ABCD1 mutations and the X-linked adrenoleukodystrophy mutation database: role in diagnosis and clinical correlations.

X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ABCD1 gene, which encodes a peroxisomal ABC half-transporter (ALDP) involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement. There is no apparent correlation between genotype and phenotype. In males, unambiguous diagnosis can be achieved by demonstration of elevated levels of VLCFA in plasma. In 15 to 20% of obligate heterozygotes, however, test results are false-negative. Therefore, mutation analysis is the only reliable method for the identification of heterozygotes. Since most X-ALD kindreds have a unique mutation, a great number of mutations have been identified in the ABCD1 gene in the last seven years. In order to catalog and facilitate the analysis of these mutations, we have established a mutation database for X-ALD ( http://www.x-ald.nl). In this review we report a detailed analysis of all 406 X-ALD mutations currently included in the database. Also, we present 47 novel mutations. In addition, we review the various X-ALD phenotypes, the different diagnostic tools, and the need for extended family screening for the identification of new patients.

Single-tube multiplex-PCR screen for common deletional determinants of alpha-thalassemia.

Alpha-thalassemia is very common throughout all tropical and subtropical regions of the world. In Southeast Asia and the Mediterranean regions, compound heterozygotes and homozygotes may have anemia that is mild to severe (hemoglobin [Hb] H disease) or lethal (Hb Bart's hydrops fetalis). We have developed a reliable, single-tube multiplex-polymerase chain reaction (PCR) assay for the 6 most frequently observed determinants of alpha-thalassemia. The assay allows simple, high throughput genetic screening for these common hematological disorders. (Blood. 2000;95:360-362)

Accurate DNA-based diagnostic and carrier testing for X-linked adrenoleukodystrophy.

X-linked adrenoleukodystrophy is a serious and often fatal disorder, affecting the white matter of the nervous system, the adrenal cortex, and the testis. The gene mutated in X-ALD encodes a peroxisomal membrane protein, ALDP. The presence of very long chain fatty acids in plasma is highly diagnostic for affected males and carrier females, but exclusion of carrier status biochemically is unreliable. Molecular analysis of the X-ALD gene has the potential to either identify or rule out carrier status accurately, but is complicated by the existence of autosomal paralogs. We have developed and validated a robust DNA diagnostic test for this disorder involving nonnested genomic amplification of the X-ALD gene, followed by fluorescent dye-primer sequencing and analysis. This protocol provides a highly reliable means of determining carrier status in women at risk for transmitting X-ALD and is applicable to a clinical diagnostic laboratory.

Switch from monoallelic to biallelic human IGF2 promoter methylation during aging and carcinogenesis.

We have previously linked aging, carcinogenesis, and de novo methylation within the promoter of the estrogen receptor (ER) gene in human colon. We now examine the dynamics of this process for the imprinted gene for insulin-like growth factor II (IGF2). In young individuals, the P2-4 promoters of IGF2 are methylated exclusively on the silenced maternal allele. During aging, this promoter methylation becomes more extensive and involves the originally unmethylated allele. Most adult human tumors, including colon, breast, lung, and leukemias, exhibit increased methylation at the P2-4 IGF2 promoters, suggesting further spreading during the neoplastic process. In tumors, this methylation is associated with diminished or absent IGF2 expression from the methylated P3 promoter but maintained expression from P1, an upstream promoter that is not contained within the IGF2 CpG island. Our results demonstrate a remarkable evolution of methylation patterns in the imprinted promoter of the IGF2 gene during aging and carcinogenesis, and provide further evidence for a potential link between aberrant methylation and diseases of aging.

Cystic fibrosis carrier population screening in the primary care setting.

To determine the receptivity of prenatal care providers and their patients to carrier testing for cystic fibrosis (CF), we offered free carrier screening, followed by genetic counseling of carriers, to all prenatal care providers in Rochester, NY, for all their female patients of reproductive age, pregnant or not. Of 124 prenatal care providers, only 37 elected to participate, but many of these offered screening only to pregnant women. The acceptance rate among pregnant women was approximately 57%. The most common reasons for accepting screening were to obtain reassurance (50.7%) and to avoid having a child with CF (27.8 %). The most common reasons for declining screening were not intending to terminate a pregnancy for CF (32.4%) and believing that the chance of having a CF child was very low (32.2%). Compared with decliners, acceptors were more likely to have no children, regarded having a child with CF as more serious, believed themselves more susceptible to having such a child, knew more about CF, would be more likely to terminate a pregnancy if the fetus were shown to have CF, and more strongly supported offering CF screening to women of reproductive age. Of 4,879 women on whom results were obtained, 124 were found to be carriers. Of these 124 carriers, the partners of 106 were tested. Of the five at-risk couples, four requested prenatal diagnosis and one requested neonatal diagnosis. No woman found to be a carrier whose partner tested negative requested prenatal diagnosis. Except for the imperfect knowledge of those testing negative, none of the adverse outcomes predicted for CF carrier testing in the general population were observed in this study.

A new retrotransposable human L1 element from the LRE2 locus on chromosome 1q produces a chimaeric insertion.

We have found a 2 kilobase insertion containing a rearranged L1 element in the dystrophin gene of a muscular dystrophy patient. We cloned the precursor of this insertion, the second known active human L1 element. The locus, LRE2, has one allele derived from the patient which matches the insertion sequence exactly. LRE2 has a perfect 13-15 bp target site duplication, two open reading frames, and an unusual 21 bp truncation of the 5' end, suggesting that a slightly truncated element can still retrotranspose. It differs from LRE1 by approximately 0.7%. There is an L1 element at LRE2 on approximately 66% of human chromosomes 1q, and the element is absent from chimpanzee and gorilla genomes. These data demonstrate that multiple active L1 elements exist in the human genome, and that a readthrough transcript of an active element is capable of retrotransposition.

Frequency and stability of the fragile X premutation.

Although considered the most common heritable cause of neurodevelopmental disability, precise prevalence figures for the FMR1 mutation in the general population are lacking. Since no fragile X premutation alleles have yet been observed to originate from FMR1 alleles within the normal size range, there is also little information available about the origin of the fragile X premutation and mechanisms leading to instability of the FMR1 trinucleotide repeat region. In this study, 977 genetically unrelated individuals from families unselected for mental retardation or fragile X were analyzed with Southern blot analysis for the presence of FMR1 mutations. A subgroup of subjects with evidence of a large CGG repeat number, and any available relatives, were further studied with PCR to investigate the stability of the trinucleotide repeat segment of FMR1. One subject had a 75 repeat length which was unstable (increased in size) when passed to subsequent generations. This includes one male descendent who had a premutation/full mutation mosaic pattern. Two other alleles with > or = 46 repeats from different subjects were also found to be unstable and increased in size in subsequent generations. Considering all three unstable alleles to be indicative of an evolving or actual premutation, the estimated frequency of the fragile X premutation is one in 510 X chromosomes. However, since 11 other alleles with > or = 46 repeats were found to be stable through at least one meiotic transmission, repeat length appears to be an important but not sufficient condition leading to instability of the FMR1 gene.

Increased echogenicity in the fetal abdomen: use of DNA analysis to establish a diagnosis of cystic fibrosis.

The sonographic finding of increased echogenicity within the fetal abdomen presents a diagnostic dilemma, with a differential diagnosis ranging from normal variation to CF. We report the diagnostic evaluation of four cases, two of which were found to be the result of CF. On the basis of this experience, we believe that persistence of an echogenic bowel pattern, especially with bowel dilation, after 20 weeks' gestation should prompt an evaluation for CF. Using DNA analysis, approximately 75% of the cases involving CF can be detected with noninvasive studies of the parents, and confirmation by amniocentesis is performed only in those cases in which both parents are carriers of known mutations.

Familial neurofibromatosis type 1: clinical experience with DNA testing.

To determine how DNA testing for familial neurofibromatosis type 1 (NF-1) would be used in a clinical setting by patients and physicians, we performed confirmatory DNA testing on 24 individuals with a family history of NF-1 and on nine couples who requested DNA testing for current or future prenatal diagnosis. A further eight families were unsuitable for DNA linkage testing because of their pedigree structure. For the majority of persons the certainty of the test result was 95% to 99%. In five individuals, only one of whom was less than 6 years of age, the DNA-based diagnosis was discrepant with the clinical diagnosis at the time of referral. In all five cases, results of subsequent clinical re-examinations were consistent with the DNA diagnosis. We conclude that DNA testing by linkage analysis may be most useful as an adjunct to the clinical diagnosis of familial NF-1 (1) in children less than 6 years of age in whom the full manifestations may not yet be apparent, (2) in NF-1 families interested in prenatal testing, and (3) when the resources available for a complete clinical examination are limited.

The molecular basis of genetic disease.

The pace of localization and characterization of genes affected in human genetic disorders is quickening. Many important genes were localized or characterized recently: genes for in cystic fibrosis, NF-2, Marfan's syndrome and xeroderma pigmentosum, to name a few. Also, in the past 15 months, the CFTR gene affected in cystic fibrosis has been isolated, the first disease gene to be isolated without use of previous cytogenetic clues, such as deletions or translocations in sporadic cases. Other examples should follow, although we have been disappointed to date by the difficulties encountered in the isolation of Huntington's disease gene which was localized a number of years ago to distal chromosome 4p. It is still very difficult to isolate a disease gene without critical cytogenetic information. New improved techniques for finding the desired expressed sequences in a large cloned segment of human DNA are needed. Our ability to find mutant alleles of a given sequence has expanded greatly with the recent technical advances in denaturing gradient gel electrophoresis, chemical cleavage, and single-stranded conformational electrophoresis. One would predict that information derived from the human genome project will have a major impact upon the isolation of further disease genes. As whole regions of human chromosomes or indeed entire chromosomes are physically mapped and cloned as continuous, overlapping YACs (yeast artificial chromosomes), isolation of disease genes will become easier and easier.(ABSTRACT TRUNCATED AT 250 WORDS)

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.

Use of polymerase chain reaction for diagnosis of inherited disorders.

The polymerase chain reaction (PCR) is a rapid method for generating a 10(6)- to 10(7)-fold increase in the number of copies of a discrete DNA or RNA sequence. The technique is being used for rapid prenatal diagnosis and carrier testing of several inherited disorders. After PCR, mutations producing single-gene disorders can be detected by several different methods, including endonuclease digestion and gel electrophoresis (applicable when a mutation affects an endonuclease recognition site), gel electrophoresis (used for detection of deletions), and hybridization to an oligonucleotide probe specific for a mutation. Less often, gene sequencing of a PCR product is used to rapidly identify a mutation. In addition, the PCR technique can be applied to polymorphism analysis to provide diagnosis by linkage analysis. In other areas, PCR is being used to detect and characterize microbial pathogens and to characterize mutations associated with carcinogenesis. The PCR method is useful in situations in which the amount of DNA sample is limited, such as in forensics and prenatal testing, or in which the quality of the DNA sample is poor.

Phenylketonuria in the Greek population. Haplotype analysis of the phenylalanine hydroxylase gene and identification of a PKU mutation.

Haplotype analysis of the phenylalanine hydroxylase (PAH) gene was performed on 27 chromosomes from a sample of 14 Greek phenylketonuria (PKU) probands and their parents. The majority (94%) of the 17 mutant PAH alleles are on haplotypes 1, 2 and 4, with haplotype 1 being most common. Sixty per cent of ten control PAH alleles are on haplotypes 1, 2 and 4. Haplotype 3 was not present in either group. A new MspI restriction site was found in exon 9 of a single mutant PAH allele on haplotype 7. The mutation responsible for the restriction site alteration is a T to C transition at nucleotide 1154 of the PAH cDNA, resulting in the conversion of codon 311 from leucine to proline (L311P). The same mutation has been described on a haplotype 1 allele in a German PKU patient. A single crossover event would be required to transfer this mutation from haplotype 1 to 7. Migration of this mutation from one haplotype to another by recombination cannot be distinguished from a recurrent mutation at this site.

Identification of carriers of Duchenne muscular dystrophy: value of molecular analysis.

Currently, molecular methods are the most accurate diagnostic tools for carrier detection and prenatal diagnosis of Duchenne muscular dystrophy (DMD). This report illustrates the value of molecular diagnosis as opposed to previous diagnostic methods, the need for frequent re-evaluations as new methodologies develop, and the necessity for in-depth genetic counseling. In Family 1, the proposita was predicted to be a carrier by an indirect assay (abnormal in vitro muscle ribosomal protein synthesis). DNA analysis using restriction fragment length polymorphisms (RFLPs) indicated that she was not a carrier. She gave birth to a predicted non-affected male, who inherited the gene in question. In Family 2 the proposita, an obligate carrier, was initially evaluated by RFLP analysis. Two pregnancies were monitored by first trimester chorionic villous sampling. Re-evaluation indicated that all affected individuals, including one of the embryos, carried a deletion of the dystrophin gene. The identification of an RFLP within the region containing the deletion allowed unambiguous determination of the carrier status of all individuals.

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.