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Emery MV, Bolhofner K, Spake L, Ghafoor S, Versoza CJ, Rawls EM, Winingear S, Buikstra JE, Loreille O, Fulginiti LC, Stone AC. Targeted enrichment of whole-genome SNPs from highly burned skeletal remains. J Forensic Sci 2024; 69:1558-1577. [PMID: 38415845 DOI: 10.1111/1556-4029.15482] [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: 09/29/2023] [Revised: 01/13/2024] [Accepted: 01/19/2024] [Indexed: 02/29/2024]
Abstract
Genetic assessment of highly incinerated and/or degraded human skeletal material is a persistent challenge in forensic DNA analysis, including identifying victims of mass disasters. Few studies have investigated the impact of thermal degradation on whole-genome single-nucleotide polymorphism (SNP) quality and quantity using next-generation sequencing (NGS). We present whole-genome SNP data obtained from the bones and teeth of 27 fire victims using two DNA extraction techniques. Extracts were converted to double-stranded DNA libraries then enriched for whole-genome SNPs using unpublished biotinylated RNA baits and sequenced on an Illumina NextSeq 550 platform. Raw reads were processed using the EAGER (Efficient Ancient Genome Reconstruction) pipeline, and the SNPs filtered and called using FreeBayes and GATK (v. 3.8). Mixed-effects modeling of the data suggest that SNP variability and preservation is predominantly determined by skeletal element and burn category, and not by extraction type. Whole-genome SNP data suggest that selecting long bones, hand and foot bones, and teeth subjected to temperatures <350°C are the most likely sources for higher genomic DNA yields. Furthermore, we observed an inverse correlation between the number of captured SNPs and the extent to which samples were burned, as well as a significant decrease in the total number of SNPs measured for samples subjected to temperatures >350°C. Our data complement previous analyses of burned human remains that compare extraction methods for downstream forensic applications and support the idea of adopting a modified Dabney extraction technique when traditional forensic methods fail to produce DNA yields sufficient for genetic identification.
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Affiliation(s)
- Matthew V Emery
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
- Center for Evolution and Medicine, Arizona State University, Life Sciences C, Tempe, Arizona, USA
| | - Katelyn Bolhofner
- Center for Bioarchaeology, Arizona State University, Tempe, Arizona, USA
- School of Interdisciplinary Forensics, Arizona State University, Glendale, Arizona, USA
| | - Laure Spake
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
| | - Suhail Ghafoor
- Center for Evolution and Medicine, Arizona State University, Life Sciences C, Tempe, Arizona, USA
| | - Cyril J Versoza
- Center for Evolution and Medicine, Arizona State University, Life Sciences C, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Life Sciences C, Tempe, Arizona, USA
| | - Erin M Rawls
- School of Life Sciences, Arizona State University, Life Sciences C, Tempe, Arizona, USA
| | - Stevie Winingear
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Jane E Buikstra
- Center for Evolution and Medicine, Arizona State University, Life Sciences C, Tempe, Arizona, USA
- Center for Bioarchaeology, Arizona State University, Tempe, Arizona, USA
| | - Odile Loreille
- FBI Laboratory, DNA Support Unit, Quantico, Virginia, USA
| | - Laura C Fulginiti
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
- Maricopa County Office of the Medical Examiner, Phoenix, Arizona, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
- Center for Evolution and Medicine, Arizona State University, Life Sciences C, Tempe, Arizona, USA
- Center for Bioarchaeology, Arizona State University, Tempe, Arizona, USA
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Haarkötter C, Gálvez X, Vinueza-Espinosa DC, Medina-Lozano MI, Saiz M, Lorente JA, Álvarez JC. A comparison of five DNA extraction methods from degraded human skeletal remains. Forensic Sci Int 2023; 348:111730. [PMID: 37224759 DOI: 10.1016/j.forsciint.2023.111730] [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: 03/24/2023] [Revised: 04/19/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023]
Abstract
Extracting DNA from degraded human remains poses a challenge for any forensic genetics laboratory, as it requires efficient high-throughput methods. While little research has compared different techniques, silica in suspension has been identified in the literature as the best method for recovering small fragments, which are often present in these types of samples. In this study, we tested five DNA extraction protocols on 25 different degraded skeletal remains. Including the humerus, ulna, tibia, femur, and petrous bone. The five protocols were organic extraction by phenol/chloroform/isoamyl alcohol, silica in suspension, High Pure Nucleic Acid Large Volume silica columns (Roche), InnoXtract™ Bone (InnoGenomics), and PrepFiler™ BTA with AutoMate™ Express robot (ThermoFisher). We analysed five DNA quantification parameters (small human target quantity, large human target quantity, human male target quantity, degradation index, and internal PCR control threshold), and five DNA profile parameters (number of alleles with peak height higher than analytic and stochastic threshold, average relative fluorescence units (RFU), heterozygous balance, and number of reportable loci) were analysed. Our results suggest that organic extraction by phenol/chloroform/isoamyl alcohol was the best performing method in terms of both quantification and DNA profile results. However, Roche silica columns were found to be the most efficient method.
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Affiliation(s)
- Christian Haarkötter
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
| | - Xiomara Gálvez
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain.
| | - Diana C Vinueza-Espinosa
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
| | - María Isabel Medina-Lozano
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
| | - María Saiz
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
| | - José Antonio Lorente
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
| | - Juan Carlos Álvarez
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
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Development and validation of a SYBR green-based mitochondrial DNA quantification method by following the MIQE and other guidelines. Leg Med (Tokyo) 2022; 58:102096. [PMID: 35689884 DOI: 10.1016/j.legalmed.2022.102096] [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: 01/30/2022] [Revised: 04/11/2022] [Accepted: 05/27/2022] [Indexed: 01/28/2023]
Abstract
In forensic mitochondrial DNA (mtDNA) analysis, quantitative PCR (qPCR) is usually performed to obtain high-quality sequence data for subsequent Sanger or massively parallel sequencing. Unlike methods for nuclear DNA quantification using qPCR, a calibrator is necessary to obtain mtDNA concentrations (i.e., copies/µL). Herein, we developed and validated a mtDNA quantification method based on a SYBR Green assay by following MIQE [Bustin et al., Clin. Chem. 55 (2009) 611-22] and other guidelines. Primers were designed to amplify nucleotide positions 16,190-16,420 in hypervariable region 1 for qPCR using PowerUp SYBR Green and QuantStudio 5. The optimized conditions were 0.3 µM each primer and an annealing temperature of 60 °C under a 2-step cycling protocol. K562 DNA at 100 pg/µL was converted into a mtDNA concentration of 16,400 copies/µL using linearized plasmid DNA. This mtDNA calibrator was obtained by cloning the synthesized DNA fragments of mtDNA (positions 16,140-16,470) containing a 100-bp inversion. The linear dynamic range of the K562 standard curve was 10,000-0.1 pg/µL (r2 ≥ 0.999). The accuracy was examined using NIST SRM 2372a, and its components A, B, and C were quantified with differences of -29.4%, -35.0%, and -22.0%, respectively, against the mtDNA concentrations calculated from published NIST data. We also examined the specificity of the primers, stability of the reaction mix, precision, tolerance against PCR inhibitors, and cross-reactivity against DNA from various animal taxa. Our newly developed mtDNA quantification method is expected to be useful for forensic mtDNA analysis.
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