The origin of the major cystic fibrosis mutation (delta F508) in European populations.

delta F508 is the most frequent cystic fibrosis (CF) mutation and accounts for approximately 70% of CF chromosomes worldwide. Three highly polymorphic microsatellite markers have been used to study the origin and evolution of delta F508 chromosomes in Europe. Haplotype data demonstrate that delta F508 occurred more than 52,000 years ago, in a population genetically distinct from any present European group, and spread throughout Europe in chronologically distinct expansions, which are responsible for the different frequencies of delta F508 in Europe.

Minisatellite diversity supports a recent African origin for modern humans.

In a study of human diversity at a highly variable locus, we have mapped the internal structures of tandem-repetitive alleles from different populations at the minisatellite MS205 (D16S309). The results give an unusually detailed view of the different allelic structures represented on modern human chromosomes, and of the ancestral relationships between them. There was a clear difference in allelic diversity between African and non-African populations. A restricted set of allele families was found in non-African populations, and formed a subset of the much greater diversity seen on African chromosomes. The data strongly support a recent African origin for modern human diversity at this locus.

Y chromosome sequence variation and the history of human populations.

Binary polymorphisms associated with the non-recombining region of the human Y chromosome (NRY) preserve the paternal genetic legacy of our species that has persisted to the present, permitting inference of human evolution, population affinity and demographic history. We used denaturing high-performance liquid chromatography (DHPLC; ref. 2) to identify 160 of the 166 bi-allelic and 1 tri-allelic site that formed a parsimonious genealogy of 116 haplotypes, several of which display distinct population affinities based on the analysis of 1062 globally representative individuals. A minority of contemporary East Africans and Khoisan represent the descendants of the most ancestral patrilineages of anatomically modern humans that left Africa between 35,000 and 89,000 years ago.

Author Correction: Sex-biased patterns shaped the genetic history of Roma.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Sex-biased patterns shaped the genetic history of Roma.

The Roma population is a European ethnic minority characterized by recent and multiple dispersals and founder effects. After their origin in South Asia around 1,500 years ago, they migrated West. In Europe, they diverged into ethnolinguistically distinct migrant groups that spread across the continent. Previous genetic studies based on genome-wide data and uniparental markers detected Roma founder events and West-Eurasian gene flow. However, to the best of our knowledge, it has not been assessed whether these demographic processes have equally affected both sexes in the population. The present study uses the largest and most comprehensive dataset of complete mitochondrial and Y chromosome Roma sequences to unravel the sex-biased patterns that have shaped their genetic history. The results show that the Roma maternal genetic pool carries a higher lineage diversity from South Asia, as opposed to a single paternal South Asian lineage. Nonetheless, the European gene flow events mainly occurred through the maternal lineages; however, a signal of this gene flow is also traceable in the paternal lineages. We also detect a higher female migration rate among European Roma groups. Altogether, these results suggest that sociocultural factors influenced the emergence of sex-biased genetic patterns at global and local scales in the Roma population through time.

Age and origin of major Smith-Lemli-Opitz syndrome (SLOS) mutations in European populations.

BACKGROUND: Smith-Lemli-Opitz syndrome (SLOS) (MIM 270 400) is an autosomal recessive multiple congenital anomalies/mental retardation syndrome caused by mutations in the Delta7-sterol reductase (DHCR7, E.C.1.3.1.21) gene. The prevalence of SLOS has been estimated to range between 1:15000 and 1:60000 in populations of European origin. METHODS AND RESULTS: We have analysed the frequency, origin, and age of DHCR7 mutations in European populations. In 263 SLOS patients 10 common alleles (c.964-1G>C, p.Trp151X, p.Thr93Met, p.Val326Leu, p.Arg352Trp, p.Arg404Cys, p.Phe302Leu, p.Leu157Pro, p.Gly410Ser, p.Arg445Gln) were found to constitute approximately 80% of disease-causing mutations. As reported before, the mutational spectra differed significantly between populations, and frequency peaks of common mutations were observed in North-West (c.964-1G>C), North-East (p.Trp151X, p.Val326Leu) and Southern Europe (p.Thr93Met). SLOS was virtually absent from Finland. The analysis of nearly 8000 alleles from 10 different European populations confirmed a geographical distribution of DHCR7 mutations as reported in previous studies. The common Null mutations in Northern Europe (combined ca. 1:70) occurred at a much higher frequency than expected from the reported prevalence of SLOS. In contrast the most common mutation in Mediterranean SLOS patients (p.Thr93Met) had a low population frequency. Haplotypes were constructed for SLOS chromosomes, and for wild-type chromosomes of African and European origins using eight cSNPs in the DHCR7 gene. The DHCR7 orthologue was sequenced in eight chimpanzees (Pan troglodytes) and three microsatellites were analysed in 50 of the SLOS families in order to estimate the age of the three major SLOS-causing mutations. CONCLUSIONS: The results indicate a time of first appearance of c.964-1G>C and p.Trp151X some 3000 years ago in North-West and North-East Europe, respectively. The p.Thr93Met mutations on the J haplotype has probably first arisen approximately 6000 years ago in the Eastern Mediterranean. Together, it appears that a combination of founder effects, recurrent mutations, and drift have shaped the present frequency distribution of DHCR7 mutations in Europe.

Population structure in copy number variation and SNPs in the CCL4L chemokine gene.

The recent description of a large amount of copy number variation (CNV) in the human genome has extended the concept of genome diversity. In this study we integrate the analysis of CNV and single nucleotide polymorphisms (SNPs) in the human CCL4L chemokine gene. CCL4L is a nonallelic copy of CCL4/MIP-1beta chemokine and displays a CNV that also includes the CCL3L gene, a nonallelic copy of CCL3/MIP-1alpha. This CNV and two functionally relevant CCL4L SNPs (rs4796195 and rs3744595) have been recently associated to HIV pathology in three independent studies. We have quantified the CCL4L copy number and genotyped both SNPs in samples from HGDP-CEPH Diversity Panel. A strong correlation between CCL4L CNV and one of the SNPs analyzed is found, whereas no significant linkage disequilibrium is found between the two SNPs despite their close distance (647 bp), suggesting a recent appearance of the second SNP when the diversity in the first one and CNV had already been generated. The present study points out that in genes with CNV, it may be a key issue to combine the assessment of gene copy number with the genotyping of relevant SNPs to understand the phenotypic impact of genome variation in the immune response.

Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe.

The peopling of Europe is a complex process. One of the most dramatic demographic events, the Neolithic agricultural revolution, took place in the Near East roughly 10000 years ago and then spread through the European continent. Nevertheless, the nature of this process (either cultural or demographic) is still a matter of debate among scientists. We have retrieved HVRI mitochondrial DNA sequences from 11 Neolithic remains from Granollers (Catalonia, northeast Spain) dated to 5500 years BP. We followed the proposed authenticity criteria, and we were also able, for the first time, to track down the pre-laboratory-derived contaminant sequences and consequently eliminate them from the generated cloning dataset. Phylogeographic analysis shows that the haplogroup composition of the Neolithic population is very similar to that found in modern populations from the Iberian Peninsula, suggesting a long-time genetic continuity, at least since Neolithic times. This result contrasts with that recently found in a Neolithic population from Central Europe and, therefore, raises new questions on the heterogeneity of the Neolithic dispersals into Europe. We propose here a dual model of Neolithic spread: acculturation in Central Europe and demic diffusion in southern Europe.

A novel Gypsy founder mutation, p.Arg1109X in the CMT4C gene, causes variable peripheral neuropathy phenotypes.

BACKGROUND: Linkage, haplotype and sequencing analysis in a large Spanish Gypsy kindred with multiple members affected by autosomal recessive peripheral neuropathy led to the identification of a novel mutation, p.Arg1109X, in the CMT4C gene. The screening of further unrelated patients, and of a panel of ethnically matched controls, showed that p.Arg1109X is an ancestral mutation which occurs in Gypsy populations across Europe and is the most common cause of autosomal recessive Charcot-Marie-Tooth disease in Spanish Gypsies. OBJECTIVE: To report the identification of a novel Gypsy founder mutation causing autosomal recessive CMT4C disease in a sample of homozygous affected individuals. RESULTS: The mutation was associated with a surprisingly broad spectrum of neuropathy phenotypes, with variation in the age at onset, rate of progression, severity of muscle and sensory involvement, the presence of scoliosis, and cranial nerve involvement. CONCLUSIONS: Ascertainment and further studies of CMT4C patients in this population will provide a unique opportunity for characterising the full range of clinical manifestations of the disease in a genetically homogeneous sample.

Glucocerebrosidase pseudogene variation and Gaucher disease: Recognizing pseudogene tracts in GBA alleles.

We surveyed the genetic variability of the glucocerebrosidase pseudogene (psGBA) in a worldwide sample of 100 human chromosomes. psGBA is the non-functional duplicate of the gene responsible for Gaucher disease (GBA), the most common lipid storage disorder. The existence of only one psGBA allele described until now, together with the high homology between GBA and psGBA, often prevented recognition of the complex alleles formed by the combination of GBA and psGBA, because psGBA variants could be confused with GBA mutations. In order to determine the variability existent in psGBA, the whole psGBA DNA segment was PCR-amplified and sequenced, and the genotype for all samples was obtained. The ascertainment of the phase among the heterozygous sites was possible through cloning and sequencing a single allele. Eighteen variable sites were detected along psGBA. Two of the variants already have been reported as Gaucher-causing mutations when present in GBA alleles. The other variants were unknown. The knowledge of the psGBA variants described in this report will allow identification of psGBA-GBA complex alleles that may aid in understanding the intricate phenotype-genotype relationship in Gaucher disease.

Serotonin transporter gene and risk for bipolar affective disorder: an association study in Spanish population.

BACKGROUND: The serotonin transporter (5-HTT) is an important candidate gene for the genetic transmission of manic depressive illness. Many studies of patients with affective disorders have found abnormalities in serotonin metabolism and dysregulation of the transporter itself. In the present study, we hypothesize that genetic variation in the 5-HTT gene (17q11.1-17q12) may have an effect in the etiology of manic depression. METHODS: To test this hypothesis, we analyzed allele, genotype, and haplotype frequencies of two polymorphisms recently described in the 5-HTT gene (a variable number of tandem repeats in intron 2 and a deletion/insertion polymorphism in the transcriptional control region) in a sample of 88 patients with manic-depressive illness and 113 controls. Cases and controls were matched for ethnic and geographic origin. RESULTS: No associations were found between any of these polymorphisms, tested individually or as haplotypes, and manic depression. Moreover, the genetic analysis by sex, presence/absence of psychiatric family history, and age of onset did not reveal significant differences in allele or genotype distributions. CONCLUSIONS: Our results suggest that the genetic variability of the 5-HTT gene is not a major risk factor for manic depression.

mtDNA hypervariable region II (HVII) sequences in human evolution studies.

Variation in human mitochondrial DNA (mtDNA) has been used to infer the origin and migration patterns in human populations. mtDNA analysis has been focused mainly on the first hypervariable region (HVI). Nevertheless, although many studies of the second hypervariable region (HVII) have been carried out during recent years, the correlation between the first and the second hypervariable regions has not been well established. We have analysed 71 individuals from a relatively isolated region at the westernmost edge of continental Europe (Galicia, NW Iberian peninsula) and we have used available HVII sequence information from another 17 European and African populations. The results show high concordance between the two hypervariable regions, not only in variability levels but also in other phylogenetic aspects. The study of the population structure through an AMOVA analysis shows a low level of heterogeneity in the European populations. Nevertheless, we have found some inconsistency in the results, which are related to the mutation rate in these two hypervariable regions. These results are compatible with a high heterogeneity of mutation rates across the HVII region and stress the interest of HVII in population and forensic genetics.

Do Basque- and Caucasian-speaking populations share non-Indo-European ancestors?

Genetic evidence is consistent with the view that the Indo-European languages were propagated in Europe by the diffusion of early farmers. The existence of phylogenetic relationships between European populations speaking other languages has been proposed on linguistic and archaeological grounds, and is here tested by analyzing allele frequencies at ten polymorphic protein and blood group loci. Genetic distances between speakers of Basque and Caucasian languages are compared with those between controls, i.e. contiguous populations speaking Indo-European and Altaic. Although some statistical tests show an excess of genetic similarity between Basque and South Caucasian speakers, most results do not support their common origin. If the Basques and the Caucasian-speaking populations share common ancestors, recent evolutionary phenomena must have caused divergence between them, so that their gene frequencies do not appear more similar now than those of random pairs of populations separated by the same geographic distance.

mtDNA analysis of the Galician population: a genetic edge of European variation.

Analysis of mitochondrial DNA (mtDNA) variation has become a useful tool for human population studies. We analysed the first hypervariable region of mitochondrial DNA control region (position 16024-16383) in 92 unrelated individuals from Galicia (Spain), a relatively isolated European population at the westernmost continental edge. Fifty different sequences defined by 56 variable positions were found. The frequency of the reference sequence reaches in Galicians its maximum value in Europe. Moreover, several genetic indexes confirm the low variability of our sample in comparison to data from 11 European and Middle Eastern populations. A parsimony tree of the sequences reveals a high simplicity of the tree, with few and small well defined clusters. These results place Galicians on the genetic edge of the European variation, bringing together all the traits of a cul-de-sac population with a striking similarity to the Basque population. The present results are fully compatible with a population expansion model in Europe during the Upper Paleolithic age. The genetic evidence revealed by the analysis of mtDNA shows the Galician population at the edge of a demographic expansion towards Europe from the Middle East.

Evidence for a common origin of most Friedreich ataxia chromosomes in the Spanish population.

Haplotype analysis is a powerful approach to understand the spectrum of mutations accounting for a disease in a homogeneous population. We show that haplotype variation for 10 markers linked to the Friedreich ataxia locus (FRDA) argues in favor of an important mutation homogeneity in the Spanish population, and positions the FRDA locus in the region where it has been recently isolated. We also report the finding of a new single nucleotide polymorphism called FAD1. The new marker shows a very strong linkage disequilibrium with Friedreich ataxia (FA) in both the Spanish and French populations. suggesting the existence of an ancient and widespread FRDA mutations. Inclusion of FAD1 in the extended haplotype analysis has allowed to postulate that this main FRDA mutation could account for 50-90% of the disease chromosomes. The results indicate that FA, despite clinical heterogeneity, could have originated from a few initial mutations.

Genetic structure of north-west Africa revealed by STR analysis.

We have analysed a large set of autosomal short tandem repeat (STR) loci in several Arabic and Berber-speaking groups from north-west Africa (ie Moroccan Arabs, northern-central and southern Moroccan Berbers, Saharawis, and Mozabites). Two levels of analysis have been devised using two sets of 12STR loci, (D3S1358, vWA, FGA, THO1, TPOX, CSF1PO, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820) and 21 (the former set plus D9S926, D11S2010, D13S767, D14S306, D18S848, D2S1328, D4S243, F13A1, and FES/FPS). For each set, data for a number of external reference populations were gathered from the literature. Several methods of analysis based on genetic distances (neighbour-joining trees, principal coordinate analysis, boundary detection), as well as AMOVA, showed that genetic differentiation among NW African populations was very low and devoid of any spatial pattern. When the NW African populations were grouped according to cultural or linguistic differences, the partition was not associated with genetic differentiation. Thus, it is likely that Arabisation was mainly a cultural process. A clear genetic difference was found between NW African populations and Iberians, which underscores the Gilbraltar Straits as a strong barrier to genetic exchange; nonetheless, some degree of gene flow into Southern Iberia may have existed. NW Africans were genetically closer to Iberians and to other Europeans than to African Americans.

Association analysis of the catechol O-methyltransferase gene and bipolar affective disorder.

OBJECTIVE: Catechol O-methyltransferase (COMT) is an enzyme that inactivates catecholamines. Two common COMT alleles determine high and low activity of the enzyme. Previous studies using biochemical methods found lower enzyme activity in patients with major depression and bipolar disorder in comparison with control values, suggesting that a dysfunction in catecholamine metabolism may be related to the etiology of depression. METHOD: The authors studied two recently described DNA polymorphisms at the COMT gene (a silent C256G mutation and a structural mutation, Val-108-Met) in 88 patients with bipolar disorder and in 113 healthy comparison subjects, all of Spanish origin. RESULTS: The frequency of the C256 allele was 0.58 in the patients and 0.54 in the comparison subjects. The frequency of the Val108 variant was 0.57 for both the patients and the comparison subjects. No allelic or genotypic associations were observed. CONCLUSIONS: The lack of association suggests that the COMT gene is not a major risk factor for bipolar disorder.

Unravelling migrations in the steppe: mitochondrial DNA sequences from ancient central Asians.

This study helps to clarify the debate on the Western and Eastern genetic influences in Central Asia. Thirty-six skeletal remains from Kazakhstan (Central Asia), excavated from different sites dating between the fifteenth century BC to the fifth century AD, have been analysed for the hypervariable control region (HVR-I) and haplogroup diagnostic single nucleotide polymorphisms (SNPs) of the mitochondrial DNA genome. Standard authentication criteria for ancient DNA studies, including multiple extractions, cloning of PCR products and independent replication, have been followed. The distribution of east and west Eurasian lineages through time in the region is concordant with the available archaeological information: prior to the thirteenth-seventh century BC, all Kazakh samples belong to European lineages; while later an arrival of east Eurasian sequences that coexisted with the previous west Eurasian genetic substratum can be detected. The presence of an ancient genetic substratum of European origin in West Asia may be related to the discovery of ancient mummies with European features in Xinjiang and to the existence of an extinct Indo-European language, Tocharian. This study demonstrates the usefulness of the ancient DNA in unravelling complex patterns of past human migrations so as to help decipher the origin of present-day admixed populations.