Screening For Known Mutations Research Articles

Can intensive exercise harm the heart? You can get too much of a good thing.

Can intensive exercise harm the heart? You can get too much of a good thing.

Severe retinal degeneration in females with c.2543del mutation in the RPGR gene

AbstractPurpose To describe the genotype‐phenotype correlation and serial observations in a five‐generation Czech family with retinitis pigmentosa (RP) associated with total blindness in females.Methods Comprehensive ophthalmological examination was performed in sixteen family members (nine females and seven males). Autosomal dominant inheritance was suspected and screening for known mutations by genotyping microarray was performed. Next, direct sequencing of ORF15 RPGR exon was undertaken.Results The c.2543delA, in ORF15 of the RPGR gene was detected. Three females became bilaterally totally blind in the sixth decade. Four examined females and five males showed pigmentary deposits, progressive visual field constriction, moderate to high myopia and myopic astigmatism. Three other females had moderate to high myopia and myopic astigmatism but without the presence of bone spicule formation. Only one 34 year old female carrier had clinically normal fundus findings.Conclusion The c.2543delA in RPGR is associated with severe phenotype in females in the studied family. The presence of refractive errors, especially high myopia and astigmatism in the absence of male to male transmission may be indicative of an X‐linked inheritance.

APCR, factor V gene known and novel SNPs and adverse pregnancy outcomes in an Irish cohort of pregnant women

BackgroundActivated Protein C Resistance (APCR), a poor anticoagulant response of APC in haemostasis, is the commonest heritable thrombophilia. Adverse outcomes during pregnancy have been linked to APCR. This study determined the frequency of APCR, factor V gene known and novel SNPs and adverse outcomes in a group of pregnant women.MethodsBlood samples collected from 907 pregnant women were tested using the Coatest® Classic and Modified functional haematological tests to establish the frequency of APCR. PCR-Restriction Enzyme Analysis (PCR-REA), PCR-DNA probe hybridisation analysis and DNA sequencing were used for molecular screening of known mutations in the factor V gene in subjects determined to have APCR based on the Coatest® Classic and/or Modified functional haematological tests. Glycosylase Mediated Polymorphism Detection (GMPD), a SNP screening technique and DNA sequencing, were used to identify SNPs in the factor V gene of 5 APCR subjects.ResultsSixteen percent of the study group had an APCR phenotype. Factor V Leiden (FVL), FV Cambridge, and haplotype (H) R2 alleles were identified in this group. Thirty-three SNPs; 9 silent SNPs and 24 missense SNPs, of which 20 SNPs were novel, were identified in the 5 APCR subjects. Adverse pregnancy outcomes were found at a frequency of 35% in the group with APCR based on Classic Coatest® test only and at 45% in the group with APCR based on the Modified Coatest® test. Forty-eight percent of subjects with FVL had adverse outcomes while in the group of subjects with no FVL, adverse outcomes occurred at a frequency of 37%.ConclusionsKnown mutations and novel SNPs in the factor V gene were identified in the study cohort determined to have APCR in pregnancy. Further studies are required to investigate the contribution of these novel SNPs to the APCR phenotype. Adverse outcomes including early pregnancy loss (EPL), preeclampsia (PET) and intrauterine growth restriction (IGUR) were not significantly more frequent in subjects with APCR compared to normal pregnant women however Pregnancy induced hypertension (PIH) was found to be associated with FVL in our study group.

Juvenile-onset neuronal ceroid lipofuscinosis with infantile CLN1 mutation and palmitoyl-protein thioesterase deficiency

Accurate diagnosis, especially in progressive hereditary diseases, is essential for the treatment and genetic counseling of the patient and the family. Neuronal ceroid lipofuscinoses (NCL) are amongst the most common groups of neurodegenerative diseases. Infantile, juvenile, and adult-onset types with multiple genotype-phenotype associations have been described. A fluorimetric enzyme assay for palmitoyl protein thioesterase (PPT) from leukocytes and fibroblasts has been previously developed to confirm the diagnosis of infantile NCL. We describe a patient with juvenile-onset NCL phenotype with a new CLN1 mutation and deficient PPT activity. Over 40 different mutations have been found in patients with PPT deficiency, indicating that screening for known mutations is not an efficient way to diagnose this disorder. Therefore, PPT enzyme analysis should precede mutation analysis in suspected PPT deficiency, particularly in patients with granular osmiophilic deposits (GROD) or in patients who have negative ultrastructural data. The use of enzyme assay led to the diagnosis of this patient with juvenile-onset Finnish variant NCL with PPT deficiency, and we expect that greater awareness of the utility of the enzymatic assay may lead to identification of other similar cases awaiting a definitive diagnosis.

Estimation of the total number of disease‐causing mutations in ornithine transcarbamylase (OTC) deficiency. Value of the OTC structure in predicting a mutation pathogenic potential

Ornithine transcarbamylase deficiency (OTCD), the X-linked, most frequent urea cycle error, results from mutations in the OTC gene, encoding a 354-residue polypeptide. To date 341 OTCD clinical mutations, including 222 missense single nucleotide changes (mSNCs), have been compiled (Hum Mutat 2006;27:626). OTCD mutation detection might be simplified if the entire repertoire of OTCD-causing mutations were known. We estimate the size of this repertoire from 23 new OTCD patients exhibiting 22 different mutations, of which 9, including 4 mSNCs, are novel. The complete repertoire of OTCD-causing mutations is estimated as 560 mutations (95% confidence interval, 422-833 mutations), including 290 mSNCs (95% confidence interval, 230-394 mSNCs). Thus, OTCD diagnosis based on the screening for known mutations might attain 90% sensitivity in <5 years. Since disease-causing mSNCs represent <20% of the 2064 possible OTC mSNCs, simple approaches are essential for discrimination between causative and trivial mSNCs. Observation of the OTC structure appears a simple approach for such discrimination, comparing favourably in our sample with three formalized structure-based and/or sequence-based in silico assessment methods, and supporting the causation of complete deficiency by the mutations p.Pro305Arg and p.Ser96Phe, and of partial deficiency by p.Asp41Gly, p.Glu122Gly, p.Leu179Phe, p.Pro220Thr and p.Glu273del. Five non-mSNC novel mutations (p.Gly71X, a 7-nucleotide and a 10-nucleotide duplication and deletion in exon 5, G>A transitions at bases +1 and +5 of introns 4 and 9, respectively) are obviously pathogenic. The previously reported mSNCs p.Arg26Gln, p.Arg40His, p.Glu52Lys, pLys88Asn, p.Arg129His, p.Asn161Ser, p.Thr178Met, p.His202Tyr, p.Ala208Thr and p.His302Arg, found in our cohort, are also discussed.

AB1-6: Screening for known mutations in LQTS: A novel way to fast and low cost genotyping?

AB1-6: Screening for known mutations in LQTS: A novel way to fast and low cost genotyping?

Screening for known mutations in EIF2Bgenes in a large panel of patients with premature ovarian failure

BackgroundPremature Ovarian Failure (POF), defined as the development of hypergonadotropic amenorrhea before the age of 40 years, occurs in about 1% of all women. Other than karyotype abnormalities, very few genes are known to be associated with this ovarian dysfunction. Recently, in seven patients who presented with POF and white matter abnormalities on MRI (ovarioleukodystrophy) eight mutationswere found in EIF2B2, 4 and 5.MethodsTo further test the involvement of known mutations of EIF2B genes in POF, we screened 93 patients with POF who did not have identified leukodystrophy or neurological symptoms. We evaluated these eight mutations and two additional mutations that had been found in patients with milder forms of eIF2B-related disorders. We used restriction enzymes and direct sequencing.ResultsNone of the known mutations in EIF2B genes, either homozygous or heterozygous, were identified in our 93 patients with pure 46,XX POF. The upper 95 % confidence limit of the proportion 0/93 is 3.2%.ConclusionsWe conclude that eIF2B mutations, already described in cases of POF associated with white matter abnormalities, are an uncommon cause of pure spontaneous premature ovarian failure.

Molecular genetic study in Japanese patients with Alexander disease: a novel mutation, R79L

Since the first report by Brenner et al. of mutations in the glial fibrillary acidic protein (GFAP) gene in patients with Alexander disease, several molecular genetic studies have been performed in different ethnic groups. We previously reported a Japanese patient with a mutation, R239C, which is identical to one commonly found in American patients. Here we have analyzed four additional Japanese patients by screening for known mutations or, if no known mutation was found, by sequencing of all exons of the GFAP gene. We detected three missense mutations; one was a novel mutation, R79L, and two were previously reported mutations, R239C and R79C. All of our patients were heterozygous for their mutations. Together with the novel mutation, R79L, four different nucleotide changes altering the R79 residue have been reported, implying that any alternation of this arginine residue can give the GFAP protein a dominant negative effect, leading to accumulation of GFAP as Rosenthal fibers. We conclude that molecular genetic analysis of the GFAP gene is feasible for antemortem diagnosis of Alexander disease in Japanese patients.

Phenotype-genotype correlation in 91 patients with familial Mediterranean fever reveals a high frequency of cutaneomucous features.

To describe the clinical manifestations of familial Mediterranean fever (FMF) in 91 patients from 47 families and provide data from the genetic study. P:atients and methods. We conducted a retrospective chart review of 91 patients (including 83 children aged <15 yr) from 47 families through a questionnaire and a specific database. The genetic analysis included complete screening of known mutations of the MEFV gene on chromosome 16p13.3. A positive diagnosis required at least two mutations, one on each chromosome. Our panel included 52 females and 39 males, with a mean age of 7.27 yr. Of the 47 families, 31 were non-Ashkenazi Jews, 10 were Armenians and six were from other ethnic groups. Clinical features included fever (100%), peritonitis (86%), pleuritis (56%), arthritis (34%) and myalgias (27%). We observed a high rate of cutaneous manifestations (47%); erythema, oedema and recurrent oral ulcers were the most frequent. Phenotype-genotype correlations showed a significant association of M694V homozygosity with earlier age of onset (P: = 0.044), fever >39 degrees C (P: = 0. 002), pleural crisis (P: = 0.0044), splenomegaly (P: = 0.0005) and arthritis (P: = 0.001). Associations with mucocutaneous features were as follows: erysipelas-like erythema (P: = 0.012), oedema (P: = 0.61, not significant) and oral ulcers (P: = 0.45, not significant). New phenotype-genotype correlations emerged from our study: homozygosity for the M694V mutation was associated with intensity of fever, splenomegaly and with erysipelas-like erythema. Apart from erysipelas-like erythema, no significant association was found between other cutaneous features and the genotype.

Screening for the beta-39 mutation in thalassemia by capillary electrophoresis in free solution in strongly acidic, isoelectric buffers.

A novel method is reported for screening for point mutations in genomic DNA: free-zone capillary electrophoresis in very acidic buffers. This method exploits the charge difference among the four different bases (C, T, A, G) in a pH window between 2.5 and 3.5, where the four titration curves fan out. The method is applied to the detection of the beta-39 missense mutation in the beta-globin gene in thalassemias. A 60-mer fragment straddling the mutation site has been amplified. In an isoelectric buffer (iminodiacetic acid) of pH 3.3, partial resolution between the wild type and mutated strands is obtained. In a pH 3.0 phosphate buffer, baseline resolution is achieved between the two strands in a heterozygous individual. Due to the short size of the amplified fragment, this method can only be applied to routine screening for known mutations because resolution was lost in a fragment 100 bases long.

Chemical mismatch cleavage combined with capillary electrophoresis: detection of mutations in exon 8 of the cystathionine β-synthase gene

Mutation detection by chemical mismatch cleavage (CMC) is based on the chemical modification and cleavage at the site of mismatched C or T in heteroduplexes, using hydroxylamine or osmium tetroxide (OsO4) as chemical probes. In the present study, we evaluated CMC in combination with capillary electrophoresis (CE) by determining the common T833C and G919A mutations in exon 8 of the cystathionine beta-synthase gene in heterozygous and homozygous samples. A 186-bp fragment encompassing exon 8 was amplified by PCR with both primers labeled with 5'-fluorescein. Labeled single strands of 40 and 61 nucleotides (nt) were formed from the coding strand of the T833C sample and non-coding strand from the G919A sample, respectively. These single-stranded DNA (ssDNA) products were analyzed under denaturing conditions by CE with short-chain linear polyacrylamide as the sieving matrix and were detected by laser-induced fluorescence (LIF), using a sensitive, one-channel sheath-flow detector. The CE-LIF format afforded relatively high resolution of ssDNA (down to 1 nt), precise size assessment of CMC products, sensitive detection with small sample requirements, and fast analysis. Thus, CMC combined with CE-LIF is suitable for screening of known mutations, giving expected CMC products, but will also detect unknown mutations, the locations of which are indicated by the fragment sizes.

High-throughput screening for known mutations by automated analysis of single sequencing reactions.

This work shows that single sequencing reactions analyzed on an automated DNA sequencer can be an efficient way of screening PCR products for known mutations. We have analyzed a mutation in exon 10 of the human aromatase gene and show that an unambiguous genotype could be elucidated in more than 90% of the analyzed samples. Compared to analysis by full sequencing, 4 times more samples can be analyzed per gel, so that the sample capacity of the gel is approaching that of alternative gel-based methods for genotype analysis. Unlike many of these, the method offers direct identification of the variant sequence position and on-line analysis without the need of post-electrophoretic processing of the gel.

Update on low density lipoprotein receptor mutations.

Recent research has focused on the rapid detection of new LDL receptor gene variants and large scale screening for known mutations. Whether the nature of the mutation in the LDL receptor gene in familial hypercholesterolaemia determines clinical variability has been examined, as well as the potential value of detecting mutation carriers for clinical practice. There is also evidence that some patients with clinical familial hypercholesterolaemia do not have detectable defects in the LDL receptor or apolipoprotein B.

Recurrent strokes in a 34-year-old man

mitochondrial disease have an A to G point mutation of mtDNA at nucleotide positions 3243, but stroke-like episodes may also be a feature of other mtDNA mutations. Blood screening for the A3243G mutation may give false-negative results. Many patients with pathogenetic mtDNA mutations have a mixture of mutant and wild-type mtDNA within each cell (heteroplasmy), and as a result, they have different concentrations of mutant mtDNA in different organs. High concentrations of mutant mtDNA may be present in skeletal muscle and the central nervous system, with lower levels in blood, and approximately 4% of affected individuals have levels of mutant mtDNA in blood below the lower limit of detection by the non-radioactive method (6% mutant mtDNA). Investigation of patients with strokes and possible mitochondrial disease requires an integrated approach of clinical evidence, results of biochemical studies, and screening for known mutations in blood. A muscle biopsy is often necessary. Molecular genetic analysis of skeletal muscle DNA is likely to give the highest diagnostic yield, and if clinical suspicion is strong enough, investigations should include the direct sequencing of mitochondrial genes. Establishing such a diagnosis will help avoid unnecessary treatments and their accompanying side-effects. Although no specific treatment is currently available for patients with mtDNA disease, identifying a mitochondrial cause for a stroke will affect management and prognosis.

Screening for known mutations in the LDL receptor gene causing familial hypercholesterolemia

Screening for known mutations in the LDL receptor gene causing familial hypercholesterolemia

Screening for known mutations in the LDL receptor gene causing familial hypercholesterolemia

Familial hypercholesterolemia (FH) is caused by defective low density lipoprotein (LDL) receptors and is characterized by hypercholesterolemia and premature coronary heart disease. Two strategies can be used to identify the mutation in the LDL receptor gene underlying FH. One strategy is to search for novel mutations by DNA sequencing with or without prior mutation screening. The other strategy is to screen for known mutations. In this study we employed the latter strategy to screen 75 unrelated, Norwegian FH subjects for 38 known mutations. Three of the 38 mutations were detected in our group of FH subjects. Two subjects had FH-Padova, one had FH-Cincinnati-2 and one had FH-Gujerat. When additional unrelated FH heterozygotes were screened for the three mutations, the gene frequencies were 1.3%, 1.0% and 3.0%, respectively. In addition to identifying known mutations we also detected a novel stop codon in codon 541 (S541X). We conclude that screening for known mutations in the LDL receptor gene should be used as a complementary strategy to screening for novel mutations in order to understand the molecular genetics of FH.

Maple syrup urine disease (MSUD): screening for known mutations in Italian patients.

Maple syrup urine disease (MSUD) is an autosomal recessive disease due to deficiency of the branched-chain alpha-ketoacid dehydrogenase (BCKDH) caused by a large number of mutations. In the present study, DNA from Italian patients and their relatives was examined for three point mutations (Y393N in the E1 alpha gene, T841G and G1031A in the E2 gene) and two deletions (-G at the intron/exon border of exon 8 in the E2 gene and an 11 bp deletion in exon 1 of the E1 beta gene) using the polymerase chain reaction (PCR) followed by allele-specific oligonucleotide (ASO) hybridization, gene-scanning size analysis of fluorescent-tagged PCR products and/or automated DNA sequence analysis. Our results show that two different mutations account for 7 of the 20 mutant MSUD alleles. Two unrelated affected children, two of their parents and one sibling were carriers for the 11 bp deletion in the E1 beta gene, one patient and her mother were heterozygous for Y393N in E1 alpha, while T841G, G1031A and the -G deletion in E2 were not detected. This study is the first attempt to characterize at a nucleic acid level MSUD mutations in Italy. Our results indicate that additional defects are present in the Italian population and that, unlike the Mennonites, a number of different MSUD mutations exist in Italians.