Rapid detection of Flt3 mutations in acute myeloid leukemia patients by denaturing HPLC

BACKGROUND: fms-related tyrosine kinase 3 (Flt3) is the most commonly mutated gene in human acute myeloid leukemia (AML) and has been implicated in its pathogenesis. Because screening of Flt3 in AML patients by PCR followed by gel electrophoresis is time-consuming and fails to detect some very small internal tandem duplications (ITDs), we developed a method for screening of FLT3 receptor mutations with PCR plus denaturing HPLC (D-HPLC). METHODS: Total mRNAs extracted from 34 AML patients were first analyzed for the presence of juxtamembrane length mutations and tyrosine kinase domain point mutations by a conventional method involving PCR amplification, restriction enzyme digestion, and agarose gel electrophoresis (PCR-RED-AGE). Subsequently, the same patient panel was analyzed by D-HPLC, using specifically designed primers and optimized running temperatures for the length and point mutation analysis. RESULTS: Thirty-four patients were analyzed by PCR-RED-AGE; 9 were positive for known Flt3 mutations: 6 of 34 (18%) for ITDs in exon 14 and 3 of 34 (9%) for point mutations in exon 20. The same patient panel was analyzed by D-HPLC, and additional nucleotide changes were discovered; in total, 14 sequence variations were identified: 7 of 34 (21%) for ITDs in exon 14; 2 of 34 (6%) for point mutations in exon 20; 1 of 34 (3%) for a new point mutation in exon 16; and 4 of 34 (12%) for polymorphisms in exons 13 and 14. Direct sequencing analysis identified nucleotide alterations in each of the "D-HPLC positives" but in none of the "D-HPLC negatives", yielding a specificity and sensitivity of 100% for D-HPLC-based screening. CONCLUSIONS: This novel D-HPLC-based procedure, which is optimized for identification of new point mutations in the catalytic and regulatory domains of FLT3 receptor, could potentially be useful for studies involving precise genotype determination, which could be critical for selection of innovative AML therapies targeting the FLT3 protein.     

Exhaustive screening of exon 10 CFTR gene mutations and polymorphisms by denaturing gradient gel electrophoresis: applications to genetic counselling in cystic fibrosis.

Several mutations in the cystic fibrosis (CF) gene have been reported. Ten, including the most prevalent mutation in Caucasians, delta F508, are located in exon 10 of the gene, in addition to five sequence polymorphisms. We have previously presented a strategy based on denaturing gradient gel analysis for the rapid detection of any nucleotide variation in all the exons and their immediate flanking regions. We now report the application of this method to the simultaneous detection of all mutations and polymorphisms located in exon 10, together with the use of exon 10 polymorphisms, especially the most frequent one (M470V), as intragenic markers for prenatal diagnosis of cystic fibrosis in families with at least one affected child and unknown disease-causing mutations.     

Use of TP53 reference materials to validate mutations in clinical tissue specimens by single-strand conformational polymorphism analysis.

BACKGROUND: As genetic information moves from basic research laboratories in to the clinical testing environment, there is a critical need for reliable reference materials for the quality assurance of genetic tests. A panel of 12 plasmid clones containing wild-type or point mutations within exons 5-9 have been developed as reference materials for the detection of TP53 mutations. AIM: The goal of this study was to validate the reference materials in providing quality assurance for the detection of TP53 mutations in clinical specimens. METHODS: We studied 33 gynecological samples, 11 apparently normal samples and 22 malignant tumors of various origins. Mutations were identified using single-strand conformational polymorphism analysis with both slab gel and capillary electrophoresis. All DNA samples were amplified with fluorescently labeled PCR primers specific for exons 5-9 for mutation detection. RESULTS: Of the 33 patient samples tested, mutations and polymorphisms were found in six specimens in three of the five exons scanned; no mutations were found in exons 7 or 9. Both a mutation and polymorphism were found in non-malignant specimens from the control group. The mutations were confirmed by DNA sequence analysis of the regions scanned. CONCLUSIONS: Mutations and polymorphisms were detected in the clinical samples. All of the mutations were silent except for one non-conservative mutation in exon 5, codon 181. This study demonstrates the usefulness of the National Institute of Standards and Technology (NIST) TP53 reference panel in TP53 mutation detection in clinical tissue specimens.     

A mutation analysis on GYPC, the gene encoding the Gerbich blood group antigens

The four exons of GYPC genomic DNA were amplified together with their flanking sequences and analysed by denaturing gradient gel electrophoresis (DGGE) or single-strand conformational analysis (SSCA). Exons 2 and 3 were amplified by a common set of primers so as to provide an internal control for exon deletion mutants. Ge:-2,-3,4 (Ge) and Ge:-2,3,4 (Yus) phenotypes were always associated with exon 3 and exon 2 deletions, respectively, as determined by DGGE. Ge:-2,-3,-4 (Leach) was associated with a deletion of exons 3 and 4. Two single base mutations within exon 2 were detected, one of which represented the An ^a allele and encoded an amino acid substitution. A previously undetected single base mutation in exon 3 encoded a Val61Ile substitution within the membrane spanning domain. DGGE analysis of exon 4 product revealed two distinct haplotypes of frequencies 41% and 59%. DGGE was not found suitable for analysis of exon 1, so SSCA was utilized. This method distinguished the single base mutation responsible for Wb antigen, but not that responsible for Dh^a.     

Comparison of genetic polymorphisms of CYP2E1, ADH2, and ALDH2 genes involved in alcohol metabolism in Koreans and four other ethnic groups

Background and objectives:  Recent studies of the genetics of alcoholism have considered genetic factors in alcohol metabolism and have identified functional polymorphisms in genes encoding enzymes involved in ethanol metabolism. The aim of this study was to estimate the genotype and allele frequencies of polymorphisms of three major ethanol-metabolizing enzymes (ADH2, ALDH2 and CYP2E1) in Koreans and to compare them with those of other ethnic groups.
Methods:  We chose three polymorphisms, ADH2 (*2), ALDH2 (*2) and CYP2E1 (c2), which are most likely to affect alcohol metabolism. To evaluate the allele frequencies of these single-nucleotide polymorphisms, 342 healthy Korean volunteers were recruited. Each genotype was determined by the TaqMan or SNaPshot method with genomic DNA extracted from peripheral leucocytes. We compared these allele frequencies with those of other ethnic groups registered on the International HapMap database.
Results and discussion:  The allele frequencies in Koreans were 80·3% for the ADH2 (*2), 13·9% for ALDH2 (*2), and 20·9% for CYP2E1 (c2). Other Asians, including Japanese and Chinese populations, show similar frequencies (Japanese, 73·9%, 22·7%, and 20·5% respectively and Chinese, 76·7%, 15·6%, and 28·9% respectively), whereas African and European groups have quite different frequencies (Europeans, 0%, 0%, and 5·1% respectively and African, 0%, 0%, and 0% respectively).
Conclusion:  Our current observations provide data on the prevalence of polymorphisms of ethanol-metabolizing enzymes, which should be useful in assessing the comparative susceptibility of different populations to diseases related to ethanol consumption.     

Genetic polymorphisms of alcohol metabolising enzymes: their role in susceptibility to oesophageal cancer.

BACKGROUND: Alcohol is a major risk factor for susceptibility to oesophageal cancer in the South African population. The role of polymorphisms in alcohol metabolising enzymes, alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH2) in predisposition of this population to oesophageal cancer is unknown. Alcohol metabolising enzymes exhibit polymorphisms that result in variant alleles with either increased or decreased activity. METHODS: The role of these polymorphisms in increased risk of oesophageal cancer was investigated in 238 patients and 268 controls from Black and Mixed Ancestry South Africans, using the PCR/RFLP technique. RESULTS: The ADH3*2/*2 genotype was significantly associated with increased risk for oesophageal cancer amongst Black subjects (odds ratio, 2.19; p=0.004). The low activity ALDH2*2 allele was significantly associated with increased risk for oesophageal cancer amongst the Black subjects (odds ratio, 2.35; p=0.0084). CONCLUSIONS: It was observed that ADH variants, ADH2*1 and ADH3*2, were associated with increased risk for oesophageal cancer, possibly due to the tolerance of the carriers of these alleles to alcohol consumption compared to those with high activity alleles (ADH2*2 and ADH2*3) which are associated with higher production of the unpleasant acetaldehyde intermediate.     

Simultaneous genotyping of alcohol dehydrogenase 2 and aldehyde dehydrogenase 2 by single-strand conformation polymorphism analysis

Alcohol dehydrogenase (ADH; EC 1.1.1.1) and aldehyde dehydrogenase (ALDH; EC 1.2.1.3) have important roles in the elimination of ingested ethanol. These enzymes have polymorphisms resulting from single-point mutations that cause kinetic differences in their respective enzyme activities. Simultaneous observation of these enzymes would be useful in investigating the association between these enzyme polymorphisms and alcohol-related problems. In this study amplified genomic DNA was amplified from nail clippings with two sets of primers for ADH2 and ALDH2 genes, respectively, in a micro test tube and the accuracy of the amplification was verified by direct sequencing. The PCR products were separated into four distinct bands by single-strand conformation polymorphism analysis. This genotyping method is fast, accurate. reliable and inexpensive, and requires the same amount of template DNA as non-simultaneous methods. In other words, the required amount of template DNA for this method is only half that required for the separate genotyping of ADH2 and ALDH2.     

Mutation analysis of the Vangl2 coding region revealed no common cause for Tetralogy of Fallot

Vangl2 (Van Gogh-like 2) protein acts via non-canonical Wnt signalling to regulate polarized cell movements during development of the proximal outflow tract in vertebrate embryos. Recently, it has been shown that mutations of the Vangl2 gene cause aortic arch defects that are characteristic of the loop-tail (Lp) mouse and they have also became a strong candidate for causing congenital outflow tract defects in humans. Thus, in this study Tetralogy of Fallot (ToF), which comprises a group of syndromes that constitutes the most frequent cause of congenital cardiac outflow abnormalities in humans, was analysed for mutations within all coding regions of the Vangl2 gene. Based on direct sequencing data from a combination of 20 patients with ToF and 22 healthy people, three polymorphisms have been identified in exon 6 and exon 7 which do not change the amino acid sequence. It was concluded, therefore, that there is no specific mutation responsible for the ToF phenotype in the Vangl2 gene.     

Genotyping of the 19-bp insertion/deletion polymorphism in the 5' flank of beta-hydroxylase gene by dissociation analysis of allele-specific PCR products.

The 19-bp insertion/deletion polymorphism in the 5' flank of the dopamine beta-hydroxylase (DBH) gene has been associated with psychiatric disorders. We have developed a simple, reliable and inexpensive closed-tube assay for genotyping of this polymorphism based upon T(m) determination of amplified DNA fragments. Mistyping of heterozygote samples due to preferential allele amplification was prevented by use of an optimized concentration of Mg(2+), addition of dimethyl sulfoxide and annealing/extension at an appropriate temperature. Comparison of results achieved by the closed-tube assay and a conventional approach based upon agarose gel electrophoresis of amplified fragments revealed complete concordance between the two procedures. The insights obtained in this study may be utilized to develop assays based upon dissociation analysis of PCR products for genotyping of other insertion/deletion polymorphisms.     

Simultaneous genotyping of alcohol dehydrogenase 2 and aldehyde dehydrogenase 2 by single‐strand conformation polymorphism analysis

Alcohol dehydrogenase (ADH; EC 1.1.1.1) and aldehyde dehydrogenase (ALDH; EC 1.2.1.3) have important roles in the elimination of ingested ethanol. These enzymes have polymorphisms resulting from single‐point mutations that cause kinetic differences in their respective enzyme activities. Simultaneous observation of these enzymes would be useful in investigating the association between these enzyme polymorphisms and alcohol‐related problems. In this study amplified genomic DNA was amplified from nail clippings with two sets of primers for ADH2 and ALDH2 genes, respectively, in a micro test tube and the accuracy of the amplification was verified by direct sequencing. The PCR products were separated into four distinct bands by single‐strand conformation polymorphism analysis. This genotyping method is fast, accurate, reliable and inexpensive, and requires the same amount of template DNA as non‐simultaneous methods. In other words, the required amount of template DNA for this method is only half that required for the separate genotyping of ADH2 and ALDH2.     

Molecular basis of polymorphisms of human complement component C3

C3 exhibits two common allotypic variants that may be separated by gel electrophoresis and are called C3 fast (C3 F) and C3 slow (C3 S). C3 F, the less common variant, occurs at appreciable frequencies only in Caucasoid populations (gene frequency = 0.20). An increased prevalence of the C3 F allele has been reported in patients with partial lipodystrophy, IgA nephropathy, and Indian childhood hepatic cirrhosis. Studies of the genomic organization of the human C3 gene led to the identification of a single change (C to G) between C3 S and C3 F at nucleotide 364 in exon 3. This leads, at the translation level, to the substitution of an arginine residue (positively charged) in C3 S for a glycine residue (neutral) in C3 F. This substitution results in a polymorphic restriction site for the enzyme HhaI. The resulting restriction fragment length polymorphism (RFLP) was investigated using genomic DNA, amplified using the polymerase chain reaction; there was absolute concordance between the genomic polymorphism and the distribution of C3 S and C3 F in 50 normal subjects. The molecular basis of a second structural polymorphism, defined by the monoclonal antibody HAV 4-1, was also characterized. The polymorphic determinant was identified at codon 314 in the exon 9 of the beta chain where a leucine residue (HAV 4-1+) is substituted for a proline residue (HAV 4-1-). Identification of the amino acid sequences of these polymorphic variants will facilitate characterization of possible functional differences between different allotypes of C3. Three RFLPs (BamHI, EcoRI, and SstI) were located to introns in the C3 gene. There was no allelic association between these three RFLPs, or between the RFLPs and the C3 F/S polymorphic site. Genetic equilibration of these polymorphisms has occurred within a gene of 41 kb.     

Comparative semi-automated analysis of (CAG) repeats in the Huntington disease gene: use of internal standards.

Huntington disease (HD) belongs to the group of neurodegenerative disorders characterized by unstable expanded trinucleotide repeats. In the case of HD, the expansion of a CAG repeat occurs in the IT15 gene. The detection of the expanded CAG repeats has usually involved the electrophoretic separation of polymerase chain reaction (PCR) amplification products using conventional agarose and acrylamide gel electrophoresis. We have undertaken the comparative analysis of sizing CAG repeats of the IT15 gene using radioactive and fluorescent PCR amplification, and the subsequent separation of these products by slab gel and capillary electrophoresis. The assays have been performed on both cloned and sequenced CAG repeats, as well as genomic DNA from HD patients with a wide range of repeat lengths. The mobility of the CAG repeat amplification products of the IT15 gene is greater using capillary electrophoresis compared to slab gel electrophoresis. The analysis of 40 DNA samples from HD patients indicates that the mobility difference increases with the length of the repeat. However, we have devised an allele ladder for sizing the CAG repeats. This ladder provides a mandatory internal calibration system for diagnostic purposes and enables the confident use of either capillary or slab gel electrophoresis for sizing HD alleles.     

Porphobilmogen deaminase gene mutations in Brazilian acute intermittent porphyria patients

Acute intermittent porphyria (AIP) is an autosomal dominant disorder resulting from porphobilmogen deaminase (PBGD) deficiency. Seven unrelated Brazilian patients were investigated regarding PBGD gene mutations by polymerase chain reaction (PCR) and single strand conformation polymorphism (SSCP) analysis followed by direct DNA sequencing. The PBG gene screening disclosed abnormal SSCP patterns in exons 7, 9, 12, 13, and 15, as well as in introns 3 and 10. Direct DNA sequencing revealed the occurrence of three nonsense mutations (R149X, R225X, and R325X) in exons 9, 12, and 15, respectively, and one missense mutation G111R in exon 7. The G111R mutation was detected in two unrelated patients. Intragenic polymorphisms (3119G/T in intron 2, 3581G/A in intron 3, 7052A/G and 7064C/A in intron 10, and -65C/T in exon 1) were also observed. In addition, two silent mutations (V202V in exon 10 and A266A in exon 13) were found. The latter has not heretofore been reported. Thus, this study revealed the mutations involved in Brazilian symptomatic AIP patients, as well as the intragenic polymorphisms found in the patients.     

Alcohol Dehydrogenase 2 Genotype and Risk for Migraine

( Headache 2010;50:85-91)
Background/Objectives.— Alcohol has been traditionally considered a possible migraine trigger factor. Alcohol-dehydrogenase (ADH) enzymes are thought to play important roles in the metabolism of ethanol. Relevant polymorphism has been found only for 2 of the ADH genes (mapped on chromosome ): ADH 1B, betapolypeptide ( ADH2 ) and ADH3 . The polymorphism rs1229984, located in the third exon of the human ADH2 gene, causes the amino acid substitution Arg48His. The aim of this study was to investigate the possible association between ADH2 polymorphism and the risk for migraine and for triggering migraine attacks.
Methods.— We studied the frequency of the ADH2 genotypes and allelic variants in 197 patients with migraine and 255 healthy controls using allele-specific PCR amplification and Msl I-RFLP's analyses.
Results.— The frequencies of ADH2 Arg/His genotype and of ADH2 His allele were significantly lower in patients with migraine when compared with those of controls, and were unrelated with the age of onset of migraine attacks, family history of migraine or presence of aura. The frequency of the allelic variant ADH2 His ( ADH2*2 ) was significantly higher in the group of patients who reported triggering of migraine by alcohol when compared with the group who reported no effect.
Conclusion.— The results of the present study suggest that ADH2 Arg/His genotype should be associated with a decreased risk for migraine, while the ADH2 His allelic variant should be related with the risk for triggering migraine attacks after alcohol consumption in our population of migraine patients.     

Evaluation of a capillary zone electrophoresis system versus a conventional agarose gel system for routine serum protein separation and monoclonal component typing

Capillary zone electrophoresis of serum proteins is increasingly gaining impact in clinical laboratories. During 2003, we compared the fully automated capillary electrophoresis (CE) system from Beckman (Paragon CZE 2000) with the method agarose gel electrophoresis Sebia (Hydrasis-Hyris, AGE). This new study focused on the evaluation of analytical performance and a comparison including 115 fresh routine samples (group A) and a series of 97 frozen pathologic sera with suspicion of monoclonal protein (group B). Coefficients of variation (CVs %) for the five classical protein fractions have been reported to be consistenly < 9% in within-run and < 10% in between-run imprecision studies with the Paragon 2000 system. The results of the comparison study (group A) demonstrated a good correlation between the CE system and AGE, except for beta-globulin (r = 0.65). Among the 97 pathologic serum samples (group B), there were 90 in which we detected a monoclonal protein by immunofixation (IF) (immunosubtraction (IS) was not used). AGE and Paragon 2000 failed to detect 7 and 12 monoclonal proteins, respectively, leading to a concordance to 92% for AGE and 87% for Paragon 2000 for identifying electrophoretic abnormalities in this group. Beta-globulin abnormalities and M paraprotein were well detected with Paragon 2000. Only 81% (21 vs 26) of the gammopathies were immunotyped with IS by two readers blinded to the IF immunotype. The Paragon 2000 is a reliable alternative to conventional agarose gel electrophoresis combining the advantages of full automation (rapidity, ease of use and cost) with high analytical performance. Qualified interpretation of results requires an adaptation period which could further improve concordance between the methods. Recently, this CE system has been improved by the manufacturer (Beckman) concerning the migration buffer and detection of beta-globulin abnormalities.     

Cluster Headache is Associated With the Alcohol Dehydrogenase 4 (ADH4) Gene

(Headache 2010;50:92‐98) Background/Objectives.— Alcohol is a well‐known trigger factor for cluster headache attacks during the active phases of the disease. The alcohol dehydrogenase (ADH) pathway, which converts alcohol to the toxic substance acetaldehyde, is responsible for most of the alcohol breakdown in the liver. Humans have 7 ADH genes, tightly clustered on chromosome 4q21‐q25, that encode different ADH isoforms. The ADH4 gene encodes the class II ADH4 pi subunit, which contributes, in addition to alcohol, to the metabolization of a wide variety of substrates, including retinol, other aliphatic alcohols, hydroxysteroids, and biogenic amines. The purpose of this study was to investigate the association of genetic variants within the ADH4 gene with cluster headache susceptibility and phenotype. Methods.— A total of 110 consecutive unrelated cluster headache patients and 203 age‐ and sex‐matched healthy controls of Caucasian origin were involved in the study. Patients and controls were genotyped for 2 bi‐allelic single nucleotide polymorphisms (SNPs) of the ADH4 gene: SNP1 – rs1800759 and SNP2 – rs1126671. Allele, genotype, and haplotype frequencies of the examined polymorphisms were compared between cases and controls. Results.— Genotype frequencies of the rs1126671 polymorphism resulted significantly different between cluster headache patients and controls (χ² = 10.269, P = .006). The carriage of the AA genotype, in comparison with remaining genotypes, was associated with a significantly increased disease risk (OR = 2.33, 95% CI: 1.25‐4.37). Haplotype analysis confirmed the association between the ADH4 gene and the disease. No association between different clinical characteristics of cluster headache and the examined polymorphisms was found. Conclusion.— Our data suggest that cluster headache is associated with the ADH4 gene or a linked locus. Additional studies are warranted to elucidate the role of this gene in the etiopathogenesis of the disease.     

Mutation analysis in a small cohort of New Zealand patients originating from the United Kingdom demonstrates genetic heterogeneity in familial hypercholesterolemia

Familial hypercholesterolemia (FH) and familial defective apolipoprotein B-100 (FDB) are relatively common lipid disorders caused by mutations in the low-density lipoprotein receptor (LDLR) and apolipoprotein B (apo B) genes, respectively. Molecular analysis at these loci was performed in eight New Zealand subjects with clinical features of heterozygous FH. Utilization of an in vitro lymphocyte receptor assay demonstrated normal receptor function in four patients, three of whom screened positive for the founder-type apo B mutation, R3500Q, causing FDB. Four patients with reduced LDLR function, consistent with heterozygous FH, revealed three previously documented mutations in exons 3 (W66X), 6 (C292Y) and 7 (G322S) of the LDLR gene and, a novel 2-bp deletion (TC or CT) after nucleotide 1204 (or 1205) in exon 9. The remaining patient was found to be FH/FDB negative after extensive mutation screening using both denaturing gradient gel electrophoresis and heteroduplex-single strand conformation polymorphism analysis. Haplotype analysis at the LDLR and apo B loci finally excluded the likelihood that mutations in these two genes underlie the FH phenotype in the molecularly uncharacterized New Zealand family originating from the United Kingdom. This family represents a valuable source of material for future genetic dissection of autosomal dominant hypercholesterolemia (ADH), shown to be a heterogeneous disease through molecular analysis.