ABSTRACT
European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.
Subject(s)
DNA, Ancient , Databases, Genetic , Genetic Drift , Genome, Human , White People/genetics , Animals , Genome-Wide Association Study , History, Ancient , Human Genetics , Humans , Italy , Neanderthals/geneticsABSTRACT
The human ZC3HAV1 gene encodes an antiviral protein. The longest splicing isoform of ZC3HAV1 contains a C-terminal PARP-like domain, which has evolved under positive selection in primates. We analyzed the evolutionary history of this same domain in humans and in Pan troglodytes. We identified two variants that segregate in both humans and chimpanzees; one of them (rs3735007) does not occur at a hypermutable site and accounts for a nonsynonymous substitution (Thr851Ile). The probability that the two trans-specific polymorphisms have occurred independently in the two lineages was estimated to be low (P = 0.0054), suggesting that at least one of them has arisen before speciation and has been maintained by selection. Population genetic analyses in humans indicated that the region surrounding the shared variants displays strong evidences of long-standing balancing selection. Selection signatures were also observed in a chimpanzee population sample. Inspection of 1000 Genomes data confirmed these findings but indicated that search for selection signatures using low-coverage whole-genome data may need masking of repetitive sequences. A case-control study of more than 1,000 individuals from mainland Italy indicated that the Thr851Ile SNP is significantly associated with susceptibility to multiple sclerosis (MS) (odds ratio [OR] = 1.47, 95% confidence intervals [CI]: 1.08-1.99, P = 0.011). This finding was confirmed in a larger sample of 4,416 Sardinians cases/controls (OR = 1.18, 95% CI: 1.037-1.344, P = 0.011), but not in a population from Belgium. We provide one of the first instances of human/chimpanzee trans-specific coding variant located outside the major histocompatibility complex region. The selective pressure is likely to be virus driven; in modern populations, this variant associates with susceptibility to MS, possibly via the interaction with environmental factors.
Subject(s)
Genetic Predisposition to Disease , Multiple Sclerosis/genetics , Polymorphism, Single Nucleotide , RNA-Binding Proteins/genetics , Selection, Genetic , Acebutolol , Animals , Case-Control Studies , Gene-Environment Interaction , Genetic Association Studies , Genome, Human , Haplotypes , Humans , Linkage Disequilibrium , Models, Genetic , Odds Ratio , Pan troglodytes/genetics , Phylogeny , Protein Isoforms/chemistry , Protein Isoforms/genetics , Protein Structure, Tertiary , RNA-Binding Proteins/chemistry , Sequence Analysis, DNAABSTRACT
Variation within intron 19 of the CLEC16A (KIAA0350) gene region was recently found to be unequivocally associated with type 1 diabetes (T1D) in genome-wide association (GWA) studies in Northern European populations. A variant in intron 22 that is nearly independent of the intron 19 variant showed suggestive evidence of association with multiple sclerosis (MS). Here, we genotyped the rs725613 polymorphism, representative of the earlier reported associations with T1D within CLEC16A, in 1037 T1D cases, 1498 MS cases and 1706 matched controls, all from the founder, autoimmunity-prone Sardinian population. In these Sardinian samples, allele A of rs725613 is positively associated not only with T1D (odds ratio=1.15, P one-tail=5.1 x 10(-3)) but also, and with a comparable effect size, with MS (odds ratio=1.21, P one-tail 6.7 x 10(-5)). Taken together these data provide evidence of joint disease association in T1D and MS within CLEC16A and underline a shared disease pathway.
Subject(s)
Diabetes Mellitus, Type 1/genetics , Genetic Variation , Genome-Wide Association Study , Lectins, C-Type/genetics , Monosaccharide Transport Proteins/genetics , Multiple Sclerosis/genetics , Adult , Age of Onset , Alleles , Case-Control Studies , Family , Female , Humans , Italy , Male , Odds Ratio , Polymorphism, Genetic , ProbabilityABSTRACT
Y-chromosomal DNA polymorphisms, especially Y-STRs are well established in forensic routine case work. The STRs are used for identification in paternity deficiency cases and stain analysis with complicate mixtures of male and female DNA. In contrast, Y-chromosomal SNPs are a new tool in forensic investigations. At present, Y-SNPs are mainly used in molecular anthropology for evolutionary studies. Nevertheless, these markers could also provide very useful information for the analysis of forensic cases. The aim of the presented study was to test Y-SNP-typing for stain analyses using different methods-SNaPshot and MALDI-TOF MS. Both methods are based on the principle of minisequencing. The selected Y-SNP markers are suited to define the most important European haplogroups.
Subject(s)
Chromosomes, Human, Y , DNA Fingerprinting/methods , Polymorphism, Single Nucleotide , DNA/analysis , DNA Primers , Genetic Markers , Genotype , Haplotypes , Humans , Male , Polymerase Chain Reaction , White PeopleABSTRACT
OBJECTIVES: Multiple sclerosis (MS) is a chronic demyelinating disease of the central nervous system which is widely believed to have a T-cell-mediated etiology. The cytotoxic T-lymphocyte antigen-4 (CTLA-4) antigen molecule plays a key role in the downregulation of T-cell responses. To examine the genetic association of the CTLA-4 gene locus with MS, we analyzed an exon 1 (A49G) transition. MATERIAL AND METHODS: One hundred and fifty-two MS patients and 154 controls were examined. The A/G transition was genotyped by a polymerase chain reaction followed by labeling with a SNaPshot kit and detection using a capillary genetic analyzer. RESULTS: The genotype, allele and phenotype frequencies did not differ significantly between MS patients and controls. Those MS patients with AA and AG genotypes had 4.36 times greater risk of progressing from the relapsing-remitting to the secondary progressive form of the disease than those with the GG genotype. CONCLUSION: The results of our study indicate that CTLA-4 (A49G) exon 1 polymorphism is associated with MS progression.
