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PubMed2005

Noninvasive genotyping and Mendelian analysis of microsatellites in African savannah elephants.

We obtained fresh dung samples from 202 (133 mother-offspring pairs) savannah elephants (Loxodonta africana) in Samburu, Kenya, and genotyped them at 20 microsatellite loci to assess genotyping success and errors. A total of 98.6% consensus genotypes was successfully obtained, with allelic dropout and false allele rates at 1.6% (n = 46) and 0.9% (n = 37) of heterozygous and total consensus genotypes, respectively, and an overall genotyping error rate of 2.5% based on repeat typing. Mendelian analysis revealed consistent inheritance in all but 38 allelic pairs from mother-offspring, giving an average mismatch error rate of 2.06%, a possible result of null alleles, mutations, genotyping errors, or inaccuracy in maternity assignment. We detected no evidence for large allele dropout, stuttering, or scoring error in the dataset and significant Hardy-Weinberg deviations at only two loci due to heterozygosity deficiency. Across loci, null allele frequencies were low (range: 0.000-0.042) and below the 0.20 threshold that would significantly bias individual-based studies. The high genotyping success and low errors observed in this study demonstrate reliability of the method employed and underscore the application of simple pedigrees in noninvasive studies. Since none of the sires were included in this study, the error rates presented are just estimates.

Animals↗
PubMed1998

Cytochrome P4501A1 and glutathione S-transferase M1 genotypes as risk factors for prostate cancer in Japan.

BACKGROUND: The p53 mutation spectrum of prostate cancers developing in Japan indicates a role for environmental factors. This suggests there might be differences in susceptibility due to genetic polymorphisms in metabolic activation enzyme genes. We analyzed genetic polymorphisms of the xenobiotic-metabolizing enzymes, CYP1A1 and GSTM1. METHOD: Genotyping of CYP1A1 and GSTM1 was investigated by using allele-specific PCR in 115 prostate cancer (PCa) patients and 204 control patients. RESULTS: The CYP1A1 Val/Val genotype significantly increased the risk for PCa (OR = 2.6; 95% CI = 1.11-6.25) and the Ile/Val genotype showed a similar tendency (OR = 1.4; CI = 0.86-2.29). Individuals with the GSTM1 (0/0) genotype demonstrated a slightly increased risk (OR = 1.3; CI = 0.82-2.04). The combination of the CYP1A1 Val allele and GSTM1 (0/0) genotype was associated with a higher risk (OR = 2.3; CI = 1.18-4.48) than the CYP1A1 Val allele alone. When cases were analyzed by age at initial diagnosis, the relative risks with both the CYP1A1 Val allele and the GSTM1 (0/0) genotype were higher in the young group than in the old group (CYP1A1; OR = 1.7, CI = 0.89-3.17: GSTM1; OR = 1.6, CI = 0.84-2.99). The frequency of the GSTM1 (0/0) genotype was also higher in patients with advanced stage disease. In stage D, the OR was 1.7 with a CI of 0.93-3.17 and in stages A and B, the OR was 0.8 with a CI of 0.40-1.62. CONCLUSIONS: These results suggest that CYP1A1 and GSTM1 polymorphisms are linked to a propensity for PCa development.

Aged↗
PubMed2002

Ecophysiological analysis of genotypic variation in peach fruit growth.

Cultivated varieties generally differ greatly from wild genotypes of the same closely related species. However, the processes responsible for these differences have not been elucidated. To analyse variations in fruit mass, fruit growth was characterized in a peach cultivar, a wild related species non-cultivated, and four hybrids derived by crossing them. These genotypes offer a wide range of agronomic values. An ecophysiological model of peach fruit growth in dry mass was used. This model simulates carbon partitioning at the 'shoot-bearing fruit' level by considering three compartments: fruits, 1-year-old stems and leafy shoots. The experimental measurements showed considerable variation between genotypes for fruit mass at maturity, fruit growth and source activity. The parameters of the ecophysiological model for each genotype were estimated from experimental data,. The model made it possible to account for genotypic variations in fruit growth and for genotype x fruit load interactions. Using the model, it was shown that the main processes explaining fruit growth variations among the genotypes studied were differences in potential fruit growth.

Algorithms↗
PubMed2000

Full flexibility genotyping of single nucleotide polymorphisms by the GOOD assay.

Recently a facile method for genotyping single nucleotide polymorphisms (SNPs) using MALDI mass spectrometry, termed the GOOD assay, was developed. It does not require any purification and is performed with simple liquid handling, thermal incubation and cycling steps. Although this method is well suited to automation and high-throughput analysis of SNPs, it did not allow full flexibility due to lack of certain reagents. A complete set of ss-cyanoethyl phosphoramidites is presented herein that give this SNP genotyping method full sequence and multiplex capabilities. Applications to SNP genotyping in the prion protein gene, the ss-2-adrenergic receptor gene and the angiotensin converting enzyme gene using the GOOD assay are demonstrated. Because SNP genotyping technologies are generally very sensitive to varying DNA quality, the GOOD assay has been stabilised and optimised for low quality DNA. A template extraction method is introduced that allows genotyping from tissue that was taken while placing an ear tag on an animal. This dramatically facilitates the application of genotyping to animal agricultural applications, as it demonstrates that expensive and cumbersome DNA extraction procedures prior to genotyping can be avoided.

Animals↗
PubMed2004

A web-based genotyping resource for viral sequences.

The Genotyping tool at the National Center for Biotechnology Information is a web-based program that identifies the genotype (or subtype) of recombinant or non-recombinant viral nucleotide sequences. It works by using BLAST to compare a query sequence to a set of reference sequences for known genotypes. Predefined reference genotypes exist for three major viral pathogens: human immunodeficiency virus 1 (HIV-1), hepatitis C virus (HCV) and hepatitis B virus (HBV). User-defined reference sequences can be used at the same time. The query sequence is broken into segments for comparison to the reference so that the mosaic organization of recombinant sequences could be revealed. The results are displayed graphically using color-coded genotypes. Therefore, the genotype(s) of any portion of the query can quickly be determined. The Genotyping tool can be found at: http://www.ncbi.nih.gov/projects/genotyping/formpage.cgi.

Algorithms↗
PubMed2004

Real-time PCR genotyping using displacing probes.

Simple and reliable genotyping technology is a key to success for high-throughput genetic screening in the post-genome era. Here we have developed a new real-time PCR genotyping approach that uses displacement hybridization-based probes: displacing probes. The specificity of displacing probes could be simply assessed through denaturation analysis before genotyping was implemented, and the probes designed with maximal specificity also showed the greatest detection sensitivity. The ease in design, the simple single-dye labeling chemistry and the capability to adopt degenerated negative strands for point mutation genotyping make the displacing probes both cost effective and easy to use. The feasibility of this method was first tested by detecting the C282Y mutation in the human hemochromatosis gene. The robustness of this approach was then validated by simultaneous genotyping of five different types of mutation in the human beta-globin gene. Sixty-two human genomic DNA samples with nine known genotypes were accurately detected, 32 random clinical samples were successfully screened and 114 double-blind DNA samples were all correctly genotyped. The combined merits of reliability, flexibility and simplicity should make this method suitable for routine clinical testing and large-scale genetic screening.

Amino Acid Substitution↗
PubMed2006

Genetic variation among broiler genotypes in susceptibility to colibacillosis.

Selection for reduced susceptibility to colibacillosis in broilers may contribute to the prevention of colibacillosis. Such selection should focus on the responses to Escherichia coli rather than the associated primary agent(s). The purpose of the current study was to examine whether genetic variation is present in the susceptibility to colibacillosis. This was achieved through an evaluation of the susceptibility to primary colibacillosis in 5 pure broiler lines, a slow-growing line, and two 2-way crosses of the pure lines (altogether referred to as genotypes). A challenge experiment was executed in 2 trials. Per trial, 24 chicks per genotype were challenged and 20 chicks per genotype were controls. At 7 d of age, challenged chicks were intratracheally inoculated with 0.3 mL of E. coli O78K80 solution, and controls with 0.3 mL of PBS. All chicks were euthanized at 14 or 15 d. Traits measured were mortality, lesion scores (airsacculitis, pericarditis, and perihepatitis) at 14 or 15 d, and BW at 1, 4, 7, 10, 12, and 14 or 15 d. An effect of genotype on mortality, lesion prevalence, and growth retardation was found, indicating the presence of genetic variation in susceptibility to colibacillosis, and suggesting that selection for reduced susceptibility is possible. There were large between-genotype differences in mortality (up to 46%) and in lesion prevalence (up to 41%). Growth retardation was not observed for any genotype in chicks without lesions, whereas genotypes differed from none to 20% growth retardation for chicks with airsacculitis but no systemic lesions, and up to 13% for chicks with systemic lesions. The heterosis in susceptibility and growth retardation was found to be either negative or absent, indicating that crossbreeding would not be an advantage for the selection for reduced susceptibility, and that test crossing is essential.

Animals↗
PubMed2004

Neuregulin genotype and medication response in Finnish patients with schizophrenia.

Neuregulin 1 is involved both in neurodevelopment and neurotransmitter mechanisms in the brain. There is evidence of an association between neuregulin 1 genotype and schizophrenia. We compared neuregulin 1 genotypes in patients with schizophrenia (n=94) and control subjects (n=395) of Finnish origin by using one SNP (SNP8NRG221533) as a genetic marker. We also analyzed NRG1 genotype with regard to age at onset and between responders and non-responders to conventional antipsychotics. The NRG1 genotype or allele frequencies showed similar distributions between patient and control groups. Age at onset was not associated with NRG1 genotype. The TT genotype was overrepresented in the non-responders group compared with the responders (p=0.013). Further studies are needed to ascertain the significance of neuregulin genotype in medication response to schizophrenia.

Adult↗
PubMed1993

Phylogenetic analysis of gag genes from 70 international HIV-1 isolates provides evidence for multiple genotypes.

OBJECTIVE: To determine the extent of genetic variation among internationally collected HIV-1 isolates, to analyse phylogenetic relationships and the geographic distribution of different variants. DESIGN: Phylogenetic comparison of 70 HIV-1 isolates collected in 15 countries on four continents. METHODS: To sequence the complete gag genome of HIV-1 isolates, build multiple sequence alignments and construct phylogenetic trees using distance matrix methods and maximum parsimony algorithms. RESULTS: Phylogenetic tree analysis identified seven distinct genotypes. The seven genotypes were evident by both distance matrix methods and maximum parsimony analysis, and were strongly supported by bootstrap resampling of the data. The intra-genotypic gag distances averaged 7%, whereas the inter-genotypic distances averaged 14%. The geographic distribution of variants was complex. Some genotypes have apparently migrated to several continents and many areas harbor a mixture of genotypes. Related variants may cluster in certain areas, particularly isolates from a single city collected over a short time. CONCLUSIONS: The genetic variation among HIV-1 isolates is more extensive than previously appreciated. At least seven distinct HIV-1 genotypes can be identified. Diversification, migration and establishment of local, temporal 'blooms' of particular variants may all occur concomitantly.

Africa↗
PubMed1995

Genotypes of hepatitis C virus in Taiwan and the progression of liver disease.

The existence of four genotypes of hepatitis C virus (HCV)--types 1a, 1b, 2a, and 2b--has been suggested based on variations in nucleotide sequences of the core region. The aim of this study was to investigate the prevalence of HCV genotypes in chronic type C liver disease in Taiwan and correlate distinct genotypes to severity of liver disease. The genotypes of 175 patients with chronic type C liver disease were determined by a polymerase chain reaction with type-specific primers. The prevalence of each genotype in Taiwan was as follows: type 1a, n = 1 (0.6%); 1b, n = 125 (71.4%); 2a, n = 21 (12%); 2b, n = 6 (3.4%); mixed types, n = 18 (10.3%); and unclassified, n = 4 (2.3%). The demographic and clinical features were comparable between patients with different genotypes, except that the mean peak serum transaminase levels of patients with double viruses and type 1b HCV infections were significantly higher than were those of patients with type 2a virus. Moreover, type 1b HCV was more prevalent in patients with liver cirrhosis alone or with hepatocellular carcinoma. In conclusion, type 1b virus is the predominant genotype in chronic hepatitis C in Taiwan, and type 1b virus and mixed infection may trigger more severe liver disease.

Adult↗
PubMed1999

Hepatitis C virus seroconversion and genotype prevalence in patients and staff on chronic hemodialysis.

The prevalence of hepatitis C virus (HCV)-RNA positivity among hemodialysis patients varies between 10 and 70%. Few previous surveys revealed high frequency of seroconversion of HCV-RNA-negative patients over the years of hemodialysis. Only few studies reported HCV genotype variability. We evaluated all 65 patients on chronic hemodialysis in our dialysis unit. All sera positive to anti-HCV on ELISA were retested by reverse transcriptase polymerase chain reaction to HCV-RNA. Sixteen patients were found anti-HCV positive on ELISA, and 8 of them were also PCR positive. Three of these eight patients seroconverted during the year 1995. Four patients had both 1a and 1b genotypes of HCV, coexistence of genotypes 1b and 4a in one patient and genotypes 1a, 1b and 2a in the remaining three patients. Mean serum aminotransferase, duration of dialysis, and number of blood units transfused were significantly higher in the HCV-PCR-positive patients compared with the HCV-PCR-negative patients. Because strict isolation methods were initiated at the end of 1995, not one new case of HCV among dialysis patients was found in 1998, although new hemodialysis patients were diagnosed as having HCV. In conclusion, genotypes 1a and 1b, as is true for the general population in Israel, were also the predominant genotypes among hemodialysis patients; the coexistence of more than one genotype is common among hemodialysis patients; seroconversion is common among these patients and strict isolation methods are efficient and should be recommended.

Antibodies, Viral↗
PubMed2001

Tumor necrosis factor-alpha gene mutations and genotype changes in renal cell carcinoma.

PURPOSE: We tested the hypothesis that genotype changes in the promoter region of tumor necrosis factor-alpha and exon 1 are associated with renal cell carcinoma. MATERIALS AND METHODS: We analyzed genotypic changes at the 3 polymorphic loci of tumor necrosis factor-alpha -238, -308 and 488 using tumor and normal tissues from 81 Japanese patients with renal cell carcinoma. RESULTS: Of the 81 patients 14 (17%) had point mutations from G to A, including 8 (57%) with point mutations at multiple loci. Six of the 8 patients (75%) with point mutations at multiple loci were classified with stage 4 renal cell carcinoma. Of the 81 patients 14 were classified with stage 4 carcinoma, including 9 (64%) with point mutation from G to A. Normal tissue from cancer patients showed an increased frequency of the GA genotype at loci -238 and 488 compared to healthy controls (37% versus 9% and 30% versus 12%, respectively). The relative risk of renal cell carcinoma was 6.5-fold higher in patients with the GA genotype at locus -238 (p <0.001) and 2.9-fold higher in those with the GA genotype at locus 488 (0.01 < p <0.025) when comparing normal tissue from renal cell carcinoma patients with that of healthy controls. CONCLUSIONS: Point mutation from G to A, and the GA genotype at loci -238 and 488 of the TNF-alpha gene were common in patients with advanced renal cell carcinoma. The genotype change at loci -238 and 488 of the TNF-alpha gene are associated with renal cancer pathogenesis.

Adult↗
PubMed2002

Screening and genotyping of genital Chlamydia trachomatis in urine specimens from male and female clients of youth-health centers in Stockholm County.

BACKGROUND: The current study was conducted in the context of the current increase in cases of Chlamydia trachomatis infections, the development of new diagnostic strategies, and an outreach to community-based youth center screening sites. GOAL: The goal was to define the prevalence of genital C trachomatis infection among clients of youth-health clinics and to evaluate the feasibility of implementing genotyping as a tool for epidemiologic studies with use of urine specimens. STUDY DESIGN: This was a prospective pilot study at two community-based youth-health clinics for teenagers and adolescents. Enrollment followed a high school educational program and public advertising campaign on the common occurrence of nonsymptomatic or only mildly symptomatic chlamydial infection among sexually active young people. Voluntary, confidential, free screening of first-void urine was provided, and the samples were tested by polymerase chain reaction (PCR). Demographic and behavioral data were obtained. Positive samples were differentiated into genovars by genotyping with restriction fragment length polymorphism analysis of the PCR-amplified omp1 gene. RESULTS: The prevalence of nonsymptomatic or mildly symptomatic chlamydial infection was 6.0% among women and 9.3% among men. A significant increase in the risk of infection was associated with a history of sexually transmitted disease (STD) (P < 0.01). There was no statistical risk correlating with partner change during the past year, infrequent or inconsistent condom use during the past year, present use of contraceptive pills, smoking habits, or recent alcohol consumption. Genotype E was most common (60%) among both sexes. Genotypes F and K were second most prevalent for men (20%), and genotype D was second most prevalent for women (15%). Genotype K or F was found in 23% of cases. CONCLUSION: Screening programs targeting sexually active adolescents attending youth-health clinics are important for detection of C trachomatis. Genotyping might become an efficient tool in epidemiologic studies. The impact of educational school- and community-based programs on STD among young people needs further evaluation.

Adolescent↗
PubMed1993

Correlation between N-acetyltransferase activity and NAT2 genotype in Chinese males.

Eighty-four healthy Chinese male control subjects derived from an occupation-based case-control study of bladder cancer were evaluated for hepatic N-acetyltransferase activity by dapsone and for NAT2 genotype using allele-specific amplification of peripheral leukocyte DNA by the polymerase chain reaction. Fifty-nine percent of the overall variation in acetylation activity was explained by genotype (p < 0.0001). The remaining variation in acetylation was not associated with dapsone N-hydroxylation activity, age, current smoking status, or weight in the study population, or within any genotype subgroup. Although acetylation activity in the homozygous mutant group did not overlap with the other genotype categories, there was moderate overlap in acetylation between the heterozygous mutant and wildtype groups, and substantial variation in acetylation within them. Considering all subjects with the identical NAT2 genotype as phenotypically similar and all subjects with differing NAT2 genotypes as phenotypically distinct may result in misclassification of metabolic risk factors in epidemiological investigations. As such, it would seem prudent, where possible, to collect both acetylation phenotype and NAT2 genotype data, since the advantages and limitations of these two sources of information complement, and serve to assess the accuracy of each other.

Aged↗
PubMed1995

Distribution of GSTM1 null genotype in relation to gender, age and smoking status in Japanese lung cancer patients.

GSTM1 gene deficiency has been shown to occur in approximately half of the populations of various ethnic origins and has been implicated as a factor for elevated risk for lung cancers. However the results have been variable or even conflicting between the studies. In an attempt to explore the reason for such a diversity, we studied the distribution of GSTM1 genotypes in relation to gender, age and smoking status in 447 Japanese lung cancer patients and 469 community controls. We found: (1) that in squamous and small cell carcinomas GSTM1 null genotype distributed markedly more in females than males especially among the patients aged < 70 years (male 57.4%, female 100.0%); (2) that GSTM1 null genotype distributed generally more in patients aged < 70 years (58.3%) than those aged > or = 70 years (50.0%) irrespective of histologies except for small cell carcinoma; and (3) that proportion of GSTM1 null genotype increased dependent on the extent of tobacco smoke exposure in male patients having squamous and small cell carcinomas aged < 70 years, and remained high but independent of the smoking index in adenocarcinoma and unchanged in never- or exsmokers from the control level (48.6%). The present study thus suggests that composition of GSTM1 genotypes in patients is significantly affected by gender, age and smoking status, which should be taken into consideration in any attempt to determine the association of GSTM1 genotypes for risk assessment. With the diverse of GSTM1 null genotype variability between patients of different histologies, our results were also suggestive of different carcinogenic involvement of GSTM1 deficiency among different histological cell types.

Age Factors↗
PubMed2001

Glutathione S-transferase genotypes and stomach cancer in a population-based case-control study in Warsaw, Poland.

Glutathione S-transferases are important in the detoxification of a wide range of human carcinogens. Previous studies have shown inconsistent associations between the GSTT1 and GSTM1 null genotypes and stomach cancer risk. We investigated the relationship between these and related genotypes and stomach cancer risk in a population-based case-control study in Warsaw, Poland, where stomach cancer incidence and mortality rates are among the highest in Europe. DNA from blood samples was available for 304 stomach cancer patients and 427 control subjects. We observed a 1.48-fold increased risk for stomach cancer (95% confidence interval 0.97-2.25) in patients with the GSTT1 null genotype but no evidence of increased risk associated with the GSTM1, GSTM3 or GSTP1 genotypes. Furthermore, the stomach cancer risk associated with the GSTT1 null genotype varied by age at diagnosis, with odds ratios of 3.85, 1.91, 1.78 and 0.59 for those diagnosed at ages less than 50, 50-59, 60-69 and 70 years or older, respectively (P trend = 0.01). This was due to a shift in the GSTT1 genotype distribution across age groups among stomach cancer patients only. These results suggest that the GSTT1 null genotype may be associated with increased risk of stomach cancer.

Adult↗
PubMed2003

Adherence to and dosing of beta-hydroxy-beta-methylglutaryl coenzyme A reductase inhibitors in the general population differs according to apolipoprotein E-genotypes.

Discontinuation and poor adherence to therapy are major problems during long-term treatment, particularly with cholesterol lowering drugs. Several studies have indicated that the cholesterol lowering effect of statins differs according to apolipoprotein (apo)E genotypes. Low-density lipoprotein-cholesterol lowering capacity appears to be smaller in subjects with the epsilon(4) allele. To assess whether the use of statins in daily practice differs according to apoE genotypes, we used data from the Rotterdam Study, a population-based prospective cohort study in the Netherlands, which started in 1990 and included 7983 subjects aged 55 years or more. During follow-up, there were 798 subjects who started to use statins. We used a Cox proportional hazard model to determine the rate of discontinuation in the first 3 years of statin use. Subjects on statin therapy with epsilon(2)epsilon(2) and epsilon(4)epsilon(4) genotypes showed a trend towards higher dosages than subjects with the other genotypes. Relative to subjects with the epsilon(2)epsilon(3) genotype, those with the epsilon(4)epsilon(4) genotype had a risk of 2.28 [95% confidence interval (CI) 1.02-5.12] to discontinue statins within 3 years. In women, this relative risk was 1.70 (CI 0.53-5.42) versus 3.18 (CI 1.01-10.03) in men. The apoE genotype is associated with discontinuation of statins. This suggests that subjects who are genetically prone to develop hypercholesterolemia show the highest risk of discontinuation of treatment.

Apolipoproteins E↗
PubMed2003

CYP2E1 and NQO1 genotypes, smoking and bladder cancer.

BACKGROUND: Cytochrome P450 2E1 (CYP2E1) and NAD(P)H:quinone oxidoreductase (NQO1) catalyze the activation of some environmental procarcinogens present in tobacco smoke (i.e. nitrosoamines and heterocyclic amines). We conducted a hospital based case-control study to evaluate the potential association between genetic polymorphisms of CYP2E1 (C1019T in the 5' flanking region) and NQO1 (C609T in exon 6) and bladder cancer risk in Asian population. METHODS: The study population was comprised of 218 histologically confirmed prevalent bladder cancer cases and 199 controls without cancer or systemic illness. PCR-restriction fragment length polymorphism based methods were used for the genotyping analyses and unconditional logistic regression model for the statistical evaluations. RESULTS: The risk of bladder cancer increased with the amount of smoking (P for trend < 0.01). The frequency of CYP2E1 c1/c1 genotype was significantly higher in bladder cancer patients (57.9%) than in the controls (47.9%) (OR = 1.8, 95% CI = 1.1-2.9). Similarly, the NQO1 C/C genotypes were significantly more prevalent in the patients (45.8%) than in the controls (37.6%) (OR = 1.6, 95% CI = 1.0-2.7). The risk for bladder cancer increased with the number of the putative risk genotypes (P for trend = 0.03); the most remarkable risk was observed for heavy smokers with both CYP2E1 c1/c1 and NQO1 C/C genotypes (OR = 13.8, 95% CI = 3.9-48.6) when compared to non/light smokers with other genotypes. CONCLUSION: Our findings suggest that CYP2E1 and NQO1 genotypes may play an important role in development of smoking related bladder cancer among Korean men.

Asian People↗