Regional localization on the human X chromosome and polymorphism of the coagulation factor IX gene (hemophilia B locus)

Current Status and Challenges in Delivering Comprehensive Care for Patients with Hemophilia

The importance of comprehensive care as a treatment strategy for patients with hemophilia is recognized worldwide. Comprehensive care entails addressing full spectrum of medical and psychological aspects impacting both patients and their families. The primary objective of comprehensive care for individuals with hemophilia is to enable them to lead their daily lives just as anyone else would. To achieve this goal, it is necessary to have a positive and collaborative approach across various healthcare disciplines. This extends beyond clinical specialists, encompassing pediatricians, hematologists, orthopedic surgeons, dental and oral surgeons, gynecologists, nurses, physical therapists, clinical psychologists, and other professionals from diverse fields. This review article discusses the current status and challenges associated with comprehensive care for patients with hemophilia. We categorize these challenges as follows: hemophilic arthritis, rehabilitation, oral care, transitioning from pediatric to adult care, addressing carrier issues, and providing psychological care. There is still substantial work to be undertaken in addressing these hurdles and advancing the quality of comprehensive care for hemophilia patients.

Genetic analysis of carrier status in female members of Japanese hemophilia families

BACKGROUND

Genetic characteristics and genetic carrier diagnosis in Japanese hemophilia female carriers have not been evaluated.

OBJECTIVES

To provide genetic information on Japanese hemophilia female carriers and demonstrate the advantages of genetic testing in carrier diagnosis.

METHODS

DNA sequencing combined with long polymerase chain reaction for inversion and multiplex ligation-dependent probe amplification for large mutations.

RESULTS

Genetic analysis was performed in 69 male hemophiliac patients (48 hemophilia A [HA] and 21 hemophilia B [HB]) and 112 female family members (FFM) (80 from 50 families with HA and 32 from 22 families with HB). In 72 hemophiliac families, the identified F8 mutations were inversion (42%), missense (26%), and other variations (32%), while 74% of F9 mutations were point mutations. Among the 112 FFM, 53/80 (66%) with HA and 21/32 (66%) with HB were diagnosed genetically as carriers based on detection of heterozygous mutations. Low factor VIII activity (FVIII:C) levels (<50 IU/dL) were detected in only 10% of gene-confirmed carriers, suggesting that FVIII:C is not suitable for HA carrier prediction. Low FVIII/von Willebrand factor ratio (<0.9) was observed in 67% of gene-confirmed carriers. Half of the gene-confirmed HB carriers had low FIX:C (<60 IU/dL). Importantly, 32 mothers of 37 sporadic cases (86%) (24/27 [89%] HA and 8/10 [80%] HB) showed the relevant mutations, suggesting low incidence of de novo mutations in males.

CONCLUSIONS

This study is the first to provide genetic information on Japanese hemophilia female carriers. Gene analysis is the gold standard for carrier diagnosis as it well identifies undetected female carriers based on pedigree information and hemostatic measurements.

Comprehensive analysis of phenotypes and genetics in 21 Chinese families with haemophilia B: characterization of five novel mutations

Molecular characterization of haemophilia B (HB) at the factor IX gene (F9) is essential to establish diagnosis, confirm genotype-phenotype correlations and to advise in genetic counselling. This study aimed to identify the causative mutations in 21 Chinese families with HB and to analyse the association of these mutations with clinical phenotype. Phenotypic analyses were performed using one-stage assay for factor IX (FIX) activity (FIX: C) and enzyme-linked immunosorbent assay for FIX antigen (FIX: Ag). Direct sequencing of the F9 gene was carried out. For those suspected to have a large deletion, multiplex ligation-dependent probe amplification (MLPA) was performed. Predicting the causal impact of new changes was studied by bioinformatics approaches. We also assessed the effect of the F9 mutations on the FIX protein structure and function. Causative mutations were detected in all study patients. There were 14 point mutations, three small deletions, one large deletion and one small in-frame duplication that together comprised a total of 19 unique variants, of which five were novel. The structural and functional defects of novel missense and in-frame deletion/duplication mutations were demonstrated by bioinformatics approaches. The 12 missense mutations include five purely quantitative mutations, five predominantly qualitative abnormalities and two combined defects. Our data confirmed the genetic heterogeneity of the F9 mutations. Quantitative missense mutations were found to be in different regions of precursor FIX compared with qualitative and combined ones.

The evolution of the search for novel genes in mammalian sex determination: from mice to men

Disorders of sex determination are a genetically heterogeneous group of rare disorders, presenting with sex-specific phenotypes and variable expressivity. Prior to the advent of the Human Genome Project, the identification of novel mammalian sex determination genes was hindered by the rarity of disorders of sex determination and small family sizes that made traditional linkage approaches difficult, if not impossible. This article reviews the revolutionary role of the Human Genome Project in the history of sex determination research and highlights the important role of inbred mouse models in elucidating the role of identified sex determination genes in mammalian sex determination. Next generation sequencing technologies has made it possible to sequence complete human genomes or exomes for the purpose of providing a genetic diagnosis to more patients with unexplained disorders of sex determination and identifying novel sex determination genes. However, beyond novel gene discovery, these tools have the power to inform us on more intricate and complex regulation-taking place within the heterogeneous cells that make up the testis and ovary.

Skewed X chromosome inactivation in fraternal female twins results in moderately severe and mild haemophilia B

Female carriers of haemophilia B are usually asymptomatic; however, the disease resulting from different pathophysiological mechanisms has rarely been documented in females. In this study, we investigated the mechanisms responsible for haemophilia B in fraternal female twins. We sequenced the factor IX gene (F9) of the propositus, her father, a severe haemophilia B patient and the other family members. X chromosome inactivation was assessed by the methylation-sensitive HpaII-PCR assay using X-linked polymorphisms in human phosphoglycerate kinase 1 gene (PGK1) and glutamate receptor ionotropic AMPA 3 gene (GRIA3). The twins were found to be heterozygotes with a nonsense mutation (p.Arg384X) inherited from their father. The propositus, more severely affected twin, exhibited a significantly higher percentage of inactivation in the maternally derived X chromosome carrying a normal F9. The other twin also showed a skewed maternal X inactivation, resulting in a patient with mild haemophilia B. Thus, the degree of skewing of maternal X inactivation is closely correlated with the coagulation parameters and the clinical phenotypes of the twins. Furthermore, we identified a crossing-over in the Xq25-26 region of the maternal X chromosome of the more severely affected twin. This crossing-over was absent in the other twin, consistent with their fraternal state. Differently skewed X inactivation in the fraternal female twins might cause moderately severe and mild haemophilia B phenotypes, respectively.

DNA variation in a 13-Mb region including the F9 gene: inferring the genealogical history and causal role of a hemophilia B mutation (IVS 5+13 A-->G)

About 5.5% of all UK hemophilia B patients have the base substitution IVS 5+13 A-->G as the only change in their factor (F)IX gene (F9). This generates a novel donor splice site which fits the consensus better than the normal intron 5 donor splice. Use of the novel splice site should result in a missense mutation followed by the abnormal addition of four amino acids to the patients' FIX. In order to explain the prevalence of this mutation, its genealogical history is examined. Analysis of restriction fragment length polymorphism in the 21 reference UK individuals (from different families) with the above mutation showed identical haplotypes in 19 while two differed from the rest and from each other. In order to investigate the history of the mutation and to verify that it had occurred independently more than once, the sequence variation in 1.5-kb segments scattered over a 13-Mb region including F9 was examined in 18 patients and 15 controls. This variation was then analyzed with a recently developed Bayesian approach that reconstructs the genealogy of the gene investigated while providing evidence of independent mutations that contribute disconnected branches to the genealogical tree. The method also provides minimum estimates of the age of the mutation inherited by the members of coherent trees. This revealed that 17 or 18 mutant genes descend from a founder who probably lived 450 years ago, while one patient carries an independent mutation. The independent recurrence of the IVS5+13 A-->G mutation strongly supports the conclusion that it is the cause of these patients' mild hemophilia.

Factor IX gene polymorphisms in Indian population

Hemophilia B is an X-linked, recessive disorder of hemostasis, caused by a defect in coagulation factor IX. To date, several restriction fragment length polymorphisms (RFLPs) have been identified within the gene for human factor IX. The incidence of these RFLPs differs significantly in different populations. In the present study, we analyzed the heterozygosity frequency and the allele frequency of three common intra- and extragenic polymorphic sites of the factor IX gene in Indian population. The main objective was to test the informativeness of two intragenic markers Dde I and Xmn I and one extragenic marker Hha I for carrier detection and prenatal diagnosis. The method used was polymerase chain reaction (PCR) and RFLP, which is economical yet simple to perform. In Indian population Dde I marker showed an informativeness of 69.0% followed by 38.0% for Hha I and 23.0% for Xmn I. The cumulative informativeness of these three markers was found to be 80 to 82%. A comparison of the heterozygosity rates of these three markers with the other ethnic groups showed that Indian population had almost similar pattern with the Caucasians and American blacks but differed significantly from the Orientals including Japanese, Chinese and Malays.

Identification of twenty-one new mutations in the factor IX gene by SSCP analysis

In this study we have analyzed the factor IX gene from 84 hemophilia B patients of Spanish origin. It included single-strand conformation polymorphism (SSCP) analysis of all functional regions of the gene and further sequencing of all fragments showing abnormal migration. In 76 patients (90.4%), it was possible to identify molecular alterations leading to the appearance of the disease. Twenty-one new mutations were identified, including 13 missense mutations, two nonsense mutations, three splice-site mutations, one frameshift deletion, one frameshift insertion, and one non-frameshift deletion. The approach appears to be very suitable for molecular diagnosis of hemophilia B.

Germline mutations in Peruvian patients with hemophilia B: pattern of mutation in AmerIndians is similar to the putative endogenous germline pattern

Exogenous (e.g., environmental) mutagens produce characteristic patterns of mutation. In contrast, endogenous mutation processes likely are associated with an invariant pattern of mutation. Analysis of factor IX gene mutations among large samples of hemophilia B patients from multiple, widely divergent geographic and ethnic populations reveals a remarkably constant mutational pattern, suggesting that the primary germline mutational process results from endogenous processes rather than environmental mutagens. To test this hypothesis further, we have initiated a study of hemophilia B patients from Peru because relatively large populations of AmerIndians can be found with low admixtures of other races. To determine if the factor IX (FIX) germline mutational pattern in AmerIndians differs from the common and putative endogenous pattern, FIX gene mutations were characterized in an initial sample of 10 AmerIndian Peruvian patients with hemophilia B. A minimum of 2.2 kb of the FIX gene was examined by PCR and direct sequencing of all eight exons, the splice junctions, and the promoter region. The pattern of germline mutation in AmerIndians was similar to the pattern of FIX germline mutations from larger U. S. Caucasian or Mexican Hispanic samples (P=0.55 and 0.63, respectively). The similar pattern in this initial sample of the Peru AmerIndian population provides additional support for the inference that the FIX germline mutational pattern results from predominantly endogenous processes rather than exogenous mutagens.

Direct mutation analysis as the preferred method for carrier diagnosis in families with isolated cases of haemophilia B

Approximately one-third of haemophilia B cases are described as isolated due to their occurrence in families with no prior history of the disorder. In this report, two families with isolated haemophilia B were studied by the standard method of restriction fragment length polymorphism (RFLP) analysis coupled with factor IX activity and antigen levels with the aim of achieving carrier diagnoses. The limitations of using this approach in the determination of carrier status were highlighted by diagnostic problems arising in both families. The problems included difficulty in interpreting bioassay results, homozygosity for the RFLP marker in a key family member and the possibility of germline mosaicism. Unequivocal carrier diagnosis in the two families was ultimately achieved by direct mutation analysis.

Prenatal and molecular diagnosis of hemophilia B

Prenatal diagnosis was carried out on a woman who had previously given birth to a son with a spontaneous mutation of C-->T transition at nt 31133 of the factor IX (F.IX) gene. The diagnosis was performed on chorionic villi sampling by the method of amplification-created restriction site (ACRS). It revealed a female fetus with a normal F.IX gene, as confirmed by DNA sequencing after delivery. Meanwhile, a survey using the ACRS method to evaluate the inheritance of 63 individuals from 8 hemophilia B families was done. A different single-point mutation in each family was proved by DNA sequencing. One individual had a mutation with a naturally-created restriction site. In each of the remaining patients, we were able to show an enzyme-cutting site in their DNA amplification product for ACRS with the designed mutagenesis primers. All patients and carriers could be diagnosed accurately by comparing ACRS results with clinical and laboratory findings. There were new novel mutations among the patients.

Are some apparently simple deletions actually two concerted deletions that result from interacting RY(i) hairpin loops?

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Carrier detection and feasibility of prenatal diagnosis of hemophilia B by multiplex polymerase chain reaction

Since direct diagnosis based on detection of factor IX mutations by direct sequencing is currently performed in a few laboratories only, restriction fragment length polymorphisms are still useful for carrier detection and prenatal diagnosis of hemophilia B. We analyzed 29 women from 20 families at risk of hemophilia B with three intragenic (MnlI, DdeI, TaqI) and two extragenic (HhaI, BamHI) restriction fragment length polymorphisms, all by the polymerase chain reaction. This analysis confirmed 10 possible carriers and excluded 16 as carriers. The diagnosis was made in 17 of the 20 families (85%). The combination of three polymorphisms indicated that MnlI/DdeI/HhaI and TaqI/DdeI/HhaI were the most informative (15/20 families, 75% and 14/20 families, 70%). For carrier detection with the most useful polymorphism combination (TaqI/DdeI/HhaI) we devised a multiplex polymerase chain reaction that uses two or three sets of primers, allowing carrier diagnosis in one step with 99% reliability. Our results indicate that the combination of five restriction fragment length polymorphisms makes carrier detection and prenatal diagnosis possible for 85% of families at risk of hemophilia B, with 99% reliability. With multiplex polymerase chain reaction such diagnoses can be obtained faster.

The pattern of spontaneous germ-line mutation: relative rates of mutation at or near CpG dinucleotides in the factor IX gene

Mutations at CpG dinucleotides were delineated in the factor IX gene of 38 hemophilia B patients. When transitions at CpG were considered with those previously reported by us and those compiled in the factor IX mutation database, the following patterns emerged. Many CpG sites were mutated with high frequency, while two CpG sites were infrequently mutated (R29-->Q and R116-->TGA). Of the 6 possible nonsense mutations and the 14 missense mutations that would produce a nonconservative change at conserved amino acids, all have been observed to cause hemophilia B except A-10-->T and R338-->Q. By contrast, none of the 6 missense changes at nonconserved amino acids have been observed to cause hemophilia B. At those CpG sites that are frequently mutated, the rate of transitions is estimated to be 20-fold higher than transitions at non-CpG sites. Point mutations in close proximity to CpG dinucleotides did not seem elevated.

Linkage mapping of a severe X-linked mental retardation syndrome

A four-generation Swedish family with a new type of X-linked mental retardation syndrome was recently reported by Gustavson et al. The complex syndrome includes microcephaly, severe mental retardation, optical atrophy with decreased vision or blindness, severe hearing defect, characteristic facial features, spasticity, seizures, and restricted joint motility. The patients die during infancy or early in childhood. Twenty-one family members, including two affected males, were available for study. Linkage analysis was conducted in the family by using 11 RFLP markers and 10 VNTR markers spread along the X chromosome. A hypervariable short tandem repeat of DXS294 at Xq26 showed a peak two-point lod score of 3.35 at zero recombination fraction. Calculations using the same markers revealed a multipoint peak lod score of 3.65 at DXS294. Crossover events with the centromeric marker DXS424 and the telomeric marker DXS297 delimit a probable region for the gene localization. It is noteworthy that hte disease loci of two other syndromes with overlapping clinical manifestations recently were shown by Turner et al. and Pettigrew et al. to be linked to markers at Xq26.

Functional disomy of Xp22-pter in three males carrying a portion of Xp translocated to Yq

A number of Xp22;Yq11 translocations involving the transposition of Yq material to the distal short arm of the X chromosome have been described. The reciprocal product, i.e. the derivative Y chromosome resulting from the translocation of a portion of Xp to Yq, has never been recovered. We searched for this reciprocal product by performing dosage analysis of Xp22-pter loci in 9 individuals carrying a non-fluorescent Y chromosome. In three mentally retarded and dysmorphic patients, dosage analysis indicated the duplication of Xp22 loci. Use of the highly polymorphic probe CRI-S232 demonstrated the inheritance of paternal Xp-specific alleles in the probands. In situ hybridization, performed in one case, confirmed that 29CL pseudoautosomal sequences were present, in addition to Xpter and Ypter, in the telomeric portion of Yq. To our knowledge, these are the first cases in which the translocation of Xp material to Yq has been demonstrated. The X and Y breakpoints were mapped in the three patients by dosage and deletion analysis. The X breakpoint falls, in the three cases, in a region of Xp22 that is not recognized as sharing sequence similarities with the Y chromosome, thus suggesting that these translocations are not the result of a homologous recombination event.

Variations among Japanese of the factor IX gene (F9) detected by PCR-denaturing gradient gel electrophoresis

In the course of feasibility studies to examine the efficiencies and practicalities of various techniques for screening for genetic variations, the human coagulation factor IX (F9) genes of 63 Japanese families were examined by PCR-denaturing gradient gel electrophoresis (PCR-DGGE). Four target sequences with lengths of 983-2,891 bp from the F9 genes of 126 unrelated individuals from Hiroshima and their 100 children were amplified by PCR, digested with restriction enzymes to approximately 500-bp fragments, and examined by DGGE--a total of 6,724 bp being examined per individual. GC-rich sequences (GC-clamps) of 40 bp were attached to both ends of the target sequences, as far as was feasible. Eleven types of new nucleotide substitutions were detected in the population, none of which produced RFLPs or caused hemophilia B. By examining two target sequences in a single lane, approximately 8,000 bp in a diploid individual could be examined. This approach is very effective for the detection of variations in DNA and is applicable to large-scale population studies.

Single-strand conformation polymorphism (SSCP) analysis of the molecular pathology of hemophilia B

In the present study, we report the application of polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis to the screening of seven functionally important factor IX gene (FIX) regions (total length 2.66 kb) in 9 unrelated haemophilia B patients of Portuguese or African origin. In eight of the patients an altered migration pattern of single-stranded DNA was observed. Direct sequencing of the relevant DNA fragments unveiled the following sequence alterations: two novel mutations, namely FIXBarcelos Thr-380-Pro and FIXLousada 9bp insertion at position 31,309 or 31,318; five mutations previously reported in other ethnic groups (FIXPorto Arg-145-His, FIXLuanda Gly-207-Arg, FIXPenafiel Arg-248-Gln, FIXSesimbra Arg-333-Gln, FIXCascais Arg-333-Stop); and a normal variant, G-->T transvertion at position 6,596 in intron 2. We propose hypothetical models for the generation of the 9 bp duplication (FIXLousada). We have performed molecular modeling studies in order to predict the structure of the variant FIX molecules.

Linkage and risk assessment in fragile X families using new DNA probes at Xq27

Until recently few polymorphic loci had been genetically mapped close to the fragile X syndrome locus [FRAXA]. Six polymorphic loci, DXS369, DXS297, DXS296, DXS304, IDS and DXS374, have now been mapped closer to the fragile X FRAXA than in the present study. We report the results of genetic linkage analysis of 32 fragile X [fra(X)] families using 12 polymorphic loci including these new markers. Cytogenetic and molecular data were combined in two-point linkage analysis for the estimation of lod scores and carrier probabilities in potential carriers. Combined with results from previous studies, recombination fractions (0) corresponding to the maximum lod scores (Z max) were obtained for each of the 12 loci versus FRAXA. Recombination fractions between marker loci in the families were also calculated. The data were evaluated to determine the efficacy of using the strategy suggested by Suthers et al. (1991a) for molecular studies in fra(X) families. The large proportion of females heterozygous for at least one locus (83%) and of females heterozygous for flanking loci (60%) indicate that this is a very useful diagnostic strategy. Use of these new marker loci substantially changed the carrier risk estimates for members of 7 of the 32 families from the risk estimates previously calculated on the basis of less closely linked probes available prior to 1989.

Why does the human factor IX gene have a G + C content of 40%?

The factor IX gene has a G + C content of approximately 40% in all mammalian species examined. In human factor IX, C----T and G----A transitions at the dinucleotide CpG are elevated at least 24-fold relative to other transitions. Can the G + C content be explained solely by this hot spot of mutation? Using our mathematical model, we show that the elevation of mutation at CpG cannot alone lower the G + C content below 45%. To search for other hot spots of mutation that might contribute to the reduction of G + C content, we assessed the relative rates of base substitution in our sample of 160 families with hemophilia B. Seventeen independent single-base substitutions are reported herein for a total of 96 independent point mutations in our sample. The following conclusions emerge from the analysis of our data and, where appropriate, the data of others: (1) Transversions at CpG are elevated an estimated 7.7-fold relative to other transversions. (2) The mutation rates at non-CpG dinucleotides are remarkably uniform; none of the observed rates are either more than twofold above the median for transitions or more than threefold above the median for transversions. (3) The pattern of recent mutation is compatible with the pattern during mammalian evolution that has maintained the G + C content of the factor IX gene at approximately 40%.

Missense mutations and evolutionary conservation of amino acids: evidence that many of the amino acids in factor IX function as "spacer" elements

We report 31 point mutations in the factor IX gene and explore the relationship between the level of evolutionary conservation of an amino acid and the probability of a mutation causing hemophilia B. From our total sample of 125 hemophiliacs and from those reported by others, we identify 95 independent missense mutations, 94 of which occur at amino acids that are evolutionarily conserved in the available mammalian factor IX sequences. The likelihood of a missense mutation causing hemophilia B depends on whether the residue is also conserved in the factor IX-related proteases: factor VII, factor X, and protein C. Most of the possible missense mutations in generically conserved residues (i.e., those conserved in factor IX and in all the related proteases) should cause disease. In contrast, missense mutations in factor IX-specific residues (i.e., those conserved in human, cow, dog, and mouse factor IX but not in the related proteases) are sixfold less likely to cause disease. Missense mutations at nonconserved residues are 33-fold less likely to cause disease. At least three models are compatible with these observations. A comparison of sequence alignments from four and nine species of factor IX and an examination of the missense mutations occurring at CpG residues suggest a model in which most residues fall on opposite ends of a spectrum. In about 40% of residues, virtually any missense mutation in a minority of the residues will cause disease, while virtually no missense mutations will cause disease in most of the remaining residues. Thus, many of the residues in factor IX are spacers; that is, the main chains are presumably necessary to keep other amino acid interactions in register, but the nature of the side chain is unimportant.

The varying frequencies of five DNA polymorphisms of X-linked coagulant factor IX in eight ethnic groups

Five RFLPS of X-linked coagulation factor IX were evaluated in more than 500 normal persons (723-804 X chromosomes) of both sexes who belonged to eight ethnic groups: Anglo-Americans, Basques, Swedes, African-Americans, East Africans, East Indians, Chinese, and Malays. The polymorphisms, 5' to 3', were BamHI, XmnI, TaqI, MnlI, and HhaI. A PCR procedure was developed for three previously described RFLPs-XmnI, TaqI, and MnlI; a PCRP procedure was developed for BamHI, and a PCRP which had been described by others was used for HhaI. Europeans were the most polymorphic, African-Americans and East Africans were intermediate, and Orientals were the least polymorphic. Extragenic 3' HhaI was highly polymorphic in most groups, and extragenic 5' BamHI was polymorphic only in persons with African ancestry. Two major haplotypes predominated among 247 men, and the expected and observed heterozygosities were concordant among women. Allelic association was very strong between the three intragenic PCRPs; it was present but weak between 5' extragenic BamHI and XmnI. No association was found between 3' extragenic HhaI and MnlI.

Intrachromosomal rearrangements fusing L-myc and rlf in small-cell lung cancer

Chromosomal abnormalities affecting proto-oncogenes are frequently detected in human cancer. Oncogenes of the myc family are activated in several types of tumors as a result of gene amplification or chromosomal translocation. We have recently found the L-myc gene involved in a gene fusion in small-cell lung cancer (SCLC). This results in a chimeric protein with amino-terminal sequences from a novel gene named rif joined to L-myc. Here we present a preliminary structural characterization of the rlf-L-myc fusion gene, which has been found only in cells with an amplified L-myc gene. In addition, we have used somatic cell hybrids to assign the normal rlf locus to the same chromosome (chromosome 1) on which L-myc resides. Finally, we have been able to establish a physical linkage between rif and L-myc with pulsed-field gel electrophoresis. Our results demonstrate that normal rlf and L-myc genes are separated by less than 800 kb of DNA. Thus, the rlf-L-myc gene fusions are due to similar but not identical intrachromosomal rearrangements at 1p32. The presence of independent genetic lesions that cause the formation of identical chimeric rlf-L-myc proteins suggests a role for the fusion protein in the development of these tumors.

Intrachromosomal rearrangements fusing L-myc and rlf in small-cell lung cancer

Chromosomal abnormalities affecting proto-oncogenes are frequently detected in human cancer. Oncogenes of the myc family are activated in several types of tumors as a result of gene amplification or chromosomal translocation. We have recently found the L-myc gene involved in a gene fusion in small-cell lung cancer (SCLC). This results in a chimeric protein with amino-terminal sequences from a novel gene named rif joined to L-myc. Here we present a preliminary structural characterization of the rlf-L-myc fusion gene, which has been found only in cells with an amplified L-myc gene. In addition, we have used somatic cell hybrids to assign the normal rlf locus to the same chromosome (chromosome 1) on which L-myc resides. Finally, we have been able to establish a physical linkage between rif and L-myc with pulsed-field gel electrophoresis. Our results demonstrate that normal rlf and L-myc genes are separated by less than 800 kb of DNA. Thus, the rlf-L-myc gene fusions are due to similar but not identical intrachromosomal rearrangements at 1p32. The presence of independent genetic lesions that cause the formation of identical chimeric rlf-L-myc proteins suggests a role for the fusion protein in the development of these tumors.

Fine structure mapping of the hypoxanthine-guanine phosphoribosyltransferase (HPRT) gene region of the human X chromosome (Xq26)

The Xq26-q27 region of the X chromosome is interesting, as an unusually large number of genes and anonymous RFLP probes have been mapped in this area. A number of studies have used classical linkage analysis in families to map this region. Here, we use mutant human T-lymphocyte clones known to be deleted for all or part of the hypoxanthine-guanine phosphoribosyltransferase (hprt) gene, to order anonymous probes known to map to Xq26. Fifty-seven T-cell clones were studied, including 44 derived from in vivo mutation and 13 from in vitro irradiated T-lymphocyte cultures. Twenty anonymous probes (DXS10, DXS11, DXS19, DXS37, DXS42, DXS51, DXS53, DXS59, DXS79, DXS86, DXS92, DXS99, DXS100d, DXS102, DXS107, DXS144, DXS172, DXS174, DXS177, and DNF1) were tested for codeletion with the hprt gene by Southern blotting methods. Five of these probes (DXS10, DXS53, DXS79, DXS86 and DXS177) showed codeletion with hprt in some mutants. The mutants established the following unambiguous ordering of the probes relative to the hprt gene: DXS53-DXS79-5'hprt3'-DXS86-DXS10-DXS177 . The centromere appears to map proximal to DXS53. These mappings order several closely linked but previously unordered probes. In addition, these studies indicate that rather large deletions of the functionally haploid X chromosome can occur while still retaining T-cell viability.

Restriction fragment length polymorphisms associated with the factor VIII and factor IX genes in Polynesians

New Zealand Maoris (72 X chromosomes) have been compared with Pacific Island Polynesians (121 X chromosomes) and Caucasian New Zealanders (51 X chromosomes) as a control group to determine the allelic frequency of six RFLPs associated with the genes for two X linked diseases (haemophilia A and haemophilia B). RFLPs examined were BclI, XbaI, and BglI within the factor VIII gene, the factor VIII extragenic TaqI system, and the factor IX intragenic TaqI and XmnI sites. The information obtained facilitates the design of strategies for both carrier detection and prenatal diagnosis of haemophilia A within these groups. Strong linkage disequilibrium was observed between the factor VIII BclI and XbaI sites in Polynesians. Genetic counselling for Polynesians with haemophilia B continues, however, to rely on phenotypic diagnosis. The RFLP data from the two separate loci on the X chromosome in Polynesians show similarities with Chinese and Japanese populations, reinforcing theories of an early Polynesian ancestry originating in east Asia.

Single nucleotide primer extension to detect genetic diseases: experimental application to hemophilia B (factor IX) and cystic fibrosis genes

In this report, we describe an approach to detect the presence of abnormal alleles in those genetic diseases in which frequency of occurrence of the same mutation is high (e.g., cystic fibrosis and sickle cell disease), and in others in which multiple mutations cause the disease and the sequence variation in an affected member of a given family is known (e.g., hemophilia B). Initially, from each subject, the DNA fragment containing the putative mutation site is amplified by the polymerase chain reaction. For each fragment two reaction mixtures are then prepared. Each contains the amplified fragment, a primer (18-mer or longer) whose sequence is identical to the coding sequence of the normal gene immediately flanking the 5' end of the mutation site, and either an alpha-32P-labeled nucleotide corresponding to the normal coding sequence at the mutation site or an alpha-32P-labeled nucleotide corresponding to the mutant sequence. Single nucleotide primer extensions are then carried out and analyzed by denaturing polyacrylamide gel electrophoresis and autoradiography. As predicted by the Watson-Crick base-pair rule, in the wild type only the normal base, in an affected member only the mutant base, and in carriers both the normal and the mutant base are incorporated into the primer. Thus, an essential feature of the present methodology is that the base immediately 3' to the template-bound primer is one of those altered in the mutant, since in this way an extension of the primer by a single base will give an extended molecule characteristic of either the mutant or the wild type. The method is rapid and should be useful in carrier detection and prenatal diagnosis of every genetic disease with a known sequence variation.

Segments containing alternating purine and pyrimidine dinucleotides: patterns of polymorphism in humans and prevalence throughout phylogeny

Tandem dinucleotide repeats of GT or AC [(GT)n/(AC)n] where n greater than or equal to 14 are highly polymorphic and other simple repeats such as (CT)n/(AG)n and (A)n(T)n are also polymorphic. The uniformity of these sequences precludes a mechanistic differentiation between recombination or polymerase slippage. Since (GT)n/(AC)n or (CT)n/(AG)n segments of desired size were not available in our gene of interest, we analyzed a 187+ bp segment in the factor IX gene with multiple short dinucleotide repeats. This sequence contains a melody of short dinucleotide repeats which includes a 142+ bp segment of alternating purines and pyrimidines. Amplification of this sequence in 167 individuals of different ethnicity and direct sequencing of 106 individuals (23 kb of sequence) failed to reveal simple variation in the number of tandem dinucleotide repeats. However, polymorphism in the 142+ alternating purine and pyrimidine segment (RY)n was detected due to the insertion of two related repeat units of 24 bp (A) and 26 bp (B). Two previously described alleles (AB, A2B2) and two novel presumptive recombinants were found (A2B, A3B2) for a total of four alleles. An analysis of (RY)n segments in GenBank revealed an extraordinary enrichment in the genome of mammals, invertebrates, and yeast and a marked reduction in bacteria. Rodent (RY)n were larger and substantially more frequent than those in primates. When a second (RY)n was examined in the exon 8 of human factor IX gene, it was polymorphic at short repeats of (GT)n/(AC)n (n = 3-6) in Western Europeans and Koreans. In addition, an (RY)n in the dystrophin gene had four polymorphic alleles involving AT and GT dinucleotides. Thus (RY)n segments appear to be abundant and highly polymorphic. The asymmetric patterns of polymorphism and the absence of simple dinucleotide variation in 23 kb of sequence are compatible with recombination or sister chromatid exchange, but not polymerase slippage. By inference, recombination should underlie the polymorphisms at (GT)n/(AC)n since they are a subset of (RY)n and they commonly occur in the context of longer (RY)n.

Mapping the gene encoding the human erythroid transcriptional factor NFE1-GF1 to Xp11.23

The X-linked NFE1 gene encodes an erythroid factor involved in globin gene transcription. Using a human cDNA clone encoding this factor, we show, by in situ hybridization and by analysis of human-rodent hybrid cell lines, that this gene is located in Xp11.23. In the absence of polymorphisms in the NFE1 gene, these results allow the study of the possible relationships between NFE1 mutations and X-linked hereditary persistence of fetal hemoglobin by linkage analysis with RFLP markers of the region. A female patient, hemizygous for the NFE1 locus, shows essentially normal hematological parameters.

DNA linkage analysis of 26 families with fragile X syndrome

Linkage data using the markers F9 (factor IX), DXS105 (cX55.7), DXS98 (4D-8), DXS52 (St14), DXS15 (DX13), and DXS134 (cpX67) are presented from 26 pedigrees segregating with fragile X (fra[X]) syndrome. Cytogenetic and DNA data were combined in 2-point linkage analysis for the estimation of lod scores and carrier probabilities in potential carriers. Recombination fractions (theta) corresponding to the maximum lod scores (Z) were obtained for F9 (Z = 2.78, theta = 0.15), DXS105 (Z = 1.72, theta = 14), DXS98 (Z = 3.74, theta = 0.00), DXS52 (Z = 3.53, theta = 0.17), DXS15 (Z = 4.03, theta = 0.11), and DXS134 (Z = 2.12, theta = 0.16) and for the fragile X locus (FRAXA). Recombination fractions between marker loci in the families are also presented. Discordance between the results of cytogenetic and DNA analyses in 2 potential carrier females was investigated by reexamination of the fragile site expression and was concluded to be due to the expression of the common fragile site at Xq27.2.

An HhaI polymorphism is present in factor IX genes of Asian subjects

Hemophilia B is caused by decreased factor IX procoagulant activity. An HhaI restriction site polymorphism near the factor IX gene has been detected by the polymerase chain reaction. Frequency and linkage data already observed in Caucasians are confirmed and the polymorphism is also prevalent in the factor IX genes of Black and Asian populations.

The gene for 17 beta-hydroxysteroid dehydrogenase maps to human chromosome 17, bands q12-q21, and shows an RFLP with ScaI

The gene encoding human 17 beta-hydroxysteroid dehydrogenase (17-HSD; EC 1.1.1.62) is assigned to chromosome 17 by Southern blotting analyses of panels of human x rodent somatic cell hybrids and independently to 17q12-q21 using chromosomal in situ hybridization. A search for physical linkage between 17-HSD and the proto-oncogenes. THRA1 and ERBB2 (both reported to be located in this region of chromosome 17) was performed by pulsed-field gel electrophoresis (PFGE) using several rare-cutting restriction endonucleases. Because all three genes hybridized to DNA fragments of different lengths it seems unlikely that the gene for 17-HSD is located very close to THRA1 and ERBB2. Further evidence for this assumption was obtained from the absence of any coamplification of the 17-HSD gene in 9 breast tumors with amplification of the ERBB2 gene. Analyses of Southern blots of ScaI-digested DNAs from unrelated individuals from Northern Finland revealed a relatively infrequent diallelic restriction fragment length polymorphism, the allele frequencies of which were 0.04 (A1) and 0.96 (A2).

Localization of transcription initiation sites in the human coagulation factor IX gene

The transcription start sites of the human gene coding for the coagulation factor IX have been identified. Three major transcription initiation sites within a small area of approximately 30 nucleotides were found by S1 nuclease analysis and primer extension studies.

Mutations causing hemophilia B: direct estimate of the underlying rates of spontaneous germ-line transitions, transversions, and deletions in a human gene

Spontaneous mutation provides the substrate for evolution on one hand and for genetic susceptibility to disease on the other hand. X-linked diseases such as hemophilia B offer an opportunity to examine recent germ-line mutations in humans. By utilizing the direct sequencing method of genomic amplification with transcript sequencing, eight regions (2.46 kb) of likely functional significance in the factor IX gene have been sequenced in a total of 60 consecutive, unrelated hemophiliacs. The high frequency of patient ascertainment from three regions in the midwestern United States and Canada suggests that the sample is representative of hemophiliacs of northern European descent. Twenty-six of the delineated mutations are reported herein, and the group of 60 is analyzed as a whole. From the pattern of mutations causing disease and from a knowledge of evolutionarily conserved amino acids, it is possible to reconstruct the underlying pattern of mutation and to calculate the mutation rates per base pair per generation for transitions (27 x 10(-10)), transversions (4.1 x 10(-10), and deletions (0.9 x 10(-10)) for a total mutation rate of 32 x 10(-10). The proportion of transitions at non-CpG nucleotides is elevated sevenfold over that expected if one base substitution were as likely as another. At the dinucleotide CpG, transitions are elevated 24-fold relative to transitions at other sites. The pattern of spontaneous mutations in factor IX resembles that observed in Escherichia coli when the data are corrected for ascertainment bias. The aggregate data hint that most mutations may be due to endogenous processes. The following additional conclusions emerge from the data: (1) Although in recent decades reproductive fitness in individuals with mild and moderate hemophilia has been approximately normal, the large number of different mutations found strongly suggest that these levels of disease substantially compromised reproduction in previous centuries. (2) Mutations which putatively affect splicing account for at least 13% of independent mutations, indicating that the division of the gene into eight exons presents a significant genetic cost for the organism. In one individual a "silent" mutation at lysine 5 is likely to cause hemophilia by generating a perfect splice donor consensus sequence in exon b. (3) All the missense mutations occurred at evolutionarily conserved amino acids. As additional data are generated on the pattern of mutations caused by specific mutagens, it will be possible to utilize the pattern of spontaneous mutation to estimate the maximal contribution of that mutagen during the past century.

A past mutation at isoleucine 397 is now a common cause of moderate/mild haemophilia B

Of the factor IX sequence changes that we have identified in 65 consecutive males with haemophilia B, 11 (17%) are the same mutation. This mutation is a T----C transition at base 31311 which substitutes threonine for isoleucine397 (ile397) in the factor IX molecule. The 11 patients are of Western European descent and have the same haplotype: Hinf1 (-), Xmn1 (-), Taq1 (-), BamH1 (+), Malmö allele = thr148. The frequency of this haplotype was estimated and the probability of the same mutation occurring independently 11 times in this haplotype was miniscule. We conclude that these patients have a common ancestor despite the lack of overlapping pedigrees. The clinical symptoms of the disease were consistently moderate/mild in these 11 patients, whereas factor IX coagulation values obtained from the medical records varied more than sixfold between individuals. However, when plasma from five individuals was assayed by the same laboratory concurrently, the values varied less than twofold. Thus, in routine practice, clinical severity may correlate better with the presence of a given mutation than the factor IX coagulant activity. The high frequency of the mutation at ile397 indicates that carrier testing in families of Northern European descent with moderate/mild haemophilia B can be expedited by first determining whether this particular mutation is present. We demonstrate here that the technique of polymerase chain reaction (PCR) amplification of specific alleles (PASA) can be used to rapidly perform carrier testing in families with the ile397 mutation.

Recurrent nonsense mutations at arginine residues cause severe hemophilia B in unrelated hemophiliacs

Direct sequencing of the regions of the factor IX gene of likely functional significance was performed in four patients with severe hemophilia B. In two of the individuals, a transition at the dinucleotide CpG caused a nonsense mutation at arginine 333. In the other two individuals, a transition at CpG caused a nonsense mutation at arginine 29. Since these patients are all unrelated, as shown by differing alleles of the TaqI polymorphism in intron four or extensive nonoverlapping pedigrees, the mutations arose independently. In addition, the origin of one arginine 333 mutation in one family has been traced to the germline of the maternal grandfather. The frequent occurrence of mutations at arginine codons that contain the sequence CGN can be explained by the dramatic elevation of transitions at CpG. As a result, approximately one in four individuals with hemophilia B is expected to have a mutation at arginine and nonsense mutations at one of six arginine residues should be common causes of severe hemophilia.

Diagnosis of haemophilia B using the polymerase chain reaction

The polymerase chain reaction (PCR) was used to amplify specific DNA sequences within the factor IX gene of haemophilia B patients and their relatives. Three of the amplified fragments contain polymorphic sites, which can be used as markers in segregation analyses. These restriction fragment length polymorphisms (RFLPs) were until recently detected by Southern blotting after digestion with the restriction enzymes Taq I, Dde I and Xmn I. All three RFLP's are located in introns of the factor IX gene and together are informative in approximately 70% of all cases. Each of the polymorphisms was successfully used in carrier detection studies after amplification of the relevant fragments. This method is also suitable for rapid antenatal diagnosis. Additionally we were able to amplify all eight exons of the factor IX gene including the splice junctions and a part of the 5'-region. Large deletions or insertions can be detected without further analysis. Several possibilities for the rapid detection of point mutations after DNA amplification have been described recently. The complete amplification of all functional parts of the Factor IX gene in combination with these new techniques should enable us to detect the majority of mutations leading to haemophilia B.

Cytogenetic and molecular analysis of an unbalanced translocation (X;7) (q28;p15) in a dysmorphic girl

A severely retarded and dysmorphic girl, carrying an unbalanced X/7 translocation with breakpoints at Xq28 and 7p14, was analyzed by cytogenetic, biochemical and molecular techniques. The X/7 translocated chromosome was found to replicate consistently late in the 105 metaphases analyzed. In 83 of these cells, late replication was limited to the X portion of the abnormal chromosome, whereas in 22 cells incomplete spreading into the autosomal fragment was observed. Southern blot and in situ hybridization experiments with probe G80 (locus D7S373) (previously localized to 7p13-15) and G98 (localized to 7p14-15) assigns the former to 7p15 and the latter to 7p14, thus suggesting the order 7ter-G80-G98-cen. The activity of the enzyme phosphoserine phosphatase localized to 7pter-p14 was increased. Southern blotting experiments with 19 probes spanning the entire X chromosome demonstrated that the translocated chromosome had lost a portion of Xq28 (locus DXS51) but still retained part of Xq27 (F9 locus). The results confirm that the proband is trisomic for the region 7p15-pter and monosomic for the region Xq28-qter. Comparing her phenotype with those of other cases of partial trisomy or monosomy 7p, we confirm that band 7q21 is probably involved in skull development.

Close linkage of probe p212 (DXS178) to X-linked agammaglobulinemia

Segregation analysis was performed in three families affected in X-linked agammaglobulinemia (XLA) with five polymorphic DNA probes linked to the disease locus. In agreement with previous studies, no recombination was observed with either pXG12 (DXS94) or S21 (DXS17). Segregation analysis was also performed with a marker, p212 (DXS178), which has been shown to be closely linked to pXG12 in normal families. No cross-over with XLA was observed in these three families and in five additional families previously analyzed with DXS17 and DXS94 (z = 5.92 at theta = 0). These data provide evidence against genetic heterogeneity in XLA and indicate the value of probe p212 for carrier detection and prenatal diagnosis of XLA. We were able to estimate the carrier status of six females (out of six) in the three previously unreported families.

Contiguous gene syndromes due to deletions in the distal short arm of the human X chromosome

Mendelian inherited disorders due to deletions of adjacent genes on a chromosome have been described as "contiguous gene syndromes." Short stature, chondrodysplasia punctata, mental retardation, steroid sulfatase deficiency, and Kallmann syndrome have been found as isolated entities or associated in various combinations in 27 patients with interstitial and terminal deletions involving the distal short arm of the X chromosome. The use of cDNA and genomic probes from the Xp22-pter region allowed us to identify 12 different deletion intervals and to confirm, and further refine, the chromosomal assignment of X-linked recessive chondrodysplasia punctata and Kallmann syndrome genes. A putative pseudoautosomal gene affecting height and an X-linked non-specific mental retardation gene have been tentatively assigned to specific intervals. The deletion panel described is a useful tool for mapping new sequences and orienting chromosome walks in the region.

The gene encoding the human preproacrosin (ACR) maps to the q13-qter region on chromosome 22

Human proproacrosin is specified by a single gene (ACR). Using a series of human-rodent somatic cell hybrids containing variant complements of human chromosomes, the preproacrosin gene was found to cosegregate with human chromosome 22. Somatic cell hybrids containing translocation chromosomes carrying parts of chromosome 22 were used to locate the preproacrosin gene to the region 22q13-22qter. By probing the DNA of 82 individuals, a restriction fragment length polymorphism was found with SstI in 14 cases.

Direct carrier testing in 14 families with haemophilia B

Direct carrier testing was done in 54 at-risk female relatives of haemophilic patients by initially analysing 2.46 kb of the factor IX gene in 1 haemophiliac per family by genomic amplification with transcript sequencing. A presumptive mutation was found in all 14 haemophiliacs examined. Analyses were then done either by sequencing the appropriate region in at-risk female relatives or by detection of an altered restriction site. A simulation indicated that the mutation will be associated with an altered restriction site in about half the families. The technique has clinical application.

The human lysozyme gene. Sequence organization and chromosomal localization

We have isolated two overlapping recombinant lambda-phage clones from a genomic lambda-EMBL3 library containing 25 kb of the human lysozyme gene region. Furthermore a full-lenght human lysozyme cDNA clone of 1.5 kb was isolated from a human placenta cDNA library. Nucleotide sequences of the entire structural gene and the cDNA clone were determined. The human lysozyme gene spans 5856 bp and its sequence organization with four exons and three introns is homologous to the chicken lysozyme gene and the human alpha-lactalbumin gene. Human and chicken lysozyme genes differ mainly in the size of their introns and 3' non-coding region. Four Alu repetitive elements were found in the human lysozyme gene, one in each intron and one on the fourth exon. Lysozyme transcripts of 1.6 kb and 0.6 kb in size were detected in human myeloid cell lines U-937, HL-60 and THP-1 and surprisingly in human hepatoma cell lines HepG2 and Hep3B. The lysozyme gene locus was assigned to human chromosome 12 by hybridization to a panel of DNAs from human-rodent somatic cell hybrids.

Detection of polymorphisms at cytosine phosphoguanadine dinucleotides and diagnosis of haemophilia B carriers

The polymerase chain reaction procedure (PCR) was used to detect a polymorphic Hha I site adjacent to the factor IX locus in a panel of 33 phenotypically normal caucasian individuals. This technique was also applied to a haemophilia B family pedigree. The Hha I polymorphic site was located 8 kb 3' to the factor IX gene, and the proportion of female subjects expected to be heterozygous at this site was 0.48. The Hha I locus was in linkage equilibrium with the other polymorphic loci on the factor IX gene. These findings, besides increasing the proportion of caucasian individuals whose haemophilia B carrier state can be diagnosed from 79% to 89%, demonstrate this widely applicable use of PCR for the detection of DNA polymorphism at cytosine phosphoguanadine dinucleotides irrespective of the methylation status.