Assessing population substructure in the Lebanese population: A population study using data on 23 autosomal short tandem repeats

BACKGROUND

Understanding the genetic substructure of a population is essential for proper forensic genetic analysis. The Lebanese population has a high rate of endogamous and consanguineous marriages and is segregated based on religious belongings. However, no genetic population studies have been performed up to date to estimate the degree of genetic substructure and inbreeding coefficients.

METHODS

The present study analyzed a compendium of 23 autosomal STRs typed in 1400 individuals belonging to the seven major Lebanese religious subcommunities. Inbreeding coefficients such as F statistics were estimated.

RESULTS

Results showed a Fst (theta) value of 0.002, indicating a low genetic subdivision within the Lebanese population.

CONCLUSION

This study aimed at assessing the genetic substructure of the Lebanese population by analyzing 1400 Lebanese citizens' samples using 23 STR markers. F statistics were computed to evaluate the degree of genetic substructure. Results showed a Fst value of 0.002, indicating a low genetic subdivision within the Lebanese population.

Genetic variations and population data on five supplementary STR markers in Lebanon

Population representative short tandem repeat (STR) allele frequencies are crucial for proper probabilistic interpretation of DNA forensic evidence. STR allele frequencies also provide information about the genetic diversity of a given population. The Lebanese population is characterized by the presence of more than 18 religious communities that have high recorded rates of endogamous and consanguineous marriages, where the choice of marriages is mainly influenced by their respective geographical distributions and religious affiliation. These factors could have led to an increase in complex DNA cases, whereby high numbers of STR markers are needed to help clear the case. Allele frequencies for 23 STR loci in the Lebanese population were recently estimated and published. The present study aims at estimating the STR allele frequencies for five supplementary STRs, namely, the LPL, F13B, FESFPS, F13A01, and Penta C STR markers, which are mainly used to resolve complex kinship investigations. A DNA database representative of the Lebanese population that comprises 505 Lebanese unrelated individuals was used to amplify the five STR systems, using the CS7 kit released by Promega. The allele frequencies for these STR systems were estimated, and a significant departure from the Hardy-Weinberg equilibrium was detected after Bonferroni correction for multiple tests at locus LPL, F13A01, and Penta C. The newly added systems appeared to have variation in their discriminative power among Lebanese individuals. Penta C showed the highest power of discrimination, whereas FESFPS showed the lowest power of discrimination. The estimated frequencies and population data could provide local DNA relationship testing laboratories with additional tools that help resolve complex DNA cases.

Genotyping irregularities observed in STR markers used in forensics and human identification in the Lebanese population

Forensic DNA analysis is based on the evaluation of DNA profiles obtained from reference samples or crime scene traces. Profiles are determined using different commercial STR multiplex kits, which includeallelic ladders for the correct designation of alleles ofa given STR system. However, some new STR variants could be observed and their identification is essential for proper allele size calling in casework interpretation and cases of kinship matching or relationship testing. A total of 6392 samples were analyzedas part of the DNA work at our DNA testing facility from 2004 until 2016, where one hundred and twelvenew different STR variant alleles of 20STR loci wereobserved in the Lebanese population. Forty-fiveof these variant alleles were internationally reported in the STR-base whereas the remainingsixty-sevenalleles were observed for the first time. The loci included D3S1358, D19S433, D21S11, D13S317, TPOX, FGA, D7S820, D18S51, CSF1PO, D2S1338, D10S1248, D12S391, D22S1045, D2S441, Penta-D, Penta-E, SE33, D1S1656, vWA, and THO1.Also, four triallelic patterns were observed at D21S11, D12S391, D13S317 and Penta-D loci. Primer binding site mismatch that resulted in a discordance between the amplification of different kits was observed once attheD19S433 locus.

A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.