Use of denaturing gradient gel electrophoresis to detect point mutations in the factor VIII gene

Point mutations in the factor VIII gene are responsible for the majority of cases of hemophilia A, and only a small fraction of these mutations can be recognized by restriction endonuclease analysis. We have now used polymerase chain reaction and denaturing gradient gel electrophoresis to characterize single nucleotide substitutions in the factor VIII gene. Five regions of the gene were studied: exon 8, the 3' end of exon 14, exon 17, exon 18, and exon 24. A GC clamp was attached to the 5' PCR primer to allow detection of the majority of single base changes in DNA fragments ranging from 249 to 356 bp. Ten of eleven known point mutations were definitively separated. Fifty-two patients with unknown mutations were then studied by these methods, and the disease-producing mutation was found in three. First, we identified a new missense mutation in exon 14 which is the likely cause of hemophilia A in one patient (tyrosine changed to cysteine at amino acid residue 1709). Second, we found a new missense mutation in exon 18 in one patient (asparagine to aspartic acid at amino acid residue 1922). Third, a previously described mutation in exon 24 was detected (arginine changed to glutamine at amino acid residue 2209). In addition, a new polymorphic nucleotide substitution was found in intron 7. Moreover, these mutations can be detected when the GC-clamped PCR products from all five regions are run in the same denaturing gel. Our results indicate that denaturing gradient gel electrophoresis can be successfully applied to the analysis of point mutations in large genes whose transcripts are not readily available.

Characterization of a thrombin cleavage site mutation (Arg 1689 to Cys) in the factor VIII gene of two unrelated patients with cross-reacting material-positive hemophilia A

The molecular defect responsible for moderate and severe hemophilia A has been identified for two unrelated patients with the CRM-positive form of this disorder (factor VIII activity of 0.02 and 0.05 U/mL with factor VIII antigen of 0.87 and 2.20 U/mL). In both cases, the immunopurified dysfunctional factor VIII protein is abnormal, in that the 80 Kd light chain is not cleaved by thrombin at arginine-1689. The basis for this failure was identified by polymerase chain reaction amplification of exon 14 of the variant factor VIII genes and direct sequencing of the amplified products. In both cases, a single base substitution (C to T) was identified that produces an arginine to cysteine substitution at amino acid residue 1689. These data identify the molecular defects of the two identical factor VIII variant proteins. The dysfunctional factor VIII has been designated "Factor VIII-East Hartford," the residence of the patient in whom the defect was first identified.

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.

Phylogeny of human beta-globin haplotypes and its implications for recent human evolution

The evolutionary histories and relationships among African, Eurasian, and Pacific Island populations are investigated by using observations on five polymorphic restriction sites in the beta-globin gene cluster. We present new data on 222 chromosomes from a global sample and combine these with previously published observations on 591 chromosomes. It is shown that the data are rich in rare haplotypes and that rare variants are not helpful for standard methods of population structure analysis. Consequently, a new approach is developed. We first consider the phylogeny of beta-globin haplotypes. The roles of mutation, gene conversion, and recombination in the generation of haplotype diversity are specifically focused upon. The relationships among human populations are then inferred from the phylogenetic relationships among the haplotypes, their presence or absence, and frequencies within populations. Questions regarding whether or not a phyletic process can account for relationships among the major geographical populations and whether or not an extant human population exhibits the qualities that would be expected of an ancestral group are addressed. The results of this analysis support an African origin for modern Homo sapiens and a phyletic structuring of the major geographical regions. However, it is shown that divergence times for the various populations cannot be determined from these data.

MspI polymorphic site in intron 22 of the factor VIII gene in the Japanese population

A novel MspI DNA polymorphic site has been found in intron 22 of the human factor VIII gene. This site is informative almost exclusively in the Japanese population (heterozygosity 0.45) and will be of considerable importance in carrier detection and prenatal diagnosis of hemophilia A in this population.

Single-sperm typing: determination of genetic distance between the G gamma-globin and parathyroid hormone loci by using the polymerase chain reaction and allele-specific oligomers

The frequency of recombination between the G gamma-globin (HBG2) and parathyroid hormone (PTH) loci on the short arm of human chromosome 11 was estimated by typing greater than 700 single-sperm samples from two males. The sperm-typing technique employed involves the polymerase chain reaction and allele-specific oligonucleotide hybridization. Our maximum likelihood recombination fraction estimate of 0.16 (95%) confidence interval, 0.13-0.19) falls well within previous estimates based on family studies. With current technology and a sample size of 1000 sperm, recombination fractions down to approximately 0.009 can be estimated with statistical reliability; with a sample size of 5000 sperm, this value drops to about 0.004. Reasonable technological improvements could result in the detection of recombination frequencies less than 0.001.

Linkage to the Huntington's disease locus in a family with unusual clinical and pathological features

We used the anonymous DNA probe, D4S10 (G8), known to be linked to the Huntington's disease (HD) locus, to confirm inheritance at that locus in a family in whom most affected individuals had atypical clinical and pathological features. Their clinical features were similar to the Westphal variant (usually seen in juvenile-onset HD) but they had onset in adult life, and in contrast to juvenile-onset HD, their course of illness was prolonged. Most family members had been repeatedly misdiagnosed during life because of the absence of chorea and prominence of long-tract signs. In 2 patients who died, neuropathological examination at autopsy revealed prominent involvement of brainstem and spinal cord structures, and in 1, mild neostriatal atrophy relative to duration of the disease. The study demonstrates the usefulness of genetic linkage analysis as a diagnostic tool in families with atypical forms of HD. This method allows study of phenotypic variations that can be inherited at or near the HD locus and implies either multiple alleles at the locus gene, modifiers of a single allele, or another locus in the same region causing a dominantly inherited neurodegenerative disease.

Presymptomatic diagnosis of delayed-onset disease with linked DNA markers. The experience in Huntington's disease

Clinical medicine in the 21st century is almost certain to include wide-scale use of molecular genetic diagnostic tests. In September 1986, The Johns Hopkins University School of Medicine initiated a voluntary program of presymptomatic genetic testing for Huntington's disease for persons at 50% risk. DNA analyses using the D4S10 (G8), D4S43, and D4S95 locus probes have been performed for 55 people. Twelve of the tests have yielded positive results, 30 were negative, and 13 were uninformative. Initial reactions ranged from joy and relief to disappointment, sadness, and demoralization. Thus far, there have been no severe depressive reactions. Although the sample size is small, our data suggest that people who receive genetic test results cope well, at least over the short term, when the testing is performed in a clinical context that includes education, pretest counseling, psychological support, and regular follow-up.

Direct characterization of factor VIII in plasma: detection of a mutation altering a thrombin cleavage site (arginine-372----histidine)

An immunoadsorbent method has been developed for the direct analysis of normal and variant plasma factor VIII. Using this method, the molecular defect responsible for mild hemophilia A has been identified for a patient whose plasma factor VIII activity is 0.05 unit/ml, even though the factor VIII antigen content is 3.25 units/ml. Although the variant factor VIII has an apparently normal molecular mass and chain composition, the 92-kDa heavy chain accumulates when the variant protein is incubated with thrombin and the 44-kDa heavy chain fragment cannot be detected. In contrast, thrombin cleavage of the 80-kDa light chain to the 72-kDa fragment is normal. As these data indicate a loss of factor VIII cleavage by thrombin at arginine-372, the genetic defect was determined by polymerase-chain-reaction amplification of exon 8 of the factor VIII gene and direct sequencing of the amplified product. A single-base substitution (guanine----adenine) was identified that produces an arginine to histidine substitution at amino acid residue 372. These data identify the molecular basis of an abnormal factor VIII, "factor VIII-Kumamoto," that lacks procoagulant function because of impaired thrombin activation.

Characterization of a nondeleterious L1 insertion in an intron of the human factor VIII gene and further evidence of open reading frames in functional L1 elements

We have characterized an insertional event in IVS-10 of the factor VIII gene in a pedigree containing a hemophilia A patient (JH-25). The inserted DNA is a 5' truncated L1 element that is 681 bp long followed by a 3'66-bp poly(A) tract. The L1 element is inserted 154 bp 5' to the start of exon 11 and is flanked by a 13- to 17-bp target site duplication. The L1 insertion is present in four generations of the patient's family. The maternal grandfather who carries the insertion does not have hemophilia A, indicating that the insertion is not the cause of hemophilia A in the patient. We have sequenced this insertion and two previously reported de novo L1 insertions in the factor VIII gene in patients JH-27 (3785 bp) and JH-28 (2132 bp). The three nucleotide sequences differ by 0.2-0.8%. All three of these L1 insertions have open reading frames (ORFs) (1192, 642, and 157 aa) and the three derived amino acid sequences are 98-99% identical. The previously reported sequence similarity between L1 3' ORFs and the polymerase domain of reverse transcriptases is maintained in the ORFs of the JH-27 and JH-28 L1 insertions. The presence of open reading frames and the close sequence similarity of these recently inserted L1 elements provide indirect evidence for the existence of a set of functional L1 elements that encode one or more proteins necessary for their retrotransposition.

Hinf I polymorphism 3' to the human beta-globin gene detected by the polymerase chain reaction (PCR)

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Molecular mechanism in the formation of a human ring chromosome 21

We have characterized the structural rearrangements of a chromosome 21 that led to the de novo formation of a human ring chromosome 21 [r(21)]. Molecular cloning and chromosomal localization of the DNA regions flanking the ring junction provide evidence for a long arm to long arm fusion in formation of the r(21). In addition, the centromere and proximal long arm region of a maternal chromosome 21 are duplicated in the r(21). Therefore, the mechanism in formation of the r(21) was complex involving two sequential chromosomal rearrangements. (i) Duplication of the centromere and long arm of one maternal chromosome 21 occurred forming a rearranged intermediate. (ii) Chromosomal breaks in both the proximal and telomeric long arm regions on opposite arms of this rearranged chromosome occurred with subsequent reunion producing the r(21).

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.

Mild hemophilia A resulting from Arg-to-Leu substitution in exon 26 of the factor VIII gene

Polymerase chain reaction amplification and nucleotide sequencing were used to identify the molecular defect in a Japanese patient with mild hemophilia A and an alteration of a TaqI site in exon 26 of the factor VIII gene. The mutation was a G-to-T transversion in codon 2326 of the factor VIII gene resulting in an Arg-to-Leu substitution at amino acid 2307 of the protein. The mutation, which is not of the common CG-to-TG type, is at the same codon in which both nonsense and a different missense (Arg to Gln) have previously been observed.

Beta-thalassemia due to two novel nucleotide substitutions in consensus acceptor splice sequences of the beta-globin gene

We have identified two novel RNA-splicing mutations affecting a critical nucleotide (nt) in the acceptor consensus sequences at both the IVS-1/exon 2 and IVS-2/exon 3 junctions of the human beta-globin gene. Both mutations are single nt substitutions, T to G and C to A, at position -3 adjacent to the invariant AG dinucleotide. For the IVS-2/exon 3 mutation abnormal splicing into the cryptic splice site at IVS-2 nt 579 is documented. Identification of these two mutations provides further support for the importance of the location of specific nucleotides within the consensus sequences in splice site selection and RNA processing.

Homozygous beta-thalassemia without anemia

A 37-year-old man of Guyanese origin was found to have homozygous beta-thalassemia without anemia. There were no physical stigmata of thalassemia. The hematocrit value was 41 to 45.8, the mean corpuscular volume was 61 fL, and the mean corpuscular hemoglobin was 18.9 pg. The HbF was 45% with a G gamma:A gamma ratio of 3:1. An acid elution preparation of the peripheral blood showed heterogeneous distribution of HbF, but all erythrocytes stained for fetal hemoglobin. The beta/alpha synthesis ratio in the peripheral blood was 0.25; the (beta + gamma)/alpha ratio was 0.55. Haplotype analysis revealed homozygosity for the -+-+ + + + pattern (Senegal, type IX) at seven polymorphic restriction sites within the beta-like gene complex. Digestion of DNA with Xmnl indicated that the -158 C-to-T transition was present in both beta-globin gene clusters. Oligomer hybridization analysis demonstrated homozygosity for the -29 A-to-G mutation in the beta-globin promoter region. Although this form of thalassemia can cause transfusion-requiring anemia, the high-HbF, high-G gamma phenotype associated with the linked +-+ + subhaplotype and -158 C-to-T substitution appears to have ameliorated the disease in this subject.

Accuracy and limitations of pulsed field gel electrophoresis in sizing partial deletions of the factor VIII gene

Pulsed field gel electrophoresis (PFGE) has been recently used to separate DNA fragments ranging from 100 to 2000 kb in size. In order to assess the accuracy of the sizes of the DNA fragments and the resolving capability of this technique, we used PFGE combined with Southern blotting and probe hybridization techniques to determine the size and approximate location of four partial deletions of the factor VIII gene. This gene was chosen because of its large size (186 kb) and the availability of hemophiliac patients with well-characterized partial deletions. The sizes of three deletions estimated by PFGE (55 kb, 60 kb and 133 to 145 kb) were within 10% of the sizes calculated from conventional restriction analysis. Therefore, concatemers of lambda DNA and intact chromosomal DNA of Saccharomyces cerevisiae provide a relatively accurate system (within 10%) for sizing mammalian DNA fragments that are 100 to 550 kb in size. However, analysis of the fourth deletion (9 to 12 kb) revealed that it is difficult to detect changes in the size of mammalian DNA fragments of 8% or less using Southern blotting and PFGE.

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

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.

Molecular basis and prenatal diagnosis of beta-thalassemia

The molecular characterization of mutations producing beta-thalassemia in world populations is nearing completion. We expect that new rare alleles in thoroughly studied groups and other alleles in less studied groups, eg, inhabitants of New Guinea, Latin America, and certain Pacific Islands, will be found. Knowledge of the molecular basis of the disease and new technology that allows rapid detection of single nucleotide changes in genomic DNA have led to the reality of prenatal diagnosis by direct mutation detection even in the heterogeneous US population. Programs aimed at prevention of beta-thalassemia should be facilitated by these developments.

Macrorestriction mapping of COL4A1 and COL4A2 collagen genes on human chromosome 13q34

The genes for the alpha-1 and alpha-2 chains of type IV collagen (COL4A1 and COL4A2) map to the same chromosomal band (13q34) and have a high degree of nucleotide homology. We have used pulsed field gel electrophoresis and cloned COL4A1 and COL4A2 DNA fragments as molecular probes to construct a 1200-kb macrorestriction map which encompasses both genes. The two genes are located within a 340-kb region with the 3' end of COL4A2 and the 5' region of COL4A1 separated by at least 100 kb but not more than 160 kb. These genes, therefore, are two members of a gene cluster on chromosome 13q34.

Diagnosis of sickle cell anemia and beta-thalassemia with enzymatically amplified DNA and nonradioactive allele-specific oligonucleotide probes

We have developed a simple and rapid nonradioactive method for detecting genetic variation and have applied it to the diagnosis of sickle cell anemia and beta-thalassemia. The procedure involves the selective amplification of a segment of the human beta-globin gene with oligonucleotide primers and a thermostable DNA polymerase, followed by hybridization of the amplified DNA with allele-specific oligonucleotide probes covalently labeled with horseradish peroxidase. The hybridized probes were detected with a simple colorimetric assay. We demonstrated the usefulness of this method in a retrospective analysis of two pregnancies at risk for beta-thalassemia and one at risk for sickle cell anemia, as well as in an analysis of nine DNA samples simulating three family sets.

New amber mutation in a beta-thalassemic gene with nonmeasurable levels of mutant messenger RNA in vivo

We have identified a beta-thalassemia gene that carries a novel nonsense mutation in a Chinese patient. This mutation, a G to T substitution at the first position of codon 43, changes the glutamic acid coding triplet (GAG) to a terminator codon (TAG). Based on oligonucleotide hybridization studies of 78 Chinese and Southeast Asian beta-thalassemia chromosomes, we estimate that this mutation accounts for a small minority of the beta-thalassemia mutations in that population. Study of the expression of this cloned gene in a transient expression system demonstrated a 65% decrease in levels of normally spliced mutant beta-globin mRNA. However, the study of reticulocyte RNA isolated from an individual heterozygous for this mutation demonstrated a total absence of this mutant mRNA in vivo. The basis for this big discrepancy between the level of accumulated mRNA in vivo and in vitro is probably the result of differences in the stabilities of the mutant mRNA in erythroid cells.