Flavio De Angelis

First genetic insight into Libyan Tuaregs: a maternal perspective

The Tuaregs are a semi‐nomadic pastoralist people of northwest Africa. Their origins are still a matter of debate due to the scarcity of genetic and historical data. Here we report the first data on the mitochondrial DNA (mtDNA) genetic characterization of a Tuareg sample from Fezzan (Libyan Sahara). A total of 129 individuals from two villages in the Acacus region were genetically analysed. Both the hypervariable regions and the coding region of mtDNA were investigated. Phylogeographic investigation was carried out in order to reconstruct human migratory shifts in central Sahara, and to shed light on the origin of the Libyan Tuaregs. Our results clearly show low genetic diversity in the sample, possibly due to genetic drift and founder effect associated with the separation of Libyan Tuaregs from an ancestral population. Furthermore, the maternal genetic pool of the Libyan Tuaregs is characterized by a major „European” component shared with the Berbers that could be traced to the Iberian Peninsula, as well as a minor ‘south Saharan’ contribution possibly linked to both Eastern African and Near Eastern populations.

Haplotypes in SLC24A5 Gene as Ancestry Informative Markers in Different Populations

Ancestry informative markers (AIMs) are human polymorphisms that exhibit substantially allele frequency differences among populations. These markers can be useful to provide information about ancestry of samples which may be useful in predicting a perpetrator’s ethnic origin to aid criminal investigations. Variations in human pigmentation are the most obvious phenotypes to distinguish individuals. It has been recently shown that the variation of a G in an A allele of the coding single-nucleotide polymorphism (SNP) rs1426654 within SLC24A5 gene varies in frequency among several population samples according to skin pigmentation. Because of these observations, the SLC24A5 locus has been evaluated as Ancestry Informative Region (AIR) by typing rs1426654 together with two additional intragenic markers (rs2555364 and rs16960620) in 471 unrelated individuals originating from three different continents (Africa, Asia and Europe). This study further supports the role of human SLC24A5 gene in skin pigmentation suggesting that variations in SLC24A5 haplotypes can correlate with human migration and ancestry. Furthermore, our data do reveal the utility of haplotype and combined unphased genotype analysis of SLC24A5 in predicting ancestry and provide a good example of usefulness of genetic characterization of larger regions, in addition to single polymorphisms, as candidates for population-specific sweeps in the ancestral population.

Human GST loci as markers of evolutionary forces: GSTO1*E155del and GSTO1*E208K polymorphisms may be under natural selection induced by environmental arsenic

Over the last two decades, significant data has been accumulated linking Glutatione S-Transferases (GSTs) with the development of several diseases. Contemporary studies have demonstrated the impact of ethnicity on GST allele frequencies. The aim is to verify if the variability of GST genes reflects population demographic history or rather selective pressures. GST genes (GSTM1, GSTO1 GSTO2, GSTT1) were analysed in three Ecuadorian populations (Cayapas, n = 114; Colorados, n = 104; African-Ecuadorian, n = 77) and compared with HapMap data. GST SNPs were determined using the PCR-RFLP method while GST null phenotype was determined using a Multiplex PCR. The population relationship achieved using GSTM1 positive/null, GSTO1*A140D, GSTO2*N142D and GSTT1 positive/null are in agreement with the data obtained using neutral polymorphisms: Amerindians are close to Asian populations and African-Ecuadorians to African populations. To what concerns GSTO1*del155 and GSTO1*K208 variants, allele frequencies never exceeded 10%, showing no significant differences in the Ecuadorian groups and in worldwide populations. The features of GSTO1*del155 and GSTO1*K208 variants and their association with arsenic biotransformation deficiency suggest the presence of a selection mechanism towards these loci. In particular, this hypothesis is strengthened by a possible linkage between these alleles and the susceptibility of arsenic-induced male infertility.

Functional variability of glutathione S-transferases in basque populations

Glutathione S‐transferases (GSTs) are enzymes involved in Phase II reactions. They play a key role in cellular detoxification. Various studies have shown that genes coding for the GST are highly polymorphic and some of these variants are directly associated with a decrease of enzyme activity making individuals more susceptible to different clinical phenotypes. The aim of this study is to investigate the genetic variability of GST genes among human populations. We have focused our attention on the polymorphic variants of the GSTA1, GSTM1, GSTO1, GSTO2, GSTP1, GSTT1, and GSTT2B genes.

Haplotype differences for copy number variants in the 22q11.23 region among human populations: a pigmentation-based model for selective pressure

Two gene clusters are tightly linked in a narrow region of chromosome 22q11.23: the macrophage migration inhibitory factor (MIF) gene family and the glutathione S-transferase theta class. Within 120 kb in this region, two 30-kb deletions reach high frequencies in human populations. This gives rise to four haplotypic arrangements, which modulate the number of genes in both families. The variable patterns of linkage disequilibrium (LD) between these copy number variants (CNVs) in diverse human populations remain poorly understood. We analyzed 2469 individuals belonging to 27 human populations with different ethnic origins. Then we correlated the genetic variability of 22q11.23 CNVs with environmental variables. We confirmed an increasing strength of LD from Africa to Asia and to Europe. Further, we highlighted strongly significant correlations between the frequency of one of the haplotypes and pigmentation-related variables: skin color (R2=0.675, P<0.001), distance from the equator (R2=0.454, P<0.001), UVA radiation (R2=0.439, P<0.001), and UVB radiation (R2=0.313, P=0.002). The fact that all MIF-related genes are retained on this haplotype and the evidences gleaned from experimental systems seem to agree with the role of MIF-related genes in melanogenesis. As such, we propose a model that explains the geographic and ethnic distribution of 22q11.23 CNVs among human populations, assuming that MIF-related gene dosage could be associated with adaptation to low UV radiation.

Polymorphisms of the COL1A2, CYP1A1 and HS1,2 Ig enhancer genes in the Tuaregs from Libya

Background: Restriction fragment length polymorphisms (RFLPs) of the COL1A2 and CYP1A1 and short tandem repeats of HS1,2 Ig enhancer genes are proving to be useful markers for describing human populations and thus are of interest for anthropogenetic research. Moreover, they can provide useful information in identifying alleles and haplotypes associated with particular forms of common diseases or for pharmacogenomics studies. Aim: The objective of this study was to define the genetic structure of Libyan Tuaregs and to establish the degree of genetic homogeneity amongst the El Awaynat and Tahala groups. Subjects and methods: Tuareg individuals from El Awaynat (n = 99) and Tahala (n = 18), in Libyan Sahara, were analysed for the RFLPs of COL1A2 and CYP1A1 and short tandem repeats of HS1,2 Ig enhancer genes. In order to provide a clearer picture of COL1A2, CYP1A1 and HS1,2 Ig enhancer allele and haplotype frequency distributions in various human groups distributed over a wide geographic area, comparisons with other African, European and Asian populations were carried out by analysis of molecular variance (AMOVA) and genetic distance analysis. Results: No significant level of differentiation was evident between the two Libyan Tuareg groups according to AMOVA. For the CYP1A1 gene, a possible new haplotype was observed, even though at a very low frequency. Linkage disequilibrium was assessed only for COL1A2, since CYP1A1 turned out to be poorly polymorphic for m2 and m3. Conclusions: Statistical analyses showed that Tuaregs from Libya are located in a intermediate position between south Saharan populations on one side and the Europeans and the Asians on the other.

Most recent common ancestor of TTR Val30Met mutation in Italian population and its potential role in genotype-phenotype correlation

Abstract Introduction: Transthyretin (TTR)-related amyloidosis is characterized by autosomal transmission of amyloidogenic mutated TTR. Val30Met is one of the most common amyloidogenic TTR mutations, showing a worldwide distribution with phenotypic heterogeneity among human populations. Multiple founder mutations for Val30Met foci have been hypothesized and the different origins may explain the phenotypic variability. The aim of our study is to determine the origin of Italian Val30Met and to analyze the genetic relationship of other Val30Met foci. Methods: We analyzed the origin of Italian Val30Met through 11 microsatellite markers around the TTR gene in 29 patients and 34 healthy controls. Results: Our genetic analysis showed an estimated age of origin of 34–36 generations ago for the Italian Val30Met. Comparing Italian Val30Met haplotypes with those from Sweden and Portugal highlights relevant differences that seem to be consistent with an independent origin of Italian Val30Met mutation. This genetic evidence agrees with the disease phenotypic variation in these populations. Discussion and conclusions: Italian Val30Met mutation should have originated before the Portuguese and Swedish Val30Met ones (which arose through independent mutational events). This indicates a genetic diversity in the surrounding regions of three different Val30Met mutations, supporting the hypothesis that TTR non-coding regions may contribute to phenotypic heterogeneity.

Traces of forgotten historical events in mountain communities in Central Italy: A genetic insight

Analysis of human genetic variation in mountain communities can shed light on the peopling of mountainous regions, perhaps revealing whether the remote geographic location spared them from outside invasion and preserved their gene pool from admixture. In this study, we created a model to assess genetic traces of historical events by reconstructing the paternal and maternal genetic history of seven small mountain villages in inland valleys of Central Italy.

Phenotype versus Genotype Methods for Copy Number Variant Analysis of Glutathione S‐Transferases M1

Several variants have been identified for genes encoding Glutathione S‐transferase (GST) enzymes; some are associated with significant alteration of protein function. One of the most extensively studied is a copy number variant (CNV) in the GSTM1 gene. In this study, we compared phenotype (positive, null) and genotype (1/1, 1/0, 0/0) methods in order to assess dissimilarities obtained using these two different approaches to evaluate possible methodology‐related bias. We analyzed a sample of 1947 individuals belonging to 18 human populations with different ethnic origins. We also evaluated whether the presence of missense substitutions in the GSTM1 gene might influence the association of the CNV with phenotype distribution.

Non-coding variants contribute to the clinical heterogeneity of TTR amyloidosis

Coding mutations in TTR gene cause a rare hereditary form of systemic amyloidosis, which has a complex genotype–phenotype correlation. We investigated the role of non-coding variants in regulating TTR gene expression and consequently amyloidosis symptoms. We evaluated the genotype–phenotype correlation considering the clinical information of 129 Italian patients with TTR amyloidosis. Then, we conducted a re-sequencing of TTR gene to investigate how non-coding variants affect TTR expression and, consequently, phenotypic presentation in carriers of amyloidogenic mutations. Polygenic scores for genetically determined TTR expression were constructed using data from our re-sequencing analysis and the GTEx (Genotype-Tissue Expression) project. We confirmed a strong phenotypic heterogeneity across coding mutations causing TTR amyloidosis. Considering the effects of non-coding variants on TTR expression, we identified three patient clusters with specific expression patterns associated with certain phenotypic presentations, including late onset, autonomic neurological involvement, and gastrointestinal symptoms. This study provides novel data regarding the role of non-coding variation and the gene expression profiles in patients affected by TTR amyloidosis, also putting forth an approach that could be used to investigate the mechanisms at the basis of the genotype–phenotype correlation of the disease.