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Mini review article, past, present, and future of dna typing for analyzing human and non-human forensic samples.

• 1 Department of Biological Sciences, Florida International University, Miami, FL, United States
• 2 International Forensic Research Institute, Florida International University, Miami, FL, United States

Forensic DNA analysis has vastly evolved since the first forensic samples were evaluated by restriction fragment length polymorphism (RFLP). Methodologies advanced from gel electrophoresis techniques to capillary electrophoresis and now to next generation sequencing (NGS). Capillary electrophoresis was and still is the standard method used in forensic analysis. However, dependent upon the information needed, there are several different techniques that can be used to type a DNA fragment. Short tandem repeat (STR) fragment analysis, Sanger sequencing, SNapShot, and capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) are a few of the techniques that have been used for the genetic analysis of DNA samples. NGS is the newest and most revolutionary technology and has the potential to be the next standard for genetic analysis. This review briefly encompasses many of the techniques and applications that have been utilized for the analysis of human and nonhuman DNA samples.

Introduction

Forensic genetics applies genetic tools and scientific methodology to solve criminal and civil litigations ( Editorial, 2007 ). Locard’s Exchange Principle states that every contact leaves a trace, making any evidence a key component in forensic analysis. Biological evidence can comprise of cellular material or cell-free DNA from crime scenes, and as technologies improved, genetic methodologies were expanded to include human and non-human forensic analyses. Although these methodologies can be used for any genome, the prevalence of databases and standard guidelines has allowed human DNA typing to become the gold standard. This review will discuss the historical progression of DNA analysis techniques, strengths and limitations, and their possible forensic applications applied to human and non-human genetics.

Methodologies to Detect Genetic Differences in Humans Is the “Gold Standard”

“dna fingerprinting”: the beginning of human forensic dna typing.

“DNA fingerprinting” was serendipitously discovered in 1984 ( Jeffreys, 2013 ). What they found propelled DNA “fingerprinting,” or DNA typing, to the forefront in legal cases to become the “gold standard” for forensic genetics in a court of law. Jeffreys first used restriction enzymes to fragment DNA, a method in which restriction endonucleases (RE) enzymes fragment the genomic DNA, producing restriction fragment length polymorphisms (RFLP) patterns. Since each RE recognizes specific DNA sequences to enzymatically cut the DNA, then inherent differences between gene sequences, due to evolutionary changes, will produce different fragment lengths. If the enzyme site is present in one individual but has changed in a different individual, the fragment lengths, once separated and visualized, will differ. While this technique was useful for some studies, Jeffreys did not find it useful for his particular genetic studies. Subsequently when working with the myoglobin gene in seals, he discovered that a short section of that gene – a minisatellite – was conserved and when isolated and cloned could be used to detect inherited genetic lineages as well as individualize a subject. Fragment length separation by electrophoresis, followed by transfer to Southern blot membranes, hybridized with a specific or non-specific complementary isotopic DNA probe, allowed for DNA fragments visualization ( Jeffreys et al., 1985b ). Upon careful analysis, Jeffreys determined that the fragments represented different combinations of DNA repetitive elements, unique to each individual, and could be used to better identify individuals or kinship lineages ( Jeffreys et al., 1985b ). Jeffreys’ technology was used in several subsequent paternity, immigration, and forensic genetics cases ( Gill et al., 1985 ; Jeffreys et al., 1985a ; Evans, 2007 ). This was just the beginning of a whole new era in DNA typing.

Restriction Fragment Length Polymorphism (RFLP) Analysis: The Past

After Jeffreys’ discoveries, many DNA analyses methods involving electrophoretic fragment separation were discovered. Many were based on RFLP principles ( Botstein et al., 1980 ), e.g., amplified fragment length polymorphism (AFLP) ( Vos et al., 1995 ), and terminal restriction fragment length polymorphism (TRFLP) ( Liu et al., 1997 ). Others like length heterogeneity- polymerase chain reaction (LH-PCR) ( Suzuki et al., 1998 ) were based on intrinsic insertions and deletions of bases within specific genetic markers. Sanger sequencing ( Sanger and Coulson, 1975 ), and single-strand conformational polymorphism (SSCP) analysis ( Orita et al., 1989 ), while separated by electrophoresis, are theoretically based on single base sequence changes rather than insertions, deletions or RE site differences. While Jeffrey’s DNA fingerprinting method provided a very high power of discrimination, the main limitations were it was very time-consuming and required at least 10–25 ng of DNA to be successful ( Wyman and White, 1980 ). With these limitations, RFLP was not always feasible for forensic cases.

Short Tandem Repeat (STR) Analysis: The Present

The polymerase chain reaction (PCR) was discovered by Kary Mullis in 1985 and helped transform all DNA analyses ( Mullis et al., 1986 ). The current standard for human DNA typing is short tandem repeat (STR) analysis ( McCord et al., 2019 ). This method amplifies highly polymorphic, repetitive DNA regions by PCR and separates them by amplicon length using capillary electrophoresis. These inheritable markers are a series of 2–7 bases tandemly repeated at a specific locus, often in non-coding genetic regions. Forensic STRs are commonly tetranucleotide repeats ( Goodwin et al., 2011 ), chosen because of their technical robustness and high variation among individuals ( Kim et al., 2015 ). The combined DNA index system (CODIS) uses 20 core STR loci, expanded in 2017, and several commercial kits are available that contain these STRs ( Oostdik et al., 2014 ; Ludeman et al., 2018 ). After amplification, different fluorochromes on each primer set allow for visualization of STRs after deconvolution, creating a STR profile consisting of a combination of genotypes ( Gill et al., 2015 ). This method has become the gold standard for human forensics. Its greatest strength is the standardization of loci used by all laboratories and an extremely large searchable database of genetic profiles. However, some limitations and challenges are faced when dealing with highly degraded or low template DNA samples. To overcome these technical challenges, standardized mini-STR kits have been developed which use shorter versions of the core STRs and can be used in the same manner for forensic cases ( Butler et al., 2007 ; Constantinescu et al., 2012 ). Keep in mind, DNA typing of humans – a single species – is the gold standard because of (a) the concerted scientific effort to standardize loci to analyze, (b) the development of commercial kits that can produce the same results regardless of instrumentation or laboratory performing the work, (c) a compatible and very large database that provides allelic frequencies for all sub-populations of humans, (d) standardized statistical methods used to report the results and (e) many court cases that have accepted human DNA typing evidence in a court of law – setting the precedent for future cases to use DNA typing results.

Methodologies to Detect Genetic Differences in Non-Humans: Past and Present

Amplified fragment length polymorphism (aflp) analysis.

It was not long before scientists realized that non-human DNA could provide informative genetic evidence in forensic cases. Applications include bioterrorism, wildlife crimes, human identification through skin microorganisms, and so much more ( Arenas et al., 2017 ). Since large quantities of biological materials are frequently not found at crime scenes, successful RFLP analyses were unlikely. Combining restriction enzymes and PCR technology, a process known as AFLP analysis ( Vos et al., 1995 ), became a method for DNA fingerprinting using minute amounts of unknown sourced DNA. REs digest genomic DNA, then ligation of a constructed adapter sequence to the ends of all fragments allows the annealing of primers designed to recognize the adaptor sequences. Subsequent amplification generates many amplicons ranging in length when separated and visualized in an electropherogram or on a gel ( Vos et al., 1995 ; Butler, 2012 ). AFLP markers for plant forensic DNA typing have been used because it provides high discrimination, requires only small amounts of DNA and the method is reproducible, all forensically important characteristics ( Datwyler and Weiblen, 2006 ). For example, since most cannabis is clonally propagated, subsequent generations will have identical genetic profiles as seen with AFLP ( Miller Coyle et al., 2003 ), providing useful intelligence links back to the source population. But there are significant variation between cultivars and within populations, so not having a standard database representing the species’ diversity for statistical comparisons greatly limits the method’s applicability. Another forensic example of its use is differentiating between marijuana and hemp, two morphologically and genetically similar plants, one an illicit drug while the other is not. In this study, three populations of hemp and one population of marijuana were analyzed with AFLP producing 18 bands that were specific to hemp samples. Additionally, 51.9% of molecular variance occurred within populations indicating these polymorphisms were useful for forensic individualization ( Datwyler and Weiblen, 2006 ).

Terminal Restriction Fragment Length Polymorphism (TRFLP) Analysis

As a result of the anthrax letter attacks of 2001, microbial forensics came to the forefront ( Schmedes et al., 2016 ), a discipline that combines multiple scientific specialties – microbiology, genetics, forensic science, and analytical chemistry. One method used to compare microbial communities is TRFLP ( Liu et al., 1997 ; Osborn et al., 2000 ; Butler, 2012 ). With this method, the DNA is amplified using “universal,” highly conserved primer sequences shared across all organisms of interest, i.e., the 16S rRNA genes in bacteria and Archaea, and then uses REs to fragment the PCR products ( Table 1 ). Separated by capillary electrophoresis, only the fluorescently tagged terminal restricted fragments are visualized ( Mrkonjic Fuka et al., 2007 ), reducing the profile complexity and providing high discrimination. TRFLP has been used to characterize complex microbial communities for forensic applications by linking the similarity of the amplicon patterns generated from the intrinsic soil communities to the evidence from a crime scene ( Meyers and Foran, 2008 ; Habtom et al., 2017 ). This method does provide a distinct pattern reflective of the microbial community, useful for forensic genetics but the method does not provide any sequence information. Another limitation is no standardization of which primer pairs or REs are used, making direct comparisons between studies difficult. This lack of standardization also hinders the development of a database for species identification. Additionally, the method is time-consuming due to the additional step of restriction digestion and the possibility of incomplete enzymatic digestion can complicate the interpretation of results ( Osborn et al., 2000 ; Moreno et al., 2006 ).

Table 1. The basis of differentiation, advantages, and disadvantages of past and current technologies.

Length Heterogeneity-Polymerase Chain Reaction (LH-PCR)

Another methodology has been used to characterize microbial communities is length heterogeneity- polymerase chain reaction (LH-PCR) ( Suzuki et al., 1998 ). Universal primers complementary to highly conserved domains within genomes are used to amplify hypervariable sequences within specific sequence domains. The 16S/18S rRNA genes, the chloroplast genes or Internal Transcribed Spacer (ITS) regions are commonly used. This technique is based on the natural sequence length variation due to insertions and deletions of bases that occur within a domain ( Moreno et al., 2006 ). It has been used to characterize microbial communities for forensic soil applications where a correlation between geographic location and microbial profiles has proven to be more discriminating than elemental soil analysis ( Moreno et al., 2006 , 2011 ; Damaso et al., 2018 ). With LH-PCR, metagenomic DNA extracted from the soil is amplified using fluorescently labeled universal primers with amplicon peaks within the electropherogram representing the minimum diversity within the community. However, specific sequence information is not known as many peaks of the same size could represent more than one species, thereby masking the community’s actual taxonomic diversity. A recent study showed the intrinsic diversity of a microbial mat, masked by LH-PCR, could be further resolved by the inherent sequence differences using capillary electrophoresis-single strand conformational polymorphism (CE-SSCP) analysis ( Damaso et al., 2014 ) and confirmed by sequencing. The advantage of LH-PCR is it is a fast and reproducible method that can correlate geographical areas to microbial patterns with bioinformatics ( Damaso et al., 2018 ); but a soil database would need to be developed to be useful beyond specific geographical areas.

Methodologies to Detect Intersequence Variation: The Past and Present

Sanger sequencing and single nucleotide polymorphism (snp) variation.

The basis of genomic differentiation is the intrinsic order of base pairs within a region that can be evaluated by sequencing. Sanger sequencing has been the gold standard since the 1970s ( Sanger and Coulson, 1975 ). Sanger sequencing was termed the gold standard because of the ability for single base pair resolution allowing for full sequence information to be determined. Robust and extensive databases are also readily available for comparison, i.e., GenBank, to identify an organism. However, it does have some limitations such as the short length (<500–700 bp) and it cannot sequence mixtures of organisms, for example, without cloning, so it would not be useful for sequencing complex microbial communities without intense time, effort and cost.

Other approaches use the ability to identify intrinsic single base sequence variation using single nucleotide polymorphisms (SNPs) within four forensically relevant SNP classes: identity-testing, ancestry informative, phenotype informative, and lineage informative. SNPs are particularly useful when typing degraded DNA or increasing the amount of genetic information retrieved from a sample ( Budowle and van Daal, 2008 ; Goodwin et al., 2011 ). SNaPshot TM is a commercially available SNP kit that can identify known SNPs using single base extension (SBE) technology ( Daniel et al., 2015 ; Fondevila et al., 2017 ). Wildlife forensics has used SNaPshot TM to identify endangered or trafficked species that are illegally poached to support criminal prosecutions. Elephant species identification from ivory and ivory products ( Kitpipit et al., 2017 ) or differentiating wolf species from dog subspecies ( Jiang et al., 2020 ) are both examples of SNaPshot TM assays developed for wildlife forensics. By using species-specific SNPs, the samples could be identified. But yet again, the limitation becomes the need for species-specific reference databases and the monumental task of developing a robust database for each species. Human SNPs databases with allele frequencies, as seen in dbSNP, however, are available making their forensic application more feasible in some cases.

Next-Generation Sequencing: The Present

Massively parallel sequencing (MPS) or next-generation sequencing (NGS) allows for mixtures of genomes of any species to be sequenced in one analysis ( Ansorge, 2009 ). This technology can sequence thousands of genomic regions simultaneously, allowing for whole-genome, metagenomic sequencing or targeted amplicon sequencing ( Gettings et al., 2016 ). Various NGS technologies are available each using slightly different technologies to sequence DNA ( Heather and Chain, 2016 ). Verogen has developed kits explicitly for human forensic genomics using Illumina’s MiSeq FGx system ( Guo et al., 2017 ; Moreno et al., 2018 ). The FBI recently approved DNA profiles generated by Verogen forensic technology to be uploaded into the National DNA Index System (NDIS) ( SWGDAM, 2019 ), making it the first NGS technology approved for NDIS.

Short tandem repeat mixture deconvolution, degraded, low template samples, and even microbial community samples are just a few of the potential NGS applications for forensic genomics and metagenomics ( Borsting and Morling, 2015 ). In human STR analyses, the greatest challenge is mixture deconvolution. NGS technology presents an increased power of discrimination of STR alleles using the intrinsic SNPs genetic microhaplotypes – a combination of 2–4 closely linked SNPs within an allele ( Kidd et al., 2014 ; Pang et al., 2020 ). However, the acceptance of analyses programs to deconvolve mixtures has not been standardized to the same level as it has for STRs.

Microbes are the first responders to changes in any environment because they are rapidly affected by the availability of nutrients and their intrinsic habitats. This makes them excellent indicators for studies investigating post-mortem interval (PMI) or as an indicator of soil geographical provenance ( Giampaoli et al., 2014 ; Finley et al., 2015 ). In decaying organisms, shifts in epinecrotic communities or the thanatomicrobiome are becoming increasingly critical components in investigating PMI ( Javan et al., 2016 ). Sequencing of the thanatomicrobiome revealed the Clostridium spp. varied during different stages human decomposition, the “Postmortem Clostridium Effect” (PCE), providing a time signature of the thanatomicrobiome, which could only have been uncovered through NGS ( Javan et al., 2017 ). However, the lack of consensus in analyses techniques must be addressed before NGS methodologies can be introduced into the justice system ( Table 1 ).

Future Directions and Concluding Remarks

Forensic DNA typing has progressed quickly within a short timeframe ( Figure 1 ), which can be attributed to the many advancements in molecular biology technologies. As these techniques advance, forensic scientists will analyze more atypical forms of evidence to answer questions deemed unresolvable with traditional DNA analyses. For example, epigenetics and DNA methylation markers have been proposed to estimate age, determine the tissue type, and even differentiate between monozygotic twins ( Vidaki and Kayser, 2018 ). However, since epigenetic patterns are also influenced by environmental factors, they can be dynamic, and a number of confounding factors have the potential to affect predictions and must be taken into account when preparing prediction models (i.e., age estimation). Additionally, phenotype informative SNPs across the genome can infer physical characteristics like eye, hair, and skin color, even age, from an unknown source of DNA retrieved from a crime scene. But this technology could pose an “implicit bias” toward minorities, especially in “societies where racism and xenophobia are now on the rise” ( Schneider et al., 2019 ) if not ethically and judicially implemented. With the increased sensitivity of NGS, low biomass samples from environmental DNA (eDNA) – DNA from soil, water, air – can complement and enhance intelligence gathering or provenance in criminal cases. Pollen and dust are two types of eDNA recently explored for their future forensic potential ( Alotaibi et al., 2020 ; Young and Linacre, 2021 ). However, if used in criminal investigations where the eDNA collected has had interaction with other environments, there must be some protocol or quality control established to account for variability that is likely to occur. This makes the prudent validation of this type of DNA analysis, essential. Limitations also arise due to lack of a database for comparison of samples and statistical analyses to evaluate the strength of a match like in the analysis of human STR profiles.

Figure 1. Timeline of the evolution of DNA typing technologies from the 1970’s to the present.

DNA has long been the gold standard in human forensic analysis because of the standardization of DNA markers, databases and statistical analyses. It has laid the foundation for these promising new technologies that will significantly enhance intelligence gathering and species identification – human and non-human – in forensic cases. In order for these methodologies to be useful in criminal investigations, they must adhere to the legal standards such as the Frye or Daubert Standards which determines if an expert testimony or evidence is admissible in court. A method can be deemed acceptable if it follows forensic guidelines set by organizations such as NIST’s Organization Scientific Area Committees (OSAC), Society for Wildlife Forensic Sciences (SWFS), Scientific Working Group on DNA Analysis Methods (SWGDAM), and the International Society for Forensic Genetics (ISFG) ( Linacre et al., 2011 ) just to name a few. These committees provide the guidelines for validation, interpretation, and quality assurance, all necessary components for DNA analysis. The US Fish and Wildlife forensic laboratory has standardized protocols for crimes against federally endangered or threatened species 1 . However, the more common limiting factors in the development of standard guidelines of non-human forensic genetic analyses across different state laboratories are the lack of consensus in methodologies, supporting allelic databases and standardized statistical analyses. Addressing those issues could lay the foundation for non-human analyses to be on par with human analyses.

Author Contributions

DJ designed and wrote the manuscript. DM edited and contributed to the writing of the manuscript. Both authors contributed to the article and approved the submitted version.

Conflict of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Acknowledgments

We would like to acknowledge the invitation by the editors to contribute to this special edition. DJ was supported by the Florida Education Fund’s McKnight Doctoral Fellowship.

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Keywords : forensic genetics, DNA typing, metabarcoding, soil, microbes, minisatellites, next-generation sequencing

Citation: Jordan D and Mills D (2021) Past, Present, and Future of DNA Typing for Analyzing Human and Non-Human Forensic Samples. Front. Ecol. Evol. 9:646130. doi: 10.3389/fevo.2021.646130

Received: 25 December 2020; Accepted: 02 March 2021; Published: 22 March 2021.

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Copyright © 2021 Jordan and Mills. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) . The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: DeEtta Mills, [email protected]

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Life and Death: New Perspectives and Applications in Forensic Science

Genetic Fingerprinting for Human Diseases: Applications and Implications

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DNA fingerprinting traditionally refers to the identification of individuals from blood and/or tissue samples for forensic purposes. But genetic fingerprinting can also include characterization of the genetic basis of human diseases, especially the inherited disorders. Some of the variants or haplotypes identified may run in families and thereby also have pathological or phenotypic connotations. The DNA sequencing technologies have evolved over the years, and nowadays, high-throughput techniques and applications are available with increased automation. Thus, genetic fingerprinting can have various connotations in relation to human diseases. The genetic testing done would depend on the clinical situation or phenotype, and what we are looking for in a specific patient or individual. Pretest and posttest counseling are important to facilitate decision-making.

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Roewer L (2013) DNA fingerprinting in forensics: past, present, and future. Investig Genet 4:22. https://doi.org/10.1186/2041-2223-4-22

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Thanks to all families whose clinical details have been discussed as cases in this write up. Appropriate consent was taken for publication as per ethical guidelines from parents/guardian. Also, thanks to the individuals/labs for the molecular testing in the patients.

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Panigrahi, I. (2018). Genetic Fingerprinting for Human Diseases: Applications and Implications. In: Dash, H., Shrivastava, P., Mohapatra, B., Das, S. (eds) DNA Fingerprinting: Advancements and Future Endeavors. Springer, Singapore. https://doi.org/10.1007/978-981-13-1583-1_8

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DNA fingerprinting in forensics: past, present, future

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DNA fingerprinting, one of the great discoveries of the late 20th century, has revolutionized forensic investigations. This review briefly recapitulates 30 years of progress in forensic DNA analysis which helps to convict criminals, exonerate the wrongly accused, and identify victims of crime, disasters, and war. Current standard methods based on short tandem repeats (STRs) as well as lineage markers (Y chromosome, mitochondrial DNA) are covered and applications are illustrated by casework examples. Benefits and risks of expanding forensic DNA databases are discussed and we ask what the future holds for forensic DNA fingerprinting.

The past - a new method that changed the forensic world

'“I’ve found it! I’ve found it”, he shouted, running towards us with a test-tube in his hand. “I have found a re-agent which is precipitated by hemoglobin, and by nothing else”,’ says Sherlock Holmes to Watson in Arthur Conan Doyle’s first novel A study in Scarlet from1886 and later: 'Now we have the Sherlock Holmes’ test, and there will no longer be any difficulty […]. Had this test been invented, there are hundreds of men now walking the earth who would long ago have paid the penalty of their crimes’ [ 1 ].

The Eureka shout shook England again and was heard around the world when roughly 100 years later Alec Jeffreys at the University of Leicester, in UK, found extraordinarily variable and heritable patterns from repetitive DNA analyzed with multi-locus probes. Not being Holmes he refrained to call the method after himself but 'DNA fingerprinting’ [ 2 ]. Under this name his invention opened up a new area of science. The technique proved applicable in many biological disciplines, namely in diversity and conservation studies among species, and in clinical and anthropological studies. But the true political and social dimension of genetic fingerprinting became apparent far beyond academic circles when the first applications in civil and criminal cases were published. Forensic genetic fingerprinting can be defined as the comparison of the DNA in a person’s nucleated cells with that identified in biological matter found at the scene of a crime or with the DNA of another person for the purpose of identification or exclusion. The application of these techniques introduces new factual evidence to criminal investigations and court cases. However, the first case (March 1985) was not strictly a forensic case but one of immigration [ 3 ]. The first application of DNA fingerprinting saved a young boy from deportation and the method thus captured the public’s sympathy. In Alec Jeffreys’ words: 'If our first case had been forensic I believe it would have been challenged and the process may well have been damaged in the courts’ [ 4 ]. The forensic implications of genetic fingerprinting were nevertheless obvious, and improvements of the laboratory process led already in 1987 to the very first application in a forensic case. Two teenage girls had been raped and murdered on different occasions in nearby English villages, one in 1983, and the other in 1986. Semen was obtained from each of the two crime scenes. The case was spectacular because it surprisingly excluded a suspected man, Richard Buckland, and matched another man, Colin Pitchfork, who attempted to evade the DNA dragnet by persuading a friend to give a sample on his behalf. Pitchfork confessed to committing the crimes after he was confronted with the evidence that his DNA profile matched the trace DNA from the two crime scenes. For 2 years the Lister Institute of Leicester where Jeffreys was employed was the only laboratory in the world doing this work. But it was around 1987 when companies such as Cellmark, the academic medico-legal institutions around the world, the national police, law enforcement agencies, and so on started to evaluate, improve upon, and employ the new tool. The years after the discovery of DNA fingerprinting were characterized by a mood of cooperation and interdisciplinary research. None of the many young researchers who has been there will ever forget the DNA fingerprint congresses which were held on five continents, in Bern (1990), in Belo Horizonte (1992), in Hyderabad (1994), in Melbourne (1996), and in Pt. Elizabeth (1999), and then shut down with the good feeling that the job was done. Everyone read the Fingerprint News distributed for free by the University of Cambridge since 1989 (Figure  1 ). This affectionate little periodical published non-stylish short articles directly from the bench without impact factors and resumed networking activities in the different fields of applications. The period in the 1990s was the golden research age of DNA fingerprinting succeeded by two decades of engineering, implementation, and high-throughput application. From the Foreword of Alec Jeffreys in Fingerprint News , Issue 1, January 1989: 'Dear Colleagues, […] I hope that Fingerprint News will cover all aspects of hypervariable DNA and its application, including both multi-locus and single-locus systems, new methods for studying DNA polymorphisms, the population genetics of variable loci and the statistical analysis of fingerprint data, as well as providing useful technical tips for getting good DNA profiles […]. May your bands be variable’ [ 5 ].

Cover of one of the first issues of Fingerprint News from 1990.

Jeffreys’ original technology, now obsolete for forensic use, underwent important developments in terms of the basic methodology, that is, from Southern blot to PCR, from radioactive to fluorescent labels, from slab gels to capillary electrophoresis. As the technique became more sensitive, the handling simple and automated and the statistical treatment straightforward, DNA profiling, as the method was renamed, entered the forensic routine laboratories around the world in storm. But, what counts in the Pitchfork case and what still counts today is the process to get DNA identification results accepted in legal proceedings. Spectacular fallacies, from the historical 1989 case of People vs. Castro in New York [ 6 ] to the case against Knox and Sollecito in Italy (2007–2013) where literally DNA fingerprinting was on trial [ 7 ], disclosed severe insufficiencies in the technical protocols and especially in the DNA evidence interpretation and raised nolens volens doubts on the scientific and evidentiary value of forensic DNA fingerprinting. These cases are rare but frequent enough to remind each new generation of forensic analysts, researchers, or private sector employees that DNA evidence is nowadays an important part of factual evidence and needs thus intense scrutiny for all parts of the DNA analysis and interpretation process.

In the following I will briefly describe the development of DNA fingerprinting to a standardized investigative method for court use which has since 1984 led to the conviction of thousands of criminals and to the exoneration of many wrongfully suspected or convicted individuals [ 8 ]. Genetic fingerprinting per se could of course not reduce the criminal rate in any of the many countries in the world, which employ this method. But DNA profiling adds hard scientific value to the evidence and strengthens thus (principally) the credibility of the legal system.

The technological evolution of forensic DNA profiling

In the classical DNA fingerprinting method radio-labeled DNA probes containing minisatellite [ 9 ] or oligonucleotide sequences [ 10 ] are hybridized to DNA that has been digested with a restriction enzyme, separated by agarose electrophoresis and immobilized on a membrane by Southern blotting or - in the case of the oligonucleotide probes - immobilized directly in the dried gel. The radio-labeled probe hybridizes to a set of minisatellites or oligonucleotide stretches in genomic DNA contained in restriction fragments whose size differ because of variation in the numbers of repeat units. After washing away excess probe the exposure to X-ray film (autoradiography) allows these variable fragments to be visualized, and their profiles compared between individuals. Minisatellite probes, called 33.6 and 33.15, were most widely used in the UK, most parts of Europe and the USA, whereas pentameric (CAC)/(GTG) 5 probes were predominantly applied in Germany. These so-called multilocus probes (MLP) detect sets of 15 to 20 variable fragments per individual ranging from 3.5 to 20 kb in size (Figure  2 ). But the multi-locus profiling method had several limitations despite its successful application to crime and kinship cases until the middle of the 1990s. Running conditions or DNA quality issues render the exact matching between bands often difficult. To overcome this, forensic laboratories adhered to binning approaches [ 11 ], where fixed or floating bins were defined relative to the observed DNA fragment size, and adjusted to the resolving power of the detection system. Second, fragment association within one DNA fingerprint profile is not known, leading to statistical errors due to possible linkage between loci. Third, for obtaining optimal profiles the method required substantial amounts of high molecular weight DNA [ 12 ] and thus excludes the majority of crime-scene samples from the analysis. To overcome some of these limitations, single-locus profiling was developed [ 13 ]. Here a single hypervariable locus is detected by a specific single-locus probe (SLP) using high stringency hybridization. Typically, four SLPs were used in a reprobing approach, yielding eight alleles of four independent loci per individual. This method requires only 10 ng of genomic DNA [ 14 ] and has been validated through extensive experiments and forensic casework, and for many years provided a robust and valuable system for individual identification. Nevertheless, all these different restriction fragment length polymorphism (RFLP)-based methods were still limited by the available quality and quantity of the DNA and also hampered by difficulties to reliably compare genetic profiles from different sources, labs, and techniques. What was needed was a DNA code, which could ideally be generated even from a single nucleated cell and from highly degraded DNA, a code, which could be rapidly generated, numerically encrypted, automatically compared, and easily supported in court. Indeed, starting in the early 1990s DNA fingerprinting methods based on RFLP analysis were gradually supplanted by methods based on PCR because of the improved sensitivity, speed, and genotyping precision [ 15 ]. Microsatellites, in the forensic community usually referred to short tandem repeats (STRs), were found to be ideally suited for forensic applications. STR typing is more sensitive than single-locus RFLP methods, less prone to allelic dropout than VNTR (variable number of tandem repeat) systems [ 16 ], and more discriminating than other PCR-based typing methods, such as HLA-DQA1 [ 17 ]. More than 2,000 publications now detail the technology, hundreds of different population groups have been studied, new technologies as, for example, the miniSTRs [ 18 ] have been developed and standard protocols have been validated in laboratories worldwide (for an overview see [ 19 ]). Forensic DNA profiling is currently performed using a panel of multi-allelic STR markers which are structurally analogous to the original minisatellites but with much shorter repeat tracts and thus easier to amplify and multiplex with PCR. Up to 30 STRs can be detected in a single capillary electrophoresis injection generating for each individual a unique genetic code. Basically there are two sets of STR markers complying with the standards requested by criminal databases around the world: the European standard set of 12 STR markers [ 20 ] and the US CODIS standard of 13 markers [ 21 ]. Due to partial overlap, they form together a standard of 18 STR markers in total. The incorporation of these STR markers into commercial kits has improved the application of these markers for all kinds of DNA evidence with reproducible results from as less than three nucleated cells [ 22 ] and extracted even from severely compromised material. The probability that two individuals will have identical markers at each of 13 different STR loci within their DNA exceeds one out of a billion. If a DNA match occurs between an accused individual and a crime scene stain, the correct courtroom expression would be that the probability of a match if the crime-scene sample came from someone other than the suspect (considering the random, not closely-related man) is at most one in a billion [ 14 ]. The uniqueness of each person’s DNA (with the exception of monozygotic twins) and its simple numerical codification led to the establishment of government-controlled criminal investigation DNA databases in the developed nations around the world, the first in 1995 in the UK [ 23 ]. When a match is made from such a DNA database to link a crime scene sample to an offender who has provided a DNA sample to a database that link is often referred to as a cold hit. A cold hit is of value as an investigative lead for the police agency to a specific suspect. China (approximately 16 million profiles, the United States (approximately 10 million profiles), and the UK (approximately 6 million profiles) maintain the largest DNA database in the world. The percentage of databased persons is on the increase in all countries with a national DNA database, but the proportions are not the same by the far: whereas in the UK about 10% of the population is in the national DNA database, the percentage in Germany and the Netherlands is only about 0.9% and 0.8%, respectively [ 24 ].

Multilocus DNA Fingerprint from a large family probed with the oligonucleotide (GTG) 5 ( Courtesy of Peter Nürnberg, Cologne Center for Genomics, Germany ).

Lineage markers in forensic analysis

Lineage markers have special applications in forensic genetics. Y chromosome analysis is very helpful in cases where there is an excess of DNA from a female victim and only a low proportion from a male perpetrator. Typical examples include sexual assault without ejaculation, sexual assault by a vasectomized male, male DNA under the fingernails of a victim, male 'touch’ DNA on the skin, and the clothing or belongings of a female victim. Mitochondrial DNA (mtDNA) is of importance for the analyses of low level nuclear DNA samples, namely from unidentified (typically skeletonized) remains, hair shafts without roots, or very old specimens where only heavily degraded DNA is available [ 25 ]. The unusual non-recombinant mode of inheritance of Y and mtDNA weakens the statistical weight of a match between individual samples but makes the method efficient for the reconstruction of the paternal or maternal relationship, for example in mass disaster investigations [ 26 ] or in historical reconstructions. A classic case is the identification of two missing children of the Romanov family, the last Russian monarchy. MtDNA analysis combined with additional DNA testing of material from the mass grave near Yekaterinburg gave virtually irrefutable evidence that the two individuals recovered from a second grave nearby are the two missing children of the Romanov family: the Tsarevich Alexei and one of his sisters [ 27 ]. Interestingly, a point heteroplasmy, that is, the presence of two slightly different mtDNA haplotypes within an individual, was found in the mtDNA of the Tsar and his relatives, which was in 1991 a contentious finding (Figure  3 ). In the early 1990s when the bones were first analyzed, a point heteroplasmy was believed to be an extremely rare phenomenon and was not readily explainable. Today, the existence of heteroplasmy is understood to be relatively common and large population databases can be searched for its frequency at certain positions. The mtDNA evidence in the Romanov case was underpinned by Y-STR analysis where a 17-locus haplotype from the remains of Tsar Nicholas II matched exactly to the femur of the putative Tsarevich and also to a living Romanov relative. Other studies demonstrated that very distant family branches can be traced back to common ancestors who lived hundreds of years ago [ 28 ]. Currently forensic Y chromosome typing has gained wide acceptance with the introduction of highly sensitive panels of up to 27 STRs including rapidly mutating markers [ 29 ]. Figure  4 demonstrates the impressive gain of the discriminative power with increasing numbers of Y-STRs. The determination of the match probability between Y-STR or mtDNA profiles via the mostly applied counting method [ 30 ] requires large, representative, and quality-assessed databases of haplotypes sampled in appropriate reference populations, because the multiplication of individual allele frequencies is not valid as for independently inherited autosomal STRs [ 31 ]. Other estimators for the haplotype match probability than the count estimator have been proposed and evaluated using empirical data [ 32 ], however, the biostatistical interpretation remains complicated and controversial and research continues. The largest forensic Y chromosome haplotype database is the YHRD ( http://www.yhrd.org ) hosted at the Institute of Legal Medicine and Forensic Sciences in Berlin, Germany, with about 115,000 haplotypes sampled in 850 populations [ 33 ]. The largest forensic mtDNA database is EMPOP ( http://www.empop.org ) hosted at the Institute of Legal Medicine in Innsbruck, Austria, with about 33,000 haplotypes sampled in 63 countries [ 34 ]. More than 235 institutes have actually submitted data to the YHRD and 105 to EMPOP, a compelling demonstration of the level of networking activities between forensic science institutes around the world. That additional intelligence information is potentially derivable from such large datasets becomes obvious when a target DNA profile is searched against a collection of geographically annotated Y chromosomal or mtDNA profiles. Because linearly inherited markers have a highly non-random geographical distribution the target profile shares characteristic variants with geographical neighbors due to common ancestry [ 35 ]. This link between genetics, genealogy, and geography could provide investigative leads for investigators in non-suspect cases as illustrated in the following case [ 36 ]:

Screenshot of the 16169 C/T heteroplasmy present in Tsar Nicholas II using both forward and reverse sequencing primers ( Courtesy of Michael Coble, National Institute of Standards and Technology, Gaithersburg, USA ).

Correlation between the number of analyzed Y-STRs and the number of different haplotypes detected in a global population sample of 18,863 23-locus haplotypes.

Screenshot from the YHRD depicting the radiation of a 9-locus haplotype belonging to haplogroup J in Southern Europe.

In 2002, a woman was found with a smashed skull and covered in blood but still alive in her Berlin apartment. Her life was saved by intensive medical care. Later she told the police that she had let a man into her apartment, and he had immediately attacked her. The man was subletting the apartment next door. The evidence collected at the scene and in the neighboring apartment included a baseball cap, two towels, and a glass. The evidence was sent to the state police laboratory in Berlin, Germany and was analyzed with conventional autosomal STR profiling. Stains on the baseball cap and on one towel revealed a pattern consistent with that of the tenant, whereas two different male DNA profiles were found on a second bath towel and on the glass. The tenant was eliminated as a suspect because he was absent at the time of the offense, but two unknown men (different in autosomal but identical in Y-STRs) who shared the apartment were suspected. Unfortunately, the apartment had been used by many individuals of both European and African nationalities, so the initial search for the two men became very difficult. The police obtained a court order for Y-STR haplotyping to gain information about the unknown men’s population affiliation. Prerequisites for such biogeographic analyses are large reference databases containing Y-STR haplotypes also typed for ancestry informative single nucleotide markers (SNP) markers from hundreds of different populations. The YHRD proved useful to infer the population origin of the unknown man. The database inquiry indicated a patrilineage of Southern European ancestry, whereas an African descent was unlikely (Figure  5 ). The police were able to track down the tenant in Italy, and with his help, establish the identity of one of the unknown men, who was also Italian. When questioning this man, the police used the information retrieved from Y-STR profiling that he had shared the apartment in Berlin with a paternal relative. This relative was identified as his nephew. Because of the close-knit relationship within the family, this information would probably not have been easily retrieved from the uncle without the prior knowledge. The nephew was suspected of the attempted murder in Berlin. He was later arrested in Italy, where he had committed another violent robbery.

Information on the biogeographic origin of an unknown DNA could also be retrieved from a number of ancestry informative SNPs (AISNPs) on autosomes or insertion/deletion polymorphisms [ 37 , 38 ] but perhaps even better from so-called mini-haplotypes with only <10 SNPs spanning small molecular intervals (<10 kb) with very low recombination among sites [ 39 ]. Each 'minihap’ behaves like a locus with multiple haplotype lineages (alleles) that have evolved from the ancestral human haplotype. All copies of each distinct haplotype are essentially identical by descent. Thus, they fall like Y and mtDNA into the lineage-informative category of genetic markers and are thus useful for connecting an individual to a family or ancestral genetic pool.

Benefits and risks of forensic DNA databases

The steady growth in the size of forensic DNA databases raises issues on the criteria of inclusion and retention and doubts on the efficiency, commensurability, and infringement of privacy of such large personal data collections. In contrast to the past, not only serious but all crimes are subject to DNA analysis generating millions and millions of DNA profiles, many of which are stored and continuously searched in national DNA databases. And as always when big datasets are gathered new mining procedures based on correlation became feasible. For example, 'Familial DNA Database Searching’ is based on near matches between a crime stain and a databased person, which could be a near relative of the true perpetrator [ 40 ]. Again the first successful familial search was conducted in UK in 2004 and led to the conviction of Craig Harman of manslaughter. Craig Harman was convicted because of partial matches from Harman’s brother. The strategy was subsequently applied in some US states but is not conducted at the national level. It was during a dragnet that it first became public knowledge that the German police were also already involved in familial search strategies. In a little town in Northern Germany the police arrested a young man accused of rape because they had analyzed the DNA of his two brothers who had participated in the dragnet. Because of partial matches between crime scene DNA profiles and these brothers they had identified the suspect. In contrast to other countries, the Federal Constitutional Court of Germany decided in December 2012 against the future court use of this kind of evidence.

Civil rights and liberties are crucial for democratic societies and plans to extend forensic DNA databases to whole populations need to be condemned. Alec Jeffreys early on has questioned the way UK police collects DNA profiles, holding not only convicted individuals but also arrestees without conviction, suspects cleared in an investigation, or even innocent people never charged with an offence [ 41 ]. He also criticized that large national databases as the NDNAD of England and Wales are likely skewed socioeconomically. It has been pointed out that most of the matches refer to minor offences; according to GeneWatch in Germany 63% of the database matches provided are related to theft while <3% related to rape and murder. The changes to the UK database came in the 2012’s Protection of Freedoms bill, following a major defeat at the European Court of Human Rights in 2008. As of May 2013 1.1 million profiles (of about 7 million) had been destroyed to remove innocent people’s profiles from the database. In 2005 the incoming government of Portugal proposed a DNA database containing samples from every Portuguese citizen. Following public objections, the government limited the database to criminals. A recent study on the public views on DNA database-related matters showed that a more critical attitude towards wider national databases is correlated with the age and education of the respondents [ 42 ]. A deeper public awareness on the benefits and risks of very large DNA collections need to be built and common ethical and privacy standards for the development and governance of DNA databases need to be adopted where the citizen’s perspectives are taken into consideration.

The future of forensic DNA analysis

The forensic community, as it always has, is facing the question in which direction the DNA Fingerprint technology will be developed. A growing number of colleagues are convinced that DNA sequencing will soon replace methods based on fragment length analysis and there are good arguments for this position. With the emergence of current Next Generation Sequencing (NGS) technologies, the body of forensically useful data can potentially be expanded and analyzed quickly and cost-efficiently. Given the enormous number of potentially informative DNA loci - which of those should be sequenced? In my opinion there are four types of polymorphisms which deserve a place on the analytic device: an array of 20–30 autosomal STRs which complies with the standard sets used in the national and international databases around the world, a highly discriminating set of Y chromosomal markers, individual and signature polymorphisms in the control and coding region of the mitochondrial genome [ 43 ], as well as ancestry and phenotype inference SNPs [ 44 ]. Indeed, a promising NGS approach with the simultaneous analysis of 10 STRs, 386 autosomal ancestry and phenotype informative SNPs, and the complete mtDNA genome has been presented recently [ 45 ] (Figure  6 ). Currently, the rather high error rates are preventing NGS technologies from being used in forensic routine [ 46 ], but it is foreseeable that the technology will be improved in terms of accuracy and reliability. Time is another essential factor in police investigations which will be considerably reduced in future applications of DNA profiling. Commercial instruments capable of producing a database-compatible DNA profile within 2 hours exist [ 47 ] and are currently under validation for law enforcement use. The hands-free 'swab in - profile out’ process consists of automated extraction, amplification, separation, detection, and allele calling without human intervention. In the US the promise of on-site DNA analysis has already altered the way in which DNA could be collected in future. In a recent decision the Supreme court of the United States held that 'when officers make an arrest supported by probable cause to hold for a serious offense and bring the suspect to the station to be detained in custody, taking and analyzing a cheek swab of the arrestee’s DNA is, like fingerprinting and photographing, a legitimate police booking procedure’ (Maryland v. Alonzo Jay King, Jr.). In other words, DNA can be taken from any arrestee, rightly or wrongly arrested, as a part of the normal booking procedure. Twenty-eight states and the federal government now take DNA swabs after arrests with the aim of comparing profiles to the CODIS database, creating links to unsolved cases and to identify the person (Associated Press, 3 June 2013). Driven by the rapid technological progress DNA actually becomes another metric of quick identification. It remains to be seen whether rapid DNA technologies will alter the way in which DNA is collected by police in other countries. In Germany for example the DNA collection is still regulated by the code of the criminal procedure and the use of DNA profiling for identification purposes only is excluded. Because national legislations are basically so different, a worldwide system to interrogate DNA profiles from criminal justice databases seems currently a very distant project.

Schematic overview of Haloplex targeting and NGS analysis of a large number of markers simultaneously. Sequence data are shown for samples from two individuals and the D3S1358 STR marker, the rs1335873 SNP marker, and a part of the HVII region of mtDNA ( Courtesy of Marie Allen, Uppsala University, Sweden ).

At present the forensic DNA technology directly affects the lives of millions people worldwide. The general acceptance of this technique is still high, reports on the DNA identification of victims of the 9/11 terrorist attacks [ 48 ], of natural disasters as the Hurricane Katrina [ 49 ], and of recent wars (for example, in former Yugoslavia [ 50 ]) and dictatorship (for example, in Argentina [ 51 ]) impress the public in the same way as police investigators in white suits securing DNA evidence at a broken door. CSI watchers know, and even professionals believe, that DNA will inevitably solve the case just following the motto Do Not Ask, it’s DNA, stupid! But the affirmative view changes and critical questions are raised. It should not be assumed that the benefits of forensic DNA fingerprinting will necessarily override the social and ethical costs [ 52 ].

This short article leaves many of such questions unanswered. Alfred Nobel used his fortune to institute a prize for work 'in ideal direction’. What would be the ideal direction in which DNA fingerprinting, one of the great discoveries in recent history, should be developed?

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• DNA fingerprinting
• Forensic DNA profiling
• Short tandem repeat
• Lineage markers
• Ancestry informative markers
• Forensic DNA database
• Privacy rights

Investigative Genetics

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DNA Fingerprinting: An Introduction

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DNA fingerprinting is a revolutionary technique that enables scientists to match minute tissue samples and facilitates scientific studies on the composition, Reproduction, and evolution of animal and plant populations. As a tool for positive identification of criminals, it plays a particularly important role in Forensic science. The first book to be published in the field, , DNA Fingerprinting is a practical guide to basic principles and laboratory methods as applied to a variety of fields including Forensic analysis, paternity testing, Medical diagnostics, animal and Plant Sciences, and Wildlife Poaching.

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Modern (1940’s-present)

Diane Scalera; Elsa Saine; Ava Niebrzydowski; Dylan Berry; Grace Young; and Caitlin Kelly

introduction

“Eureka!” shouted scientist Alec Jeffreys in his lab in Leicester, England, on a September day in 1984. Jeffreys had discovered a technique to biologically identify any individual using only a small sample of their DNA : the DNA fingerprint . While Sir Alec was studying hereditable diseases in families, he noticed the repetitive patterns of DNA, Variable Number of Tandem Repeats (VNTR’s), were present in every human being. Each DNA pattern differed in every individual, leading to Jeffreys’ realization that each variation of DNA could be used to identify a specific individual. (“An Evening with Alec Jefferies”, 2016)

The first DNA profiling technique developed by Alec Jeffreys in the 1980’s evolved into

the basis of forensic science , revolutionizing forensic investigations and criminal prosecutions for the protection of society by addressing concerns that existed, its contribution to forensic science, and its influence on the criminal justice system.

Jeffrey’s new DNA fingerprinting technique was known as the multi-locus probe (MLP) technique . DNA was dissolved into fragments via restriction enzymes , chemical “scissors”. The MLP technique visualized sequences of DNA and compared its sizes. The result of the technique was a complex pattern of bands from markers that bound to chromosomal sites. The two samples could be compared to identify a specific individual. Jeffreys and other supporters of his technique believed this technique was completely reliable and never wrong.  (Roewer, 2013)

Societal concerns regarding DNA technology

While the technique of DNA fingerprinting was a phenomenal technological advance for forensic science, the introduction of any new technology to society is likely to raise concerns. The introduction of DNA fingerprinting, by Alec Jeffreys was no different, as it raised social, economic, and ethical concerns among members of society ( National Research Council , 1992). Economical concerns included expansion in the number of laboratories and experts in the field, as well as the cost of equipment, training programs, and supplies. There were concerns about supplying the court with reliable assistance to evaluate DNA, along with the overall increase in cost of criminal justice (Lynch, 2003).

It was decided that DNA profiling did not violate any fundamental ethical principles, however, ethics was a matter in question. There was apprehension about intrusions of privacy and breaches of confidentiality involving DNA. Many people questioned whether the rights of the subject were enhanced or endangered. Society was also concerned about the potential abuse and misuse of DNA technology. Invaders gaining unauthorized access to databanks and the threat of unauthorized disclosure of information posed a problem, as well ( National Research Council , 1992).

The most prevalent issue brought about by DNA fingerprinting was that of trust . Who and what should a court trust when making major decisions about an individual’s fate and the protection of society? Could members of society trust the validity of DNA fingerprinting? Why were these concerns brought about and what did this mean for society?

At first, courts in many countries were hesitant towards the new technology. Their main concern involved trusting that DNA fingerprinting was a legitimate and reliable source of evidence (Lynch 2003). The use of DNA technology was challenged in court several times, planting seeds of doubt in many people’s minds. However, Sir Alec Jeffreys, along with the scientific community, supported the error-free method of personal identification and backed the technology with extensive research. Scientific research supported Jeffreys’ postulation that DNA could be used for personal identification. Eventually, judges, juries, and the public placed their trust in the scientific evidence, too.

“The courts trusted fingerprint experts not so much because of the examiners’ esteemed personal qualities, but because fingerprints were believed to be a certain means of individual identification and the job of detecting fingerprint matches was deemed trivial for trained persons, given sufficient evidence. (Lynch, 2003, p. 94).

The validity of DNA technology  became   established as the courts and members of government broadcasted their belief in the technology. They trusted fingerprint examiners because their judgments were expressed as absolute determinations. DNA fingerprinting was viewed as an unquestioned method of identifying an individual based on the MLP technique. 

“A forensic scientist testifying in an early death-penalty rape–murder trial made a claim about a DNA profile match, saying that detecting it was a ‘very simple straightforward operation…there are no objective standards about making a visual match. Either it matches or it doesn’t. It’s like you walk into a parking lot and see two blue Fords parked next to each other’ “(Lynch 2003, p. 96).

Once the trust between DNA technology and society was established, the overall consensus about DNA fingerprinting was that of excitement and hope in the fight against crime.

DNA TECHNOLOGY AND PATERNITY TESTING

One major area advanced by DNA technology is paternity testing. Paternity testing has historically been conducted by taking blood samples and analyzing inherited traits. The tests involved the analysis of blood types and subtypes, as well as examining how the traits have been inherited from a person’s parents. However, such methods were not entirely accurate and typically were not used in a court of law (Asen, 2019). Later advancements in DNA fingerprinting have allowed for the widespread use and acceptance of paternity testing, solidifying it as a highly impactful and accurate way of determining a person’s biological father.

Modern paternity testing has become widely accessible, as tests can be taken in a variety of ways. Testing for legal reasons must be conducted in a medical setting, and DNA samples are collected by a nurse or other third party. This ensures that the identity of the person tested can be verified, thus enabling the test to be used and presented in a court of law (Nigerian Tribune, 2017). Legal testing thus enables people to gain legal rights to child support, custody, and other benefits. At-home tests are also an option when these issues are not of worry to individuals. These tests are typically made to be affordable, are taken for peace of mind, and can also help establish trust between individuals (Cleveland Clinic, 2020).

The accessibility of paternity testing has proven increasingly relevant in many parts of the world. Nigeria serves as an example of this, as paternity testing has seen an increase in popularity due to the increased rate of divorce, immigration, and even the influence of western culture. This increase in popularity has somewhat had an impact on Nigerian culture, from protecting wills and estates to breaking the notion that only a mother can truly know who fathers her children. As a result, Nigerian companies and establishments are beginning to make efforts to invest in paternity testing and the necessary skill sets needed to perform it (Nigerian Tribune, 2017).

Dna technology’s role in forensic science

Although DNA profiling was a controversial innovation, the technology revolutionized forensic science investigations and criminal prosecutions for the betterment of society. Since Jeffreys’ DNA profiling technique, DNA testing has become an established component of the criminal justice process. DNA profiling allows for exoneration of the innocent and conviction of the guilty. A major use for DNA evidence is the use in exoneration cases. In criminal context the term exonerate refers to a state where a person convicted of a crime is later proved to be innocent. Since Jeffreys used DNA evidence for the first time, there has been 367 people released from prison for crimes that they did not commit. Not only is this number growing, the technique is getting progressively faster, leading to more numbers of people getting exonerated and freed. Investigators use DNA evidence as a main point in their exoneration case.

The courtroom has the ability to use evidentiary material to identify victims of crime, disaster, and war (Trent, 2012).  DNA technology is not only used for recognizing criminals, but also serves as a positive resource. It is a technology that has many applications for the betterment of society. 

Before Jeffreys’ “eureka moment”, DNA evidence had never been used in the court of law. In an interview with Alison Woollard, Sir Alec Jeffreys recalls a time when his scientific peers refused to entertain the idea of using DNA technology to benefit the justice system. When he explained his idea to his peers they laughed in his face and said, “ You just don’t use DNA in criminal investigations; that’s stupid” (“An Evening with Alec Jefferys, 2016). 

The  scientific community’s reaction only fueled Jeffreys’ determination to successfully use DNA in criminal investigations. By 1998, DNA test results had been used in more than one-hundred cases in the United States, all without much challenge from defense attorneys (Norris 2017). Now,  DNA fingerprinting is the absolute standard in criminal investigations and has been since the 1990’s. This wide acceptance can be attributed to a deeper public awareness of the scientific evidence behind DNA technology along with its benefits, and society’s eventual trust in the technology due the presented scientific evidence. However, not all were impressed with the new technology and the New York Times printed an extensive article by Lawrence Altman on February 4, 1986 critiquing the new DNA technology (Altman, 1986).

The increasing approval and use of DNA technology enabled a variety of new developments and advancements to be made. One essential development is the analysis and use of microsatellites, also known as short tandem repeats. These microsatellites are small, repeating segments of DNA that are unique to each individual (Saad, 2005). Advancements like microsatellites and methods related to paternity testing were used to aid in the identification of the remains of Joseph Mengele, a Nazi prison camp doctor nicknamed the “Angel of Death.” When his suspected remains were first located, they had decomposed and aged to the point that any DNA samples taken were barely usable. However, blood specimens from Mengele’s wife and son were used to reconstruct portions of his DNA in what was essentially a “reverse paternity test.” The results were conclusive, and the remains were later confirmed to belong to Mengele (Saad, 2005).

DNA technology in the criminal justice system

The first time DNA technology was used in the court of law was in England in 1996 to contribute to a rape case. Two girls were raped and strangled on two separate occasions in 1983 and 1996. The suspect admitted to the rape and murder of the first female, but not the second. Since Alec Jeffreys had just discovered the technique of DNA fingerprinting, he was called in to demonstrate his new technique with hopes of convicting the criminal responsible. The results of the DNA test indicated that both crime scene samples matched each other, but they did not match the suspect. The first time DNA was used in the criminal justice system was to prove innocence   (Norris, 2017). The technique of DNA fingerprinting was originally thought of to identify criminals and convict them or their evildoing. The first case where DNA technology was utilized broadened the horizons of the technology by introducing the concept that it could aid in the exoneration of the innocent.

In criminal investigations, DNA fingerprinting provides a crucial evidentiary link between the suspect and the scene of the crime. In a crime scene, sometimes there are only reminiscence of blood, hair, or semen. The physical trace of the suspect left at the scene is uplifted by investigators, DNA is extracted from the sample, and then a DNA fingerprint is made from the sample. Each DNA fingerprint provides a sample unique and identifiable to an individual person (Singh, 1992). DNA technology allows investigators to identify persons of interest and liberate the falsely accused. According to Singh,

“The significance of this development for forensic analysis is staggering for if the two patterns match the possibility of error – that is, the chance that they do not come from the same individual – is less than one in thirty billion.” (p.91)

DNA evidence provides a definite identification of an individual, with very little chance of inaccuracy, although, upon early development of the technique some uncertainty was presented in matters of sexual offenses. When a semen stain was taken from a vaginal swab, it was found that the result was not always sex specific, reducing the certainty of who the sperm originated from. However, a chemical process separating sperm nuclei from the female component was developed, completely eliminating any chance of confusion or doubt (Singh, 1992). As of modern day, newer technological advances and scientific explorations advocate for the validity and benefit of DNA technology utilized in the criminal justice system.

A fascinating case of the use of DNA technology is the Malcolm Alexander case. Malcolm was in jail for 38 years before being exonerated by DNA evidence. Malcolm was only 19 years old when he was convicted of rape, a crime that he did not commit. During his trial, there was a deeply flawed, unreliable identification procedure which led to him being convicted of the charge. Being only 19 years old, with little help to prove his innocence, Malcolm went on to spend 38 years in jail before the Innocence Project helped him out. In 2013, they found hair evidence that was stored at a local police station which did not match Malcolm nor the victim. The three hairs that they tested did not match Malcolm, so they brought the case to court and got Malcolm exonerated.

A more modern example of the use of DNA technology in the criminal justice system involves the case of Ivey v. Commonwealth. The case involves the abuse of 13-year-old Karen by a man named Ivey, who was in a relationship with her mother. Karen eventually became pregnant, and later revealed that the father of the child was Ivey. Her mother immediately contacted both the Garrard County and Hardin County police departments and they were quickly able to obtain a warrant to collect necessary DNA samples. Two additional paternity tests were ordered and obtained, and the case was presented in court. Expert testimony quickly showed that the tests determined Ivey to be the father with a 99.9999% probability. The court accepted the evidence, and Ivey was sentenced to life in prison (Ivey v. Commonwealth, 2016). This case stands as a testament to the accuracy of modern methods of DNA fingerprinting and paternity testing. It contrasts from the previously skeptical attitudes that were held about the technology’s accuracy and applicability and cements its acceptance and usefulness in modern day society.

THe Evolution of DNA Fingerprinting

DNA fingerprinting has evolved in a variety of ways since its discovery. Improvements in technology and science have allowed for it to be easy to detect in crime scenes, and the use of DNA fingerprinting has also served as a catalyst for other forms of DNA to be used as evidence in crime scenes. Other forms of DNA that have been collected for evidence at crime scenes include blood, hair, skin, etc. The use of DNA forms being used as evidence has helped exonerate over 150 wrongly convicted people, and has been helpful in a more truthful, accurate trial (Your DNA Fingerprint). As told by CEN, “Today, investigators can retrieve DNA profiles from skin cells left behind when a criminal merely touches a surface.” Other improvements to DNA fingerprinting have helped to make it easier for samples of DNA to be taken at crime scenes (Arnaud). It has evolved since its discovery to be more beneficial and efficient to use in crime scenes and forensic science. Through improved scientific research, smaller samples can be used to gather information, different kinds of DNA can be used, and it has also made it easier to predict different genes in individuals.

DNA can now be used to predict genetics in forensics. Certain models can now even predict eye color 90% of the time and hair color 80% of the time (Your DNA Fingerprint). These models are currently being observed to create more models that can predict more complex facial features and make it even easier to analyze and use DNA in forensics. The goal for the future is to use DNA from crime scenes to help create an accurate description of potential suspects of unidentified victims from scratch. As found on WMD, “DNA phenotyping has evolved from DNA fingerprinting and can help identify victims more efficiently and quickly.” The use of DNA testing has helped forensics science and proven to be a powerful tool for catching criminals. Sophisticated software that has evolved over time can use probabilistic genotype matching, and this is used to help correctly identify a suspect (Your DNA Fingerprint). This helps determine if two samples come from the same person and can help with identifying people through DNA accurately.

As DNA fingerprinting technology has progressed, scientists are now able to create fingerprints with smaller samples. Instead of a pint of blood that was used originally for DNA fingerprinting, a suspect can be identified from a pint of blood (Arnaud). Originally, DNA fingerprinting required samples to be in perfection. To be an accurate reading, almost a pint of blood was required and a large sample that is not mixed. Technology and new scientific research have helped make it easier for forensic scientists to use gathered evidence at crime scenes as DNA evidence. The improvement of PCR to be less sensitive in testing has helped make it possible for a drop of blood to be used and analyzed by forensic scientists (Arnaud).

DNA can be found in various forms at crime scenes today to help identify a suspect. Investigators can retrieve DNA profiles from skin cells left behind when a criminal touches a surface. The improved technology makes it possible to distinguish a suspect from a mixed sample. DNA can be used as evidence in skin cells, blood, hair, nails, etc (Evolution at the Scene of a Crime). There are many ways that DNA can be collected and used for crime scenes today, making it easier to identify suspects and easier for them to get caught as well. It is almost impossible to leave a crime scene without DNA being left behind, making it so much harder for criminals to commit crimes.

The improvement of DNA fingerprinting has helped society have a better, safe environment because it has ultimately made it easier for a criminal to be identified correctly. The accuracy of DNA is useful in other aspects of society today, branching out from its original purpose of being used in fingerprinting to solve crimes. It can also be used for organ donations, identifying bodies, it can aid in finding cures for disease, it can identify family genetics and hereditary diseases, help identify a crime suspect, etc (Your DNA Fingerprint). It’s many purposes have grown from its discovering in 1984, and it ultimately has helped to evolve society for the better.

Race and the digital divide in dna databases

DNA fingerprinting is a practice that will always be controversial due to different racial, social, and ethical opinions circling around America today. One specific connection to DNA fingerprinting in particular has caused discussion about these three standpoints, and that is DNA fingerprinting databases. Hundreds of scholars, advocates, and scientists have experimented with trying to perform DNA database research properly, but there are still concerns about racial equity when it comes to the topic. A study done by Erin Murphy and Jun H. Tong found that there are “dramatic disparities in racial composition of DNA databases”, and this includes the fact that information about black Americans in DNA databases is collected at two-three times the rate that information about white Americans is (Murphy, E., & Tong, J. H., 2020). Knowing that 14.2% of all Americans total are black, this is a stunning statistic. Furthermore, DNA databases are used to find near matches of the actual perpetrator in a crime. When a professional uses a DNA database to try and identify the people involved in a crime, they take evidence from the scene and try to match it to any existing DNA already in the database to try to find people who may be related to the perpetrator (Murphy, E., & Tong, J. H., 2020). This process is very controversial because in doing so, it makes all relatives of the preparator suspects in a crime case, and it is not always 100% accurate (Murphy, E., & Tong, J. H., 2020).  Additionally, research indicated that black Americans have much more representation in DNA databases, which means that they have more family members in the databases (Murphy, E., & Tong, J. H., 2020). This puts black Americans more at risk during investigation and puts them at a much higher probability of becoming a suspect in a criminal case. Not only are there racial disparities within DNA databases, there are also inequities according to gender. DNA databases hold much more information on males than they do on females (Murphy, E. E., 2010). While one may argue that males tend to be more reckless and therefore get into more trouble, this disparity can be a big problem especially when professionals use the near match technique for finding a perpetrator. When an official uses the near match technique where they identify people related to the DNA found at the crime scene using DNA databases, more males in the family will automatically be labeled as suspects due to the fact that there is more male data in DNA databases than there is for females (Murphy, E. E., 2010).

In addition to racial disparities within DNA databases, the databases also tend to make the digital divide larger. To have a digital divide means that there is a gap between middle class and higher Americans and underprivileged Americans when it comes to technology. Underprivileged Americans tend to not have as much easy access to technology and the internet, so completely relying on DNA databases in crime can set them apart even more than they already are right now (Chow-White, P. A., & Duster, T., 2011). Some of the groups that can be affected by this growing divide are racial and eithnic minorities, unemployed citizens, and the working class (Chow-White, P. A., & Duster, T., 2011). Technology is something that is meant to connect the world and make communication easier, not divide the world further. Connection to the internet is a basic need in society today, and unfortunately there are inequities in who has access to different amounts of technology (Chow-White, P. A., & Duster, T., 2011). Therefore, these DNA databases can really make this gap between different classes of Americans even larger, and have the opposite effect of the intended goal with technology.

Race and DNA Databases

DNA fingerprinting technologies have been critical in proving innocence or guilt in the courts; however, we often downplay the adverse effects of this technology, especially on racial minorities in the United States. The impact of DNA fingerprinting on society is particularly evident by the racial and ethnic makeup of forensic DNA databases that is disproportionate to the American population. The demographic composition of these databases exacerbates racial disparities and reinforces stereotypes linking race and crime.

Large forensic databases like CODIS (the Combined DNA Index System) contain several million DNA samples, and it is this abundance of data that makes these databases so important in criminal investigations. Thus, police departments utilize DNA fingerprinting/profiling techniques to collect samples from felons, arrestees, and sometimes even suspects in order to further expand their databases (Ossorio, 2005). However, analyzing the composition of these databases reveals that the proportion of DNA fingerprints that are from African Americans is between two and three times larger than the fraction of African Americans in the total population of every state (Murphy, 2020). On the other hand, even though white persons make up 62% of the US population, less than half of the samples in forensic databases belong to white people (Murphy, 2020). Thus, one can conclude that officers collect DNA profiles from African Americans much more frequently than they do from white people and that this technology has a much more significant effect on communities of color. Forensic DNA databases have disproportionately more data from African Americans, while the opposite is true for DNA collections used in biomedical and health research, where there is a distinct lack of diversity. These statistics lead to questions concerning the causes for the racial discrepancies in forensic databases in particular.

The most obvious reason is that these databases reflect and “mirror racial disparities in arrest practices and incarceration rates” (Chow-White, 2011). Over the past three decades, the racial makeup of prisons has shifted due to changes in policing. Policing occurs with higher frequency in black neighborhoods, and black Americans have much higher arrest rates than white Americans. For example, “buy and bust” police tactics, which are common in black neighborhoods, rarely occur in white communities even though drug use is often higher in these areas. Thus, when police collect DNA profiles from convicted felons and arrestees, they are disproportionately gathering DNA from nonwhite populations (Chow-White, 2011). Part of the issue may be the compulsory collection laws, which were ruled constitutional by the Supreme Court in Maryland v. King and encourage police officers to collect DNA from arrestees. In fact, some police will consistently solicit a DNA sample from every person they stop in order to add these samples to their databases (Thompson, 2019). This would not necessarily be an issue if not for racial profiling, in which people of minority races are more likely to be stopped by police and then compelled to give up their DNA. Forensic databases were created to help uncover the truth when it comes to crime. However, the nature of the databases is such that it places more suspicion on African Americans since they are unfairly represented. Hence, there is increasing fear that DNA profiling is one of several new technologies that instead of “ameliorating social inequalities, … would exacerbate them” (Chow-White, 2011).

Inequality can be an unintentional result of some criminal investigations that utilize familial searches of forensic databases. When police cannot find an exact DNA match for a criminal, they will instead search their databases for a partial match in DNA to identify a relative of the offender who could lead them to the culprit. However, this method disproportionately places suspicion on the innocent relatives of current or former black convicts since black Americans are excessively represented in the databases. Familial searches essentially allow for “‘genetic surveillance’… [that] would be concentrated on particular demographic populations” (Murphy, 2020). Thus, this technique can lead to police making assumptions about the race of the criminal, usually in cases where they have minimal knowledge or evidence about their offender (Murphy, 2010). Ultimately, familial searches can result in a cycle of increased policing of communities of color, leading to more arrests and thus a higher collection of DNA samples in these neighborhoods (Ossorio, 2005).

Likewise, DNA dragnets is another investigative technique utilizing DNA that, like familial searches, has dangerous implications in furthering racial inequities. As mentioned previously, DNA databases have a limited number of samples compared to the total population of possible suspects, so it is commonly the case that police do not find a DNA match to their criminal within the database. However, DNA dragnets involve requesting DNA samples from a large number of individuals around the geographical location of the crime and matching their DNA with that of the offender (Ossorio, 2005). However, as could be assumed, there is often a “racially targeted manner in which these samples were collected” (Ossorio, 2005) since investigators will request DNA from specific demographics to which they think their suspect belongs. Because this method has been called out and criticized for how it leads to investigators collecting DNA profiles from those primarily belonging to racial minorities, this technique is no longer used. However, both familial searches and DNA dragnets reveal how DNA databases and DNA profiling have been used in racially targeted manners.

The unbalanced racial makeup of DNA databases and how these samples are often racially categorized in investigations can lead to dangerous assumptions linking race, biology, and crime. Race is dependent on the individual’s self-identification, so its use in forensic studies is illogical and leads to the incorrect belief that we all have an inherent and natural race. Our genes do not establish a decided few racial categories of which each person belongs (Ossorio, 2005). In fact, any two humans will have nucleotide sequences that are 99.9% identical, and the variation that is there is most likely to be based on geography, not race (Murphy, 2010). Utilizing DNA profiling technologies in criminal investigations and then studying this data through a racial lens based on the makeup of the DNA databases runs the risk of people making assumptions that biology, race, and criminality are mutually influential. In her research paper about familial searches, Erin Murphy warns that “overtly racializing biological evidence in the criminal justice system risks embarking on a dangerous path that biologizes and pathologizes crime along racial grounds” (Murphy, 2010). It is important to emphasize that there are no genetic markers that are unique to different races (particularly concerning predisposition to criminal behavior) because there are in fact no distinct racial groupings according to our DNA.

Even small police forces now use DNA fingerprinting techniques to catch criminals, thus its wide usage makes it essential to analyze the effects of these technologies on different populations. The intention of DNA fingerprinting in police work was to bring about greater objectivity (Thompson, 2019), but in the hands of humans, who each have some form of implicit bias, DNA profiling technologies are not as objective as we would like to believe. Particularly in criminal investigations, they tend to “lump groups of individuals together into a racialized suspect population” (M’Charek, 2008). Although there are a lot of benefits to DNA fingerprinting, it is important to also acknowledge its detrimental effects, especially on underrepresented populations.

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• TECHNOLOGY FEATURE
• 08 May 2024

Powerful ‘nanopore’ DNA sequencing method tackles proteins too

• Caroline Seydel 0

Caroline Seydel is a science writer in Los Angeles, California.

You can also search for this author in PubMed   Google Scholar

A nanopore sequencing device is typically used for sequencing DNA and RNA. Credit: Anthony Kwan/Bloomberg/Getty

With its fast analyses and ultra-long reads, nanopore sequencing has transformed genomics, transcriptomics and epigenomics. Now, thanks to advances in nanopore design and protein engineering, protein analysis using the technique might be catching up.

“All the pieces are there to start with to do single-molecule proteomics and identify proteins and their modifications using nanopores,” says chemical biologist Giovanni Maglia at the University of Groningen, the Netherlands. That’s not precisely sequencing, but it could help to work out which proteins are present. “There are many different ways you can identify proteins which doesn’t really require the exact identification of all 20 amino acids,” he says, referring to the usual number found in proteins.

In nanopore DNA sequencing, single-stranded DNA is driven through a protein pore by an electrical current. As a DNA residue traverses the pore, it disrupts the current to produce a characteristic signal that can be decoded into a sequence of DNA bases.

Proteins, however, are harder to crack. They cannot be consistently unfolded and moved by a voltage gradient because, unlike DNA, proteins don’t carry a uniform charge. They might also be adorned with post-translational modifications (PTMs) that alter the amino acids’ size and chemistry — and the signals that they produce. Still, researchers are making progress.

Water power

One way to push proteins through a pore is to make them hitch a ride on flowing water, like logs in a flume. Maglia and his team engineered a nanopore 1 with charges positioned so that the pore could create an electro-osmotic flow that was strong enough to unfold a full-length protein and carry it through the pore. The team tested its design with a polypeptide containing negatively charged amino acids, including up to 19 in a row, says Maglia. This concentrated charge created a strong pull against the electric field, but the force of the moving water kept the protein moving in the right direction. “That was really amazing,” he says. “We really did not expect it would work so well.”

Super-speedy sequencing puts genomic diagnosis in the fast lane

Chemists Hagan Bayley and Yujia Qing at the University of Oxford, UK, and their colleagues have also exploited electro-osmotic force, this time to distinguish between PTMs 2 . The team synthesized a long polypeptide with a central modification site. Addition of any of three distinct PTMs to that site changed how much the current through the pore was altered relative to the unmodified residues. The change was also characteristic of the modifying group. Initially, “we’re going for polypeptide modifications, because we think that’s where the important biology lies”, explains Qing.

And, because nanopore sequencing leaves the peptide chain intact, researchers can use it to determine which PTMs coexist in the same molecule — a detail that can be difficult to establish using proteomics methods, such as ‘bottom up’ mass spectrometry, because proteins are cut into small fragments. Bayley and Qing have used their method to scan artificial polypeptides longer than 1,000 amino acids, identifying and localizing PTMs deep in the sequence. “I think mass spec is fantastic and provides a lot of amazing information that we didn’t have 10 or 20 years ago, but what we’d like to do is make an inventory of the modifications in individual polypeptide chains,” Bayley says — that is, identifying individual protein isoforms, or ‘proteoforms’.

Molecular ratchets

Another approach to nanopore protein analysis uses molecular motors to ratchet a polypeptide through the pore one residue at a time. This can be done by attaching a polypeptide to a leader strand of DNA and using a DNA helicase enzyme to pull the molecule through. But that limits how much of the protein the method can read, says synthetic biologist Jeff Nivala at the University of Washington, Seattle. “As soon as the DNA motor would hit the protein strand, it would fall off.”

Nivala developed a different technique, using an enzyme called ClpX (see ‘Read and repeat’). In the cell, ClpX unfolds proteins for degradation; in Nivala’s method, it pulls proteins back through the pore. The protein to be sequenced is modified at either end. A negatively charged sequence at one end allows the electric field to drive the protein through the pore until it encounters a stably folded ‘blocking’ domain that is too large to pass through. ClpX then grabs that folded end and pulls the protein in the other direction, at which point the sequence is read. “Much like you would pull a rope hand over hand, the enzyme has these little hooks and it’s just dragging the protein back up through the pore,” Nivala says.

Source: Ref. 3

Nivala’s approach has another advantage: when ClpX reaches the end of the protein, a special ‘slip sequence’ causes it to let go so that the current can pull the protein through the pore for a second time. As ClpX reels it back out again and again, the system gets multiple peeks at the same sequence, improving accuracy.

Last October 3 , Nivala and his colleagues showed that their method can read synthetic protein strands of hundreds of amino acids in length, as well as an 89-amino-acid piece of the protein titin. The read data not only allowed them to distinguish between sequences, but also provided unambiguous identification of amino acids in some contexts. Still, it can be difficult to deduce the amino-acid sequence of a completely unknown protein, because an amino acid’s electrical signature varies on the basis of both its surrounding sequence and its modifications. Nivala predicts that the method will have a ‘fingerprinting’ application, in which an unknown protein is matched to a database of reference nanopore signals. “We just need more data to be able to feed these machine-learning algorithms to make them robust to many different sequences,” he says.

NatureTech hub

Stefan Howorka, a chemical biologist at University College London, says that nanopore protein sequencing could boost a range of disciplines. But the technology isn’t quite ready for prime time. “A couple of very promising proof-of-concept papers have been published. That’s wonderful, but it’s not the end.” The accuracy of reads needs to improve, he says, and better methods will be needed to handle larger PTMs, such as bulky carbohydrate groups, that can impede the peptide’s movement through the pore.

How easy it will be to extend the technology to the proteome level is also unclear, he says, given the vast number and wide dynamic range of proteins in the cell. But he is optimistic. “Progress in the field is moving extremely fast.”

Nature 629 , 492-493 (2024)

doi: https://doi.org/10.1038/d41586-024-01280-5

Sauciuc, A., Morozzo della Rocca, B., Tadema, M. J., Chinappi, M. & Maglia, G. Nature Biotechnol . https://doi.org/10.1038/s41587-023-01954-x (2023).

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Martin-Baniandres, P. et al. Nature Nanotechnol. 18 , 1335–1340 (2023).

Article   PubMed   Google Scholar  

Motone, K. et al. Preprint at bioRxiv https://doi.org/10.1101/2023.10.19.563182 (2023).

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Google DeepMind’s new AlphaFold can model a much larger slice of biological life

AlphaFold 3 can predict how DNA, RNA and other molecules interact, further cementing its leading role in drug discovery and research. Who will benefit?

• James O'Donnell archive page

Google DeepMind has released an improved version of its biology prediction tool, AlphaFold, that can predict the structures not only of proteins but of nearly all the elements of biological life.

It’s a development that could help accelerate drug discovery and other scientific research. The tool is currently being used to experiment with identifying everything from resilient crops to new vaccines. 

While the previous model, released in 2020, amazed the research community with its ability to predict proteins structures, researchers have been clamoring for the tool to handle more than just proteins. 

Now, DeepMind says, AlphaFold 3 can predict the structures of DNA, RNA, and molecules like ligands, which are essential to drug discovery. DeepMind says the tool provides a more nuanced and dynamic portrait of molecule interactions than anything previously available. 

“Biology is a dynamic system,” DeepMind CEO Demis Hassabis told reporters on a call. “Properties of biology emerge through the interactions between different molecules in the cell, and you can think about AlphaFold 3 as our first big sort of step toward [modeling] that.”

AlphaFold 2 helped us better map the human heart , model antimicrobial resistance , and identify the eggs of extinct birds , but we don’t yet know what advances AlphaFold 3 will bring. 

Mohammed AlQuraishi, an assistant professor of systems biology at Columbia University who is unaffiliated with DeepMind, thinks the new version of the model will be even better for drug discovery. “The AlphaFold 2 system only knew about amino acids, so it was of very limited utility for biopharma,” he says. “But now, the system can in principle predict where a drug binds a protein.”

Isomorphic Labs, a drug discovery spinoff of DeepMind, is already using the model for exactly that purpose, collaborating with pharmaceutical companies to try to develop new treatments for diseases, according to DeepMind. 

AlQuraishi says the release marks a big leap forward. But there are caveats.

“It makes the system much more general, and in particular for drug discovery purposes (in early-stage research), it’s far more useful now than AlphaFold 2,” he says. But as with most models, the impact of AlphaFold will depend on how accurate its predictions are. For some uses, AlphaFold 3 has double the success rate of similar leading models like RoseTTAFold. But for others, like protein-RNA interactions, AlQuraishi says it’s still very inaccurate. 

DeepMind says that depending on the interaction being modeled, accuracy can range from 40% to over 80%, and the model will let researchers know how confident it is in its prediction. With less accurate predictions, researchers have to use AlphaFold merely as a starting point before pursuing other methods. Regardless of these ranges in accuracy, if researchers are trying to take the first steps toward answering a question like which enzymes have the potential to break down the plastic in water bottles, it’s vastly more efficient to use a tool like AlphaFold than experimental techniques such as x-ray crystallography. 

A revamped model  

AlphaFold 3’s larger library of molecules and higher level of complexity required improvements to the underlying model architecture. So DeepMind turned to diffusion techniques, which AI researchers have been steadily improving in recent years and now power image and video generators like OpenAI’s DALL-E 2 and Sora. It works by training a model to start with a noisy image and then reduce that noise bit by bit until an accurate prediction emerges. That method allows AlphaFold 3 to handle a much larger set of inputs.

That marked “a big evolution from the previous model,” says John Jumper, director at Google DeepMind. “It really simplified the whole process of getting all these different atoms to work together.”

It also presented new risks. As the AlphaFold 3 paper details, the use of diffusion techniques made it possible for the model to hallucinate, or generate structures that look plausible but in reality could not exist. Researchers reduced that risk by adding more training data to the areas most prone to hallucination, though that doesn’t eliminate the problem completely. 

Restricted access

Part of AlphaFold 3’s impact will depend on how DeepMind divvies up access to the model. For AlphaFold 2, the company released the open-source code , allowing researchers to look under the hood to gain a better understanding of how it worked. It was also available for all purposes, including commercial use by drugmakers. For AlphaFold 3, Hassabis said, there are no current plans to release the full code. The company is instead releasing a public interface for the model called the AlphaFold Server , which imposes limitations on which molecules can be experimented with and can only be used for noncommercial purposes. DeepMind says the interface will lower the technical barrier and broaden the use of the tool to biologists who are less knowledgeable about this technology.

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