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PubMed2000

[A molecular epidemiologic study of TT virus in various population].

To investigate infection and sequence divergence of TT virus in various population, a nested polymerase chain reaction (nPCR) assay with primers from TTV ORF1 genome was used to detect serum TTV DNA. TTV DNAs from various population were cloned and sequenced. Six gene sequences derived from two patients with non-A through non-E and non-G hepatitis, a hepatitis patient with HBsAg, a normal blood donor, an intravenous drug user and a woman prostitute, were compared with known sequence of TTV isolate (N22) reported by Okamoto, Japan. The nucleotide homology were 96%-98% and the whole sequences belonged to la genotype. The data indicate that TTV DNA from various population in China might chiefly be la genotype. There is no correlation between genotype and disease transmission and development.

Adult↗
PubMed2004

Genetic variation in clinical varicella-zoster virus isolates collected in Ireland between 2002 and 2003.

Analysis of genetic variation in 16 varicella-zoster virus (VZV) isolates selected at random and circulating in the Irish population between March 2002 and February 2003 was carried out. A 919 bp fragment of the glycoprotein E gene (open reading frame 68) encompassing codon 150, at which a non-synonymous mutation defines the escape mutant VZV-MSP, and including two other epitope regions e1 and c1, was sequenced. No new single nucleotide polymorphisms (SNPs) were detected, indicating stability of these epitopes in clinical isolates of VZV. However, when four informative polymorphic markers consisting of defined regions from genes 1, 21, 50, and 54 were sequenced 14 variable nucleotide positions were identified. Phylogenetic analysis showed the presence of three highly supported clades A, B, and C circulating in the Irish population. Approximately one third (6/16; 37.5%) of the Irish VZV isolates in this study belonged to genotype C, 4/16 (25%) to genotype A, and 4/16 (25%) to genotype B. A smaller number 2/16 (12.5%) belonged to genotype J1. This indicates remarkable heterogeneity in the Irish population given the small sample size. No evidence was found to suggest any of the 16 isolates was a recombinant. These findings have implications for the model of geographic isolation of VZV clades to certain regions as the circulating Irish VZV population appears to comprise approximately equal numbers of each of the main genotypes. This data is inconsistent with a model of strict geographical separation of VZV genotypes and suggests that VZV diversity is more pronounced in certain areas than had been thought previously.

Adult↗
PubMed2005

Use of extreme patient samples for outcome prediction from gene expression data.

MOTIVATION: Patient outcome prediction using microarray technologies is an important application in bioinformatics. Based on patients' genotypic microarray data, predictions are made to estimate patients' survival time and their risk of tumor metastasis or recurrence. So, accurate prediction can potentially help to provide better treatment for patients. RESULTS: We present a new computational method for patient outcome prediction. In the training phase of this method, we make use of two types of extreme patient samples: short-term survivors who got an unfavorable outcome within a short period and long-term survivors who were maintaining a favorable outcome after a long follow-up time. These extreme training samples yield a clear platform for us to identify relevant genes whose expression is closely related to the outcome. The selected extreme samples and the relevant genes are then integrated by a support vector machine to build a prediction model, by which each validation sample is assigned a risk score that falls into one of the special pre-defined risk groups. We apply this method to several public datasets. In most cases, patients in high and low risk groups stratified by our method have clearly distinguishable outcome status as seen in their Kaplan-Meier curves. We also show that the idea of selecting only extreme patient samples for training is effective for improving the prediction accuracy when different gene selection methods are used.

Biomarkers, Tumor↗
PubMed1996

Phylogenetic analysis of hepatitis C virus isolates and their correlation to viremia, liver function tests, and histology.

Nucleotide sequence analysis of hepatitis C virus (HCV) strains showed substantial variability leading to a classification into several genotypes and subtypes. The data correlating HCV genotypes and subtypes with hepatitis C viremia levels, demographic characteristics of patients (age, mode of transmission, duration of infection), and severity of liver disease are conflicting. The interpretation of several studies is further complicated because the molecular methods used lacked specificity for genotyping/subtyping and underestimated viremia levels, especially in patients infected with HCV genotypes 2 and 3. In the present study we investigated 97 consecutive patients with chronic hepatitis C using molecular "gold standard" methods. HCV subtyping was performed by sequence and phylogenetic analysis of the nonstructural (NS)-5 region and serum HCV-RNA concentration was assessed by a validated genotype-independent quantitative reverse-transcription-polymerase chain reaction assay using an internal RNA standard. Patients infected with subtypes HCV-1b, HCV-2a-c, and HCV-4 were older than patients infected with HCV-1a and HCV-3a. Serum HCV-RNA levels ranged from 1.5 x 10(4) to 1.0 x 10(8) copies/mL with no significant differences between median serum HCV-RNA concentrations in patients infected with different genotypes/subtypes. Although patients infected with HCV-1b were older, no biochemical or histological evidence was obtained that this subtype is associated with more severe liver disease. Furthermore, the present study showed a lack of correlation between the serum HCV-RNA concentration, biochemical parameters, and liver histology. The median serum HCV-RNA levels in patients with chronic persistent hepatitis, chronic active hepatitis, and liver cirrhosis were 5.0 x 10(6) copies/mL, 2.5 x 10(6) copies/mL, and 5.0 x 10(6) copies/mL, respectively. These differences were not significant. In conclusion, using optimized and validated molecular techniques, the present cross-sectional study showed no correlation between HCV genotypes/subtypes, viremia, liver function test results, and histology.

Adult↗
PubMed1996

Tissue deposition rates in relation to muscle fibre and fat cell characteristics in lean female pigs (Sus scrofa) following treatment with porcine growth hormone (pGH).

Two experiments were conducted to examine the effect of porcine growth hormone (pGH) on performance, carcase composition, muscle and fat deposition rates, muscle fibre characteristics, and fat cell volume in pigs. In the first experiment, ten pairs of littermates were treated with vehicle (saline buffer) or 80 micrograms pGH per kg live weight per day for 42 days starting at 50 kg live weight. In the second experiment, twelve pairs of littermates were untreated or treated with 3 mg pGH per day from approximately 56 kg live weight to slaughter at approximately 103 kg live weight. All pigs were fed ad libitum. In Experiments 1 and 2, respectively, feed intake decreased (10 and 11%) and the feed/grain ratio improved (8 and 13%), while daily gain was unaltered. There was an increase in deposition rates of muscle (11 and 22%), skin (27 and 23%), and bone (15% in both), and a decrease in deposition rates of intermuscular (48 and 24%) and subcutaneous (82 and 50%) fat. This resulted in a change in carcase composition towards more muscle (5 and 9%), bone (6 and 4%), and skin (18 and 12%), and less intermuscular (30 and 16%) and subcutaneous fat (51 and 32%). The increased muscle mass was due to enhanced hypertrophy of all muscle fibre types, while pGH did not affect the frequency of the different muscle fibre types. The reduction in subcutaneous fat was reflected in a similar reduction in fat cell volume. In contrast to the majority of pigs used in pGH experiments, the genotype used in the present experiments did not respond with respect to daily gain following pGH treatment. Furthermore, the increase in muscle deposition was rather low compared to results reported in pigs of other genotypes. These data together with published data on the cross-sectional area of muscle fibres indicate that genotypes with relatively large muscle fibres are less responsive to pGH treatment than genotypes with relatively small muscle fibres.

Adipocytes↗
PubMed1998

Analysis of a biallelic polymorphism in the tumor necrosis factor alpha promoter and HIV type 1 disease progression.

The relevance of a TNF-alpha promoter polymorphism, a G-to-A polymorphic sequence at position-308, was examined to test whether variant alleles of TNF-alpha affect susceptibility to infection with HIV-1 and progression to AIDS. Analysis of specimens from cohorts of HIV-1 positive homosexual men demonstrated that 3 of the 32 (9.4%) HIV-1-infected long-term nonprogressors (LTNPs) were homozygous for the uncommon TNF-2 allele compared with 3 of the 196 (1.5%) HIV-1-seronegative blood donors and uninfected homosexual men (p < 0.05). There was no difference in heterozygosity among HIV-1-seropositive or -seronegative groups, although some of the seropositive men heterozygous for the TNF2 genotype were also heterozygous for CCR5delta32. However, no significant association was found between TNF genotypes and time of survival, CD4 slopes, or viral loads when seroincident (n = 109) and seroprevalent cases (n = 442) from the Chicago MACS were analyzed. Functional analysis of lymphocytes from the seronegative group revealed no difference in endogenous or mitogen-induced TNF-alpha production, as well as susceptibility to in vitro HIV-1 infection between different TNF-genotype donors. These data suggest that TNF genotypes do not play a direct role in HIV-1 disease progression; however, they could potentially be part of a multigenic linkage that may be involved in delaying progression to AIDS.

Acquired Immunodeficiency Syndrome↗
PubMed2004

Sliding window discretization: a new method for multiple band matching of bacterial genotyping fingerprints.

Microbiologists have traditionally applied hierarchical clustering algorithms as their mathematical tool of choice to unravel the taxonomic relationships between micro-organisms. However, the interpretation of such hierarchical classifications suffers from being subjective, in that a variety of ad hoc choices must be made during their construction. On the other hand, the application of more profound and objective mathematical methods--such as the minimization of stochastic complexity--for the classification of bacterial genotyping fingerprints data is hampered by the prerequisite that such methods only act upon vectorized data. In this paper we introduce a new method, coined sliding window discretization, for the transformation of genotypic fingerprint patterns into binary vector format. In the context of an extensive amplified fragment length polymorphism (AFLP) data set of 507 strains from the Vibrionaceae family that has previously been analysed, we demonstrate by comparison with a number of other discretization methods that this new discretization method results in minimal loss of the original information content captured in the banding patterns. Finally, we investigate the implications of the different discretization methods on the classification of bacterial genotyping fingerprints by minimization of stochastic complexity, as it is implemented in the BinClass software package for probabilistic clustering of binary vectors. The new taxonomic insights learned from the resulting classification of the AFLP patterns will prove the value of combining sliding window discretization with minimization of stochastic complexity, as an alternative classification algorithm for bacterial genotyping fingerprints.

Bacteria↗
PubMed2000

CYP17 promotor polymorphism and ovarian cancer risk.

The CYP17 gene encodes the cytochrome P450c17alpha enzyme, which functions at 2 different points in the steroid biosynthesis pathway, and is considered a candidate susceptibility gene for endocrine-related tumors. A T to C substitution polymorphism exists in the 5' promoter region of this gene, and creates an additional Sp1-type motif. Several studies have examined this polymorphism as a risk factor for breast cancer, but results have been conflicting. We examined 319 cases of ovarian cancer and 298 unaffected controls for the T-C polymorphism. There was no significant difference between cases and controls for the allele frequencies (p = 0.6), or for genotype distribution (p = 0.9). The odds ratio (95% confidence interval) for ovarian cancer was 1.13 (0.70-1.82) for the putative "cancer susceptibility" CC genotype and 1.07 (0.77-1.48) for any C allele (CC or CT genotype). Results were little different after adjustment for age. Stratification of the ovarian cancer cases according to form (benign, low malignant potential or invasive), histology, grade or stage failed to reveal any heterogeneity with respect to CYP17 genotype. Our data provide no evidence for an association between ovarian cancer risk and the genotype defined by the CYP17 5' promoter region T-C polymorphism.

Adenocarcinoma↗
PubMed2005

Genetic variation in the IL-10 pathway modulates severity of acute graft-versus-host disease following hematopoietic cell transplantation: synergism between IL-10 genotype of patient and IL-10 receptor beta genotype of donor.

We have previously shown that the interleukin 10 (IL-10)/-592*A allele of the recipient is associated with less severe acute graft-versus-host disease (GVHD) and a lower risk of nonrelapse mortality after hematopoietic cell transplantation (HCT) from an HLA-identical sibling. In the present study, we examined variation in the IL-10 receptor beta gene as a further test of the hypothesis that the IL-10 pathway regulates the risk of acute GVHD. A single nucleotide polymorphism (A/G) at cDNA position 238 of the IL-10 receptor beta gene (IL10RB/c238) was genotyped in 953 HC transplant recipients and their HLA-identical sibling donors. IL-10/-592 and IL10RB/c238 genotypes were tested for association with GVHD by multivariable analysis. The IL-10/-592*A allele of the recipient and IL10RB/c238*G allele of the donor were significantly associated with a lower risk of grades III-IV acute GVHD (trend P < .001 and P = .02, respectively). The donor IL10RB/c238*G allele provided protection among patients with the IL-10/-592 A/C or A/A genotypes but not among patients with the high-risk IL-10/-592 C/C genotype. These data suggest an interaction of the patient IL-10/-592 and donor IL10RB/c238 genotypes on risk of GVHD, further supporting the hypothesis that the IL-10 pathway plays an important role in controlling the severity of acute GVHD.

Adolescent↗
PubMed1996

Association of Trp64Arg mutation of the beta3-adrenergic-receptor with NIDDM and body weight gain.

A possible pathogenic mutation in the beta 3-adrenergic-receptor gene (Trp64Arg) has been reported to be associated with an earlier age of onset of non-insulin-dependent diabetes mellitus (NIDDM) and clinical features of the insulin resistance syndrome in Pima Indian, Finnish and French subjects. Since marked heterogeneity has been reported in the association of mutations of candidate genes with NIDDM between Japanese and other ethnic groups, we investigated the association of Trp64Arg with NIDDM in Japanese subjects. The allele frequency of the mutation (Arg) was slightly, but not significantly, higher in NIDDM than in control subjects (70 out of 342 alleles [20.5%] vs 40 out of 248 [16.1%], respectively, p > 0.2). When our data were combined with those of Pima Indian and Finnish subjects, however, the Arg/Arg genotype was significantly associated with NIDDM as compared with the other two genotypes (p < 0.005, relative risk [RR] 2.13, 95% confidence interval [CI] 1.28-3.55). The Arg allele was also associated with NIDDM (p < 0.05, RR 1.27, 95% CI 1.06-1.52). Japanese subjects homozygous for the mutation had a significantly higher body mass index (mean +/- SD: 25.5 +/- 3.9 kg/m2) than heterozygotes (22.6 +/- 4.1, p < 0.05) and normal homozygotes (22.8 +/- 3.8, p < 0.05). NIDDM patients homozygous for the mutation tended to have an earlier age of onset of NIDDM than those with other genotypes. These data suggest that the Trp64Arg mutation not only contributes to weight gain and age-at-onset of NIDDM but is also associated with susceptibility to NIDDM.

Age of Onset↗
PubMed2005

Bayesian and maximum likelihood estimation of genetic maps.

There has recently been increased interest in the use of Markov Chain Monte Carlo (MCMC)-based Bayesian methods for estimating genetic maps. The advantage of these methods is that they can deal accurately with missing data and genotyping errors. Here we present an extension of the previous methods that makes the Bayesian method applicable to large data sets. We present an extensive simulation study examining the statistical properties of the method and comparing it with the likelihood method implemented in Mapmaker. We show that the Maximum A Posteriori (MAP) estimator of the genetic distances, corresponding to the maximum likelihood estimator, performs better than estimators based on the posterior expectation. We also show that while the performance is similar between Mapmaker and the MCMC-based method in the absence of genotyping errors, the MCMC-based method has a distinct advantage in the presence of genotyping errors. A similar advantage of the Bayesian method was not observed for missing data. We also re-analyse a recently published set of data from the eggplant and show that the use of the MCMC-based method leads to smaller estimates of genetic distances.

Algorithms↗
PubMed2006

AccuTyping: new algorithms for automated analysis of data from high-throughput genotyping with oligonucleotide microarrays.

Microarray-based analysis of single nucleotide polymorphisms (SNPs) has many applications in large-scale genetic studies. To minimize the influence of experimental variation, microarray data usually need to be processed in different aspects including background subtraction, normalization and low-signal filtering before genotype determination. Although many algorithms are sophisticated for these purposes, biases are still present. In the present paper, new algorithms for SNP microarray data analysis and the software, AccuTyping, developed based on these algorithms are described. The algorithms take advantage of a large number of SNPs included in each assay, and the fact that the top and bottom 20% of SNPs can be safely treated as homozygous after sorting based on their ratios between the signal intensities. These SNPs are then used as controls for color channel normalization and background subtraction. Genotype calls are made based on the logarithms of signal intensity ratios using two cutoff values, which were determined after training the program with a dataset of approximately 160,000 genotypes and validated by non-microarray methods. AccuTyping was used to determine >300,000 genotypes of DNA and sperm samples. The accuracy was shown to be >99%. AccuTyping can be downloaded from http://www2.umdnj.edu/lilabweb/publications/AccuTyping.html.

Algorithms↗
PubMed2001

A transmission/disequilibrium test that allows for genotyping errors in the analysis of single-nucleotide polymorphism data.

The present study assesses the effects of genotyping errors on the type I error rate of a particular transmission/disequilibrium test (TDT(std)), which assumes that data are errorless, and introduces a new transmission/disequilibrium test (TDT(ae)) that allows for random genotyping errors. We evaluate the type I error rate and power of the TDT(ae) under a variety of simulations and perform a power comparison between the TDT(std) and the TDT(ae), for errorless data. Both the TDT(std) and the TDT(ae) statistics are computed as two times a log-likelihood difference, and both are asymptotically distributed as chi(2) with 1 df. Genotype data for trios are simulated under a null hypothesis and under an alternative (power) hypothesis. For each simulation, errors are introduced randomly via a computer algorithm with different probabilities (called "allelic error rates"). The TDT(std) statistic is computed on all trios that show Mendelian consistency, whereas the TDT(ae) statistic is computed on all trios. The results indicate that TDT(std) shows a significant increase in type I error when applied to data in which inconsistent trios are removed. This type I error increases both with an increase in sample size and with an increase in the allelic error rates. TDT(ae) always maintains correct type I error rates for the simulations considered. Factors affecting the power of the TDT(ae) are discussed. Finally, the power of TDT(std) is at least that of TDT(ae) for simulations with errorless data. Because data are rarely error free, we recommend that researchers use methods, such as the TDT(ae), that allow for errors in genotype data.

Alleles↗
PubMed2002

Association of the platelet glycoprotein Ia C807T/G873A gene polymorphism and thrombosis in Behçet patients.

Thrombosis is a common complication of Behçet disease and the pathogenic mechanism of thrombotic tendency in Behçet disease is not well known. Several platelet membrane glycoprotein gene polymorphisms have been identified as risk factors for thrombosis. This study aimed to evaluate the possible role of the GP Ia C807T/G873A polymorphism as a risk factor for thrombosis in Behçet disease. We determined the prevalence of platelet glycoprotein Ia C807T/G873A gene polymorphism in Behçet patients. Genomic DNA was obtained from 20 patients with Behçet disease and 61 controls. All individuals were of Turkish ancestry and were genotyped for the GP Ia C807T/G873A polymorphism with real-time PCR method by LightCycler system. The 807 CC, CT and TT genotypes corresponded with 873 GG, GA and AA genotypes, respectively. Complete linkage between the 807 and 873 sites was found in all samples. The 807CC(873 GG), 807CT(873GA), 807TT(873AA) genotypes found to be 45.9%, 45.9% and 8.1% in controls and 30.0%, 55.0% and 15.0% in patients with Behçet disease, respectively. The Odds Ratio for BD (OR = 1.97; 95% confidence interval (CI): 0.42-9.13) is high for the 807 TT genotype compared with controls. Thrombosis was found in 7 cases of Behçet disease group: five cases have 807CT, one case has 807TT genotype and one case has 807CC genotype. Our data indicate hat patients with BD are affected by the glycoprotein Ia gene 807TT genotypes and carrying 807T allele. The risk of thrombosis is significantly higher in patients who have 807TT and 807CT genotypes than in patients who have 807CC genotype.

Behcet Syndrome↗
PubMed2001

Description of three data sets: Collaborative Study on the Genetics of Asthma (CSGA), the German Affected-Sib-Pair Study, and the Hutterites of South Dakota.

Three different data sets with clinical data and markers from genome-wide screens were submitted for analysis at Genetic Analysis Workshop 12. In each study, participants were carefully characterized for asthma and related phenotypes. Testing for bronchial hyper-responsiveness using methacholine and standardized protocols was performed. Total serum IgE levels were measured using standardized techniques. In addition, similar questionnaire data on symptoms and relevant environmental exposures were obtained. Relevant clinical data and genotypes for the polymorphic markers used for each genome-wide screen were submitted. The data set from the United States Collaborative Study on the Genetics of Asthma represents a heterogeneous population consisting of both Caucasian and African American families ascertained through two siblings with clinical asthma from multiple centers. Likewise, the families from the German Asthma Genetics Group were also ascertained through two siblings with asthma at multiple centers. In a contrast to these data sets, Dr. Carole Ober and her collaborators submitted data from the inbred Hutterite population in South Dakota.

Adolescent↗
PubMed1999

Hepatitis B virus: genotypes and subtypes in Brazilian hemodialysis patients.

There are no data concerning the genotypic analysis of hepatitis B virus (HBV) infection in Brazilian dialysis centers. Serum samples from all hemodialysis patients (n = 282) in Goiânia City, Central Brazil, were tested for hepatitis B surface antigen (HBsAg). An overall prevalence of 12.0% was found, ranging from 0 to 33.3% depending on dialysis centers. Positive samples (n = 34) were submitted to serological subtyping by monoclonal ELISA and HBV DNA detection by polymerase chain reaction (PCR). Among 30 PCR-positive samples, 26 were genotyped by use of the line probe assay technology (INNO-LiPA HBV, Innogenetics, Gent, Belgium). HBV genotypes A (50. 0%) and D (46.2%) were the most frequently found whereas genotype F (3.8%) was rare in this population. Serological subtypes adw2 (44. 1%) and ayw3 (41.2%) were dominant. By contrast, adw4 and ayw2 were found at a low frequency (2.9%). A correlation was observed in the distribution of genotypes and subtypes by dialysis center. Genotype D and subtype ayw3 were predominant in 2 hemodialysis centers whereas genotype A and subtype adw2 were predominant in the others. The findings of high HBsAg prevalence rates restricted to certain dialysis centers and the data obtained through genotyping and serological subtyping suggest HBV nosocomial transmission in these hemodialysis centers.

Adolescent↗
PubMed2006

Rectal lymphogranuloma venereum surveillance in France 2004-2005.

Lymphogranuloma venereum (LGV) is a sexually transmitted infection (STI) caused by Chlamydia trachomatis strains belonging to the L1, L2 or L3 genotype. An alert about an outbreak of LGV among MSM in the Netherlands was published in January 2004. The first cases of rectal LGV in France were retrospectively diagnosed in March 2004 and sentinel surveillance for LGV was implemented in April 2004. Most of the participating centres were located in the cities of Paris and Bordeaux. Only confirmed rectal LGV cases were included in the surveillance. Rectal specimens from men that were found to be positive for C trachomatis by PCR were sent to the National Reference Centre for Chlamydia infection for genotyping. Simple epidemiological data provided by clinicians and genotyping results were sent to the Institut de Veille Sanitaire (InVS) where data were anonymously recorded. A total of 328 C. trachomatis rectal strains isolated in men were genotyped by the end of December 2005. Of these, 244 (74%) were LGV strains belonging to the L2 genotype. No L1 or L3 C. trachomatis genotype was found. Diagnosis was made retrospectively for 46 cases. The median age of patients with LGV was 39 years. HIV status was known for 96 patients: 82/96 (85%) were HIV-infected. Most LGV cases were diagnosed in the Paris area (92%). Among the remaining 26% C. trachomatis strains, genotypes Da and G were the most frequent. As with syphilis in recent years, the emergence of LGV in Europe is mainly affecting HIV-infected MSM. The screening and treatment of STIs should be included in the clinical follow-up of all HIV-infected MSM.

Adult↗
PubMed1998

Type 1 Gaucher disease: phenotypic expression and natural history in Japanese patients.

Gaucher disease is caused by a deficiency of glucocerebrosidase, resulting in hepatosplenomegaly, pancytopenia, growth retardation and skeletal involvement. We analyzed data on genotype and key clinical parameters in 35 Japanese patients with Gaucher disease type 1. Our data demonstrated that over 60% of patients had onset of Gaucher disease signs/symptoms at less than 5 years. Sixty percent and 46% of evaluable patients were splenectomized and developed severe bone involvement, respectively. Within mean follow-up periods of 8 years and 4 months, mean relative height and weight, severity score index and platelet count all worsened to a highly significant degree. These data suggest that type 1 Gaucher disease tends to be severe and progressive in Japanese patients, most of whom would be suitable for treatment and might indeed require earlier and more aggressive therapy.

Adult↗