Haplotype analysis of the linkage group HLA-A:HAL-B:Bf and its bearing on the interpretation of the linkage disequilibrium

HLA antigens associated with properdin factor B allotype BfF1

Linkage disequilibrium has been described between HLA-B antigens and allotypes of properdin factor B (Bf). The association between HLA-B and DR antigens and the rate allotype BfF1 was investigated. In 27 HLA-A, B and DR typed individuals only one person was found who was DR3 negative but five who were B18 negative. Family studies showed that in nine cases B18, BfF1 and DR3 segregated as a haplotype; in another family which was B18 negative, BfF1 and DR3 segregated together. It is inferred that the Bf locus is more strongly associated with HLA-DR than with HLA-B.

Genomic analysis of the F subtypes of human complement factor B

Factor B of human complement is encoded within the Major Histocompatibility Complex (MHC) and is polymorphic, with up to 30 alleles defined by electrophoretic mobility. One of the most common alleles, BF*F, is subdivided into the FA and FB subtypes, which differ at the gene level by non-synonymous base substitutions in the seventh codon. We have found at this position a new restriction site polymorphism, as a Bsl I site absent from the FB allele. Using this restriction polymorphism, we have developed a method for BF F subtype determination, based on amplification by polymerase chain reaction of the 5' end of the BF gene, and digestion with Bsl I. This new method has been applied to a panel of 29 selected BF F individuals. A single strand DNA conformation analysis of the same region of the gene allowed us to confirm the above DNA-based BF F subtyping. During this study, two BF*F1 alleles showed discrepancies between protein and DNA typing, which were confirmed by our sequencing data. These were identical, in the 5' region, to BF*S and BF*FB genes, respectively. In a comparison with two protein subtyping methods, identical results were found for only one third of the selected samples. The conflicting results may arise, in part, from previously undescribed molecular heterogeneity within BF F subtypes, or from the presence of a null allele. Our new method allows BF*F subtyping to be used with confidence in the definition of disease-associated MHC haplotypes.

HLA frequencies in Basques in Spain and in neighbouring populations

HLA antigen and gene frequencies at the A, B, and C loci are examined in a sample of 181 Basques and 102 non-Basques in Bilbao, Spain. The most common associations of genes at the A and B loci are as in western Europe generally. The results are compared with gene frequencies in other Basque and non-Basque samples in Spain and France. There is clear distinction in gene frequency between Basques and non-Basques, to which the greatest contribution is made by A1 and B35, followed by B7, B8 and B12; and a difference between Basques in France and in Spain, notably in A28, 29, 30 and 31 and B17 and 18.

Order of class III genes relative to HLA genes determined by the haplotype method

The B18 C4A3 C4BQ0 BfF1 DR3 haplotype was found to be ideal for determining the order of C4 and Bf relative to HLA-B and DR by the haplotype method. All the copies of this haplotype are assumed to be derived from a single ancestral haplotype. Sixteen of the twenty-six BfF1-containing haplotypes carried all of the alleles from this "ancestral" haplotype. Most of the other BfF1-containing haplotypes could be derived from the "ancestral" haplotype by a single crossover event for one of the two possible gene orders. This suggests that B18 C4A3 C4BQ0 BfF1 DR3 is the sole source of the BfF1 allele. The uncommon C4 type on B18 C4A3 C4BQ0 BfF1 DR3 facilitates recognition of the BfF1-containing products of recombination between Bf and C4. One such recombinant haplotype was found which shows that the orientation of the class III genes is as follows: C4 is closest to HLA-B and Bf is closest to HLA-DR. This gene order is supported by all the earlier unequivocal results obtained using the haplotype method (Olaisen et al. 1983, Marshall et al. 1984a). Combining these results with the information on class III genes obtained from overlapping cosmid clones (Carroll et al. 1984) and earlier mapping studies (Robson and Lamm 1984) shows that HLA-B is telomeric to 21B. C4B, 21A, C4A, Bf and C2 then follow 21B in that order covering 120 kb. HLA-DR is located further toward the centromere.

Two subtypes of BfF by isoelectrofocusing: differential linkage to other HLA markers

By isoelectrofocusing in agarose, the properdin factor allotype BfF could be split into two subtypes: BfFa with one major cathodic band and BfFb with the same cathodic band but in addition a major anodic band. By scanning, BfFaFb heterozygotes were distinguished from BfFbFb homozygotes by the stronger intensity of the anodic band in the latter. The two subtypes were segregated perfectly with HLA in 40 families and showed different association patterns with HLA markers. BfFa seemed to be linked to B35 while BfFb showed a strong linkage with all the components of the following haplotype: HLA-A29, Cw-, B44, BfFb, C4A3B1, DR7. The frequency of BfFa among BfFS heterozygotes was 41% (46/113) and that of BfFb 59% (67/113).

Estimation of haplotype frequencies

Maximum likelihood estimates of haplotype frequencies in multilocus systems are often zero and so may be genetically inacceptable. Estimation problems are discussed, and preferable estimates are derived.

The BF locus and HLA: rare alleles coding for functionally active and inactive factor-B products

The genetic polymorphism of properdin factor B (BF) was studied in different populations. The rarer alleles, BF*F1 and BF*S1, occurred in Caucasians, were less frequent in North American blacks, and were not demonstrated in any of three Oriental populations studied. Two further alleles of BF, termed BF*FM and BF*SM, were found to exist in these populations. The BF*FM allele, which was found only in Caucasians, codes for a functionally inactive factor-B product, whereas the BF*SM allele (found in a single Chinese individual), like other alleles of BF, codes for a functionally active product. HLA haplotype analyses in individuals carrying the rarer alleles of BF revealed not only a strong association between BF*F1 and HLA-B18 and BF*S1 and HLA-Bw50 but an even stronger association between these BF alleles and alleles of the two C4 loci. BF*F1 occurred most frequently on a C4A*3,B*Q0 haplotype, whereas the BF*S1 allele was usually found on a C4A*2,B*1/B*Q0 haplotype. HLA haplotypes carrying the BF*FM and BF*SM alleles all carried the more common C*4A3,B*1 haplotype.

Polymorphism of properdin factor B in Japanese. Description of a rare variant and data of association with HLA and C2

Polymorphism of the properdin factor B (BF) was investigated using an agarose gel immunofixation electrophoresis in 487 unrelated healthy adult Japanese who were already typed for HLA-A, -B, -C and C2. Besides the previously reported phenotypes in Japanese (S, FS, and F), a rare heterozygous phenotype (tentatively maned FTS) was observed once. The estimated allele frequencies for BS*S, BF*F, and FB*FT (F Tokyo) were 0.801, 0.198, and 0,001 respectively. The relative electrophoretic mobility of the variant band of type FTS was measured by Dr. G Mauff to be F 0.75. The conversion fragment Bb of the type showed a double-banded pattern. BF hemolytic activity of the FTS individual was at the same level as other phenotypes. Statistical tests for the phenotypic data of BF with HLA-A, -B, -C, and C2 indicated the presence of the following significant associations in Japanese: Aw33-BF*F, A11-BF*S, Aw24-BF*S, B15-BF*F, B17-BF*F, Bw44-BF*F, B7-BF*S, Bw52;-BF*S, BW54-BF*S, BW59-BF*S, Cw3-BF*F, C2*AT-BF*F, and C2*A'-BF*F.

HLA-linked genetic markers in Chinese and other Oriental populations

The polymorphic variants of the HLA-linked genetic markers Bf, C2, C4 and GLO-I were studied in three mongoloid populations. Analysis of linkage dis-equilibrium between these markers and HLA-A, B, C and DR antigens was carried out on test results from 140 unrelated Chinese individuals. The phenotypes BfS and GLO-2 were found at significantly higher frequencies than in Caucasians. BfS was associated with B12 in Japanese but not in Chinese. A single individual with the rare Bf variant S1 was found. No C2 deficient individuals were observed. The C2C (common) allele occurred at a gene frequency of 0.949 and the more basic allele C2B at 0.039. The acidic variant, C2A, was observed at a frequency of 0.011 and appeared to be associated with BfF. Eighty-nine per cent of the Chinese were phenotypically C4FS. In contrast to Bf and C2, each of which is coded for by codominant alleles at a single genetic locus, C4 is coded for by two genes, C4F (Rodgers) and C4S (Chido). The C4F locus allele, C4F1 (extra fast), was strongly associated with HLA-B17, as has been found in other populations, but a new association of the C4S locus deficiency allele, C4so (Ch-), with B17 was also observed. All HLA-B17;C4so haplotypes were BfS position. As has been previously found in Caucasian populations, individuals of the C4F phenotype (i.e. genotypically FsoFso) were all found to be Chido negative. The frequencies of the various HLA-linked genetic markers, however, as much as the frequencies and associations of the HLA antigens themselves, distinguish these populations from other ethnic groups.

Haplotype study. linkage between HLA--A, B, C and Bf alleles: results obtained by different statistical methods

325 HLA-A, B and Bf haplotypes obtained from family studies were investigated. In addition, 216 of these were tested for HLA-Cw2, Cw4, Cw5. Four different statistical methods were employed to study 2, 3 or 4 loci gametic associations in order to compare the results obtained by these different methods. Our results were then compared with those of other authors who employed similar methods. Piazza's method, used to identify gametic associations, was not able to show any 3 loci associations in our material. The Delta Standard Method employed in conjunction with Factorial Correspondence Analysis was found suitable for the study of chromosomal prevalence in a population.

Properdin factor B polymorphism in continental Italy and Sardinia

A sample of healthy unrelated individuals (882 from Continental Italy and Sicily, and 139 from Sardinia) were typed for HLA and Bf polymorphisms. Bf gene frequencies in Continental Italy and Sicily show an intermediate position among European populations, with Lapps on one side and Basques on the other side; while a very peculiar pattern is observed among Sardinians, with an impressive similarity with French Basques and with the highest F1 gene frequency so far observed. The HLA:Bf gametic associations in Italy and Sardinia are also reported, which confirm the different ethnic background of these populations.

Strong linkage disequilibria among HLA-Bw50, BfS1, and HLA-DR3/DR7, and mapping of the Bf locus

Based on genotypic and phenotypic studies we have found strong linkage disequilibria in Caucasians among the genes HLA-Bw50, BfS1, and HLA-DR3 and/or -DR7. The relative disequilibria, which are among the highest described in man, are delta r (BfS1, DR7) = 0.51, delta r (Bw50, BfS1, DR7) = 0.36, delta r (Bw50, DR3 or 7) = 0.72, delta r (BfS1, DR3 or 7) = 0.91, delta r (Bw50, BfS1, DR3 or 7) = 0.73. The previously described high delta r (Bw50, BfS1) and delta r (Bw50, DR7) have also been confirmed. A B parallel DR crossover family is also presented that, together with previously reported recombinant families, confirms that the Bf locus resides between HLA-B and HLA-DR. These data suggest the existence of a supergene complex of Bw50, BfS1, DR3/7 (or MB2), and hypotheses to account for the observed disequilibria are discussed.

The location of C2, C4, and BF relative to HLA-B and HLA-D

The loci for HLA-A,B,C,D, and DR are known to be closely linked to the structural loci for the complement components C2, BF, and the duplicated loci for C4, C4A and C4B. Conflicting evidence has been presented for the order of these genes. However, new techniques have made possible identification of markers in the HLA-D and C4 region for nearly all identified haplotypes. In our population we have confirmed five HLA-B-D crossovers and in each case informative allotypes of C2, BF, or C4A and C4B segregated with HLA-D or DR suggesting that the loci for these proteins lie close to HLA-D and DR. These findings may be of importance for resolving problems encountered in the assignment of HLA-D alleles.

Bf polymorphism and its relationship with HLA antigens in a sample of the Spanish Population: high BfF1 frequencies

Bf allele frequencies were studied in a sample of the normal Spanish population and in family haplotypes. BfF1 shows a frequency higher than in other Caucasoid populations and closer to that found in Negroids. Basques show an even higher BfF1 frequency BfF1 is in strong linkage disequilibrium with B18. HLA-Bw44 is found to be the B12 split in linkage disequilibrium with BfF and Bw50-BfS1 association is confirmed. DR3--BfF1 are not in linkage disequilibrium in the normal Spanish population, in contrast to DR3--BfF1 in linkage found in a diabetic Spanish population. Results are discussed on the bases of the paleo-North African Iberian population origins and of the use of Bf to define B12 and Bw21 splits.

The genetics of diabetes mellitus in man

The genetics of diabetes mellitus in man has been reviewed. The evidence for genetic heterogeneity on clinical, biochemical and HLA (histocompatibility leukocyte antigens) data is presented. An attempt is made to interpret the meaning of the associations of the disease and certain HLA antigens and the complement factor, properdin in populations and in families. The population data can be best explained by the linkage disequilibrium hypothesis requiring tight linkage between the DS (diabetes susceptibility) locus and those in the MHC (major histocompatibility complex). Linkage between the DS locus and MHC from family data is estimated to be about 14%, which is not likely tight enough to be compatible with the population data; and a one locus or one allele hypothesis and genetic heterogeneity is postulated as the best explanation of the incompatibility between population and family data. It is still impossible to precisely define the exact genetic hypothesis for diabetes in man.

High frequency of the properdin factor Bf F1 and its linkage to HLA in French Basques

We studied 201 unrelated French Basque individuals for HLA and Bf polymorphisms. The haplotypes of eighty-seven of them were deduced from family studies. The results show the frequency of the Bf F1 allele (0.1393) which is the highest one currently reported. They confirm the high frequencies of HLA-Aw19.2 and B18 previously reported in that population and show that a whole haplotype with strong linkage disequilibria, namely Aw19.2, Cw5, B18, Bf F1, DRw3 is frequent. On the other hand, the gene frequency of Bf S is decreased (0.5497) as compared with the other European Caucasoïd populations, while a slight increase in the Bf F gene frequency (0.2960) appears. These results point out that it is of importance to consider the genetic background choosing the population where linkage disequilibria are to be studied.

Linkage disequilibria between HLA-B and the rarer properdin factor B alleles, BfF1 and BfS1

Phenotypic association and highly significant linkage disequilibria have been demonstrated for HLA-B18 and BfF1 and HLA-Bw50 and BfS1 alleles among Caucasians from Australia and the United States (San Francisco Bay area). The HLA-B18, BfF1 association appears to be associated with HLA-Aw30. It is possible that BfS1 arose as a mutation, after the evolutionary splitting of HLA-Bw21, on an HLA-Bw50 haplotype, and that BfF1 arose on an HLA-Aw30, B18 haplotype.

Genetic linkage between Bf S0.7 (Bf S1) and HLA-Bw50

Two hundred and one unrelated French Basque individuals were studied for HLA-A, B, C, DR and Bf polymorphisms. The results show that the Bf S0.7 (Bf S1) variant, which is known to be associated with HLA-Bw21, presents a highly significant linkage disequilibrium with a subtypic specificity, i.e., Bw50 (delta = 0.0123, delta S=100%, P less than 10(-8)). As neither Bf S0.7 variant nor Bw50 antigen is found in Mongoloid populations, it is suggested that in evolutionary terms, the Bf S0.7 mutation is a more recent event than the HLA-Bw21 split.

HLA-A, B, Bf three point association of 1,072 haplotypes in a German population

Altogether 1,072 HLA-A, B, Bf haplotypes in 536 parents of 268 German families were analyzed by gene and haplotype counting in order to investigate the two and three point association of HLA-A and B antigens with Bf alleles. In agreement with previously published data (Albert et al. 1975, Bender et al. 1977) significant positive linkage disequilibria were found for HLA-A3 and BfF, B7 and BfS, B8 and BfS, Bw35 and BfF, whereas significant negative Delta values appeared to exist for HLA-A3 and BfS, B7 and BfF, B8 and BfF, B12 and BfS, as well as Bw35 and BfS. Significant positive three point Delta values were found for the following haplotypes: HLA-A11, Bw35, BfS, HLA-Aw23, Bw35, BfS, HLA-A28, B12, BfS, HLA-A2, B17, BF, HLA-A3, Bw35, BfF, HLA-Aw24, b12, BfF and HLA-A29, B12, BfF. According to the large number of comparisons performed calculating the level of significance of the three point associations, these data have to be corroborated by further investigation. The three point Delta values, obtained by calculation from the patients' phenotypes differed markedly from those results obtained by haplotype counting.

Strong linkage disequilibrium between HLA-Dw2 and and BfS in multiple sclerosis and in the normal population

An increased frequency of the S allele of Properdin factor B (BfS) was found amongst 162 patients with multiple sclerosis (MS) compared with 470 normal controls. This increase was shown to be due to a strong linkage disequilibrium (LD) between BfS and HLA-Dw2 in 77 patients typed for both systems (delta = 3.84%, P = .0002). The same LD was demonstrated amongst 100 normal controls (delta = 2.24%, P = .0049) and 31 patients with idiopathic demyelination of the peripheral nervous system (IDPN). A total of 70 haplotypes with HLA-Dw2 were encountered (40 MS, seven IDPN and 23 normal controls) and all contained BfS. In the MS patient group, a much weaker association was noted between BfS and HLA-B7 suggesting either that the Bf locus is musch closer to the HLA-D than the HLA-B locus or (and) that HLA-D and Bf products selectively interact (perhaps on the surface of B lymphocytes) with evolutionary advantage or disadvantage resulting from certain allelic combinations. Strong associations between BfS1 and HLA-Bw21 (P = .0000) and BfF1 and HLA-B18 (P = .0001), both previously reported, were confirmed in the current study. No increase in the frequency of a glyoxalase (GLO) allele was found amongst the MS patients and no LD was encountered between HLA-Dw2 and a GLO allele. The possibility that the HLA-Dw2, BfS disequilibrium has resulted from a selective advantage conferred on the general community but at the expense of increasing susceptibility to MS should be considered.

Properdin factor B-polymorphism. An indication for the existence of a Bf O-allele

The polymorphism of the properdin factor B (Bf, C3-proactivator, GBG = glycin-rich-beta-glycoprotein) has been investigated by high voltage agarose gel immunofixation electrophoresis in 1115 unrelated persons from Southern Germany. Seven phenotypes were observed; the allele frequencies were calculated as BfS = 0.8094, BfF = 0.1790, BfSI = 0.0094, BfFI = 0.0022. A study of 94 parents with 98 children and 420 mother-child combinations showed no deviation from the assumed autosomal codominant mode of inheritance. In one additional family the findings suggested the existence of a silent allele at the Bf-locus.

Population genetic data on properdin factor B (Bf) in northern Germany

Properdin factor B phenotypes were determined in 1,112 unrelated individuals and in 151 mother/child combinations from Northern Germany. Gene frequencies were : F = 0.1960, S= 0.7905, F1 = 0.0072, S1 = 0.0063. The data of the mother/child combinations are in full accordance with the postulated gene model.

Estimation of haplotype frequency and linkage disequilibrium parameter in the HLA system

Conventional formulae currently employed were extended to calculate the haplotype frequency and the corresponding variance for an arbitrary number (n) of loci when unrelated individuals were investigated. A formula is presented for the variance for the degree of three locus linkage disequilibrium.

A haplotype study of HLA complex with special reference to the HLA-DR series and to Bf. C2 and glyoxalase I polymorphisms

Fifty-three French families were typed for alleles at seven loci of the HLA complex (HLA-A, -B, -C, -DR, -Bf, -C2 and -GLO) and 212 haplotypes were demonstrated. Eleven recombinations were observed (two A/B, two A/C, two B/Bf, one Bf/D and four D/GLO). The linkage disequilibrium was calculated not only between two alleles (delta) but between three, four...seven alleles (D). In order to compare the intensity of D values in the various haplotypes, the influence of the differences in gene frequencies was eliminated by the introduction of the standardized Ds (Ds = D/D max). The number of haplotypes in disequilibrium is relatively limited since most of the significant Ds involved about 17 haplotypes. For some haplotypes, the disequilibrium covered the whole distance from A to GLO but the stronger disequilibrium concerns the C to Bf or C to DR segment. Three hypotheses (isolation, admixture of population and selection) concerning the formation and maintenance of the disequilibria are discussed.

Screening of inbred rat strains for electrophoretic protein polymorphisms

Nineteen inbred strains of the laboratory rat (Rattus norvegicus) were investigated for genetic differences by starch and agarose gel electrophoretic techniques. For six out of 21 loci, interstrain differences were observed: Tf, 6PGD, Es-1, Es-4, Es-5, and Svp. The variants are briefly described and the allelic distributions are tabulated. The 6GPD locus was found to be linked neither to the major histocompatibility gene region nor to the coat color genes c, a, h.

Analysis of the HLA-ABC linkage disequilibrium: decreasing strength of gametic association with increasing map distance

1242 HLA-ABC haplotypes of the North German population (Hambrug) as deduced by family analyses are described. They are in perfect agreement with recently published data by Mayr (1977) from Austria (Vienna) in all parameters tested: frequency of the single HLA-alleles, haplotype distribution and linkage disequilibrium values. Gametic association studies revealed that 69.4% of the B and C genes (map distance 0.2cM) 36.9% of the A and C genes (0.6 cM), but only 23.2% of the A and B genes (0.8 cM) were significantly more often combined than expected due to their frequencies. From these findings it seems likely that the linkage disequilibrium within the MHC is rather due to a short evolutionary period than to selective forces. Some observations as to the most common European haplotype A1,B8 are discussed.

Bf types of HLA haplotyped individuals in an isolated Newfoundland population

Five hundred and fourteen individuals from an isolated NewFoundland population have been typed and haplotyped for HLA and Factor B (Bf locus). The Bf gene frequencies were: S0.704, F0.226, F1 0.052 and S1 0.018. Tracing the haplotypes backwards on the various pedigrees it was shown that 202 HLA/Bf haplotypes had been introduced into the study population. Some HLA alleles always appeared in association with particular Bf alleles and vice versa. Bf S1 had entered the population four times, always with HLA--A9, B12. Bf F1 had entered three times, always with HLA--B18. There were 17 entries of HLA--Al, B8 that had given rise to the 78 such haplotypes that were now present in the population; all were Bf S. There were 68 family units informative for Bf. They accounted for 240 children and 304 informative meioses. There were three recombinants in the HLA region but none could be shown to have occurred between the HLA-B and Bf loci.

No evidence for linkage disequilibrium between Bf and GLO in African negroids

A sample of South African Negroids (n = 791) was scored for each individual's Bf and GLO phenotype. (The genes for the Bf and GLO olymorphisms are included in a known cluster of linked genes on chromosome 6.) Following a x2-test the respective two series of alleles were found to be disturbed at random, i.e., there was no evidence for a linkage disequilibrium. This result is discussed in terms of the linkage relationships and map distances of the genetic markers involved.