Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genotyping performance”

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

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

At least 127 records · Page 7Linked to original sources
PubMed2001

CTLA-4 gene expression is influenced by promoter and exon 1 polymorphisms.

CTLA-4, expressed mainly on activated T cells, helps maintain, through its inhibitory function, immune-system homeostasis. Polymorphisms in the CTLA-4 gene (CTLA4) are known to be important in several autoimmune diseases, including multiple sclerosis (MS). Here, we have performed genotyping for CTLA4 polymorphisms, and investigated expression by peripheral blood mononuclear cells of CTLA-4 mRNA and protein, in patients with MS and myasthenia gravis and in healthy controls. Expression levels for mRNA and protein were similar in the patient and control groups; however, there was a clear relationship between genotype and CTLA-4 expression. Specifically, individuals carrying thymine at position -318 of the CTLA4 promoter (T(-318)) and homozygous for adenine at position 49 in exon 1 showed significantly increased expression both of cell-surface CTLA-4 after cellular stimulation and of CTLA-4 mRNA in non-stimulated cells. The association was seen most clearly for unsorted CD3(+) cells and was absent in the CD8(+) subset. The T(-318) allele has been shown to be negatively associated with susceptibility to MS in an earlier study by our group. Thus, we propose that the susceptibility-influencing role of CTLA4 in MS may be related to genotypically conditioned promoter function, whereby high gene expression may decrease the risk of disease.

Abatacept↗
PubMed2003

CR1 Knops blood group alleles are not associated with severe malaria in the Gambia.

The Knops blood group antigen erythrocyte polymorphisms have been associated with reduced falciparum malaria-based in vitro rosette formation (putative malaria virulence factor). Having previously identified single-nucleotide polymorphisms (SNPs) in the human complement receptor 1 (CR1/CD35) gene underlying the Knops antithetical antigens Sl1/Sl2 and McC(a)/McC(b), we have now performed genotype comparisons to test associations between these two molecular variants and severe malaria in West African children living in the Gambia. While SNPs associated with Sl:2 and McC(b+) were equally distributed among malaria-infected children with severe malaria and control children not infected with malaria parasites, high allele frequencies for Sl 2 (0.800, 1,365/1,706) and McC(b) (0.385, 658/1706) were observed. Further, when compared to the Sl 1/McC(a) allele observed in all populations, the African Sl 2/McC(b) allele appears to have evolved as a result of positive selection (modified Nei-Gojobori test Ka-Ks/s.e.=1.77, P-value <0.05). Given the role of CR1 in host defense, our findings suggest that Sl 2 and McC(b) have arisen to confer a selective advantage against infectious disease that, in view of these case-control study data, was not solely Plasmodium falciparum malaria. Factors underlying the lack of association between Sl 2 and McC(b) with severe malaria may involve variation in CR1 expression levels.

Amino Acid Sequence↗
PubMed2001

Linkage and association of HLA class II genes with vitiligo in a Dutch population.

BACKGROUND: Serological typing of HLA has shown discrepancies in HLA associations with vitiligo in different ethnic populations. OBJECTIVES: To perform genotyping of HLA class II genes on a Dutch vitiligo population in order clearly to identify susceptible and protective HLA alleles in vitiligo. METHODS: HLA typing was carried out by amplifying genomic DNA by polymerase chain reaction (PCR) followed by dot-blot hybridization with sequence-specific oligonucleotides (SSO). Fifty Dutch vitiligo probands, and their parents (150 individuals) and 204 healthy controls were studied. RESULTS: Family-based case-control association studies and linkage disequilibrium analysis showed the linkage and association of DRB4*0101 allele with vitiligo (P(c) = 0.0016, relative risk = 2.21). The family-based association study also provided evidence for linkage and association of DQB1*0303 allele with vitiligo (chi(2) = 7.36, P = 0.006). We measured the clinical relevance of the test by calculating the prevalence corrected positive predictive values (PcPPV). The PcPPV of disease for the DRB4*0101 allele was 0.017 and for the DRB4*0101/0101 genotype was 0.0358. In other words, a DRB4*0101/0101 genotype carries a 3.58% risk of developing vitiligo. CONCLUSIONS: Both DRB4*0101 and DQB1*0303 alleles provide significant susceptibility for vitiligo.

Adolescent↗
PubMed2002

Coagulation factor XIII polymorphisms and the risk of myocardial infarction and ischaemic stroke in young women.

The inconsistent findings among association studies that have examined the relationship between factor XIIIA Val34Leu and thrombosis may be owing to (1) population differences in the prevalence of other risk factors that modify the association with Val34Leu, or (2) linkage disequilibrium with other functional factor XIIIA polymorphisms. We therefore performed genotyping for factor XIIIA Val34Leu, Tyr204Phe and Pro564Leu in a population-based study of myocardial infarction (MI) and ischaemic stroke among white women <45-years of age and 345 demographically similar controls, and examined potential interactions with other risk factors. The presence of the factor XIIIA Leu34 allele was associated with a slight decreased risk of MI [odds ratio (OR) = 0.80] that was most pronounced among women with traditional cardiovascular risk factors. Paradoxically, women carrying two copies of the Leu34 allele had a nearly fourfold increased risk of ischaemic stroke relative to the Val34/Val34 genotype. Heterozygosity for factor XIIIA Phe204 was associated with a milder increased risk of ischaemic stroke, and analysis of a kindred with congenital dysfibrinogenaemia suggested that co-inheritance of the factor XIIIA Phe204 allele may increase susceptibility to ischaemic stroke. Our results suggest that the factor XIIIA Val34Leu variant may be associated with a decreased risk of MI among young women with other risk factors. The relationship of factor XIIIA polymorphisms to cerebrovascular disease requires further study.

Adolescent↗
PubMed2002

Molecular analysis of syndromic congenital heart disease using short tandem repeat markers and semiquantitative polymerase chain reaction method.

BACKGROUND: Velo-cardiofacial syndrome (VCFS) and DiGeorge syndrome (DGS) are developmental disorders characterized by craniofacial anomalies and conotruncal heart defects. Many of them have hemizygous deletions within chromosome 22q11.2, suggesting that haploinsufficiency in this region are responsible for their etiologies. METHODS: To effectively understand the molecular basis for the chromosomal deletions, a semiquantitative fluores-cent polymerase chain reaction (PCR) method using 11 highly polymorphic markers located in 22q11.2 to perform genotyping analysis on 10 probands (five VCFS and five DGS) and their unaffected relatives were designed. RESULTS: Two VCFS and four DGS patients have a 3-Mb deletion; the other DGS patient has a 1.5-Mb deletion and a cross-over occurs in the same interval at the other allele. CONCLUSION: This results supports that the specific regions in 22q11.2 are susceptible to rearrangement and the deletions might be the genetic etiology of these syndromes. Most important of all, the new method, semiquantitative fluorescent PCR, is an effective method for detecting chromosomal microdeletions and has the following features: (i) the cost is inexpensive; (ii) the testing time is short; and (iii) the result is accurate.

Chromosome Deletion↗
PubMed2006

Disease outcome of inflammatory bowel disease patients: general outline of a Europe-wide population-based 10-year clinical follow-up study.

OBJECTIVE: To give a general outline of a 10-year clinical follow-up study of a population-based European cohort of inflammatory bowel disease (IBD) patients and to present the first results in terms of clinical outcome parameters and risk factors. MATERIALS AND METHODS: A population-based cohort of newly, prospectively, diagnosed cases was initiated between 1991 and 1993. The 2201 patients with IBD (706 had Crohn's disease (CD), 1379 had ulcerative colitis (UC) and 116 had indeterminate colitis) originated from 20 different areas in 11 different European countries and Israel. For the 10-year follow-up of this cohort, electronic data-collecting instruments were made available through an Internet-based website. Data concerning vital status, disease activity, medication use, surgical events, cancer, pregnancy, fertility, quality of life and health-care costs were gathered. A blood sample was obtained from patients and controls to perform genotypic characterization. RESULTS: Thirteen centres from eight European countries and Israel participated. In 958 (316 CD and 642 UC) out of a total of 1505 IBD patients (64%) from these 13 centres, a complete dataset was obtained at follow-up. Even though an increased mortality risk was observed in CD patients 10 years after diagnosis, a benign disease course was observed in this patient group in terms of disease recurrence. A correlation between ASCA and CARD15 variants in CD patients and complicated disease course was observed. A north-south gradient was observed regarding colectomy rates in UC patients. Direct costs were found to be highest in the first year after diagnosis and greater in CD patients than in UC patients, with marked differences between participating countries. CONCLUSIONS: This 10-year clinical follow-up study of a population-based European cohort of IBD patients provides updated information on disease outcome of these patient groups.

Adult↗
PubMed2000

Hepatitis C virus serotypes in haemodialysis patients in South-East Italy.

Hepatitis C virus (HCV) infection is highly prevalent in haemodialysis patients. To date, only a few studies involving a small number of subjects have characterized HCV-infected dialysis patients by serotyping. The spread of HCV serotypes in 114 HCV-positive dialysis patients from the same geographical area was evaluated by Murex HCV serotyping assay. Serotypes were detected in 102 subjects (89.5%), with type 1 being the most frequent (37.7%), followed by types 2 (19.3%), 4 (8.8%) and 3 (7.9%). Types 5 and 6 were the least prevalent (3.5%). Ten samples (8.8%) revealed mixed infections: type 1 was detectable in all and the co-infecting HCV types were types 2, 3 and 4 in 3, 4 and 3 cases, respectively. These results suggest that the serotyping assay as an alternative method of distinguishing the major types of HCV, also for particular risk groups and especially in laboratories that lack the specific expertise to perform genotyping methods. Age-related differences in patients with type 5 compared with those with types 3 and 6 may provide evidence of a more recent spread of these latter types.

Adult↗
PubMed2006

Polymorphisms in four candidate genes in young patients with essential hypertension.

AIM: To determine whether four potential genetic factors (polymorphisms in genes for alpha-adducin, beta-adducin, the G-protein beta-3 subunit and nitric oxide synthase) are important for the development of essential hypertension (EH) in Slovenian children and young adults with EH. METHODS: Both a nuclear families approach and case-control study have been performed. Genotyping of common polymorphisms in these genes using polymerase chain reaction was carried out in 104 nuclear families (an affected child, both parents) and in 200 control patients. RESULTS: Using the transmission disequilibrium test, no statistically significant differences were found between the frequencies of transmitted and non-transmitted alleles in nuclear families for all four investigated polymorphisms. In addition, the distributions of genotypes and alleles for the four polymorphisms did not differ significantly between our children and 200 healthy control patients. The allele frequencies of all polymorphisms were concordant with those observed in some other Caucasian populations. CONCLUSION: We found no association between the investigated gene variants and EH, so we conclude that they do not confer a significantly increased risk of the development of EH in the Slovenian population of hypertensive children.

Adolescent↗
PubMed2003

Influence of the TNF-alpha and TNF-beta polymorphisms upon infectious risk and outcome in surgical intensive care patients.

BACKGROUND: Tumor necrosis factor-alpha (TNF-alpha) is a well-documented central inflammatory mediator in sepsis. Specific polymorphisms of the TNF-alpha and TNF-beta genes (TNF2 and LTA + 250, respectively) have been suggested to correlate with higher mortality in septic shock. This study sought to determine whether these polymorphisms of the TNF-alpha and -beta genes are associated with an increased risk of infection in an at-risk surgical intensive care population. MATERIALS AND METHODS: Forty-four consecutive patients with systemic inflammatory response syndrome were enrolled prospectively in the study. Genomic DNA was isolated from whole blood samples using standard phenol/chloroform extraction techniques. Specific fragments including the polymorphic sites of each gene were amplified by polymerase chain reaction, and restriction enzyme digestions were performed. Genotypes were determined by gel electrophoresis and confirmed by direct sequencing. RESULTS: Eighty-six percent of the patients were TNF1 homozygotes (G:G at -308 of the TNF-alpha promoter region), whereas 9% of the patients were homozygous for TNF2 (A:A). There was no difference in the incidence of sepsis, septic shock, or mortality between patients bearing the various alleles. Only 13.6% of the patients exhibited the G:G alleles for TNF-beta, whereas the homozygous A:A was present in 45.4% of the patients. CONCLUSION: The presence of the A allele at these polymorphic sites did not predispose critically ill surgical patients to either infection or septic shock.

Aged↗
PubMed2002

Association of polymorphisms of the oestrogen receptor alpha gene with the age of menarche.

BACKGROUND: The age of menarche may be subject to hereditary influences, but the specific genetic determinants are largely unknown. We evaluated whether the XbaI and PvuII polymorphisms of the estrogen receptor alpha gene are associated with the age of menarche. METHODS: We performed genotyping for XbaI and PvuII in a cohort of 145 adolescent females from a closed community in North-Western Greece. RESULTS: There was strong linkage disequilibrium between the two polymorphisms. Menarche occurred later in girls with the XX genotype than in girls with the Xx or xx genotype (mean +/- SD: 13.36 +/- 1.24 versus 12.80 +/- 1.14 and 12.75 +/- 1.35 years respectively; P = 0.017). Menarche also tended to occur later in PP homozygotes than in Pp and pp subjects, but the difference was not significant (mean +/- SD: 13.09 +/- 1.29 versus 12.80 +/- 1.19 and 12.85 +/- 1.33 years respectively). The strongest effect was seen when the PX haplotype was considered [mean +/- SD: 13.43 +/- 1.18 years for homozygotes versus 12.76 +/- 1.25 years in heterozygotes and in subjects without the PX allele, P = 0.006]. CONCLUSIONS: We document that the XbaI polymorphism, and possibly PvuII, may be genetic determinants of the age of menarche.

Adolescent↗
PubMed1999

Glutathione-S-transferase (GSTM1) genetic polymorphisms do not affect human breast cancer risk, regardless of dietary antioxidants.

Glutathione-S-transferases catalyze the detoxication of carcinogen metabolites and reactive oxygen species (ROS) produced through a number of mechanisms. Glutathione-S-transferase (GST) M1 is polymorphic, and the null allele results in a lack of enzyme activity. Because there are indications that ROS may be involved in breast carcinogenesis, we sought to determine whether the GSTM1 null allele was associated with increased breast cancer, particularly among women with lower consumption of dietary sources of alpha-tocopherol, carotenoids and ascorbic acid. In a study of diet and cancer in western New York, women with primary, incident, histologically confirmed breast cancer (n = 740) and community controls (n = 810) were interviewed and an extensive food-frequency questionnaire administered. A subset of these women provided a blood specimen. DNA was extracted and genotyping performed for GSTM1. Data were available for 279 cases and 340 controls. The null allele did not increase breast cancer risk, regardless of menopausal status. There were also no differences in associations between the polymorphism and risk among lower and higher consumers of dietary sources of antioxidants or smokers and nonsmokers. These results indicate that GSTM1 genetic polymorphisms are not associated with breast cancer risk, even in an environment low in antioxidant defenses.

Antioxidants↗
PubMed2004

Lack of association between the ITPA 94C>A polymorphism and adverse effects from azathioprine.

A 94C>A missense mutation in the ITPA gene which encodes inosine triphosphate pyrophosphatase has been associated with adverse effects from azathioprine, specifically flu-like symptoms, pancreatitis and rash. We hypothesized that this association may also be present in a larger, population-based group of inflammatory bowel disease patients intolerant of thiopurine drugs. We performed genotyping for this polymorphism and TPMT*2 and TPMT*3 in 73 such patients and 74 patients with inflammatory bowel disease who have tolerated azathioprine. We could not demonstrate a significant association between the ITPA94C>A genotype and any adverse effects (Odds ratio (OR) 1.015, 95% confidence interval (CI) 0.360-2.867, P = 0.593), flu-like symptoms (OR 1.547, 95%CI 0.368-6.496, P = 0.398), rash (no ITPA 94C>A polymorphism identified) or pancreatitis (no ITPA 94C>A polymorphism identified). We found no significant association between the ITPA 94C>A polymorphism and adverse effects to thiopurine drugs.

Azathioprine↗
PubMed2003

Limited evolution of HIV antiretroviral drug resistance-associated mutations during the performance of drug resistance testing.

We investigated the evolution of HIV reverse transcriptase (RT)- and protease-associated antiretroviral (ARV) drug resistance mutations during the time taken to perform genotypic drug resistance testing. Thirty treatment-experienced patients who were adherent to therapy and who underwent genotypic drug resistance testing provided blood samples at randomization and when reviewing the test results (baseline). Patients remained on their existing therapy between randomization and baseline. The predominant HIV strains in 10 patients (33%) either lost and/or gained primary RT inhibitor (RTI)- or protease inhibitor (PI)-associated resistance mutations during the testing period. Of the 9 patients with RT mutations, 2 lost, 5 gained, and 2 both lost and gained RTI resistance mutations. One patient gained a significant PI-associated resistance mutation on an existing PI-resistant background. The evolution that occurred in the RT may have altered the effectiveness of subsequent ARV therapy in some patients. Neither viral load at randomization, ARV drug class used at randomization, time between collection of blood samples, duration of current therapy, nor number of ARV drugs used influenced gain or loss of resistance mutations. There was a significant association between duration of previous ARV therapy and gain of RTI-associated resistance mutations ( p =.02), however. In general, our results suggest that patients should continue current therapy until test results are available. A few patients would be expected to gain ARV drug-associated resistance mutations during this time, however.

Adult↗
PubMed2004

Human papillomavirus and abnormal Pap test results in Vietnamese-American women: a pilot case-control study.

OBJECTIVE: To evaluate the relationship between abnormal Pap test results and human papillomavirus (HPV) in Vietnamese-American women, who have the highest cervical cancer incidence in the United States. MATERIALS AND METHODS: In 2001, we obtained specimens from 117 Vietnamese women, 24 with abnormal Pap test results including atypical squamous cells of undetermined significance (cases) and 93 with normal Pap test results (controls), as classified by the 1991 Bethesda System. We used L1 consensus primers MY09/MY11 to perform HPV polymerase chain reaction analysis and type-specific probes to perform genotyping. RESULTS: Thirteen cases (54%) and 6 controls (6%) were HPV positive (p < .001). Ten of 24 cases (42%) and 0 controls (0%) had high-risk HPV types (16, 18, 45, 53, 56, or 66; p < .001). High-risk HPV types were significantly associated with increasing severity of Pap test results. CONCLUSIONS: Compared with those with normal Pap test results, Vietnamese-American women with abnormal Pap test results were more likely to have high-risk HPV types. Higher cervical cancer incidence among these women is likely the result of less frequent Pap screening rates and not different biology.

Journal Article↗
PubMed2006

Patterns of primary antiretroviral drug resistance in antiretroviral-naive HIV-1-infected individuals in a midwest university clinic.

A total of 192 HIV-1-infected antiretroviral-naive individuals had genotyping performed in our midwest university clinic between 2003 and 2005. The overall prevalence of resistance with either a reverse transcriptase or major protease mutation was 18%. There did not seem to be a significant difference in primary resistance patterns between different modes of HIV transmission (heterosexual versus men who have sex with men), gender or between white and African-American individuals.

Adult↗
PubMed2006

Polymorphisms of heat shock protein-70 (HSPA1B and HSPA1L loci) do not influence infection or outcome risk in critically ill surgical patients.

Heat shock proteins (HSP) are induced in various stress conditions and have many cytoprotective effects, including formation of protein complexes for antigen presentation, stabilizing intracellular proteins, and facilitating protein folding. The HSP-70 gene exhibits polymorphisms at the HSPA1B and HSPA1L loci that reportedly influence cytokine levels and clinical outcomes in critically ill patients. These HSP variations also have been linked to TNF-beta polymorphisms associated with poor outcomes. This study further evaluated outcomes and risk of infection of HSP polymorphisms in critically ill patients. Seventy-six consecutive surgical intensive care unit uninfected patients with established systemic inflammatory response features were prospectively enrolled. Genomic DNA was isolated from whole blood samples and specific fragments, including the relevant polymorphic sites, were amplified by PCR, and restriction digestions were performed. Genotypes were determined by electrophoresis and all were confirmed by direct sequencing. Plasma cytokine levels for TNF-alpha were assayed in a subset of patients by enzyme-linked immunoabsorbent assay. None of the HSP alleles bore a significant relationship to nosocomial infection rates, organ specific dysfunctions, or mortality. No linkage of HSP genotype to common TNF-alpha or TNF-beta genotypes could be demonstrated, although the HSPA1L CT polymorphism was associated with higher levels of TNF-alpha compared with the TT genotype. These data suggest that polymorphisms of the HSPA1L or HSPA1B loci do not influence infection or other highly morbid outcomes in surgical intensive care unit patients.

Aged↗
PubMed2004

Refined localization of dyschromatosis symmetrica hereditaria gene to a 9.4-cM region at 1q21-22 and a literature review of 136 cases reported in China.

BACKGROUND: Dyschromatosis symmetrica hereditaria (DSH) is an autosomal dominant pigmentary genodermatosis characterized by hyperpigmented and hypopigmented macules on the extremities, which has recently been mapped to an 11.6-cM interval on chromosome 1q11-21. So far, most cases of DSH have been reported in Japan and dermatologists around the world might think this disorder mainly occurs in Japan. In fact, there are 17 DSH families including 136 cases reported in China since 1980, but most of them are described in Chinese. OBJECTIVES: To refine the previously mapped region that facilitates the identification of the DSH gene and to delineate the clinical and genetic features of Chinese DSH cases by a literature review of 136 cases reported in China. METHODS: We performed genotyping and linkage analysis using polymorphic microsatellite markers at 1q11-22 in two Chinese DSH families, and reviewed all of the DSH cases reported in China since 1980. RESULTS: A cumulative maximum two-point lod score of 3.68 was produced with marker D1S506 at a recombination frequency of theta = 0.00 in these two families. Haplotype analysis refined the DSH locus to a 9.4-cM interval flanked by D1S2343 and D1S2635. The genetic and clinical features of Chinese cases with DSH were summarized. In some Chinese cases, hyperpigmented and hypopigmented macules were scattered on the neck and chest, but among Japanese patients there were no similar skin lesions to be reported on these sites. CONCLUSIONS: This study confirms linkage of DSH to a previously mapped region and refines the DSH gene to a 9.4-cM interval at 1q21-22. Likewise, the literature review indicates that DSH is not an uncommon disorder in China and the differences in the distribution of skin lesions could be related to race and environment.

Adult↗
PubMed2004

Refinement of a locus for Marie Unna hereditary hypotrichosis to a 1.1-cM interval at 8p21.3.

BACKGROUND: Marie Unna hereditary hypotrichosis (MUHH) is a rare autosomal congenital alopecia with progressive hair loss starting in early childhood and accelerating at puberty. A locus for MUHH has been mapped on chromosome 8p21 but no genes for MUHH have been identified to date. OBJECTIVES: To refine the MUHH locus to a narrow chromosome region to facilitate cloning of the gene. METHODS: We performed genotyping and linkage analysis in a multigeneration Chinese family with MUHH, using 18 high-density microsatellite markers spanning the previously mapped interval at 8p21. RESULTS: Significant evidence for linkage was observed in this region, with a maximum two-point LOD score of 3.01 (theta = 0). Haplotype analysis localized the MUHH locus within the region defined by D8S282 and D8S1839. This region overlaps by 1.1-cM with the previously reported MUHH region and represents a physical distance of about 380 kb. CONCLUSIONS: This study provides a refined map location (1.1 cM) for isolation of the gene causing MUHH. These data also indicate the existence of a common MUHH locus at 8p21.3 between affected caucasian and Chinese families.

Aged↗