Abstract

Due to the haploid nature of the human male determinant chromosome, Y chromosome Short Tandem Repeats (Y-STRs) are interesting genetic markers for the identification of potential suspects in certain forensic investigations. Furthermore, being a haploid chromosome, the presence of more than one fragment size in Y-STR analysis is often indicative of a mixture of male DNA. Certain events during DNA replication may lead to the appearance of allelic variants in certain markers that could result in duplications, microvariants or null alleles. In particular, duplications may raise complications in the study of Y-STR markers in forensic investigations. Here we find that certain duplications may be found in higher frequencies than previously described, which could be cause for concern in future or present investigations in forensic genetics.

Keywords1. Introduction

Certain areas of the human genome present a high level of variability between individuals. Short Tandem Repeats (STRs), are repetitive DNA sequences that can be used to identify suspects in ongoing criminal cases, unidentified or undocumented individuals, or to infer paternity in forensic contexts.

In the human males, the Y chromosome is mostly preserved during meiotic division due to its haploid status. It can then be passed on through generations mostly unchanged, barring occasional mutations [[1]Review Sex Chromosome Specialization and Degeneration in Mammals.]. Furthermore, Y chromosome analysis eliminates the need for differential extraction in cases in which there is an excess of female DNA in a mixture, such as rape investigations [[2]Y chromosome STR typing in crime casework.].

Y-STR markers with more than one amplified fragment may be indicative of a mixture of male DNA. However, there are instances in which there may be certain allelic variations. In particular, duplications can lead to the initial misinterpretation of male DNA mixtures in these samples.

This study looks to analyse the Y-STR markers of African descendants residing in Central and Southern Portugal, as they represent nearly 21 % of immigrants in this country and therefore may influence the structure of the overall host population [[3]Base De Dados De Portugal Contemporâneo.]. As results have shown, these populations reveal a higher than expected frequency of duplications in specific Y-STR markers. Here we try to elucidate how these variations may affect future or even current forensic investigations.2. Materials and methodsWe extracted and analysed DNA from 400 blood samples of individuals descendant from African countries residing in Central and Southern Portugal. DNA extraction was done through the Chelex 100® method [[4]Walsh P.S. Metzger D.A. Higuchi R. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material.]. Quantification was done with the Real-Time PCR amplification kit, Quantifiler™ Trio DNA Quantification Kit (Applied Biosystems), and the subsequent Y-STR marker amplification with the PowerPlex® Y23 System (Promega) amplification kit, and capillary electrophoresis was performed using the 3130 xl sequencer (Applied Biosystems) [,[6]Quantifiler TM HP and Trio DNA Quantification Kits USER GUIDE [Internet].]. Samples in with marker variants were re-extracted and amplified with the Y Filer™ Plus (Applied Biosystems) amplification kit [[7]Yfiler TM Plus PCR Amplification Kit USER GUIDE [Internet].]. Data analysis was performed with the Arlequin 3.5.2.2 software.3. ResultsOf the 400 samples studied, 10 % of the haplotypes presented allelic variants, of which 26 were duplications, 8 were microvariants and 5 were found to be null alleles (Fig.1).

Fig. 1Rate of Null Alleles, Duplications and Microvariants analysed in the studied sample.

About 79 % of the duplications were found in the DYS448 genetic marker, being that haplotypes containing a 1920 duplication in this marker represented 4.75 % of the studied samples. Other, less prominent duplications were found in the DYS389 II genetic marker (of which two were found to contain a duplication in the DYS439 marker as well), and in the DYS549 marker. Microvariants were observed in the DYS458 and DYS385 markers, while null alleles were found within the DYS448 and DYS392 markers.

4. Discussion and conclusionAccording to the National Institute of Standards and Technology’s STRBase database, DYS448 1920 duplication variants were only reported twice with the same amplification kit and sequencer, and twice more with different equipment and amplification kits []. The results shown in this study pertain to a much higher frequency than would be predicted with the information provided in this database, meaning that, at least in African descendant individuals, this may be a more common variant.

Due to absence of recombination in Y chromosome, two unrelated male individuals could potentially present a very similar or even identical haplotype, depending on the amplification kit used. In fact, during the course of this study, certain individuals shared a haplotype when analysed through the genetic markers contained in the Promega amplification kit, yet differed in certain markers when amplified with the Applied Biosystems amplification kit. It is possible that, when more individualising methods are not an option, the presence of duplications in Y-STR markers can lead to delays in the analysis of such samples.

That being said, it is worth noting that these allelic variants are not overtly prominent in the populations. If taken into consideration, these can be used to obtain more accurate profile matches. Their presence in a sample from an ongoing investigation can offer a higher probability of that sample belonging to a suspect known to have these variations.

Many forensic genetics tools are also not yet equipped to take these variants into account. The Y-chromosome STR Haplotype Reference Database itself contains tools for population comparison, yet it does not account for the presence of allelic variants when analysing samples through AMOVA & MDS. It is important that the study of forensic and population genetics be prepared for such instances in order to provide more accurate results, seeing as they prove to be more common than previously thought.

Declaration of Competing Interest

None.

References

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Published online: November 27, 2019

Accepted: November 27, 2019

Received in revised form: November 26, 2019

Received: September 19, 2019

Identification

DOI: https://doi.org/10.1016/j.fsigss.2019.11.016

Copyright

© 2019 Elsevier B.V. All rights reserved.

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