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PubMed2004

Interleukin-10 production genotype protects against acute persistent rejection after lung transplantation.

BACKGROUND: Our previous studies demonstrated that cytokine gene polymorphisms are related to acute rejection in pediatric heart transplantation; a decreased tumor necrosis factor (TNF)-alpha production genotype combined with an increased or intermediate interleukin (IL)-10 production genotype was associated with the smallest incidence of acute rejection. The objective of this study was to determine whether cytokine genotypes TNF-alpha, IL-10, IL-6, interferon-gamma, and transforming growth factor beta were associated with acute persistent rejection after lung transplantation. METHODS: Cytokine genotyping was performed in 119 adult lung transplantation recipients who underwent surveillance transbronchial biopsies during their first year after transplantation. We categorized recipients with acute persistent rejection if they had 2 consecutive biopsy specimens at >/=Grade A2 despite anti-rejection treatment. We performed cytokine genotyping using the polymerase chain reaction-sequence specific primers technique, with a commercially available kit. RESULTS: We analyzed the IL-10 genotype in 116 patients. For the increased IL-10 production genotype, 7 of 20 patients (35%) were persistent rejecters. In comparison, 57 of 96 patients (59%) with intermediate or decreased IL-10 production genotype had acute persistent rejection (p = 0.046). For IL-10 haplotypes associated with intermediate IL-10 production, 30 of 45 patients with GCC/ACC haplotype (67%) had acute persistent rejection compared with 10 of 22 patients with GCC/ATA (45%). In the patients with intermediate IL-10 production, 17 of 22 (77%) with IL-10 GCC/ACC and IL-6 G/C had acute persistent rejection, whereas only 2 of 7 patients (29%) with IL-10 GCC/ATA and IL-6 G/G had acute persistent rejection (p = 0.018). CONCLUSIONS: In lung transplant recipients, the increased IL-10 production genotype protects against acute persistent rejection when compared with the intermediate or decreased IL-10 production genotypes. The intermediate IL-10 production genotype in lung transplant recipients can be differentiated into 2 haplotype responses, with the GCC/ACC haplotype associated more with acute persistent rejection. In lung transplant recipients, the immunomodulatory effects of IL-6 are differentiated in the G/C and G/G alleles in conjunction with IL-10 haplotypes, with G/C being associated with more acute persistent rejection in conjunction with the IL-10 GCC/ACC haplotype. Future pharmacogenomic models may incorporate these associations with acute persistent rejection in lung transplant recipients to formulate individualized therapeutic regimens.

Acute Disease↗
PubMed2002

Hybrid Capture II HPV Test detects at least 15 human papillomavirus genotypes not included in its current high-risk probe cocktail.

BACKGROUND: Hybrid Capture II HPV Test (HCII) (Digene Corporation, Gaithersburg, MD) is a signal amplified hybridization microplate-based assay designated to detect 18 human papillomavirus (HPV) genotypes using two probe cocktails, for high-risk HPV genotypes 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59 and 68 and low-risk HPV genotypes 6, 11, 42, 43 and 44. At present, HCII is the only commercially available HPV assay with sufficient scientific data to support its performance in the clinical setting. OBJECTIVES: To determine the specificity and accuracy of HCII high-risk probe cocktail for detection of 13 HPV genotypes included in the high-risk probe cocktail. STUDY DESIGN: Cervical samples obtained from 325 women recognized as HPV positive using the HCII high-risk probe cocktail were included in the study. HPV genotypes were determined by restriction fragment analysis of PGMY09/PGMY11 polymerase chain reaction (PCR) products using seven restriction endonucleases. RESULTS: A 450 bp fragment of HPV L1 gene was successfully amplified from 312 out of 325 samples. Of the 312 PCR-positive samples, 280 samples were associated with the expected high-risk HPV genotypes and 32 samples with the HPV genotypes not included in the HCII high-risk probe cocktail. Thus, HPV53 was detected in 8 samples, HPV66 in 4 samples, HPV54 in 3 samples, HPV6, HPV26, HPV70 each in 2 samples, and HPV11, HPV40, HPV42, HPV61, HPV73, HPV81, MM4, IS39, CP6108 each in 1 sample. In 2 samples, we were not able to determine the HPV genotype. CONCLUSIONS: Our study shows that HCII high-risk probe cocktail detects at least 15 HPV genotypes not included in the current HCII high-risk probe cocktail. The potential impact of HCII high-risk probe cocktail cross-reactivity with phylogenetically related and unrelated HPV genotypes, including genotypes currently considered to be low-risk HPVs, remains to be determined.

Cross Reactions↗
PubMed1997

cDNA sequencing of the 5' noncoding region (5' NCR) to determine hepatitis C genotypes in patients with chronic hepatitis C.

Reports suggest that response to interferon-alpha therapy is influenced by both hepatitis C viral genotype and titer. Our aim was to determine if direct, automated, cycle sequencing of the PCR product from an HCV RNA detection assay could be used to reliably determine HCV genotype. In addition, the approach was used to determine the HCV genotype distribution in our patient population and to learn if there was a correlation between HCV genotype and RNA titer that could be used to predict response to treatment. In all 143 consecutive patients were tested for both HCV RNA titer and genotype. Automated, cycle sequencing of PCR product was highly effective and failed to yield a genotype in only 3 (2%) patients. The distribution of HCV genotypes was: 1a (40%), 1b (39%), 2a (2%), 2b (6%), 3a (4%). There were significant differences in the median HCV RNA titers between genotypes 1, 2, and 3. High HCV RNA titers >4.4 x 10(6) copies/ml were only seen in genotype 1. However, the HCV RNA level should not be used as a surrogate marker of genotype because of a significant overlap of titers within the genotypes.

Base Sequence↗
PubMed1999

Utility of the predictors of coronary heart disease mortality in a longitudinal study of elderly Finnish men aged 65 to 84 years is dependent on context defined by Apo E genotype and area of residence.

A common assumption underlying most genetic studies is that individuals with different genotypes respond similarly to exposure to internal (epigenetic and background genotype effects) and external (ecological) environments. Here we evaluate whether this assumption is true in individuals with different genotypes of the gene coding for the apolipoprotein E (Apo E) molecule, an important determinant of the metabolic fate of plasma lipids and lipoproteins. We addressed whether the utility of known risk factors of coronary heart disease (CHD) in the prediction of CHD death in a 5-year follow-up is the same for the two most common Apo E genotypes, epsilon3/3 and epsilon4/3, in two cohorts of elderly Finnish men (age at baseline: 65-84 years), one in Eastern and the other in Southwestern Finland. The CHD mortality rate was higher in the epsilon4/3 than in the epsilon3/3 genotype in both cohorts (11.1 versus 7.8%, Pr = 0.281 in the Eastern cohort and 19.6 versus 8.2%, Pr = 0.002 in the Southwestern cohort). In the Eastern cohort, serum high density lipoprotein (HDL) cholesterol level was identified as a strong predictor of CHD death in the epsilon3/3 genotype (beta = -2.155, Pr = 0.019). In the Southwestern cohort, age (beta = 0.139, Pr = 0.006), body mass index (BMI) (beta = 0.149, Pr = 0.016), and serum total cholesterol level (beta = 0.453, Pr = 0.051) were identified as strong predictors in the epsilon3/3 genotype, as were smoking (beta = 0.236, Pr = 0.008) and BMI (beta = -0.124, Pr = 0.057) in the epsilon4/3 genotype. The latter observation indicates that in Southwestern Finland the probability of CHD death decreases with increasing BMI in elderly men with the epsilon4/3 genotype, while in their counterparts with the epsilon3/3 genotype the risk increases with increasing BMI. This difference was statistically significant (Pr = 0.002). These observations clearly argue against the assumption that individuals with different genotypes respond similarly to exposures to internal and/or external environments. These observations are consistent with a complex pathobiology of CHD involving biochemical and physiological agents that are under the influence of interactions between genetic and environmental factors. Information about these interactions is necessary for developing a more precise risk assessment and ultimately to improve public health and clinical strategies to prevent this devastating disease both at the individual and population levels.

Aged↗
PubMed2002

Distribution of genotypes of F-specific RNA bacteriophages in human and non-human sources of faecal pollution in South Africa and Spain.

AIMS: To assess whether the distribution of genotypes of F-specific RNA bacteriophages reflects faecal pollution of human and animal origin in water environments. METHODS AND RESULTS: Stool samples, animal feedlot waste slurries and a wide variety of faecally polluted waters were studied in South Africa and Spain. Genotyping was performed by plaque and spot hybridization with genotype-specific probes. Only genotypes II and III were detected in human stool. Animal faeces contained predominantly, but not exclusively, genotypes I and IV. Raw hospital and municipal sewage contained mostly genotypes II and III, whereas genotypes I and II prevailed in settled sewage, secondary treated sewage and non-point diffuse effluents from developing communities. Abattoir wastewaters contained mostly genotypes I and IV. No differences were observed between the distribution of genotypes in Spain and South Africa. CONCLUSIONS: Although the association of genotypes II and III with human excreta and I and IV with animal excreta was statistically significant, the results suggest that the association cannot be used for absolute distinction between faecal pollution of human and animal origin. SIGNIFICANCE AND IMPACT OF THE STUDY: This study contributes greatly to understanding the usefulness of genotypes of F-specific RNA bacteriophages in source tracking of faecal wastes.

Animals↗
PubMed1997

Hepatitis C virus genotypes in Australia.

The relative distribution of Australian hepatitis C virus (HCV) genotypes was determined for 500 isolates. Genotyping was performed using a commercial reverse phase hybridization assay after amplification of the 5' untranslated region of HCV by the polymerase chain reaction. Australian isolates comprised, predominantly, genotype 1 (55%) and genotype 3 (38%) with genotype 2 accounting for only 7%. Genotype 3a was the most common subtype. When the major risk groups of injecting drug users or transfusion-acquired hepatitis C were compared, there was a significantly higher incidence of genotype 1b in the transfusion-acquired group (P < 0.03). When the age of the patients was analysed, genotype 3a was more prevalent in the 21-40-year age group than the 41-60-year age group (P < 0.05). There was no significant difference in genotype distribution between males and females. HCV genotypes 1, 2 and 3 are most often found in developed countries but the relatively high prevalence of genotype 3a in Australia is unusual.

Adult↗
PubMed1999

Hepatitis C virus genotypes in France: relationship with epidemiology, pathogenicity and response to interferon therapy. The GEMHEP.

The aim of this study was to investigate the following in a large population of French patients with chronic hepatitis C: the geographical distribution of hepatitis C virus (HCV) genotypes; the relationship between HCV genotypes and epidemiological characteristics; severity of the disease; and response to interferon (IFN) therapy. Data from 14 tertiary referral centres, corresponding to 1872 patients with chronic hepatitis C, were prospectively collected from 1989 to 1997. HCV genotyping was performed using the line probe assay (LiPA). HCV genotypes 1b, 3, 1a, 2, 4 and a mixed infection were found in 41%, 22%, 16%, 11%, 4% and 4% of our population, respectively. HCV genotype distribution was homogeneous, except for genotype 2 that was found more frequently in the southwest than in the other regions (21% vs 9.2%) (P=0.001). HCV distribution was associated with gender, age, and source and duration of infection. In multivariate analysis, these correlations were related to the source of infection, which was the only independent factor significantly associated with genotype (P=0.001). Genotype 1b was significantly more common in patients with cirrhosis, but in multivariate analysis cirrhosis was independently related to older age at exposure and longer duration of infection (P=0.001). A sustained response to IFN therapy was observed in 11% of patients infected with genotypes 1a or 1b vs 32% of those infected with genotypes 2 or 3 (P=0.001). This study shows that HCV genotype is mainly related to the source infection, but not to the intrinsic pathogenicity of HCV, and is a strong predictor of sustained response to therapy.

Adult↗
PubMed1999

Distribution of fungal endophyte genotypes in doubly infected host grasses.

Fungal endophytes of the genus Epichloë live intercellulary in above ground plant parts of many pooid 'grasses of the temperate regions. The associations are characterized by single genotype entities since a given host individual normally contains a single endophyte genotype. They can persist over the life span of the hosts. This study examines whether two fungal genotypes can co-exist within a host plant, and how fungal genotypes are distributed within a host in the case of double infections. We selected four Epichloë bromicola strains that we identified as unique genotypes through RAPD' analysis. Young Bromus erectus plants, derived from callus cultures, were artificially inoculated with all possible double-strain mixtures of these fungal genotypes. For identification of fungal genotypes in planta, we designed genotype-specific primer pairs that flanked size-variable loci in the fungal genomes. Diagnostic PCR revealed that only one fungal genotype was present in most inoculated plants, but double infections were also observed with a frequency of 8% of all infected plants. Subsequent analyses of individual tillers of doubly infected plants revealed that, in a given tiller, both the leaf-blade and the leaf-sheath were colonized with only one endophyte genotype. Tillers without any detectable fungal DNA were also observed. Thus, co-existence of multiple endophyte genotypes within a single host plant is governed by mutual exclusion at the tiller level.

Ascomycota↗
PubMedDate not supplied

Development of a Chlamydophila psittaci species-specific and genotype-specific real-time PCR.

A Chlamydophila psittaci species-specific real-time PCR targeting the rDNA ribosomal spacer was developed as well as a genotype-specific real-time PCR targeting the Cp. psittaci outer membrane protein A (ompA) gene. The SYBR Green-based species-specific real-time PCR detected Cp. psittaci genotypes A to F, and the recently discovered E/B genotype. The genotype-specific real-time PCR could easily distinguish genotypes C, D, F by use of TaqMan probes. Genotypes A, B and E could not be distinguished from each other by simply using TaqMan probes. For this purpose, non-fluorescent competitor oligonucleotides, had to be used next to the TaqMan probes. Genotype E/B could only be detected by use of a minor groove binder (MGB) probe. Both real-time PCR assays allowed reproducible, sensitive (10 rDNA or ompA copies/microL DNA extract) and specific detection of Cp. psittaci DNA. The genotype-specific real-time PCR was compared to ompA sequencing and ompA restriction fragment length polymorphism (RFLP) analysis using five Cp. psittaci field isolates (99, 61/8, 7344/2, 8615/1 and 7778B15) each consisting of two different genotypes. The currently developed real-time PCR assays were used in a case study on a veterinary school and a turkey farm. In the veterinary school, Cp. psittaci genotypes D, E/B and F infection were detected in all five groups of turkeys, and one veterinarian who was taking care of all these turkeys. On the turkey farm, the presence of two Cp. psittaci genotype B infection waves was demonstrated in one randomly selected turkey, the first wave at the age of 6 weeks, and the second at the age of 12 weeks.

Animals↗
PubMed2004

Clinical relevance of hepatitis B virus genotype in children with chronic infection and hepatocellular carcinoma.

BACKGROUND & AIMS: The aim of this study was to investigate the influence of hepatitis B virus (HBV) genotypes on the clinical outcome of chronic childhood HBV infection and hepatocellular carcinoma (HCC). METHODS: A total of 460 HBV carrier children were followed-up for 15 years and 26 children with HBV-related HCC were recruited. HBV genotyping was examined at enrollment and the latest follow-up of these carrier children and at diagnosis in HCC children. Viral load was checked at enrollment for the carrier children. These carriers were grouped based on their initial hepatitis B e antigen (HBeAg) and antibody to hepatitis B e antigen (anti-HBe) status. The HBeAg positive (+) group was divided further into an HBeAg(+/+) group and HBeAg(+/-) group, depending on whether spontaneous HBeAg seroconversion occurred during the follow-up period. RESULTS: Genotype B constituted 73%, 86%, and 76% in the HBeAg(+/+), HBeAg(+/-), and anti-HBe(+) groups, respectively. Genotype C was found in 27%, 8%, and 6% in the HBeAg(+/+), HBeAg(+/-), and anti-HBe(+) group, respectively. Genotype C carriers were more prevalent in the HBeAg(+/+) group than the other 2 groups (P = .01), and had a delayed HBeAg seroconversion compared with the genotype B carriers (P < .001). Changes of genotype during the follow-up period were rare (2.8%). In those with HCC, genotype B was also the major type (74%). There was no difference in the baseline viral load between genotypes B and C. CONCLUSIONS: Although HBV genotype B dominates in children with chronic HBV infection and HCC in Taiwan, genotype C delays HBeAg seroconversion in pediatric chronic HBV infection.

Carcinoma, Hepatocellular↗
PubMed2000

Effect of bilirubin UDP glucuronosyltransferase 1 gene TATA box genotypes on serum bilirubin concentrations in chronic liver injuries.

TATA box abnormality in the promoter region of the bilirubin UDP glucuronosyltransferase 1 gene has been reported to cause Gilbert's syndrome in white subjects. It has also been reported that the majority of Japanese patients with Gilbert's syndrome are heterozygous for Gly71Arg in the coding region of this gene. On the other hand, some patients with chronic hepatitis often show signs of unexpected hyperbilirubinemia. The aims of this study were to determine which of the genetic variations, TATA box genotype or codon 71 genotype, is most closely related to serum bilirubin concentrations, and whether the TATA box genotype has an effect on serum bilirubin concentrations in patients with hepatitis C-associated chronic liver diseases. In a sample of 300 individuals selected from among the general Japanese population, mean concentrations of total serum bilirubin differed significantly among TATA box genotypes, but not among codon 71 genotypes. Concentration of total serum bilirubin was significantly correlated with TATA box genotypes. In 211 patients with hepatitis C-associated chronic liver diseases, mean concentrations of total serum bilirubin also differed significantly among TATA box genotypes. In patients with chronic hepatitis C, concentration of total serum bilirubin was significantly correlated with TATA box genotypes. In summary, TATA box genotypes, but not codon 71 genotypes, are closely related to serum bilirubin concentrations. TATA box genotypes should therefore be considered when evaluating hepatic function by serum bilirubin concentrations in cases of hepatitis C-associated chronic liver diseases.

Adult↗
PubMed2002

Hepatitis C virus genotype 3 is cytopathic to hepatocytes: Reversal of hepatic steatosis after sustained therapeutic response.

On the basis of cross-sectional studies, it has been proposed that hepatic steatosis is a cytopathic effect of hepatitis C virus (HCV) genotype 3 but not genotype 1 infections. We tested this hypothesis by examining whether antiviral treatment altered hepatic steatosis in chronic hepatitis C. In 28 patients with genotype 1 and 34 with genotype 3 HCV, we determined the severity of steatosis in pre- and posttreatment liver biopsies using computer-assisted morphometric image analysis as well as conventional semiquantitative scoring. Before treatment, hepatic steatosis was present in 16 (57%) patients infected with HCV genotype 1 and 21 (62%) of those with genotype 3. Sustained viral response (SVR) was achieved in 9 (32%) patients with genotype 1 and 22 (65%) with genotype 3. In neither group were there significant changes in body weight or alcohol consumption between pre- and posttreatment biopsies. In patients with HCV genotype 1, there was no change in hepatic steatosis after treatment, irrespective of the treatment response. Among those infected with genotype 3, SVR significantly reduced steatosis (P <.001), but there was no change in steatosis among those without a SVR. By logistic regression analysis, SVR was the only variable predictive of improvement in hepatic steatosis (OR = 36, 95% CI = 2.7-481, P =.007). In conclusion, these data provide strong support for a direct causal association between HCV genotype 3 infection and hepatic steatosis.

Adult↗
PubMed2003

Influence of hepatitis B virus genotypes on the progression of chronic type B liver disease.

To investigate the hepatitis B virus (HBV) genotype-related differences in the progression of liver disease, 585 patients with chronic HBV infection including 258 with histologically verified chronic liver disease (CLD) and 74 with hepatocellular carcinoma (HCC) were examined. The mean ages of both patients with advanced fibrosis (F3 or F4) and with HCC were significantly older in genotype B than in genotype C patients (P =.018, P =.024, respectively). Both the hepatitis B e antigen (HBeAg) negativity rate at biopsy and the cumulative HBe seroconversion rate in patients with CLD were significantly higher in genotype B patients than genotype C patients (P <.01, P =.022, respectively). Multivariate analysis revealed that genotype B, presence of precore mutation, high ALT levels, and severe histologic activity were independent factors for HBe seroconversion. Among all the biopsy-proven CLD patients, the ratio of patients with advanced fibrosis in genotype B was significantly lower than that in genotype C (4/30 vs. 74/224, respectively; P =.034). This difference was more remarkable in younger patients (< or =45 years; 1/25 vs. 47/180, respectively; P =.020), and there was no difference in older patients (>45 years). The distribution of each genotype between CLD and HCC was very similar (B and C: 11.2% and 87.0% vs. 10.8% and 89.2%, respectively). In conclusion, our results suggest that, although the patients with genotype B experience earlier HBe seroconversion, slower progression of liver fibrosis, and slower development of HCC, the life-long risk of progression to advanced fibrosis and development of HCC may not differ among genotypes B- and C-related chronic liver disease.

Adult↗
PubMed2000

Helicobacter pylori vacA genotypes and cagA gene in a series of 383 H. pylori-positive patients.

BACKGROUND: Only 10-15% of all patients infected with Helicobacter pylori develop peptic ulcer disease (PUD) or gastric cancer. Apart from immunological factors in the host, virulence determinants of H. pylori such as the vacuolating cytotoxin (VacA) or the cytotoxin-associated protein A (CagA) might represent a predisposition for the development of PUD. METHODS: We studied antral biopsies of 383 H. pylori-positive patients with peptic ulcer disease (PUD) or other H. pylori-related diseases for H. pylori vacA genotypes and the presence of the cagA gene by PCR. RESULTS: VacA genotypes and cagA status could be completely determined in 357 (93.2%) of the patients. In 91 (93.8%) of 97 patients with PUD, the vacA s1 genotype (s1m1, 45; s1m2, 46 patients) was present. The vacA s2m2 genotype was found in only 6 (6.2%) of 97 patients with PUD. In contrast, 180 (75.3%) of 239 patients (s1m1, 89; s1m2, 91 patients) without PUD and without gastric malignancies harbored strains with the vacA s1 genotype. The vacA genotype s2m2 was found in 59 (24.7%) of these patients. The presence of the cagA gene was closely associated with the vacA genotype s1 and found in 124 (88.6%) and in 113 (80.7%) of patients with the s1m1 or s1m2 genotypes, respectively, whereas strains with the genotype s2m2 were almost exclusively cagA negative. CONCLUSION: Most H. pylori strains found in patients with PUD possess the vacA s1 genotype and the cagA gene. Patients with this type of H. pylori strain but without PUD might be at higher risk of developing PUD. In contrast, the risk for PUD might be significantly decreased in those patients who are infected by H. pylori strains with the vacA s2 genotype lacking the cagA gene.

Adult↗
PubMed2004

Histological findings, genotype distribution and percentage of patients fulfilling the treatment criteria among patients with chronic hepatitis C virus infection in a single Swedish centre.

BACKGROUND: Genotype distribution of chronic hepatitis C in Sweden has shown a predominance of genotype non-1. With recent improvements in therapy, genotypes 2 and 3 infections can, according to consensus, be treated without histological assessment. The aim of this study was to evaluate the genotype distribution, histological stage and grade, and the percentage of patients fulfilling the histological treatment criteria. METHOD: A total of 323 patients with chronic hepatitis C were tested for genotype, histological findings and the percentage fulfilling the histological treatment criteria as stated by Swedish consensus; i.e. having fibrosis stage II or more, or fibrosis stage I with inflammation grade II or more. RESULTS: The patients had a mean age of 45 years (range 16-71 years) and 62% were males. Genotypes were determined in 79% of patients and genotype 2b or 3a was found to predominate, comprising 56%. Former intravenous drug use was found to be the predominant mode of acquisition, noted in 60%. The mean disease duration was 21 years (range 3-40) after which time 14% of patients had developed cirrhosis (stage IV). In the total material, 77% fulfilled the histological treatment criteria, 76% and 86%, respectively, among genotype I and genotype non-1 (2b and 3a) patients. CONCLUSIONS: Genotype non-1 (2b or 3a) predominated among Swedish patients, 14% of whom developed cirrhosis after a mean follow-up time of 21 years. Furthermore, an absolute majority fulfilled the histological criteria used to judge patients' eligibility for antiviral therapy, supporting the recent Swedish consensus decision to treat genotypes 2 and 3 infected patients without a previous biopsy.

Adolescent↗
PubMed2006

JC virus in the Irish population: significant increase of genotype 2 in immunocompromised individuals.

The human polyomavirus JC virus (JCV) is ubiquitous and can be shed in the urine of more than 40% of the healthy population. Amplification and sequencing of JCV from urine has allowed a distinctive map of the distribution of JCV genotypes worldwide. To define the frequency of JCV urinary excretion and genotype distribution in Ireland, urines from 121 healthy individuals and from 94 immunocompromised individuals (human immunodeficiency virus [HIV]-positive patients and rheumatoid arthritis patients) were collected. JCV DNA was detected by polymerase-chain reaction (PCR) with subsequent nucleotide sequencing of a fragment of the major capsid protein (VP1). JCV was detected in 20.7% of healthy individuals and was found significantly more often in the urine of HIV-positive patients (54.2%; P < .001) and rheumatoid arthritis patients (54.4%; P < .001). In healthy Irish individuals genotype 1 was the predominant genotype in 62.5%, followed by genotype 4 in 16.7% and genotype 2 in 12.5%. In contrast, genotype 2 was significantly more often isolated from the urine of both HIV-positive patients (60%) and rheumatoid arthritis patients (54.4%; P < .01). The pattern of genotype distribution among healthy Irish individuals is in agreement with data reported from other European countries, whereas the overall level of JCV urinary excretion is lower. Previous studies have found genotype 2 significantly more often in cerebrospinal (CSF) samples of patients with progressive multifocal leukoencephalopathy (PML). Here the authors report an increased frequency of genotype 2 in urine samples of immunocompromised non-PML patients. This finding further underlines the hypothesis that there could be biologic differences between JCV genotypes.

Amino Acid Sequence↗
PubMed2002

Probability of detection of genotyping errors and mutations as inheritance inconsistencies in nuclear-family data.

Gene-mapping studies routinely rely on checking for Mendelian transmission of marker alleles in a pedigree, as a means of screening for genotyping errors and mutations, with the implicit assumption that, if a pedigree is consistent with Mendel's laws of inheritance, then there are no genotyping errors. However, the occurrence of inheritance inconsistencies alone is an inadequate measure of the number of genotyping errors, since the rate of occurrence depends on the number and relationships of genotyped pedigree members, the type of errors, and the distribution of marker-allele frequencies. In this article, we calculate the expected probability of detection of a genotyping error or mutation as an inheritance inconsistency in nuclear-family data, as a function of both the number of genotyped parents and offspring and the marker-allele frequency distribution. Through computer simulation, we explore the sensitivity of our analytic calculations to the underlying error model. Under a random-allele-error model, we find that detection rates are 51%-77% for multiallelic markers and 13%-75% for biallelic markers; detection rates are generally lower when the error occurs in a parent than in an offspring, unless a large number of offspring are genotyped. Errors are especially difficult to detect for biallelic markers with equally frequent alleles, even when both parents are genotyped; in this case, the maximum detection rate is 34% for four-person nuclear families. Error detection in families in which parents are not genotyped is limited, even with multiallelic markers. Given these results, we recommend that additional error checking (e.g., on the basis of multipoint analysis) be performed, beyond routine checking for Mendelian consistency. Furthermore, our results permit assessment of the plausibility of an observed number of inheritance inconsistencies for a family, allowing the detection of likely pedigree-rather than genotyping-errors in the early stages of a genome scan. Such early assessments are valuable in either the targeting of families for resampling or discontinued genotyping.

Alleles↗
PubMed2006

Effects of glutathione S-transferase A1 (GSTA1) genotype and potential modifiers on breast cancer risk.

Glutathione S-transferases (GSTs) are phase II enzymes that are involved in the detoxification of a wide range of carcinogens. The novel GSTA1*A and GSTA1*B genetic polymorphism results in differential expression, with lower transcriptional activation of GSTA1*B (variant) than that of GSTA1*A (common) allele. Considering that cruciferous vegetables induce GSTs, which metabolize tobacco smoke carcinogens, we hypothesized that the variant GSTA1*B genotype may predispose women to breast cancer, particularly among low cruciferous vegetable consumers and among smokers. Thus, we evaluated potential relationships between GSTA1 polymorphisms and breast cancer risk, in relation to vegetable consumption and smoking status in the Long Island Breast Cancer Study Project (1996-1997), a population-based case-control study. Genotyping (1036 cases and 1089 controls) was performed, and putative breast cancer risk factors and usual dietary intakes were assessed. Having GSTA1*A/*B or *B/*B genotypes was not associated with increased breast cancer risk, compared to having the common *A/*A genotype. However, among women in the lowest two tertiles of cruciferous vegetable consumption, *B/*B genotypes were associated with increased risk (OR (95% CI)=1.73 (1.10-2.72) for 0-1 servings/week), compared to women with *A/*A genotypes. Among women with *B/*B genotypes, a significant inverse trend between cruciferous vegetable consumption and breast cancer risk was observed (P for trend=0.05), and higher consumption (4+ servings/week) ameliorated the increased risk associated with the genotype. Current smokers with *B/*B genotypes had a 1.89-fold increase in risk (OR (95% CI)=1.89 (1.09-3.25)), compared with never smokers with *A/*A genotypes. These data indicate that GSTA1 genotypes related to reduced GSTA1 expression are associated with increased breast cancer primarily among women with lower consumption of cruciferous vegetables and among current smokers.

Alleles↗