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From Forensic Epigenetics to Forensic Epigenomics: Broadening DNA Investigative Intelligence Athina Vidaki* and Manfred Kayser

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From Forensic Epigenetics to Forensic Epigenomics: Broadening DNA Investigative Intelligence Athina Vidaki* and Manfred Kayser Vidaki and Kayser Genome Biology (2017) 18:238 DOI 10.1186/s13059-017-1373-1 OPINION Open Access From forensic epigenetics to forensic epigenomics: broadening DNA investigative intelligence Athina Vidaki* and Manfred Kayser In contrast to genetics, epigenetics has been explored Abstract slowly in the forensic field [11, 12]. DNA methylation is Human genetic variation is a major resource in forensics, preferred in forensics over other epigenetic modifica- but does not allow all forensically relevant questions tions (such as changes in chromatin structure or histone to be answered. Some questions may instead be modifications) for both in vitro stability and high sensi- addressable via epigenomics, as the epigenome acts tivity in terms of DNA amounts required. Currently, as an interphase between the fixed genome and the only a limited number of DNA methylation markers are dynamic environment. We envision future forensic applied for a few forensic purposes, using technologies applications of DNA methylation analysis that will that enable the analysis of a small number of such broaden DNA-based forensic intelligence. Together with markers. These approaches can be classified as forensic genetic prediction of appearance and biogeographic epigenetics, and include DNA methylation profiling for ancestry, epigenomic lifestyle prediction is expected tissue determination [13], age prediction [14], and differ- to increase the ability of police to find unknown entiation between monozygotic twins [15]. The concept perpetrators of crime who are not identifiable using of personalized epigenomics, which is already used in current forensic DNA profiling. medical research [16], has not yet been recognized in the forensic field. Provided that scientific and technological progress in Introduction human epigenomics continues to advance rapidly, we Human genetic variation provides high discriminatory envision the establishment of an “epigenomic finger- power in identifying known persons, such as perpetra- print” [17] from crime scene traces as a promising ap- tors of crime [1, 2]. Although less established, it can also proach to address various forensically relevant questions aid in predicting appearance traits and biogeographic an- that cannot be answered through genetics. We also ex- cestry, which is useful for finding unknown persons who pect that in the near future novel technologies will be are not identifiable with standard DNA profiling [3, 4]. developed to allow the detection of large-scale DNA While the genome is typically non-informative regarding methylation variation in forensic-type DNA for many lifelong environmental influences on the body, which more forensic purposes—that is, forensic epigenomics can provide forensically relevant information, the epige- will emerge. These purposes are likely to include the “ ” nome acts as an interphase between the mostly fixed prediction of forensically informative lifestyle and envir- “ ” genome and the principally dynamic environment [5]. onmental information of an unknown trace donor (Fig. 1) For example, lifelong molecular responses to environ- to help further overcome the principle limitation of the mental exposure via varying DNA methylation levels at current use of DNA in human forensics. Current foren- thousands of cytosines across the genome result in indi- sic DNA profiling is completely comparative; that is, it – vidual epigenome variation [6 10]. aims to match DNA profiles from crime scene traces with that of known suspects, such as those included in forensic DNA databases [1, 2]. In consequence, perpetra- * Correspondence: [email protected] tors whose DNA profiles are unknown to the investiga- Department of Genetic Identification, Erasmus MC University Medical Center tors cannot be identified. Together with current Rotterdam, Room Ee1051, PO Box 2040, 3000 CA Rotterdam, The emergence of genetic prediction of appearance traits [3] Netherlands © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Vidaki and Kayser Genome Biology (2017) 18:238 Page 2 of 13 Fig. 1 Questions to which forensic epigenomics is envisioned to provide answers in the future and biogeographic ancestry [4], as well as epigenetic pre- DNA tests possible. In consequence, multiplex genotyp- diction of chronological age [3], epigenomic prediction ing methods for the simultaneous analysis of several epi- of lifestyle and environmental exposures will allow fur- genetic markers at once are required in forensic analysis ther characterization of unknown perpetrators from since single markers typically do not deliver enough fo- DNA, which is useful in criminal cases where no DNA rensically useful information. However, currently avail- profile match has been obtained. If put into practice, able technologies for the simultaneous analysis of a large such broadened DNA-based intelligence is expected to number of epigenetic markers, such as DNA methyla- guide police investigations towards the most likely group tion microarrays and whole-genome bisulfite sequen- of potential suspects. cing, are not suitable for forensic trace analysis because of the large input amounts of high-quality DNA they re- Forensic requirements of epigenetic/epigenomic quire. At the same time, current epigenetic analysis tech- analysis nologies that are able to deal with low-quality/quantity There are several requirements of forensic DNA ana- DNA, such as bisulfite pyrosequencing, methylation lysis, which are determined by the low quality and quan- quantitative PCR, and EPITYPER®, are limited in their tity of DNA that is typically available from crime scene multiplexing capacities (fewer than 20 markers), which traces, which has consequences for the type and number are often insufficient to fully address a forensic question of markers that can be analyzed, and the technology that of interest [18]. can be used. These requirements also apply to forensic Amounts of DNA obtained from crime scene traces are epigenetic/epigenomic analyses (Fig. 2). Moreover, there often low, typically in the picrogram–nanogram range. are additional technological challenges given the quantita- Therefore, highly sensitive technologies are needed in fo- tive outcome of epigenetic/epigenomic analysis, in contrast rensics to allow for reliable detection of DNA variation, to forensic genetics analysis, which is mostly qualitative. including DNA methylation levels. Methods such as The limited amount of human biological material methylation SNaPshot with (albeit limited) multiplexing available at crime scenes restricts the number of separate capacity currently have sensitivities down to a few Vidaki and Kayser Genome Biology (2017) 18:238 Page 3 of 13 Fig. 2 Challenges and considerations in developing and implementing forensic epigenomics. CpG cytosine-phosphate-guanine, pg picogram nanograms of DNA input per PCR [13, 19]. However, of the epigenetic analysis depends on a direct comparison most current epigenetic methodologies require bisulfite between crime scene material and reference samples, sam- conversion prior to marker analysis; the efficiency of con- ples from the same tissue type should be used. However, verting unmethylated cytosines into uracils strongly de- additional challenges in interpretation can be encountered pends on the DNA input. Typically, bisulfite conversion when analyzing heterogeneous forensic-type samples such kits require a minimum of 50–200 ng DNA for reliable as whole blood, consisting of different cell types with dis- performance. Reduced DNA input leads to increased tech- tinct epigenomes [25, 26]. nical variation and thus an increased error range of the When it comes to predictive DNA analysis in forensics subsequent DNA methylation analysis. Highly sensitive (and beyond), the accuracy of predicting a trait from technologies allowing for simultaneous analysis of large DNA, including methylation markers, should be as high numbers of DNA methylation markers from low-quality/ as possible. Prediction accuracy should be investigated quantity DNA do not yet exist. via different approaches and estimated via different mea- Crime scenes traces can consist of different cell types. sures in as many test samples as possible. Potential con- While cell/tissue-type composition is mostly not restrict- founding DNA methylation effects [27] caused by a ive in genetic analysis, it can be challenging in epigenetic combination of factors such as age or environmental ex- analysis. Forensic epigenetic tests have to work equally posures should also be taken into account during inter- well in all forensically relevant cell or tissue types or, if pretation, and properly tested before implementation. that is impossible, need to be tailored to specific tissue However, forensic DNA prediction is generally applied in types, requiring tissue-type determination prior to epi- cases where the police have little or no knowledge of the genetic analysis. Some DNA methylation sites can show identity of the trace donor and how to find him/her.
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