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Forensic Genomics

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Technologies and Resources for Genetics".

Deadline for manuscript submissions: closed (31 December 2017) | Viewed by 124161

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Special Issue Editors

Prof. Dr. Manfred Kayser

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Guest Editor

Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
Interests: forensic genetics; forensic molecular biology; forensic epigenetics; forensic microbiome analysis; forensic DNA phenotyping; forensic Y-chromosome analysis; forensic tissue identification; genetic ancestry inference; genetic appearance prediction

Prof. Dr. Walther Parson

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Guest Editor

Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, 6020 Innsbruck, Austria
Interests: forensic genetics; mitochondrial DNA; human identification; forensic DNA phenotyping

Special Issue Information

Dear Colleagues,

Although being a conservative field per se due to serving law enforcement, forensic genetics is slowly transitioning into forensic genomics. With this Special Issue of Genes, we acknowledge and appreciate this rather recent development. Genomic, transcriptomic, and epigenomic principles, data, and technologies are applied to identify and analyse useful DNA and RNA markers to address various forensic questions that cannot be answered, or only in a limited way, via genetic or other approaches. Human genome data produced with SNP microarray technologies, and increasingly whole exome and whole genome data established via massively parallel sequencing (MPS) technologies, are used to identify DNA markers for individual identification, as well as for appearance and ancestry prediction. The latter is forensically relevant for finding unknown perpetrators of crime who are unidentifiable with standard DNA profiling. Human transcriptome data of various tissues generated with expression microarray technologies, and increasingly with whole transcriptome sequencing via MPS technologies, are used to identify RNA markers to determine the cellular source of crime scene sample. This is forensically relevant for reconstructing the course of events that may have happened at the scene of crime and to support the use of DNA at the activity level of evidence interpretation. Human epigenome data established with DNA methylation microarray technologies, and increasingly by whole epigenome sequencing via MPS technologies, are used to identify DNA methylation markers for forensic tissue identification, for predicting lifetime age suitable for finding unknown perpetrators and for differentiating identical twins, the latter two cannot be identified via standard DNA profiling. Targeted MPS technologies, partly combined with hybridization capture and primer extension capture technologies, are applied to analyse forensic DNA and RNA markers with increased throughput, which improves various forensic applications, such as individual and lineage identification, appearance and ancestry prediction, as well as the interpretation of DNA mixtures produced from more than one person. Non-human genomic and transcriptomic data, such as those from insects or microbes, are useful in the forensic context, e.g., to estimate time of death, and for microbial species and strain identification to solve cases of bioterrorism. Several of these developments are covered by the articles collated in this Special Issue we have the privilege to serve as guest editors for. Thus, we not only aim to introduce the field of forensics to the wider community of geneticists, but do so by emphasizing on topics where genomic principles, methods, and dataset are started to be employed in the forensic context.

Prof. Manfred Kayser
Prof. Walther Parson
Guest Editors

Manuscript Submission Information

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Keywords

Forensics
Genomics
Transcriptomics
Epigenomics
Massive parallel sequencing (MPS)
Next generation sequencing (NGS)
Individual identification
Lineage identification
Missing person identification
Ancestry prediction
Appearance prediction
Time of death
Post mortem interval
Bioterrorism

Published Papers (11 papers)

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Editorial

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138 KiB

Open AccessEditorial

Transitioning from Forensic Genetics to Forensic Genomics

by Manfred Kayser and Walther Parson

Genes 2018, 9(1), 3; https://doi.org/10.3390/genes9010003 - 22 Dec 2017

Cited by 6 | Viewed by 4981

Abstract

Due to its support of law enforcement, forensics is a conservative field; nevertheless, driven by scientific and technological progress, forensic genetics is slowly transitioning into forensic genomics. With this Special Issue of Genes we acknowledge and appreciate this rather recent development by not only introducing the field of forensics to the wider community of geneticists, but we do so by emphasizing on different topics of forensic relevance where genomic, transcriptomic, and epigenomic principles, methods, and datasets of humans and beyond are beginning to be used to answer forensic questions. Full article

(This article belongs to the Special Issue Forensic Genomics)

Research

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20 pages, 1329 KiB

Open AccessArticle

Fragmented Nuclear DNA Is the Predominant Genetic Material in Human Hair Shafts

by Michael D. Brandhagen, Odile Loreille and Jodi A. Irwin

Genes 2018, 9(12), 640; https://doi.org/10.3390/genes9120640 - 18 Dec 2018

Cited by 41 | Viewed by 7593

Abstract

While shed hairs are one of the most commonly encountered evidence types, they are among the most limited in terms of DNA quantity and quality. As a result, nuclear DNA short tandem repeat (STR) profiling is generally unsuccessful and DNA testing of shed hair is instead performed by targeting the mitochondrial DNA control region. Although the high copy number of mitochondrial DNA relative to nuclear DNA routinely permits the recovery of mitochondrial DNA (mtDNA) data in these cases, mtDNA profiles do not offer the discriminatory power of nuclear DNA profiles. In order to better understand the total content and degradation state of DNA in single shed hairs and assess the feasibility of recovering highly discriminatory nuclear DNA data from this common evidence type, high throughput shotgun sequencing was performed on both recently collected and aged (approximately 50-year-old) hair samples. The data reflect trends that have been demonstrated previously with other technologies, namely that mtDNA quantity and quality decrease along the length of the hair shaft. In addition, the shotgun data reveal that nuclear DNA is present in shed hair and surprisingly abundant relative to mitochondrial DNA, even in the most distal fragments. Nuclear DNA comprised, at minimum, 88% of the total human reads in any given sample, and generally more than 95%. Here, we characterize both the nuclear and mitochondrial DNA content of shed hairs and discuss the implications of these data for forensic investigations. Full article

(This article belongs to the Special Issue Forensic Genomics)

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25 pages, 4477 KiB

Open AccessArticle

Investigating the Epigenetic Discrimination of Identical Twins Using Buccal Swabs, Saliva, and Cigarette Butts in the Forensic Setting

by Athina Vidaki, Vivian Kalamara, Elena Carnero-Montoro, Timothy D. Spector, Jordana T. Bell and Manfred Kayser

Genes 2018, 9(5), 252; https://doi.org/10.3390/genes9050252 - 14 May 2018

Cited by 19 | Viewed by 7528

Abstract

Monozygotic (MZ) twins are typically indistinguishable via forensic DNA profiling. Recently, we demonstrated that epigenetic differentiation of MZ twins is feasible; however, proportions of twin differentially methylated CpG sites (tDMSs) identified in reference-type blood DNA were not replicated in trace-type blood DNA. Here we investigated buccal swabs as typical forensic reference material, and saliva and cigarette butts as commonly encountered forensic trace materials. As an analog to a forensic case, we analyzed one MZ twin pair. Epigenome-wide microarray analysis in reference-type buccal DNA revealed 25 candidate tDMSs with >0.5 twin-to-twin differences. MethyLight quantitative PCR (qPCR) of 22 selected tDMSs in trace-type DNA revealed in saliva DNA that six tDMSs (27.3%) had >0.1 twin-to-twin differences, seven (31.8%) had smaller (<0.1) but robustly detected differences, whereas for nine (40.9%) the differences were in the opposite direction relative to the microarray data; for cigarette butt DNA, results were 50%, 22.7%, and 27.3%, respectively. The discrepancies between reference-type and trace-type DNA outcomes can be explained by cell composition differences, method-to-method variation, and other technical reasons including bisulfite conversion inefficiency. Our study highlights the importance of the DNA source and that careful characterization of biological and technical effects is needed before epigenetic MZ twin differentiation is applicable in forensic casework. Full article

(This article belongs to the Special Issue Forensic Genomics)

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19 pages, 7562 KiB

Open AccessArticle

Dating Pupae of the Blow Fly Calliphora vicina Robineau–Desvoidy 1830 (Diptera: Calliphoridae) for Post Mortem Interval—Estimation: Validation of Molecular Age Markers

by Barbara K. Zajac, Jens Amendt, Marcel A. Verhoff and Richard Zehner

Genes 2018, 9(3), 153; https://doi.org/10.3390/genes9030153 - 09 Mar 2018

Cited by 18 | Viewed by 5373

Abstract

Determining the age of juvenile blow flies is one of the key tasks of forensic entomology when providing evidence for the minimum post mortem interval. While the age determination of blow fly larvae is well established using morphological parameters, the current study focuses on molecular methods for estimating the age of blow flies during the metamorphosis in the pupal stage, which lasts about half the total juvenile development. It has already been demonstrated in several studies that the intraspecific variance in expression of so far used genes in blow flies is often too high to assign a certain expression level to a distinct age, leading to an inaccurate prediction. To overcome this problem, we previously identified new markers, which show a very sharp age dependent expression course during pupal development of the forensically-important blow fly Calliphora vicina Robineau–Desvoidy 1830 (Diptera: Calliphoridae) by analyzing massive parallel sequencing (MPS) generated transcriptome data. We initially designed and validated two quantitative polymerase chain reaction (qPCR) assays for each of 15 defined pupal ages representing a daily progress during the total pupal development if grown at 17 °C. We also investigated whether the performance of these assays is affected by the ambient temperature, when rearing pupae of C. vicina at three different constant temperatures—namely 17 °C, 20 °C and 25 °C. A temperature dependency of the performance could not be observed, except for one marker. Hence, for each of the defined development landmarks, we can present gene expression profiles of one to two markers defining the mentioned progress in development. Full article

(This article belongs to the Special Issue Forensic Genomics)

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18 pages, 2151 KiB

Open AccessArticle

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

by Odile Loreille, Shashikala Ratnayake, Adam L. Bazinet, Timothy B. Stockwell, Daniel D. Sommer, Nadin Rohland, Swapan Mallick, Philip L.F. Johnson, Pontus Skoglund, Anthony J. Onorato, Nicholas H. Bergman, David Reich and Jodi A. Irwin

Genes 2018, 9(3), 135; https://doi.org/10.3390/genes9030135 - 01 Mar 2018

Cited by 34 | Viewed by 57033

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 (R_X and R_Y), 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. Full article

(This article belongs to the Special Issue Forensic Genomics)

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20 pages, 2811 KiB

Open AccessArticle

Deep-Coverage MPS Analysis of Heteroplasmic Variants within the mtGenome Allows for Frequent Differentiation of Maternal Relatives

by Mitchell M. Holland, Kateryna D. Makova and Jennifer A. McElhoe

Genes 2018, 9(3), 124; https://doi.org/10.3390/genes9030124 - 26 Feb 2018

Cited by 27 | Viewed by 5478

Abstract

Distinguishing between maternal relatives through mitochondrial (mt) DNA sequence analysis has been a longstanding desire of the forensic community. Using a deep-coverage, massively parallel sequencing (DCMPS) approach, we studied the pattern of mtDNA heteroplasmy across the mtgenomes of 39 mother-child pairs of European decent; haplogroups H, J, K, R, T, U, and X. Both shared and differentiating heteroplasmy were observed on a frequent basis in these closely related maternal relatives, with the minor variant often presented as 2–10% of the sequencing reads. A total of 17 pairs exhibited differentiating heteroplasmy (44%), with the majority of sites (76%, 16 of 21) occurring in the coding region, further illustrating the value of conducting sequence analysis on the entire mtgenome. A number of the sites of differentiating heteroplasmy resulted in non-synonymous changes in protein sequence (5 of 21), and to changes in transfer or ribosomal RNA sequences (5 of 21), highlighting the potentially deleterious nature of these heteroplasmic states. Shared heteroplasmy was observed in 12 of the 39 mother-child pairs (31%), with no duplicate sites of either differentiating or shared heteroplasmy observed; a single nucleotide position (16093) was duplicated between the data sets. Finally, rates of heteroplasmy in blood and buccal cells were compared, as it is known that rates can vary across tissue types, with similar observations in the current study. Our data support the view that differentiating heteroplasmy across the mtgenome can be used to frequently distinguish maternal relatives, and could be of interest to both the medical genetics and forensic communities. Full article

(This article belongs to the Special Issue Forensic Genomics)

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13 pages, 812 KiB

Open AccessArticle

Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models

by Aeriel Belk, Zhenjiang Zech Xu, David O. Carter, Aaron Lynne, Sibyl Bucheli, Rob Knight and Jessica L. Metcalf

Genes 2018, 9(2), 104; https://doi.org/10.3390/genes9020104 - 16 Feb 2018

Cited by 75 | Viewed by 9415

Abstract

Death investigations often include an effort to establish the postmortem interval (PMI) in cases in which the time of death is uncertain. The postmortem interval can lead to the identification of the deceased and the validation of witness statements and suspect alibis. Recent research has demonstrated that microbes provide an accurate clock that starts at death and relies on ecological change in the microbial communities that normally inhabit a body and its surrounding environment. Here, we explore how to build the most robust Random Forest regression models for prediction of PMI by testing models built on different sample types (gravesoil, skin of the torso, skin of the head), gene markers (16S ribosomal RNA (rRNA), 18S rRNA, internal transcribed spacer regions (ITS)), and taxonomic levels (sequence variants, species, genus, etc.). We also tested whether particular suites of indicator microbes were informative across different datasets. Generally, results indicate that the most accurate models for predicting PMI were built using gravesoil and skin data using the 16S rRNA genetic marker at the taxonomic level of phyla. Additionally, several phyla consistently contributed highly to model accuracy and may be candidate indicators of PMI. Full article

(This article belongs to the Special Issue Forensic Genomics)

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19 pages, 2982 KiB

Open AccessArticle

Applications of Probe Capture Enrichment Next Generation Sequencing for Whole Mitochondrial Genome and 426 Nuclear SNPs for Forensically Challenging Samples

by Shelly Y. Shih, Nikhil Bose, Anna Beatriz R. Gonçalves, Henry A. Erlich and Cassandra D. Calloway

Genes 2018, 9(1), 49; https://doi.org/10.3390/genes9010049 - 22 Jan 2018

Cited by 39 | Viewed by 13066 | Correction

Abstract

The application of next generation sequencing (NGS) for the analysis of mitochondrial (mt) DNA, short tandem repeats (STRs), and single nucleotide polymorphism (SNPs) has demonstrated great promise for challenging forensic specimens, such as degraded, limited, and mixed samples. Target enrichment using probe capture rather than PCR amplification offers advantages for analysis of degraded DNA since two intact PCR primer sites in the template DNA molecule are not required. Furthermore, NGS software programs can help remove PCR duplicates to determine initial template copy numbers of a shotgun library. Moreover, the same shotgun library prepared from a limited DNA source can be enriched for mtDNA as well as nuclear markers by hybrid capture with the relevant probe panels. Here, we demonstrate the use of this strategy in the analysis of limited and mock degraded samples using our custom probe capture panels for massively parallel sequencing of the whole mtgenome and 426 SNP markers. We also applied the mtgenome capture panel in a mixed sample and analyzed using both phylogenetic and variant frequency based bioinformatics tools to resolve the minor and major contributors. Finally, the results obtained on individual telogen hairs demonstrate the potential of probe capture NGS analysis for both mtDNA and nuclear SNPs for challenging forensic specimens. Full article

(This article belongs to the Special Issue Forensic Genomics)

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2651 KiB

Open AccessArticle

Flanking Variation Influences Rates of Stutter in Simple Repeats

by August E. Woerner, Jonathan L. King and Bruce Budowle

Genes 2017, 8(11), 329; https://doi.org/10.3390/genes8110329 - 17 Nov 2017

Cited by 18 | Viewed by 3983

Abstract

It has been posited that the longest uninterrupted stretch (LUS) of tandem repeats, as defined by the number of exactly matching repeating motif units, is a better predictor of rates of stutter than the parental allele length (PAL). While there are cases where this hypothesis is likely correct, such as the 9.3 allele in the TH01 locus, there can be situations where it may not apply as well. For example, the PAL may capture flanking indel variations while remaining insensitive to polymorphisms in the repeat, and these haplotypic changes may impact the stutter rate. To address this, rates of stutter were contrasted against the LUS as well as the PAL on different flanking haplotypic backgrounds. This study shows that rates of stutter can vary substantially depending on the flanking haplotype, and while there are cases where the LUS is a better predictor of stutter than the PAL, examples to the contrary are apparent in commonly assayed forensic markers. Further, flanking variation that is 7 bp from the repeat region can impact rates of stutter. These findings suggest that non-proximal effects, such as DNA secondary structure, may be impacting the rates of stutter in common forensic short tandem repeat markers. Full article

(This article belongs to the Special Issue Forensic Genomics)

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1355 KiB

Open AccessArticle

Human Organ Tissue Identification by Targeted RNA Deep Sequencing to Aid the Investigation of Traumatic Injury

by Erin Hanson and Jack Ballantyne

Genes 2017, 8(11), 319; https://doi.org/10.3390/genes8110319 - 10 Nov 2017

Cited by 14 | Viewed by 4053

Abstract

Molecular analysis of the RNA transcriptome from a putative tissue fragment should permit the assignment of its source to a specific organ, since each will exhibit a unique pattern of gene expression. Determination of the organ source of tissues from crime scenes may aid in shootings and other investigations. We have developed a prototype massively parallel sequencing (MPS) mRNA profiling assay for organ tissue identification that is designed to definitively identify 10 organ/tissue types using a targeted panel of 46 mRNA biomarkers. The identifiable organs and tissues include brain, lung, liver, heart, kidney, intestine, stomach, skeletal muscle, adipose, and trachea. The biomarkers were chosen after iterative specificity testing of numerous candidate genes in various tissue types. The assay is very specific, with little cross-reactivity with non-targeted tissue, and can detect RNA mixtures from different tissues. We also demonstrate the ability of the assay to successful identify the tissue source of origin using a single blind study. Full article

(This article belongs to the Special Issue Forensic Genomics)

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