Y-chromosome polymorphisms and ethnic group – a combined STR and SNP approach in a population sample from northern Italy

Aim To find an association between Y chromosome polymorphisms and some ethnic groups. Methods Short tandem repeats (STR) and single-nucleotide polymorphisms (SNP) on the Y chromosome were typed in 311 unrelated men from four different ethnic groups – Italians from northern Italy, Albanians, Africans from the Maghreb region, and Indo-Pakistanis, using the AmpFlSTR® Yfiler PCR Amplification Kit and the SNaPshot Multiplex Kit. Results STRs analysis found 299 different haplotypes and SNPs analysis 11 different haplogroups. Haplotypes and haplogroups were analyzed and compared between different ethnic groups. Significant differences were found among all the population groups, except between Italians and Indo-Pakistanis and between Albanians and Indo-Pakistanis. Conclusions Typing both STRs and SNPs on the Y chromosome could become useful in determining ethnic origin of a potential suspect.

Determining the ethnic origin of a suspect through DNA analysis of biological stains left at the crime scene is an important part of criminal investigations. To discriminate between different ethnic groups, short tandem repeat (STR) autosomal marker analysis (1-6) can be complemented by single-nucleotide polymorphism (SNP) assays, which have have been demonstrated to be more useful for this purpose (7,8). The introduction of new markers, mostly from the Y chromosome, offers a better power of discrimination to define even sub-populations of different ethnic groups (9-11). This study aims to compare a sample of Italian men from Brescia (northern Italy) with a sample of men from each of three main ethnic groups living in Brescia county (Albanians, North Africans, Indo-Pakistanis), through STRs and SNPs Y chromosome typing, in order to find the data useful in defining the ethnic origin.

MAteriAls AND MethoDs
The study was conducted on samples collected during routine forensic work of the Department of Forensic Medicine of Brescia, Italy, over the period between 2010 and 2012. A total of 311 men from four different ethnic groups were evaluated: 107 Italians, 83 Albanians, 77 Africans from Maghreb, and 44 Indo-Pakistanis. The participants were not related and the samples were of sufficient quality and quantity to be included in the statistical analysis.
DNA was extracted from buccal swabs or blood using the Chelex® 100 procedure (12).  Table 1, Table   2, Table 3, and Table 4. Haplotypes of the four population groups were compared using the ARLEQUIN Software (18) ( Table 5).
No significant differences were found between Italians and Indo-Pakistanis, as opposed to Italians and Albanians, between whom significant differences were found, as well as between Italians and North Africans. Significant differences were found between North Africans' haplotypes and all other populations.
Haplogroup prediction starting from haplotype is theoretically possible under certain conditions (21,22) and if Y-STRs are routinely tested in forensic laboratories, they could be greatly useful for forensic investigations. No strong correlations were observed in the data set between STRs-specific alleles and haplogroups. Haplogroup prediction from the haplotype was not calculated in this study since a simple Bayes theorem calculation would be strongly affected by a sampling error due to the small data set.
In conclusion, SNPs analysis seems to be a powerful tool to infer the ethnic origin of an unknown sample but the number of samples for each of these four populations needs to be increased for a better resolution. Our results showed a low discrimination considering the haplotype and the haplogroup independently. Otherwise, the combination of the two systems enabled good discrimination between Italian men from northern Italy and men belonging to other three ethnic groups, which has potential usefulness in crime scene investigations. Further autochthonous population studies are needed to highlight the most informative loci.
Funding None.
ethical approval Not required.
Declaration of authorship VC and AM were in charge of technical organization of the study. AV, NC and FDF were in charge of organization aspects of the study.

Competing interests All authors have completed the Unified Competing
Interest form at www.icmje.org/coi_disclosure.pdf (available on request from the corresponding author) and declare: no support from any organization for the submitted work; no financial relationships with any organizations that might have an interest in the submitted work in the previous years; no other relationships or activities that could appear to have influenced the submitted work.