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PubMed2005

Epidermal growth factor receptor gene polymorphisms predict pelvic recurrence in patients with rectal cancer treated with chemoradiation.

An association between epidermal growth factor receptor (EGFR) signaling pathway and response of cancer cells to ionizing radiation has been reported. Recently, a polymorphic variant in the EGFR gene that leads to an arginine-to-lysine substitution in the extracellular domain at codon 497 within subdomain IV of EGFR has been identified. The variant EGFR (HER-1 497K) may lead to attenuation in ligand binding, growth stimulation, tyrosine kinase activation, and induction of proto-oncogenes myc, fos, and jun. A (CA)(n) repeat polymorphism in intron 1 of the EGFR gene that alters EGFR expression in vitro and in vivo has also been described. In the current pilot study, we assessed both polymorphisms in 59 patients with locally advanced rectal cancer treated with adjuvant or neoadjuvant chemoradiation therapy using PCR-RFLP and a 5'-end [gamma-(33)P]ATP-labeled PCR protocol. We tested whether either polymorphism alone or in combination can be associated with local recurrence in the setting of chemoradiation treatment. We found that patients with HER-1 497 Arg/Arg genotype or lower number of CA repeats (both alleles <20) tended to have a higher risk of local recurrence (P = 0.24 and 0.31, respectively). Combined analysis showed the highest risk for local recurrence was seen in patients who possessed both a HER-1 497 Arg allele and <20 CA repeats (P = 0.05, log-rank test). Our data suggest that the HER-1 R497K and EGFR intron 1 (CA)(n) repeat polymorphisms may be potential indicators of radiosensitivity in patients with rectal cancer treated with chemoradiation.

Adult↗
PubMed1995

[Diagnosis of hemophilia A carrier state using analysis of intergenic and intergenic polymorphism of factor VIII gene].

Carrier state of haemophilia A was assessed in women at risk by using Bcl I polymorphism of factor VIII gene in intron 18, CA repeating sequence polymorphism in intron 13, and intergenic polymorphism at DXS52 locus. Appropriate fragments of DNA in intron 18 and 13 were amplified by PCR. Polymorphism at DXS52 locus was determined by the method of Southern after digesting DNA with endonuclease Taq I and employing F814 and ST14-1 probes. The diagnosis of carrier state of haemophilia A was made in 12 women from 9 families.

Adult↗
PubMed1999

Frequent allelic loss at chromosome 3p distinct from genetic alterations of the 8-oxoguanine DNA glycosylase 1 gene in head and neck cancer.

Cigarette smoking is the major known risk factor for head and neck cancer. Tobacco promotes oxidative stress and enhances tissue levels of 8-hydroxyguanine (8-OH-G) in smokers. The presence of 8-OH-G does not impede replication but leads to an accumulation of G-->T transversions. Recently, the gene for human 8-oxoguanine DNA glycosylase 1 (hOGG1), an enzyme involved in the repair of 8-OH-G in humans, was cloned and mapped to chromosome 3p. In head and neck tumors, the hOGG1 gene locus is often targeted by loss of heterozygosity (LOH), and the spectrum of mutations in the p53 gene shows a bias in favor of G:C-->T:A transversions, as would be expected if HOGG1 repair functions were disabled. To test the involvement of hOGG1 in head and neck carcinogenesis, we had previously screened 56 tumors for LOH at 3p. From these tumors and two others, we selected 33 tumors demonstrating LOH for further mutational analysis of this gene. No somatic inactivating mutation was found in hOGG1. Polymorphisms involving intron 4 and exon 7 were present in 30% of the patients. A new polymorphism was identified in one patient in exon 6 and led to the amino-acid change G308E. Similar repair activities were found for the wild-type and exon 6-variant enzymes. Therefore, the involvement of hOGG1 in head and neck carcinogenesis is not strongly supported by this work.

Alleles↗
PubMed2001

[The association between polymorphism of endothelial nitric oxide synthase gene and diabetic nephropathy].

OBJECTIVE: To investigate the association between a 894 G-->T mutation at exon 7 and a 27 base pair(bp) repeat polymorphism in intron 4 of the eNOS gene and diabetic nephropathy in Chinese. METHODS: A case control study of 228 Chinese subjects (including 143 type 2 diabetes mellitus with or without nephropathy and 85 normal controls) was performed. The number of 894 G-->T mutation allele and 27 bp repeat polymorhism alleles were determined by polymerasechain reaction restriction fragment lenth polymorphism(PCR-RFLP) method and PCR combined with 4% agarose electrophoresis. RESULTS: The frequency of the T allele and TG genotype at exon 7 and the a allele and ab genotype in intron 4 were significantly higher in diabetic nephropathy positive (DN+) group than in diabetic nephropathy negative (DN-) group and control subjects(P < 0.05). Diabetic patients with coexistence of the T and a alleles had a higher incidence of diabetic nephropathy(P < 0.05) than those with only one of the two alleles or without any of the two alleles. Multivariate logistic regression analysis showed that blood glucose, GHbA1c, SBP, TC, 894 G-->T mutation at exon 7 and a 27 base pair(bp) repeat polymorphism in intron 4 of the eNOS gene are independent risk factors for diabetic nephropathy. CONCLUSIONS: The T allele at exon 7 and a allele in intron 4 are related to diabetic nephropathy in Chinese patients with type with 2 diabetes mellitus. The incidence of diabetic nephropathy is higher in patients who have both T and a alleles than patients who have either T or a allele alone.

Aged↗
PubMed2004

Polymorphism R92Q of the tumour necrosis factor receptor 1 gene is associated with myocardial infarction and carotid intima-media thickness--the ECTIM, AXA, EVA and GENIC Studies.

The TNFRSF1A gene was screened for polymorphisms in 95 subjects with premature myocardial infarction (MI), who also had one parent who had an MI. A total of 10 polymorphisms were found: three in the promoter region, two in exons and five in introns. All polymorphisms were genotyped in ECTIM, a case-control study of MI (1815 subjects). The nonsynonymous 92Q allele was found in 1.8, 1.0 and 1.7% of controls from Strasbourg, Belfast and Glasgow - respectively; in cases: 4.2, 2.2 and 3.2%. The population-adjusted odds ratio (OR) for MI associated with allele Q carrying was 2.15 (95% CI: 1.09-4.23). To check its possible implication in atherosclerosis, this polymorphism was then genotyped in the AXA Study (ultrasound examinations of carotid and femoral arteries in the context of an employment medical examination, 733 subjects), the EVA Study (ultrasound examinations of carotid arteries in a study of cognitive and vascular ageing, 1092 subjects) and the GENIC Study (on brain infarction (BI), 912 subjects). In the AXA Study, among smokers, carrying the 92Q allele was positively associated with the presence of a carotid plaque (OR 5.07; 95% CI: 1.64-15.63) and with a thickening of the carotid intima-media thickness (IMT) (0.59 (0.11) vs 0.54 (0.11), P=0.045). In the EVA Study, carriers of allele 92Q had an increased mean carotid IMT (0.70 (0.09) vs 0.67 (0.13), P=0.02). No significant association of the 92Q allele was found with BI in the GENIC Study. Overall, these results may suggest that carriers of the 92Q allele may be at increased risk of atherosclerosis.

Adult↗
PubMed2005

Three novel polymorphisms in the beta globin gene.

We report on three novel polymorphisms in and around the beta globin gene. Two of them are intronic (IVS2) polymorphisms (IVS 2 nt 200-203 (-CTTT) and IVS2 82-83 (-AG)). The third is a novel G-->C substitution at nt +1707 related to the beta globin cap site. This +1707 G-->C polymorphism was detected in 23.5% of chromosomes among 140 samples from India. It seems to be a novel but common polymorphism among Indians. There was no linkage between these novel polymorphisms and any beta thalassemia mutation.

Adult↗
PubMed2007

Angiotensin I-converting enzyme insertion-related genotypes and allele are associated with higher susceptibility of endometriosis and leiomyoma.

Endometriosis and leiomyoma display features similar to malignancy, requiring neovascularization to proliferation and growth. Altered vascular-related genes might be related to the development of endometriosis and leiomyoma. Polymorphisms of the angiotensin-converting enzyme (ACE) insertion/deletion (I/D) genes have been linked with some vascular diseases. This study investigates whether ACE I/D gene polymorphisms could be used as markers of susceptibility in endometriosis and leiomyoma. Women were divided into three groups: (1) endometriosis (n = 125); (2) leiomyoma (n = 120); (3) normal controls (n = 128). Genomic DNA was obtained from peripheral leukocyte. ACE I/D gene polymorphisms in intron 16 were amplified by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) Genotypes and allelic frequencies in both groups were compared. We observed the genotype distribution and allele frequency of ACE I/D gene polymorphisms in both groups were significantly different. Proportions of ACE*I homozygote/heterozygote/D homozygote in both groups were: (1) 50.4/24/25.6%; (2) 25/23.33/51.67%; (3) 10.2/29.7/60.1%. Proportions of I/D alleles in each group were: (1) 62.4/37.6%; (2) 36.7/63.3%; (3) 25/75%. We concluded that ACE*I/D gene polymorphisms are associated with endometriosis and leiomyoma susceptibilities. ACE*I-related genotypes and allele are strongly related to the occurrence of endometriosis and moderately related to the occurrence of leiomyoma.

Endometriosis↗
PubMed1994

Rapid detection of loss of heterozygosity of chromosome 17p by polymerase chain reaction-based variable number of tandem repeat analysis and detection of single-strand conformation polymorphism of intragenic p53 polymorphisms.

Intragenic restriction site polymorphisms in amino acid residue 72 in exon 4 and a Mspl polymorphism in intron 6 of the p53 tumour suppressor gene can both serve as polymorphic markers. Probe YNZ22 (D17S5) is a highly polymorphic, variable number of tandem repeat (VNTR) marker which maps to chromosome 17p13.1 where the p53 gene is located. Locus specific amplification by polymerase chain reaction (PCR) technique and subsequent non-isotopic single-strand conformation polymorphism analysis of the PCR fragments was used for the detection of loss heterozygosity (LOH) of 17p including the p53 gene locus. In combination with a PCR-based method for the analysis of the VNTR locus D17S5 using unique sequences flanking the polymorphic region of YNZ22 we investigated tumour DNA and corresponding constitutional DNA from 69 patients, including 39 patients with gastric cancer, 21 patients with osteosarcomas and 9 patients with Ewing's sarcomas. Using all three methods, 49/69 (71%) patients were informative for LOH, which revealed allelic loss in 5/39 (12.8%) gastric cancers, 1/9 (11.1%) Ewing's sarcoma, and 4/20 (20%) osteosarcomas.

Base Sequence↗
PubMed2006

Prevalence and spectrum of mutations in the sarcomeric troponin T and I genes in a cohort of Spanish cardiac hypertrophy patients.

We sequenced the coding exons of the cardiac troponins T (TNNT2) and I (TNNI3) genes in 115 Spanish HCM-patients (32% with a family history of the disease). Only two (2%) had mutations in the TNNT2 (Arg278>Cys and Arg92>Lys). These mutations were associated with variable clinical outcomes. No patient had TNNI3-mutation. We also genotyped these patients and 320 healthy controls for a 5 bp insertion/deletion (I/D) polymorphism in intron 3 of TNNT2. DD-homozygotes for the 5 bp I/D polymorphism were significantly more frequent among the patients (OR=1.83, 95% CI=2.10-5.16).

Adolescent↗
PubMed1996

Association analyses of the polymorphisms of angiotensin-converting enzyme and angiotensinogen genes with diabetic nephropathy in Japanese non-insulin-dependent diabetics.

To investigate predictive genetic markers for diabetic nephropathy, we studied the genetic polymorphisms of angiotensin-converting enzyme (ACE) and angiotensinogen (AGN) in Japanese subjects with non-insulin-dependent diabetes mellitus (NIDDM) with and without nephropathy. Genotype distributions were studied in 132 unrelated NIDDM patients of three groups with normoalbuminuria ([Normo] n = 53), microalbuminuria ([Micro] n = 54), and macroalbuminuria ([Macro] n = 25). The ACE insertion/deletion (I/D) polymorphism of intron 16 was identified by polymerase chain reaction, and the AGN M235T polymorphism was identified by restriction fragment length polymorphism analysis. There were no significant associations between AGN 235 allele or genotype and diabetic nephropathy. The D allele of ACE was significantly more frequent in the Micro (P = .003) and Macro (P = .009) group than in the Normo group. Overall frequencies of the ACE genotype did not differ significantly between the Micro and Macro groups. There were significant relationships between I/D polymorphism and plasma ACE activity; the DD genotype had the highest activity. A multiple logistic regression analysis revealed that the D allele is a strong and independent risk factor for abnormal albuminuria in NIDDM patients. These results suggested that ACE I/D polymorphism, but not AGN M235T polymorphism, is a possible genetic risk factor for diabetic nephropathy in Japanese NIDDM patients.

Aged↗
PubMed1997

Host specificity, evolutionary relationships and macrogeographic differentiation among Ascaris populations from humans and pigs.

We describe a variety of restriction site polymorphisms in the introns of Ascaris nuclear genes and in the ribosomal DNA spacers. We use these markers, in addition to previously described mitochondrial variation, to clarify our understanding of the epidemiology of Ascaris in Guatemalan villages where humans and pigs occur in sympatry and to describe the genetic structure of host-associated Ascaris populations from world-wide locations. Intron sequences were amplified from individual worms and alleles defined by endonuclease digestion. Two loci were monomorphic, while 4 length variants and 22 point mutations were detected in the other 7 loci. Within sympatric Guatemalan populations no single locus from either the nuclear or mitochondrial genome was fixed for alternative alleles, although allele frequencies were significantly different at many loci. Phenograms constructed from multilocus nuclear genotypes of individual worms failed to reveal a single case of cross-infection, and demonstrate that divergent mtDNA genotypes are segregating within host-associated populations. On a world-wide scale, the data suggest that extant worm populations result from a single host shift, although characterization of genetic variation in additional loci will be necessary to confirm this. The direction and the geographical origin of the host shift were unresolved. Overall 65% of nuclear genetic variation was found within populations, host (human or pig) explained 18%, while geographical variation within host-associated populations explained 17%. The results (a) demonstrate the utility of introns for studying the epidemiology of parasites showing limited allozyme variation (b) suggest that programmes aiming to control Ascaris infection in the human population can safely ignore zoonotic infection from pigs and (c) illustrate the problems inherent in using single genetic markers to make inferences about the epidemiology of closely related parasite taxa.

Animals↗
PubMed2003

Exclusion of PTPN11 mutations in Costello syndrome: further evidence for distinct genetic etiologies for Noonan, cardio-facio-cutaneous and Costello syndromes.

Costello syndrome (CS) is a rare, multiple congenital anomaly syndrome with characteristic dysmorphic features, cardiac anomalies and a tendency to develop certain cancers. Phenotypically there is some overlap with other genetic disorders, notably cardio-facio-cutaneous (CFC) syndrome and Noonan syndrome (NS), suggesting that these syndromes may be allelic. We recently identified PTPN11, which encodes the non-receptor protein tyrosine phosphatase, SHP-2, as a major NS disease gene. In this report, we screened a cohort of 27 patients, with the clinical diagnosis of CS, for PTPN11 mutations using denaturing high performance liquid chromatography analysis. No mutations of the PTPN11 gene were found in the CS patients. Common polymorphisms in introns 6 and 7 and exon 8 were identified in four individuals. With our previous exclusion of PTPN11 mutations in CFC syndrome, these data suggest distinct genetic etiologies for Noonan, CFC and Costello syndromes.

Abnormalities, Multiple↗
PubMed2004

Identification of polymorphisms in the human glucocorticoid receptor gene (NR3C1) in a multi-racial asthma case and control screening panel.

The glucocorticoid receptor (GR) gene (NR3C1) maps to 5q31, a region genetically linked to asthma. In this study, NR3C1 exons 1A, 1B, and exons 1C to 9 (alpha and beta) were sequenced in a screening panel of asthmatics and unaffected controls from US Caucasian, African American, US Hispanic, and Dutch Caucasian populations to identify polymorphisms for genetic association studies. Eight polymorphisms were identified in exon 1A, but none were located in putative transcription regulatory sites. Thirty-four polymorphisms were identified in exons 1B to 9 (alpha and beta), 17 of which were novel. Eight coding polymorphisms were identified (4 non-synonymous). One novel mutation (Ala229Thr) was identified in a Hispanic individual. Linkage disequilibrium (LD) was strongest between polymorphisms spanning intron 2 to exon 9beta. This data shows the variability of NR3C1 polymorphism frequencies between racial groups and confirms that NR3C1 non-synonymous coding polymorphisms are generally rare in mild/moderate asthmatics and unaffected controls.

Black or African American↗
PubMed2006

The alanine/threonine polymorphism of the alpha-1-antichymotrypsin (SERPINA3) gene and ruptured intracranial aneurysms in the Japanese population.

BACKGROUND: Serine protease inhibitor member 3 of clade A (SERPINA3), also known as alpha-1-antichymotrypsin, inhibits the activity of cathepsin G. The release of neutrophil cathepsin G (proteolytic enzyme) can destroy the vascular matrix through degradation, platelet aggregation and coagulation disorders. In a previous report there was evidence that an alanine/threonine polymorphism was associated with the risk factor for aneurysmal subarachnoid hemorrhage (SAH) in a Polish population. We performed this study to determine whether this A15T polymorphism shows the same association in a Japanese population. METHODS: A total of 437 patients with an aneurysmal SAH and 405 control cases of Japanese origin were genotyped for the A15T polymorphism and 2 further intronic single nucleotide polymorphisms by using polymerase chain reaction and direct sequencing. RESULTS: In the patients with intracranial aneurysms the SERPINA3 A15T allele and genotype distribution did not differ significantly from the controls. CONCLUSION: In the Japanese population the A15T polymorphism of the SERPINA3 gene is not associated with aneurysmal SAH.

Alanine↗
PubMed1992

Analysis of the PvuII restriction fragment-length polymorphism and exon structure of the estrogen receptor gene in breast cancer and peripheral blood.

The presence of estrogen receptor (ER) is a well-known predictor of clinical outcome in human breast cancer. We examined the ER gene in 26 primary breast cancers (14 ER-positive, 12 ER-negative) to determine if alterations of the gene are associated with the ER-negative status. In tumor biopsies and peripheral blood DNA obtained from the same patients we analyzed the ER exon structure using polymerase chain reaction amplification, restriction endonuclease digestion, and agarose gel electrophoresis. All blood and tumor samples, regardless of ER status, showed a complete set of eight exons of normal sizes, ruling out deletions or rearrangements of the ER gene in excess of +/- 20 nucleotides. Previous reports indicate that the two-allele ER PvuII polymorphism could be associated with ER expression in breast cancer (Hill et al., Cancer Res., 49: 145-148, 1989) as well as with patient age at time of tumor diagnosis (Parl et al., Breast Cancer Res. Treat., 14: 57-64, 1989). We localized the PvuII polymorphism in intron 1, 0.4 kilobase upstream of exon 2. Sequence analysis showed the polymorphism to result from a point mutation (T----C) at the fifth position of the restriction site (CATCTG). We determined the PvuII restriction fragment-length polymorphism genotype in 257 primary breast cancers and 140 peripheral blood DNA samples obtained from women without breast cancer. The results indicate that the PvuII polymorphism is not associated with ER content or patient age at tumor diagnosis.

Adult↗
PubMedDate not supplied

Distribution of plasma alpha 1-antichymotrypsin levels in Alzheimer disease patients and controls and their genetic controls.

Alzheimer's disease (AD) is a complex multifactorial disease in which many genetic and environmental factors are involved. Recent studies have shown that alpha(1)-antichymotrypsin (ACT) is one of the candidate genes for AD. Elevated levels of ACT have been widely, but not universally reported in the cerebrospinal fluid and plasma of AD patients. The genetic association between the ACT/codon -17*A allele of the signal peptide polymorphism and AD has been shown in some studies. One hypothesis is that the ACT/codon -17*A allele is in linkage disequilibrium with unknown functional mutation(s) in the ACT gene. Alternatively, the more hydrophobic character of the alanine (codon -17*A) may enhance ACT translocation into the endoplasmic reticulum and the Golgi apparatus, thus being secreted at higher levels. Therefore, this study was undertaken to determine the distribution of ACT plasma levels in cases (n = 397) and controls (n = 118) and the impact of ACT polymorphisms, including codon -17, on plasma ACT levels. In our cohort, plasma ACT levels were significantly higher in AD patients than controls (542.13 +/- 7.11 mg/liter vs. 496.62 +/- 12.79 mg/liter; P = 0.002). The ACT/codon -17 polymorphism showed significant association with ACT levels in male AD patients, while the effect of the intron 4 polymorphism was significant in both male and female patients. Codon 227 polymorphism was associated with lower ACT levels in AD patients. In conclusion, ACT may play an important role in the AD pathogenesis and genetic variation in the ACT gene appears to have some effect on plasma ACT concentrations.

Aged↗
PubMed1990

Genomic carrier detection and prenatal diagnosis of haemophilia A in families at risk using the polymerase chain reaction (PCR).

The polymerase chain reaction (PCR) was applied in genomic analysis of families at risk for haemophilia A using the intragenic Bel I and Hind III polymorphism in introns 18 and 19, respectively, of factor VIII gene. For the latter the primers derived from exon 19 and 20 sequences allowed to amplify the whole intron 19 resulting in a 730 bp fragment. Hind III restriction of this fragment provides polymorphic fragments of 250 bp or 160 bp and 90 bp respectively. An also occurring 480 bp fragment can be used as internal control to circumvent misdiagnosis due to incomplete or failure of restriction. The Hind III polymorphism was successfully used in prenatal diagnosis of an affected male in the first trimenon of pregnancy. Fetal sexing was also performed by PCR technique using Y specific primers.

Base Sequence↗