ABCMdb

PMID: 1715309

Reiss J, Cooper DN, Bal J, Slomski R, Cutting GR, Krawczak M
Discrimination between recurrent mutation and identity by descent: application to point mutations in exon 11 of the cystic fibrosis (CFTR) gene.
Hum Genet. 1991 Aug;87(4):457-61., [PubMed]

Sentences

No. Mutations Sentence Comment

2 ABCC7 p.Gly551Asp ABCC7 p.Arg553* ABCC7 p.Arg553* ABCC7 p.Arg553* These Caucasian patients were found to possess an identical haplotype background for two common mutations (G551D, R553X) constistent with their being identical by descent. However, a different R553X associated haplotype found in American black patients was suggestive of recurrent mutation, a postulate supported by the location of the R553X alteration in a hypermutable CpG dinucleotide. Login to comment 3 ABCC7 p.Arg553* Likelihood estimates for recurrent mutation and identity by descent were compared and strongly supported the hypothesis of recurrent R553X mutation. Login to comment 15 ABCC7 p.Gly551Asp ABCC7 p.Arg553* In this study, we report the frequency of G551D and R553X mutations on CF chromosomes from Western Germany and use derived restriction fragment length polymorphism (RFLP) haplotype data in an attempt to distinguish between the alternative hypotheses of recurrent mutation and identity by descent. Login to comment 26 ABCC7 p.Gly551Asp ABCC7 p.Arg553* Results PCR amplification products of exon 11 of the CFTR gene from 59 unrelated CF patients who had previously been identified as carrying at least one non-AFS08 mutation (Wagner et al. 1990; Reis et al. 1990), were analysed with restriction enzymes HincII to screen for mutations R553X and G551D, and DdeI for mutations of codon $549 (Table 1). Login to comment 29 ABCC7 p.Gly551Asp In four of these, a novel MboI site was also apparent (sample digests are shown in Fig. 1), identifying the mutations unequivocally as G551D. Login to comment 30 ABCC7 p.Arg553* For the remaining 10 chromosomes, sequence alterations other than that responsible for R553X are possible; these would result in the loss of a HincII site without the creation of a MboI site. Login to comment 31 ABCC7 p.Arg553* However, R553X is the only mutation of this kind so far described that occurs at a significant frequency in population studies. Login to comment 32 ABCC7 p.Arg553* Moreover, PCR/direct sequencing of five of these alleles confirmed the presence of a R553X nonsense mutation (data not shown). Login to comment 34 ABCC7 p.Gly551Asp ABCC7 p.Arg553* Frequency of exon 11 mutations on non-AF508chromo- somes of German CF patients Detection Loss ofHincII site Loss of DdeI site Absence of Presence of MboI site MboI site Corresponding R553X G551D - mutation Frequency 10out of 75 4 out of 75 0 out of 75 Fig.la, b. Login to comment 38 ABCC7 p.Gly551Asp ABCC7 p.Gly551Asp ABCC7 p.Arg553* ABCC7 p.Arg553* Unless otherwise indicated, the underlined alleles indicate haplotypes derived by homozygosity Acronym AF508 KM19 XV2c pJ3.11 (PstI) (TaqI) (PstI/mspId) R553X 1226(homozygous) -/- _1-_1 _1-_1 2-2 1570 -/m 1-2a 1-1 1-2 2063 -/m 1-2b 1-1 1-2a 3946 -/- 1-2a 1-2 1-2 3986 -/m 1-2a 1-1 2-2 4133 -/- 1-2 1-1 2-2 4773 -/m 1-2a 1-1 2-2 5416 -/m 1-2a 1-1 1-2 5426 -/m 1-2a 1-1 1-2a Associated with R553X 1 1 2 G551D 2547 -/- 2-2 1-1 2-2 3937 -/m 2-2 2-1b'c 1-2a 4701 -/m 2-2 1-1 1-2a 5172 -/m 2-2 1-1 2-2 Associated with G551D 2 1 2 a Family genotyping b Subtraction of the KM19(2)-XV2c(1) haplotype (b) associated with the AF508deletion (Reis et al. 1990) c Recombination (illustrated in Fig. 2) d Not distinguished in population studies on account of strong linkage disequilibrium (Northrup et al. 1989) Results from a combined haplotype analysis are shown in Table 2. Login to comment 39 ABCC7 p.Gly551Asp ABCC7 p.Arg553* Evaluation of homozygous alleles, family genotyping or subtraction of the well-established AF508- associated haplotype (Krawczak et al. 1988; Wagner et al. 1990) from heterozygotes revealed the haplotypes associated with mutations R553X and G551D. Login to comment 40 ABCC7 p.Gly551Asp One possible exception was found for G551D in a family exhibiting recombination between KM19 and XV2C (see Fig. 2). Login to comment 41 ABCC7 p.Arg553* A detailed description of patient 1226, identified as a homozygote for the R553X mutation, will be presented elsewhere (Bal et al., in press). Login to comment 42 ABCC7 p.Arg553* R553X is associated with the 1(KM19)-l(XV2c)- 2(p J3.11) haplotype on all Caucasian chromosomes analysed. Login to comment 43 ABCC7 p.Gly551Asp This is consistent with these mutant alleles being identical by descent. However, on two chromosomes 1,1 1,2 II,1 [I,2 II,3 xvzc (1 ~) (1 2) (i 2)(1 ~) (i z) KMI9 1 2 2 1 1 2 2 2 2 2 MP6d9 1 2 2 I I 2 2 2 2 2 ~F508 - + - - - + - § - + b G551D - - + - - - + - + - Fig.2a, b. Pedigree (a) and genotypes (b) of the recombination bearing family. Login to comment 45 ABCC7 p.Arg553* For alleles in brackets,the phase could not be determined from American black CF patients, R553X was observed on a 2(KM19)-2(XV2c) haplotype, one of which additionally carried a 1(pJ3.11) allele. Login to comment 46 ABCC7 p.Arg553* ABCC7 p.Arg553* Were two R553X- bearing chromosomes with different marker haplotypes to be traced back generation by generation, then at least one of these lineages must have originated either in a recurrent mutation creating a new R553X substitution on a different haplotype background, or in recombination events, in this case involving markers on both sides of the CFTR gene. Login to comment 49 ABCC7 p.Arg553* If we assume that the population frequency of R553X (i.e. 10-3) has remained relatively constant over a reasonable period of time, then the likelihood for a recombination event can be estimated as Li = 10-3 x 10-4 x 10-2 = 10-9 per meiosis, neglecting RFLP allele frequencies. Login to comment 51 ABCC7 p.Arg553* Moreover, the C to T transition responsible for R553X is consistent with the model of methylation-mediated deamination. Login to comment 56 ABCC7 p.Gly551Asp In contrast to the situation described above, it can be demonstrated that all G551D mutations observed in our German population sample have a high probability of being identical by descent, despite the postulated occurrence of the one deviating haplotype. Login to comment 57 ABCC7 p.Gly551Asp G551D mutations result from a GGT to GAT substitution, a mutational event that has been estimated to occur at a rate of approximately 10-9 (Cooper and Krawczak 1990). Login to comment 77 ABCC7 p.Arg553* The R553X substitution was first described by Cutting et al. (1990) in two American black patients both of whom carried the mutation on identical haplotypes for 4 informative sites including KM19 and XV2c (both allele 2). Login to comment 89 ABCC7 p.Gly551Asp The haplotype found on 10 G551D bearing chromosomes (Cutting et al. 1990; this study) is homogeneous. Login to comment 95 ABCC7 p.Gly551Asp 1, assuming that the mother carries the CF gene bearing haplotype G551D-KM19(2)-XV2c(2). Login to comment 96 ABCC7 p.Gly551Asp Another possible explanation is germ line mosaicism, the mother carrying the haplotype G551D-KM19(2)-XV2c (1) but with a recombination taking place in one precursor cell during early development. Login to comment 98 ABCC7 p.Gly551Asp However, even assuming that the deviating haplotype is linked to the G551D mutation, the likelihood of recurrent mutation remains virtually the same as for identical haplotypes. Login to comment 99 ABCC7 p.Gly551Asp Only a limited number of patients bearing the G551D mutation have been examined so far, but the preliminary data justify the use of haplotype information in this case, e.g. if the rapid identification of the diesase-causing mutation is essential for diagnostic reasons. Login to comment