Linkage disequilibrium between cystic fibrosis and linked DNA polymorphisms in Italian families: A collaborative study

The locus D7S23 includes a CpG-enriched methylation-free island that maps midway between the markers J3.11 and met and is genetically very close to the mutation causing cystic fibrosis (CF). We have studied the linkage disequilibrium between four polymorphic markers from this locus (KM.19, CS.7, XV-2c, and PT-3) and the CF mutation (CF) in 127 Italian families. Strong linkage disequilibrium is found between KM.19, CS.7, and CF, and weaker but significant disequilibrium is found between XV-2c, PT-3, and CF. The disequilibrium between markers and CF for the Italian population provides additional information on the origin and homogeneity of the CF defect. This panel of probes is sufficiently informative to permit accurate prenatal diagnosis of CF in most families with an affected person, and the disequilibrium also allows indirect carrier detection/exclusion in some cases.     

Cystic fibrosis typing with DNA probes and screening for ΔF508 deletion in families from Southern France

Summary A sample of 235 individuals from 49 French cystic fibrosis (CF) families with at least one living affected child was typed with probes for restriction fragment length polymorphisms (RFLPs) known to be linked to the CF gene, and was screened for the ΔF508 mutation. Using a combination of six probes, 44 out of the 49 families were sufficiently informative to enable prenatal diagnosis or carrier determination. As in many other populations, linkage disequilibrium was found between the CF locus and the haplotype B (XV2c: allele 1; KM19: allele 2), which accounts for about 78% of CF chromosomes in our families. The ΔF508 deletion was present in 64.3% of CF chromosomes.     

Genotyping of the Spanish cystic fibrosis population at the ΔF508 mutation site and RFLP linked loci

Summary Spanish families (n = 75) with at least one affected cystic fibrosis (CF) child were typed for restriction fragment length polymorphisms (RFLPs) by the probes XV2c, KM19, and pMP6d-9. These families were also studied at the 508 mutation site by the polymerase chain reaction method. We have studied the linkage disequilibrium between these markers and the CF mutations, the probable number of independent secondary CFX (non-ΔF508) mutations, and the genetic differences between Spain and Western Europe.     

Haplotypes in cystic fibrosis patients with or without pancreatic insufficiency from four European populations

We examined the allele and haplotype frequencies of five polymorphic DNA markers in 355 European cystic fibrosis (CF) patients (from Belgium, the German Democratic Republic, Greece, and Italy) who were divided into two groups according to whether they were or not taking supplementary pancreatic enzymes. The level of linkage disequilibrium between each polymorphism and the CF mutation varied among the different populations; there was no significant association between KM.19 and CF in the Greek population. The distributions of alleles and haplotypes derived from the polymorphisms revealed by probes KM.19 and XV.2c were always different in patients with or without pancreatic insufficiency (PI) in all the populations studied. In particular, among 32 patients without PI, only 9 (or 28%) were homozygous for the KM.19-XV.2c = 2-1 haplotype (which was present in 73% of all the CF chromosomes in our sample) compared to 162 of 252 patients (or 64%) with PI. These findings are consistent with the hypothesis that pancreatic insufficiency or sufficiency may be determined by different mutations at the CF locus.     

Molecular analysis of cystic fibrosis in the Hungarian population

Summary Hungarian cystic fibrosis (CF) families (n = 33) including 114 family members have been analysed for the presence of the F508 mutation within the cystic fibrosis transmembrane conductance regulator (CFTR) gene, and have been haplotyped with probes for restriction fragment length polymorphisms (RFLPs) known to be linked to the CFTR gene. The F508 deletion was present in 64% of CF chromosomes. As in many other populations, linkage disequilibrium was found between the CF locus and the haplotype B (XV-2c: allele 1, KM1-9: allele 2), which accounts for 95% of F508 CF chromosomes in our families.     

The cystic fibrosis ΔF508 mutation in the French population

Summary French families (n = 129) with at least one cystic fibrosis (CF) affected child and 44 unrelated subjects from the general population were tested for the presence of the ΔF508 mutation by the polymerase chain reaction. The ΔF508/CF mutation ratio (CF: uncharacterised CF mutations) was tested in the CF families with and without meconium ileus. The association between ΔF508 and CF mutations and restriction fragment length polymorphism haplotypes (XV2c and KM19) has been estimated; these data suggest that the CF chromosomes include a panel of independent and probably different mutations.     

Analysis of DNA polymorphism haplotypes linked to the cystic fibrosis locus in North American black and Caucasian families supports the existence of multiple mutations of the cystic fibrosis gene.

Strong linkage disequilibrium (LD) was found between DNA marker XV2c and the cystic fibrosis (CF) locus (delta = 0.46) and between DNA marker KM19 and CF (delta = 0.67) in 157 CF and 138 normal chromosomes from U.S. Caucasians. DNA haplotypes with nine polymorphic sites were created in 54 Caucasian families. There is a strong LD between the haplotypes and the presence of the mutant CF genes. This implies that the DNA polymorphisms examined are close to the CF gene and that one mutation of the CF gene predominates in the Caucasian population. Haplotype analysis can also be used to refine estimates of CF carrier risk in Caucasians. Data for XV2c and MET markers in 16 American black patients and their families revealed a different haplotype distribution and LD pattern with the CF locus. These data suggest that racial admixture alone does not explain the occurrence of CF in American blacks and that multiple alleles of the CF gene may exist in this population.     

Allele polymorphism of the DNA loci MET, D7S8, D7S23, linked to the cystic fibrosis gene in some populations of the USSR, in high risk families and in cystic fibrosis patients

RELP analysis of DNA loci MET, D7S8 and D7S23 was carried out in Leningrad population and partially in populations of Moscow, Azerbaijan, Ukraine, Buryatia as well as in individuals from high risk families and in cystic fibrosis (CF) patients by means of blot hybridization and polymerase chain reaction. Allelic polymorphism of all loci studied in these three groups was found to be quite similar to that in the North-Western Europe and in whites of the North America. Linkage disequilibrium of the alleles studied with the CF gene was especially pronounced for alleles of the D7S23 locus and gradually decreases from KM-19 through CS-7 to XV-2c DNA probes. The data witness genetic homogeneity of the CF mutation in European populations of the USSR and its similarity to this mutation in Western Europe. The significance of these data for potential diagnosis of CF and for heterozygous carrier detection is discussed.     

Studies of cystic fibrosis in Hutterite families by using linked DNA probes.

Several multigenerational S-leut Hutterite families with cystic fibrosis (CF) were ascertained. Linkage studies with DNA marker loci MET and pJ3.11 (D7S8) were performed to determine whether (1) the CF gene in this inbred population is linked to DNA markers on chromosome 7, as it is in outbred populations of European origins, and (2) ancestral origin(s) of the CF gene could be determined. Our results indicate that the CF gene in Hutterite families segregates with chromosome 7 markers, identified by probes metH and pJ3.11. Thus, the CF mutation in Hutterites is likely to be either at the same locus as or at one closely linked to that reported in outbred populations. Heterozygous carriers could be distinguished from normal homozygous sibs of affected individuals. In the families studied, three different chromosome 7 haplotypes carried the CF mutation, raising the possibility that the CF gene may have been introduced into this population by as many as three different ancestors.     

Cystic fibrosis: typing 89 German families with linked DNA probes

Summary Three hundred and ninety-two subjects from 89 German families were typed for restriction fragment length polymorphisms (RFLPs) detected by the probes pmetH, pmetD, pJ3.11, KM19, and XV2c known to be tightly linked to the cystic fibrosis (CF) gene. The analysis of the predictive value of this typing in individual CF families indicates that the combined use of these probes provides a powerful diagnostic system for both carrier detection and prenatal diagnosis. In 45 families the complete haplotype including all RFLPs was available. Of them 41 (91.1%) were fully informative and 4 were partly informative.     

Different haplotypes for cystic fibrosis-linked DNA polymorphisms in Polish and Dutch populations

Summary We analyzed DNA from 34 Polish and 63 Dutch cystic fibrosis (CF) patients and their families using the polymorphic markers XV2c and KM19, which are in linkage disequilibrium with the CF mutation. Strong linkage disequilibrium was found in the Dutch population sample, but the haplotypes of the Polish chromosomes showed a significantly less extreme disequilibrium. Our data and previous studies indicate that the highest degree of homogeneity of the CF defect and hence the best possible use of the XV2c/KM19/CF linkage disequilibrium for CF carrier detection/exclusion is in populations of northern European origin.     

ΔF508 deletion in cystic fibrosis in Italian families

Summary In 20 Italian families with cystic fibrosis (CF), restriction fragment length polymorphisms were detected by five linked markers; a strong linkage disequilibrium is observed between the haplotype B (alleles 2/1 with respect to KM19/XV2c) and CF. The frequency of the ΔF508 deletion in CF chromosomes of this sample is 50%. A significant correlation is found between the absence of the ΔF508 mutation and pancreatic sufficiency.     

Identification of carriers by screening for delta F508 deletion in a multi-generation cystic fibrosis family

Samples from 30 members of a french cystic fibrosis (CF) family had to be typed with probes for restriction fragment length polymorphisms (RFLPs) known to be linked to the CF gene, to fulfill the expectations of twenty-two low-risk relatives who were asking for carrier testing. Classical linkage-disequilibrium data between KM-19 and XV-2c polymorphisms and the CF locus were not informative enough for some individuals, and other RFLPs had to be analyzed to determine which chromosomes carried the deficient gene in the family. We report the retrospective screening for delta F508 mutation in this extended family to illustrate the drastic improvements that the direct detection of the major mutation responsible for CF has on genetic counselling of relatives of patients with cystic fibrosis.     

Marker haplotype association with growth in German cystic fibrosis patients

Summary In 84 families with 101 children with cystic fibrosis (CF) and 103 unaffected siblings, the haplotype of CF chromosomes was determined with six restriction fragment length polymorphism (RFLP) markers that span the CF gene locus. Patient groups with different genotypes in the more distant flanking marker loci MET D, MET H, and D7S8 differed significantly from each other with respect to percentile height and weight, and percentage of weight for height. Patients homozygous 1-1 in met D (TaqI) and met H (TaqI) were thin and tall when homozygous 1-1 in J3.11 (MspI), and small when homozygous 2-2 in J3.11. Heterozygosity in 3.11 and met H and homozygosity 1-1 in met D segregated with the most severe growth retardation. In contrast, growth was normal in patients who were heterozygous in met D and/or had an uncommon KM.19/XV-2c haplotype. Most patients with pancreatic sufficiency and/or borderline sweat test values were carrying rare haplotypes on their CF chromosomes. Adult patients clustered in genotype groups with normal height percentile distributions. This association between haplotype and clinical severity of CF in the German population provides evidence for genetic microheterogeneity of the CF locus, either because of the existence of multiple alleles of the CF gene itself and/or because of the existence of closely linked polymorphic genes that control growth and development and hence modulate the clinical course and prognosis of CF.     

Cystic fibrosis DNA markers in Alabama blacks

DNA samples from unrelated Alabama blacks with no family history of cystic fibrosis (CF) were analyzed with DNA markers linked to cf. Allelic frequencies of genetic markers detected by probes pmetH, pmetD, XV2c, KM19, and pJ3.11 were compared to those of other populations. Allelic frequencies for pJ3.11, XV2c, and KM19 in Alabama blacks and previously studied Caucasian populations were similar. In contrast, the met locus allelic frequencies in Alabama blacks were markedly different from those in Caucasian populations.     

Cystic fibrosis: typing 48 German families with linked DNA probes

Summary Two hundred and thirty five subjects from 48 German cystic fibrosis (CF) families were typed for restriction fragment length polymorphisms (RFLPs) detected by the probes pmet H, pmet D, and pJ 3.11, known to be tightly linked to the CF gene. Gene and haplotype frequencies suggest a linkage disequilibrium with the CF locus. The analysis of the predictive value of this typing in individual CF families indicates that the combined use of these probes provides a powerful diagnostic system both for carrier detection and prenatal diagnosis. In 33 out of 48 families carriers and non-carriers could be identified, and in 26 of these 33 families prenatal diagnosis could discriminate between affected and unaffected offspring.     

Cystic fibrosis mutation ΔF508 in Finland: other mutations predominate

Summary The frequency of mutation ΔF508 was determined in all 20 Finnish cystic fibrosis (CF) families with living affected children (19 with pancreatic insufficiency). ΔF508 was detected in 18 out of 40 CF chromosomes (45%). At least two different mutations associated with pancreatic insufficiently have occurred in a rare haplotype defined by XV2c, CS.7, KM19 alleles 1 2 2. Geographical clustering of ΔF508 and other mutations suggested that a founder effect and genetic drift have influenced the frequency of mutations causing CF in Finland.     

Intra- and extragenic marker haplotypes of CFTR mutations in cystic fibrosis families

Summary In order to facilitate the screening for the less common mutations in the cystic fibrosis (CF) gene viz., the CF transmembrane conductance regulator gene (CFTR), marker haplotypes were determined for German nonCF (N) and CF chromosomes by polymerase chain reaction analysis of four polymorphisms upstream of the CF gene (XV-2c, KM.19, MP6-D9, J44) and six intragenic polymorphisms (GATT, TUB9, M470V, T854T, TUB18, TUB20) that span the CFTR gene from exon 6 through exon 21. Novel informative sequence variants of CFTR were detected in front of exons 10 (1525-61 A or G), 19 (3601-65 C or A), and 21 (4006-200 A or G). The CF locus exhibits strong long-range marker-marker linkage disequilibrium with breakpoints of recombination between XV-2c and KM.19, and between exons 10 and 19 of CFTR. Marker alleles of GATT-TUB9 and TUB18-TUB20 were found to be in absolute linkage disequilibrium. Four major haplotypes encompass more than 90% of German N and CF chromosomes. Fifteen CFTR mutations detected on 421 out of 500 CF chromosomes were each identified on one of these four predominant 7-marker haplotypes. Whereas all analysed F508 chromosomes carried the same KM.19-D9-J44-GATT-TUB9-M470V-T854T haplotype, another frequent mutation in Germany, R553X, was identified on two different major haplotypes. Hence, a priori haplotyping cannot exclude a particular CF mutation, but in combination with population genetic data, enables mutations to be ranked by decreasing probability.     

Genetic homogeneity of cystic fibrosis.

We studied large Amish/Mennonite/Hutterite kindreds that segregate cystic fibrosis (CF) for linkage between CF and the polymorphic DNA markers pJ3.11 and 7C22 located on chromosome 7. These inbred pedigrees consist of more than 300 members including 30 affected individuals. In these families, linkage between the CF locus and the chromosome 21 marker D21S5 and between CF and the marker at the met oncogene locus on chromosome 7 had been previously indicated. We now report linkage between CF and pJ3.11 (Z = 4.92, theta = 0) and between CF and 7C22 (Z = 3.42, theta = 0). Therefore, CF segregates in these large pedigrees in a manner consistent with data from smaller outbred families with respect to the markers on chromosome 7 closest to CF. These data are consistent with locus homogeneity for the defect causing CF in the populations that have been examined to date.     

The ΔF508 mutation in cystic fibrosis patients of Southern Italy

Summary Fifty one independent cystic fibrosis (CF) families originating from a restricted area of Southern Italy (Campania) have been analyzed for KM19 and XV2c haplotypes and the ΔF508 mutation: 54% of the total CF chromosomes show the ΔF508 mutation. No significative correlations were obtained when clinical score, radiological score,Pseudomonas colonization, or clinical symptoms at presentation were matched with the presence or absence of the ΔF508 mutation.