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 505 records · Page 28Linked to original sources
PubMed2006

An AFLP-based database of Shigella flexneri and Shigella sonnei isolates and its use for the identification of untypable Shigella strains.

Amplified fragment length polymorphism (AFLP) can be used to assess the genetic diversity of closely related microbial genomes. In this study, the first of its kind for identification of Shigella, the high discriminatory power of AFLP has been used to determine the genetic relatedness of 230 isolates of Shigella flexneri and Shigella sonnei strains. An AFLP database was generated to demonstrate its utility in the discrimination of closely related strains. Based on AFLP, S. flexneri strains could be grouped into separate clusters according to their serotypes. Within each serotype, strains demonstrated 80-100% similarity indicating that identical strains and closely related strains could be distinguished by this technique. S. flexneri 6 formed a distinct cluster with 55% similarity to the rest of the S. flexneri strains showing significant divergence from the rest of the S. flexneri strains. Significantly, S. sonnei isolates formed a distinct group and showed approximately the same level of genetic linkage to S. flexneri as Escherichia coli strains. Untypable isolates that showed conflicting agglutination reactions with conventional typing sera were identifiable by AFLP. Thus AFLP can be used for genetic fingerprinting of Shigella strains and aid in the identification of variant untypable isolates.

Bacterial Typing Techniques↗
PubMed2004

Identification of two novel allelic variants of ESX1L in the human placenta: lack of an association with intrauterine growth restriction.

Intrauterine growth restriction (IUGR) is a leading cause of neonatal morbidity and mortality. Although epidemiological studies implicate an important role for genetic factors in determining birth weight, few candidate genes for IUGR have been identified. ESX1L, the orthologue of Esx1, is an X chromosome-linked human homeobox gene expressed in the placenta and testis. The present study was undertaken to determine if aberrations in the ESX1L gene were associated with idiopathic IUGR because targeted deletion of Esx1 in the mouse leads to abnormal placental development and consequent IUGR. Genotyping analysis of ESX1L gene was performed on placental samples from 22 normal term and 12 IUGR term fetuses. Two allelic variants were identified, and they contain an insertion and a deletion, respectively, of the same 27 nucleotides in the highly repetitive region of exon-4 that encodes the previously identified 12 contiguous repeats of a unique 9-amino acid motif, PPMAP(V/L)PPG. Thus, the insertion and deletion variants were predicted to code for an aberrant ESX1L protein containing 13 and 11 contiguous repeats, respectively. However, both variants were detectable and evenly distributed in normal as well as IUGR placentae, indicating that these two variants of ESX1L do not contribute to genetic susceptibility to idiopathic IUGR. Furthermore, no single nucleotide polymorphisms were identified, and there was no difference in the level of ESX1L mRNA between control and IUGR placentae. Taken together, these findings provide the first evidence that two allelic variants of ESX1L exist in the human placenta but they are not associated with idiopathic IUGR.

Alleles↗
PubMed2003

Identification in eggplant of a variant of citrus exocortis viroid (CEVd) with a 96 nucleotide duplication in the right terminal region of the rod-like secondary structure.

Analysis of eggplants, kept for years under greenhouse conditions after having been mechanically inoculated with nucleic acid preparations from field-grown eggplants containing two viroids, Eggplant latent viroid (ELVd) and Citrus exocortis viroid (CEVd), revealed the presence of an additional larger viroid RNA. Molecular characterization of this RNA showed that it is a stable 467-nt variant of CEVd with a 96-nt duplication of the right terminal region (CEVd-D96) that preserves the rod-like secondary structure. The coexistence in eggplant of CEVd (371nt) and CEVd-D96, and the fact that they have an almost identical sequence, strongly suggests the emergence of the latter from the former through an internal recombination mediated by a jumping RNA polymerase with low processivity. CEVd-D96 from eggplant is similar to the CEVd-D92 variant characterized previously in a hybrid tomato, suggesting that certain hosts may play a critical role in selecting and replicating this class of enlarged variants.

Base Sequence↗
PubMed2005

Genetic analysis of three genes causing isolated methylmalonic acidemia: identification of 21 novel allelic variants.

Isolated methylmalonic aciduria (MMA) is an inborn error of metabolism due to the impaired isomerization of l-methylmalonyl-CoA to succinyl-CoA. This reaction is catalyzed by the mitochondrial protein methylmalonyl-CoA mutase (MCM, EC 5.4.99.2), an adenosylcobalamin-dependent enzyme. Four different forms of isolated MMA have been described: mut MMA associated with defects in the MCM apoenzyme, and phenotypically divided into two subtypes mut- and mut0 MMA, and three different defects involved in the synthesis of the active form of the cofactor adenosylcobalamin, termed cbl MMA, and classified into three different complementation groups cblA, cblB, and cblH associated with defects in the MMAA and MMAB genes and with an unidentified protein, respectively. In this work we describe the genetic analysis of 25 MMA patients, mainly from Spain. Using biochemical and cellular approaches our patients have been classified, identifying 13 mut MMA, 7 cblA, 2 cblB, and 3 noncblA, noncblB deficient patients. cDNA and genomic DNA sequence analysis of the MUT, MMAA, and MMAB genes have allowed us to identify 27 different changes, 21 novel ones. Among the missense mutations identified in the MUT gene only one, the c.970G>A (p.A324T) variant located in the substrate binding domain is likely a mut- mutation. The remaining missense mutations c.326A>G (p.Q109R), c.983T>C (p.L328P), c.1846C>T (p.R616C), and c.1850T>G (p.L617R) are probably mut0. In the MMAA patients analyzed, frameshift mutations are prevalent. We have explored the genotype-phenotype correlation for this clinically heterogeneous disease.

Acidosis↗
PubMed2002

Identification of the novel splicing variants for the hPXR in human livers.

The human pregnane X receptor (hPXR) plays a key role in the regulation of both drug metabolism and efflux by inducing the expression of CYP3A4 and MDR1 gene. Using reverse transcription-polymerase chain reaction (RT-PCR) analysis, we identified seven novel splicing variants of hPXR in tissue from a single human liver. The expression of hPXR-related transcripts in the liver samples of 15 Caucasian individuals was subsequently determined by RT-PCR assays. The pattern of expression levels of these transcripts varied among liver samples. These results suggest that the hPXR is expressed as several different transcripts in liver tissues, apparently due to alternative as well as defective gene splicing. Furthermore, because this study provides the possibility of interindividual differences in hPXR transcript profiles, these alternative splicings for hPXR may largely contribute to the interindividual variability in CYP3A4 and P-glycoprotein induction.

Alternative Splicing↗
PubMed1998

Genotyping human arylamine N-acetyltransferase type 1 (NAT1): the identification of two novel allelic variants.

Human arylamine N-acetyltransferase (NAT) is known to exist as two isoenzymes, NAT1 and NAT2, with different though overlapping substrate specificities. NAT1 and NAT2 are polymorphic at both genetic and phenotypic levels with four distinct alleles described in Caucasians for NAT1. Though clear genotype/phenotype associations exist for NAT2, the same remains unclear for NAT1. Whole blood taken from 32 individuals were NAT1 genotyped and compared to previously obtained NAT1 activities using p-aminobenzoic acid as a substrate. The NAT1 alleles of one individual, who had low NAT1 activity, were sequenced and compared to the wild type allele NAT1*4. A novel, non-conservative, substitution was present in both alleles at nucleotide position 560 and results in the exchange of an arginine for a glutamine at amino acid position 187. A glutamine is found in NAT2 at amino acid position 187 and has been implicated in substrate binding. This report describes a simple and effective genotyping method which detects the four previously reported NAT1 polymorphisms, and the described novel low acetylating polymorphism, by either NAT1 allele specific-PCR amplification or restriction fragment length polymorphism analysis of PCR amplified products. We suggest that NAT1 genotype/phenotype correlations will become more clear as further allelic variants are determined.

Alleles↗
PubMed1997

Identification and expression of a variant isoform of the levocabastine-sensitive neurotensin receptor in the mouse central nervous system.

This work describes the molecular cloning of a variant isoform of the low-affinity levocabastine-sensitive neurotensin receptor isolated from mouse brain. Although the corresponding mRNA encodes for a 282 amino acid protein unable to bind neurotensin after transient transfection in COS-7 cells, this non-functional neurotensin receptor is expressed in cerebral neocortex, cerebellum, olfactory bulb, striatum and hypothalamus with a level similar to that of the full-length low-affinity neurotensin receptor. By contrast, this receptor form is very weakly expressed in mesencephalon and absent in the pituitary, but is the major product in the spinal cord.

Amino Acid Sequence↗
PubMed1999

Identification and characterization of splice variants of ephrin-A3 and ephrin-A5.

Ephrins and Eph receptors have been implicated to play important roles in axon guidance. A variable spacer region exists that differs significantly among distinct ephrins. An ephrin-A5 isoform has previously been isolated which lacks 27 amino acids within the spacer region. The expression and biological activities of this isoform, as well as the existence of isoforms for other ephrins that show variation within the spacer region, remain unknown. We report here a novel alternatively spliced isoform of ephrin-A3 which lacks the corresponding variable region. When compared to the longer isoforms, the shorter isoforms of both ephrin-A3 and ephrin-A5 remained less prominent in the brain during development, though their expression increased at postnatal stages. In addition, they could inhibit neurite outgrowth of dorsal root ganglia (DRG) neurons, suggesting that the corresponding variable regions were not essential for their axon guidance activities.

Alternative Splicing↗
PubMed1998

Familial hyperinsulinism with apparent autosomal dominant inheritance: clinical and genetic differences from the autosomal recessive variant.

We describe three families with hypoglycemia caused by familial hyperinsulinism (HI) in whom vertical transmission of the disorder occurred, suggesting autosomal dominant (AD) inheritance. We therefore examined the relationship between the apparent AD disorder and the more common autosomal recessive (AR) form of HI, which has recently been linked to the sulfonylurea receptor on chromosome 11p15.1. The clinical features of the 11 patients with AD HI were milder than those seen in 14 patients with AR HI. Hypoglycemia was readily controlled with either diet alone or with diazoxide in 10 of 11 patients with AD HI but in none of those with the AR form. In one large pedigree, analysis of genomic DNA with polymorphic simple sequence repeat markers excluded linkage of AD HI to the SUR locus in a dominant manner. The possibility of linkage to the SUR locus could not be absolutely excluded in the two smaller pedigrees. None of the published mutations of the SUR gene identified in patients with AR HI were detected in the patients with the AD form. We conclude that the AD form of hyperinsulinism is phenotypically different from the AR variant. The identification of more families with this form of HI may make it possible to locate the responsible gene by the use of linkage analysis.

Adolescent↗
PubMed2003

Comparative study of different methods to genotype hepatitis C virus type 6 variants.

Hepatitis C virus (HCV) genotype 6a is found frequently in Southeast Asia. In Thailand, however, genotype 6 variants may exist which posses a genotype 1 like sequence in the 5' non-coding region. In order to genotype correctly these viruses, four different methods; INNO-LiPA assay, two RFLP assays on the core region (using different restriction enzymes) and phylogenetic analysis of the core sequences were compared. Samples from 17 chronic HCV patients from the Netherlands and Thailand and 18 anti-HCV positive blood donors recruited from Thailand were tested. The INNO-LiPA could not distinguish genotype 6 variants. The RFLP methods used could not, or only in combination with 5'NCR genotyping methods, identify type 6 variants. In conclusion, for identification of type 6 variants at least two different regions of the HCV genome have to be analyzed (both 5'NCR and core).

5' Untranslated Regions↗
PubMedDate not supplied

Neuroendocrine vs. paracrine control of follicle-stimulating hormone.

In spite of the pivotal role FSH plays in the regulation of gametogenesis, we are far from understanding the regulatory mechanisms involved in the control of its synthesis, secretion, and functions. Part of the problem relates to its molecular heterogeneity and the unavailability of assay methods capable of distinguishing the various isoforms of FSH. Recent work has confirmed the existence of two modes of FSH secretion, the basal and the episodic modes. The major portion of FSH secretion appears to be in the basal mode. The episodic mode appears to consist of both GnRH-associated and non-GnRH-associated pulses of FSH. The intracellular mechanisms by which differential release of LH and FSH are facilitated by GnRH are just beginning to be unraveled and may involve different second-messenger systems. Local pituitary regulators such as activins, inhibins, and follistatins are receiving considerable attention in recent years as a means by which differential release of LH and FSH can be facilitated by GnRH and other neuroendocrine factors. In parallel, the search for a selective FSH-releasing factor (FSH-RF) continues. Identification of variant forms of GnRH in recent years has opened up the possibility that one GnRH variant may be the long-sought-after FSH-RF. From a functional aspect, an understanding of how FSH heterogeneity is regulated is also important, as the different mixes of FSH isoforms have the ability to fine-tune the follicular recruitment and selection process. This review focuses on the recent advances made in the neuroendocrine and paracrine regulation of FSH synthesis/secretion/heterogeneity and pinpoints areas of gaps in our knowledge.

Activins↗
PubMed2001

Identification of two novel splicing variants of human type II iodothyronine deiodinase mRNA.

Human type II iodothyronine deiodinase (hDII) belongs to a family of selenoproteins. It catalyzes 5'-deiodination of thyroxine to generate an active thyroid hormone, 3,3',5-triiodothyronine. Two novel splice variants of hDII gene transcript; namely hDII-b and hDII-c, were identified. Three distinct DNA fragments (hDII-a-c) were amplified by a reverse transcription-polymerase chain reaction (RT-PCR) with hDII intron-spanning primers using total-RNA from human umbilical vein endothelial cell line, ECV304. The sequence of hDII-a was identical to that of previously reported hDII. hDII-b and hDII-c had an additional insertion of 108 and 242 bp, respectively. The insertion sequences were found in the intron of hDII gene, therefore, two novel exons exist between exons 1 and 2 of hDII gene. The splice sites of new exons (b and c) conserved the consensus sequences of splice acceptor and donor sites. hDII-b contains exon b with an in-frame TGA codon that may encode an extra selenocysteine. hDII-c contained exons b and c and the predicted open reading frame is interrupted by a stop codon (TAA) produced by a frame shift. RT-PCR analysis showed that hDII-a and hDII-b mRNAs are expressed in human tissues including brain, kidney, lung and trachea. The mRNA abundance of hDII-c was lower than that of hDII-a or hDII-b. Thus, the new variants of hDII transcripts suggest the presence of two short exons between exons 1 and 2 of hDII gene, and of functional variant of hDII.

Alternative Splicing↗
PubMed1999

The tau gene in progressive supranuclear palsy: exclusion of mutations in coding exons and exon 10 splice sites, and identification of a new intronic variant of the disease-associated H1 haplotype in Italian cases.

Mutations in coding exons or exon 10 5'-splice-site of the gene for microtubule-associated protein tau can cause chromosome 17-linked frontotemporal dementia and parkinsonism (FTDP-17). We sequenced the 11 coding exons plus exon-intron boundaries of the tau gene in 15 cases of progressive supranuclear palsy (PSP), and found no mutations in coding exons or exon ten 5'-splice sites. These data indicate that typical PSP is not associated with tau gene mutations similar to those causing FTDP-17. We also observed a +39deltaG base change in the intron following exon 4 in three out of 69 PSP cases (all three Italians), whereas it was not found in 150 Dutch controls and once in 112 Italian controls. The +39deltaG variant arose in the context of the PSP-associated tau H1 haplotype. Although a pathogenic role cannot be entirely excluded, +39deltaG is likely to be a rare polymorphism that may be in linkage disequilibrium with a biologically relevant locus inside or near to the tau gene.

Aged↗
PubMed2002

Identification of an alternative splicing variant of cathepsin C/dipeptidyl-peptidase I.

Cathepsin C/dipeptidyl-peptidase I is a papain-like lysosomal cysteine proteinase implicated in the processing of various proenzymes to their active forms. In this study, we identified an alternative splicing variant of cathepsin C in both human and mouse species for the first time. The variant messenger RNA (mRNA) encodes 137 amino acids corresponding to the first and second exons, followed by additional 31 amino acids. The two newly recognized exons are located in the former intron 2. The variant mRNA is distributed ubiquitously, but predominantly in kidney, placenta, and lymph nodes. Furthermore, both interleukin 4 (IL-4) and IL-13, but not a range of cytokines induce expression of the variant in bronchial epithelial cells. These results indicate that the variant may play a role in regulating the biological activities of cathepsin C, involved in the pathogenesis of bronchial asthma.

Alternative Splicing↗
PubMed2001

A permutation procedure for the haplotype method for identification of disease-predisposing variants.

Once a genetic region involved in a complex disease has been localized through linkage or association studies, we need methods to help us identify the actual disease predisposing genetic variant(s) in the region. A large number of single nucleotide polymorphic (SNP) sites may exist in this region. It is important to identify genetic variants directly involved in disease from those in linkage disequilibrium, and thus associated with, the disease predisposing variant(s). A question of great interest is to test whether a SNP, or a combination of SNPs, that influence the trait under investigation have been identified. For many complex HLA-associated diseases, patterns of amino acid site variability raise the possibility that HLA-variation association with a disease may not be due to a given allele but rather one or more variable amino acid sites occurring on several alleles. Here the question is whether an amino acid variant or a combination of amino acid variants involved in disease are identified. To address this question, this paper proposes a permutation procedure for the haplotype method, to test whether all the sites involved in the disease have been identified using the haplotypic data of patients and controls. The method is based on the theoretical result of Valdes and Thomson, that, for each haplotype combination containing all the amino acid sites involved in the disease process, the relative frequencies of amino acid variants at sites not involved in disease, but in linkage disequilibrium with the disease-predisposing sites, are expected to be the same in patients and controls. This procedure takes into account the non-independence of the sites sampled and is robust to mode of inheritance and penetrance of the disease, and can definitely specify when all the disease predisposing sites have not been identified. Application to both simulated data and real data sets on type 1 diabetes and alcoholism indicates that the proposed procedure works well in testing the important null hypothesis of whether all the predisposing sites are identified.

Alcohol Dehydrogenase↗
PubMed2001

Identification of seventeen novel KIR variants: fourteen of them from two non-Caucasian donors.

The killer-cell immunoglobulin-like receptors (KIR) expressed by human natural killer (NK) cells are encoded by a family of genes on chromosome 19. The number of KIR genes varies with haplotype and the individual genes exhibit polymorphism. To investigate KIR diversity we studied KIR cDNA and genes of four human donors: two Caucasians, one Black American and one Asian Indian. From analysis of these donors seventeen novel KIR variants were identified and characterized. Fifteen of the new variants appear to have a simple allelic relationship with a known KIR, whereas two of them combine the sequences of two different KIR genes. Fourteen of the seventeen KIR variants were isolated from the two non-Caucasoid blood donors. These data show that much human KIR diversity remains to be characterized, particularly in non-Caucasoid populations.

Alleles↗
PubMed2001

Experimental annotation of the human genome using microarray technology.

The most important product of the sequencing of a genome is a complete, accurate catalogue of genes and their products, primarily messenger RNA transcripts and their cognate proteins. Such a catalogue cannot be constructed by computational annotation alone; it requires experimental validation on a genome scale. Using 'exon' and 'tiling' arrays fabricated by ink-jet oligonucleotide synthesis, we devised an experimental approach to validate and refine computational gene predictions and define full-length transcripts on the basis of co-regulated expression of their exons. These methods can provide more accurate gene numbers and allow the detection of mRNA splice variants and identification of the tissue- and disease-specific conditions under which genes are expressed. We apply our technique to chromosome 22q under 69 experimental condition pairs, and to the entire human genome under two experimental conditions. We discuss implications for more comprehensive, consistent and reliable genome annotation, more efficient, full-length complementary DNA cloning strategies and application to complex diseases.

Algorithms↗