined that accommodates the addition or deletion of whole motifs in addition to single-nucleotide edits. A dynamic programming implementation is developed for computing this distance between sequences. The novelty of this algorithm is in handling the complex interactions that arise between multiple- and single-character edits. Forensic examples illustrate the purpose and use of the Restricted Forensic Levenshtein (RFL) distance measure, but applications extend to sequence alignment and string similarity in other biological areas, as well as dynamic programming algorithms more broadly.
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10
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Perry J, Munshi T, Haizel T, Iyavoo S. Validation of reduced volume VeriFiler™ Express PCR Amplification Kit for buccal swab samples extracted using Prep-n-Go™ Buffer. J Forensic Sci 2022; 67:1971-1978. [PMID: 35735089 PMCID: PMC9546378 DOI: 10.1111/1556-4029.15084] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022]
Abstract
The efficiency of reduced volume PCR amplification was studied using the VeriFiler™ Express PCR Amplification Kit. Full (25 μL) and reduced (5 μL) volumes were tested in parallel to identify any differences in template DNA sensitivity and other electropherogram parameters. Both volumes produced full DNA profiles down to 0.08 ng/μL DNA concentration at 26 PCR cycles; however, reduced volume produced higher peak heights due to increased signal intensities. Significant difference (p‐value ≤ 0.05) in heterozygote peak height ratios was observed between both volumes, where the reduced volume threshold was lowered to 0.6 to accommodate all data points. However, no significant difference (p‐value > 0.05) was identified in the stutter ratios between both volumes. The analytical threshold for reduced volume was also determined to be 150 RFU with the presence of template DNA in PCR amplification. When the optimized reduced volume parameters were tested on DNA extracted from buccal swab samples using Prep‐n‐Go™ Buffer, good quality DNA profiles were produced. Overall, the reduced volume not only showed better results compared to the full volume, but also enable more samples to be processed with a PCR amplification kit, thus reduced the cost.
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Affiliation(s)
- Jessica Perry
- School of Chemistry, College of Science, University of Lincoln, Lincolnshire, UK
| | - Tasnim Munshi
- School of Chemistry, College of Science, University of Lincoln, Lincolnshire, UK
| | - Thomas Haizel
- IDna Genetics Limited, Scottow Enterprise Park, Norfolk, UK
| | - Sasitaran Iyavoo
- School of Chemistry, College of Science, University of Lincoln, Lincolnshire, UK.,IDna Genetics Limited, Scottow Enterprise Park, Norfolk, UK
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11
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Agudo MM, Aanes H, Roseth A, Albert M, Gill P, Bleka Ø. A comprehensive characterization of MPS-STR stutter artefacts. Forensic Sci Int Genet 2022; 60:102728. [DOI: 10.1016/j.fsigen.2022.102728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/03/2022] [Accepted: 05/24/2022] [Indexed: 11/04/2022]
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12
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Luttman AM, Komine M, Thaiwong T, Carpenter T, Ewart SL, Kiupel M, Langohr IM, Venta PJ. Development of a 17-Plex of Penta- and Tetra-Nucleotide Microsatellites for DNA Profiling and Paternity Testing in Horses. Front Vet Sci 2022; 9:861623. [PMID: 35464354 PMCID: PMC9021955 DOI: 10.3389/fvets.2022.861623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Tetranucleotide and pentanucleotide short tandem repeat (hereafter termed tetraSTR and pentaSTR) polymorphisms have properties that make them desirable for DNA profiling and paternity testing. However, certain species, such as the horse, have far fewer tetraSTRs than other species and for this reason dinucleotide STRs (diSTRs) have become the standard for DNA profiling in horses, despite being less desirable for technical reasons. During our testing of a series of candidate genes as potentially underlying a heritable condition characterized by megaesophagus in the Friesian horse breed, we found that good tetraSTRs do exist in horses but, as expected, at a much lower frequency than in other species, e.g., dogs and humans. Using a series of efficient methods developed in our laboratory for the production of multiplexed tetraSTRs in other species, we identified a set of tetra- and pentaSTRs that we developed into a 17-plex panel for the horse, plus a sex-identifying marker near the amelogenin gene. These markers were tested in 128 horses representing 16 breeds as well as crossbred horses, and we found that these markers have useful genetic variability. Average observed heterozygosities (Ho) ranged from 0.53 to 0.89 for the individual markers (0.66 average Ho for all markers), and 0.62-0.82 for expected heterozygosity (He) within breeds (0.72 average He for all markers). The probability of identity (PI) within breeds for which 10 or more samples were available was at least 1.1 x 10−11, and the PI among siblings (PIsib) was 1.5 x 10−5. Stutter was ≤ 11% (average stutter for all markers combined was 6.9%) compared to the more than 30% typically seen with diSTRs. We predict that it will be possible to develop accurate allelic ladders for this multiplex panel that will make cross-laboratory comparisons easier and will also improve DNA profiling accuracy. Although we were only able to exclude candidate genes for Friesian horse megaesophagus with no unexcluded genes that are possibly causative at this point in time, the study helped us to refine the methods used to develop better tetraSTR multiplexed panels for species such as the horse that have a low frequency of tetraSTRs.
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Affiliation(s)
- Andrea M. Luttman
- Microbiology and Molecular Genetics, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- Genetics and Genomic Sciences, Michigan State University, East Lansing, MI, United States
| | - Misa Komine
- Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Tuddow Thaiwong
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- *Correspondence: Tuddow Thaiwong
| | - Tyler Carpenter
- Microbiology and Molecular Genetics, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University College of Human Medicine, Grand Rapids, MI, United States
| | - Susan L. Ewart
- Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Matti Kiupel
- Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Ingeborg M. Langohr
- Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Patrick J. Venta
- Microbiology and Molecular Genetics, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
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13
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Assessing non-LUS stutter in DNA sequence data. Forensic Sci Int Genet 2022; 59:102706. [DOI: 10.1016/j.fsigen.2022.102706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/16/2022] [Accepted: 04/11/2022] [Indexed: 11/23/2022]
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14
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Xia R, Tao R, Qu Y, Zhang X, Yu H, Yuan C, Zhang S, Li C. Development and Validation of a Novel and Fast Detection Method for Cannabis sativa: A 19-Plex Short Tandem Repeat Typing System. FRONTIERS IN PLANT SCIENCE 2022; 13:837945. [PMID: 35295633 PMCID: PMC8918947 DOI: 10.3389/fpls.2022.837945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
In recent years, influenced by the legalization of Cannabis sativa in some countries and regions, the number of people who smoke or abuse C. sativa has continuously grown, cases of transnational C. sativa trafficking have also been increasing. Therefore, fast and accurate identification and source tracking of C. sativa have become urgent social needs. In this study, we developed a new 19-plex short tandem repeats (STRs) typing system for C. sativa, which includes 15 autosomal STRs (D02-CANN1, C11-CANN1, 4910, B01-CANN1, E07-CANN1, 9269, B05-CANN1, H06-CANN2, 5159, nH09, CS1, ANUCS 305, 3735, and ANUCS 302 and 9043), two X-chromosome STRs (ANUCS 501 and 1528), one sex-determining marker (DM016, on Y-chromosome), and a quality control marker (DM029, on autosome). The whole polymerase chain reaction (PCR) process could finish within 1 h, making the system suitable for fast detection. The PCR products were detected and separated with an Applied Biosystems 3500XL Genetic Analyser. Developmental validation studies indicated that the 19-plex typing system was accurate, reliable and sensitive, which could also deconvolute mixed C. sativa samples. Specifically, the sensitivity study showed that a full genotyping profile was obtainable with as low as 125 pg of C. sativa DNA. The species specificity study demonstrated that this multiplex has no cross-reactivity with common non C. sativa DNA. In the population study, a total of 162 alleles at 15 autosomal STRs and 14 alleles at two X-chromosome STRs were detected among 85 samples. The efficiency parameters, including the total discrimination power (TDP) and the combined power of exclusion (CPE) of the system, were calculated to exceed 0.999 999 999 999 988 and 0.998 455 889 684 078, respectively, further proving that the system could meet the needs of individual identification. To the extent of the known studies, this is the first study that included the C. sativa sex-determining marker. In conclusion, the developed new 19-plex STR typing system can successfully achieve the purposes of species identification, gender determination, and individual identification, which could be a powerful tool in tracing trade routes of particular drug syndicates or dealers or in linking certain C. sativa to a crime scene.
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Affiliation(s)
- Ruocheng Xia
- Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Ruiyang Tao
- Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Yiling Qu
- Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Xiaochun Zhang
- Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Huan Yu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, China
| | - Chunyan Yuan
- Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Suhua Zhang
- Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Chengtao Li
- Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
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15
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Holland MM, Tiedge TM, Bender AJ, Gaston-Sanchez SA, McElhoe JA. MaSTR™: an effective probabilistic genotyping tool for interpretation of STR mixtures associated with differentially degraded DNA. Int J Legal Med 2022; 136:433-446. [DOI: 10.1007/s00414-021-02771-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022]
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16
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Hölzl-Müller P, Bodner M, Berger B, Parson W. Exploring STR sequencing for forensic DNA intelligence databasing using the Austrian National DNA Database as an example. Int J Legal Med 2021; 135:2235-2246. [PMID: 34436655 PMCID: PMC8523457 DOI: 10.1007/s00414-021-02685-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/12/2021] [Indexed: 11/29/2022]
Abstract
Here, we present the results from a population study that evaluated the performance of massively parallel sequencing (MPS) of short tandem repeats (STRs) with a particular focus on DNA intelligence databasing purposes. To meet this objective, 247 randomly selected reference samples, earlier being processed with conventional capillary electrophoretic (CE) STR sizing from the Austrian National DNA Database, were reanalyzed with the PowerSeq 46Y kit (Promega). This sample set provides MPS-based population data valid for the Austrian population to increase the body of sequence-based STR variation. The study addressed forensically relevant parameters, such as concordance and backward compatibility to extant amplicon-based genotypes, sequence-based stutter ratios, and relative marker performance. Of the 22 autosomal STR loci included in the PowerSeq 46GY panel, 99.98% of the allele calls were concordant between MPS and CE. Moreover, 25 new sequence variants from 15 markers were found in the Austrian dataset that are yet undescribed in the STRSeq online catalogue and were submitted for inclusion. Despite the high degree of concordance between MPS and CE derived genotypes, our results demonstrate the need for a harmonized allele nomenclature system that is equally applicable to both technologies, but at the same time can take advantage of the increased information content of MPS. This appears to be particularly important with regard to database applications in order to prevent false exclusions due to varying allele naming based on different analysis platforms and ensures backward compatibility.
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Affiliation(s)
- Petra Hölzl-Müller
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstrasse 44, 6020, Innsbruck, Austria
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstrasse 44, 6020, Innsbruck, Austria
| | - Burkhard Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstrasse 44, 6020, Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstrasse 44, 6020, Innsbruck, Austria.
- Forensic Science Program, The Pennsylvania State University, State College, PA, USA.
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17
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Huang Y, Chen X, Li X, Shu P, Wang H, Hou T, Wang Y, Song F, Zhang J. A proof-of-principle study on implementing polymerase chain displacement reaction (PCDR) to improve forensic low-template DNA analysis. Forensic Sci Int Genet 2021; 56:102609. [PMID: 34717077 DOI: 10.1016/j.fsigen.2021.102609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 10/06/2021] [Accepted: 10/18/2021] [Indexed: 11/26/2022]
Abstract
Polymerase chain reaction (PCR) plays an important role in forensic DNA analysis. However, the amplification of low-template DNA (LTDNA) samples usually encounters unsatisfactory results for the limited efficiency of PCR, which would interfere with the subsequent profile interpretation. Polymerase chain displacement reaction (PCDR) is a highly-efficient technique characterized by combining PCR and strand displacement reaction into a single PCDR cycle. This study explored the feasibility of PCDR for improving forensic LTDNA analysis. STR markers commonly used in forensic genetics were subjected to PCDR amplification and capillary electrophoresis detection. The results of singleplex reactions indicated that PCDR surpassed original PCR in efficiency for STR amplification. The average peak height of alleles in PCDR profiles was linearly correlated to the number of outer primers adopted for initiating the strand displacement process. Further, we assessed the multiplexing potential of PCDR by incorporating 17 STRs included in the expanded CODIS core loci and Amelogenin gene into a multiplex PCDR system. For pristine DNA templates ranged from 200 pg to 12.5 pg, the multiplex PCDR system consistently exhibited higher allele peak height as well as less allele dropout compared to the multiplex PCR references. Meanwhile, a significant reduction of stutter ratio was extensively observed in PCDR profiles. We also tested mock casework samples to verify the practical ability of multiplex PCDR for LTDNA detection. With DNA input varying from 48.1 pg to 6.6 pg, the multiplex PCDR system consistently obtained more allelic information than multiplex PCR methods. Our data collectively suggested that it is feasible to apply PCDR in forensic LTDNA analysis.
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Affiliation(s)
- Yuguo Huang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xiaogang Chen
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xi Li
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Panyin Shu
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Haoyu Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Tingyun Hou
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuting Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Feng Song
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
| | - Ji Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
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18
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Gill P, Benschop C, Buckleton J, Bleka Ø, Taylor D. A Review of Probabilistic Genotyping Systems: EuroForMix, DNAStatistX and STRmix™. Genes (Basel) 2021; 12:1559. [PMID: 34680954 PMCID: PMC8535381 DOI: 10.3390/genes12101559] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 11/24/2022] Open
Abstract
Probabilistic genotyping has become widespread. EuroForMix and DNAStatistX are both based upon maximum likelihood estimation using a γ model, whereas STRmix™ is a Bayesian approach that specifies prior distributions on the unknown model parameters. A general overview is provided of the historical development of probabilistic genotyping. Some general principles of interpretation are described, including: the application to investigative vs. evaluative reporting; detection of contamination events; inter and intra laboratory studies; numbers of contributors; proposition setting and validation of software and its performance. This is followed by details of the evolution, utility, practice and adoption of the software discussed.
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Affiliation(s)
- Peter Gill
- Forensic Genetics Research Group, Department of Forensic Sciences, Oslo University Hospital, 0372 Oslo, Norway;
- Department of Forensic Medicine, Institute of Clinical Medicine, University of Oslo, 0315 Oslo, Norway
| | - Corina Benschop
- Division of Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, The Netherlands;
| | - John Buckleton
- Department of Statistics, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand;
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
| | - Øyvind Bleka
- Forensic Genetics Research Group, Department of Forensic Sciences, Oslo University Hospital, 0372 Oslo, Norway;
| | - Duncan Taylor
- Forensic Science SA, GPO Box 2790, Adelaide, SA 5001, Australia;
- School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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19
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Ralf A, Zandstra D, Weiler N, van Ijcken WFJ, Sijen T, Kayser M. RMplex: An efficient method for analyzing 30 Y-STRs with high mutation rates. Forensic Sci Int Genet 2021; 55:102595. [PMID: 34543845 DOI: 10.1016/j.fsigen.2021.102595] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Y-chromosomal short tandem repeats (Y-STRs) with high mutation rates are recognized as valuable genetic markers for differentiating paternally related men, who typically cannot be separated with standard Y-STRs, and were shown to provide paternal lineage differentiation on a higher resolution level than standard Y-STRs. Both features make Y-STRs with high mutation rates relevant in criminal casework, particularly in sexual assault cases involving highly unbalanced male-female DNA mixtures that often fail autosomal forensic STR profiling for the male donor. Previously, the number of known Y-STRs with mutation rates higher than 10-2 per locus per generation termed rapidly mutating Y-STRs (RM Y-STRs) was limited to 13, which has recently been overcome by the discovery and characterization of 12 additional RM Y-STRs. Here, we present the development and validation of RMplex, an efficient genotyping system for analyzing 30 Y-STRs with high mutation rates, including all currently known RM Y-STRs, using multiplex PCR with capillary electrophoresis (CE) or massively parallel sequencing (MPS), overall targeting a total of 44 male-specific loci. If previously unavailable, repeat number assignations were provided based on newly generated MPS data. Validation tests based on the CE method demonstrated that the results were both repeatable and reproducible, full profiles were achieved with minimal input DNA of 250 pg for RMplex 1 and 100 pg for RMplex 2, and in the presence of inhibitors, or with a surplus of female DNA, the assays performed reasonably well. Application of RMplex to differentiate between paternally related men was exemplified in 32 males belonging to five different paternal pedigrees. Given further successful forensic validation testing, we envision the future application of RMplex in criminal cases where it is suspected, or cannot be excluded, that the crime scene trace originated from a male relatives of the suspect who is highlighted with standard Y-STR matching. Other applications of RMplex are in criminal cases without known suspects to differentiate between male relatives highlighted in familial searching based on standard Y-STR matching.
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Affiliation(s)
- Arwin Ralf
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Dion Zandstra
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Natalie Weiler
- Division of Biological Traces, Netherlands Forensic Institute, The Hague, the Netherlands
| | - Wilfred F J van Ijcken
- Center for Biomics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Titia Sijen
- Division of Biological Traces, Netherlands Forensic Institute, The Hague, the Netherlands; University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
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20
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Alaeddini R, Yang M, Puza B. Bayesian regression analysis of stutter in DNA mixtures. COMMUN STAT-THEOR M 2021. [DOI: 10.1080/03610926.2019.1710760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | - Mo Yang
- School of Finance, Dongbei University of Finance and Economics, Dalian, China
| | - Borek Puza
- Research School of Finance, Actuarial Studies & Statistics, The Australian National University, Canberra, ACT, Australia
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21
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Yang Q, Yu H, Qu Y, Zhang X, Xia R, Wang Z, Tan R, Xiong L, Xi S, Wu J, Gao Y, Zhang S, Li C. Developmental validation of the novel six-dye Goldeneye TM DNA ID System 35InDel kit for forensic application. Forensic Sci Res 2021; 7:673-684. [PMID: 36817233 PMCID: PMC9930762 DOI: 10.1080/20961790.2021.1945723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Insertion/deletion polymorphisms (InDels) have been treated as a prospective and helpful genetic marker in the fields of forensic human identification, anthropology and population genetics for the past few years. In this study, we developed a six-dye multiplex typing system consisting of 34 autosomal InDels and Amelogenin for forensic application. The contained InDels were specifically selected for Chinese population with the MAF ≥ 0.25 in East Asia, which do not overlap with the markers of Investigator® DIPplex kit. The typing system was named as GoldeneyeTM DNA ID System 35InDel Kit, and a series of developmental validation studies including repeatability/reproducibility, concordance, accuracy, sensitivity, stability, species specificity and population genetics were conducted on this kit. We confirmed that the 35InDel kit is precise, sensitive, species specific and robust for forensic practice. Moreover, the 35InDel kit is capable of typing DNA extracted from forensic routine case-type samples as well as degraded samples and mixture samples. All markers are proved to be highly polymorphic with an average observed heterozygosity (He) of 0.4582. The combined power of discrimination (CPD) is 0.999 999 999 999 978 and the combined power of exclusion in duos (CPED) and trios (CPET) are 0.978 837 and 0.999573, respectively, which are higher than those of the Investigator® DIPplex kit. Thus, the GoldeneyeTM DNA ID System 35InDel kit is suitable for forensic human identification and could serve as a supplementary typing system for paternity testing. Supplemental data for this article is available online at https://doi.org/10.1080/20961790.2021.1945723 .
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Affiliation(s)
- Qi Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China,Department of Forensic Science, Medical School of Soochow University, Suzhou, China
| | - Huan Yu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China,Department of Forensic Science, Medical School of Soochow University, Suzhou, China
| | - Yiling Qu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China,Department of Forensic Science, Medical School of Soochow University, Suzhou, China
| | - Xiaochun Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China,Department of Forensic Science, Medical School of Soochow University, Suzhou, China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China,Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, China
| | - Ziwei Wang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China,Department of Forensic Science, Medical School of Soochow University, Suzhou, China
| | - Rui Tan
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China,Department of Forensic Science, Medical School of Soochow University, Suzhou, China
| | - Lei Xiong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China,School of Basic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Shihan Xi
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China,Clinical Medical School, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Jun Wu
- PEOPLESPOTINC, Beijing, China
| | - Yuzhen Gao
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China,CONTACT Suhua Zhang ; Chengtao Li
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China,Department of Forensic Science, Medical School of Soochow University, Suzhou, China
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22
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Jedrzejczak-Silicka M, Lepczynski A, Gołębiowski F, Dolata D, Dybus A. Application of PCR-HRM method for microsatellite polymorphism genotyping in the LDHA gene of pigeons (Columba livia). PLoS One 2021; 16:e0256065. [PMID: 34411134 PMCID: PMC8376019 DOI: 10.1371/journal.pone.0256065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 08/01/2021] [Indexed: 11/19/2022] Open
Abstract
High-resolution melting (HRM) is a post-PCR method that allows to discriminate genotypes based on fluorescence changes during the melting phase. HRM is used to detect mutations or polymorphisms (e.g. microsatellites, SNPs, indels). Here, the (TTTAT)3-5 microsatellite polymorphism within intron 6 of the LDHA gene in pigeons was analysed using the HRM method. Individuals (123 homing pigeons) were genotyped using conventional PCR. Birds were classified into groups based on genotype type and the results were tested by qPCR-HRM and verified using sequencing. Based on the evaluated protocol, five genotypes were identified that vary in the number of TTTAT repeat units (3/3, 4/4, 3/4, 4/5, and 5/5). Sequencing have confirmed the results obtained with qPCR-HRM and verified that HRM is a suitable method for identification of three-allele microsatellite polymorphisms. It can be concluded that the high-resolution melting (HRM) method can be effectively used for rapid (one-step) discrimination of the (TTTAT)3-5 microsatellite polymorphism in the pigeon’s LDHA gene.
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Affiliation(s)
- Magdalena Jedrzejczak-Silicka
- Faculty of Biotechnology and Animal Husbandry, Laboratory of Molecular Biology, West Pomeranian University of Technology, Szczecin, Poland
- * E-mail:
| | - Adam Lepczynski
- Department of Physiology, Cytobiology and Proteomics, West Pomeranian University of Technology, Szczecin, Poland
| | | | | | - Andrzej Dybus
- Faculty of Biotechnology and Animal Husbandry, Department of Genetics, West Pomeranian University of Technology, Szczecin, Poland
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23
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Shang S, Jiang R, Luo R, Jia S, Irwin DM, Wang Z, Zhang S. Development of a 19-plex short tandem repeat typing system for individual identification and parentage testing of horses (Equus caballus). Anim Genet 2021; 52:754-758. [PMID: 34268790 DOI: 10.1111/age.13119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 12/01/2022]
Abstract
Individual identification of horses for pedigree verification and registration is important for the sustainable development of the horse industry. Horse individual identification and parentage tests commonly use the 17 short tandem repeats (STRs) recommended by the International Society for Animal Genetics (ISAG) and the locus LEX33. While many multiplex STR typing systems have been established for the horse, a sex determining marker is usually absent, and none of them can simultaneously detect all 17 ISAG recommended loci and the locus LEX33. Here, we present a 19-plex STR typing system that contains the 17 ISAG recommend loci, the locus LEX33 and amelogenin as sex determining loci. The results of our sensitivity, species specificity, stutter analysis and population data analysis, indicate that this system is a specific, sensitive, and robust tool for the identification of individuals, parentage testing and genetic research in the horse.
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Affiliation(s)
- S Shang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - R Jiang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - R Luo
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - S Jia
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - D M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Z Wang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - S Zhang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
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24
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Low stutter ratio by SuperFi polymerase. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2021. [DOI: 10.1016/j.fsir.2021.100201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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25
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Lin MH, Lee SI, Zhang X, Russell L, Kelly H, Cheng K, Cooper S, Wivell R, Kerr Z, Morawitz J, Bright JA. Developmental validation of FaSTR™ DNA: Software for the analysis of forensic DNA profiles. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2021. [DOI: 10.1016/j.fsir.2021.100217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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26
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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).
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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
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27
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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] [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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Qu Y, Tao R, Yu H, Yang Q, Wang Z, Tan R, Zhang X, Xia R, Xiong L, Xi S, Wu J, Gao Y, Zhang S, Li C. Development and validation of a forensic six-dye multiplex assay with 29 STR loci. Electrophoresis 2021; 42:1419-1430. [PMID: 33864289 DOI: 10.1002/elps.202100019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/05/2021] [Accepted: 04/10/2021] [Indexed: 11/10/2022]
Abstract
This paper describes the development and validation of a novel 31-locus, six-dye STR multiplex system, which is designed to meet the needs of the rapidly growing Chinese forensic database. This new assay combines 20 extended-CODIS core loci (D3S1358, D5S818, TPOX, CSF1PO, TH01, vWA, D7S820, D21S11, D8S1179, D18S51, D16S539, D13S317, FGA, D1S1656, D2S441, D2S1338, D10S1248, D12S391, D19S433, and D22S1045), nine highly polymorphic loci in Chinese Han population (D3S3045, D6S1043, D6S477, D8S1132, D10S1435, D15S659, D19S253, Penta D, and Penta E), and two gender determining markers, amelogenin and Y-Indel, which could amplify DNA from extracts, as well as direct amplification from substrates. To demonstrate the suitability for forensic applications, this system was validated by precision and accuracy evaluation, concordance tests, case sample tests, sensitivity, species specificity, stability, stutter calculation, and DNA mixtures, according to the guidelines described by the Scientific Working Group on DNA Analysis Methods (SWGDAM) and regulations published by the China Ministry of Public Security. The validation results indicate the robustness and reliability of this new system, and it could be a potentially helpful tool for human identification and paternity testing in the Chinese population, as well as facilitating global forensic DNA data sharing.
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Affiliation(s)
- Yiling Qu
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - RuiYang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Huan Yu
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Qi Yang
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Ziwei Wang
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Rui Tan
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Xiaochun Zhang
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China.,Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, P. R. China
| | - Lei Xiong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China.,School of Basic Medicine, Inner Mongolia Medical University, Hohhot, P. R. China
| | - Shihan Xi
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China.,Clinical Medical School of Inner Mongolia University for the Nationalities, Tongliao, P. R. China
| | - Jun Wu
- PeopleSpot Inc., Beijing, P. R. China
| | - Yuzhen Gao
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Chengtao Li
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
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29
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Moura-Neto R, King JL, Mello I, Dias V, Crysup B, Woerner AE, Budowle B, Silva R. Evaluation of Promega PowerSeq™ Auto/Y systems prototype on an admixed sample of Rio de Janeiro, Brazil: Population data, sensitivity, stutter and mixture studies. Forensic Sci Int Genet 2021; 53:102516. [PMID: 33878618 DOI: 10.1016/j.fsigen.2021.102516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 03/06/2021] [Accepted: 03/29/2021] [Indexed: 02/01/2023]
Abstract
Forensic DNA typing typically relies on the length-based (LB) separation of PCR products containing short tandem repeat loci (STRs). Massively parallel sequencing (MPS) elucidates an additional level of STR motif and flanking region variation. Also, MPS enables simultaneous analysis of different marker-types - autosomal STRs, SNPs for lineage and identification purposes, reducing both the amount of sample used and the turn-around-time of analysis. Therefore, MPS methodologies are being considered as an additional tool in forensic genetic casework. The PowerSeq™ Auto/Y System (Promega Corp), a multiplex forensic kit for MPS, enables analysis of the 22 autosomal STR markers (plus Amelogenin) from the PowerPlex® Fusion 6C kit and 23 Y-STR markers from the PowerPlex® Y23 kit. Population data were generated from 140 individuals from an admixed sample from Rio de Janeiro, Brazil. All samples were processed according to the manufacturers' recommended protocols. Raw data (FastQ) were generated for each indexed sample and analyzed using STRait Razor v2s and PowerSeqv2.config file. The subsequent population data showed the largest increase in expected heterozygosity (23%), from LB to sequence-based (SB) analyses at the D5S818 locus. Unreported allele was found at the D21S11 locus. The random match probability across all loci decreased from 5.9 × 10-28 to 7.6 × 10-33. Sensitivity studies using 1, 0.25, 0.062 and 0.016 ng of DNA input were analyzed in triplicate. Full Y-STR profiles were detected in all samples, and no autosomal allele drop-out was observed with 62 pg of input DNA. For mixture studies, 1 ng of genomic DNA from a male and female sample at 1:1, 1:4, 1:9, 1:19 and 1:49 proportions were analyzed in triplicate. Clearly resolvable alleles (i.e., no stacking or shared alleles) were obtained at a 1:19 male to female contributor ratio. The minus one stutter (-1) increased with the longest uninterrupted stretch (LUS) allele size reads and according to simple or compound/complex repeats. The haplotype-specific stutter rates add more information for mixed samples interpretation. These data support the use of the PowerSeqTM Auto/Y systems prototype kit (22 autosomal STR loci, 23 Y-STR loci and Amelogenin) for forensic genetics applications.
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Affiliation(s)
- Rodrigo Moura-Neto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Isadora Mello
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Victor Dias
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Benjamin Crysup
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - August E Woerner
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Rosane Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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30
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Woerner AE, Mandape S, King JL, Muenzler M, Crysup B, Budowle B. Reducing noise and stutter in short tandem repeat loci with unique molecular identifiers. Forensic Sci Int Genet 2020; 51:102459. [PMID: 33429137 DOI: 10.1016/j.fsigen.2020.102459] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/28/2020] [Accepted: 12/21/2020] [Indexed: 12/24/2022]
Abstract
Unique molecular identifiers (UMIs) are a promising approach to contend with errors generated during PCR and massively parallel sequencing (MPS). With UMI technology, random molecular barcodes are ligated to template DNA molecules prior to PCR, allowing PCR and sequencing error to be tracked and corrected bioinformatically. UMIs have the potential to be particularly informative for the interpretation of short tandem repeats (STRs). Traditional MPS approaches may simply lead to the observation of alleles that are consistent with the hypotheses of stutter, while with UMIs stutter products bioinformatically may be re-associated with their parental alleles and subsequently removed. Herein, a bioinformatics pipeline named strumi is described that is designed for the analysis of STRs that are tagged with UMIs. Unlike other tools, strumi is an alignment-free machine learning driven algorithm that clusters individual MPS reads into UMI families, infers consensus super-reads that represent each family and provides an estimate the resulting haplotype's accuracy. Super-reads, in turn, approximate independent measurements not of the PCR products, but of the original template molecules, both in terms of quantity and sequence identity. Provisional assessments show that naïve threshold-based approaches generate super-reads that are accurate (∼97 % haplotype accuracy, compared to ∼78 % when UMIs are not used), and the application of a more nuanced machine learning approach increases the accuracy to ∼99.5 % depending on the level of certainty desired. With these features, UMIs may greatly simplify probabilistic genotyping systems and reduce uncertainty. However, the ability to interpret alleles at trace levels also permits the interpretation, characterization and quantification of contamination as well as somatic variation (including somatic stutter), which may present newfound challenges.
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Affiliation(s)
- August E Woerner
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.
| | - Sammed Mandape
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Melissa Muenzler
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Benjamin Crysup
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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31
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Lewis DH, Jarvis DE, Maughan PJ. SSRgenotyper: A simple sequence repeat genotyping application for whole-genome resequencing and reduced representational sequencing projects. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11402. [PMID: 33344093 PMCID: PMC7742204 DOI: 10.1002/aps3.11402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/13/2020] [Indexed: 05/13/2023]
Abstract
PREMISE Many programs can identify simple sequence repeat (SSR) motifs in genomic data. SSRgenotyper extends SSR identification to en masse genotyping from resequencing data for diversity panels and linkage mapping populations. METHODS AND RESULTS SSRgenotyper will find and genotype SSRs from SAM files and an SSR reference FASTA. Several outputs are possible, including a simple table with the SSR marker name, position, and SSR alleles, defined by the repeat number of the repeat motif. Specific output files include a GENEPOP-formatted file for downstream genetic diversity analyses and a traditional A, H, B mapping file output that is phased to the parents of the population for biparental linkage map construction. Linkage maps produced using SSRgenotyper genotypes were highly collinear with physical maps and correctly inferred known phylogenies. CONCLUSIONS SSRgenotyper provides an easy-to-use, accurate, and scalable SSR genotyping platform for whole-genome resequencing data. SSRgenotyper is freely available at https://github.com/dlewis27/SSRgenotyper.
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Affiliation(s)
- Daniel H. Lewis
- Department of Plant and Wildlife SciencesBrigham Young UniversityProvoUtah84058USA
| | - David E. Jarvis
- Department of Plant and Wildlife SciencesBrigham Young UniversityProvoUtah84058USA
| | - Peter J. Maughan
- Department of Plant and Wildlife SciencesBrigham Young UniversityProvoUtah84058USA
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32
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Lenz KA, Rabbach DR, Liu C, Xu Q, Zeng Y, Steffen CR, Storts DR. Developmental validation of the VersaPlex™ 27PY system. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2020. [DOI: 10.1016/j.fsir.2020.100156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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33
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Ballard D, Winkler-Galicki J, Wesoły J. Massive parallel sequencing in forensics: advantages, issues, technicalities, and prospects. Int J Legal Med 2020; 134:1291-1303. [PMID: 32451905 PMCID: PMC7295846 DOI: 10.1007/s00414-020-02294-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 04/03/2020] [Indexed: 12/13/2022]
Abstract
In the last decade, next-generation sequencing (NGS) technology, alternatively massive parallel sequencing (MPS), was applied to all fields of biological research. Its introduction to the field of forensics was slower, mainly due to lack of accredited sequencers, kits, and relatively higher sequencing error rates as compared with standardized Sanger sequencing. Currently, a majority of the problematic issues have been solved, which is proven by the body of reports in the literature. Here, we discuss the utility of NGS sequencing in forensics, emphasizing the advantages, issues, the technical aspects of the experiments, commercial solutions, and the potentially interesting applications of MPS.
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Affiliation(s)
- David Ballard
- King's Forensic Genetics, Faculty of Life Sciences and Medicine, King's College London, 150 Stamford Street, London, UK
| | - Jakub Winkler-Galicki
- Laboratory of High Throughput Technologies, Faculty of Biology, Adam Mickiewicz, University Poznan, 6 Uniwersytetu Poznanskiego Street, Poznan, Poland
| | - Joanna Wesoły
- Laboratory of High Throughput Technologies, Faculty of Biology, Adam Mickiewicz, University Poznan, 6 Uniwersytetu Poznanskiego Street, Poznan, Poland.
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34
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Daunay A, Duval A, Baudrin LG, Buhard O, Renault V, Deleuze JF, How-Kit A. Low temperature isothermal amplification of microsatellites drastically reduces stutter artifact formation and improves microsatellite instability detection in cancer. Nucleic Acids Res 2020; 47:e141. [PMID: 31584085 PMCID: PMC6868440 DOI: 10.1093/nar/gkz811] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/03/2019] [Accepted: 09/11/2019] [Indexed: 12/28/2022] Open
Abstract
Microsatellites are polymorphic short tandem repeats of 1–6 nucleotides ubiquitously present in the genome that are extensively used in living organisms as genetic markers and in oncology to detect microsatellite instability (MSI). While the standard analysis method of microsatellites is based on PCR followed by capillary electrophoresis, it generates undesirable frameshift products known as ‘stutter peaks’ caused by the polymerase slippage that can greatly complicate the analysis and interpretation of the data. Here we present an easy multiplexable approach replacing PCR that is based on low temperature isothermal amplification using recombinase polymerase amplification (LT-RPA) that drastically reduces and sometimes completely abolishes the formation of stutter artifacts, thus greatly simplifying the calling of the alleles. Using HT17, a mononucleotide DNA repeat that was previously proposed as an optimal marker to detect MSI in tumor DNA, we showed that LT-RPA improves the limit of detection of MSI compared to PCR up to four times, notably for small deletions, and simplifies the identification of the mutant alleles. It was successfully applied to clinical colorectal cancer samples and enabled detection of MSI. This easy-to-handle, rapid and cost-effective approach may deeply improve the analysis of microsatellites in several biological and clinical applications.
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Affiliation(s)
- Antoine Daunay
- Laboratory for Genomics, Foundation Jean Dausset - CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
| | - Alex Duval
- Sorbonne-Université, Université Pierre et Marie Curie - Paris 6, Paris, France, INSERM, UMRS 938-Centre de Recherche Saint-Antoine, Equipe 'Instabilité des Microsatellites et Cancers', Equipe labellisée par la Ligue Nationale contre le Cancer, and SIRIC CURAMUS, Paris, France Université Pierre et Marie Curie, Paris, France
| | - Laura G Baudrin
- Laboratory for Genomics, Foundation Jean Dausset - CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France.,Laboratory of Excellence GenMed, Paris, France
| | - Olivier Buhard
- Sorbonne-Université, Université Pierre et Marie Curie - Paris 6, Paris, France, INSERM, UMRS 938-Centre de Recherche Saint-Antoine, Equipe 'Instabilité des Microsatellites et Cancers', Equipe labellisée par la Ligue Nationale contre le Cancer, and SIRIC CURAMUS, Paris, France Université Pierre et Marie Curie, Paris, France
| | - Victor Renault
- Laboratory for Bioinformatics, Foundation Jean Dausset - CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
| | - Jean-François Deleuze
- Laboratory for Genomics, Foundation Jean Dausset - CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France.,Centre National de Recherche en Génomique Humaine, CEA-Institut François Jacob, Evry, France
| | - Alexandre How-Kit
- Laboratory for Genomics, Foundation Jean Dausset - CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
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35
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Grass RN, Heckel R, Dessimoz C, Stark WJ. Genomic Encryption of Digital Data Stored in Synthetic DNA. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Robert N. Grass
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 1 8093 Zurich Switzerland
| | - Reinhard Heckel
- Department of Electrical and Computer Engineering Rice University 6100 Main Street Houston TX 77005 USA
- Department of Electrical and Computer Engineering Technical University of Munich Munich Germany
| | - Christophe Dessimoz
- Department of Computational Biology and Center for Integrative Genomics University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
- Department of Genetics, Evolution & Environment and Department of Computer Science University College London UK
| | - Wendelin J. Stark
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 1 8093 Zurich Switzerland
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36
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Grass RN, Heckel R, Dessimoz C, Stark WJ. Genomic Encryption of Digital Data Stored in Synthetic DNA. Angew Chem Int Ed Engl 2020; 59:8476-8480. [PMID: 32083389 DOI: 10.1002/anie.202001162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Indexed: 01/17/2023]
Abstract
Today, we can read human genomes and store digital data robustly in synthetic DNA. Herein, we report a strategy to intertwine these two technologies to enable the secure storage of valuable information in synthetic DNA, protected with personalized keys. We show that genetic short tandem repeats (STRs) contain sufficient entropy to generate strong encryption keys, and that only one technology, DNA sequencing, is required to simultaneously read the key and the data. Using this approach, we experimentally generated 80 bit strong keys from human DNA, and used such a key to encrypt 17 kB of digital information stored in synthetic DNA. Finally, the decrypted information was recovered perfectly from a single massively parallel sequencing run.
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Affiliation(s)
- Robert N Grass
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Reinhard Heckel
- Department of Electrical and Computer Engineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA.,Department of Electrical and Computer Engineering, Technical University of Munich, Munich, Germany
| | - Christophe Dessimoz
- Department of Computational Biology and Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Genetics, Evolution & Environment and Department of Computer Science, University College, London, UK
| | - Wendelin J Stark
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
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37
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Venta PJ, Nguyen AK, Senut MC, Poulos WG, Prukudom S, Cibelli JB. A 13-plex of tetra- and penta-STRs to identify zebrafish. Sci Rep 2020; 10:3851. [PMID: 32123258 PMCID: PMC7052278 DOI: 10.1038/s41598-020-60842-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/09/2020] [Indexed: 11/09/2022] Open
Abstract
The zebrafish species Danio rerio has become one of the major vertebrate model organisms used in biomedical research. However, there are aspects of the model that need to be improved. One of these is the ability to identify individual fish and fish lines by DNA profiling. Although many dinucleotide short tandem repeat (diSTR) markers are available for this and similar purposes, they have certain disadvantages such as an excessive polymerase slippage ("stutter") that causes difficulties in automated genotyping and cross-laboratory comparisons. Here we report on the development of a 13-plex of tetranucleotide and pentanucleotide STRs (tetraSTRs and pentaSTRs, respectively) that have low stutter. The system uses an inexpensive universal primer labelling system, which can easily be converted to a direct labeling system if desired. This 13-plex was examined in three zebrafish lines (NHGRI-1, kca33Tg, and kca66Tg, originally obtained from ZIRC). The average observed heterozygosity (Ho) and expected heterozygosity (He) in these highly inbred lines were 0.291 and 0.359, respectively, which is very similar to what has been found with diSTRs. The probability of identity (PI) for all fish tested was 2.1 × 10-5 and the PI for siblings (PIsib) was 6.4 × 10-3, as calculated by the Genalex package. Ninety percent of the fish tested were correctly identified with their respective strains. It is also demonstrated that this panel can be used to confirm doubled-haploid cell lines. This multiplex should find multiple uses for improving the accuracy and reproducibility of studies using the zebrafish model.
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Affiliation(s)
- Patrick J Venta
- Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48823, USA. .,Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, 48823, USA.
| | - Anthony K Nguyen
- Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48823, USA
| | - Marie-Claude Senut
- Biomilab LLC, Lansing, MI, 48910, USA.,Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48823, USA
| | - William G Poulos
- Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48823, USA
| | - Sukumal Prukudom
- Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University (CASAF, NRU-KU), Bangkok, 10900, Thailand
| | - Jose B Cibelli
- Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48823, USA. .,Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, 48823, USA.
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38
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Silvery J, Ganschow S, Wiegand P, Tiemann C. Developmental validation of the monSTR identity panel, a forensic STR multiplex assay for massively parallel sequencing. Forensic Sci Int Genet 2020; 46:102236. [PMID: 31986344 DOI: 10.1016/j.fsigen.2020.102236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/07/2020] [Accepted: 01/12/2020] [Indexed: 12/11/2022]
Abstract
The 21-plex STR panel monSTR was designed for high-fidelity forensic genotyping on the Illumina MiSeq platform. In this study, the panel's performance was validated according to the recommended validation guidelines of the Scientific Working Group for DNA Analysis Methods (SWGDAM). Concordance, repeatability and reproducibility, sensitivity of detection, mixture analysis, species-specificity, and the ability to analyze mock samples were assessed. Sequence data was analyzed using the genotyping software toaSTR. The assay performance was evaluated by measuring the read on-target ratio, the genotype accuracy, the inter-locus balance, the heterozygosity balance, and the signal-to-noise ratio. Results showed that profiles of NIST reference DNA samples as well as GEDNAP proficiency samples were fully concordant with CE-based methods. In addition, inter-run and intra-run variation experiments indicated high precision. Furthermore, full profiles could be obtained using 62.5 pg of DNA input amount with proper inter-locus balance and read on-target ratio; 76.4% of alleles were correctly called with 7.8 pg DNA input amount. It was demonstrated that 94.4% of minor contributor alleles were resolved accurately in a 1:49 mixture. Results suggested that the minor contribution could be precisely calculated based on the minor component allele frequency. Validation results described here demonstrate that the monSTR forensic identity panel is a valid tool for forensic STR genotyping using massively parallel sequencing.
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Affiliation(s)
- Janine Silvery
- LABCON-OWL Analytik, Forschung und Consulting GmbH, Siemensstraße 40, 32105 Bad Salzuflen, Germany; Institute of Legal Medicine, University Hospital of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Sebastian Ganschow
- LABCON-OWL Analytik, Forschung und Consulting GmbH, Siemensstraße 40, 32105 Bad Salzuflen, Germany
| | - Peter Wiegand
- Institute of Legal Medicine, University Hospital of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Carsten Tiemann
- LABCON-OWL Analytik, Forschung und Consulting GmbH, Siemensstraße 40, 32105 Bad Salzuflen, Germany; Faculty of Engineering and Mathematics, Bielefeld University of Applied Science, Interaktion 1, 33619 Bielefeld, Germany
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Li R, Wu R, Li H, Zhang Y, Peng D, Wang N, Shen X, Wang Z, Sun H. Characterizing stutter variants in forensic STRs with massively parallel sequencing. Forensic Sci Int Genet 2019; 45:102225. [PMID: 31865225 DOI: 10.1016/j.fsigen.2019.102225] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 11/19/2019] [Accepted: 12/08/2019] [Indexed: 11/28/2022]
Abstract
Despite improvements in characterizing stutters of short tandem repeats (STRs), the relationships among the amounts of stutter variants and the relationships among motifs are not well understood yet. In the present study, 750 peripheral blood samples from human subjects were included to characterize the stutters of 58 STRs via the ForenSeq DNA Signature Prep Kit on a MiSeq FGx instrument. Alleles and corresponding stutter products were identified with a sequence simplification procedure. After screening, 26,921 alleles were included, that resulted in over 50 million reads, among which 8.69% were stutter products. Among these stutter products, 83.44% were N-1 stutters. Additionally, N-4, N-3, N-2, N0, N + 1, and N + 2 variants accounted for 0.11%, 0.77%, 6.45%, 3.01%, 5.95%, and 0.25% of the stutter products, respectively. For backward stutters, stutter products correlated best with the corresponding one-unit-longer stutter (or parental allele), which may represent a good predictor for backward stutters. For forward stutters, the N + 2 stutter correlated best with the N + 1 stutter, whereas the N + 1 stutter correlated best with the N-1 stutter rather than the expected parental allele, which indicated that the patterns were more complex for forward stutters. Additionally, some interesting findings were obtained for D21S11. For two adjacent contiguous motifs, co-stuttering patterns were observed where one motif tended to increase one repeat unit while the other motif decreased one repeat unit, whereas the inter-motif dependency was not significant for interrupted motifs. In conclusion, with massively parallel sequencing technology and our sequence simplification strategy, sequence variations within alleles and stutter products were identified, which was useful to determine the origin of stutters, identify more stutter variants, and explore the relationships among motifs. These findings may be helpful for allele designation, a deeper understanding of the mechanism of stutter, and improving resolution in forensic mixture analyses.
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Affiliation(s)
- Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong, People's Republic of China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, Guangdong, People's Republic of China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong, People's Republic of China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, Guangdong, People's Republic of China
| | - Haixia Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong, People's Republic of China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, Guangdong, People's Republic of China
| | - Yinming Zhang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong, People's Republic of China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, Guangdong, People's Republic of China
| | - Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong, People's Republic of China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, Guangdong, People's Republic of China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong, People's Republic of China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, Guangdong, People's Republic of China
| | - Xuefeng Shen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong, People's Republic of China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, Guangdong, People's Republic of China
| | - Zhiyuan Wang
- Forensic Science Center of Foshan Municipal Public Security Department, Foshan 528000, Guangdong, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong, People's Republic of China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, Guangdong, People's Republic of China.
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40
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Understanding the behavior of stutter through the sequencing of STR alleles. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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41
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Alsafiah HM, Aljanabi AA, Hadi S, Alturayeif SS, Goodwin W. An evaluation of the SureID 23comp Human Identification Kit for kinship testing. Sci Rep 2019; 9:16859. [PMID: 31727926 PMCID: PMC6856129 DOI: 10.1038/s41598-019-52838-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 10/21/2019] [Indexed: 01/16/2023] Open
Abstract
Short tandem repeat (STR) profiling has been routinely used in kinship testing since the introduction of commercial kits in the mid-1990s. While 15 to 23 STR loci normally give definitive results in simple kinship testing, additional loci are sometimes required to resolve complex cases. The SureID 23comp Human Identification Kit, recently released by Health Gene Technologies (China), multiplexes amelogenin and 22 autosomal STRs, 17 of which are non-CODIS STRs. This enables the profiling of 38–40 loci when used in conjunction with widely used commercial kits. In this study, the kit was evaluated for kinship applications as a supplementary STR kit following the minimum criteria for validation recommended by the European Network of Forensic Science Institutes (ENFSI) and the Scientific Working Group on DNA Analysis Methods (SWGDAM) using 500 samples. Performance was comparable with other commercial kits demonstrating: repeatability and reproducibility; precision (maximum s.d. 0.1048 nt); accuracy, all alleles were within ±0.41 nt compared to the actual sizes; heterozygous peak balances at all loci >68%; stutter ratios ranged from 3.8% to 16.15%; full profiles were generated with 125 pg DNA (95.12% of alleles at 62 pg),; and we found 100% concordance over 5 common STRs with the GlobalFiler kit.
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Affiliation(s)
- Hussain M Alsafiah
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston, United Kingdom. .,Forensic Genetics Laboratory, General Administration of Criminal Evidences, Public Security, Ministry of Interior, Riyadh, Saudi Arabia.
| | - Ali A Aljanabi
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston, United Kingdom
| | - Sibte Hadi
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston, United Kingdom
| | - Saleh S Alturayeif
- Forensic Genetics Laboratory, General Administration of Criminal Evidences, Public Security, Ministry of Interior, Riyadh, Saudi Arabia
| | - William Goodwin
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston, United Kingdom.
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42
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Rodriguez JJRB, Bright JA, Salvador JM, Laude RP, De Ungria MCA. Data on likelihood ratios of two-person DNA mixtures interpreted using semi- and fully continuous systems. Data Brief 2019; 26:104455. [PMID: 31667227 PMCID: PMC6811899 DOI: 10.1016/j.dib.2019.104455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/19/2019] [Accepted: 08/22/2019] [Indexed: 12/05/2022] Open
Abstract
In the paper, "Probabilistic approaches to interpreting two-person DNA mixtures from post-coital specimens" [1], we analysed 102 two-person DNA samples from simulated mixtures and male-female and male-male post-coital specimens. We report here data on profile characteristics of these samples and likelihood ratios (LRs) generated using semi- and fully continuous systems. Both log10 LRs from true and non-contributor tests are presented. These data may supplement studies comparing performance of different probabilistic systems for DNA evidence interpretation.
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Affiliation(s)
- Jae Joseph Russell B. Rodriguez
- DNA Analysis Laboratory, Natural Sciences Research Institute, College of Science, University of the Philippines Diliman, Quezon City, 1101, Philippines
- Genetics and Molecular Biology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, 4031, Philippines
| | - Jo-Anne Bright
- Institute of Environmental Science and Research Ltd., Mt. Albert Science Centre, Auckland, New Zealand
| | - Jazelyn M. Salvador
- DNA Analysis Laboratory, Natural Sciences Research Institute, College of Science, University of the Philippines Diliman, Quezon City, 1101, Philippines
| | - Rita P. Laude
- Genetics and Molecular Biology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, 4031, Philippines
| | - Maria Corazon A. De Ungria
- DNA Analysis Laboratory, Natural Sciences Research Institute, College of Science, University of the Philippines Diliman, Quezon City, 1101, Philippines
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43
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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]
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44
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Rodriguez JJRB, Bright JA, Salvador JM, Laude RP, De Ungria MCA. Probabilistic approaches to interpreting two-person DNA mixtures from post-coital specimens. Forensic Sci Int 2019; 300:157-163. [PMID: 31112838 DOI: 10.1016/j.forsciint.2019.04.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 03/26/2019] [Accepted: 04/29/2019] [Indexed: 01/23/2023]
Abstract
Biological samples submitted for sexual assault investigation typically involve mixtures of DNA from the victim and the assailant/s. Providing a statistical weight to such evidence may be mathematically complex and may be affected by subjective judgment of a human analyst. Software tools have been developed to address these issues. To contribute towards improving the system for routine DNA testing of sexual assault cases, we evaluated two likelihood ratio (LR) approaches: a semi-continuous model using LRmix Studio and a fully continuous approach employed in STRmix™ for interpreting two-person DNA mixtures. LRs conditioned on the presence of the receptive partner's DNA were calculated for a total of 102 two-person DNA samples from simulated mixtures and various post-coital samples. Our results highlight the importance of maximising information provided into the LR calculation to generate strong support for the true hypothesis. This can be achieved by recovering sufficient DNA from a sample to minimise risk of drop-out and increase peak intensities and by implementing a statistical model that utilises as much of the electropherogram information as possible. LRmix is open-source and can handle profiles with allelic drop-out and drop-ins, however stuttering is not modelled and requires manual removal by a DNA analyst especially for mixtures with low template components. STRmix™ makes effective use of all available information by incorporating into its biological model complicating aspects of a DNA profile such as degradation, allele drop-out and drop-in, stutters, and peak height variability.
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Affiliation(s)
- Jae Joseph Russell B Rodriguez
- DNA Analysis Laboratory, Natural Sciences Research Institute, College of Science, University of the Philippines Diliman, Quezon City, 1101 Philippines; Genetics and Molecular Biology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, 4031 Philippines.
| | - Jo-Anne Bright
- Institute of Environmental Science and Research Ltd., Mt. Albert Science Centre, Auckland, New Zealand.
| | - Jazelyn M Salvador
- DNA Analysis Laboratory, Natural Sciences Research Institute, College of Science, University of the Philippines Diliman, Quezon City, 1101 Philippines.
| | - Rita P Laude
- Genetics and Molecular Biology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, 4031 Philippines.
| | - Maria Corazon A De Ungria
- DNA Analysis Laboratory, Natural Sciences Research Institute, College of Science, University of the Philippines Diliman, Quezon City, 1101 Philippines.
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45
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Development and validation of a novel panel of 16 STR markers for simultaneous diagnosis of β-thalassemia, aneuploidy screening, maternal cell contamination detection and fetal sample authenticity in PND and PGD/PGS cases. Sci Rep 2019; 9:7452. [PMID: 31092881 PMCID: PMC6520367 DOI: 10.1038/s41598-019-43892-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 05/03/2019] [Indexed: 11/09/2022] Open
Abstract
Prenatal diagnosis (PND) may be complicated with sample mix-up; maternal cell contamination, non-paternity and allele drop out at different stages of diagnosis. Aneuploidy screening if combined with PND for a given single gene disorder, can help to detect any common aneuploidy as well as aiding sample authenticity and other probable complications which may arise during such procedures. This study was carried out to evaluate the effectiveness of a novel panel of STR markers combined as a multiplex PCR kit (HapScreen™ kit) for the detection of β-thalassemia, aneuploidy screening, ruling in/out maternal cell contamination (MCC), and sample authenticity. The kit uses 7 STR markers linked to β-globin gene (HBB) as well as using 9 markers for quantitative analysis of chromosomes 21, 18, 13, X and Y. Selection of the markers was to do linkage analysis with β-globin gene, segregation analysis and to perform a preliminary aneuploidy screening of fetal samples respectively. These markers (linked to the β-globin gene) were tested on more than 2185 samples and showed high heterozygosity values (68.4-91.4%). From 2185 fetal cases we found 3 cases of non-paternity, 5 cases of MCC, one case of sample mix-up and one case of trisomy 21 which otherwise may have end up to misdiagnosis. This kit was also successfully used on 231 blastomeres for 29 cases of pre-implantation genetic diagnosis (PGD) and screening (PGS). The markers used for simultaneous analysis of haplotype segregation and aneuploidy screening proved to be very valuable to confirm results obtained from direct mutation detection methods (i.e. ARMS, MLPA and sequencing) and aneuploidy screening.
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46
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Compound stutter in D2S1338 and D12S391. Forensic Sci Int Genet 2018; 39:50-56. [PMID: 30554027 DOI: 10.1016/j.fsigen.2018.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/06/2018] [Accepted: 12/06/2018] [Indexed: 11/22/2022]
Abstract
Compound repeats provide a testing ground for evaluating hypotheses on the causes and consequences of stutter. As compound repeats have two repeating motifs, each motif may produce stutter variants; thus as the repeat within the locus is compound, so is the resultant stutter. Further, the rates of stutter formation between these motifs may not be independent. This lack of independence may complicate modeling strategies, thus contributing to the challenges of mixture interpretation that rely on nucleotide sequence. This study evaluates compound stutter in two STR loci: D2S1338 and D12S391. The effects of flanking variation, as well as possible interactions between the two different uninterrupted stretches (US) and their respective stutter variants are assessed. Multivariate multiple linear regression (MMLR) was used to show that, as with simple repeats, the rate of stutter product formation of a particular repeating motif is not solely a function of the US of that repeat. The nucleotides adjacent to the repeating motif also appear to influence the rate of stutter formation of that motif, with those nucleotides sometimes including the other motif. MMLR was used to estimate the size of these effects and to construct an example of a two-dimensional (thus, a compound) stutter prediction. This example may merit further investigation in the application of massively parallel sequencing data to mixture interpretation and probabilistic genotyping.
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47
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Four model variants within a continuous forensic DNA mixture interpretation framework: Effects on evidential inference and reporting. PLoS One 2018; 13:e0207599. [PMID: 30458020 PMCID: PMC6245789 DOI: 10.1371/journal.pone.0207599] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 10/13/2018] [Indexed: 12/11/2022] Open
Abstract
Continuous mixture interpretation methods that employ probabilistic genotyping to compute the Likelihood Ratio (LR) utilize more information than threshold-based systems. The continuous interpretation schemes described in the literature, however, do not all use the same underlying probabilistic model and standards outlining which probabilistic models may or may not be implemented into casework do not exist; thus, it is the individual forensic laboratory or expert that decides which model and corresponding software program to implement. For countries, such as the United States, with an adversarial legal system, one can envision a scenario where two probabilistic models are used to present the weight of evidence, and two LRs are presented by two experts. Conversely, if no independent review of the evidence is requested, one expert using one model may present one LR as there is no standard or guideline requiring the uncertainty in the LR estimate be presented. The choice of model determines the underlying probability calculation, and changes to it can result in non-negligible differences in the reported LR or corresponding verbal categorization presented to the trier-of-fact. In this paper, we study the impact of model differences on the LR and on the corresponding verbal expression computed using four variants of a continuous mixture interpretation method. The four models were tested five times each on 101, 1-, 2- and 3-person experimental samples with known contributors. For each sample, LRs were computed using the known contributor as the person of interest. In all four models, intra-model variability increased with an increase in the number of contributors and with a decrease in the contributor’s template mass. Inter-model variability in the associated verbal expression of the LR was observed in 32 of the 195 LRs used for comparison. Moreover, in 11 of these profiles there was a change from LR > 1 to LR < 1. These results indicate that modifications to existing continuous models do have the potential to significantly impact the final statistic, justifying the continuation of broad-based, large-scale, independent studies to quantify the limits of reliability and variability of existing forensically relevant systems.
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48
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Buckleton JS, Bright JA, Gittelson S, Moretti TR, Onorato AJ, Bieber FR, Budowle B, Taylor DA. The Probabilistic Genotyping Software STRmix: Utility and Evidence for its Validity. J Forensic Sci 2018; 64:393-405. [PMID: 30132900 DOI: 10.1111/1556-4029.13898] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/14/2018] [Accepted: 07/17/2018] [Indexed: 01/08/2023]
Abstract
Forensic DNA interpretation is transitioning from manual interpretation based usually on binary decision-making toward computer-based systems that model the probability of the profile given different explanations for it, termed probabilistic genotyping (PG). Decision-making by laboratories to implement probability-based interpretation should be based on scientific principles for validity and information that supports its utility, such as criteria to support admissibility. The principles behind STRmix™ are outlined in this study and include standard mathematics and modeling of peak heights and variability in those heights. All PG methods generate a likelihood ratio (LR) and require the formulation of propositions. Principles underpinning formulations of propositions include the identification of reasonably assumed contributors. Substantial data have been produced that support precision, error rate, and reliability of PG, and in particular, STRmix™. A current issue is access to the code and quality processes used while coding. There are substantial data that describe the performance, strengths, and limitations of STRmix™, one of the available PG software.
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Affiliation(s)
- John S Buckleton
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland, 1142, New Zealand.,Department of Statistics, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Jo-Anne Bright
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland, 1142, New Zealand
| | - Simone Gittelson
- Centre for Forensic Science, University of Technology Sydney, P.O. Box 123, Broadway, NSW, 2007, Australia
| | - Tamyra R Moretti
- DNA Support Unit, Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135
| | - Anthony J Onorato
- DNA Support Unit, Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135
| | - Frederick R Bieber
- Center for Advanced Molecular Diagnostics, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA, 02115
| | - Bruce Budowle
- Center for Human Identification, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107
| | - Duncan A Taylor
- Forensic Science South Australia, 21 Divett Place, Adelaide, SA, Australia.,Flinders University - School of Biology, Stuart Road, Bedford Park, Adelaide, SA, Australia
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49
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Ganschow S, Silvery J, Kalinowski J, Tiemann C. toaSTR: A web application for forensic STR genotyping by massively parallel sequencing. Forensic Sci Int Genet 2018; 37:21-28. [PMID: 30071493 DOI: 10.1016/j.fsigen.2018.07.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 01/29/2023]
Abstract
Massively parallel sequencing (MPS) is emerging within the forensic community as a promising technique for high-resolution short tandem repeat (STR) genotyping, discovering both length and sequence polymorphisms. Conversely, the application of MPS to routine casework poses new challenges to the DNA analyst in view of the complex sequence data that is generated with this technology. We developed the web application toaSTR to help forensic experts work with MPS data simply and efficiently. An intuitive graphical user interface guides through the STR genotyping workflow. This versatile software handles data from various popular MPS platforms and supports both commercial and in-house multiplex PCR kits. Users can define locus-specific stutter thresholds and create custom sets of STR markers to be analyzed. toaSTR's innovative sequence-based stutter model predicts and identifies common stutter variants. The algorithm automatically differentiates biological (iso-)alleles from stutter and other artefacts to assist the interpretation of mixed samples. toaSTR features a comprehensive data visualization with interactive diagrams and a dynamic tabular overview of sequence observations. The software provides an interface to biostatistics tools and enables PDF result export in compliance with the sequence notation recommended by the International Society for Forensic Genetics (ISFG). An initial compatibility and concordance study confirmed the software's independent functionality and precise allele calling with data of different MPS platforms, STR amplification kits, and library preparation chemistries. Discussion of genotyping results for single source and mixed samples demonstrates toaSTR's advantages and includes suggestions for future MPS software development. The beta version of toaSTR is freely accessible at www.toastr.online.
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Affiliation(s)
- Sebastian Ganschow
- LABCON-OWL Analytik, Forschung und Consulting GmbH, Siemensstr. 40, 32105 Bad Salzuflen, Germany.
| | - Janine Silvery
- LABCON-OWL Analytik, Forschung und Consulting GmbH, Siemensstr. 40, 32105 Bad Salzuflen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
| | - Carsten Tiemann
- LABCON-OWL Analytik, Forschung und Consulting GmbH, Siemensstr. 40, 32105 Bad Salzuflen, Germany
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50
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Vilsen SB, Tvedebrink T, Eriksen PS, Bøsting C, Hussing C, Mogensen HS, Morling N. Stutter analysis of complex STR MPS data. Forensic Sci Int Genet 2018; 35:107-112. [DOI: 10.1016/j.fsigen.2018.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/13/2018] [Accepted: 04/06/2018] [Indexed: 11/29/2022]
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