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PCR-RFLP
Terms modified by PCR-RFLP Selected AbstractsPhylogenetic Reanalysis of the Saudi Gazelle and Its Implications for ConservationCONSERVATION BIOLOGY, Issue 4 2001Robert L. Hammond The Saudi gazelle ( Gazella saudiya) was endemic to the Arabian peninsula but is now considered extinct in the wild and is potentially a candidate for captive breeding and reintroduction. Using 375 base pairs of mitochondrial DNA (mtDNA) cytochrome b gene derived from museum samples collected from the wild prior to the presumed extinction of this species, we show that G. saudiya is the sister taxon of the African dorcas gazelle ( G. dorcas). Reciprocal monophyly of G. saudiya mtDNA haplotypes with G. dorcas, coupled with morphological distinctiveness, suggests that it is an evolutionarily significant unit. These data indicate that captive populations identified previously as potential sources of G. saudiya for captive breeding appear incorrectly designated and are irrelevant to the conservation of G. saudiya. The polymerase chain reaction,restriction fragment length polymorphism ( PCR-RFLP) analysis of several private collections of living gazelles in Saudi Arabia provides no evidence for the survival of G. saudiya. We recommend that field surveys be undertaken to establish whether G. saudiya is indeed extinct in the wild and that other private collections within the Arabian peninsula be screened genetically. We urge caution when captive animals of unknown provenance are used to investigate the phylogenetics of cryptic species groups. Resumen: La identificación de poblaciones taxonómicamente apropiadas de especies en peligro para programas de reproducción en cautiverio y de reintroducción es fundamental para su éxito. La Gacela Saudi (Gazella saudiya) fue endémica a la península de Arabia pero ahora está considerada como extinta en su medio y es un candidato potencial para reproducción en cautiverio y reintroducción. Utilizando 375 pares de bases de ADN mitocondrial (ADNmt) del gene citocromo b derivados de muestras de museos colectadas en el medio silvestre antes de la extinción de la especie, mostramos que G. saudiya es el taxón hermano de la gacela dorcas africana (G. dorcas). La monofilia recíproca de haplotipos de ADNmt de G. saudiya con G. dorcas, aunado a diferencias morfológicas, sugiere que es una unidad evolutiva significativa. Estos datos indican que las poblaciones cautivas identificadas previamente como fuente potencial de G. saudiya para reproducción en cautiverio están incorrectamente identificadas y son irrelevantes para la conservación de G. saudiya. El análisis PCR-RFLP de varias colecciones privadas de gacelas vivas en Arabia Saudita no proporcionan evidencia para la supervivencia de G. saudiya. Recomendamos que se realicen muestreos en el campo para establecer si en efecto G. saudiya está extinta en su hábitat y que se examinen genéticamente las otras colecciones privadas en la península Arábiga. Recomendamos precaución cuando animales cautivos de origen desconocido son utilizados para investigar la filogenia de grupos de especies crípticas. [source] Islet autoimmunity and genetic mutations in Chinese subjects initially thought to have Type 1B diabetesDIABETIC MEDICINE, Issue 1 2006D. Zhang Abstract Aims To explore the contribution of islet autoimmunity and genetic mutations in Chinese patients initially thought to have Type 1B diabetes. Methods A group of 33 Chinese patients with newly diagnosed Type 1B diabetes, were identified by the absence of autoantibodies to glutamic acid decarboxylase (GAD), IA-2, insulin, thyroid globulin or thyroid peroxidase, or high-risk HLA-DQ haplotypes. The cohort was further characterized by measurement of autoantibodies to carboxypeptidase H (CPH) and SOX13 using radioligand assays, and testing for genetic mutations associated with MODY3/MODY6 and mitochondrial diabetes. Mutations of HNF-1, (MODY3) and neuroD1/,2 (MODY6) genes were screened using the single-strand conformation polymorphism (SSCP) technique and sequencing. Mitochondrial DNA mutations were analysed with polymerase chain reaction,restriction fragment length polymorphism (PCR-RFLP). Results Within the cohort, we found one patient with a novel mutation, R321H (CGC,CAC) in exon 5 of the HNF-1, gene, one with ND1 mt3316 G,A mutation in mitochondrial DNA, five with Ala45Thr polymorphisms in the neuroD1/,2 gene, and two patients with autoantibodies to SOX13. Conclusions Some of the Chinese patients originally thought to have Type 1B diabetes do have other evidence of islet autoimmunity and genetic mutations involved in the underlying aetiology. This suggests that more rigorous screening for these conditions is needed before classifying subjects as having Type 1B diabetes. [source] The p73 polymorphisms are not associated with susceptibility to esophageal squamous cell carcinoma in a high incidence region of ChinaDISEASES OF THE ESOPHAGUS, Issue 4 2007H. Ge SUMMARY., P73, a p53 homolog, has some p53-like activities and plays an important role in modulating cell cycle, apoptosis and DNA repair. The two linked polymorphisms in the non-coding region of exon2 of p73 gene, named G4C14-A4T14, may alter translation efficiency of the gene. The transcription of p73 gene is initiated by three promoters, termed P1-P3. There is a single nucleotide substitution (,386G/A) in the P3 promoter region with unknown function. To test the hypothesis that the genetic variations in the exon2 and P3 promoter play a role in the etiology of esophageal squamous cell carcinoma (ESCC), we conducted a population-based case-control study in 348 ESCC patients and 583 healthy controls from a high incidence region of Hebei province, China. The p73 polymorphisms were genotyped by polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP). The results showed that the family history of upper gastrointestinal cancer (UGIC) significantly increased the risk of developing ESCC (the age, sex and smoking status adjusted OR = 2.02, 95% CI = 1.54,2.67). The overall distribution of the p73 genotype, allelotype and haplotype in cancer patients and controls were not significantly different (all P -values are above 0.05). Stratification analysis by smoking status and family history of UGIC also did not show the significant influence of the polymorphisms on the risk of ESCC development. The results suggested that the p73 exon2 G4C14-A4T14 and P3 promoter ,386G/A polymorphisms might not be used as potential markers to predicate the risk of ESCC development in northern China. [source] Vascular endothelial growth factor gene polymorphisms are associated with the risk of developing adenomyosisENVIRONMENTAL AND MOLECULAR MUTAGENESIS, Issue 5 2009Shan Kang Abstract Vascular endothelial growth factor (VEGF), a major mediator of angiogenesis and vascular permeability, may play a key role in the development of adenomyosis. The aim of this study was to investigate whether these four VEGF polymorphisms (,2578C/A, ,1154G/A, ,460C/T, and +936C/T) were associated with the risk of adenomyosis development. Genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay in 174 adenomyosis patients and 199 frequency-matched control women. There were significant differences between patients and control group in allele frequencies and genotype distributions of the ,2578C/A polymorphisms (P = 0.010 and 0.044, respectively). Compared with the C/C genotype, the A/A + C/A genotype could significantly modify the risk of developing adenomyosis [odds ratio (OR) = 0.64, 95% confidence interval (CI) = 0.42,0.97]. For the ,1154G/A polymorphism, the allele frequencies and genotype distributions in patient group were significant different from those of the controls (P = 0.001 and 0.007, respectively). Compared with the G/G genotype, the A/A + G/A genotype could significantly decrease the risk of developing adenomyosis (OR = 0.51, 95% CI = 0.33,0.80). However, the genotype distributions and allele frequencies of the ,460C/T and +936C/T polymorphisms did not significantly differ between controls and patients (all P value > 0.05). The haplotype analysis suggested that the TGA (VEGF ,460/,1154/,2578) and CGA haplotypes exhibited a significant decrease in the risk of developing adenomyosis compared with the haplotype of TGC (OR = 0.64, 95% CI = 0.41,1.00; OR = 0.44, 95% CI = 0.21,0.93, respectively). The study indicated that the ,2578A or ,1154A allele of VEGF gene could significantly decrease the risk of adenomyosis and might be potentially protective factors for adenomyosis development. Environ. Mol. Mutagen., 2009. © 2009 Wiley-Liss, Inc. [source] Polymorphisms in the thymidylate synthase promoter and the DNA repair genes XRCC1 and XPD in a Brazilian populationENVIRONMENTAL AND MOLECULAR MUTAGENESIS, Issue 9 2006Renata Canalle Abstract Polymorphisms in genes responsible for maintaining genomic integrity are potential modifiers of disease risk. Since considerable interindividual and interethnic variation in DNA repair capacity has been associated with polymorphic alleles, we evaluated the frequency of the 2R/3R variants in the TS promoter, Arg194Trp and Arg399Gln in the XRCC1 gene, and Asp312Asn and Lys751Gln in the XPD gene in 364 healthy individuals from a Brazilian population separated by ethnicity (European ancestry and African ancestry). The genotypes were determined by PCR (TS) or by PCR-RFLP (XRCC1 and XPD). The frequency of the TS 3R allele was 0.56 for whites and 0.51 for nonwhites. In the case of the XRCC1 MspI polymorphism, the allele frequencies were 0.09 for 194Trp in both nonwhites and whites and 0.27 and 0.28 for 399Gln in nonwhites and whites, respectively. For the XPD 312Asn allele, we found a frequency of 0.25 in white individuals, which was significantly different (P = 0.025) from that seen in nonwhites (0.15). Similarly, the 751Gln polymorphic allele of the XPD gene was significantly more frequent (P < 0.002) in whites (0.30) than in nonwhites (0.20). The genotype frequencies were within Hardy,Weinberg equilibrium. We concluded that the genotype and allele frequencies of XPD gene polymorphism differed between white and nonwhite Brazilians, and that the frequencies of the XPD 312Asn and XRCC1 399Gln alleles in this Brazilian population showed ethnic variability when compared with those observed in other populations. Environ. Mol. Mutagen., 2006. © 2006 Wiley-Liss, Inc. [source] Identification of economically important Liriomyza species by PCR-RFLP analysis,EPPO BULLETIN, Issue 1 2005L. F. F. Kox Only adult males of Liriomyza bryoniae, L. huidobrensis, L. sativae and L. trifolii can be identified with certainty on basis of their genitalia. Female adults, pupae and larvae can only be identified on the level of groups of species (L. bryoniae and L. huidobrensis vs. L. sativae and L. trifolii). Species identification in all developmental stages is possible using molecular biological techniques. Our method is a PCR amplification of a 790-bp fragment of mitochondrial cytochrome oxidase II (COII) DNA followed by RFLP analysis. The method was tested on single larvae, pupae and adults and proved to be applicable to these three life stages. The specificity of the assay was assessed by comparing the results of the PCR-RFLP analysis with those of morphological analysis using 60 Liriomyza specimens. Molecular and morphological identification agreed for all specimens analysed. PCR-RFLP is a powerful diagnostic tool for rapid and reliable identification of all life stages of economically important Liriomyza species. [source] Functional C3435T polymorphism of MDR1 gene: an impact on genetic susceptibility and clinical outcome of childhood acute lymphoblastic leukemiaEUROPEAN JOURNAL OF HAEMATOLOGY, Issue 5 2004Krzysztof Jamroziak Abstract: The significance of genetic background in childhood acute lymphoblastic leukemia (ALL) is not well understood. Polymorphisms of genes encoding for xenobiotics and drug transporters are potential factors, which can influence the risk of developing ALL and its clinical outcome. P-glycoprotein (P-gp) is an adenosine triphosphate-binding cassette (ABC)-family transporter involved in protection against xenobiotics and multi-drug resistance. Recently, the single-nucleotide polymorphism C3435T of MDR1 gene has been found to be associated with altered tissue expression and function of P-gp. To evaluate whether C3435T MDR1 polymorphism is associated with the occurrence and outcome of ALL, 113 children with ALL (median age 5.1 yr) and 175 healthy individuals of Polish Caucasian origin were studied by polymerase chain reaction-restriction fragment-length polymorhism (PCR-RFLP) assay. The mutant homozygous TT genotype was found to be associated with occurrence of ALL (OR, 95% CI; 1.8, 1.1,3.1; P = 0.037). Besides, the analysis of factors influencing clinical outcome of our ALL patient cohort showed that CC genotype carriers had significantly lower event-free survival probability (pEFS) (0.62 vs. 0.87; P = 0.007) and overall survival probability (pOS) (0.72 vs. 0.91; P = 0.006). The Cox proportional hazards model-based analysis revealed that the hazard ratios for lower pEFS and lower pOS among CC homozygous subjects were 3.9 (P = 0.008) and 3.3 (P = 0.02), respectively. In conclusion, the results of the present study provide evidence that C3435T MDR1 polymorphism may involve both the susceptibility to and the clinical outcome of childhood ALL. Carriers of the TT genotype are more at risk of developing ALL than other individuals, whereas CC genotype carriers are supposed to have worse prognosis. [source] PAX9 polymorphisms and susceptibility to sporadic tooth agenesis: a case,control study in southeast ChinaEUROPEAN JOURNAL OF ORAL SCIENCES, Issue 2 2008Yongchu Pan Tooth agenesis is one of the most common developmental disorders in humans. The PAX9 gene, which plays an important role in odontogenesis, is associated with familial and sporadic tooth agenesis. A case,control study was performed in 102 subjects with tooth agenesis (cases) and 116 healthy controls. We genotyped four PAX9 gene polymorphisms using a polymerase chain reaction,restriction fragment length polymorphism (PCR-RFLP) assay. The allele and genotype frequencies of the four polymorphisms were not significantly different between the controls and the subjects with tooth agenesis. Similar results were observed in a subgroup analysis of test subjects only with mandibular incisor agenesis. Further analysis showed no significant difference in the haplotype distribution between the controls and the subjects with tooth agenesis or mandibular incisor agenesis. However, we found that the AGGC haplotype was associated with a decreased risk of tooth agenesis, compared with the most common haplotype, AGCC (odds ratio, 0.14; 95% confidence interval: 0.00,0.95). These results suggest that the four PAX9 polymorphisms alone have a non-significant main effect on the risk of tooth agenesis but that the AGGC haplotype may have a protective effect associated with a decreased risk of tooth agenesis. [source] Structure and activity of the nitrate-reducing community in the rhizosphere of Lolium perenne and Trifolium repens under long-term elevated atmospheric pCO2FEMS MICROBIOLOGY ECOLOGY, Issue 3 2004Kathrin Deiglmayr Abstract Rhizosphere soil was sampled in monocultures of Lolium perenne and Trifolium repens in June and October 2002, at two different nitrogen fertilisation levels (14 and 56 g N m,2 year,1) and under two pCO2 atmospheres (360 and 600 ppmv) at the Swiss FACE (Free Air Carbon dioxide Enrichment) site. Directly extracted soil DNA was analysed with restriction fragment length polymorphism (PCR-RFLP) by use of degenerated primers for the narG gene encoding the active site of the membrane-bound nitrate reductase. The corresponding enzyme activity of the nitrate reductase was determined colorimetrically after 24 h of anaerobic incubation. The narG PCR-RFLP fingerprints showed that the structure of the nitrate-reducing community was primarily affected by season and pH of the sampling site, whereas CO2 enrichment, plant species or fertiliser treatment had no apparent effect. In contrast, the nitrate reductase activity responded to N fertilisation, CO2 enrichment and plant species in October, whereas in June drought stress most likely kept the enzyme activity at a low level in all treatments. Apparently, the respiratory nitrate-reducing community adapted to different treatments primarily by altered enzyme activity. [source] Distribution and diversity of type III secretion system-like genes in saprophytic and phytopathogenic fluorescent pseudomonadsFEMS MICROBIOLOGY ECOLOGY, Issue 3 2004Sylvie Mazurier Abstract Type three secretion systems (TTSSs) are protein translocation mechanisms associated with bacterial pathogenicity in host plants, and hypersensitive reactions in non-host plants. Distribution and diversity of TTSS-like genes within a collection of saprophytic and phytopathogenic fluorescent pseudomonads were characterized. This collection included 16 strains belonging to 13 pathogenic species, and 87 strains belonging to five saprophytic species isolated from plant rhizosphere and soil. Presence of conserved hypersensitive reaction/pathogenicity (hrp) genes (hrc RST) was assessed both by PCR using primers designed to amplify the corresponding sequence and by dot-blot hybridization using a PCR-amplified hrc RST fragment as a probe. PCR allowed the detection of TTSS-like genes in 75% and 32% of the phytopathogenic and saprophytic strains, respectively, and dot-blot hybridization in 100% and 49% of the phytopathogenic and saprophytic strains, respectively. The restriction fragment length polymorphism (RFLP) of 26 amplified hrc RST fragments revealed a considerable diversity. Twenty-one distinct RFLP types were identified and one hrc RST fragment was sequenced per RFLP type. The obtained hrc RST sequences clustered into three groups. Two of these groups included both phytopathogenic and saprophytic strains. The diversity of 16S rRNA genes, commonly used as an evolution marker, was characterized using PCR-RFLP. Polymorphism of the 16S rRNA genes corresponded to that of hrc RST genes, suggesting that these genes have followed a similar evolution. However, the occurrence of few mismatches suggests that sometimes TTSS-like genes might have undergone horizontal genetic transfer. [source] Genetic diversity of the hyperparasite Sphaerellopsis filum on Melampsora willow rustsFOREST PATHOLOGY, Issue 5 2004M. Liesebach Summary The non-specific rust hyperparasite Sphaerellopsis filum occurs naturally on Melampsora rusts of many species of the genus Salix as well as on a large range of other rust genera worldwide. To study the genetic diversity of the hyperparasitic fungus 77 S. filum isolates collected from rusts on willow clones from plantations, clone collections and natural habitats of different sites were investigated using polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) analysis of the rDNA internal transcribed spacer regions including 5.8S rDNA and sequence analysis. Additionally, strains from Melampsora poplar rusts (4) and strains of Puccinia abrupta from Parthenium hysterophorus (5) and of P. obscura from Bellis perennis (1) were used for comparisons. Results of genetic analysis demonstrated distinct variation within the S. filum isolates. Two main groups with more than 32% difference between their nucleotide sequences were distinguished, indicating two taxa within S. filum. Within the first main group three profiles (I, II, III) were detected. The differences between these profiles were about 12%. The variation within each profile was very low (less than 2%). The second main group comprised two profiles (IV, V), which differed in 12 to 16% of their nucleotide positions. The isolates of group IV possessed a higher variation (up to 5%) within the group than those of the first main group (I, II, III). Group V was only represented by a single isolate. Neither interrelations between the S. filum profiles and the Melampsora genotypes nor a spatial distribution could be detected. It is remarkable that the six strains of S. filum from Puccinia rusts belong to one subgroup. Résumé Sphaerellopsis filum est un hyperparasite non spécifique des rouilles qui se rencontre naturellement sur les Melampsora affectant le genre Salix ainsi que sur une large gamme d'autres genres de rouille dans le monde entier. Pour caractériser la diversité de ce champignon hyperparasite, 77 isolats de S. filum, récoltés à partir de lésions de rouille sur des clones de plantation, des collections de clones et dans des sites naturels, ont étéétudiés par analyse PCR-RFLP des régions ITS de l'ADNr, incluant le 5.8S rDNA, et par analyse de séquences. Des souches provenant de Melampsora des peupliers (4), de Puccinia abrupta sur Parthenium hysterophorus (5) et de P. obscura sur Bellis perennis (1) ont également été utilisées pour comparaison. L'analyse génétique démontre une variation entre isolats de S. filum. Deux groupes principaux, avec plus de 32% de différence dans leur séquence nucléotidique, se distinguent, indiquant l'existence de deux taxons au sein de S. filum. A l'intérieur du premier groupe, trois profils (I, II, III) sont mis en évidence, avec une différence d'environ 12% entre profils mais très peu de variation (moins de 2%) à l'intérieur d'un profil. Le deuxième groupe comprend deux profils (IV, V) qui différent de 12 à 16% pour leur séquence nucléotidique. Les isolats du groupe IV présentent une variation intra-groupe plus importante (jusqu'à 5%) que ceux des groupes I, II et III. Le groupe V n'est représenté que par un isolat. Aucune relation n'a pu être établié entre les profils de S. filum et les génotypes de Melampsora ou la distribution spatiale. Il est à noter que les six isolats de S. filum provenant de rouilles àPuccinia appartiennent à un seul sous-groupe. Zusammenfassung Der Hyperparasit Sphaerellopsis filum kommt natürlich auf Melampsora -Rostpilzen bei Salicaceae und auf zahlreichen anderen Rostgattungen weltweit vor. Um die genetische Vielfalt dieses hyperparasitischen Pilzes zu untersuchen, wurden 77 S. filum -Proben, die von Weidenrosten in Plantagen, Klonsammlungen und von verschiedenen natürlichen Standorten stammen, isoliert. Die 5.8S-ITS-Abschnitte der rDNA wurden mit Hilfe der PCR-RFLP untersucht und Sequenzen analysiert. Zum Vergleich wurden vier Isolate von Pappelrosten sowie fünf Isolate von Puccinia abrupta von Parthenium hysterophorus und ein Isolat von Puccinia obscura von Bellis perennis herangezogen. Die Ergebnisse der genetischen Untersuchungen zeigten eine deutliche Variation zwischen den S. filum -Isolaten. Zwei Gruppen mit über 32% Unterschied in der Nukleotid-Sequenz ließen sich unterscheiden. Dies deutet auf zwei taxonomische Einheiten von Sphaerellopsis hin. Die erste Gruppe ließ sich in drei Untergruppen (I, II, III) einteilen, deren 5.8S-ITS-Profile im Mittel 12% Unterschied aufwiesen. Die Variation innerhalb dieser drei Profile war sehr gering (,2%). Die zweite Gruppe umfasste zwei Profile (IV, V), die sich an 12 bis 16% Positionen ihrer Nukleotid-Abfolge unterschieden. Die Variation innerhalb von Profil IV war höher (bis 5%) als die der Untergruppen I - III, Profil V war nur durch ein Isolat vertreten. Eine Beziehung des S. filum -Genotyps zum Melampsora -Genotyp der Weide oder der Pappel ließ sich bei dem untersuchten Material nicht nachweisen, ebenso konnte keine geographische Differenzierung gefunden werden. Auffällig ist, dass alle sechs Puccinia -Isolate einer Untergruppe angehörten. [source] Glutathione S-transferase P1 and alpha gene variants; role in susceptibility and tumor size development of oral cancerHEAD & NECK: JOURNAL FOR THE SCIENCES & SPECIALTIES OF THE HEAD AND NECK, Issue 8 2010Mu-Kuan Chen MD Abstract Background. The aim of this study was to estimate the relationship of glutathione S-transferases (GST)P1, GSTA1, GSTM1, and GSTT1 gene polymorphisms to oral cancer risk. Methods. Polymerase chain reaction,restriction fragment length polymorphism (PCR-RFLP) was used to measure these 4 gene polymorphisms in 274 controls and 164 oral cancer patients. Results. Individuals with at least 1 varied G allele of GSTP1 had a 1.53-fold risk (95% confidence interval [CI] = 1.01,2.31) of developing oral cancer compared with patients with wild-type A/A homozygotes. Oral cancer patients with at least 1 varied T allele of GSTA1 gene had a 0.42-fold risk (95% CI = 0.18,0.95) of having a tumor size >2 cm compared with patients with C/C homozygotes. Conclusions. The varied G allele of GSTP1 may be considered as a factor contributing to increased susceptibility, whereas the T allele of GSTA1 could be a protective factor for tumor size progression in Taiwanese with oral cancer. © 2009 Wiley Periodicals, Inc. Head Neck, 2010 [source] Association of estrogen receptor , polymorphisms with susceptibility to chronic hepatitis B virus infectionHEPATOLOGY, Issue 2 2004Guohong Deng Several studies have demonstrated that estrogen receptor , (ESR1) participates in the pathogenesis of persistent hepatitis B virus (HBV) infection. To examine whether polymorphisms at the ESR1 gene locus are associated with persistent HBV infection, we resequenced ESR1 genomic region for single nucleotide polymorphisms (SNPs) in 27 unrelated Chinese. Two haplotype-tagged SNPs (htSNP), T29C and A252966G, were selected for genotyping in 1,277 persistent HBV-infected cases, 748 spontaneously recovered controls, and 293 nuclear families using polymerase chain reaction (PCR)-restriction fragment length polymorphism (PCR-RFLP) analysis. We observed that the subjects bearing ESR1 29T/T genotype had an increased susceptibility to persistent HBV infection compared to those bearing at least one 29C allele (odds ratio 1.41; 95% CI, 1.17-1.71, P < .001). Consistent with the results of population-based association study, a significantly greater than expected transmission of the 29T allele (56.4%) from heterozygous parents to offspring with persistent HBV infection was observed (,2 = 4.60, P = .033) using the transmission-disequilibrium test (TDT) in 293 nuclear families. Linkage disequilibrium (LD) mapping analysis indicated that the T29C polymorphism contained within a LD block located from promoter region to intron 3 of ESR1, suggesting that the strong association detected with T29C in ESR1 originated from ESR1 itself. In conclusion, our results suggest that the genetic variation at the ESR1 locus influences susceptibility to persistent HBV infection in a Chinese population. (HEPATOLOGY 2004;40:318,326.) [source] Absence of deafness-associated connexin-26 (GJB2) gene mutations in the Omani population ,,HUMAN MUTATION, Issue 6 2001Mehmet Simsek Abstract We have investigated the prevalence of mutations in the connexin 26 (GJB2) gene in Omani population using both PCR-RFLP and direct DNA sequencing methods. Two common GJB2 gene mutations (35delG and 167delT) were screened in 280 healthy controls and 95 deaf patients using two different PCR-RFLP methods. To investigate other GJB2 mutations, we have amplified and sequenced DNA from 51 unrelated deaf patients and 17 control subjects. None of the samples studied, either by RFLP or sequencing, revealed any deafness-associated mutations in the coding region of the GJB2 gene. These findings disagree with many reports on the GJB2 gene, describing various mutations as the cause of congenital recessive deafness. Although, an amino acid substitution (S86T) was identified by sequencing, we conclude that this change could not be associated with deafness since it was present in all the control and patient samples sequenced. © 2001 Wiley-Liss, Inc. [source] Compound heterozygosity in sibling patients with recessive dystrophic epidermolysis bullosa associated with a mild phenotypeINTERNATIONAL JOURNAL OF DERMATOLOGY, Issue 3 2006Y. Shibusawa MD We describe two cases of a 3-year-old Japanese boy and his 1-year-old sister presenting recessive dystrophic epidermolysis bullosa; a relatively mild phenotype. Blistering and scarring were limited to the acral region, and some fingernails and toenails were lost. PCR-RFLP and DNA sequencing analyses revealed compound heterozygotes for a splice-site mutation (6573 +1GtoC) and a nonsense mutation (E2857X) in the type VII collagen gene (COL7A1). Both mutations caused a premature termination codon (PTC). The mutation E2857X was located behind the candidate cleavage site within the NC-2 domain required for the assembly of anchoring fibrils. This PTC position may explain their mild phenotype. [source] NRAMP1 (SLC11A1) gene polymorphisms that correlate with autoimmune versus infectious disease susceptibility in tuberculosis and rheumatoid arthritisINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 1 2009Ö. Ates Summary NRAMP1 gene has multiple pleiotropic effects on macrophage activation pathways. These pleiotropic effects may increase resistance to infections such as tuberculosis (TB), but may also lead to susceptibility of autoimmune diseases such as rheumatoid arthritis (RA). It has been hypothesized that allele 3 would be associated with autoimmune diseases, whereas allele 2 would be associated with infectious diseases, and genetic factors that enhanced survival in the epidemics of TB might have led to susceptibility for the development of RA. We analysed four NRAMP1 gene polymorphisms including 5, promoter (GT)n (rs34448891), INT4 (469 + 14G/C) (rs3731865), 3,UTR (1729 + 55del4) (rs17235416) and D543N (codon 543, Asp to Asn) (rs17235409) in 112 patients with TB, 98 patients with RA, 80 healthy controls for TB and 122 healthy controls for RA using ARMS-PCR and PCR-RFLP. We found a significant association between INT4 and RA (P = 0.004, odds ratio: 2.06, 95% CI: 1.24,3.41), but no significant differences between 5, promoter, D543N, 3,UTR polymorphisms and RA. There were no associations between NRAMP1 gene polymorphisms and TB. Similarly, no significant differences were observed between NRAMP1 polymorphisms and rheumatoid factor positivity and erosive disease in RA and localization of TB. INT4 polymorphism may be associated with RA in Turkish patients. [source] The effects of RANTES/CCR5 promoter polymorphisms on HIV disease progression in HIV-infected KoreansINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 2 2008D. H. Jang Summary Recent studies have reported that two single nucleotide polymorphisms (SNPs) in the RANTES gene promoter region, ,403G/A and ,28C/G, are associated with a slower rate of decline in CD4+ T-cell number, whereas genetic polymorphisms within the CCR5 promoter are linked to acceleration of AIDS progression. In this study, we investigated the distribution of SNPs in the RANTES and CCR5 promoters and the association between these SNPs and HIV-1 disease progression in HIV-infected Koreans. Twenty-seven long-term non-progressors (LTNPs), 29 AIDS patients and 39 HIV-uninfected persons were enrolled in this study. SNPs for the RANTES and CCR5 promoters were determined by polymerase chain reaction,restriction fragment length polymorphism (PCR-RFLP) and a direct sequencing method. In the analysis of RANTES promoter polymorphisms, the genotypic and allelic frequencies of the RANTES ,28G mutation were significantly lower in HIV-infected patients than in HIV-uninfected persons (P = 0.005 and P = 0.001, respectively). The genotypic frequencies of RANTES ,28G and ,403A mutations did not differ significantly between LTNPs and AIDS patients. The frequencies of three CCR5 promoter polymorphisms, designated 59029 G/A, 59353T/C, and 59402G/A, did not differ significantly between HIV-uninfected and HIV-infected patients. However, the allelic frequency of CCR559353C was significantly higher in AIDS patients than in LTNPs (P = 0.003). These results suggest that RANTES-28G and CCR5 59353C mutations might be associated with HIV infection or pathogenesis in the Korean population. [source] Promoter polymorphism of the IL-18 gene is associated with atopic asthma in Tunisian childrenINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 1 2008J. Lachheb Summary Several lines of evidence point to a relevant role of IL-18 in the process of asthma. Some studies suggest that the polymorphism in the gene of IL-18 can be involved in many inflammatory and atopic diseases such as asthma. The aim of our study is to estimate the frequency of the IL-18- 607 C/A (rs 1946518) promoter polymorphism in Tunisian children with asthma. We investigated whether the presence of this polymorphism -607 C/A was associated with asthma or atopy and whether this polymorphism influenced the severity of asthma in affected children. We examined also the relationship between the IL-18 gene polymorphism and the serum total IgE level. The IL-18/-607 C/A polymorphism was analysed by polymerase chain reaction and restriction fragment-length polymorphism (PCR-RFLP) analysis. A total of 105 asthma patients and 112 controls as part of the whole children population were studied in a case-control study. Among the 105 children with asthma, 40 were also studied for linkage analyses with their respective parents. We noted that the A allele was associated with statistically significant increases in the risk of asthma in the case-control study (odd ratio (OR) = 1.55, 95% confidence interval (CI) 1.03,2.33. Moreover, the A allele was also associated with atopic asthma (P = 0.008), but not with asthma severity. The transmission disequilibrium test (TDT) analysis in this family study did not suggest a preferential transmission of the IL-18/ -607 C/A polymorphism to affected children. There is no correlation between the IgE level and the IL-18 - 607 C/A promoter polymorphism. Our data indicate that IL-18 - 607 C/A promoter polymorphism is associated with susceptibility to developing asthma in Tunisian population. [source] No association of SUMO4 M55V with autoimmune diabetes in Asian-Indian patientsINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 2 2007S. K. Sedimbi Summary Autoimmune diabetes [type 1 diabetes mellitus (T1DM), latent autoimmune diabetes in adults (LADA) and part of malnutrition-related diabetes] has been shown to have genetic predisposition. Studies in IDDM 5 have lead to the discovery of a novel polymorphism 163 A,G, of SUMO4 (small ubiquitin-related modifier) gene, associated with risk to T1DM in Asians, but not in Caucasians. We studied patients with T1DM (n = 134), patients with LADA (n = 101), patients with malnutrition-modulated diabetes mellitus (n = 66) and patients with fibrocalculous pancreatic diabetes (n = 43) and healthy controls subjects (n = 114) from Cuttack, India. Polymerase chain reaction,sequence-specific primer (PCR-SSP) was used to amplify the 163 A,G sequences. Restriction fragment length polymorphism (RFLP) was performed using restriction enzyme Taq I (PCR-RFLP). Differences in the allelic frequencies of the A and the G alleles were tested statistically using Fisher's exact test or chi-squared test wherever appropriate. P -values were considered significant when equal to or less than 0.05. No significant association was detected between SUMO4 M55V and T1DM susceptibility in Asian-Indians. Comparison of the A and G alleles with HLA DR3-DR4 did not result in any significant P -values. No significant association was found between SUMO4 M55V and LADA or malnutrition-related diabetes mellitus (MRDM). Our results show that Asian-Indians with T1DM are different from other Asian populations. Asian-Indians show more similarity to Caucasians with respect to the association of SUMO4 M55V variant in T1DM. Association studies on Asian-Indian patients with LADA and MRDM showed no significant difference in the presence of the A and the G alleles when compared to healthy controls. [source] Cattle MHC genes DOA and DOB: sequence polymorphisms and assignments to the class IIb regionINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 3 2001A. Gelhaus Summary In a study of the genetic polymorphism of the second exons of the cattle DOA and DOB genes, two and four allelic variants were detected, respectively. In the predicted amino acid sequence, the DOA polymorphism corresponded to variation at the respective residue position, whereas the nucleotide substitutions in the DOB gene were non-informative. PCR-RFLP assays were developed for DOA and DOB typing, and both loci were genetically mapped to the BoLA class IIb region by linkage analysis in the International Bovine Reference Panel. The single nucleotide polymorphisms detected in the BoLA-DOA and - DOB genes enable these loci to be used as markers in genetic trait analyses. [source] A new HpaII PCR-RFLP within the porcine prolactin receptor (PRLR) gene and study of its effect on litter size and number of teatsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 1 2002L. PUTNOVÁ DNA polymorphism of the porcine prolactin receptor gene (PRLR) was investigated and used to study its effect on litter size and number of teats in pigs. By means of PRLR gene sequence homology in pig, human and other species, primers were designed for PCR amplification within 5, unknown (to date) part of the prolactin receptor gene in pigs. In this part of the gene, a new polymorphism with HpaII restriction endonuclease was detected. AluI polymorphism described before and our new HpaII polymorphism were used to study the associations with reproduction traits. The PCR restriction fragment length polymorphism (PCR-RFLP) method was used to genotype AluI and HpaII loci of the PRLR gene in line A with 83 sows of Landrace breed and in two lines (B and C) with 75 and 86 Large White sows, respectively. Statistical analysis of 1020 litters showed that AluI locus was associated with litter size mainly in Landrace and affected the first parities, while HpaII locus of the gene was associated with the same traits in Landrace and Large White pigs and mainly affected numbers of weaned of pigs. The magnitude of the effect varied by population with the effects exceeding two pigs per litter in Landrace line and 1 pig per litter in Large White populations. Ein neuer HpaII PCR-RFLP innerhalb des porcinen Prolaktionrezeptorgens (PRLR), und Zusammenhänge zur Wurfgröße und Zitzenzahl DNA-Polymorphismen im porcinen Prolaktionrezeptorgen (PRLR) wurden untersucht und für die Analyse von Einflüssen auf Wurfgröße und Zitzenzahl bei Schweinen verwendet. Auf der Basis der PRLR -Gensequenzhomologie zwischen Schwein, Mensch und anderen Spezies wurden Primer für die PCR-Amplifikation aus dem 5, Bereich des Prolaktionrezeptorgens abgeleitet, der bisher beim Schwein noch unbekannt ist. In diesem Teil des Gens wurde mittels HpaII-Restriktionsendonuklease ein neuer Polymorphismus dargestellt. AluI Polymorphismus und der neue HpaII Polymorphismus wurden für Assoziationsstudien in Bezug auf Reproduktionsmerkmale verwendet. Mittels PCR-RFLP wurden in Linie A 83 Sauen der Landrasse und die Linien B und C mit 75 bzw. 86 Large White Sauen unter Verwendung von AluI und HpaII am PRLR -Gen genotypisiert. Die statistische Analyse von 1.020 Würfen zeigte, dass der AluI-Polymorphismus insbesondere in der Landrasse mit der Wurfgröße assoziiert ist, sowie die ersten Trächtigkeiten beeinflusst, während der HpaII Polymorphismus die gleichen Merkmale in der Landrasse und Large White Schweinen und insbesondere die Zahl an abgesetzten Ferkeln beeinflusste. Die Auswirkungen des Effekts variierten innerhalb Population, wobei der Effekt 2 Ferkel je Wurf in der Landrasse-Linie und 1 Ferkel je Wurf in der Large White Populationen überstieg. [source] The molecular diversity of the methanogenic community in a hypereutrophic freshwater lake determined by PCR-RFLPJOURNAL OF APPLIED MICROBIOLOGY, Issue 5 2004C. Whitby Abstract Aims:, To combine database-held sequence information with a programme of experimental molecular ecology to define the methanogenic community of a hypereutrophic lake by a PCR-restriction fragment length polymorphism (RFLP) analysis. Methods and Results:, Methanogen diversity in a hypereutrophic freshwater lake was analysed using 16S rDNA PCR-RFLP. Database-held 16S rRNA gene sequences for 76 diverse methanogens were analysed for specific restriction sites that permitted unequivocal differentiation of methanogens. Restriction digestion and agarose gel electrophoresis of the 16S rDNA from selected methanogen pure cultures generated observed restriction profiles that corroborated the expected patterns. This method was then tested by analysing methanogen diversity in samples obtained over 1 year from sediment and water samples taken from the same sampling site. Conclusions:, Restriction analysis of the 16S rRNA gene sequences from 157 methanogen clones generated from lakewater and sediment samples showed that over 50% were similar to Methanoculleus spp. Furthermore, a total of 16 RFLP types (1,16) were identified, eight of which contained no cultured representative archaeal 16S rRNA gene sequences. Significance and Impact of the Study:, This RFLP strategy provides a robust and reliable means to rapidly identify methanogens in the environment. [source] Estrogen Receptor , Gene Polymorphisms and Peak Bone Density in Chinese Nuclear Families,JOURNAL OF BONE AND MINERAL RESEARCH, Issue 6 2003Yue-Juan Qin Abstract PBD is an important determinant of osteoporotic fractures. Few studies were performed to search for genes underlying PBD variation in Chinese populations. We tested linkage and/or association of the estrogen receptor , gene polymorphism with PBD in 401 Chinese nuclear families. This study suggests the ER-, gene may have some minor effects on PBM variation in the Chinese population. Low peak bone density (PBD) in adulthood is an important determinant of osteoporotic fractures in the elderly. PBD variation is mainly regulated by genetic factors. Extensive molecular genetics studies have been performed to search for genes underlying PBD variation, largely in whites. Few studies were performed in Chinese populations. In this study, we simultaneously test linkage and/or association of the estrogen receptor , (ER -,) gene polymorphism with PBD in 401 Chinese nuclear families (both parents plus their female children) of 1260 subjects, with the 458 children generally between 20 and 40 years of age. All the subjects were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) at polymorphic PvuII and XbaI sites inside the ER -, gene. Bone mineral density was measured at the lumbar spine (L1-L4) and hip (femoral neck, trochanter, and intertrochanteric region). Raw bone mineral density values were adjusted by age, height, and weight as covariates. We detected marginally significant results for within-family association (transmission disequilibrium; p = 0.054) between the spine bone mineral density variation and the ER -, XbaI genotypes. For the hip bone mineral density variation, significant (p < 0.05) linkage results were generally found for the two intragenic markers. Analyses of the haplotypes defined by the two markers confer further evidence for linkage of the ER -, with the hip PBD variation. In conclusion, this study suggests that the ER -, gene may have minor effects on PBD variation in our Chinese population. [source] Common single nucleotide polymorphisms in cyclooxygenase-2 and risk of severe chronic periodontitis in a Chinese populationJOURNAL OF CLINICAL PERIODONTOLOGY, Issue 3 2009Cheng-Jie Xie Abstract Aim: Several common single nucleotide polymorphisms (SNPs) of the cyclooxygenase-2 (COX-2) gene have been reported to be functional. The association between ,1195GA, ,765GC and 8473TC of COX-2, and severe chronic periodontitis (CP) in a Chinese population was investigated. Material and Methods: 148 cases of healthy controls (control group) and 146 cases of severe CP were recruited in this study. Genotypes of ,1195GA, ,765GC and 8473TC were determined by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP). The distributions of genotypes and haplotypes were compared by ,2 test and the odds ratios (ORs) were calculated by logistic regression analysis. Results: The prevalence of the ,1195A was more prevalent in CP group (60.62%) than control group (51.35%), and the distributions of the ,765C and 8473C were higher in control group (6.76% and 21.96%) compared with CP group (3.08% and 15.07%). Only genotype distribution of ,1195GA was significant when p -value was corrected for multiple testing (pc=0.033). The adjusted ORs for the ,1195AA/GA, ,765GC and 8473CC/TC were 2.49 (95% CI=1.33,4.69, p=0.005), 0.45 (95% CI=0.20,1.04, p=0.061) and 0.67 (95% CI=0.41,1.11, p=0.118). Subjects with the haplotype AGT had a significantly higher risk of periodontitis than those with the most common haplotype GGT (OR=1.91, 95% CI=1.32,2.76, pc<0.001). Conclusions: It suggests the ,1195A variant is associated with an increased risk for severe CP. [source] Single-nucleotide polymorphisms in the IL-4 and IL-13 promoter region in aggressive periodontitisJOURNAL OF CLINICAL PERIODONTOLOGY, Issue 6 2007J. R. Gonzales Abstract Introduction: IL-4 and IL-13 polymorphisms have been shown to influence the susceptibility to systemic diseases. In this study, possible associations between the IL-4 ,590 C,T, IL-4 ,34 C,T, IL-13 ,1112 C,T and IL-13 ,1512 A,C promoter polymorphisms were investigated in subjects with generalized aggressive periodontitis (AgP) compared with healthy individuals. Material and Methods: Fifty-eight patients with diagnosis of generalized AgP and 51 matched healthy controls participated in the study. Blood samples were collected and DNA isolated. Molecular analyses were performed by PCR-RFLP in a blind fashion. Genotype and allele frequencies among study groups were compared using Fisher's exact test (, value: 0.05). Pearson's ,2 test was used for analysis of Hardy,Weinberg equilibrium. Results: The frequency of the IL-4 ,590 T/T and IL-4 ,34 T/T genotypes differed significantly between groups (p=0.05, 0.02, respectively), although the allele frequencies were similar. There was a higher frequency of the IL-4 ,590 T/T and IL-4 ,34 T/T genotypes in patients with AgP compared with controls. The genotype and allele frequencies of the IL-13 polymorphisms did not differ between groups. Conclusions: This study demonstrated an association between the IL-4 ,590 T/T and IL-4 ,34 T/T genotypes and AgP. Further research is necessary to prove if there is an association of these polymorphisms with AgP, and if the polymorphisms have a functional effect. [source] Below-ground ectomycorrhizal community structure in a recently burned bishop pine forestJOURNAL OF ECOLOGY, Issue 6 2000P. Grogan Summary 1,The effects of wildfire ash on ectomycorrhizal (EM) associations were investigated by sampling bishop pine (Pinus muricata, D. Don) seedlings from control and ash-removed plots 1.5 years after a severe fire in a northern Californian P. muricata forest. The below-ground community composition of EM at the site was characterized using molecular techniques (PCR-RFLP and nucleotide sequencing). 2,A total of 30 fungal taxa were observed, many of which differed in their distribution between treatment and control seedlings. However, most of the taxa that were distinctive to either treatment or control seedlings occurred only once across the site, precluding statistical detection of potential ash effects on EM community composition. There were no significant effects of ash removal on plot-level mycorrhizal community richness or diversity, and there were no distinct treatment-related clusters in a principal components analysis. 3,Analysis of the combined data indicated that numbers of fungal taxa per seedling, numbers of successive root depth increments colonized by the same taxon, and distances to neighbouring seedlings colonized by the same taxon, were randomly distributed across the site for the majority of mycorrhizal fungi. These distributional patterns suggest that the post-fire mycorrhizal community structure on P. muricata arose primarily from successful colonization by randomly distributed point-source fungal inocula within the upper mineral soil layer of the forest floor. 4,By comparison with pre-fire studies from similar P. muricata sites nearby, our data indicate that severe wildfire disturbance resulted in marked changes in mycorrhizal community composition, and a sharp increase in the relative biomass of ascomycetous fungi. [source] PCR-RFLP genotypes associated with quinolone resistance in isolates of Flavobacterium psychrophilumJOURNAL OF FISH DISEASES, Issue 3 2007S Izumi Abstract A novel genotyping method for epizootiological studies of bacterial cold-water disease caused by Flavobacterium psychrophilum and associated with quinolone resistance was developed. Polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) was performed on 244 F. psychrophilum isolates from various fish species. PCR was performed with primer pair GYRA-FP1F and GYRA-FP1R amplifying the A subunit of the DNA gyrase (GyrA) gene, which contained the quinolone resistance determining region. Digestion of PCR products with the restriction enzyme Mph1103I showed two genotypes, QR and QS. The difference between these genotypes was amino acid substitutions at position 83 of GyrA (Escherichia coli numbering). The genotype QR indicated an alanine residue at this position associated with quinolone resistance in F. psychrophilum isolates. Of the 244 isolates tested in this study, the number of QR genotype isolates was 153 (62.7%). In isolates from ayu (n = 177), 146 (82.5%) were genotype QR. With combination of this technique and previously reported PCR-RFLP genotyping, eight genotypes were observed in F. psychrophilum isolates. Using this genotyping system, the relationships between genotype and host fish species, or locality of isolation, were analysed and are discussed. [source] Rapid PCR-RFLP Method for the Identification of 5 Billfish SpeciesJOURNAL OF FOOD SCIENCE, Issue 4 2005Hung-Sheng Hsieh ABSTRACT: A rapid and reliable polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was developed to identify billfish species Xiphias gladius (swordfish), Makaira nigricans (blue marlin), Makaira indica (black marlin), Istiophorus platypterus (sailfish), and Tetrapturus audax (striped marlin). After DNA extraction and amplifying, the 348-bp PCR products from gene encoding of cytochrome b were subjected to restriction enzyme analysis. No single enzyme tested was able to distinguish the 5 species at the same time, but the combination of results obtained from the digests of Bsa JI and Cac 81 could be used to differentiate the 5 billfish species. This sensitive, rapid, and valid method can be used to detect fraudulent substitutes. [source] Polymorphism of human leptin receptor gene is associated with type 2 diabetic patients complicated with non-alcoholic fatty liver disease in ChinaJOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, Issue 2 2009Hongyun Lu Abstract Background and Aim:, To investigate the relationship between human leptin receptor (LEPR) gene G3057A polymorphism and type 2 diabetes mellitus (T2DM) patients complicated with or without non-alcoholic fatty liver disease (NAFLD). Methods:, Two hundred and sixteen cases of newly diagnosed T2DM patients (104 cases complicated with NAFLD) and 108 cases of normal glucose tolerances (NGT) were recruited. Hemi-nested polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) and PCR-direct sequence analysis were conducted to detect the polymorphism of LEPR G3057A variation. Plasma leptin levels were measured by enzyme-linked immunosorbent assay kit. Plasma lipid and glucose metabolic parameters were measured routinely. Liver ultrasound was carried out for all subjects. Results:, T2DM patients complicated with NAFLD had higher plasma insulin, leptin, triglycerides (TG) and low-density lipoprotein cholesterol (LDL-C) levels than those without NAFLD and NGT subjects. The variant frequency at nucleotide 3057 G,A transversion was 76.0% in type 2 diabetic patients complicated with NAFLD, which was also significantly higher than those without NAFLD (62.1%) and NGT cases (53.2%). There was also significant difference in genotype distribution between the three groups (,2 = 14.63, P < 0.01). Conclusion:, The polymorphism of LEPR gene 3057 probably contributes to the onset of NAFLD by regulating lipid metabolism and affecting insulin sensitivity. [source] Influence of cancer-related gene polymorphisms on clinicopathological features in colorectal cancerJOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, Issue 6 2008Gen Yoshiya Abstract Background and Aim:, Single nucleotide polymorphisms (SNP) are shown to be related with cancer incidence. It has been reported that CCND1, p21cip1DCC, MTHFR, and EXO1 are related with the risk of malignant neoplasm, but few studies have mentioned the prognosis of the patients. We investigated the SNP of patients and related this to clinicopathological features, including survival rate. Method:, DNA from the tissues of primary colorectal cancer was obtained from surgical resections of 114 patients (68 males and 46 females, 29,83 years). The CCND1 polymorphism was analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and those of other genes were investigated by the TaqMan method. The polymorphisms obtained were statistically analyzed for the relationship with clinicopathological features. Results:, The CG + GG allele was more invasive than the CC allele in histological tumor depth in the DCC codon 201 (P = 0.0086). The 677TT allele in MTHFR had a larger tumor size than the 677CC allele (P = 0.028). In EXO1 P757L polymorphism, patients with the TT allele had a statistically reduced survival rate compared with the other alleles. In CCND1 polymorphisms, we found no statistical significance in clinicopathological features. Conclusions:, From these preliminary data, these polymorphisms would be candidates predicting the clinicopathological features of colorectal cancer, but further more systematic gene analyses are warranted. [source] | ||||||||||||||||||||||||||||||||||||||||