Molecular genetic analysis of factor X deficiency: gene deletion and germline mosaicism

Summary A case of homozygous factor X deficiency arising from the inheritance of two non-identical gene deletions from heterozygous parents is described. One, a partial gene deletion, was localized to exons VII and VIII by a combination of Southern blotting and polymerase chain reaction (PCR) amplification of exon sequences. The other deletion, of maternal origin, probably involves the entire factor X gene. Restriction fragments associated with the exon VII + VIII deletion were present in three siblings including the homozygous proband. These fragments were however absent from the somatic cells of the father, a finding consistent with germline mosaicism.     

Somatic origin of inherited haemophilia A

Summary We found a partial deletion of the clotting factor VIII gene of about 2000 bp, spanning exon 5 and part of intervening sequence 4 and 5 in an isolated patient with severe haemophilia A. The mother of the patient, who appeared to be a non-carrier on the basis of coagulation assays and restriction fragment length polymorphism analysis in the family, turned out to be a mosaic for the deletion, not only in her germ cells, but also in various somatic cells. These findings suggest that the mutation is the result of an event in early embryogenesis. If mosaicism for a mutation, either gonadal or somatic, proves to be a common phenomenon in human genetics, it is imperative to reconsider genetic risks for (future) sibs of any apparently new mutant of a hereditary disease.     

Restriction endonuclease mapping of six novel deletions of the factor VIII gene in hemophilia A

Summary Hemophilia A is an X-linked disease of blood coagulation caused by deficiency of factor VIII. Using cloned cDNA, genomic and synthetic oligonucleotide factor VIII probes, we have identified six novel partial gene deletions in patients with severe hemophilia A. We have previously reported six other deletions of the factor VIII gene. The number of gross molecular defects (deletions, insertions) in the factor VIII gene in our series of 240 patients is 17 (3 insertions and 2 complicated deletions will be described elsewhere). No association was observed between the size or location of the deletions and the presence of inhibitors to factor VIII. No deletion breakpoint hotspots have been identified by restriction analysis. The parental origin of several of the deletions was determined.     

Moderately severe hemophilia A resulting from Glu----Gly substitution in exon 7 of the factor VIII gene.

To define the molecular basis of a TaqI site alteration in the factor VIII gene of a patient with moderately severe hemophilia A, we used a combination of genomic amplification followed by direct sequencing and oligonucleotide hybridization, to demonstrate an A-to-G substitution in exon 7 (codon 291) of this gene. This mutation generates a Gly in place of Glu at amino acid 272 of the mature factor VIII protein. The mutation arose de novo in a germ cell of the patient's mother.     

First experiences in application of RFLP analysis for carrier detection in preparation of prenatal diagnosis of hemophilia A in the GDR

The application of the intragenic probe F8 e16-19 of factor VIII gene is reported for carrier detection in preparation of prenatal diagnosis of hemophilia A in a family at risk. The proband's mother is heterozygous for the Bcl I polymorphism and prenatal diagnosis can be offered to this family.     

A deletion/insertion leading to the generation of a direct repeat as a result of slipped mispairing and intragenic recombination in the factor VIII gene

A deletion/insertion in the human factor VIII gene was found in a patient with severe hemophilia A; 316 bp were removed, viz., those enclosing part of intron 15 and the first 7 bp of exon 16. In addition to the deletion, 6 bp were added to the deletion breakpoints; this resulted in the duplication of an existing 13-bp unit. Thus, an overlapping 13-bp direct repeat was generated at the deletion junction. Moreover, the deleted fragment itself was flanked by two homologous 6-bp sequences, one unit being lost by the deletion. A combination of slipped mispairing during replication and an intragenic recombination is discussed to describe this deletion/insertion process. Received: 4 January 1999 / Accepted: 22 March 1999     

Escherichia coli endonuclease VIII: cloning, sequencing, and overexpression of the nei structural gene and characterization of nei and nei nth mutants.

Escherichia coli possesses two DNA glycosylase/apurinic lyase activities with overlapping substrate specificities, endonuclease III and endonuclease VIII, that recognize and remove oxidized pyrimidines from DNA. Endonuclease III is encoded by the nth gene. Endonuclease VIII has now been purified to apparent homogeneity, and the gene, nei, has been cloned by using reverse genetics. The gene nei is located at 16 min on the E. coli chromosome and encodes a 263-amino-acid protein which shows significant homology in the N-terminal and C-terminal regions to five bacterial Fpg proteins. A nei partial deletion replacement mutant was constructed, and deletion of nei was confirmed by genomic PCR, activity analysis, and Western blot analysis. nth nei double mutants were hypersensitive to ionizing radiation and hydrogen peroxide but not as sensitive as mutants devoid of base excision repair (xth nfo). Single nth mutants exhibited wild-type sensitivity to X rays, while nei mutants were consistently slightly more sensitive than the wild type. Double mutants lacking both endonucleases III and VIII exhibited a strong spontaneous mutator phenotype (about 20-fold) as determined by a rifampin forward mutation assay. In contrast to nth mutants, which showed a weak mutator phenotype, nei single mutants behaved as the wild type.     

Screening for nonsense mutations in patients with severe hemophilia A can provide rapid,direct carrier detection

Summary Despite marked genetic heterogeneity in families with hemophilic patients, transition mutations in CG dinucleotides occur frequently. Of 71 CG dinucleotides in the factor VIII cDNA, a C-to-T transition in 12 would lead to a new Stop codon (CGA to TGA). Using restriction enzyme digestion of 11 amplified DNA fragments, seven point mutations were localized among 60 patients with severe hemophilia A. Five were detected as loss of a natural or introduced TaqI site at codons -5, 583, 1941, 2116, and 2209 and were confirmed as CGA (Arg) to TGA (Stop) nonsense mutations by DNA sequencing. A novel C-to-T nonsense mutation was detected as loss of the RsaI site at codon 1966 and confirmed by sequence in two unrelated individuals. Two partial gene deletions were detected as selective failure to amplify exon 1 and exons 15–22, respectively. In an additional (61st) patient who was subsequently found to have mild (instead of severe) hemophilia, digests suggested a mutation in codon 1696. Upon sequencing, this codon contained a novel missense mutation, a C-to-G transversion changing CGA (Arg 1696) to GGA (Gly). In four families with women available for testing, carrier status was rapidly determined by direct screening for the point mutation. In two of three with sporadic occurrences, the mother was a carrier as were two of four sisters. In the other family, the mother and a sister were homozygous for the TaqI cleavage site in their amplified exon 24 fragment, indicating a de novo C-to-T transition in codon 2209 in the patient's factor VIII gene. This final patient's sister was a noncarrier even though by linkage analysis she inherited the same factor VIII gene as her brother.These results have already been published in part in abstract form: Reiner AP, Thompson AR (1990) Circulation Research 82:304     

Characterization of mutations in the factor VIII gene by direct sequencing of amplified genomic DNA

In order to search for mutations resulting in hemophilia A that are not detectable by restriction analysis, three regions of the factor VIII gene were chosen for direct sequence analysis. Short segments of genomic DNA of 127 unrelated patients with hemophilia A were amplified by polymerase chain reaction. A total of 136,017 nucleotides were sequenced, and four mutations leading to the disease were found: a frameshift at codon 360 due to deletion of two nucleotides (GA), a nonsense codon 1705 due to a C----T transition, and two missense codons at positions 1699 and 1708. The first missense mutation (A----T) results in a Tyr----Phe substitution at a putative von Willebrand factor binding site. The second results in an Arg----Cys substitution at a thrombin cleavage site. In addition, we identified three rare sequence variants: a silent C----T transition at codon 34 which does not result in an amino acid change, a G----C change at codon 345 (Val----Leu), and an A----G change at the third nucleotide of intron 14. Direct sequence analysis of amplified DNA is a powerful but labor-intensive method of identifying mutations in large genes such as the human factor VIII gene.     

Thrombin cleavage analysis of a novel antihaemophilic factor variant, factor VIII delta II

Factor VIII delta II is a genetically engineered deletion variant of factor VIII expressed by recombinant Chinese hamster ovary cells, in which a major portion of the central (B) domain and a part of the light chain (Pro771-Asp1666) are missing. After immunoaffinity purification, the kinetics of thrombin cleavage of the novel molecule was analysed by SDS/PAGE, Western blotting and N-terminal amino acid sequencing. Thrombin first cleaves factor VIII delta II at Arg740-Ser741 to generate the 90-kDa heavy chain and an 80-kDa fusion polypeptide consisting of the remaining portion of the B domain and the 73-kDa light chain. The 90-kDa fragment is further cleaved, giving rise to 50-kDa and 40-kDa fragments while the 80-kDa fragment generates a 71/73-kDa doublet. The 71/73-kDa doublet, 50-kDa and 40-kDa fragments were further analysed by N-terminal amino acid sequencing and found to correspond to the predicted amino acid sequences. Our study shows that, in spite of the 900 amino acid deletion present in factor VIII delta II, the essential structural elements required for thrombin activation are conserved.     

Characterisation of a 5-bp deletion in exon 4 of the factor VIII gene: concordance with slipped-mispairing at DNA replication

In an attempt to characterize disease producing mutations in the factor VIII gene we screened exons 4, 7, 8, 11, 12 and 16 by PCR-SSCP (polymerase chain reactionsingle strand conformation polymorphism), in 12 randomly selected haemophilia A patients. These exons were chosen because they have been reported to harbour a disproportionately high number of mutations relative to their size. Using this strategy we detected a frame-shifting 5-bp deletion (TACCT, involving nucleotides 519–523), which is predicted to result in a severely truncated factor VIII polypeptide, terminating approximately midway through the conserved A1 domain and resulting in the observed severe phenotype. We also showed that the sequence in the vicinity of the observed deletion is concordant with the modified slipped-mispairing at DNA replication model of Krawczak and Cooper.     

A case of female hemophilia with a 46,XXr karyotype studied with X-chromosome DNA probes

Summary A case of female hemophilia with a 46,XXr/45,X karyotype and signs of Turner syndrome, has been followed for the past 10 years. One of her brothers also has hemophilia A. A study with polymorphic DNA probes located in the Xq27-qter region has enabled us to demonstrate that the ring chromosome is of paternal origin and that the factor VIII gene region is deleted. The hemizygous state allowed expression of the hemophilia A mutation, present on the morphologically normal X chromosome, inherited from her carrier mother.     

A complete deletion of the factor IX gene and new TaqI variant in a hemophilia B kindred

Summary We report a hemophilia B kindred in which the proband has a complete deletion of the factor IX gene extending a minimum of 80 kilobase pairs (kb) 3 of the gene. This individual has severe factor IX deficiency with no detectable circulating factor IX protein. In common with one previous report, despite a total deletion of the factor IX gene, this patient has not developed antibodies to factor IX. The mother of the proband was found to have a new TaqI variant of the factor IX gene on the nondeletion-bearing X chromosome. The location of the altered TaqI site was found to be 5 of exon IV between residues 9731-9734 and does not affect the function of the factor IX protein. The familial natures of both the variant allele and the deletion were established. In addition a study of this kindred at the DXS99 locus demonstrated the first reported recombination event between this site and the factor IX gene.     

A very small frame-shifting deletion within exon 19 of the Duchenne muscular dystrophy gene

We report the molecular characterization of a Japanese Duchenne muscular dystrophy (DMD) patient. The analysis of genomic gene by polymerase chain reaction indicates that the individuals have a limited deletion within an amplified region, which encompasses exon 19 of DMD gene. The amplified region was sequenced. Comparison of the deletion joint sequence with the normal amplified region sequence indicates that both 5' and 3' deletion end points are present within exon 19 and the deletion removes total 52 bp out of 88 bp of exon 19. Both his mother and sister are carriers of the deletion-containing allele. The mutation introduces a termination codon at residue 791 in exon 20, and is predicted to result in the production of a severely truncated protein. This sort of deletion (designated as DMD-Kobe) might be classified as a new type of DMD gene abnormality.