Rapid detection of medium chain acyl-CoA dehydrogenase gene mutations by non-radioactive, single strand conformation polymorphism minigels.

Medium chain acyl-CoA dehydrogenase (MCAD) deficiency is a common inherited metabolic disorder affecting fatty acid beta oxidation. Identification of carriers is important since the disease can be fatal and is readily treatable once diagnosed. Twelve molecular defects have been identified in the MCAD gene; however, a single highly prevalent mutation, A985G, accounts for > 90% of mutant alleles in the white population. In order to facilitate the molecular diagnosis of MCAD deficiency, oligonucleotide primers were designed to amplify the exon regions encompassing the 12 mutations enzymatically, and PCR products were then screened with a single strand conformation polymorphism (SSCP) based method. Minigels were used allowing much faster run times, and silver staining was used after gel electrophoresis to eliminate the need for radioisotopic labelling strategies. Our non-radioactive, minigel SSCP approach showed that normals can be readily distinguished from heterozygotes and homozygotes for all three of the 12 known MCAD mutations which were detected in our sampling of 48 persons. In addition, each band pattern is characteristic for a specific mutation, including those mapping in the same PCR product like A985G and T1124C. When necessary, the molecular defect was confirmed using either restriction enzyme digestion of PCR products or by direct DNA sequence analysis or both. This rapid, non-radioactive approach can become routine for molecular diagnosis of MCAD deficiency and other genetic disorders.     

Identification of CYP21 mutations,one novel,by single strand conformational polymorphism (SSCP) analysis

Congenital adrenal hyperplasia due to 21‐hydroxylase deficiency is a common autosomal recessive disorder (MIM# 201910) due to mutations in the 21‐hydroxylase (CYP21) gene (GDB Accession # M12792). Using our protocol for single strand conformational polymorphism (SSCP) analysis, we have identified two mutations not known to exist in the 21‐hydroxylase pseudogene (CYP21P). One mutation involving codon 169, TGC to AC appears to be novel. The 46,XX patient carried the codon 169 mutation on her paternal allele and a large gene deletion/conversion event on her maternal allele. This patient had been referred in the immediate neonatal period for the evaluation of genital ambiguity and had developed hyponatremia and hyperkalemia. The second patient presented with premature pubic hair. She carried R356Q on her maternal allele and V281L on her paternal allele. © 1998 Wiley‐Liss, Inc.     

Characterisation of CAH alleles with non-radioactive DNA single strand conformation polymorphism analysis of the CYP21 gene.

The major cause of congenital adrenal hyperplasia (CAH), a common recessive genetic disease, is the deficiency of steroid 21-hydroxylase (21OH), a microsomal enzyme encoded by the CYP21 gene. Although several CAH causing mutations have been identified in the CYP21 gene of patients with 21OH deficiency, genotyping of the 21OH locus is quite complex because of the high frequency of gene conversion and the presence of multiple mutations on single CAH alleles. In order to perform the complete characterisation of the CYP21 gene coding region more simply, we developed a highly sensitive, non-radioactive method allowing DNA single strand conformation polymorphism (DNA-SSCP) analysis. This method was applied to the characterisation of all the exons and intron-exon junctions of the CYP21 gene in five patients affected by the simple virilising form and one affected by the salt wasting form. In all samples showing SSCP signals, direct sequence analysis showed the presence of more than one single sequence variant. In particular, four mutations which are already known to cause the disease, 16 polymorphisms, and one newly identified C to T transition at position 849 were detected. A random sequence analysis, performed on 31 out of 81 exons showing a normal SSCP pattern, shows the method to be highly sensitive: no sequence variant was detected, thus confirming the validity of this non-radioactive DNA-SSCP analysis in characterising the CYP21 gene in patients with steroid 21OH deficiency. Notwithstanding the complete characterisation of all exons and exon/intron junctions of the CYP21 gene, no complete genotype/phenotype correlation was found in the panel of patients analysed, thus suggesting that characterisation of CAH alleles must be extended to outside the coding region of the CYP21 gene, most probably into the promoter region.     

Identification of CYP21 mutations, one novel, by single strand conformational polymorphism (SSCP) analysis. Mutations in brief no. 218. Online

Congenital adrenal hyperplasia due to 21-hydroxylase deficiency is a common autosomal recessive disorder (MIM# 201910) due to mutations in the 21-hydroxylase (CYP21) gene (GDB Accession # M12792). Using our protocol for single strand conformational polymorphism (SSCP) analysis, we have identified two mutations not known to exist in the 21-hydroxylase pseudogene (CYP21P). One mutation involving codon 169, TGC to AC appears to be novel. The 46,XX patient carried the codon 169 mutation on her paternal allele and a large gene deletion/conversion event on her maternal allele. This patient had been referred in the immediate neonatal period for the evaluation of genital ambiguity and had developed hyponatremia and hyperkalemia. The second patient presented with premature pubic hair. She carried R356Q on her maternal allele and V281L on her paternal allele.     

Utilities for high throughput use of the single strand conformational polymorphism method: screening of 791 patients with familial hypercholesterolaemia for mutations in exon 3 of the low density lipoprotein receptor gene.

We have modified several aspects of the single strand conformational polymorphism (SSCP) method to increase the speed with which the technique can be used for mutation detection. The methods attain high resolution of small mobility differences using long (30 cm) gels and use a modified polymerase reaction to maximise detection sensitivity using a minimised quantity of 32P. By using custom cut "sharktooth" combs (4.5 mm between teeth) as the slot formers, commercially available multichannel pipettes (9 mm tip to tip) can be used to load eight or 12 samples at a time from standard microtitre plates. PCR products that have been prepared and radiolabelled using simplified protocols are loaded on to the gel, and after a precalculated time of electrophoresis another set of samples can be loaded, either with combs moved across 2.25 mm or onto the same gel tracks. The run conditions are calculated so that there is no overlap between the bands produced by the two loadings, thus doubling the amount of information that can be gained from one gel. A computer program has been developed to solve equations to determine suitable timings for repetitive loadings. Finally, a modification of the gel pouring system is described so that two gels can be poured between three standard glass plates, with both gels run simultaneously. Of the order of 1000 PCR reactions can be prepared and analysed in 24 man hours using five 40 cm x 30 cm gel tanks. The application of these techniques is described to detect SSCPs in exon 3 of the low density lipoprotein receptor (LDLR) gene in 791 patients with familial hypercholesterolaemia (FH). Eight different SSCP patterns were seen, one of which was caused by the previously described E80K mutation, which was present in 11 patients (1.4%). In total, 32 patients (4%) were identified with exon 3 mutations.     

Rapid investigation of hepatitis A virus outbreak by single strand conformation polymorphism analysis

Investigation of hepatitis A virus (HAV) outbreaks often implies nucleotide sequence analysis. As an alternative method for the identification of related strains, single strand conformation polymorphism method (SSCP) was compared to sequence analysis. Twenty-three strains from sporadic and outbreak cases were studied retrospectively. SSCP, sequence identity and phylogenetic analyses were conducted on a 267 bp fragment of the VP1-2A variable region. The results of SSCP pattern comparison and sequence identity were highly correlated (r = 0.92, P < 0.001). If SSCP showed similar patterns, the VP1-2A fragments had a high and significant probability to have a sequence identity over 99.6%. Results were concordant for outbreak strains. The only discordant result concerned a cluster of three sporadic cases evidenced by phylogenetic analysis while SSCP showed similar patterns for only two of these three cases. A prospective SSCP analysis of a recent HAV outbreak confirmed the reliability of this technique. SSCP may thus provide a rapid and cost-effective tool for preliminary investigation of HAV outbreaks, before undertaking exhaustive nucleotide sequence analysis.     

Capillary electrophoresis-based single strand DNA conformation analysis in high-throughput mutation screening

The generation of the draft human genome sequence has created new possibilities for diagnosis, prevention, and treatment of human disease. One consequence of these new possibilities is an increasing need for methods and technology that can be used for high-throughput screening for mutations in large DNA sample materials. In recent years, a number of mutation screening methods have emerged that are based on the analysis of sequence-dependent changes in the conformation of single- and double-stranded DNA using capillary electrophoresis. Common features of these methods are high sensitivity and reproducibility as well as the possibility for automation and massive parallelization. Thus, at present they are among the most attractive technologies for high-throughput mutation screening. This review describes the recent advances in capillary electrophoresis-based single strand conformation polymorphism (CE-SSCP) for detection of unknown mutations, and assesses its practical usability for high-throughput mutation screening based on the available literature. In addition, future prospects are outlined in light of the recent advances in microchip-based capillary electrophoresis.     

Single strand conformational polymorphism analysis of human CD1 genes in different ethnic groups

CD1 molecules are able to present unusual antigens, lipids or glycolipids from mycobacterium cell walls to T lymphocytes. Previous studies have suggested that polymorphism of these genes is very limited, in contrast with classical major histocompatibility complex (MHC) antigen-presenting molecules. Our aim was to study possible allelic variations of exons 2 and 3, encoding for the alpha1 and alpha2 domains, respectively, of human CD1A, -B, -C and -D genes. We analyzed genomic samples of unrelated, healthy individuals from different ethnic background: 70 Caucasians from Europe, 33 Black Africans (13 from Tanzania and 20 Zulus), 19 Caucasians from the Sahara and 44 Asian individuals. We have found CD1A to be a biallelic locus with a common allele which was present in the majority of the individuals studied. The second allele differed from the common one by a single-point mutation, resulting in a change of Cys to Trp at position 52 in the alpha1 domain. This second allele was found in heterozygosis in 7 out of 70 Caucasians from Europe (allelic frequencies P=0.95 and q=0.05). In the Chinese population, we found the second allele present in heterozygosis in 19 from the 44 individuals studied, and we also found 6 homozygous individuals for the second allele (allelic frequencies P=0.64 and q=0.35). In addition, we detected a synonymous mutation (C to T transition) in codon 34 of CD1C exon 2 in 4 out of 20 Zulus and in 2 of the 13 Blacks from Tanzania.     

High resolution single strand conformation polymorphism analysis using formamide and ethidium bromide staining.

Single strand conformation polymorphism (SSCP) analysis using ethidium bromide can be improved by adding formamide as the denaturant. This gives higher resolution than previous SSCP methods; it had 100% sensitivity in the discrimination of 14 PCR samples from two different genes, even for a long fragment close to the upper limit of 250 base pairs. This modified procedure is a rapid, simple, safe, and yet highly sensitive method for detecting structural differences in DNA fragments.     

Screening for new mutations in the LDL receptor gene in seven French familial hypercholesterolemia families by the single strand conformation polymorphism method.

To investigate the molecular basis of familial hypercholesterolemia (FH) in France, we applied the single strand conformation polymorphism (SSCP) method to the promoter region and the 18 exons of the low density lipoprotein receptor (LDLR) gene. Seven probands, 4 heterozygotes, 2 compound heterozygotes, and 1 homozygote, belonging to FH families were tested. In all cases, previous genetic analysis and/or LDL receptor fibroblast assay had shown that the disease was due to defects in the LDLR gene. Out of the nine mutations expected, one nonsense mutation in exon 2 and six missense mutations were identified in exons 3, 6, 8, 11, and 15. Two of the latter were found in exon 6. In each family, cosegregation of the base substitution and the disease was observed. Ninety-five control subjects were screened for the presence of the six missense mutations. None was detected, implying that the mutations identified are deleterious. Our results indicate that the SSCP analysis of amplified genomic DNA fragments can be successfully used to rapidly screen mutation containing exons in large genes. Furthermore, all these mutations are newly described and demonstrate heterogeneity of LDLR gene mutations responsible for FH in the French population, as in other reported Caucasian populations.     

Single-strand conformational polymorphism and denaturing gradient gel electrophoresis in screening for variegate porphyria: identification of two new mutations

Single-strand conformational polymorphism and denaturing gel electrophoresis were used to screen for mutations in the protoporphyrinogen oxidase gene (PPOX) of three patients with clinically and biochemically proven variegate porphyria in order to select genomic regions for specific DNA sequence analysis. Two previously undescribed mutations were identified: PPOX1423-1426-delATCT and PPOX2272insG. Denaturing gel electrophoresis was able to discern the point mutation in exon 5 (PPOX2272insG) of the PPOX gene. Once an index individual has been identified, single-strand conformational polymorphism and denaturing gel electrophoresis techniques are useful to identify family members who may be unaffected carriers. Such identification can help potential cases to avoid medications and other triggers that could precipitate acute porphyric attacks.     

Site specific screening for point mutations in ornithine transcarbamylase deficiency.

Ornithine transcarbamylase (OTC) deficiency is a frequent X linked disorder of the urea cycle which is responsible for lethal neonatal hyperammonaemia in males and for various clinical symptoms in heterozygous females. In order to improve the efficiency of our screening for mutant genotypes, we focused on molecular domains of functional or structural importance in the OTC gene, namely the carbamyl phosphate binding domain (encoded by the third exon) and the MspI restriction sites (CCGG) of the coding sequence (located in exons 2 and 7 respectively), as they contain mutation hot spots (CpG doublets). Using this procedure, we were able to identify three new mutant genotypes in OTC deficient children including one nonsense mutation (E 87 K, G 50 ter, G 162 R). Since genetic counselling for OTC deficiency is frequently difficult, molecular screening directed towards specific sites of the coding sequence could allow rapid detection of mutant genotypes and help solve diagnostic problems, especially when carrier status cannot be clarified easily.     

Detection of a monocyte/macrophage differentiation antigen in routinely processed paraffin-embedded tissues by monoclonal antibody Ki-M1P

A new monoclonal antibody Ki-M1P that is raised against supernatants of detergent solubilized human lymph node tissue is described. Ki-M1P recognizes in particular monocytes and their macrophage derivatives as tested by light- and electron-microscopic immunohistochemistry. Granulocytes, dendritic cells as the accessory cells of humoral and cellular immune response, and epithelial, endothelial, neural, and mesenchymal cells do not react with Ki-M1P. In extensive application Ki-M1P has proven to be a useful marker for distinguishing monocytic leukemias within FAB groups M4 and M5. The recognized antigen is composed of five proteins with molecular masses of about 60, 92, 98, 124, and 150 kDa in blood monocytes, whereas tissue macrophages tested so far expressed only the 60-kDa protein. Because the Ki-M1P antigen is not destroyed or masked during routine fixation and paraffin embedding of biopsy tissue samples, Ki-M1P represents a useful diagnostic reagent for the identification of physiological functional and pathologic reaction forms as well as neoplastic variants of the human monocyte/macrophage system even in retrospective studies.     

Detection of RET proto-oncogene point mutations in paraffin-embedded pheochromocytoma specimens by nonradioactive single-strand conformation polymorphism analysis and direct sequencing.

The suitability of formalin-fixed and paraffin-embedded tumor material was evaluated for molecular analysis of the RET proto-oncogene. We analyzed exons 10, 11, and 16 for point mutations in seven sporadic and six multiple endocrine neoplasia (MEN) 2A-associated pheochromocytomas by a nonradioactive single-strand conformation polymorphism assay followed by nonradioactive direct sequencing of PCR-amplified DNA using an automated DNA sequencer. All MEN 2A-associated pheochromocytomas contained a heterozygous missense germline mutation within cystine codons of the cysteine-rich extracellular domain encoded by exons 10 and 11. Mutations were located in codon 619 (TGC-->TCC; Cys-->Ser) in one, in codon 635 (TGC-->CGC; Cys--Arg) in three, and in codon 635 (TGC-->TAC; Cys-->Tyr) in two pheochromocytomas. No tumor-specific (somatic) mutations were detected in exons 10, 11, and 16 of the sporadic pheochromocytomas. These data support recent findings that germline point mutations that are clustered in distinct cysteine codons of the RET proto-oncogene are involved in the neoplastic phenotype of the MEN 2A syndrome. Our results demonstrate that both nonradioactive single-strand conformation polymorphism and direct sequencing are suitable methods to detect single base substitutions in DNA extracted from archival material.     

Determination of Duchenne muscular dystrophy carrier status by single strand conformation polymorphism analysis of deleted regions of the dystrophin locus.

The molecular characterisation of the dystrophin gene, mutations in which are responsible for X linked Duchenne and Becker muscular dystrophies, has led to an array of strategies for the diagnosis of affected subjects and carriers. Initially these were based on blotting and hybridisation technologies but have recently been largely superseded by PCR based techniques which afford greater speed and sensitivity. We describe the use of single strand conformation polymorphism to detect heterozygosity in regions of the dystrophin locus which are deleted in affected males, to determine the carrier status of their female relatives.     

Intragenic single nucleotide polymorphism haplotype analysis of SUR1 mutations in familial hyperinsulinism

Familial hyperinsulinism (HI; MIM# 256450) is an autosomal recessive disorder of pancreatic β‐cell function, characterized by inadequate suppression of insulin secretion despite severe recurrent fasting hypoglycemia. Subtotal pancreatectomy is frequently required to prevent permanent neurologic sequelae. The incidence of HI in the Caucasian population is estimated at 1:50,000, however an apparent increased incidence among Ashkenazi Jews and Saudi Arabian Arabs has been reported. A locus for HI was assigned by linkage analyses to human chromosome 11p15.1. The sulfonylurea receptor (MIM# 600509, SUR1) and the potassium channel, inwardly rectifying, subfamily J member 11 (MIM# 600937, KIR6.2) genes, 2 components of the β‐cell K_ATP channel, are clustered in this chromosomal region, and mutations in these genes have been implicated in HI. We previously demonstrated that two mutations in the SUR1 gene are present on approximately 88% of HI‐associated chromosomes in Ashkenazi Jewish patients. Haplotype analysis with microsatellite markers flanking the gene revealed that one mutation (delF1388), reported only in Ashkenazi probands, occurred on two related extended haplotypes. By contrast, the second, more common mutation (3992‐9g→a) was associated with nine different intergenic haplotypes and has been reported in non‐Jewish HI patients as well. In this study, we evaluated disease‐associated chromosomes from 41 Ashkenazi Jewish and 2 non‐Jewish HI patients carrying the 3992‐9g→a mutation by assessing haplotypes defined by nine common single nucleotide polymorphisms (SNPs), six in the SUR1 gene, and three in the KIR6.2 gene. Our results indicate that all 54 chromosomes carrying the 3992‐9g→a mutation in the Jewish patients appear to have originated from one founder mutation, whereas the same mutation on chromosomes from non‐Jewish patients originated independently. Furthermore, our findings have implications concerning the HI‐associated chromosomes on which no mutation has been identified. Hum Mutat 14:23–29, 1999. © 1999 Wiley‐Liss, Inc.     

Rapid screening of fluoroquinolone resistance determinants in Streptococcus pneumoniae by PCR-restriction fragment length polymorphism and single-strand conformational polymorphism

A rapid method, using PCR-restriction fragment length and single-strand conformation polymorphism (SSCP), was applied to screen for mutations of the fluoroquinolone resistance determinants in Streptococcus pneumoniae. One hundred nonduplicate Streptococcus pneumoniae isolates with ciprofloxacin MICs of > or = 4.0 microg/ml from the Prince of Wales Hospital, Hong Kong, years 2000 to 2003, were examined. For each isolate, PCR amplicons of quinolone resistance-determining regions (QRDRs) of gyrA, gyrB, parC, and parE genes were digested with AluI, HinfI, Sau3AI, and MspI, respectively, and analyzed by SSCP. Each SSCP pattern was given a number, and each isolate obtained a four-digit code, e.g., 1111, that represented the SSCP profile. The SSCP patterns were correlated to mutations characterized from sequence analyses of PCR amplicons. The most common SSCP profile obtained was no. 5232 (40%), which included strains with two amino acid substitutions in the ParC (Lys-137-Asn) and ParE (Ile-460-Val) genes, followed by the SSCP profile 5223 (17%), which included strains with amino acid substitutions in the ParE (Ile-460-Val) gene only. Ten isolates (10%) with amino acid substitutions at GyrA and ParE (+/-ParC) genes were resistant to levofloxacin with a MIC of > or = 16 microg/ml. Other SSCP profiles were unique in distinguishing the common amino acid substitutions in GyrA (Ser-81-Phe) and ParC (Lys-137-Asn, Ser-79-Phe plus Lys-137-Asn, Asp-83-Asn plus Lys-137-Asn, Ser-79-Phe, and Glu-96-Asp). SSCP analysis of restricted fragments generated patterns that were highly discriminative for mutations present in the QRDRs of gyrA, gyrB, parC, and parE. This method provides a database of high resolution profiles on these mutations and allows rapid screening for new mutations of the fluoroquinolone resistance genes.     

Detection of missense mutations by single-strand conformational polymorphism (SSCP) analysis in five dysfunctional variants of coagulation factor VII

Five unrelated subjects with dysfunctional coagulation factorVII (FVII) were studied In order to Identify missense mutationsaffecting function. Exons 2 to 8 and the Intron-exon Junctionsof their FVIl genes were amplified from peripheral white bloodcell DNA by PCR and screened by SSCP analysis. DNA fragmentsshowing aberrant mobility were sequenced. The following mutationswere Identified: In case 1 (FVII: C <1%, FVIl:Ag 18%) a heterozygousA to G transltion at nucleotlde 8915 In exon 6 results In theamlno acid substitution Lys-137 to Glu near the C-termlnus ofthe FVlla llght chaln; In case 2 (FVII: C 7%, FVll:Ag 47%) aheterozygous A to G transltion at nucleotide 7834 In exon 5results in the substitution of Gin-100 by Arg in the secondEGF-like domain; In case 3 (FVll:C 20%, FVIl:Ag 76%) a homozygousG to A transition at nucleotide position 6055 in exon 4 wasdetected resulting in substitution of Arg-79 by Gin in the firstEGF-like domain; in case 5 (FVIl:C 10%, FVIl:Ag 52%) a heterozygousC to T transition at nucleotide position 6054 in exon 4 alsoresults in the substitution of Arg79, but in this case it isreplaced by Trp; case 4 (FVll:C <1%, FVIl:Ag 100%) was homozygousfor a previously reported mutation (G to A) at nucleotide position10715 in exon 8, substituting Gin for Arg at position 304 inthe protease domain. Cases 1,2 and 5 evidently have additionalundetected mutations.     

High-throughput single strand conformation polymorphism mutation detection by automated capillary array electrophoresis: validation of the method

Capillary array electrophoresis (CAE) is a novel technique, which allows for high throughput analysis of DNA fragments. When screening for mutations in whole populations or large patient groups it is necessary to have robust and well-characterized setups for high throughput analysis. For large-scale mutation screening, we have developed procedures for single strand conformation polymorphism (SSCP) assays using CAE (CAE-SSCP) whereby we may increase both the sensitivity and the throughput compared to conventional SSCP analysis. In this study we have validated CAE-SSCP by 1) comparing detection by slab-gel based SSCP with CAE-SSCP of mutations in the MYH7, MYL2, and MYL3 genes encoding sarcomere proteins from patients suffering from hypertrophic cardiomyopathy; and 2) by constructing a series of 185 mutants having substitution mutations, as well as insertion/deletion mutations, or some combinations of these, in different sequence contexts in four exons and different positions relative to the end of the amplicon (three from the KCNQ1 gene, encoding a cardiac potassium channel, and one from the TNNI3 gene encoding cardiac troponin I). The method identified 181 out of 185 mutations (98%), and the data suggest that the position of mutation in the fragment had no effect on the sensitivity. Analysis of the specificity of the method showed that only very few mutants could not be distinguished from each other and there were no false positives.