BstEII restriction fragment alleles and haplotypes of the human IGHG genes with reference to the BamHI/SacI RFLPs and to the Gm polymorphism

In previous studies, we have described, for each of the five human immunoglobulin IGHG (C gamma) genes, BamHI, SacI and BamHI/SacI allelic restriction fragments. Further, we have determined BS (BamHI/SacI) linkage groups of alleles for the whole of the IGHG loci and we have demonstrated correlation with the Gm alleles and haplotypes. In this paper we characterize more precisely the polymorphism of the IGHG genes and, consequently, the structure and evolution of this multigene family, using the restriction enzyme BstEII and two different probes, a IGHG (C gamma) probe and a G3 (C gamma 3) specific probe. Alleles and haplotypes of the BstEII restriction fragments have been defined with reference to the BS alleles and haplotypes. New RFLPs of the IGHG genes are described and unambiguous correlations have been established with most of the Gm alleles and haplotypes. Thus, the IGHG gene RFLPs strengthen the Gm polymorphisms as powerful tools for the characterization of populations, disease and genetic marker linkage analyses, forensic medicine and evolution of these IGHG genes.     

Distribution of GM allotypes and deleted IGHG1 haplotypes in the Sel'kups in comparison to the Forest Nentsi of northwestern Siberia.

Northern Sel'kup people residing in the upper Taz and the tributaries of Turukhan Rivers were typed for immunoglobulin heavy chain (GM) allotypes. The Sel'kups exhibited a unique GM*-G haplotype circulating within the tribe in low but almost polymorphic frequency along with common GM*F B and GM*A T haplotypes, the former a Caucasian marker and the latter a northern Oriental population's marker. Contemporary Sel'kups show a higher frequency of GM*A T than the westwardly situated Forest Nentsi, reflecting recent historical events in the region such as admixture with the Evenki of Middle Siberia. Within the area located between lower Ob and Yenisey rivers, the unique GM*-N B haplotype, restricted to the Forest Nentsi, and the unique GM*-N' G haplotype, restricted to the Sel'kups, serve as GM markers discriminating between these two adjacent tribes.     

CD154 polymorphism in Spanish populations. Differences in the allelic distribution between Canary islanders and Peninsulars.

The CD154 gene contains a dinucleotide repeat (CA)n in the 3' untranslated region. Allelic distribution in Spanish populations from two areas with different genetic background, the Canary Islands and Peninsula, are described. Seven alleles with different allelic distribution between the two groups, were found. This represents a highly polymorphic marker, useful for genetic studies on a critical molecule in immunity.     

Genetic relationship between the Canary Islanders and their African and Spanish ancestors inferred from mitochondrial DNA sequences

Nucleotide sequences of the hypervariable segment I of the control region of the mtDNA were determined in 101 individuals: 54 Canary Islanders, 18 North African Berbers, 18 Spanish mainlanders and 11 sub-Saharan Guineans. In spite of the fact that only members of the Fang tribe were analysed, nucleotide diversity in Guineans (θ× 100 = 2·33)is one of the highest found in African populations.
Estimates of genetic contribution to the Canarians from their putative parental populations based on mtDNA (43·25 ± 1·38% Berbers, 35·54 ± 0·55% Spanish, 21·21 ± 1·92% Guineans) showed an important North African substrate. These mtDNA results, when compared with data based on nuclear markers, point to a strong male-female asymmetry, 75% of the Spanish nuclear contribution was due to males and practically all the Berber and Guinean was due to females. These results are in agreement with the way that the Canary Islands were conquered.
Pairwise difference distributions in Guineans and Berbers are compatible with the model of populations in expansion. Departures from a Poisson distribution for the Canarians and Spanish can be explained by admixture and the way of sampling respectively.     

Analysis of the diversity of African streak mastreviruses using PCR-generated RFLPs and partial sequence data

Maize streak virus (MSV) is the most economically significant member of a diverse group of African grass-infecting Mastrevirus species in the family Geminiviridae. We designed a single set of degenerate primers which enables the PCR amplification of an approximately 1300 bp DNA fragment spanning both conserved (the RepA gene) and variable (the long intergenic region and MP gene) portions of these viruses' genomes. Using restriction fragment length polymorphism (RFLP) analysis of PCR products obtained from 39 MSV, one SSV, and two PanSV isolates, it was possible to both identify the different virus species, which differ in nucleotide sequence by up to 40%, and to differentiate between MSV isolates sharing up to 99% sequence identity. The reliability of the RFLP data for typing the MSV isolates was verified by the phylogenetic analysis of the partial genomic nucleotide sequences of a representative subset of the MSV isolates. Based on both the RFLP and sequence data, the MSV isolates could be clearly differentiated into the four groups: these were a group of predominantly maize-infecting isolates, and three groups containing grass/wheat-infecting isolates. RFLP analysis also revealed a number of mixed virus infections in which, in certain instances, it was possible to identify individual population members.     

Application of immunoglobulin heavy chain (GM, AM) and light chain (KM) allotypes to cases of disputed paternity

To evaluate the usefulness of extended immunoglobulin allotyping compared to the conventional number of reagents in general use, 1,896 cases of disputed paternity tested for HLA, immunoglobulin allotypes (IGH, [GM, AM] and KM) and red blood cell markers (RBC) (ABO, RH, MNS, Kidd, Duffy, Kell, Colton, Lutheran, and Lewis) were analyzed. There were 1,289 cases in which both the mother and alleged father were Black, 548 cases in which the mother and alleged father were White and 59 cases that were either mixed or of different ethnic groups. A total of 691 exclusions were observed (533 Black, 143 White and 15 other). The observed exclusion rates for the HLA system in Blacks (93.9%) and in Whites (94.9%) were similar to previous estimates of the HLA exclusion rates, indicating that these cases appear to be consistent with other studies. The observed exclusion rates for the IGH haplotypes (alleles) were the highest single system exclusion rates beside the HLA system (54.08% in Blacks and 31.47% in Whites). Further, the values were higher than any single blood group system, or electrophoretic system in common usage. The combined IGH and KM observed exclusion rates were 57.50% for Black cases and 37.06% for White cases. The value of the combined immunoglobulin allotypes in Blacks almost exceeds the combined exclusion rate for all RBC antigens tested. The importance of doing extended immunoglobulin allotyping in Black cases is demonstrated by the fact that 76.5% of the exclusions would have been missed if only G1M A, F and X and G3M B0 and G had been used in the Black cases. The inclusion of additional markers in the White cases increased the observed IGH exclusion rate from 23.78 to 31.47%. The increase was primarily due to the addition of G2M N.     

DNA sequence variability of IGHG3 alleles associated to the main G3m haplotypes in human populations.

The present study investigates the molecular basis of the G3m polymorphism expressed by the heavy constant domains of human immunoglobulins gamma 3 chains. By using a new protocol allowing the specific cloning of IGHG3 genes, a total of 51 full-length IGHG3 genomic sequences (about 2 kb) isolated from African, Siberian, West Asian and European population samples were sequenced. IGHG3 sequences were assigned precise G3m haplotypes on the basis of specific associations between G3m allotypes and IGHG3 RFLPs. Specific DNA substitutions involved in the expression of G3m(5), G3m(6), G3m(15), G3m(16), G3m(21), G3m(24) and G3m(28) allotypes were then deduced, elucidating almost completely the determination of the G3m polymorphism at the DNA level. The molecular evolution of G3m haplotypes was investigated by a maximum likelihood phylogeny of IGHG3 sequences. Sequence clusters are shown to be G3m haplotype-specific, corroborating the Gm molecular model deduced from serology, and showing that populations differentiation is much more recent than G3m haplotypes differentiation. The widely distributed G3m(5,10,11,13,14) haplotype is likely to be ancestral to the other G3m haplotypes presently found at high frequencies in different continental areas.     

UDP-glucuronosyltransferase genetic variation in North African populations: a comparison with African and European data

Background: Genetic variation in glucuronosyltransferases (UGT) is crucial in drug metabolism and risk of some diseases.

Aim: To examine genetic variation in UGT in North African populations.

Subjects and methods: Allele frequencies of SNPs UGT1A4^24Thr, UGT1A4^48Val, UGT2B15^85Tyr, UGT2B15^523Thr and UGT2B17 CNV deletion from Morocco, Algeria, Tunisia and Libya were compared to European and Sub-Saharan populations.

Results: North Africans are the group with the highest genetic heterogeneity given by internal differences in the occurrence of UGT2B17 deletion, UGT1A4^48Val and UGT1A4 haplotypes. UGT2B15 SNPs differentiate Sub-Saharans from the rest of the populations.

Conclusion: North African populations show a high frequency of carriers of UGT2B15^523Thr, a variant linked to an increased risk of prostate cancer. High Atlas Moroccans and Algerians show low frequency of UGT2B17^del, a variant associated with high concentrations of testosterone and oestradiol.     

Differentiation between African populations is evidenced by the diversity of alleles and haplotypes of HLA class I loci

The allelic and haplotypic diversity of the HLA-A, HLA-B, and HLA-C loci was investigated in 852 subjects from five sub-Saharan populations from Kenya (Nandi and Luo), Mali (Dogon), Uganda, and Zambia. Distributions of genotypes at all loci and in all populations fit Hardy-Weinberg equilibrium expectations. There was not a single allele predominant at any of the loci in these populations, with the exception of A*3002 [allele frequency (AF) = 0.233] in Zambians and Cw*1601 (AF = 0.283) in Malians. This distribution was consistent with balancing selection for all class I loci in all populations, which was evidenced by the homozygosity F statistic that was less than that expected under neutrality. Only in the A locus in Zambians and the C locus in Malians, the AF distribution was very close to neutrality expectations. There were six instances in which there were significant deviations of allele distributions from neutrality in the direction of balancing selection. All allelic lineages from each of the class I loci were found in all the African populations. Several alleles of these loci have intermediate frequencies (AF = 0.020-0.150) and seem to appear only in the African populations. Most of these alleles are widely distributed in the African continent and their origin may predate the separation of linguistic groups. In contrast to native American and other populations, the African populations do not seem to show extensive allelic diversification within lineages, with the exception of the groups of alleles A*02, A*30, B*57, and B*58. The alleles of human leukocyte antigen (HLA)-B are in strong linkage disequilibrium (LD) with alleles of the C locus, and the sets of B/C haplotypes are found in several populations. The associations between A alleles with C-blocks are weaker, and only a few A/B/C haplotypes (A*0201-B*4501-Cw*1601; A*2301-B*1503-Cw*0202; A*7401-B* 1503-Cw*0202; A*2902-B*4201-Cw*1701; A*3001-B*4201-Cw*1701; and A*3601-B*5301-Cw*0401) are found in multiple populations with intermediate frequencies [haplotype frequency (HF) = 0.010-0.100]. The strength of the LD associations between alleles of HLA-A and HLA-B loci and those of HLA-B and HLA-C loci was on average of the same or higher magnitude as those observed in other non-African populations for the same pairs of loci. Comparison of the genetic distances measured by the distribution of alleles at the HLA class I loci in the sub-Saharan populations included in this and other studies indicate that the Luo population from western Kenya has the closest distance with virtually all sub-Saharan population so far studied for HLA-A, a finding consistent with the putative origin of modern humans in East Africa. In all African populations, the genetic distances between each other are greater than those observed between European populations. The remarkable current allelic and haplotypic diversity in the HLA system as well as their variable distribution in different sub-Saharan populations is probably the result of evolutionary forces and environments that have acted on each individual population or in their ancestors. In this regard, the genetic diversity of the HLA system in African populations poses practical challenges for the design of T-cell vaccines and for the transplantation medical community to find HLA-matched unrelated donors for patients in need of an allogeneic transplant.     

Molecular genetic studies of natives on Easter Island: evidence of an early European and Amerindian contribution to the Polynesian gene pool

Most archaeological and linguistic evidence suggest a Polynesian origin of the population of Easter Island (Rapanui), and this view has been supported by the identification of Polynesian mitochondrial DNA (mtDNA) polymorphisms in prehistoric skeletal remains. However, some evidence of an early South American contact also exists (the sweet potato, bottle gourd etc.), but genetic studies have so far failed to show an early Amerindian contribution to the gene pool on Easter Island. To address this issue, we analyzed mtDNA and Y chromosome markers and performed high-resolution human leukocyte antigen (HLA) genotyping of DNA harvested from previously collected sera of 48 reputedly nonadmixed native Easter Islanders. All individuals carried mtDNA types and HLA alleles previously found in Polynesia, and most men carried Y chromosome markers of Polynesian origin, providing further evidence of a Polynesian origin of the population of Easter Island. A few individuals carried HLA alleles and/or Y chromosome markers of European origin. More interestingly, some individuals carried the HLA alleles A*0212 and B*3905, which are of typical Amerindian origin. The genealogy of some of the individuals carrying these non-Polynesian HLA alleles and their haplotypic backgrounds suggest an introduction into Easter Island in the early 1800s, or earlier. Thus, there may have been an early European and Amerindian contribution to the Polynesian gene pool of Easter Island.     

Study of GM immunoglobulin allotypic system in Berbers and Arabs from Morocco.

The GM immunoglobulin allotype polymorphism was investigated in four Moroccan populations: three Berber groups from Khenifra (Middle Atlas), Amizmiz (High Atlas), and Bouhria (Beni Snassen) and one Arabic-speaking sample from the Doukkala area (Abda, Chaouia, Doukkali, and Tadla districts in south-central Morocco). In order to characterize the genetic relationships between the populations, our results were compared with those obtained for other North African groups (from Morocco, Algeria, Tunisia, and Niger) and for Middle-East Africans, sub-Saharans, and Southwest Europeans. Based on GM haplotype frequencies, Factorial Correspondence Analyses, F(ST) significance testing, and hierarchical analyses of variance were performed. Our results reveal that Moroccan populations have heterogeneous GM profiles with high frequencies of GM haplotypes in Europeans (from 76% for Doukkala to 88% for Bouhria) and relatively high frequencies of GM haplotypes in sub-Saharans (from 11% for Bouhria to 23% for Amizmiz). The genetic diversity observed among Moroccans is not significantly correlated with either geographic or linguistic differentiation. In spite of their cultural and historical differentiation, we did not discover any significant genetic differences between Berbers and Arabic-speakers from Morocco. However, when large geographical areas are considered, our population samples are integrated in the North African GM variation, significantly distant from sub-Saharan groups but with a close relationship with Southwest European populations.     

Uncommon Gm* haplotypes in the Tunisian population: further contribution to the genetics of the IgG immunoglobulins

In this work, eight family studies were conducted to establish the suspected unusual Gm* haplotypes in 13 persons (among 418) showing uncommon Gm phenotypes. Usually, the Gm (21 and 28)--or Gm (g1 and g5)--allotypes are both present or absent. Exceptions to this rule were observed: on the one hand, only the Gm (28) allotype was present in 12 persons, and on the other hand, only the Gm (21) allotype was found in 1 person. Such events could be explained, in some cases, by equal crossovers or point mutations, and, more generally and very likely, by gene conversions. Other interesting results are also presented, as, on the one hand, silent genes homozygous at the C gamma 4 locus and, on the other hand, a homozygous multigene deletion encompassing the C alpha 1, psi gamma, C gamma 2 and C gamma 4 loci.     

An evaluation of the application of the genetic algorithm to the problem of ordering genetic loci on human chromosomes using radiation hybrid data

Author to whom all correspondence should be addressed We consider the problem of ordering detectable genetic locialong a chromosome by minimizing the number of obligatory breaksthat can be inferred from radiation hybrid data. The problembears some resemblance to the travelling-salesman problem, forwhich genetic algorithms have been used with considerable success.We find that the results from other studies on closely relatedproblems are not directly transferable, and although we didfind a genetic algorithm that performed well in this applicationit would appear that this algorithm is highly sensitive to anychanges in the problem. Moreover, a very simple stochastic algorithmperformed almost as well as our much more complicated and computer-intensivegenetic algorithm and it did so in a fraction of the time. Whilewe do not dispute that genetic algorithms can work on largecomplicated problems, the various modifications and fine-tuningnecessary for good performance tend to be highly problem specificand they are often only arrived at after an exhaustive explorationof possibilities. Thus, we would dispute any claim that geneticalgorithms are robust in their form and range of applicability.     

A study of Gm allotypes and immunoglobulin heavy gamma IGHG genes in Berbers,Arabs and sub-Saharan Africans from Jerba Island,Tunisia

The Gm polymorphism of human IgG immunoglobulins was investigated in three different ethnic groups — Arabs, Berbers and ‘dark-skinned people’— on Jerba Island, Tunisia. The genetic relationships among these groups and several populations from North Africa, sub-Saharan Africa, west Asia and Europe were analysed by principal coordinate analysis, Fst significance testing, and analysis of molecular variance based on haplotype frequencies. The results revealed a non-significant genetic differentiation between Arabs and Berbers from Jerba. However, the Jerbian population of sub-Saharan African origin was close to Ethiopians. Gene flow among the three Jerbian populations, as well as an East African origin of the dark-skinned individuals, is proposed to account for the observed genetic pattern. However, the genetic diversity observed among the different Tunisian populations did not show any significant correlation with either geographic or linguistic differentiation. A preliminary analysis of the restriction fragment length polymorphism of the IGHG genes in Arabs and Berbers from Jerba confirmed the close genetic relationship between the two populations. However, it also indicated a lower level of genetic diversity in the Berbers, which may be explained by more rapid genetic drift due to longer isolation on the island.     

Allergy to dermatophagoides in a group of Spanish gypsies: genetic restrictions

BACKGROUND: Spanish gypsies have traditionally lived as nomads, a reason why few epidemiological studies were done in this ethnic group. However, the high prevalence of asthmatic diseases demonstrated in a population residing in the North of Spain induces us to analyse whether it was due to the influence of genetic loci previously implicated in other population studies as causing the disorders. METHODS: DRB1* and DQB1* HLA class II, TCR-Valpha8.1, FcepsilonRI-beta Rsa I exon 7 and intron 2, TNF-beta (LTalpha-Nco I) and CD14, were tested for association with asthma and atopy by multiple regression analysis, in 5 families comprising 87 individuals. RESULTS: Significant associations were found with DQB1*02 (p = 0.02) and DQB1*0301 (p = 0.008) and elevated levels of total serum IgE. A negative association (p = 0.02) was found between total serum IgE and DRB1*14. FcepsilonRI-beta Rsa I-In2 allele 1 was associated with high levels of total serum IgE (p = 0.04). Levels of Der p 1 IgE antibodies were negatively associated with DRB1*11-DQB1*0301 (p = 0.007), and positively with TCR Valpha-8 allele 1 (p = 0.04) and with FcepsilonRI-beta Rsa I-In2 allele 1 (p = 0.009). CONCLUSIONS: Our results do not show any association between asthma and the genetic loci studied although they do suggest the existence of multiple genetic influences on the allergic response in these families.     

A study of Gm allotypes and immunoglobulin heavy gamma IGHG genes in Berbers, Arabs and sub-Saharan Africans from Jerba Island, Tunisia.

The Gm polymorphism of human IgG immunoglobulins was investigated in three different ethnic groups--Arabs, Berbers and 'dark-skinned people'--on Jerba Island, Tunisia. The genetic relationships among these groups and several populations from North Africa, sub-Saharan Africa, west Asia and Europe were analysed by principal coordinate analysis, Fst significance testing, and analysis of molecular variance based on haplotype frequencies. The results revealed a non-significant genetic differentiation between Arabs and Berbers from Jerba. However, the Jerbian population of sub-Saharan African origin was close to Ethiopians. Gene flow among the three Jerbian populations, as well as an East African origin of the dark-skinned individuals, is proposed to account for the observed genetic pattern. However, the genetic diversity observed among the different Tunisian populations did not show any significant correlation with either geographic or linguistic differentiation. A preliminary analysis of the restriction fragment length polymorphism of the IGHG genes in Arabs and Berbers from Jerba confirmed the close genetic relationship between the two populations. However, it also indicated a lower level of genetic diversity in the Berbers, which may be explained by more rapid genetic drift due to longer isolation on the island.     

Y chromosome STR haplotypes and the genetic structure of U.S. populations of African,European, and Hispanic ancestry

To investigate geographic structure within U.S. ethnic populations, we analyzed 1705 haplotypes on the basis of 9 short tandem repeat (STR) loci on the Y-chromosome from 9-11 groups each of African-Americans, European-Americans, and Hispanics. There were no significant differences in the distribution of Y-STR haplotypes among African-American groups, whereas European-American and Hispanic groups did exhibit significant geographic heterogeneity. However, the significant heterogeneity resulted from one sample; removal of that sample in each case eliminated the significant heterogeneity. Multidimensional scaling analysis of R(ST) values indicated that African-American groups formed a distinct cluster, whereas there was some intermingling of European-American and Hispanic groups. MtDNA data exist for many of these same groups; estimates of the European-American genetic contribution to the African-American gene pool were 27.5%-33.6% for the Y-STR haplotypes and 9%-15.4% for the mtDNA types. The lack of significant geographic heterogeneity among Y-STR and mtDNA haplotypes in U.S ethnic groups means that forensic DNA databases do not need to be constructed for separate geographic regions of the U.S. Moreover, absence of significant geographic heterogeneity for these two loci means that regional variation in disease susceptibility within ethnic groups is more likely to reflect cultural/environmental factors, rather than any underlying genetic heterogeneity.