First molecular characterization of an unequal homologous alu-mediated recombination event responsible for hemophilia

The large number of Alu repeats in the human genome provides abundant opportunities for unequal homologous recombination events that are responsible of several human diseases. We here describe a novel large FVIII gene deletion from a severe hemophilia A patient in which Alu-repetitive elements are directly involved in the origin of the mutation. Using a long-fragment PCR method, a approximately 23 kb deletion was delimited between introns 24 and 25. The resulting FVIII gene had a hybrid 2317-bp intron and lacked exon 25. Absence of exon 25 was confirmed at the RNA level. Multiple sequence alignment of this hybrid intron and normal introns 24 and 25 provided evidence of an homologous recombination event between two Alu repeats and the exact breakpoints were delimited to a 16 bp region. To our knowledge, this is the first report of hemophilia caused by unequal homologous Alu/Alu recombination. This mechanism, commonly related to genetic human disorders, may be involved in a significant number of hemophilia cases considering that FVIII is coded by an Alu-rich gene.     

Factor IX Chongqing: a new mutation in the calcium-binding domain of factor IX resulting in severe hemophilia B

A Chinese patient with sporadic, severe hemophilia B was found to have a low level of total factor IX antigen (3.5 U/dl), but less apparent antigen in an assay using a calcium-dependent antibody fraction (1.1 U/dl). This suggested a defect in the factor IX Gla domain coded mainly by exon 2 of the factor IX gene. Exon 2 was therefore amplified and sequenced. An A to T substitution was found at nucleotide 6455 of the patient's factor IX gene. This transversion changes the codon for Glu 27 in normal factor IX to a codon for Val. Since Glu 27 becomes an essential Gla residue, the defect should result in altered calcium-binding or calcium-dependent conformation of the patient's factor IX. The introduction of a hydrophobic side chain also appears to affect the hemophilic protein's stability. In leukocyte DNA from the patient's mother, the nucleotide sequence of exon 2 was entirely normal. Thus, barring somatic mosaicism within her germ cells, the new mutation occurred in oogenesis of her ovary.     

F175S change and a novel polymorphism in presenilin-1 gene in late-onset familial Alzheimer's disease

We analyzed at the molecular level with presenilin-1 (PS-1) and apolipoprotein E (apoE) genotyping the affected subjects and asymptomatic relatives of an Italian family with several members affected by late-onset familial Alzheimer's disease (AD). The screen for PS-1 gene mutations revealed a novel missense substitution phenylalanine 175 to serine in 1 of the affected individuals and 2 asymptomatic sons of the patient. This change was not found in other relatives of this family, as well as in 60 individuals with sporadic late-onset AD and 40 normal controls. Furthermore, a GG/TT substitution in the 3' end of intron 6 at the boundary with exon 7 was found in all relatives of the second and third generations of this family. All the affected relatives were female homo- or heterozygotes for apoE epsilon4 allele. This study provides evidence that a PS-1 gene missense change does not necessarily associate with early-onset disease, and can occur in single cases affected by late-onset disease.     

The utility of activated partial thromboplastin time (aPTT) clot waveform analysis in the investigation of hemophilia A patients with very low levels of factor VIII activity (FVIII:C)

The lower detection limit of the conventional one-stage aPTT based clotting assay for determining FVIII:C levels is generally 1.0-2.0 IU/dl. Consequently, it has been impossible to study the clinical significance of levels of FVIII:C less than 1.0 IU/dl. Using a photo-optical automated coagulation analyzer, the Organon Teknika MDA II, we have performed qualitative and quantitative aPTT waveform analysis and measured FVIII:C levels by automated one-stage aPTT clotting assay in 36 severely affected Hemophilia A patients. Qualitative waveform analysis showed clear evidence of individual differences in the waveform profile suggesting differing coagulant activity from patient to patient. The FVIII:C level was less than 0.2 IU/dl in 23 cases and levels of FVIII:C between 0.2 and 1.0 IU/dl could be discriminated in 13 patients. The FVIII:C level in these patients was closely correlated with the minimum value of the second derivative of the aPTT waveform (Min2). This is a measure of the acceleration of change in optical transmission at the initiation of coagulation. Furthermore, the correlation of the     

Association of ADAMDEC1 haplotype with high factor VIII levels in venous thromboembolism

A suggestive locus on chromosome 8 could be shown to be associated with familial high factor VIII (FVIII) levels in venous thromboembolism. The ADAMDEC 1 gene is a candidate expressing an ectodomain sheddase. However, the ectodomain of the clearance receptor for FVIII, the low-density lipoprotein receptor-related protein (LRP), is subject to proteolysis by metalloproteases like ADAMDEC1. Other LRP-interacting proteins are lipoprotein lipase (LPL) and t-PA. For an association study, 165 thrombotic patients with high FVIII levels (from the MAISTHRO, i.e. Main-Isar-thrombosis register) were included. All patients with known causes for high FVIII levels had been previously excluded. The patients were compared with 214 healthy blood donors. Polymorphisms with usually a minor allele frequency >5%, i.e. 24 SNPs and two insertion/deletion polymorphisms of LPL gene, eight SNPs of the t-PA gene, and five SNPs of the ADAMDEC1 gene, were analyzed. Haplotype differences were calculated using PHASE. A new polymorphism in intron 7 of the t-PA gene with a minor allele frequency of 2.2% was identified. Analysis of each SNP by the Cochrane-Armitage trend test did not show any significant association between genotype and disease status. Interestingly, the ADAMDEC1 haplotype (rs12674766, rs10087305, rs2291577, rs2291578, rs3765124) differed between cases and controls (p = 0.04). In particular, the TGTGG haplotype showed a difference. In conclusion, the ADAMDEC 1 haplotype may indicate an underlying mechanism for high FVIII levels. The only moderate linkage disequilibrium may be due to a possible causal polymorphism in distant introns or the promoter region against a polygenic background.     

Autosomal dominant Emery-Dreifuss dystrophy due to mutations in rod domain of the lamin A/C gene

BACKGROUND: Autosomal dominant Emery-Dreifuss muscular dystrophy (EDMD-AD) is a disorder characterized clinically by humeropelvic weakness, contractures, and cardiomyopathy, and genetically by mutations in the lamin A/C gene on 1q21.2-q21.3. Of the 14 lamin A/C gene mutations reported thus far, the four involving the rod domain have been associated with isolated cardiomyopathy and conduction-system disease. This is the first report of rod domain mutations in patients with the full EDMD-AD phenotype. METHODS: Clinical, pathologic, and genetic data are provided on two families with EDMD-AD. RESULTS: In both families, the full clinical spectrum of EDMD-AD was demonstrated. For the proband in family 1, sequence analysis detected a mutation within exon 2 of the lamin A/C gene. The missense mutation was due to a A448C base substitution causing a Thr150Pro amino acid change. For the proband of family 2, sequence analysis detected an in-frame 3-bp deletion (AAG 778-780 or 781-783) removing one of two adjacent lysine residues (K 260 or 261) of exon 4. Both mutations were in the central rod domain of the lamin A/C gene. CONCLUSIONS: Mutations in the rod domain of the lamin A/C gene may cause the full clinical spectrum of EDMD-AD.     

X-linked myotubular myopathy due to a complex rearrangement involving a duplication of MTM1 exon 10

X-linked myotubular myopathy is a predominantly severe congenital myopathy with central nuclei on muscle biopsy due to mutations in the MTM1 gene encoding myotubularin. We report a boy with typical features of X-linked myotubular myopathy. Sequencing of the MTM1 gene did not reveal any causative mutations. Subsequent MLPA analysis identified a duplication of MTM1 exon 10 both in the patient and his mother. Additional quantitative fluorescent PCR and long-range PCR revealed an additional large deletion (2536bp) within intron 10, 143bp downstream of exon 10, and confirmed the duplication of exon 10. Our findings suggest that complex rearrangements have to be considered in typically affected males with X-linked myotubular myopathy.     

A new splice site mutation in the SMN1 gene causes discrepant results in SMN1 deletion screening approaches

In most patients with infantile spinal muscular atrophy (SMA) both exons 7 and 8 of the SMN1 gene are deleted, but the deletion may also be restricted to exon 7. We report on an SMA type I patient who was initially diagnosed to be homozygous for an exon 7 deletion only. However, multiplex ligation-dependent probe amplification (MLPA) analyses revealed a heterozygous deletion of exons 7 and 8 of the SMN1 gene. By sequencing a new subtle splice site mutation (IVS6-2A>G) was identified. This variant affects the target sequence of oligonucleotides of all applied tests in a way that it has contrary effects on the efficiencies of the different assays. The results have major impacts on genetic counselling and carrier detection of the patient's paternal relatives.     

Molecular analysis of the duchenne muscular dystrophy gene in patients with becker muscular dystrophy presenting with dilated cardiomyopathy

Molecular analysis of the Duchenne muscular dystrophy (DMD) gene was performed on 4 unrelated patients with Becker muscular dystrophy (BMD) presenting with dilated cardiomyopathy. Two patients with a deletion involving exon 1 were quite unique in that they developed fatal myocardial involvement in their teens, despite the absence of significant muscular weakness. The deletion found in these patients comprised the 3′-end of exon 1 and the greater part of intron 1. Two other patients with a deletion of exon 47 showed progressive muscular atrophy and weakness; they were considered to be typical BMD in both clinical features and the type of gene deletion. We speculate that a deletion around exon 1 may severely damage the expression and/or the function of dystrophin selectively in cardiac muscle, but not in skeletal muscle. © 1993 John Wiley & Sons, Inc.     

Intronic mutation in the PGK1 gene may cause recurrent myoglobinuria by aberrant splicing

A 33-year-old man with mental retardation and recurrent myoglobinuria demonstrated a deficiency in the phosphoglycerate kinase 1 (PGK1) activity of his muscles and erythrocytes. His PGK1 gene had intronic G-to-A substitution 5 nucleotides downstream from the normal exon 7 5' splice site (IVS7 + 5 G>A). This novel mutation results in a frame shift due to the insertion of 52 bp of intron 7 in the mature mRNA by aberrant splicing.     

Characterisation of two novel large F8 deletions in patients with severe haemophilia A and factor VIII inhibitors

Large deletions are found in approximately 5% of patients with severe haemophilia A, but only a few deletion breakpoints have been characterised precisely so far. In this study we characterised the deletion breakpoints of two patients with severe haemophilia A, large deletions and factor VIII (FVIII) inhibitors, and subsequently established deletion-specific assays for the identification of carriers. Patient 1 had a deletion of 37,410 bp comprising exon 1 and the F8 promoter region, and a 5 bp homology (GGGCC) is present at the chromosomal fusion site. In patient 2, a deletion of 22,230 bp including parts of intron 25, exon 26 and 3'-UTR was identified. No homologous repetitive elements were found at the breakpoints. However, both breakpoints were located within long terminal repeats of endogenous retroviruses and the DNA motif TTTAAA - known to be able to bend DNA molecules - was identified at the centromeric breakpoint. By deletion-specific PCR experiments we were able to identify a heterozygous state in mother 2 (carrier) while mother 1 presented only with wild-type alleles (non-carrier). Both deletions are most likely created by DNA double strand breaks and subsequent DNA repair by the non-homologous end joining DNA repair pathway (NHEJ). The exact identification of the deletion breakpoints provides a reliable diagnostic tool for carrier identification in affected families by means of a deletion-specific PCR.     

Two mutations of the factor IX gene including a donor splice consensus deletion and a point mutation in a Dutch patient with severe hemophilia B

The abnormal factor IX gene of a patient with severe hemophilia B (hemophilia B Ursem) was selected for study. All of the coding and their flanking regions and parts of the 5'- and 3'-untranslated regions of the factor IX gene were amplified from the patient's genomic DNA by using the polymerase chain reaction (PCR). By analyzing the nucleotide sequence of the PCR products we have identified two mutations in the patient's factor IX gene, viz. a tetranucleotide deletion (GAGT, nt 6492 to 6495) or (TGAG, nt 6491 to 6494) in the 5'-donor splice site consensus at the exon 2-intron B boundary, and a point mutation at nucleotide 31103 in the catalytic domain (exon 8) of factor IXa, which changes the codon for valine 328 (GTT) to one for isoleucine (ATT). PCR-amplified exon 8 from 45 normal males and 55 normal females had the codon for valine-328. We propose that the deletion within the donor splice-site consensus is the cause of the disease in this individual, whereas the substitution of valine-328 by isoleucine may be a neutral variant which is, at least, very rare in the normal population. In a family study the DNA sequence of the patient's mother shows both the G to A transition in exon 8 and the 5'-donor splice consensus deletion in intron B in one allele.     

COL6A1 genomic deletions in Bethlem myopathy and Ullrich muscular dystrophy

We have identified highly similar heterozygous COL6A1 genomic deletions, spanning from intron 8 to exon 13 or intron 13, in two patients with Ullrich congenital muscular dystrophy and the milder Bethlem myopathy. The 5' breakpoints of both deletions are located within a minisatellite in intron 8. The mutations cause in-frame deletions of 66 and 84 amino acids in the amino terminus of the triple-helical domain, leading to intracellular accumulation of mutant polypeptides and reduced extracellular collagen VI microfibrils. Our studies identify a deletion-prone region in COL6A1 and suggest that similar mutations can lead to congenital muscle disorders of different clinical severity.     

Identification and analysis of new sequence variants in the human tryptophan hydroxylase (TpH) gene

The tryptophan hydroxylase (TpH) gene codes for the rate-limiting enzyme in serotonin biosynthesis. It is one of the major candidate genes for psychiatric and behavioral disorders. A polymorphism in TpH intron 7 has been shown to be associated with suicidal attempts, aggressive behavior and psychiatric illnesses. By systematically screening the TpH genomic sequence, we identified and confirmed an earlier report of four variants in the promoter region and localized six new sequence variants, ie two in intron 1b, one in exon 1c, one in intron 8, one in intron 9 and a microsatellite in the 3' region, 5687 bp downstream of the last exon 11. We analyzed these polymorphisms, as well as the one in intron 7, by Single Strand Conformation Analysis, microsatellite or restriction analysis in a collection of 175 West European Caucasian healthy subjects. The four variants in the promoter region are in complete linkage disequilibrium (frequencies of G-T-G-T and T-C-A-G haplotypes are 0. 41 and 0.59, respectively). Deletion of GTT in intron 1b is rare (0. 7%) and so not informative. The rarer allele T of intron 1b polymorphism T3792A has a frequency of 0.34 and is in partial linkage disequilibrium with the more common alleles of intron 7, 8 and 9. The polymorphisms of these three introns are in complete linkage disequilibrium and the frequencies of haplotypes A-T-C and C-C-T are 0.36 and 0.64 respectively. We detected 10 different alleles in the microsatellite localized in the 3' region; allele '194' is in partial linkage disequilibrium with haplotype A-T-C of introns 7, 8, and 9. Analysis of these different polymorphisms will constitute an important tool for future studies between the TpH gene and psychiatric disorders. Molecular Psychiatry (2000) 5, 49-55.