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Monson KL, Ali S, Brandhagen MD, Duff MC, Fisher CL, Lowe KK, Meyer CE, Roberts MA, Tom KR, Washington AL. Potential effects of ionizing radiation on the evidentiary value of DNA, latent fingerprints, hair, and fibers: A comprehensive review and new results. Forensic Sci Int 2018; 284:204-218. [DOI: 10.1016/j.forsciint.2018.01.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 12/13/2017] [Accepted: 01/10/2018] [Indexed: 02/02/2023]
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52
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Loreille O, Ratnayake S, Bazinet AL, Stockwell TB, Sommer DD, Rohland N, Mallick S, Johnson PLF, Skoglund P, Onorato AJ, Bergman NH, Reich D, Irwin JA. Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens. Genes (Basel) 2018; 9:genes9030135. [PMID: 29494531 PMCID: PMC5867856 DOI: 10.3390/genes9030135] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/06/2018] [Accepted: 02/06/2018] [Indexed: 12/17/2022] Open
Abstract
High throughput sequencing (HTS) has been used for a number of years in the field of paleogenomics to facilitate the recovery of small DNA fragments from ancient specimens. Recently, these techniques have also been applied in forensics, where they have been used for the recovery of mitochondrial DNA sequences from samples where traditional PCR-based assays fail because of the very short length of endogenous DNA molecules. Here, we describe the biological sexing of a ~4000-year-old Egyptian mummy using shotgun sequencing and two established methods of biological sex determination (RX and RY), by way of mitochondrial genome analysis as a means of sequence data authentication. This particular case of historical interest increases the potential utility of HTS techniques for forensic purposes by demonstrating that data from the more discriminatory nuclear genome can be recovered from the most damaged specimens, even in cases where mitochondrial DNA cannot be recovered with current PCR-based forensic technologies. Although additional work remains to be done before nuclear DNA recovered via these methods can be used routinely in operational casework for individual identification purposes, these results indicate substantial promise for the retrieval of probative individually identifying DNA data from the most limited and degraded forensic specimens.
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Affiliation(s)
- Odile Loreille
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Shashikala Ratnayake
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Adam L Bazinet
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Timothy B Stockwell
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Daniel D Sommer
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Nadin Rohland
- Department of Genetics Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Swapan Mallick
- Department of Genetics Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Philip L F Johnson
- Department of Biology, University of Maryland, 1210 Biology-Psychology Building, 4094 Campus Drive, College Park, MD 20742, USA.
| | - Pontus Skoglund
- The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK.
| | - Anthony J Onorato
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Nicholas H Bergman
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - David Reich
- Department of Genetics Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
| | - Jodi A Irwin
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
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53
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Massively parallel sequencing-enabled mixture analysis of mitochondrial DNA samples. Int J Legal Med 2018; 132:1263-1272. [PMID: 29468381 DOI: 10.1007/s00414-018-1799-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 02/09/2018] [Indexed: 01/03/2023]
Abstract
The mitochondrial genome has a number of characteristics that provide useful information to forensic investigations. Massively parallel sequencing (MPS) technologies offer improvements to the quantitative analysis of the mitochondrial genome, specifically the interpretation of mixed mitochondrial samples. Two-person mixtures with nuclear DNA ratios of 1:1, 5:1, 10:1, and 20:1 of individuals from different and similar phylogenetic backgrounds and three-person mixtures with nuclear DNA ratios of 1:1:1 and 5:1:1 were prepared using the Precision ID mtDNA Whole Genome Panel and Ion Chef, and sequenced on the Ion PGM or Ion S5 sequencer (Thermo Fisher Scientific, Waltham, MA, USA). These data were used to evaluate whether and to what degree MPS mixtures could be deconvolved. Analysis was effective in identifying the major contributor in each instance, while SNPs from the minor contributor's haplotype only were identified in the 1:1, 5:1, and 10:1 two-person mixtures. While the major contributor was identified from the 5:1:1 mixture, analysis of the three-person mixtures was more complex, and the mixed haplotypes could not be completely parsed. These results indicate that mixed mitochondrial DNA samples may be interpreted with the use of MPS technologies.
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54
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Wai KT, Barash M, Gunn P. Performance of the Early Access AmpliSeq™ Mitochondrial Panel with degraded DNA samples using the Ion Torrent™ platform. Electrophoresis 2018; 39:2776-2784. [PMID: 29330875 DOI: 10.1002/elps.201700371] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/07/2017] [Accepted: 12/16/2017] [Indexed: 11/12/2022]
Abstract
The Early Access AmpliSeq™ Mitochondrial Panel amplifies whole mitochondrial genomes for phylogenetic and kinship identifications, using Ion Torrent™ technology. There is currently limited information on its performance with degraded DNA, a common occurrence in forensic samples. This study evaluated the performance of the Panel with DNA samples degraded in vitro, to mimic conditions commonly found in forensic investigations. Purified DNA from five individuals was heat-treated at five time points each (125°C for 0, 30, 60, 120, and 240 min; total n = 25). The quality of DNA was assessed via a real-time DNA assay of genomic DNA and prepared for massively parallel sequencing on the Ion Torrent™ platform. Mitochondrial sequences were obtained for all samples and had an amplicon coverage averaging between 66X to 2803X. Most amplicons (157/162) displayed high coverages (452 ± 333X), while reads with less than 100X coverage were recorded in five amplicons only (90 ± 5X). Amplicon coverage was decreased with prolonged heating. At 72% strand balance, reads were well balanced between forward and reverse strands. Using a coverage threshold of ten reads per SNP, complete sequences were recovered in all samples and resolved kinship and, haplogroup relations. Additionally, the HV1 and HV2 regions of the reference and 240-min heat-treated samples (n = 10) were Sanger-sequenced for concordance. Overall, this study demonstrates the efficacy of a novel forensic Panel that recovers high quality mitochondrial sequences from degraded DNA samples.
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Affiliation(s)
- Ka Tak Wai
- University of Technology Sydney, Centre for Forensic Science, Sydney, NSW, Australia
| | - Mark Barash
- University of Technology Sydney, Centre for Forensic Science, Sydney, NSW, Australia
| | - Peter Gunn
- University of Technology Sydney, Centre for Forensic Science, Sydney, NSW, Australia
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55
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Cho S, Kim MY, Lee JH, Lee SD. Assessment of mitochondrial DNA heteroplasmy detected on commercial panel using MPS system with artificial mixture samples. Int J Legal Med 2017; 132:1049-1056. [PMID: 29279961 DOI: 10.1007/s00414-017-1755-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/30/2017] [Indexed: 01/05/2023]
Abstract
Mitochondrial DNA (mtDNA) heteroplasmy is a potential genetic marker for forensic mtDNA analysis as well as phylogenic studies. Frequency of mtDNA heteroplasmy has been investigated in different populations through massively parallel sequencing (MPS) analysis, revealing various levels of frequency based on different MPS systems. For accurate heteroplasmy identification, it is essential to explore reliable detection threshold on various MPS systems. In addition, software solutions and pipelines need to be evaluated to analyze data effectively. In this study, heteroplasmy analysis was conducted on a commercially available mtDNA analysis system developed for forensic caseworks with artificially mixed DNA samples known for ratios and variant positions for assessment. mtDNA heteroplasmy > 10% was detectable with Torrent Variant Caller (TVC) while lower levels were identified using GeneMarker® HTS specialized software for minor variant detection. This study implies that analytical parameters and tools need to be optimized and evaluated for low-level heteroplasmy identification. Automated system with simple and efficient workflow is needed for forensic caseworks.
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Affiliation(s)
- Sohee Cho
- Institute of Forensic Science, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea
| | - Moon Young Kim
- Department of Forensic Medicine, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea
| | - Ji Hyun Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea
| | - Soong Deok Lee
- Institute of Forensic Science, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea. .,Department of Forensic Medicine, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea.
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56
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A review of bioinformatic methods for forensic DNA analyses. Forensic Sci Int Genet 2017; 33:117-128. [PMID: 29247928 DOI: 10.1016/j.fsigen.2017.12.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/30/2017] [Accepted: 12/10/2017] [Indexed: 12/20/2022]
Abstract
Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used.
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57
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Marshall C, Sturk-Andreaggi K, Daniels-Higginbotham J, Oliver RS, Barritt-Ross S, McMahon TP. Performance evaluation of a mitogenome capture and Illumina sequencing protocol using non-probative, case-type skeletal samples: Implications for the use of a positive control in a next-generation sequencing procedure. Forensic Sci Int Genet 2017; 31:198-206. [DOI: 10.1016/j.fsigen.2017.09.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/08/2017] [Accepted: 09/05/2017] [Indexed: 11/24/2022]
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58
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Sturk-Andreaggi K, Peck MA, Boysen C, Dekker P, McMahon TP, Marshall CK. AQME: A forensic mitochondrial DNA analysis tool for next-generation sequencing data. Forensic Sci Int Genet 2017; 31:189-197. [DOI: 10.1016/j.fsigen.2017.09.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/21/2017] [Accepted: 09/16/2017] [Indexed: 12/20/2022]
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59
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Gallimore JM, McElhoe JA, Holland MM. Assessing heteroplasmic variant drift in the mtDNA control region of human hairs using an MPS approach. Forensic Sci Int Genet 2017; 32:7-17. [PMID: 29024924 DOI: 10.1016/j.fsigen.2017.09.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/20/2017] [Accepted: 09/26/2017] [Indexed: 01/11/2023]
Abstract
Resolution of mitochondrial (mt) DNA heteroplasmy is possible when applying a massively parallel sequencing (MPS) approach. However, interpretation criteria for matching heteroplasmic sequences will need to be established that address a number of important topics, including the drift of variants in sample types such as human hair shafts. Prior to MPS analysis, we compared three different DNA extraction methods for hair using a custom mtDNA quantitative PCR (mtqPCR) assay, and found that a method involving bead capture significantly outperformed methods currently in place in forensic laboratories. The findings were similar for both fine (head) and coarse (pubic) hairs. Using the favored DNA extraction approach, hair shaft extracts were subjected to MPS analysis to assess heteroplasmic drift and the potential impact of the observations on interpretation of mtDNA MPS data. Hairs from different regions of the head were evaluated in individuals with varying percentages of heteroplasmy (low-level, high-level, and no detectable heteroplasmy), as measured in buccal and blood cells. The range of variant ratios was broad and was not significantly different between individuals in the low and high-level groups. While the range was also broad for the group of individuals with no heteroplasmy, the vast majority of hairs from these donors still exhibited a lack of heteroplasmy. A model was developed to predict the amount of heteroplasmy expected in hair samples when knowledge of the percentage of heteroplasmy in buccal cells is available. While significant, the model was best applied when levels of heteroplasmy in buccal cells was high. No correlation was observed between rates of heteroplasmy in blood cells and the predicted amount of heteroplasmy in hairs. Of particular interest, unexpected sites of mixed mtDNA sequence that could be interpreted as heteroplasmy were observed for 13% of the 75 hairs tested. These sites can be explained as heteroplasmy not observed in buccal or blood cells, or sites of DNA damage, with inherent heteroplasmy a likely cause, possibly due to de novo mutation events. Overall, when applying an MPS approach to hair analysis, heteroplasmic variant ratios may be quite different than those observed in blood cells, may be correlated to rates in buccal cells, and may include unexpected mixed sites. The results of this study directly impact MPS analysis of minor sequence variants from hair samples, and are particularly relevant to clinical and forensic investigations.
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Affiliation(s)
- Jamie M Gallimore
- Forensic Science Program, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA 16802, United States
| | - Jennifer A McElhoe
- Forensic Science Program, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA 16802, United States
| | - Mitchell M Holland
- Forensic Science Program, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA 16802, United States.
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60
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Eduardoff M, Xavier C, Strobl C, Casas-Vargas A, Parson W. Optimized mtDNA Control Region Primer Extension Capture Analysis for Forensically Relevant Samples and Highly Compromised mtDNA of Different Age and Origin. Genes (Basel) 2017; 8:genes8100237. [PMID: 28934125 PMCID: PMC5664087 DOI: 10.3390/genes8100237] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/06/2017] [Accepted: 09/18/2017] [Indexed: 11/24/2022] Open
Abstract
The analysis of mitochondrial DNA (mtDNA) has proven useful in forensic genetics and ancient DNA (aDNA) studies, where specimens are often highly compromised and DNA quality and quantity are low. In forensic genetics, the mtDNA control region (CR) is commonly sequenced using established Sanger-type Sequencing (STS) protocols involving fragment sizes down to approximately 150 base pairs (bp). Recent developments include Massively Parallel Sequencing (MPS) of (multiplex) PCR-generated libraries using the same amplicon sizes. Molecular genetic studies on archaeological remains that harbor more degraded aDNA have pioneered alternative approaches to target mtDNA, such as capture hybridization and primer extension capture (PEC) methods followed by MPS. These assays target smaller mtDNA fragment sizes (down to 50 bp or less), and have proven to be substantially more successful in obtaining useful mtDNA sequences from these samples compared to electrophoretic methods. Here, we present the modification and optimization of a PEC method, earlier developed for sequencing the Neanderthal mitochondrial genome, with forensic applications in mind. Our approach was designed for a more sensitive enrichment of the mtDNA CR in a single tube assay and short laboratory turnaround times, thus complying with forensic practices. We characterized the method using sheared, high quantity mtDNA (six samples), and tested challenging forensic samples (n = 2) as well as compromised solid tissue samples (n = 15) up to 8 kyrs of age. The PEC MPS method produced reliable and plausible mtDNA haplotypes that were useful in the forensic context. It yielded plausible data in samples that did not provide results with STS and other MPS techniques. We addressed the issue of contamination by including four generations of negative controls, and discuss the results in the forensic context. We finally offer perspectives for future research to enable the validation and accreditation of the PEC MPS method for final implementation in forensic genetic laboratories.
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Affiliation(s)
- Mayra Eduardoff
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria.
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria.
| | - Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria.
| | - Andrea Casas-Vargas
- Grupo de Genética de Poblaciones e Identificación, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia.
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria.
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA.
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61
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Vohr SH, Gordon R, Eizenga JM, Erlich HA, Calloway CD, Green RE. A phylogenetic approach for haplotype analysis of sequence data from complex mitochondrial mixtures. Forensic Sci Int Genet 2017; 30:93-105. [PMID: 28667863 DOI: 10.1016/j.fsigen.2017.05.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/05/2017] [Accepted: 05/26/2017] [Indexed: 12/11/2022]
Abstract
Massively parallel (next-generation) sequencing provides a powerful method to analyze DNA from many different sources, including degraded and trace samples. A common challenge, however, is that many forensic samples are often known or suspected mixtures of DNA from multiple individuals. Haploid lineage markers, such as mitochondrial (mt) DNA, are useful for analysis of mixtures because, unlike nuclear genetic markers, each individual contributes a single sequence to the mixture. Deconvolution of these mixtures into the constituent mitochondrial haplotypes is challenging as typical sequence read lengths are too short to reconstruct the distinct haplotypes completely. We present a powerful computational approach for determining the constituent haplotypes in massively parallel sequencing data from potentially mixed samples. At the heart of our approach is an expectation maximization based algorithm that co-estimates the overall mixture proportions and the source haplogroup for each read individually. This approach, implemented in the software package mixemt, correctly identifies haplogroups from mixed samples across a range of mixture proportions. Furthermore, our method can separate fragments in a mixed sample by the most likely originating contributor and generate reconstructions of the constituent haplotypes based on known patterns of mtDNA diversity.
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Affiliation(s)
- Samuel H Vohr
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA.
| | - Rachel Gordon
- Center for Genetics, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr Way, Oakland, CA 94609, USA
| | - Jordan M Eizenga
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Henry A Erlich
- Center for Genetics, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr Way, Oakland, CA 94609, USA
| | - Cassandra D Calloway
- Center for Genetics, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr Way, Oakland, CA 94609, USA; Forensic Science Graduate Program, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
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62
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Xavier C, Parson W. Evaluation of the Illumina ForenSeq™ DNA Signature Prep Kit – MPS forensic application for the MiSeq FGx™ benchtop sequencer. Forensic Sci Int Genet 2017; 28:188-194. [DOI: 10.1016/j.fsigen.2017.02.018] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/22/2017] [Accepted: 02/28/2017] [Indexed: 01/23/2023]
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63
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Holland MM, Pack ED, McElhoe JA. Evaluation of GeneMarker ® HTS for improved alignment of mtDNA MPS data, haplotype determination, and heteroplasmy assessment. Forensic Sci Int Genet 2017; 28:90-98. [PMID: 28193506 DOI: 10.1016/j.fsigen.2017.01.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 01/04/2017] [Accepted: 01/25/2017] [Indexed: 12/14/2022]
Abstract
Existing software has not allowed for effective alignment of mitochondrial (mt) DNA sequence data generated using a massively parallel sequencing (MPS) approach, combined with the ability to perform a detailed assessment of the data. The regions of sequence that are typically difficult to align are homopolymeric stretches, isolated patterns of SNPs (single nucleotide polymorphisms), and INDELs (insertions/deletions). A custom software solution, GeneMarker® HTS, was developed and evaluated to address these limitations, and to provide a user-friendly interface for forensic practitioners and others interested in mtDNA analysis of MPS data. GeneMarker® HTS generates an exportable consensus mtDNA sequence that produces phylogenetically correct SNP and INDEL calls using a customizable motif-based alignment algorithm. Sequence data from 500 individuals, with various alignment asymmetries and levels of heteroplasmy, were used to assess the software. Accuracy in producing mtDNA haplotypes, the ability to correctly identify low-level heteroplasmic sequence variants, and the user-based features of the software were evaluated. Analyzed sequences yielded correct mtDNA haplotypes, and heteroplasmic variants were properly identified with minimal manual interpretation. The software offers numerous user-defined parameters for filtering the data that address the interests of researchers and practitioners, and provides multiple options for viewing and navigating through the data.
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Affiliation(s)
- Mitchell M Holland
- Forensic Science Program, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA 16802, United States.
| | - Erica D Pack
- Forensic Science Program, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA 16802, United States
| | - Jennifer A McElhoe
- Forensic Science Program, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA 16802, United States
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64
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Madel MB, Niederstätter H, Parson W. TriXY-Homogeneous genetic sexing of highly degraded forensic samples including hair shafts. Forensic Sci Int Genet 2016; 25:166-174. [PMID: 27613970 DOI: 10.1016/j.fsigen.2016.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/01/2016] [Indexed: 02/04/2023]
Abstract
Sexing of biological evidence is an important aspect in forensic investigations. A routinely used molecular-genetic approach to this endeavour is the amelogenin sex test, which is integrated in most commercially available polymerase chain reaction (PCR) kits for human identification. However, this assay is not entirely effective in respect to highly degraded DNA samples. This study presents a homogeneous PCR assay for robust sex diagnosis, especially for the analysis of severely fragmented DNA. The introduced triplex for the X and Y chromosome (TriXY) is based on real-time PCR amplification of short intergenic sequences (<50bp) on both gonosomes. Subsequent PCR product examination and molecular-genetic sex-assignment rely on high-resolution melting (HRM) curve analysis. TriXY was optimized using commercially available multi-donor human DNA preparations of either male or female origin and successfully evaluated on challenging samples, including 46 ancient DNA specimens from archaeological excavations and a total of 16 DNA samples extracted from different segments of eight hair shafts of male and female donors. Additionally, sensitivity and cross-species amplification were examined to further test the assay's utility in forensic investigations. TriXY's closed-tube format avoids post-PCR sample manipulations and, therefore, distinctly reduces the risk of PCR product carry-over contamination and sample mix-up, while reducing labour and financial expenses at the same time. The method is sensitive down to the DNA content of approximately two diploid cells and has proven highly useful on severely fragmented and low quantity ancient DNA samples. Furthermore, it even allowed for sexing of proximal hair shafts with very good results. In summary, TriXY facilitates highly sensitive, rapid, and costeffective genetic sex-determination. It outperforms existing sexing methods both in terms of sensitivity and minimum required template molecule lengths. Therefore, we feel confident that TriXY will prove to be a reliable addition to the toolbox currently used for sex-typing in forensic genetics and other fields of research.
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Affiliation(s)
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
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65
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Peck MA, Brandhagen MD, Marshall C, Diegoli TM, Irwin JA, Sturk-Andreaggi K. Concordance and reproducibility of a next generation mtGenome sequencing method for high-quality samples using the Illumina MiSeq. Forensic Sci Int Genet 2016; 24:103-111. [DOI: 10.1016/j.fsigen.2016.06.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/27/2016] [Accepted: 06/03/2016] [Indexed: 12/11/2022]
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66
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Hairy matters: MtDNA quantity and sequence variation along and among human head hairs. Forensic Sci Int Genet 2016; 25:1-9. [PMID: 27484846 DOI: 10.1016/j.fsigen.2016.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/20/2016] [Accepted: 07/23/2016] [Indexed: 01/31/2023]
Abstract
Hairs from the same donor have been found to differ in mtDNA sequence within and among themselves and from other tissues, which impacts interpretation of results obtained in a forensic setting. However, little is known on the magnitude of this phenomenon and published data on systematic studies are scarce. We addressed this issue by generating mtDNA control region (CR) profiles of >450 hair fragments from 21 donors by Sanger-type sequencing (STS). To mirror forensic scenarios, we compared hair haplotypes from the same donors to each other, to the corresponding buccal swab reference haplotypes and analyzed several fragments of individual hairs. We also investigated the effects of hair color, donor sex and age, mtDNA haplogroup and chemical treatment on mtDNA quantity, amplification success and variation. We observed a wide range of individual CR sequence variation. The reference haplotype was the only or most common (≥75%) hair haplotype for most donors. However, in two individuals, the reference haplotype was only found in about a third of the investigated hairs, mainly due to differences at highly variable positions. Similarly, most hairs revealed the reference haplotype along their entire length, however, about a fifth of the hairs contained up to 71% of segments with deviant haplotypes, independent of the longitudinal position. Variation affected numerous positions, typically restricted to the individual hair and in most cases heteroplasmic, but also fixed (i.e. homoplasmic) substitutions were observed. While existing forensic mtDNA interpretation guidelines were found still sufficient for all comparisons to reference haplotypes, some comparisons between hairs from the same donor could yield false exclusions when those guidelines are strictly followed. This study pinpoints the special care required when interpreting mtDNA results from hair in forensic casework.
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Gandini F, Achilli A, Pala M, Bodner M, Brandini S, Huber G, Egyed B, Ferretti L, Gómez-Carballa A, Salas A, Scozzari R, Cruciani F, Coppa A, Parson W, Semino O, Soares P, Torroni A, Richards MB, Olivieri A. Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes. Sci Rep 2016; 6:25472. [PMID: 27146119 PMCID: PMC4857117 DOI: 10.1038/srep25472] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/18/2016] [Indexed: 01/29/2023] Open
Abstract
Rare mitochondrial lineages with relict distributions can sometimes be disproportionately informative about deep events in human prehistory. We have studied one such lineage, haplogroup R0a, which uniquely is most frequent in Arabia and the Horn of Africa, but is distributed much more widely, from Europe to India. We conclude that: (1) the lineage ancestral to R0a is more ancient than previously thought, with a relict distribution across the Mediterranean/Southwest Asia; (2) R0a has a much deeper presence in Arabia than previously thought, highlighting the role of at least one Pleistocene glacial refugium, perhaps on the Red Sea plains; (3) the main episode of dispersal into Eastern Africa, at least concerning maternal lineages, was at the end of the Late Glacial, due to major expansions from one or more refugia in Arabia; (4) there was likely a minor Late Glacial/early postglacial dispersal from Arabia through the Levant and into Europe, possibly alongside other lineages from a Levantine refugium; and (5) the presence of R0a in Southwest Arabia in the Holocene at the nexus of a trading network that developed after ~3 ka between Africa and the Indian Ocean led to some gene flow even further afield, into Iran, Pakistan and India.
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Affiliation(s)
- Francesca Gandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.,School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.,Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Maria Pala
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefania Brandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Balazs Egyed
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Galicia, Spain
| | - Rosaria Scozzari
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Pedro Soares
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Martin B Richards
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
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Strategies for complete mitochondrial genome sequencing on Ion Torrent PGM™ platform in forensic sciences. Forensic Sci Int Genet 2016; 22:11-21. [DOI: 10.1016/j.fsigen.2016.01.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 12/30/2015] [Accepted: 01/08/2016] [Indexed: 01/08/2023]
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Parson W, Ballard D, Budowle B, Butler JM, Gettings KB, Gill P, Gusmão L, Hares DR, Irwin JA, King JL, Knijff PD, Morling N, Prinz M, Schneider PM, Neste CV, Willuweit S, Phillips C. Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements. Forensic Sci Int Genet 2016; 22:54-63. [DOI: 10.1016/j.fsigen.2016.01.009] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 01/16/2016] [Indexed: 12/15/2022]
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70
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Massively parallel sequencing of the entire control region and targeted coding region SNPs of degraded mtDNA using a simplified library preparation method. Forensic Sci Int Genet 2016; 22:37-43. [PMID: 26844917 DOI: 10.1016/j.fsigen.2016.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 01/12/2016] [Accepted: 01/20/2016] [Indexed: 02/04/2023]
Abstract
The application of next-generation sequencing (NGS) to forensic genetics is being explored by an increasing number of laboratories because of the potential of high-throughput sequencing for recovering genetic information from multiple markers and multiple individuals in a single run. A cumbersome and technically challenging library construction process is required for NGS. In this study, we propose a simplified library preparation method for mitochondrial DNA (mtDNA) analysis that involves two rounds of PCR amplification. In the first-round of multiplex PCR, six fragments covering the entire mtDNA control region and 22 fragments covering interspersed single nucleotide polymorphisms (SNPs) in the coding region that can be used to determine global haplogroups and East Asian haplogroups were amplified using template-specific primers with read sequences. In the following step, indices and platform-specific sequences for the MiSeq(®) system (Illumina) were added by PCR. The barcoded library produced using this simplified workflow was successfully sequenced on the MiSeq system using the MiSeq Reagent Nano Kit v2. A total of 0.4 GB of sequences, 80.6% with base quality of >Q30, were obtained from 12 degraded DNA samples and mapped to the revised Cambridge Reference Sequence (rCRS). A relatively even read count was obtained for all amplicons, with an average coverage of 5200 × and a less than three-fold read count difference between amplicons per sample. Control region sequences were successfully determined, and all samples were assigned to the relevant haplogroups. In addition, enhanced discrimination was observed by adding coding region SNPs to the control region in in silico analysis. Because the developed multiplex PCR system amplifies small-sized amplicons (<250 bp), NGS analysis using the library preparation method described here allows mtDNA analysis using highly degraded DNA samples.
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71
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Chaitanya L, Ralf A, van Oven M, Kupiec T, Chang J, Lagacé R, Kayser M. Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine. Hum Mutat 2015; 36:1236-47. [PMID: 26387877 PMCID: PMC5057296 DOI: 10.1002/humu.22905] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/01/2015] [Indexed: 11/13/2022]
Abstract
Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylogenetic resolution. Most established protocols on the different massively parallel sequencing (MPS) platforms, however, invariably involve the PCR amplification of large fragments, typically several kilobases in size, which may fail due to mtDNA fragmentation in the available degraded materials. We introduce a MPS tiling approach for simultaneous whole human mt genome sequencing using 161 short overlapping amplicons (average 200 bp) with the Ion Torrent Personal Genome Machine. We illustrate the performance of this new method by sequencing 20 DNA samples belonging to different worldwide mtDNA haplogroups. Additional quality control, particularly regarding the potential detection of nuclear insertions of mtDNA (NUMTs), was performed by comparative MPS analysis using the conventional long-range amplification method. Preliminary sensitivity testing revealed that detailed haplogroup inference was feasible with 100 pg genomic input DNA. Complete mt genome coverage was achieved from DNA samples experimentally degraded down to genomic fragment sizes of about 220 bp, and up to 90% coverage from naturally degraded samples. Overall, we introduce a new approach for whole mt genome MPS analysis from degraded and nondegraded materials relevant to resolve and infer maternal genetic ancestry at complete resolution in anthropological, evolutionary, medical, and forensic applications.
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Affiliation(s)
- Lakshmi Chaitanya
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Arwin Ralf
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Mannis van Oven
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Tomasz Kupiec
- Institute of Forensic ResearchSection of Forensic GeneticsKrakówPoland
| | - Joseph Chang
- Thermo Fisher ScientificSouth San FranciscoCalifornia, USA
| | - Robert Lagacé
- Thermo Fisher ScientificSouth San FranciscoCalifornia, USA
| | - Manfred Kayser
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
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