SEARCH · PubMed Health

Results for “Polymorphism”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 163 records · Page 9Linked to original sources

PubMed1992

Insertion/deletion polymorphism and other restriction fragment length polymorphisms in the MCC gene.

The MCC gene is a candidate as a tumor suppressor gene for colorectal neoplasms. Further, MCC is tightly linked to the familial adenomatous polyposis (FAP) locus by linkage and physical analysis. Hence, restriction fragment length polymorphisms (RFLPs) of this gene might be very useful for presymptomatic diagnosis of individuals in families segregating mutant alleles of the APC gene. Here we report the identification of five polymorphic systems in MCC gene (both cDNA and genomic), one of which is an insertion/deletion polymorphism that is detectable by a polymerase chain reaction method. These five RFLP systems should be useful for linkage studies in FAP and for examining loss of heterozygosity at this locus in colonic polyps and tumors.

Adenomatous Polyposis Coli↗

PubMed1996

Characterization of Erwinia chrysanthemi by pectinolytic isozyme polymorphism and restriction fragment length polymorphism analysis of PCR-amplified fragments of pel genes.

Conserved regions about 420 bp long of the pelADE cluster specific to Erwinia chrysanthemi were amplified by PCR and used to differentiate 78 strains of E. chrysanthemi that were obtained from different hosts and geographical areas. No PCR products were obtained from DNA samples extracted from other pectinolytic and nonpectinolytic species and genera. The pel fragments amplified from the E. chrysanthemi strains studied were compared by performing a restriction fragment length polymorphism (RFLP) analysis. On the basis of similarity coefficients derived from the RFLP analysis, the strains were separated into 16 PCR RFLP patterns grouped in six clusters, These clusters appeared to be correlated with other infraspecific levels of E. chrysanthemi classification, such as pathovar and biovar, and occasionally with geographical origin. Moreover, the clusters correlated well with the polymorphism of pectate lyase and pectin methylesterase isoenzymes. While the pectin methylesterase profiles correlated with host monocot-dicot classification, the pectate lyase polymorphism might reflect the cell wall microdomains of the plants belonging to these classes.

Base Sequence↗

PubMed1998

Comparison of amplified ribosomal DNA restriction analysis, random amplified polymorphic DNA analysis, and amplified fragment length polymorphism fingerprinting for identification of Acinetobacter genomic species and typing of Acinetobacter baumannii.

Thirty-one strains of Acinetobacter species, including type strains of the 18 genomic species and 13 clinical isolates, were compared by amplified ribosomal DNA restriction analysis (ARDRA), random amplified polymorphic DNA analysis (RAPD), and amplified fragment length polymorphism (AFLP) fingerprinting. ARDRA, performed with five different enzymes, showed low discriminatory power for differentiating Acinetobacter at the species and strain level. The standardized commercially available RAPD kit clearly enabled the discrimination of all Acinetobacter genomic species but showed great polymorphism between isolates of Acinetobacter baumannii. AFLP fingerprinting with radioactively as well as fluorescently labelled primers showed high discriminatory power for the identification of 18 Acinetobacter genomic species and typing of 13 clinical Acinetobacter isolates. Compared to radioactive AFLP, fluorescent AFLP was technically fast and simple to perform, and it permitted analysis with an automated DNA sequencer. Fluorescent AFLP seems particularly well suited for studying the epidemiology of nosocomial infections and outbreaks caused by Acinetobacter species.

Acinetobacter↗

PubMed2000

Comparison of polymorphism of thymidine kinase gene and restriction fragment length polymorphism of genomic DNA in herpes simplex virus type 1.

The polymorphism of the thymidine kinase (TK) gene of herpes simplex virus type 1 (HSV-1) was analyzed and was compared with the restriction fragment length polymorphism (RFLP) of the whole genome to evaluate the relative efficiency of the TK gene as a potential probe for identification and discrimination of HSV-1. The effectiveness of using the polymorphism of the TK gene in classifying HSV-1 strains was comparable to that of RFLP analysis of 66 sites, suggesting that TK gene sequencing may have important applications in epidemiological studies of HSV-1.

DNA, Viral↗

PubMed1991

[DNA polymorphism in the Mongolian population. Restriction fragment length polymorphism analysis of mitochondrial DNA].

Restriction enzyme fragment patterns in the D loop and deletion-insertion polymorphism in the V noncoding region of human mitochondrial DNA (mt DNA) were analysed in Mongolian population using the polymerase chain reaction. Polymorphisms were detected and mt DNAs classified into 40 types using seven enzymes--AvaII, BamHI, CfrI131, KpnI, EcoRV, HaeIII RsaI and Asian specific deletion and insertion. The allele frequencies of the polymorphisms and gene diversity were determined. The data obtained for Mongolian population and the literature data were comparatively studied.

Alleles↗

PubMed1993

Deletion mapping of chromosome 8 in cancers of the urinary bladder using restriction fragment length polymorphisms and microsatellite polymorphisms.

We have used a combination of restriction fragment length polymorphism (RFLP) markers and highly informative microsatellite polymorphisms to map a common region of deletion on chromosome 8p in cancers of the urinary bladder. Analysis of loss of heterozygosity (LOH) using microsatellite polymorphisms was shown to be at least as sensitive as detection of RFLPs by Southern blotting. A total of 110 tumours was analysed for loss of heterozygosity (LOH) on 8p and 8q; 109 patients were informative for at least one marker on each chromosome arm and 29 tumours (26%) showed LOH of chromosome 8 markers, 26 of which (25%) showed LOH on 8p. Sixteen tumours (14%) showed LOH on 8q. Thirteen of these also had LOH on 8p. Of the 29 tumours with LOH, five had LOH at all informative loci, indicating loss of an entire copy of chromosome 8. An association was found between high tumour grade and stage and chromosome 8 LOH. Fifty-three per cent of grade 3 muscle-invasive tumours showed LOH compared with 11% of grade 1 non-invasive tumours (0.01 < P < 0.025 and 0.025 < P < 0.05 for grade and stage respectively). Deletion mapping of tumours with chromosome 8 LOH suggests the presence of a suppressor gene(s) for urothelial cancer within a region defined by the loci NEFL and PLAT (8p21-q11.2). If there is a common target for deletions in bladder and those in hepatocellular and colorectal tumours reported previously, this defines a common region of deletion at 8p21.3.

Base Sequence↗

PubMed2002

Electrophoretic identification of new genomic profiles with a modified selective amplification of microsatellite polymorphic loci technique based on AT/AAT polymorphic repeats.

The present paper introduces improvements of the conventional selective amplification of microsatellite polymorphic loci (SAMPL) technique, that exploit AT-rich microsatellite primers. Generally, AT/AAT microsatellites are frequent components of eukaryotic genomes, but their ubiquity and polymorphic information content (PIC) could not be exploited yet, because standard SAMPL conditions did not allow amplifications. Here we report (i) on the design of new versatile AT-rich microsatellite primers, that are combined with (ii) a modified SAMPL adapter primer (called EcoRI-Short), and (iii) special polymerase chain reaction (PCR) amplification regimes. The novel SAMPL procedure expands the range of useful microsatellite primers to AT-rich sequences and produces a high number of bands and a clear banding pattern, and detects polymorphisms in otherwise nonpolymorphic genomes of plants (Dioscorea alata, D. rotundata) and a fungus (Mycosphaerella fijiensis).

AT Rich Sequence↗

PubMed2003

A psychometrically derived impulsive trait related to a polymorphism in the serotonin transporter gene-linked polymorphic region (5-HTTLPR) in a Japanese nonclinical population: assessment by the Barratt impulsiveness scale (BIS).

Although a number of studies have shown that human impulsive traits are associated with indices of central serotonin function, few researchers have investigated the relationship between a polymorphism in the serotonin transporter gene-linked region (5-HTTLPR) and a psychometrically derived impulsive trait. We determined the 5-HTTLPR polymorphism in 123 employed Japanese male adults using the polymerase chain reaction. The distribution of allelic frequency was determined and also investigated the relationship of the 5-HTTLPR polymorphism to a impulsive trait as measured by the Barratt Impulsiveness Scale, 11th version (BIS-11). The distribution of allelic frequency was found to be almost identical to that previously reported in Japanese (the frequency for the long (L)/L, L/short (S), and S/S genotypes was: 3, 28, and 68%, respectively). In a comparison between the genotype groups, the S/S genotype group significantly higher scored for the total BIS-11 and the subscale attentional impulsiveness than the L/S + L/L genotype group. These findings suggest that individuals with a homozygous S-allele may be more impulsive than those with the other genotype.

Carrier Proteins↗

PubMed1992

A new intragenic polymorphism detected by the single-strand conformation polymorphism (SSCP) assay in the dystrophin gene.

We have employed the single strand conformation polymorphism (SSCP) technique to examine a group of patients with Duchenne or Becker muscular dystrophy who do not contain deletions detectable by multiplex PCR or Southern/cDNA, in an attempt to identify uncommon mutations within the dystrophin gene. In SSCP analysis, a mutated sequence can be detected as a change of mobility in a nondenaturing polyacrylamide gel. During the course of this investigation, we detected and characterized a new polymorphism at the 3' end of intron 16. The G-to-T base change creates a TaqI restriction site which allows for rapid typing of the polymorphism by restriction digestion and electrophoresis of PCR amplified products. Its localization inside the 5' region of the dystrophin gene and its high heterozygosity makes it a useful and easy tool for rapid carrier and prenatal diagnosis.

Base Sequence↗

PubMed1998

Detection of a high-frequency silent polymorphism (C-->T) in the kir2.1 (KCNJ2) inwardly rectifying potassium channel gene by polymerase chain reaction and single strand conformation polymorphism.

The aim of this work was to determine the frequency of a base substitution (C-->T) identified in the Kir2.1 gene (approved gene symbol: KCNJ2; OMIM number: 600681). Polymerase chain reaction (PCR) of the area of the Kir2.1 gene containing this substitution was performed on 52 genomic DNA samples. Using single strand conformation polymorphism (SSCP) analysis, the genotype and allele frequencies were subsequently determined and the polymorphism identified in this study was verified by cycle sequencing. The data demonstrate that the C-->T nucleotide change identified corresponds to a silent polymorphism with a relatively high frequency. The deduced genotype frequencies of homozygotes and heterozygotes were: C/C: 73%; T/T: 2% and C/T: 25%. The deduced allele frequencies were C: 85.6% and T: 14.4%.

DNA↗

PubMed1992

Single-strand conformational polymorphisms (SSCP): detection of useful polymorphisms at the dystrophin locus.

We searched for DNA polymorphisms in seven amplified fragments of the dystrophin gene. Three fragments exhibited variable mobilities during nondenaturing strand-separating gel electrophoresis (SSGE). These variants were due to single base changes (three transversions and one transition). Three were intronic (upstream from exons 17, 15, and 48) and one was in exon 48. The frequencies of these sequence variants were determined in a sample of 54 normal X chromosomes of Caucasian origin. One of these DNA polymorphisms was observed in every 650 bp tested and the average heterozygosity was 0.05% per base pair (0.08% if exons were excluded). Such a detection density and the fact that single-strand conformational polymorphisms do not depend on the presence of any specific sequence makes them especially valuable as genetic markers. In the dystrophin locus this approach could allow simultaneous detection of frequent deletions.

DNA, Single-Stranded↗

PubMed1992

A single base pair polymorphism in the WT1 gene detected by single-strand conformation polymorphism analysis.

The Wilms' tumor predisposition gene, WT1, was analysed exon-by-exon in a variety of tumours using the single-strand conformation polymorphism (SSCP) technique. A consistent variation in the usual band pattern for exon 7 was detected in this survey. On sequencing, a silent mutation was noted in codon 313 resulting in an A-->G transition in an arginine codon. The A-->G transition destroys an AflIII restriction enzyme recognition site, which provides a rapid means of identifying heterozygotes at this locus. Analysis of the segregation of this polymorphism in families demonstrated a co-dominant inheritance pattern. In an analysis of 21 randomly selected individuals 25% were heterozygous at this locus, which makes this polymorphism useful in a variety of genetic analyses.

Base Sequence↗

PubMed1982

Human chromosomal polymorphism. III. Chromosomal Q polymorphism in Mongoloids of northern Asia.

Q-heterochromatin variants in seven autosomes (3, 4, 13-15, 21, 22) were studied in two Mongoloid populations of northern Asia (Chukchi and Khakass). Q-staining was obtained using propylquinacrine mustard. Of 132 Chukchi individuals aged 13 to 20 years, 124 had Q-polymorphic chromosomes, while eight (6.0%) had no bands with fluorescence levels 4 and 5. The mean number of Q variants was 2.2 per individual. Of the 120 Khakass individuals aged 14 to 17 years, 112 had Q-polymorphic chromosomes, while eight (6.7%) had no Q variants with fluorescence levels 4 and 5. The mean number of Q variants was 2.5 per individual. No differences were found in the frequency of Q variants between sexes in the two populations. There was complete agreement between the observed homo- and heteromorphic frequencies and those predicted by the law of Hardy-Weinberg. As the Mongoloid populations of northern Asia showed statistically significant homogeneity both in the frequency of Q variants and the distribution of homo- and heteromorphic variants, they were examined as a single group--that of northern Mongoloids. The following questions are discussed: (1) the possible selective value of chromosomal Q-heterochromatin material in the adaptation of human populations to certain extreme environmental factors, in particular to cold and hypoxia; (2) the intraracial heterogeneity of Asian Mongoloids; (3) the taxonomic value of chromosomal Q polymorphism in ethnic anthropology.

Adolescent↗

PubMed1985

DNA polymorphism of the C2 and factor B genes. Detection of a restriction fragment length polymorphism which subdivides haplotypes carrying the C2C and factor B F alleles.

Factor B and the second component of complement (C2) in man are encoded within the major histocompatibility complex by single loci that are less than 1 kb apart. A 2.3 kb factor B-specific cDNA probe has been used to examine, by Southern blot analysis, the genomic DNA of individuals typed for C2 and factor B by protein electrophoresis. We have identified a restriction fragment length polymorphism using the endonuclease Taq I, which subdivides haplotypes carrying both the common variant of C2 (C2C) and the fast (F) variant of factor B. This DNA polymorphism has been mapped to lie in the C2 gene and represents a new genetic marker not defined by protein electrophoresis. This polymorphism may serve as a useful marker in the genetic analysis of diseases that are related to the major histocompatibility complex.

Alleles↗

PubMed1986

Polymorphisms within the HLA-DR3 haplotypes. I. HLA-DR polymorphisms detected at the protein and DNA levels are reflected by T-cell recognition.

HLA-DR molecules were isolated from eight different HLA-DR3 homozygous B-cell lines by immunoprecipitation with monoclonal antibodies, and they were subsequently analyzed by two-dimensional gel electrophoresis. We found that HLA-DR3 homozygous B-cell lines of consanguineous origin express two types of HLA-DR molecules. One type of HLA-DR molecule was present in all the cell lines tested, whereas the second DR molecule appears to be polymorphic. DNA isolated from the different HLA-DR3 homozygous cell lines was studied by Southern blot analysis to determine whether any DR beta restriction fragment length polymorphism could be observed. Polymorphisms detected at both the product and genomic level have been compared to each other, and their relations to the serological (HLA-DR) and cellular (HLA-D and LB-Q1) typing data will be discussed.

Antibodies, Monoclonal↗

PubMed1985

Bovine mitochondrial DNA polymorphism in restriction endonuclease cleavage patterns and the location of the polymorphic sites.

Cleavage patterns of mitochondrial DNA (mtDNA) by restriction endonuclease analysis were examined in four Japanese Black cows, three Japanese Shorthorn cows, and six Holstein cows. Seventeen restriction enzymes which recognize six base pairs and two restriction enzymes which recognize four base pairs were used in this study. Polymorphism was observed with three restriction enzymes, HindIII, TaqI, and MspI, and was detected within the breeds. Nucleotide substitution was determined in the HindIII polymorphic site by DNA cloning and sequencing; this is C----T at position 10126 of the URF-3 region. Furthermore, the MspI and TaqI polymorphic sites were located on the physical map.

Animals↗

PubMed2002

Association of cholecystokinin A receptor gene polymorphism with cholelithiasis and the molecular mechanisms of this polymorphism.

BACKGROUND: The etiology of gallstone formation is multifactorial, and genetic factors are involved. The genetic variations of cholecystokinin A receptor (CCK-AR) in patients having gallstones and the molecular mechanisms of this polymorhpism were examined. The involvement of CCK-AR in gallstone formation was confirmed using CCK-AR gene knockout mice. METHODS: CCK-AR gene expression was determined by Northern transfer analysis in gallbladders with or without gallstones. Genetic variations were determined by Southern blot and by direct sequencing. Molecular mechanisms in terms of the transcriptional activity and methylation status were examined. Finally, we investigated whether gallstone formation was enhanced in CCK-AR gene knockout mice. RESULTS: The gene expression of CCK-AR was significantly decreased in gallbladders with gallstones compared to those without gallstones. No genetic variations were detected in the coding region, but two sequence variations were detected in the promoter region in gallstone patients. However, no significant differences were found for the promoter activities of polymorphic promoter constructs. In contrast, less methylation in the promoter region was related to substantial expression of the CCK-AR gene. Gallstone formation was enhanced in CCK-AR gene knockout mice. The homozygote (GG/TT) polymorphism of the CCK-AR gene showed a significantly higher percentage of body fat. CONCLUSIONS: Deteriorating gallbladder contractions, possibly induced by alterations in the CCK-AR gene, as well as CCK-AR gene polymorphism, promoted gallstone formation.

Adenocarcinoma↗

PubMed1996

A novel microsatellite polymorphism in the human OB gene: a highly polymorphic marker for linkage analysis.

The mouse ob gene and its human homologue OB have recently been cloned. The mutations in the ob gene are known to be associated with extreme obesity. The relationship between the human OB gene and disease, however, is largely unknown due to the lack of suitable markers within or adjacent to the OB gene. To obtain informative markers, we searched for simple tandem repeat polymorphisms in the genomic sequence of the human OB gene and identified a novel tetranucleotide repeat in the 3' flanking region. Fifteen alleles were detected in this marker with a heterozygosity of 0.85 and polymorphism information content of 0.83, indicating a highly informative nature of this marker. Two-point linkage mapping in two Centre Etude Polymorphisme Humaine (CEPH) reference families suggested that this marker is located in the interval between D7S514 and D7S530, the same interval where the OB gene is located (recombination fractions with D7S514 and D7S530 were 0.026 and 0.034, respectively). Although allele frequency distributions of this marker did not differ between 84 control subjects and 69 NIDDM patients, there was a tendency to higher body weight in control subjects with class I/class I genotype than in those without this genotype (68.8 +/- 11.1 vs 60.8 +/- 10.3 kg, p = 0.05). The highly polymorphic nature of this marker and its location in the OB gene makes this marker useful for linkage studies of the OB gene with a number of phenotypes, such as obesity, non-insulin-dependent diabetes mellitus, hypertension and the insulin resistance syndrome.

Alleles↗