Relevance of Genetic Identification in Natural Catastrophes

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This entry is adapted from the peer-reviewed paper 10.3390/genealogy7030044

Different types of catastrophes, including from natural causes, armed conflicts and different acts of terrorism, lead not only to movement and disappearance but also to the death of civilians, demanding a prompt and effective response concerning the identification and delivery of individuals to their families.

catastrophes genetic identification kinship analysis DNA degradation

1. Human Identification in Major Human Catastrophes

In catastrophes, the main objective is to save the involved living beings. The second objective is to identify the deceased people (Mendonça 2009; Pinheiro 2009). The need to identify corpses is related to legal, criminal, civil and moral issues. In the moral and ethical scope, citizens have the right to receive the mortal remains of their relatives, whether they are victims of any type of catastrophe, disaster or emergency (Mendonça 2009; Goodwin and Simmons 2023). In the civil sphere, for example, the absence of a death certificate due to the lack of a corpse makes all civil procedures difficult, which are essential for families to deal with indemnities or pensions, among others. Concerning the legal and forensic scope, the absence of an explicit identification leads to questions related to the disappearance of the individual, for example by kidnapping for subsequent human trafficking. For this reason, it is imperative to locate and identify all individuals allegedly involved in the disaster or catastrophe.

Human identification is, at its core, a comparative exercise. Based on this methodology, by collecting individualizing and discriminating identification data, it is possible to achieve what is known in forensic sciences as “positive identification” (Mendonça 2009; Pinheiro 2009, 2013), the attribution of a unique and unequivocal identity, usually “name and surname”, associated with legal registration in a given country. For this, it is necessary to collect data from the cadaver (postmortem data), allowing forensic scientists to build a biological profile, which can be of different types: dactyloscopy (Correia and Pinheiro 2013), dental (Caldas 2013; Labajo and Perea 2022), anthropological (Hartman et al. 2011; Lloret 2018) and genetic (Mendonça 2009; Pinheiro 2009, 2013; Gomes et al. 2021, 2022; Palomo-Díez et al. 2022; Goodwin and Simmons 2023).

Traditionally, anthropology was used as a basis to identify deceased people, due to the simplicity of data collection and the use of a reduced number of materials and equipment. It was based mainly on the observation of postmortem information and the external examination of the remains found, focusing essentially on the analysis of visible phenotypic data (hair color, height, skin color, among others) and identifying physical traits (general characteristics of sex, approximate age, tattoos, scars). Although these techniques were fast, they do not allow for the identification of an individual, instead providing only a guide for the investigation, for example, “the deceased person is a man 40–50 years old”. It allows the exclusion or inclusion of the victim from certain phenotypic groups, but it did not permit the identification of the victim.

Currently, the identification of individuals is carried out using three methods, in the following order: first, fingerprints; second, dental records; and third, genetic analysis (Hartman et al. 2011; Butler 2023; Goodwin and Simmons 2023). Although fingerprints and forensic odontology are indeed considered reliable (Prajapati et al. 2018), fingerprints and/or dental samples are not always available.

2. Genetic Identification

Genetic identification plays a crucial role when the remains to be analyzed are very old or present a very advanced state of degradation, as in the case of air accidents or explosions (de Boer et al. 2018), not depending on a specific biological sample. One of the main advantages of genetic assessment is that information is found in all the nucleated cells of the body and can therefore be found in very small portions of soft tissue or bone fragments. This lets scientists determine substantially important data such as the victim’s autosomal profile, biological sex, biogeographical origin, or external phenotype, or perform kinship analysis.

However, the individual’s genetic identification can only be performed if there are samples to be compared with. It is possible to carry out a direct identification when there is a previously confirmed genetic profile belonging to the individual in question, for example, in police databases or biological samples resulting from medical diagnoses, such as biopsies. On the other hand, when it is not possible to access the individual’s biological antemortem samples, an attempt is made to carry out an identification either through assigned samples, such as clothing or other types of personal belongings of the person with whom the remains are believed to be associated or through biological relatives (Goodwin and Simmons 2023). Usually, human identification in catastrophes is performed by resorting to biological kinship analysis. One of the fundamental steps for a correct genetic analysis is the collection of information from the family of the deceased, since it is crucial for the election of the best genetic marker for each case in question to know the relationship of the person with the deceased.

2.1. Collection of Evidence at the Site of the Disaster for Genetic Analysis

At present, genetic studies are based on the comparison of two genetic profiles, that is, the comparison between postmortem samples obtained from corpses or human remains obtained from the mortuary area, and a reference sample (Hartman et al. 2011; Pinheiro 2013; Soniya and Kumar 2022; Goodwin and Simmons 2023). Despite the complications that may arise at the time of sample collection, all human remains and corpses found must be analyzed. The collection must be conducted during the autopsy by specialized personnel, always taking into account the advanced state of degradation of biological samples and the constant danger of possible contamination with exogenous DNA, both from medical personnel and during the process of genetic research (Pinheiro 2013; Soniya and Kumar 2022).

There are samples considered most suitable for genetic analysis, and the possibility of their collection will be guided by the characteristics of the catastrophe and the state of the human remains. According to the GHEP (2000) protocol, the most frequent samples are skeletal muscle, organ fragments, blood from myocardial cavities and bone and dental samples. Human hairs are not the best samples for the identification process, since there is a high probability that a hair will not have the follicle, preventing the analysis of nuclear DNA. In the case of catastrophes where corpses or human remains have remained in the water for a considerable time, the probability of using muscle samples or organs is frankly reduced, due to the different processes of saponification and putrefaction; in these cases, the sample of choice will be dental or bone pieces. Due to the characteristics of both bones and teeth, they are also the biological samples of choice in cases of high temperatures, such as fires and explosions (Schwark et al. 2011; Krishan et al. 2015; Uzair et al. 2017; Grela et al. 2021; Kumar 2022).

Regarding the reference samples of close family members, the most appropriate relatives will be direct ascendants (mother and father), descendants and the biological father/mother of these descendants, in order to discard cases of maternal/paternal incompatibility of the deceased with the descendants. Siblings of the deceased, or other relatives should be considered in the event that the previous relative’s samples could not be obtained. Usually, the biological sample taken from the biological relative is saliva, since it includes DNA from the cells of the buccal mucosa and is a quick and painless process of sample collection.

Another very important aspect in the entire identification and intervention process is the preservation of the samples; they must be correctly packaged to guarantee their correct use and arrival at the laboratory.

2.2. Nuclear DNA: The Key to Human Identification

Genetic material is present in all nucleated cells since the organization of the organism and its correct functioning depend entirely on its information. Inside the cell, DNA is located between two fundamental organelles: the nucleus (nuclear DNA) and the mitochondria (mitochondrial DNA) (Gomes et al. 2021; Palomo-Díez and López-Parra 2022; Shrivastava et al. 2022; Soniya and Kumar 2022).

Nuclear DNA contains most of an individual’s genetic information; even though mitochondria have their genome, it follows that most of the mitochondrial coding activity is carried out in strict collaboration with the nucleus, progressively, through a process of evolution (Cooper and Hausman 2017). Human beings have 46 nuclear chromosomes, which are divided into 22 pairs of homologous chromosomes, and a sexual pair, the Y and the X chromosomes in men, and two X chromosomes in women (Pinheiro 2013; Gomes et al. 2021; Gomes et al. 2022; Gomes and Arroyo-Pardo 2022; Sahajpal and Ambers 2023).

Informative Markers in Forensic Genetic Identification

Considering forensic genetics, the most informative data ae located on non-codifying regions not involving diseases or phenotypic information about the individual. Within this non-coding information, genetic identification focuses on three main types of DNA organization: STRs, SNPs and InDels.

STRs (short tandem repeats) are a class of markers based on the study of a non-codifying locus (in this case, designated “genetic marker”) formed by a certain number of base repetitions in tandem. It is important to bear in mind that it presents great variability since it can be presented in such a varied number of alleles. These motifs, together with their possibility of being amplified by PCR, make STR markers the most widely used in these cases of genetic identification (Manamperi et al. 2009; Gomes et al. 2022; Goodwin and Simmons 2023). However, there are scenarios where STRs are not the best option for analysis, such as when analyzing human remains with a high degree of degradation. In these cases, the use of markers capable of amplifying a small genetic region would be more suitable, such as SNPs or InDel polymorphisms.
SNPs (single nucleotide polymorphisms) are the most abundant genetic markers within the human genome since they are based on single-base variations. Used in multiplexes, SNPs are one of the most used tools in forensic genetics as a complement to autosomal markers (Yagasaki et al. 2022). To carry out an identification with SNPs, a much higher number of these markers is need than with STRs, due to the lower discrimination power of the SNPs (they only present six possible allelic forms) compared with STRs.
InDels are polymorphisms based on deletions or insertions on a specific genomic position. Their low level of mutation makes them very useful in the study of family relationships. Even so, this variation needs to occur in at least 1% of the population to be considered a genetic marker (Pontes et al. 2017; Gomes et al. 2021; Gomes et al. 2022). Associated with STR and SNP loci, InDels can achieve more successful results in forensic identification (Unsal Sapan 2022).

(a): Autosomal markers

Considered the markers par excellence with regard to the identification of individuals, autosomal markers are those with the greatest power of discrimination. The identification is carried out, normally, by combining two types of procedures, either by comparing the autosomal genetic profile of objects and belongings attributed to the victim and the genetic profile of the corpse or cadaveric remains (direct identification), or by comparing the autosomal profile of the corpse or cadaverous remains with those of possible relatives (indirect identification).

(b): X chromosome markers

Although scarcely used in forensic casuistry, the X chromosome markers, especially X-STRs, are used in situations where it is not possible to distinguish genealogies with autosomal markers (Pinto et al. 2010, 2011, 2012; Gomes et al. 2020; Gomes and Arroyo-Pardo 2022), due to their null power of discrimination in these situations. In cases of catastrophes, it could be a very relevant type of marker, as situations can arise where it is not possible to distinguish whether individuals are avuncular–nephew or –niece or grandparents–grandchildren.

(c): Y chromosome markers

As the Y chromosome is a lineage chromosome, Y chromosome markers do not allow identification, since all individuals of the same biological family share the same Y chromosome information via the paternal path (Palomo-Díez and López-Parra 2022). It may be useful for identification in very specific cases, where only one individual is missing in a given family and by associating this information with other family data, it can lead to a positive identification.

2.3. Non-Nuclear DNA: MtDNA

As observed for the Y chromosome, mtDNA is not a useful marker for identifying individuals in cases of catastrophes, since all family members related by maternal line will share the same genetic profile, whether women or men (Palomo-Díez and López-Parra 2022; Shrivastava et al. 2022). As described for the Y chromosome, mtDNA analysis may be useful in very specific cases, when it is necessary to identify a single person from a given family. In this case, associated with other family information, the mtDNA study could be decisive in an identification.

2.4. Problems When Studying Degraded Biological Samples from Major Catastrophes

2.4.1. DNA Fragmentation

The structural damage presented by a DNA chain is known as DNA fragmentation (Gomes 2020; Ambers 2023). This phenomenon usually occurs when the DNA has been subjected to extreme conditions that have caused its denaturation. The chemical basis of DNA denaturation is the breaking of the hydrogen bonds that stabilize the characteristic double helix structure of DNA; on the other hand, the breaking of glycosidic bonds can also occur, causing the loss of bases. The main cause of this rupture is usually high temperatures, although it can also be caused by other factors such as a very acidic or very basic pH, or the action of various microorganisms. This state of degradation is typical of cadaveric remains or bone fragments that have been exposed to environmental factors for a long time or have been subjected to high temperatures, as can occur in plane crashes or mass disasters caused by natural disasters (Gomes 2020; Ambers 2023).

The fragmentation of the genetic material is a problem for the study of samples in genetics since there is a high probability of observing allelic dropout, which often means it is not possible to carry out the identification of the individual. This is why when trying to analyze a sample with these characteristics, STR markers cannot be used due to the length and probable allelic dropout and the loss of genetic information in a particular marker. SNPs and InDels are fundamental in these studies due to their small length and being less prone to fragment, although they have a lower power of discrimination (Gomes and Arroyo-Pardo 2022).

2.4.2. Molecular Damage

After the death of the individual, DNA is subjected to numerous natural processes of chemical degradation through hydrolysis and/or oxidation reactions, as well as the action of certain enzymes such as endogenous nucleases. These reactions can be caused by certain types of ionizing radiation or also by the presence of certain free radicals from cellular reactions (Gomes 2020). The greatest danger that these reactions entail is the modification of the nitrogenous bases of DNA, which can cause erroneous results.

2.4.3. Allelic Dropout as a Consequence of Degradation

As mentioned above, the degradation of genetic material is one of the main problems that analysts must face when studying a sample in catastrophes. One of the difficulties in amplifying a DNA fragment occurs when a mutation occurs at the insertion site of the primer, preventing the correct amplification of the product or an erroneous reading of the information (Soulsbury et al. 2006).

On the other hand, allelic dropout is the most common problem when studying highly degraded samples, normally related to the degradation of the genetic material and the impossibility of accessing the information due to the allelic loss in a certain locus (Gomes 2020). This usually occurs in samples with a low DNA concentration, either because their natural DNA concentration is very low (urine, feces), or because they have undergone a degradation process that has caused a loss of DNA concentration. For this reason, forensic geneticists try to study samples that are more resistant to biological degradation, resulting in a lower probability of allelic dropout, for example, dental samples, the petrous part of the temporal bone or long bones (Gomes et al. 2019a; Gomes 2020; Soniya and Kumar 2022).

3. Kinship Analysis

3.1. Genetic Analysis of Close Relatives

The genetic analysis of close kinship consists of the study of a series of nuclear DNA markers to establish if there is a biological relationship between two individuals, usually autosomal markers, generally in paternity, maternity, or sister/brotherhood tests (Gomes and Arroyo-Pardo 2022). The more distant the kinship relationship in question, the lower the resolution power of the nuclear genetic markers, making the analysis of lineage markers more feasible (Pinheiro 2009; Gomes 2020). The most used markers when establishing parental relationships are those of the STR type (as long as researchers are not dealing with highly degraded samples) (Pinheiro 2009, 2013; Gomes 2020; Gomes and Arroyo-Pardo 2022). However, when researchers are dealing with samples in an advanced state of degradation, the results obtained through STRs may be inconclusive (Goodwin and Simmons 2023). Therefore, they must be complemented with the analysis of other markers such as SNPs or InDels.

3.2. Genetic Analysis of Non-Close Relatives

In some cases of catastrophe, it is not possible to obtain a sample from a close relative (parents, children or siblings), often due to their death or an unknown location. For this type of situation, there is the possibility of discerning whether an individual is related to the alleged father by employing an indirect test through the closest relatives, such as grandparents, paternal uncles, nephews or even a brother who is known for certain to be the biological son of the alleged father (half-brother).

The advantages of lineage markers come from their ability to estimate the biogeographical origin or exclusion in paternity/maternity testing of missing persons. Their main difficulty is their null power for establishing direct relationships between individuals (Palomo-Díez and López-Parra 2022; Shrivastava et al. 2022). When the results point to a “match” by mtDNA, differing from nuclear DNA, in the case of lineage markers, they do not refer to an individual but a group of individuals of the same maternal/paternal lineage (Shrivastava et al. 2022). In the specific case of lineage markers, mitochondrial DNA (mtDNA) and Y chromosome, these are particularly relevant when the relatives available for identification are already distant, and therefore it is not possible to carry out the study of nuclear markers (Gomes and Arroyo-Pardo 2022; Sahajpal and Ambers 2023). In this specific case, the information given by the lineage markers always indicates that the individual belongs to a certain family and lineage, making it impossible to carry out a concrete identification, that is, to say that the victim is “such a person” since all maternally and paternally related individuals will have the same mtDNA and Y chromosome genetic profile, respectively.

Despite not being one of the most used tools in forensic genetics, the X chromosome can be crucial in all cases where autosomal markers have neither exclusion nor discrimination power (Pinto et al. 2010, 2011). In case it is not possible to distinguish genealogies due to the same sharing values of identical alleles by descent, such as grandparents–grandchildren versus avuncular–nephews, the X chromosome markers, due to their particular form of transmission, are different in men and women and therefore allow the distinction of this type of genealogy (Gomes et al. 2012, 2019b, 2020; Pinto et al. 2012; Gomes 2020; Gomes and Arroyo-Pardo 2022). This type of problem can occur in cases of catastrophes where different relatives of the same family are involved in a catastrophic situation and genetic identification is the only feasible tool for identifying, for example, cadaveric remains. It is also relevant in cases where it is necessary to relate a woman to a certain paternal family, where the supposed father is inaccessible and analysis of the supposed paternal grandmother or paternal half-sisters, if they exist, may be resorted to.

However, it may also be the case that, although there are relatives close to the victim, the biological samples that can be recovered from the catastrophe do not allow the analysis of nuclear markers due to a marked degradation. In these specific cases, the most used genetic marker will be the mtDNA due to its considerable number of copies per cell, allowing not an identification, but the discarding or inclusion of the victim in a given family/maternal lineage.

Finally, in the event that no relative is found who claims a relative victim of the studied emergency, it is frankly useful to study not only nuclear markers but also lineage markers and include this information in databases of missing persons in the country(ies) affected by the disaster. Over the years, it is possible that distant relatives may donate a biological sample and identify victims, or at least place the victim in a certain family through maternal or paternal lines.

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