Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Variant identification”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4Linked to original sources
PubMed1994

[Identification of molecular variants of the enzyme glucose-6-phosphate dehydrogenase by the polymerase chain reaction technique].

BACKGROUND: An assessment of the usefulness of polymerase chain reaction (PCR) in the identification of the most frequent molecular variants of the glucose-6-phosphate dehydrogenase (G6PD) in Spain: G6PD A-, G6PD Mediterranean and G6PD Seattle through the screening of the mutations: 376 A-->G; 202 G-->A; 680 G-->T; 968 T-->C; 563 C-->T and 844 G-->C. METHODS: Three groups of patients have been studied: 1) males (40 cases); 2) relatives from the preceding group (31 cases: 7 males and 24 females), and 3) samples classified according to their fast electrophoretic mobility as G6PD A-(17 cases). The method used has been the PCR followed by digestion with specific restriction endonucleases. RESULTS: Group 1: 23 out of 40 samples (57%), were identified as G6PD Med563T variant (8 cases), G6PD A-376G/202A (13 cases) and G6PD Seattle844C (2 cases). Group 2: The study of relatives from 13 of the 23 identified samples allowed the study of additional 31 samples (7 males, 24 females): hemizygous G6PD Med563T (3 cases), heterozygous GdB/Gd Med563T (5 cases), hemizygous G6PD A-376G/202A (4 cases), heterozygous GdB/Gd A-376G/202A (11 cases), heterozygous GdB/Gd Seattle844C (1 case) and normal females (7 cases). Group 3: In all electrophoretically fast samples classified as G6PD A-was detected the 376 A-->G mutation (characteristic of G6PD A+). In 15 of these cases a second mutation was found at nucleotide 202 G-->A (G6PD A-376G/202A); and in two, at nucleotide 968 T-->C (G6PD A-376G/968C). CONCLUSIONS: The PCR method is fast and simple enough to allow the identification of known G6PD deficient variant, avoiding the need of its molecular characterization, which is more cumbersome and time consuming. In addition, the PCR is a very useful tool for demonstrating the carrier condition of G6PD deficiency in females with enzyme activity within normal range.

Base Sequence↗
PubMed1990

Enzyme immunoassay for the identification of hemoglobin variants.

We have prepared monospecific antibodies to Hbs D-Los Angeles, J-Baltimore, O-Arab and J-Paris-I and developed an enzyme immunoassay (ELISA) for their identification in hemolysates. Hbs in adult or cord blood hemolysates were coated to the wells of microtiter plates and reacted with the appropriate antisera followed by the detection system which contains anti-rabbit IgG/peroxidase conjugate and the substrate tetramethylbenzidine. Sixty-nine samples were tentatively considered to contain the above hemoglobin variants by isoelectrofocusing and the identity of 83% of them was confirmed by ELISA. Some of the non-reacting hemolysates were shown by amino acid sequence analysis to contain Hbs Korle-Bu, D-Ibadan, G-Copenhagen and the new variant Chandigarh. This ELISA offers specificity and simplicity for the confirmatory identification of hemoglobin variants.

Adult↗
PubMed1985

A new alpha 1-antitrypsin allele PI Poki: isoelectric focusing with immobilized pH gradients as a tool for identification for PI variants.

A new rare genetic variant PI Poki in the protease inhibitor system found in two Japanese subjects, was compared with some PI P variants using several electrophoresis systems. Although this variant was slightly anodal to P by separator isoelectric focusing, it could be readily distinguished by isoelectric focusing with immobilized pH gradients: the mobility of Poki became cathodal to P. This method proved to be a powerful tool for identification of PI variants.

Alleles↗
PubMed1992

The identification of a variant form of cystathionine beta-synthase in nematodes.

Characterization of the physical and catalytic properties of the enzyme responsible for nematode "activated L-serine sulfhydrase" activity (L-cysteine + R-SH-->cysteine thioether + H2S) has led to its identification as a novel, variant form (allelozyme) of cystathionine beta-synthase that is distinct from a mammalian-type synthase also present in nematodes. Additional work has demonstrated the ability of live Panagrellus redivivus to produce H2[35S] from exogenous L-[35S]cysteine and 2-mercaptoethanol, thus providing preliminary evidence for the in vivo operation of the activated L-serine sulfhydrase reaction in nematodes.

Animals↗
PubMed1997

Strategy for identification of sequence variants in COL7A1 and a novel 2-bp deletion mutation in recessive dystrophic epidermolysis bullosa.

The diagnostic hallmark of the dystrophic forms of epidermolysis bullosa (DEB), a group of heritable blistering skin diseases, is abnormalities in the anchoring fibrils at the dermal-epidermal basement membrane zone. Since type VII collagen is the major, if not the exclusive, component of the anchoring fibrils, the corresponding gene (COL7A1) is the candidate gene in DEB. Recent cloning of the type VII collagen cDNA and elucidation of the exon-intron organization of the gene have provided the basis for us to develop a novel strategy for identification of sequence variants in COL7A1. Optimization of 72 balanced primer pairs corresponding to flanking intronic sequences allowed PCR amplification of all 118 exons directly from genomic DNA. The PCR products were examined by heteroduplex analysis followed by comparative nucleotide sequencing. More than 100 sequence variants have been identified thus far in COL7A1 using this method, some of which are single base pair polymorphisms and many of which are pathogenetic mutations contributing to the blistering phenotype in DEB. The comprehensive method described is useful for rapid, reliable, and sensitive detection of sequence variants in COL7A1. We demonstrate the utility of this novel strategy in mutation detection and prenatal exclusion of RDEB in a consanguineous family at risk for recurrence.

Collagen↗
PubMed2025

Identification of intragenic variants in pediatric patients with intellectual disability in Peru.

BACKGROUND: Intellectual disability in Latin America can reach a frequency of 12% of the population, these may include nutritional deficiencies, exposure to toxic or infectious agents, and the lack of universal neonatal screening programs. In 90% of patients with intellectual disability, the etiology can be attributed to variants in the genome. OBJECTIVE: to determine intragenic variants in patients with intellectual disability between 5 and 18 years old at Instituto Nacional de Salud del Niño. METHODS: It is a descriptive cross-sectional study with convenience sampling. A total of 124 children diagnosed with intellectual disability were selected based on psychological test results and availability for whole exome sequencing. In addition, a chromosomal analysis of 6.55 M was performed on ten patients with a negative result in sequencing. Relative and absolute frequencies and measures of central tendency and dispersion were determined according to their nature. In addition, multiple linear regression and Poisson regression were used to determine the association between some clinical characteristics and the probability of occurrence in patients with positive results. RESULTS: The median age of the patients was 6.3 (IQR = 5.95), males accounted for 57.3%, and 91.9% of the cases had mild intellectual disability. Exome sequencing determined the etiology in 30.6% of patients with intellectual disability, of which 52.6% were autosomal dominant inheritance. The most frequent genes found were MECP2, STXBP1 and LAMA2. A broad genotype-phenotype correlation was identified, highlighting the genetic heterogeneity of intellectual disability in this population. The presence of dermatologic lesions, dystonia, peripheral neurological disorders, and fourth finger flexion limitation were observed more frequently in patients with intellectual disability with "positive results". CONCLUSIONS: This study shows that one-third of patients with intellectual disability exhibit intragenic variants, highlighting the importance of genetic analysis for accurate diagnosis. The identification of genes such as MECP2, STXBP1, and LAMA2 underscores the genetic heterogeneity of intellectual disability in the studied population. These findings emphasize the need for genetic testing in clinical management and the implementation of early detection programs in Peru.

Humans↗
PubMed1985

Identification of insulin variants in patients with hyperinsulinemia by reversed-phase, high-performance liquid chromatography.

We have characterized the molecular forms of circulating insulins in patients with hyperinsulinemia of diverse etiology. We have also compared the efficacy of various chromatographic conditions using reversed-phase (RP) HPLC. Using 0.2% trifluoroacetic acid (TFA) and triethylamine (TEA) with acetonitrile as the organic modifier, at an elution rate of 0.17%/min, porcine, bovine, and human insulins could be easily separated as well as abnormal insulins in the plasma of a patient (J.R.) with hyperinsulinemia of unknown etiology. When the reversed-phase C18 column was changed and a gradient of 0.33%/min was used, the abnormal insulin in patient J.R. could not be separated. By changing the solvent system to acetonitrile and isopropanol (vol:vol, 3:1) containing 0.1% TFA, omitting the TEA, and using a gentle gradient of 0.1%/min, various semisynthetic analogues of human insulin could be easily separated and the abnormal insulin could be identified in the plasma of the patient J.R. Abnormal insulin was also found in a patient with MEN-I, but in contrast, the insulins in eight patients with benign sporadic insulinomas appeared to be normal. These results suggest that certain hyperinsulinemic states may be associated with an abnormal insulin and that RP-HPLC is useful for identification of insulin variants in the circulation. However, the conditions of RP-HPLC may be critical if the abnormalities of the insulin are subtle.

C-Peptide↗
PubMed2001

Histone H2A variants and the inactive X chromosome: identification of a second macroH2A variant.

MacroH2A1 is an unusual variant of the core histone H2A which is enriched in chromatin on the inactive X chromosome of female mammals. The N-terminal third of the protein shares 65% amino acid identity with core histone H2A, while the remaining two-thirds of the protein are novel, with a small stretch of basic amino acids and a putative leucine zipper motif. We have now cloned a second macroH2A gene, encoding macroH2A2 which shares 80% amino acid identity with macroH2A1. Despite mapping to different chromosomes, the genomic organization of the macroH2A2 and macroH2A1 genes are nearly identical. The leucine zipper motif of macroH2A1 is not conserved in macroH2A2. Like macroH2A1, macroH2A2 forms a Macro Chromatin Body in the nuclei of female cells which is coincident with an X chromosome and co-localizes with macroH2A1. To address the distribution of other histone H2A variants in relation to macroH2A and the inactive X chromosome, we constructed a series of epitope-tagged versions of other histone H2A variants. Like the recently described H2A-Bbd (Barr body-deficient) variant, the histone variant H2A.Z was found to be deficient in chromatin on the inactive X chromosome in a significant proportion of female nuclei. This study provides further information about the nucleosomal composition of chromatin on the inactive X chromosome and indicates that a number of H2A variants are non-randomly distributed on the active and inactive X chromosomes.

Amino Acid Sequence↗
PubMed1999

High-throughput single-strand conformation polymorphism analysis by automated capillary electrophoresis: robust multiplex analysis and pattern-based identification of allelic variants.

Genetic diagnosis of an inherited disease or cancer often involves analysis for unknown point mutations in several genes; therefore, rapid and automated techniques that can process a large number of samples are needed. We describe a method for high-throughput single-strand conformation polymorphism (SSCP) analysis using automated capillary electrophoresis. The operating temperature of a commercially available capillary electrophoresis instrument (ABI PRISM 310) was expanded by installation of a cheap in-house designed cooling system, thereby allowing us to perform automated SSCP analysis at 14-45 degrees C. We have used the method for detection of point mutations associated with the inherited cardiac disorders long QT syndrome (LQTS) and hypertrophic cardiomyopathy (HCM). The sensitivity of the method was 100% when 34 different point mutations were analyzed, including two previously unpublished LQTS-associated mutations (F157C in KVLQT1 and G572R in HERG), as well as eight novel normal variants in HERG and MYH7. The analyzed polymerase chain reaction (PCR) fragments ranged in size from 166 to 1,223 bp. Seventeen different sequence contexts were analyzed. Three different electrophoresis temperatures were used to obtain 100% sensitivity. Two mutants could not be detected at temperatures greater than 20 degrees C. The method has a high resolution and good reproducibility and is very robust, making multiplex SSCP analysis and pattern-based identification of known allelic variants as single nucleotide polymorphisms (SNPs) possible. These possibilities, combined with automation and short analysis time, make the method suitable for high-throughput tasks, such as genetic screening.

Alleles↗
PubMed1996

Selection of monoclonal antibodies for the identification of D variants: ability to detect weak D and to split epD2, epD5 and epD6/7.

Red cells from known D variant donors were tested with 41 monoclonal anti-D reagents, 26 IgG and 15 IgM, with the view to selecting a panel to aid the identification of unusual D types. These antibodies gave reaction patterns which allowed the identification of most of the known D category cells, recognizing epD2, epD5, epD6/7, epD8 and epD9, but were unable to distinguish category III from normal D-positive cells. Reactivity with HMi, HMii, DFR, DBT and RoHar cells split epD2, epD5 and epD6/7 into two, three and eight groups, respectively. A panel comprising 15 monoclonal anti-D, 11 IgG and four IgM, was selected as representative of the antibodies tested. Reactivity of monoclonal anti-D was dependent on antibody concentration and antibody avidity. An antibody concentration of at least 12 micrograms/ml was required for optimum reactivity of the two monoclonal antibodies tested. A simple calculation of division of the titre by the antibody concentration provided a relatively simple means of establishing the reactivity performance of the antibody and correlated well with ability to detect weak D (Du) cells. A characteristic variable reduction in reaction strength with all the IgG anti-D was observed with weak D cells. The IgM antibodies, except the high avidity RUM-1, T3D2T6, D9A4 and BS226, performed poorly in detecting weak D. The majority of the IgM antibodies tested reacted with RoHarr cells, while only one IgG antibody was positive.

Antibodies, Monoclonal↗
PubMed1985

[Incidence of identification and configuration variants of the NSEP signal in relation to the recording site and measuring moment].

The component evaluation of the spinal and cortical recorded SEP-signals of thirty healthy volunteers after stimulation of the median nerve at the wrist gave information about variation of waveforms and frequency of peak identification with respect to the position of the active electrode and the repetition of the SEP recording. Basically one can distinguish three main groups of NSEP waveforms (Fig. 1). Firstly the "classical form" (i.e. N11 in the ascending part, N13 at the highest peak of the NSEP main component and N14 in the descending part of the curve). Secondly the "plateau-form" and thirdly the "polypeak form" (i.e. many peaks of the same amplitude). The latter two configurations were seen in more than a third of the evaluated NSEP maincomponents. Neither the position of the active electrode (C2 and C7) nor repetition of the SEP recording were found to have significant influence on the waveform. The position of the active electrode influenced the number of identificable peaks: the early components (N9 and N11) were more often recognisable when the recording was made over the lower neckregion (C7), N14 when the recording was made over the upper neckregion (C2). N13 was always identificable in both electrode positions. The repetition of the SEP recordings immediately after the first run is helpful if there was difficulty in identifying the peaks. The normal values of the SEP latency of the spinal and cortical recorded signals were evaluated taking above mentioned criteria into account.

Adult↗
PubMed1993

A strongly immunoreactive virion protein of human herpesvirus 6 variant B strain Z29: identification and characterization of the gene and mapping of a variant-specific monoclonal antibody reactive epitope.

We previously identified a 101-kDa apparent molecular mass polypeptide (101K) as the major immunoreactive virion protein of human herpesvirus 6 variant B strain Z29 [HHV-6B(Z29)] and found that the human immune response to this protein is HHV-6-specific (Yamamoto, M., Black, J. B., Stewart, J. A., Lopez, C., and Pellett, P. E., 1990, J. Clin. Microbiol. 28, 1957-1962). We report here the identification and characterization of the gene encoding 101K. We found 81% amino acid identity between an HHV-6B(Z29) open reading frame (ORF) and its homolog in HHV-6A strain U1102 [HHV-6A(U1102)]. The product of this gene was identified as 101K on the basis of both the reactivity of a 101K-specific monoclonal antibody (MAb C3108-103) with a bacterially expressed portion of the gene and the reactivity of polyclonal rabbit antibodies raised against the bacterially expressed protein with 101K expressed by HHV-6B(Z29)-infected cells. MAb C3108-103 reacted with eight of eight variant B isolates and none of six variant A isolates, indicating that it is a variant-specific MAb. The MAb reactivity was mapped to an eight-amino-acid segment of 101K. HHV-6A(U1102) differs from HHV-6B(Z29) by two amino acids in this region; substitution mapping with synthetic oligopeptides mapped the variant B specificity to Asp723, this explaining the failure of the MAb to react with variant A proteins. A set of transcripts appropriately sized for expression of 101K was identified and precisely mapped. The transcripts originated down-stream from either of two TATA boxes located 139 bp apart in the region 5' to the 101K ORF, with one 5'-species being much more abundant. Two independent polyadenylation sites were identified; the canonical polyadenylation signal located 3' to the 101K ORF was used much more frequently than was the atypical polyadenylation signal located within the 101K ORF. These results suggest a complex regulatory mechanism for this gene.

Amino Acid Sequence↗
PubMed2000

Identification of the novel allele HLA-B*0809 in a Caucasian individual: estimation of allogeneic potential between B*08 variants.

The identification of the new allele HLA-B*0809, which was found in a Caucasian individual, is described. In the sequence analysis the new allele differs from B*0801 by six nucleotides located in exon 3. As the structure is identical to a variety of other HLA-B alleles, it is likely that the new allele originated by gene conversion. At the protein level, the new allele has two amino acid differences compared to B*0801. Comparing the residues of the alpha1 and alpha2 domains of the B*08 variants to each other, a high degree of polymorphism was found. Three alleles differ from B*0801 by only one amino acid residue whereas the other comparisons revealed at least two disparities. B*0809 differs from the other B*08 variants by at least two amino acid residues, suggesting that mismatching may provoke alloreactivity and thus impair clinical outcome of bone marrow transplantation. Among the B*08 alleles with a single amino acid difference, the mismatch combinations B*0801 vs. B*0805 and B*0801 vs. B*0807 appear to be the most compatible based on structural data.

Alleles↗
PubMed2000

Current clinical diagnosis in Creutzfeldt-Jakob disease: identification of uncommon variants.

According to the recently established molecular basis for phenotypic heterogeneity of sporadic Creutzfeldt-Jakob disease (CJD), six different phenotypes are characterized by the size of the protease-resistant fragment of the pathological prion protein (types 1 and 2) and homozygosity or heterozygosity for methionine or valine at codon 129 of the prion protein gene (designated by MM1, MM2, MV1, MV2, W1, and W2). In the present investigation, we analyzed the value of commonly used clinical tests (electroencephalogram [EEG], detection of 14-3-3 protein in cerebrospinal fluid [CSF], and hyperintensity of the basal ganglia in magnetic resonance imaging) for the clinical diagnosis in each CJD phenotype. The detection of periodic sharp and slow wave complexes in the EEG is reliable in the clinical diagnosis of MM1 and MV1 patients only. The CSF analysis for 14-3-3 protein showed high sensitivity in all analyzed subgroups with the exception of MV2 patients. Valine-homozygous patients had a negative EEG, but most had detectable levels of neuronal proteins in the CSF. The sensitivity of the magnetic resonance imaging was 70%, irrespective of the subgroup, but was particularly reliable in the clinical diagnosis of MV2 patients. The widening spectrum of diagnostic techniques in CJD is not only useful in the increased accuracy of the clinical diagnosis but should also lead to the identification of more atypical cases of sporadic CJD.

14-3-3 Proteins↗
PubMed1994

Familial amyloid polyneuropathy in Taiwan: identification of transthyretin variant (Leu55-->Pro).

We report a family with familial amyloid polyneuropathy (FAP), showing an early-onset and a fatal outcome before age 30. Transthyretin (TTR) gene analysis showed one point mutation (T-->C change) in the second base of codon 55, and the corresponding amino acid substitution of proline (Pro) for leucine (Leu) was confirmed at the protein level. This is the first FAP family of Taiwanese origin demonstrating a causative gene abnormality, and FAP with TTR-Pro55 was considered to be more serious compared with other forms of FAP.

Adolescent↗
PubMed2001

Identification of splicing variants of Frabin with partly different functions and tissue distribution.

Frabin is a GDP/GTP exchange protein for Cdc42 small G protein with actin filament-binding activity. Frabin consists of the actin filament-binding domain, the Dbl homology domain, the first pleckstrin homology domain, the FYVE-finger domain, and the second pleckstrin homology domain in this order from the N-terminus. Frabin forms filopodia through direct activation of Cdc42 and lamellipodia through indirect activation of Rac small G protein. We isolated here two smaller splicing variants of frabin and named the original one, middle-size one, and smallest one frabin-alpha, -beta, and -gamma, respectively. Frabin-beta lacked the second pleckstrin homology domain and frabin-gamma lacked the FYVE-finger domain and the second pleckstrin homology domain. These three variants were expressed in all of the tissues examined but their expression levels are different depending on tissues. In L fibroblasts, all the three variants formed filopodia. As to lamellipodia, frabin-alpha formed them; frabin-beta formed them to a small extent; and frabin-gamma did not. In MDCK epithelial cells, frabin-alpha formed microspikes but frabin-beta or -gamma did not.

Alternative Splicing↗
PubMed2001

Molecular cloning of a member of the facilitative glucose transporter gene family GLUT11 (SLC2A11) and identification of transcription variants.

We isolated a member of the facilitative glucose transporter (GLUT) gene family (GLUT11; SLC2A11 as a HGMW-approved symbol) based on the analysis of a human genomic BAC clone KB1125A3 located on band q11.2 of human chromosome 22. The gene GLUT11/SLC2A11 consists of 12 exons spanning over 29 kb in size and is located between two genes, SMARCB1 and MIF. The deduced amino acid sequence indicated the topological features of transmembrane helices and sequence motifs which are common to the GLUT protein family. The cDNA cloning revealed the presence of three types of variation in its transcripts. The first variation is caused by the existence of three distinct first exons (SLC2A11-a, -b, and -c). PCR analysis of multi-tissue-derived cDNA panels indicated the differential expression of these transcript variants. The second variation is caused by skipping over one exon (exon 6). The third variation is caused by the premature transcription termination at a site between exon 8 and exon 9. Both exon skipping and premature termination caused frameshift, resulting in the production of truncated GLUT11/SLC2A11 transcripts. These results suggested that transcription of GLUT11/SCL2A11 gene is controlled in a complex manner.

Amino Acid Motifs↗