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.     

Genetic variants of human B component (BF system) and alpha-1-antitrypsin (PI system) in a population from Sardinia

BF- and PI-type determinations have been performed in a population from Sardinia. The corresponding allele frequencies are as follows: BF*S = 0.5783, BF*F = 0.2189, BF*SO7 = 0.0046, BF*F1 = 0.1982 and PI*M1 = 0.5872, PI*M2 = 0.2041, PI*M3 = 0.0459, PI*M4 = 0.0940, PI*S = 0.0619, PI*Z = 0.0046, PI*N = 0.0023. Whereas the BF system shows the originality of the Sardinian population with a very high BF*F1 allele frequency, the PI system does not reveal any characteristic features.     

Major histocompatibility complex (MHC) class III genetics in two Amerindian tribes from Southern Brazil: the Kaingang and the Guarani

Population genetic studies of the major histocompatibility complex (MHC) class III region, comprising C2, BF and C4 phenotypes, and molecular genetic data are rarely available for populations other than Caucasoids. We have investigated three Amerindian populations from Southern Brazil: 131 Kaingang from Ivaí (KIV), 111 Kaingang (KRC) and 100 Guarani (GRC) from Rio das Cobras. Extended MHC haplotypes were derived after standard C2, BF, C4 phenotyping and restriction fragment length polymorphism (RFLP) analysis with TaqI, together with HLA data published previously by segregation analysis. C2 and BF frequencies corresponded to other Amerindian populations. C4B*Q0 frequency was high in the GRC (0.429) but low in the Kaingang. Unusual C4 alleles were found, viz. C4A*58, A*55 and C4B*22 (presumably non-Amerindian) and aberrant C4A*3 of Amerindian origin occurring with a frequency of 0.223 in the GRC. C4A*3 bands of homo- and heterozygous individuals carrying this variant were Rodgers 1 positive and Chido 1,3 positive, showed a C4A specific lysis type and a C4A like α-chain. Polymerase chain reaction studies and sequencing showed that this is based on a C4A*3 duplication with a regular C4A*3 and a partially converted C4A*0304 carrying the C4B specific epitopes Ch 6 and Ch 1,3. Associations of class III haplotypes with particular RFLP patterns were similar to those reported for Caucasoids. The previously described association between combined C4A and CYP21P deletions and the 6.4 kb TaqI fragment was not seen in these Amerindians. This fragment occurred within a regular two locus gene structure in the Kaingang, representing a “short” gene at C4 locus I. C4 and CYP21 duplications were frequently observed. The distribution of extended MHC haplotypes provides evidence for a close relationship between the KIV and KRC and a larger genetic distance between the two Kaingang groups and the GRC. Received: 6 March 1997 / Accepted: 13 May 1997     

Genetic variants of factor B in a population of Jordan

BF phenotyping was performed in a population of Jordan. The observed allele frequencies were as follows: BF*S = 0.5457, BF*F = 0.3744, BF*SO7 = 0.0763, BF*F1 = 0.0075. These values are in agreement with the geographic position and the ethnic composition of Jordan.     

A new BF variant (F025)

A rare variant of Factor B exhibiting a mobility intermediate between BF F and BF S was described. After comparison with the mobilities of BF F and F075, this variant was designated BF F025. The allele was transmitted together with C2*C, C4A*3, and C4B*1.     

Serum protein polymorphisms in Arab Moslems and Druze of Israel: BF, F13B, AHSG, GC, PLG, PI, and TF.

We report results of typing two population samples, Israeli Arab Moslems and Arab Druze, for seven serum protein genetic variants. Data are presented in comparison with results for the same markers in a sample of Jordanian Arabs. In Israeli Moslems gene frequencies for BF (n = 169) were BF*S = 0.6361, BF*F = 0.3343, BF*S07 = 0.0296, and BF*1 = 0, and for TF (n = 90) the gene frequencies were: TF*C1 = 0.7167, TF*C2 = 0.2611, and TF*C3 = 0.0222. Allele frequencies for AHSG in Israeli Moslems (n = 155) and Druze (n = 192) were AHSG*1 = 0.9129 and 0.8750 and AHSG*2 = 0.0806 and 0.1250, respectively. Gene frequencies for PLG in Moslems (n = 149) and Druze (n = 190) were PLG*A = 0.4597 and 0.5288 and PLG*B = 0.5101 and 0.4188, respectively. The typing of Israeli Arab Druze (n = 194) for F13B resulted in F13B*1 = 0.8454, F13B*2 = 0.0387, F13B*3 = 0.0979, and F13B*4 = 0.0180. Results on the same population for PI (n = 192) were PI*M1 = 0.7839, PI*M2 = 0.1276, PI*M3 = 0.0781, PI*M4 = 0.0026, and PI*M5 = 0.0026. Observed rare alleles in various systems indicate gene flow from Europe, Africa, and Asia into the Middle East. The results on Arab populations were considered in relation to available population data in the three adjacent continents. The emerging gene frequency profile for Arabs seems to fit with the central geographic and climatic position of the Middle East.     

A new BF F variant by polyacrylamide gel isoelectric focusing

Summary Polyacrylamide gel isoelectric focusing followed by electroblotting with enzyme immunoassay was done for the investigation of allotypes of properdin factor B (BF) in serum from 326 Japanese subjects. A new BF F variant tentatively designated BF*Fb1 (b=basic) was detected, the isoelectric point of each band of homozygous BF Fb1 being higher than of BF FF. Family data were in accordance with transmission by mendelian inheritance. The allele frequencies calculated from 326 Japanese subjects were 0.7945, 0.1825, 0.0215, and 0.0015 for BF*S, BF*F, BF*Fb1, and BF*F075, respectively, with that of variant BF*Fb1 being a polymorphic frequency. The distribution of phenotypes fitted the Hardy-Weinberg equilibrium.     

Polymorphisms of serum proteins in Japanese patients with vascular diseases. I. Factor XIIIB, plasminogen and complement types in primary varicose veins.

The polymorphisms of the B subunit of coagulation factor XIII (F13B), plasminogen (PLG), complement C6, C7, factor B (BF) and factor I (IF) were studied among 21 unrelated Japanese patients with primary varicose veins (PVV) by isoelectric focusing followed by immunoblotting. The allele frequencies for F13B*2 and IF*A in PVV patients were significantly higher (F13B*2, p = 0.0047; IF*A, p = 0.0006) than those in healthy controls (n = 60). Significant associations of F13B 2 allotype [p = 0.0220, relative risk (RR) = 13.9] and IF A allotype (p = 0.0006, RR = 10.0) with PVV were observed; however, no significant association of PLG, C6, C7 or BF allotype with the disease was found.     

Factor B (BF) allotypes and multiple sclerosis in north-east England.

A significant decrease in the frequency of BF*F allele and an increase of BF*F1 allele was found in 101 clinically definite multiple sclerosis patients compared to 270 normal controls from North-East England. In Dw2 types 41 patients and 60 controls, only the rare allele BF*F1 showed a significant increase in the patients group. For the common BF*S allele a significant increase was found in Dw2+ patients compared to the Dw2- patients, but a slight similar increase observed in Dw2+ controls did not attain significance. This increase in the patient group is attributed to a strong linkage disequilibrium between BF*S and Dw2 alleles. No such linkage disequilibrium exists in the normal controls. There is a suggestion that the BF*S and Dw2+ alleles are more prevalent in chronic progressive patients, implying that in Dw2+ patients BF may influence the progression of the disease.     

Study of five haemogenetic markers (Gc, C3, Bf, Ag, and GALT) in six Indonesian populations and in 12 subgroups of Balinese

In various ethnic groups of the Indonesian archipelago and of Bali, the polymorphisms of the serum proteins Gc globulin (vitamin D-binding protein), C3 (complement component 3), Bf (complement factor B), Ag x,y (lipoprotein allotypes), and of the red cell enzyme system GALT (galactose-1P-uridyltransferase) were analysed. Among the studied proteins, the Gc system was the most informative one for the anthropologist. Besides considerable differences of frequencies of the common alleles Gc*1F, Gc*1S and Gc*2, a number of rare alleles (1A1, 1A3, 1A8, 1A9, 1A12, 1C2, 1C21, 1C24, and 2C8) and some new ones (1C28, 1C29, 1C30, 2C9) were observed. The presence of Gc*1A1 demonstrates the relationship to the Australo-Melanesian populations, but Mongolian variants (1A3, 1A8, 1A9, 1C2) were also encountered. Within the C3 system a very high frequency of the C3*S allele was observed in all populations. The rare alleles C3*F0.55, C3S1, and C3*S0.5 were observed in some groups. A new allele (C3*F0.35) was detected in a Chinese individual and in a nobleman from Bali. The frequency of the Bf*F allele was rather low in general, and the Bf*S0.7 allele was found in three Indonesian individuals only. The Ag*(x) frequencies were rather high, as it is known for Asiatic populations. Variability among subgroups was not very pronounced. The GALT*2 allele (Duarte variant of the enzyme) was observed very rarely; however, it was present in several populations. Enzyme activities could not be determined, and therefore we cannot tell whether the galactosaemia gene (GALT*0) was present or not.     

Protein subtype polymorphisms (Gc and Tf) in a Catalan population from Gerona (northeastern Spain)

The Tf and Gc polymorphic subtype variants have been examined by means of isoelectric focusing in a population sample from two subpyrenean regions in the province of Gerona (Northeast Spain). The estimated allele frequencies were Tf*C1 = 0.774, Tf*C2 = 0.167, TF*C3 = 0.055, TF*B = 0.004; Gc*1F = 0.129, Gc*1S = 0.555 and Gc*2 = 0.316. These values are in general similar to those so far reported in other Spanish populations. The comparisons between our data and those published in Spain, indicate that the present sample is closer to Barcelona than to the other groups compared.     

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.     

C3, BF and C4 polymorphisms in Tunisians

The C3, BF, C4A and C4B polymorphisms were studied in a Tunisian population sample. The allelic frequencies for C3 were S = 0.844 and F = 0.148, and for BF, S = 0.535, F = 0.331, SO7 = 0.075 and F1 = 0.041. The most frequent C4 alleles were A3 and B1 followed in a decreasing order by A2, B2 and the A and B null alleles. The results indicate that the Tunisian population is intermediate between the Caucasian and Arab populations with some trace admixture of African Blacks.     

To the research of the gene pool of the Gagauz population of Moldavia

Population genetic data on Gagauzes from Moldavia are reported here for the first time. AB0 and Rhesus blood groups, serum protein group (HP, TF, GC) and the red cell enzyme polymorphism PGM1 were determined in 190 Gagauzes. In addition to this the ability to taste PTC was tested. The following allele frequencies were found: AB0*0 = 0.5241, AB0*A = 0.3279, AB0*B = 0.1480; RH*D = 0.6083, RH*d = 0.3917; HP*1 = 0.3544, HP*2 = 0.6456; TF*C1 = 0.7472, TF*C2 = 0.1770, TF*C3 = 0.0730, TF*B = 0.0028; GC*1F = 0.1025, GC*1S = 0.5932, GC*2 = 0.3043; PGM*1+ = 0.5932; PGM*1- = 0.1000, PGM*2+ = 0.2607, PGM*2- = 0.1107. The frequency of the PTC*T allele was found to be 0.5298. These frequencies and genetic distance analyses show that the gene pool of the Gagauzes is similar to that of neighbouring southeastern European populations.     

An unusual "morphologic" variant of BF S

In the course of family studies of haplotypes of the alleles of the sixth chromosome loci HLA-A, C, B, D/DR, BF, C2, C4A, C4B, and glyoxalase I, we encountered an unusual BF variant. Its mobility was similar to BF F but it appeared to have a lesser intensity after straining with Coomassie Blue, and it was demonstrated by crossed immunoelectrophoresis to be present in lower concentration. It was therefore designated BF FQL. This variant was found on the haplotype HLA-A1, B17, DR7, BF*FQL, C2*C, C4A*6, C4B*1, GLO2. All other haplotypes of this type so far identified carry the BF variant BF S. Following activation of serum samples with zymosan, BF was analyzed by both agarose electrophoresis and isoelectric focusing and immunofixation. On both treatments, serum with BF SFQL produced a Ba pattern identical to that of a sample which was BF S. The Bb pattern for F and S are similar but differ from those of the rare variants BF F1 and BF S1. The Bb pattern of BF FQL was, thus, as expected, the same as BF F or BF S. Hence, we conclude that the variant is a mutant from BF S with mobility similar to BF F. The mutation seemed also to have resulted in a lower concentration of product than normal.     

Complement phenotypes in patients with psoriasis

Phenotype frequencies for the complement proteins C4A, C4B, Bf (factor B) and C3 were performed for 49 Caucasian patients with psoriasis. The C4*A6 allele was present in 26.6% of the patients as compared to 5.4% of healthy regional Caucasian controls, p less than 0.001, relative risk = 6.28. The C4*A6 allele is known to be in linkage disequilibrium with the HLA B17 allele and to produce a non-functional gene product when it occurs with the B17 allele. HLA B17 is known to be associated with psoriasis in many Caucasian populations. Additional findings in the present study were a significant reduction in the C4B*2 allele frequency, a non-significant increase in the Bf*F allele frequency and no difference for Bf or C3 phenotype frequencies in the patients with psoriasis as compared to the controls.     

Multiplex pyrosequencing method to determine CYP2C9*3, VKORC1*2, and CYP4F2*3 polymorphisms simultaneously: its application to a Korean population and comparisons with other ethnic groups

Warfarin is an anticoagulant that is difficult to administer because of the wide variation in dose requirements to achieve a therapeutic effect. CYP2C9, VKROC1, and CYP4F2 play important roles in warfarin metabolism, and their genetic polymorphisms are related to the variability in dose determination. In this study we describe a new multiplex pyrosequencing method to identify CYP2C9*3 (rs1057910), VKORC1*2 (rs9923231), and CYP4F2*3 (rs2108661) simultaneously. A multiplex pyrosequencing method to simultaneously detect CYP2C9*3, VKORC1*2, and CYP4F2*3 alleles was designed. We assessed the allele frequencies of the polymorphisms in 250 Korean subjects using the multiplex pyrosequencing method. The results showed 100 % concordance between single and multiplex pyrosequencing methods, and the polymorphisms identified by pyrosequencing were also validated with the direct sequencing method. The allele frequencies of these polymorphisms in this population were as follows: 0.040 for CYP2C9*3, 0.918 for VKORC1*2, and 0.416 for CYP4F2*3. Although the allele frequencies of the CYP2C9*3 and VKROC1*2 were comparable to those in Japanese and Chinese populations, their frequencies in this Korean population differed from those in other ethnic groups; the CYP4F2*3 frequency was the highest among other ethnic populations including Chinese and Japanese populations. The pyrosequencing methods developed were rapid and reliable for detecting CYP2C9*3, VKORC1*2, and CYP4F2*3. Large ethnic differences in the frequency of these genetic polymorphisms were noted among ethnic groups. CYP4F2*3 exhibited its highest allele frequency among other ethnic populations compared to that in a Korean population.     

Complement C3 polymorphism in sixteen populations of Colombia. Results of “Expedicion humana”

Blood samples of 1.022 individuals of both sexes, collected during the “Expedicion Humana” programme. Twelve Indian group, two Negroes, two urban and one mestizo populations of Colombia were C3 typed. The results showed the urban samples have C3*F genotype frequencies (17 and 20%) similar to the Spanish population. The Negroe system, with lower C3*F gene frequencies (3.5 and 7%) also resembled their parental populations in Africa. The Mestizo population reported in this study showed a lower value of the C3*F gene (2.2%) than previously studied. suggesting that the degree of admixture may vary in different regions of the country. As regards the Indian populations, there was a wide range of variation of the C3*F gene (0–19%) many tribes being monomorphic. This gene may be a marker of recent admixture in Amerindians, but there may be other genetic factors, such as selection and inbreeding in maintaining high levels of genetic polymorphism in tribes such as Guahibo.     

Haptoglobin gene subtypes in three Brazilian population groups of different ethnicities

Haptoglobin is a plasma hemoglobin-binding protein that limits iron loss during normal erythrocyte turnover and hemolysis, thereby preventing oxidative damage mediated by iron excess in the circulation. Haptoglobin polymorphism in humans, characterized by the Hp(*1) and Hp (*2) alleles, results in distinct phenotypes known as Hp1-1, Hp2-1 and Hp2-2, whose frequencies vary according to the ethnic origin of the population. The Hp(*1) allele has two subtypes, Hp (*1F) and Hp (*1S) , that also vary in their frequencies among populations worldwide. In this work, we examined the distribution frequencies of haptoglobin subtypes in three Brazilian population groups of different ethnicities. The haptoglobin genotypes of Kayabi Amerindians (n = 56), Kalunga Afro-descendants (n = 70) and an urban population (n = 132) were determined by allele-specific PCR. The Hp(*1F) allele frequency was highest in Kalunga (29.3%) and lowest in Kayabi (2.6%). The Hp(*1F)/Hp(*1S) allele frequency ratios were 0.6, 1.0 and 0.26 for the Kayabi, Kalunga and urban populations, respectively. This variation was attributable largely to the Hp(*1F) allele. However, despite the large variation in Hp(*1F) frequencies, results of F (ST) (0.0291) indicated slight genetic differentiation among subpopulations of the general Brazilian population studied here. This is the first Brazilian report of variations in the Hp(*1F) and Hp(*1S) frequencies among non-Amerindian Brazilians.     

Genetic polymorphisms of alpha-2-HS-glycoprotein, group-specific component and orosomucoid in the Han population, Chengdu, China.

The Han population in Chengdu, China, was investigated for genetic polymorphisms of alpha-2-HS-glycoprotein (A2HS), group-specific component (GC) and orosomucoid (ORM) using isoelectric focusing followed by immunofixation. The allele frequencies were: A2HS*1 = 0.6958,A2HS*2 = 0.3042, GC*1F = 0.4021, GC*1S = 0.3182, GC*2 = 0.2745, GC*1A = 0.0052, ORM1*F1 = 0.7028, ORM1*S = 0.2762, ORM1*F2 = 0.0210, ORM2*A = 0.9965, ORM2*Var = 0.0035.