Description of a simple multiplex PCR-SSCP method for AB0 genotyping and its application to the peopling of the Canary Islands

A simple and affordable multiplex polymerase chain reaction-single-strand conformation polymorphism method is proposed for the molecular study of AB0 polymorphisms. Application of this method to the peopling of the Canary Islands, analyzing a total of 2,200 chromosomes, detected that in addition to Berbers and Basques, the rare alleles 0210 and O303 are also present in the Iberian Peninsula and in the Canary Islands. Allele B101, with the highest frequency in Northwest (NW) Africa, shows a negative correlation (R = -0.822, p = 0.023) between geographic distances from this continent and insular frequencies, congruent with a main aborigine colonization from East to West still detectable today. Similar to previous autosomal studies, admixture estimations point to a major Iberian contribution (82 +/- 0.5%) to the Canary Islands, although, in some islands as La Gomera, the NW African component raised to 62 +/- 4.3%.     

Analysis of the CCR5 gene coding region diversity in five South American populations reveals two new non-synonymous alleles in Amerindians and high CCR5*D32 frequency in Euro-Brazilians

The CC chemokine receptor 5 (CCR5) molecule is an important co-receptor for HIV. The effect of the CCR5*D32 allele in susceptibility to HIV infection and AIDS disease is well known. Other alleles than CCR5*D32 have not been analysed before, neither in Amerindians nor in the majority of the populations all over the world. We investigated the distribution of the CCR5 coding region alleles in South Brazil and noticed a high CCR5*D32 frequency in the Euro-Brazilian population of the Paraná State (9.3%), which is the highest thus far reported for Latin America. The D32 frequency is even higher among the Euro-Brazilian Mennonites (14.2%). This allele is uncommon in Afro-Brazilians (2.0%), rare in the Guarani Amerindians (0.4%) and absent in the Kaingang Amerindians and the Oriental-Brazilians. R223Q is common in the Oriental-Brazilians (7.7%) and R60S in the Afro-Brazilians (5.0%). A29S and L55Q present an impaired response to β-chemokines and occurred in Afro- and Euro-Brazilians with cumulative frequencies of 4.4% and 2.7%, respectively. Two new non-synonymous alleles were found in Amerindians: C323F (g.3729G > T) in Guarani (1.4%) and Y68C (g.2964A > G) in Kaingang (10.3%). The functional characteristics of these alleles should be defined and considered in epidemiological investigations about HIV-1 infection and AIDS incidence in Amerindian populations.     

Study of red blood cell and serum enzymes in five Pyrenean communities and in a Basque population sample

Until recently, no data on genetic polymorphisms in the populations living on the northern side of the Pyrenees have been available, except for the Basques. Several investigations were done lately on rural communities in various geographic zones in the Pyrenees from the eastern to the western part. In this paper, the results for the following enzyme polymorphisms are reported: acid phosphatases, AK, ADA, PGM1 and PGM2, 6PGD, NADH diaphorase, SOD, MDH, TGP, G6PD, C5 esterase (E2 locus), serum cholinesterase (E1 locus). Significant variation in gene frequencies was observed over the distinct geographic zones for the main polymorphic system. Furthermore, some rare alleles were found: a new G6PD variant (Luz-Saint-Sauveur), the presence of ADA3 and ADA5 alleles in two groups of the Central Pyrenees, a Dia2 gene among Basques and in the Pays de Sault, a high rate of Ea1 allele in the Basque group. The values obtained for the degree of heterozygosity are in agreement with the relative isolation of the different groups studied and confirm the importance of sociocultural factors in the evolution of the genetic background of rural communities in Europe.     

Genetic variants of serum butyrylcholinesterase in Chilean Mapuche Indians

We estimated the frequencies of serum butyrylcholinesterase (BChE) alleles in three tribes of Mapuche Indians from southern Chile, using enzymatic methods, and we estimated the frequency of allele BCHE*K in one tribe using primer reduced restriction analysis (PCR-PIRA). The three tribes have different degrees of European admixture, which is reflected in the observed frequencies of the atypical allele BCHE*A: 1.11% in Huilliches, 0.89% in Cuncos, and 0% in Pehuenches. This result is evidence in favor of the hypothesis that BCHE*A is absent in native Amerindians. The frequencies of BCHE*F were higher than in most reported studies (3.89%, 5.78%, and 4.41%, respectively). These results are probably due to an overestimation of the frequency of allele BCHE*F, since none of the 20 BCHE UF individuals (by the enzymatic test) individuals analyzed showed either of the two DNA base substitutions associated with this allele. Although enzymatic methods rarely detect the presence of allele BCHE*K, PCR-PIRA found the allele in an appreciable frequency (5.76%), although lower than that found in other ethnic groups. Since observed frequencies of unusual alleles correspond to estimated percentages of European admixture, it is likely that none of these unusual alleles were present in Mapuche Indians before the arrival of Europeans.     

FMR1 CGG repeat distribution and linked microsatellite-SNP haplotypes in normal Mexican Mestizo and indigenous populations

The (CGG)n repeat size distribution in the FMR1 gene was studied in healthy individuals: 80 X chromosomes of Mexican Mestizos from Mexico City and 33 X chromosomes of Mexican Amerindians from three indigenous communities (Purepechas, Nahuas, and Tzeltales), along with alleles and haplotypes defined by two microsatellite polymorphic markers (DXS548 and FRAXAC1) and two single nucleotide polymorphisms (FMRA and FMRB). Genetic frequencies of Mestizo and Amerindian subpopulations were statistically similar in almost all cases and thus were considered one population for comparisons with other populations. Sixteen (CGG)n alleles in the 17-38 size range were observed, and the most common were the 25 (38.0%), 26 (28.3%), and 24 (12.3%) repeat alleles. This pattern differs from most other populations reported, but a closer relation to Amerindian, European, and African populations was found, as expected from the historical admixture that gave rise to Mexican Mestizos. The results of the CA repeats analysis at DXS548-FRAXAC1 were restricted to nine haplotypes, of which haplotypes 7-4 (52.2%), 8-4 (23.8%), and 7-3 (11.5%) were predominant. The modal haplotype 7-4, instead of the nearly universal haplotype 7-3, had been reported exclusively in Eastern Asian populations. Likewise, only seven different FRAXAC1-FMRA-FMRB haplotypes were observed, including five novel haplotypes (3TA, 4TA, 3 - A, 4 - A, and 5 - A), compared with Caucasians. Of these, haplotypes - A (78.7%) and 3 - A (13.2%) were the most common in the Mexican population. These data suggest a singular but relatively low genetic diversity at FMR1 in the studied Mexican populations that may be related to the recent origin of Mestizos and the low admixture rate of Amerindians.     

Frequency Distribution of Esterase-5 Alleles in Two Populations of DROSOPHILA PSEUDOOBSCURA

Statistical tests comparing allele frequencies in natural populations with those predicted by various theories of genic variation depend critically on the accurate enumeration of alleles. This study used a series of five sequential electrophoretic conditions to characterize the allele frequency distributions of esterase-5 in two large population samples of Drosophila pseudoobscura from California. In Standard chromosome lines 12 electromorphs were discriminated using a single electrophoretic condition. When four additional criteria were used, the number of electromorphs increased to 41, 33 in one population and 22 in the other. Both populations had the same two alleles in high frequency, with other alleles present in frequencies of 6% or less. Although each population had a number of unique alleles, a χ² contingency test demonstrated no significant genetic divergence between them. A statistical comparison of allele frequencies in both populations with that predicted by neutral models suggests that the individual and combined distributions deviate from neutrality in the direction of purifying selection.—Sex-Ratio chromosomes differed markedly from Standard chromosomes in both allelic content and diversity. In 32 Sex-Ratio chromosomes from one population only three alleles were found, all of which were detected under the initial "standard" electrophoretic conditions. Moreover, none of these alleles was found in the Standard chromosome lines.     

Allele and genotype frequencies of metabolic genes in Native Americans from Argentina and Paraguay

Interethnic differences in the allele frequencies of CYP2D6, NAT2, GSTM1 and GSTT1 deletions have been documented for Caucasians, Asians, and Africans population. On the other hand, data on Amerindians are scanty and limited to a few populations from southern areas of South America. In this report we analyze the frequencies of 11 allele variants of CYP2D6 and 4 allele variants of NAT2 genes, and the frequency of GSTM1 and GSTT1 homozygous deleted genotypes in a sample of 90 donors representing 8 Native American populations from Argentina and Paraguay, identified as Amerindians on the basis of their geographic location, genealogical data, mitochondrial- and Y-chromosome DNA markers. For CYP2D6, 88.6% of the total allele frequency corresponded to *1, *2, *4 and *10 variants. Average frequencies for NAT2 *4, *5, *6 and *7 alleles were 51.2%, 25%, 6.1%, and 20.1%, respectively. GSTM1 deletion ranged from 20% to 66%, while GSTT1 deletion was present in four populations in less than 50%. We assume that CYP2D6 *2, *4, *10, *14; NAT2 *5, *7 alleles and GSTM1 and GSTT1 *0/*0 genotypes are founder variants brought to America by the first Asian settlers.     

Polymorphisms of the haptoglobin peptide chains in Pyrenean populations.

This study has analyzed the haptoglobin genotype frequencies in over 900 samples from populations living on the Northern slopes of the Pyrenees. The results emphasize the importance of systematically determining the frequencies of the Hp1S, Hp1F, Hp2SS, Hp2FF, Hp2FS alleles. Hp1S was the predominant allele, the HpIS/Hp1 distribution varying between .5 and .69 as in most European populations. Hp2 alleles were observed in low frequency with differences in geographically distinct samples. Pyrenean populations in the western zones (Basques and Baronnies) were found to contain the Hp2FF allele while those in eastern regions, the Hp2SS allele. We have speculated that Hp2SS is as old as the Hp2FF, arising from southern Mediterranean areas, and suggest that Pyrenean groups have different origins.     

Primers for 12 polymorphic microsatellite DNA loci from the guppy (Poecilia reticulata)

Twelve polymorphic microsatellite DNA loci were isolated from genomic guppy DNA. We assessed the level of genetic diversity for these loci using individuals from five native Trinidadian populations. All the loci were polymorphic although there were considerable differences among loci and populations in allele frequencies. Within populations, the number of alleles ranged from 1 to 22 and observed heterozygosities ranged from 0.000 to 0.990. Allele frequencies differed substantially between populations suggesting divergence.     

HLA in Jaidukama: an Amerindian secluded Colombian population with new haplotypes and Asian and Pacific-shared alleles

America first inhabitants and peopling are still debated. In order to increase knowledge about these questions, we have aimed to detect HLA genes of an Amerindian secluded community: Jaidukama, who lives in North Colombia Equatorial forest. HLA genotyping and extended haplotype calculations were carried out in 39 healthy individuals belonging to 13 families. HLA frequencies were compared to other Amerindians and worldwide populations by calculating genetic distances, relatedness dendrograms and correspondence analyses. Only four DRB1 alleles were found (*0404, *0407, *1402 and *1602); however a total of 17 Amerindian different extended class I–class II HLA haplotypes were directly counted from the family studies, nine of them were specific of Jaidukamas. Some of the alleles or group of alleles within an extended haplotype (i.e. DQB1–DRB1) were also found in Asians and Pacific Islanders, further supporting existence of Asian and Pacific gene flow with Amerindians or a common founder effect. It is further supported that HLA extended haplotypes vary faster than alleles in populations. It is concluded that this unique model of Amerindian secluded families study suggests that rapid HLA haplotype variation may be more important than allele variation for survival (starting immune responses). This work may also be useful for future transplant programs in the area.     

Acid phosphatase, adenosine deaminase and esterase D polymorphisms in the Spanish Basque population.

The 3 red-cell polymorphic systems acid phosphatase (ACP), adenosine deaminase (ADA) and esterase D (ESD) have been studied in a random sample of 1,112 individuals from the Basque country: The allelic frequencies obtained were ACP*A = 0.275, ACP*B = 0.718 and ACP*C = 0.007; ADA*2 = 0.021, and, ESD*2 = 0.066. The allelic frequencies have been compared with those of other Basque and other European populations. In comparison with Basques, significant differences were detected only for ACP, whereas as regards other Europeans significant differences were obtained with practically all the populations compared for the 3 genetic systems studied. The low values of the less frequent alleles, especially that for the ACP*C allele which is the lowest reported in Europe, are noteworthy.     

Transferrin subtypes in 11 south China minority populations.

Transferrin subtypes were determined by isoelectric focussing (IEF) in a total of 2,121 individuals from 11 South China minority populations. The C1, C2 and DCHI alleles were present in all the populations; B alleles were lacking, C4 was found in 3 populations and C3 in 6. C2 and C4 allele frequencies are notable in these minority groups. The frequency of the C2 allele was higher (0.25-0.38) than that of Han Chinese (0.18-0.25). In Bai the C2 frequency was as high as 0.38. The C4 allele was present at a low frequency (less than 0.01), which suggests that this allele probably existed in the ancestral Mongoloid population at a low frequency and increased in frequency in Amerindians due to genetic drift or other factors.     

Distribution of group-specific component/vitamin-D-binding protein subtypes in Saudi Arabia

The distribution of group-specific component (Gc) phenotypes and the Gc allele frequencies were investigated in 1,082 individuals from five different provinces of Saudi Arabia by the combined use of isoelectric focusing and immunofixation. Between provinces variations in the Gc allele frequencies were found. Gc1S decreased and Gc1F increased from the northwest to the southeast in Saudi Arabia. The overall frequencies in Saudi Arabia were 0.236 for Gc1F, 0.610 for Gc1S, 0.150 for Gc2 and 0.004 for rare alleles. The observed frequencies did not differ significantly from those found in other population samples from the Middle East. In nine samples rare Gc variants were found.     

Protein polymorphism in quail populations selected for large body size

The polymorphism of five enzyme loci (amylase, alkaline phosphatase, albumin, for 4-week body weight was compared to that of the unselected control line (C). Three loci in the C line and two in the P line demonstrated polymorphism. Plasma amylase was separated into six bands and zymograms were classified on the basis of these bands into nine phenotypes. Three of the nine types were of relatively high activity and six were of relatively low activity. All nine types were found in the C line, whereas, all birds of the P line had only the most active type. Two alkaline phosphatase alleles (Akp-2B and Akp-2C) were segregating in the C line. Gene frequencies of alkaline phosphatase for the Akp-2B allele were 0.92 in the C line and 1.00 in the P line. Two albumin alleles (AlbQ1 and AlbQ2) were segregating in both populations. Gene frequencies for the AlbQ1 allele were 0.74 in the C line and 0.81 in the P line. Two red cell esterase-D alleles (Es-DF and Es-DS) were segregating in both populations. The gene frequency for the Es-DS allele (0.61) was higher than that of the Es-DF allele in the C line. In the P line the frequency of the Es-DF allele was higher than that of the Es-DS allele. Heterozygosities of the C and P lines were estimated as 0.2258 and 0.1560 respectively. The relative inbreeding coefficient of the P line, calculated from heterozygosities was 0.31.     

A genome-wide survey does not show the genetic distinctiveness of Basques

Basques are a cultural isolate, and, according to mainly allele frequencies of classical polymorphisms, also a genetic isolate. We investigated the differentiation of Spanish Basques from the rest of Iberian populations by means of a dense, genome-wide SNP array. We found that F _ST distances between Spanish Basques and other populations were similar to those between pairs of non-Basque populations. The same result is found in a PCA of individuals, showing a general distinction between Iberians and other South Europeans independently of being Basques. Pathogen-mediated natural selection may be responsible for the high differentiation previously reported for Basques at very specific genes such as ABO, RH, and HLA. Thus, Basques cannot be considered a genetic outlier under a general genome scope and interpretations on their origin may have to be revised.     

Genetic polymorphisms in autochthonous Basques from northern Navarre

This survey reports primary results of classical allele frequencies on ten protein loci in a Basque population sample from northern Navarre, the less known from an anthropological and genetic point of view than the populations of the other Basque territories of Spain. Since ancient times this has been a zone of Basque population settlement, and the Basque language (Euskera) still remains deeply rooted among its autochthonous population. A total of 122 blood samples from unrelated northern Navarrese with autochthonous ascendants to the third generation were typed for GC, HP, PI, TF, ACP1, AK1, CA2, ESD, PGD and PGM1 genetic systems. Basque surnames and birthplaces were the criteria used to define family origins. Genetic structure was analyzed on different population hierarchical levels. Northern Navarre seems to be the most genetically deviated area in comparison with other Basque groups. The highest level of differentiation is observed between Navarrese and Alava Basques whereas Guipúzcoa province, the territory adjacent to northern Navarre, presents the lowest genetic distance from the study area. Northern Navarrese show some distinguishing genetic characteristics in relation to other Basque relative samples, which include high frequencies for PI*M1 and TF*C1 and low levels of PGD*C and PGM1*2 alleles. When the genetic data reported here are analyzed jointly with GM allotypes frequencies, the results significantly reinforce the relative position of Navarrese Basques as well as the topology of the Basque cluster on genetic maps. The analysis of relationships among the genetic structures of Basque population samples leads us to ask ourselves which of them fits in best with the ancient Basque population. Classical geographers placed the tribe of the Vascones in the geographical region currently known as Navarre, so extant Navarrese Basques might be considered firm candidates to denote the anthropological and genomic distinctiveness of the ancient Basques.     

中国人诱导型一氧化氮合酶基因STR多态性研究

一氧化氮（nitric oxide,NO）作为一种可在细胞间自由扩散的信使分子在神经递质传递和血管舒张调节等生理与病理过程中起着重要作用。NO通过一氧化氮合酶（nitric oxide synthase,NOS）催化L-精氨酸的氧化反应而生成。目前在哺乳动物中已发现细胞来源、表达方式和活性调节不同的3种NOS同工酶,分别为神经原型NOS(meuronal NOS,nNOS）、诱导型NOS(inducible NOS,iNOS）和内皮细胞型NOS（endothelial NOS,eNOS）。3种NOS由位于不同染色体上的基因所编码。人iNOS基因位于第17号染色体长臂(17q11.2～17q12）,全长约37kb,含有26个外显子,iNOS可在多种类型的细胞中通过IL-1、IFN-a、INF-γ等细胞因子和其他介质的刺激作用而诱导表达。iNOS基因5‘-端调控区内存在一个CCTTT串联重复的多态性位点,这一多态性基因座已居北爱尔兰的糖尿病患者中证实与微血管病变有关。另有实验表明,CCTTT串联重复序列的变化对iNOS基因的转录将产生不同影响。目前在东方种族中有关iNOS基因CCTTT串联重复多态性尚未见报道。将303名中国汉族人基因组DNA用于iNOS基因CCTTT串联重复多态性分析,鉴定出了12种等位基因和49种基因型,其中重复17次、18次和19次的等位基因是在人类中首次发现的新等位基因。统计学检验和比较表明,中国汉族人iNOS基因CCTTT串联重复序列的6个等位基因频率与来自英格兰的高加索人差异显著,说明这一多态性位点的等位基因频率分布存在种族差异。在中国正常人群中获得的有关iNOS基因STR多态性的统计资料,对于进一步研究这一多态性基因座与心脑血管疾病的相关性将有重要应用价值。     

Amerindians show association to obesity with adiponectin gene SNP45 and SNP276: population genetics of a food intake control and “thrifty” gene

Adiponectin gene polymorphisms SNP45 and SNP276 have been related to metabolic syndrome (MS) and related pathologies, including obesity. However results of associations are contradictory depending on which population is studied. In the present study, these adiponectin SNPs are for the first time studied in Amerindians. Allele frequencies are obtained and comparison with obesity and other MS related parameters are performed. Amerindians were also defined by characteristic HLA genes. Our main results are: (1) SNP276 T is associated to low diastolic blood pressure in Amerindians, (2) SNP45 G allele is correlated with obesity in female but not in male Amerindians, (3) SNP45/SNP276 T/G haplotype in total obese/non-obese subjects tends to show a linkage with non-obese Amerindians, (4) SNP45/SNP276 T/T haplotype is linked to obese Amerindian males. Also, a world population study is carried out finding that SNP45 T and SNP276 T alleles are the most frequent in African Blacks and are found significantly in lower frequencies in Europeans and Asians. This together with the fact that there is a linkage of this haplotype to obese Amerindian males suggest that evolutionary forces related to famine (or population density in relation with available food) may have shaped world population adiponectin polymorphism frequencies.     

Alu insertions in the Iberian Peninsula and north west Africa--genetic boundaries or melting pot?

The Western Mediterranean Basin joins a set of ethnically different populations as Iberians and Basques in the North shore and Berbers and Arab-speakers in the South one. In spite of this differentiation, they have maintained historical contacts since ancient times. The existence of a possible common genetic background (specially for Berbers and Iberians) together with the genetic impact of the Islamic occupation of the Iberian Peninsula during 7 centuries are some of the intriguing anthropological questions that have been studied in this area using several classical and DNA markers. The aim of this work is to present the results on a survey of polymorphic Alu elements in 10 human populations of the Western Mediterranean. Recent Alu subfamilies include a significant number of polymorphic Alu insertions in humans. The polymorphic Alu elements are neutral genetic markers of identical descent with known ancestral states. This fact turns Alu insertions into useful markers for the study of human population genetics. A total number of 14 Alu insertions were analyzed in 5 Iberian populations, 3 Berber groups from North-Western Africa, an Arab-speaker population from Morocco and a sub-Saharan ethnic group from Ivory Coast. The results of this study allow the genetic characterization of Berber populations, which show a certain degree of differentiation from Arab-speaking groups of the same geographic area. Furthermore, a closer genetic distance between South Spain and Moroccan Berbers as compared with other Spanish samples supports a major genetic influx consistent with some (but not all) previous genetic studies on populations from the two shores of the Gibraltar Straits.     

Study of the association between constitutional exogenous obesity and polymorphism of the apolipoprotein B gene

An attempt was made to associate the insertion-deletion (Ins/Del) polymorphism of the apolipoprotein B gene (apoB) with obesity and to identify alleles and genotypes predisposing to this disorder. The apoB Ins/Del allele frequencies observed in the Russian population were similar to those in West European populations and significantly differed from frequencies reported for Asian populations. Patients with obesity did not differ from healthy individuals in allele and genotype frequencies regardless of whether total or sex-stratified samples were compared. Estimation of relative risk for individuals with genotype Ins/Ins did not reveal a significant association between obesity and this genotype. Thus, constitutional exogenous obesity did not prove to be associated with the Ins/Del polymorphism of the apoB gene in the Russian population.