[RT-PCR in clinical diagnosis]

Application fields of RT-PCR (reverse transcription-polymerase chain reaction) in clinical diagnosis comprises the assessment of viral load for RNA viruses and the analysis of gene transcription products. RT-PCR is also helpful when large genes have to be sequenced. Developments of quantitative approaches using real-time PCR recently led to a major widening of RT-PCR applications in clinical diagnosis. However, RT reaction is delicate due to its lack of reproducibility and to RNA lability and frequent contamination by DNA. In some cases additional difficulties come from the need to obtain a specific amplification in the presence of homologous sequences which might be present in higher amounts than the sequence of interest. These caveats have to be taken into account, when designing the RT protocol, and when choosing PCR primers and internal and/or external references. This review is aimed at helping the experimental setup of a RT-PCR based assay according to the objectives.

Treatment of dystonic syndromes by chronic electrical stimulation of the internal globus pallidus

AIM

Dystonia is a medically intractable condition causing twisting or myoclonic movements and abnormal postures. There is an important heterogeneity among etiologies of dystonia. The electrical stimulation of the globus pallidus has been used successfully in primary generalized dystonia. The aim of this study was to examine the long-term efficacy and safety of deep brain stimulation (DBS) in the treatment of primary and secondary generalized dystonia in children and adults.

METHODS

Fifty-three patients were included. Electrodes were bilaterally implanted under stereotactic guidance and connected to neurostimulators, subcutaneously inserted. Efficacy was evaluated by comparing scores on the clinical and functional Burke-Marsden-Fahn dystonia rating scales (BMFDRS) before and after implantation. Patients were divided into 3 groups: group 1 comprised 15 patients with DYT1 dystonia; group 2, 17 patients with dystonia of unknown etiology and group 3, 21 patients with secondary dystonia. The mean follow-up was 26.6+/-12.3 months for primary dystonia and 23.1+/-11.8 for secondary dystonia.

RESULTS

After 1 year, the improvement of the clinical score is 71% in group 1, 74% in group 2 and 31% in group 3. The functional score was improved by 63% in group 1, 49% in group 2 and 7% in group 3. We did not find any significant difference between children and adults. In secondary dystonia, efficacy of the stimulation is more limited. The efficacy of the stimulation improved with time for the 3 groups. COMCLUSION: Electrical stimulation of the internal globus pallidus proved to be an effective treatment for generalized dystonia and should be considered as first-line therapy.

[The varied etiologies of childhood-onset dystonia]

Dystonia is not uncommon in childhood, and identification of its etiology is an ultimate aim in the clinical evaluation of dystonia. Advances in neuroimaging, recent identification of gene or loci implicated in dystonic syndromes, and characterisation of new pathological entities (creatine deficiency, biotin-responsive basal ganglia disease) enlarge our understanding of childhood dystonia, and expend its diagnosis spectrum. Awareness of the diverse etiologic categories of childhood-onset dystonia is necessary to accurate diagnosis approach. Clinical examination and cerebral magnetic resonance imaging are the keys of this diagnosis approach. Primary dystonia is defined as syndromes in which dystonia is the sole phenotypic manifestation (especially no cognitive deterioration is observed, and brain MRI is normal); DYT1 dystonia, in which the abnormal gene is located on chromosome 9, is the most frequent childhood-onset primary dystonia; progressive generalisation of the abnormal movements occur in 70p.cent of the patients. Dopa - Responsive Dystonia are characterized by marked diurnal fluctuations of the dystonic symptoms and by their marked and sustained response to dopaminergic therapy; associated parkinsonian signs are usually observed later in the course of the disease. Clinical presentation of DRD might be atypical (mimicking cerebral palsy or isolated limb pain without diurnal fluctuation). DRD is rare, but a trial of L-dopa should be performed on all patients with childhood-onset dystonia, lasting at least one month. Secondary dystonias or heredodegenerative diseases are the most frequent etiology of childhood-onset dystonic syndromes. Among a huge range of heredodegenerative disease, those that are amenable to a specific treatment, such as Wilson's disease or creatine deficiency, should be particularly investigated. The main objective of investigation of dystonia is to identify secondary dystonias or heredodegenerative diseases. Further investigations will be performed according to the clinical characteristics of the dystonia, to the presence of associated neurological or extraneurological symptoms, and according to brain imaging; this approach must be discussed for each single patient. The aim of the diagnosis strategy is the rapid identification of the etiology of dystonia which will lead to accurate treatment and pertinent genetic counselling.

[Molecular genetics of pigmentary retinopathies: identification of mutations in CHM, RDS, RHO, RPE65, USH2A and XLRS1 genes]

PURPOSE

To evaluate the occurrence and inheritance of various types of pigmentary retinopathy in patients followed at the outpatient clinic in the university hospital, Montpellier, France. To characterize genes and mutations causing these conditions.

METHODS

Ophthalmic examination and various visual tests were performed. Mutations were sought from genomic DNA by PCR amplification of exons associated with single-strand conformation analysis and/or direct sequencing.

RESULTS

Among 315 patients over an 8-year period, cases of retinitis pigmentosa (63.2%), Usher's syndrome (10.2%), Stargardt's disease (5.4%), choroideremia (3.2%), Leber's congenital amaurosis (3.2%), congenital stationary night blindness (2.9%), cone dystrophy (2.5%), dominant optic atrophy (1.9%), X-linked juvenile retinoschisis (1.6%), Best's disease (1.6%), and others (4.3%) were diagnosed. In retinitis pigmentosa, inheritance could be determined in 54.2% of the cases including dominant autosomic (26.6%), recessive autosomic (22.6%), and X-linked cases (5%) while it could not be confirmed in 45.7% of the cases (simplex cases in the majority). For the 6 examined genes, mutations were found in 22 out of 182 propositus (12.1%). Analysis of phenotype-genotype correlations indicates that in retinitis pigmentosa, RDS is more frequently associated with macular involvement and retinal flecks, RHO with regional disease, and RPE65 with the great severity of the disease with some cases of Leber's congenital amaurosis.

CONCLUSIONS

Identification of genes may help in diagnosis and in genetic counseling, especially in simplex cases with retinitis pigmentosa. In this latter condition, molecular diagnosis will be necessary to rationalize future treatments.

Mapping of a new locus for autosomal recessive demyelinating Charcot-Marie-Tooth disease to 19q13.1-13.3 in a large consanguineous Lebanese family: exclusion of MAG as a candidate gene

Autosomal recessive Charcot-Marie-Tooth disease (CMT) type 4 (CMT4) is a complex group of demyelinating hereditary motor and sensory neuropathies presenting genetic heterogeneity. Five different subtypes that correspond to six different chromosomal locations have been described. We hereby report a large inbred Lebanese family affected with autosomal recessive CMT4, in whom we have excluded linkage to the already-known loci. The results of a genomewide search demonstrated linkage to a locus on chromosome 19q13.1-13.3, over an 8.5-cM interval between markers D19S220 and D19S412. A maximum pairwise LOD score of 5.37 for marker D19S420, at recombination fraction [theta].00, and a multipoint LOD score of 10.3 for marker D19S881, at straight theta = .00, strongly supported linkage to this locus. Clinical features and the results of histopathologic studies confirm that the disease affecting this family constitutes a previously unknown demyelinating autosomal recessive CMT subtype known as "CMT4F." The myelin-associated glycoprotein (MAG) gene, located on 19q13.1 and specifically expressed in the CNS and the peripheral nervous system, was ruled out as being the gene responsible for this form of CMT.

No missense mutation in choroideremia patients analyzed to date

PURPOSE

To elucidate the status of a previously described missense mutation (1442A>T) reported in the Rab Escort Protein 1 gene of a patient with choroideremia.

METHODS

The base substitution previously described by Donnelly et al. (Hum Mol Genet 1994;3:1017) was first confirmed by direct genomic DNA sequencing. The REP-1 cDNA region encompassing exons 10-14 was then specifically amplified from lymphocyte-derived mRNA. The effect on mRNA splicing of the mutation was analyzed by RT-PCR and cDNA sequencing.

RESULTS

The 1442A>T change located at the penultimate nucleotide of exon 11 causes complete skipping of this exon during the processing of REP-1 mRNA. Loss of exon 11 leads to the translation of a premature termination codon within exon 12.

CONCLUSION

RT-PCR analyses demonstrated that the 1442A>T transversion previously described as a possible causative missense mutation does act as a splice-site error and gives rise to a truncated REP-1 protein. The virtual absence of any missense mutation found to be responsible for choroideremia makes the RT-PCR-based protein truncation test the most relevant genotypic diagnostic procedure for identifying mutations in the CHM gene.

[Treatment of early-onset generalized dystonia by chronic bilateral stimulation of the internal globus pallidus. Apropos of a case]

Dystonia musculorum deformans is an inherited severe disease, with a wide clinical polymorphism. The most severe clinical forms with early onset carry a high risk of life-threatening complications. In the absence of any efficient medical treatment, bilateral pallidotomy has previously been reported to be of value in the management of this disease. We report the first clinical case of a severe early-onset generalized dystonia dramatically improved by a bilateral stimulation of the internal globus pallidus. In November 1996, we proposed this neurosurgical procedure for a 8-year-old girl, who had suffered since the age of 3 from severe generalized dystonia, and who progressively became totally dependent and bedridden. She had been under sedation and permanent controlled respiratory assistance for the last two months. The etiology of the disease remained unknown (the DYT1 mutation was absent). Under general anesthesia, we bilaterally implanted a four-contacts electrode in the internal globus pallidus, using the Leksell's stereotactic frame and a 1.5 tesla MRI control. A dramatic improvement was noted 6 weeks later and led us to connect the two electrodes to neurostimulators inserted under the abdominal skin.

Direct estimation of the recombination frequency between the RB1 gene and two closely linked microsatellites using sperm typing

In this study, single sperm typing has been used for high-resolution recombination analysis between the retinoblastoma gene and two closely linked extragenic microsatellites (D13S284 and D13S1307). The analysis of 1198 single sperm from three donors allowed the determination of recombination fractions between RB1.20 and D13S284 and RB1.20 and D13S1307 of 0.022 and 0.033, respectively. These results show that RB1 gene and the two microsatellites are closely linked, which validates their potential use in indirect genetic diagnosis of retinoblastoma.

Length variations of the poly(T) tract at the exon 3 splice acceptor site of the choroideremia gene

By using the single strand conformational analysis to search for point mutations in the choroideremia gene, we have identified an intronic polymorphism within the intron 2 of the CHM gene. We have studied the frequency of this polymorphism in the population from South of France.

Mosaic expression of two dystrophins in a boy with progressive muscular dystrophy

A boy with a Becker muscular dystrophy (BMD) phenotype presented unique muscular dystrophin expression. Western blot analysis showed the presence of two dystrophins of different sizes, i.e., a 400-kDa dystrophin and a 500-kDa form. An immunofluorescent study revealed mosaic expression of these dystrophins in the sarcolemma, with matching alpha-sarcoglycan and beta-dystroglycan staining patterns. DNA and RNA analysis did not reveal any mutation in the dystrophin gene, and the karyotype was normal.

Altered rep-1 expression due to substitution at position +3 of the IVS13 splice-donor site of the choroideremia (CHM) gene

PURPOSE

To characterize the effect on mRNA splicing of a yet undescribed mutation located in intron 13 splice-donor sequence (IVS13 + 3A --> C) in the Rab-Escort-protein 1 gene of a patient with choroideremia.

METHODS

The base substitution was firstly detected by the Single Strand conformation analysis from genomic DNA. A REP-1 cDNA region encompassing exons 10-14 was then specifically amplified from lymphocytes-derived mRNA.

RESULTS

We could demonstrate that this substitution affects REP-1 RNA processing. The patient revealed only one aberrantly spliced mRNA lacking exon 13 and no normal transcript.

CONCLUSION

The skipping of exon 13 results in the creation of a stop codon at the misspliced junction. This is the first case of nucleotide substitution at the +3 position of a splice donor site so far described in choroideremia.

[Update on a diagnostic test for choroideremia: the protein truncation test (PTT)]

PURPOSE

The aim of this study was to define the RT-PCR-PTT parameters for CHM gene analysis and to evaluate its interest as a method for CHM mutation screening.

METHODS

The entire CHM coding region was reversed-transcribed in three overlapping cDNA segments (RT-PCR) which were amplified and further analyzed by PTT after in vitro transcription/translation.

RESULTS

This strategy enabled us to detect a truncated peptide in each of the 6 unrelated patients from southern France who were investigated. The mutation was further characterized by direct sequencing of the RT-PCR product.

CONCLUSION

In CHM gene, all conditions are present to make the RT-PCR-PTT strategy the method of choice for mutation screening. As a result of the simplified protocol described in this study, the families of the patients could benefit from accurate carrier-status assessment.

[Rapid genetic diagnosis of females carriers related to patients with choroideremia]

PURPOSE

By using the single strand conformation analysis to search for point mutations in the choroideremia gene, we had previously identified the first truncative mutation responsible for CHM in France. The aim of the present study was to perform a simple and nonisotopic routine test to identify carriers and non carriers in the relevant family.

METHODS

We used a PCR-based restriction analysis to detect the presence or absence of the mutation in the family members, as the mutation creates a restriction site in the coding sequence of the CHM gene.

RESULTS

We could follow the segregation of the mutation in the pedigree, and unambiguously determine the genetic status of the females.

CONCLUSION

When a mutation responsible for choroideremia modifies a restriction site, the PCR-restriction provides an efficient and unexpensive one-day test to detect heterozygosity in the family.

Mutation analysis of the dystrophin gene in Southern French DMD or BMD families: from Southern blot to protein truncation test

Data from 6 years of experience in molecular diagnosis of Duchenne (DMD) and Becker (BMD) muscular dystrophy in Southern France are reported. DMD and BMD patients have been extensively analyzed for deletions and for point mutations in the dystrophin gene. By scanning the whole coding sequence as reverse-transcribed from lymphocytes or muscular RNA by the protein truncation test, we have reached a minimum of an 86% detection rate for point mutations responsible for DMD; these mutations consist of nonsense, frameshifting, and splicing mutations. Four of 12 small alterations identified in our sample are novel and described in this study. We also present an improved protocol for the automated detection of fluorescently labeled duplex polymerase chain reactions of six known intragenic microsatellites (Dys II, TG 15, STRs 44, 45, 49, and 50). Accurate sizing of the alleles at each locus was performed, and we elucidated the sequence of several repeat units. Allele frequencies at each of the six microsatellite loci and at one restriction fragment length polymorphism site (intron 16/TaqI) were defined in a sample of normal, DMD, and BMD X chromosomes from Southern France. The determination of the grandparental origin of either deletions or point mutations revealed differences depending on the type of the mutation, with most of the deletions occurring in oogenesis and most of the point mutations occurring in spermatogenesis.

The protein truncation test (PTT) as a method of detection for choroideremia mutations

The predominance of truncative mutations responsible for choroideremia (CHM) led us to investigate the use of the protein truncation test (PTT) applied to lymphocyte RNA derived from affected males as a scanning method. The entire CHM coding region was reversed-transcribed in three overlapping cDNA segments (RT-PCR) which were amplified and further analysed by PTT after in vitro transcription/ translation. This strategy enabled us to detect the CHM-causative alteration in each of the four unrelated patients from southern France who were investigated. We describe three novel mutations (E177X, 323delT, 1313delTC), and report one recurrent mutation (R267X) in CHM. We believe this to be the first attempt at applying RT-PCR-PTT to CHM mutation detection.

An exonic polymorphism (381A/G) in the choroideremia gene

By using the single strand conformational analysis (SSCA) to search for point mutations in the choroideremia gene, we have identified a previously undescribed polymorphism within exon 5a (381A/G). We have studied the frequency of this polymorphism in a population from Southern France. The sequence variation creates a new restriction site for HhaI, allowing a convenient DNA-based genetic counseling in families in which the causal disease mutation is unknown.

Recurrent PIG-A mutation (IVS5+1G-->A) in a paediatric case of paroxysmal nocturnal haemoglobinuria: detection by the protein truncation test

Paroxysmal nocturnal haemoglobinuria (PNH) is an acquired haemopoietic stem cell disorder caused by the absence of glycosyl phosphatidylinositol (GPI)-anchored surface proteins due to a deficient biosynthesis of GPI-anchor. The disease occurs predominantly in adults, and very few cases have been described in children and adolescents. Recent analyses have shown that null mutations in the X-linked PIG-A (phosphatidylinositol glycan-class A) gene are responsible for GPI-anchor deficiency in most PNH adult patients analysed. We report a young male from southern France who was diagnosed with PNH at 12 years of age during follow-up of aplastic anaemia. To further elucidate the molecular basis of PNH occurring in childhood, we used the powerful and rapid protein truncation test to scan for truncative mutations in the entire PIG-A mRNA reverse transcribed and amplified from blood mononuclear cells. The somatic defect responsible for PNH in the patient was found to be a splicing mutation. IVS5+1G-->A, which has previously been described in two Asiatic adults with PNH.

Lack of evidence for connexin 43 gene mutations in human autosomal recessive lateralization defects

Heterotaxy is the failure of the developing embryo to establish normal left-right asymmetry, which is often associated with multiple malformations. Previous studies have identified different mutations in the cytoplasmic tail of the connexin 43 (cx 43) gene in six patients from a series of six sporadic cases with defects of laterality and severe heart malformations. These cases showed that of the genes involved in lateralization defects with autosomal recessive transmission, cx 43 was the most important. This result was challenged by two different teams, which, on sequencing only the carboxyl terminal end of the cx 43 gene in 30 patients, found no mutations. To assess the responsibility of the cx 43 gene in human autosomal recessive lateralization defects, we tested its involvement in a selected group of 25 patients (19 familial cases) with a wide variety of lateralization defects and cardiovascular malformations. The whole coding sequence and direct flanking sequences were screened for mutations, both by single strand conformation analysis and direct fluorescent sequencing. We could only detect a single base pair insertion in the 3' untranslated region of one patient. To test the possibility of mutations in other parts of the cx 43 gene, the gene was located onto the physical map of chromosome 6, and flanking polymorphic markers were genotyped. Haplotype analysis excluded the cx 43 gene locus in nearly all of the familial cases of lateralization defects. Thus, our results do not support the suggestion that this gene is implicated in human autosomal recessive lateralization defects.

Transcript analysis of CFTR frameshift mutations in lymphocytes using the reverse transcription-polymerase chain reaction technique and the protein truncation test

mRNA transcripts of the cystic fibrosis transmembrane conductance regulator (CFTR) gene were analyzed from lymphocytes of two cystic fibrosis compound heterozygotes (394delTT/3195del6 and 1215delG/ 2423delG), of five related carriers heterozygous for one of these mutations, and of five normal individuals. After reverse transcription of total RNA and amplification by the polymerase chain reaction, fragments were investigated by sequencing and by the protein truncation test (PTT). The three frameshift mutants were correctly detected by PTT, as they introduced a premature termination codon resulting in shortened protein products. The PTT approach thus provides a simple and reliable alternative method for detecting frameshift, nonsense, or splice site mutations, and for ascertaining their putative effect on the reading frame of the mRNA. In addition, we have identified 6 alternatively spliced forms of CFTR mRNA, two of which (transcripts lacking 4 + 5 or 17B) have not been described previously.

Four novel dystrophin point mutations: detection by protein truncation test and transcript analysis in lymphocytes from Duchenne muscular dystrophy patients

About 30% of cases of Duchenne muscular dystrophy (DMD) result from point mutations randomly distributed in the immense dystrophin gene. As already observed for the gross rearrangements, most of the DMD point mutations identified so far give rise to truncated proteins. Here, we report results of a comprehensive search for point mutations within the dystrophin gene based on illegitimate transcript analysis by using the RT-PCR technique in combination with a method capable of selectively detecting translation-termination mutations, called the protein truncation test (PTT). The RT-PCR-PTT procedure was successful in detecting mutations in 4 out of the 6 DMD patients who were investigated. These mutations, Q2972X in exon 59, 3474insC in exon 24, delT393-G394+5 in exon/intron 3, and 2436delAG in exon 18, had not been previously described. Moreover, several alternatively spliced forms of ectopic dystrophin mRNA were characterized in normal controls or in DMD patients. Most of these differentially spliced messages consisting of exon skipping or intronic sequence insertion are reported here for the first time.

Identification of variable length polyadenosine tract at the dystrophin locus

We report the characterization of a length polymorphism in the human dystrophin gene, consisting of single-base pair increments in a polyadenosine tract located near the 3' end of exon 68. Using Single Strand Conformation Analysis (SSCA), three length alleles could be identified (10,182 + 13A9/10/11). This class of 1-bp length variant is rare among known intronic gene sequences, and has been described only once in the dystrophin gene. Furthermore, the high polymorphic content (0.56) of this novel marker and its distal localization in the 3' end of the coding sequence make it suitable for diagnostic purposes.

Protein truncation test: analysis of two novel point mutations at the carboxy-terminus of the human dystrophin gene associated with mental retardation

Approximately one-third of the mutations responsible for Duchenne muscular dytrophy (DMD) do not involve gross rearrangements of the dystrophin gene. Methods for intensive mutation screening have recently been applied to this immense gene, which resulted in the identification of a number of point mutations in DMD patients, mostly translation-terminating mutations. A number of data raised the possibility that the C-terminal region of dystrophin might be involved in some cases of mental retardation associated with DMD. Using single-strand conformation analysis of products amplified by polymerase chain reaction (PCR-SSCA) to screen the terminal domains of the dystrophin gene (exons 60-79) of 20 unrelated patients with DMD or BMD, we detected two novel point mutations in two mentally retarded DMD patients: a 1-bp deletion in exon 70 (10334delC) and a 5' splice donor site alteration in intron 69 (10294 + 1G-->T). Both mutations should result in a premature translation termination of dystrophin. The possible effects on the reading frame were analyzed by the study of reverse transcripts amplified from peripheral blood lymphocytes mRNA and by the protein truncation test.

Base substitutions in the human dystrophin gene: detection by using the single-strand conformation polymorphism (SSCP) technique

We have established the experimental conditions to screen twenty regions of the dystrophin gene using the method of single-strand conformational polymorphism (SSCP) analysis. The aim of this study was to identify point mutations in patients with Duchenne or Becker muscular dystrophy (DMD or BMD) who have no gross DNA rearrangements detectable by Southern blot analysis or multiplex exon amplification. The investigation of thirteen patients using this procedure resulted in the detection of seven sequence polymorphisms (four identified in this study) that will be useful allelic markers in familial DNA analysis. Three rare sequence variants could be found (two of them being novel variants) but we were unable to demonstrate mutations that could be clearly sufficient to be responsible for the phenotype. This analysis confirmed the efficiency of the SSCP technique for the detection of nucleotide substitutions. Application of this approach to mutation or polymorphism detection to other exons of the gene will improve carrier and prenatal diagnosis.

A new intragenic polymorphism detected by the single-strand conformation polymorphism (SSCP) assay in the dystrophin gene

We have employed the single strand conformation polymorphism (SSCP) technique to examine a group of patients with Duchenne or Becker muscular dystrophy who do not contain deletions detectable by multiplex PCR or Southern/cDNA, in an attempt to identify uncommon mutations within the dystrophin gene. In SSCP analysis, a mutated sequence can be detected as a change of mobility in a nondenaturing polyacrylamide gel. During the course of this investigation, we detected and characterized a new polymorphism at the 3' end of intron 16. The G-to-T base change creates a TaqI restriction site which allows for rapid typing of the polymorphism by restriction digestion and electrophoresis of PCR amplified products. Its localization inside the 5' region of the dystrophin gene and its high heterozygosity makes it a useful and easy tool for rapid carrier and prenatal diagnosis.

Becker muscular dystrophy: demonstration of the carrier status of a female by immunoblotting and immunostaining

Becker muscular dystrophy (BMD) often results from in-frame mutations of the dystrophin gene, leading to the production of an altered-sized protein. We examined the expression of dystrophin in a BMD patient and in his asymptomatic mother by Western blot and immunofluorescence. The combination of these techniques allowed us to demonstrate the presence of two different dystrophins, normal-sized or reduced-sized in the muscular fibers of the asymptomatic carrier. This result emphasizes the value of dystrophin analysis for carrier detection and genetic counselling of families with Becker muscular dystrophy.

Molecular deletion patterns in families from southern France with Duchenne/Becker muscular dystrophies

We studied 38 unrelated patients from southern France with Duchenne (DMD) or Becker (BMD) muscular dystrophy for intragenic deletions of the DMD/BMD gene. We used both multiplex amplification of selected exons and cDNA probes. Of the 26 (68%) unrelated individuals found to have deletions, 24 (92%) were detected by multiplex polymerase chain reaction. All these deletions have been delineated with regard to the exon-containing HindIII fragments revealed by cDNA probes, and in two cases, junction fragments of altered size were seen. The correlation between phenotype and type of deletion agreed with the reading frame theory, except for two BMD and two DMD cases.