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PubMed2002

Genotype mixtures of hepatitis B virus in patients treated with interferon.

Little is known about coinfection among several hepatitis B virus (HBV) genotypes, although previous reports of recombination and genotype shifts indicate that this should occur. In the present study, we designed a method to identify mixtures of genotype A and another genotype, regardless of whether one of them predominates. Using this method, signs of genotypic coinfection were found in 20 (67%) of 30 hepatitis B e antigen-positive patients treated with interferon (IFN). In 8 of these patients, coinfection or genotype shifts were detectable by direct sequencing or standard preS genotyping. In most of these cases, genotype changes were detected after a >2-log decrease or increase of the HBV DNA level. The presence of genotype mixtures did not significantly influence IFN response. Because quasi-species selection may occur at or shortly after transmission, patients might acquire HBV infection from subjects who appear to be infected with a different genotype. This should be considered when tracing the source of HBV infection.

Antiviral Agents↗
PubMed1998

Chlamydia trachomatis genotypes: correlation with clinical manifestations of infection and patients' characteristics.

In 1994 Chlamydia trachomatis specimens from 175 men and 135 women attending a clinic for treatment of sexually transmitted disease were genotyped by polymerase chain reaction-based restriction fragment length polymorphism of the omp1 gene. Information about the patients was collected at their initial visit. The associations between C. trachomatis genotype and patients' self-reported symptoms, clinical signs, and characteristics were studied. Genotypes E, F, and D/D-predominated (men: 71%; women: 60%). Five specimens (1.6%) showed evidence of mixed infections. Among men, complaints of urethral discharge and dysuria were most commonly associated with genotypes H and J (100% vs. 59%-68% for the other genotypes; P = .03); in addition, > or = 10 leukocytes per microscopic field were least often observed for genotypes G/Ga (19% vs. 59%-65% for the other genotypes; P = .01). Women's reports of lower abdominal pain were more often associated with F, G group genotypes (32%) than with B-complex (6%) or C-complex (13%) genotypes (P = .02). Certain symptoms of genital C. trachomatis infection were related to the infecting genotype. Further work will be necessary and should involve markers of the host immune response.

Adolescent↗
PubMed2006

Diversity of Bartonella genotypes in Richardson's ground squirrel populations.

The diversity and dynamics of Bartonella genotypes found in wild Richardson's ground squirrels (RGS), Spermophilus richardsonii were monitored at multiple sites in Saskatchewan, Canada from 2002 to 2004. Based on sequence analysis of a portion of the Bartonella citrate synthase (gltA) gene, four different genotypes were detected in 233 isolates from 176 animals. The majority (87%) of sequences were identified as genotype H, with genotypes I, J, and K accounting for 8%, 4%, and 1% of sequences, respectively. Only one animal was concurrently infected with multiple Bartonella genotypes. Of 23 animals sampled four times or more, 26% were never infected with Bartonella. Of 32 RGS infected with Bartonella at first capture and then sampled again the following month, 50% were infected with the same Bartonella genotype, 41% were no longer infected, and 9% were infected with a different Bartonella genotype in the subsequent sample. The diversity of Bartonella genotypes varied among sites. At one site almost all RGS were infected with genotype H in September, and up to 60% of the same population was infected with genotype I the following spring. We compare our results with previous studies of Bartonella infections in rodents and discuss possible explanations for the observed differences.

Animals↗
PubMed2026

LAML-Pro: joint maximum likelihood inference of cell genotypes and cell lineage trees.

MOTIVATION: Recent dynamic lineage tracing technologies use genome editing to induce heritable mutations, or edits, that accumulate across successive cell divisions. These edits are measured using single-cell sequencing or imaging, providing data to reconstruct cell lineages at single-cell resolution. Current computational approaches to infer cell lineage trees, or phylogenies, from these data perform two separate steps: (i) Identify each cell's edits (genotype) from the raw sequencing or imaging data; (ii) Infer a cell lineage tree from the cell genotypes. However, genotyping cells is an inexact process and genotype errors can yield an inaccurate lineage tree. For example, using fluorescence based-imaging to measure edits results in a high fraction (≈25%-50%) of uncertain or erroneous genotypes. RESULTS: We introduce Lineage Analysis via Maximum Likelihood with PRobabilistic Observations (LAML-Pro), an algorithm that jointly infers cell genotypes and a cell lineage tree. LAML-Pro is based on the Probabilistic Mixed-type Missing Observation (PMMO) model, which we derive to describe both the genome editing and genotype observation processes. LAML-Pro constructs lineage trees from thousands of cells in under an hour by leveraging the sparsity of transitions under the PMMO model. On simulated data, we demonstrate that LAML-Pro corrects genotype errors and infers substantially more accurate trees than existing methods which are vulnerable to genotype errors. Applied to data from two recent imaging-based lineage tracing systems, LAML-Pro reduces genotype errors by 5-fold and produces more spatially coherent lineage trees compared to existing methods. AVAILABILITY AND IMPLEMENTATION: LAML-Pro is implemented in C++ and is available as both a command-line interface and as a Python library at: github.com/raphael-group/LAML-Pro.

Cell Lineage↗
PubMed2005

Dynamic model based algorithms for screening and genotyping over 100 K SNPs on oligonucleotide microarrays.

MOTIVATION: A high density of single nucleotide polymorphism (SNP) coverage on the genome is desirable and often an essential requirement for population genetics studies. Region-specific or chromosome-specific linkage studies also benefit from the availability of as many high quality SNPs as possible. The availability of millions of SNPs from both Perlegen and the public domain and the development of an efficient microarray-based assay for genotyping SNPs has brought up some interesting analytical challenges. Effective methods for the selection of optimal subsets of SNPs spanning the genome and methods for accurately calling genotypes from probe hybridization patterns have enabled the development of a new microarray-based system for robustly genotyping over 100,000 SNPs per sample. RESULTS: We introduce a new dynamic model-based algorithm (DM) for screening over 3 million SNPs and genotyping over 100,000 SNPs. The model is based on four possible underlying states: Null, A, AB and B for each probe quartet. We calculate a probe-level log likelihood for each model and then select between the four competing models with an SNP-level statistical aggregation across multiple probe quartets to provide a high-quality genotype call along with a quality measure of the call. We assess performance with HapMap reference genotypes, informative Mendelian inheritance relationship in families, and consistency between DM and another genotype classification method. At a call rate of 95.91% the concordance with reference genotypes from the HapMap Project is 99.81% based on over 1.5 million genotypes, the Mendelian error rate is 0.018% based on 10 trios, and the consistency between DM and MPAM is 99.90% at a comparable rate of 97.18%. We also develop methods for SNP selection and optimal probe selection. AVAILABILITY: The DM algorithm is available in Affymetrix's Genotyping Tools software package and in Affymetrix's GDAS software package. See http://www.affymetrix.com for further information. 10 K and 100 K mapping array data are available on the Affymetrix website.

Algorithms↗
PubMed1997

Associations between cytochrome P4502E1 genotype, mutagen sensitivity, cigarette smoking and susceptibility to lung cancer.

Cytochrome P4502E1 (CYP2E1) is involved in the metabolic activation of carcinogenic N-nitrosoamines. We therefore assessed the genotype frequencies of PstI or RsaI CYP2E1 restriction fragment length polymorphisms and another susceptibility marker, mutagen sensitivity, in 137 lung cancer cases (92 African American and 45 Mexican American) and 206 controls (114 African American and 92 Mexican American) identified in a molecular epidemiological study of lung cancer. The CYP2E1 c1/c1 genotype was found in 86.7% of Mexican American cases, 70.6% of Mexican American controls, 89.1% of African American cases and 86.8% of African American controls. By multivariate analysis, this genotype was found to be associated with a 14.0-fold increased risk of lung cancer in Mexican Americans but not in African Americans; a 9.9-fold increased risk of lung cancer in Mexican American former smokers, but not in non-smokers or current smokers; a 15-fold increased risk of lung cancer in Mexican American males, but not in females. Patients with the susceptible genotype appeared to have developed cancer at an earlier age and with lower cigarette pack-year of exposure than did patients with the c1/c2 or c2/c2 genotypes. Stratified analysis suggested a greater than multiplicative interaction between cigarette smoking and CYP2E1 c1/c1 genotype, although not statistically significant. The odds ratios (ORs) for the CYP2E1 c1/c1 genotype, cigarette smoking and both risk factors combined were 1.3, 6.7 and 16.3, respectively. The association between CYP2E1 c1/c1 genotype and pack-years of smoking followed the same pattern. The interaction between mutagen sensitivity and CYP2E1 c1/c1 genotype was especially strong in former smokers (the ORs for the CYP2E1 c1/c1 genotype, mutagen sensitivity and both risk factors combined were 3.9, 5.4 and 23.0, respectively). Therefore, the data suggest that individuals who lack a c2 allele might be at higher risk for developing lung cancer.

Alleles↗
PubMed2001

Cyclin D1 (CCND1) genotype is associated with tumour grade in sporadic pituitary adenomas.

The cyclin D1 (CCND1) gene contains a frequent A/G polymorphism within the splice donor region of exon 4/intron 4. CCND1 genotype is associated with clinical outcome in a number of malignancies although prognostic significance varies with tumour type. We examined CCND1 allele frequencies and genotype distribution in 294 patients with sporadic pituitary adenomas of various histologies. CCND1 allele frequencies and distribution of genotypes were similar in the 294 cases compared with previously reported control populations. Analysis according to tumour subtype showed no statistical difference in allele frequencies compared with controls. However, CCND1 genotype distribution in the somatotrophinomas showed a significant difference compared with normal controls (P = 0.008). We next examined CCND1 allele frequencies and genotype distribution across the tumour grades. Within the total tumour cohort the CCND1 allele frequencies showed a significant inverse relationship across the tumour grades (P = 0.005). The CCND1 A allele progressively increased from grade 1 (0.37) through to grade 4 (0.62) tumours, whilst the CCND1 G allele frequency progressively decreased from grade 1 (0.63) through to grade 4 (0.38) tumours. Trend analysis of CCND1 genotypes showed a significant progressive increase in AA frequency from grade 1 (15%) through to grade 4 (46%) tumours (P = 0.005). The CCND1 GG genotype progressively decreased from grade 1 (41%) through to grade 4 (23%) tumours (P = 0.204). No statistical significance was observed between CCND1 AG genotype and tumour grades. While the functional significance of the observed segregation of the CCND1 A/G polymorphism and tumour grade is unclear, our data suggest that CCND1 allele frequencies and genotype distributions show significant differences between tumour grades in sporadic pituitary adenomas. Since CCND1 genotype may be determined by analysis of peripheral blood samples it may provide a useful predictive marker for those tumours likely to show invasive behaviour. This may be clinically useful in indicating which tumours should receive adjunctive treatment (e.g. radiotherapy) immediately after surgical resection.

Adenoma↗
PubMed2005

Accurate genotyping from paraffin-embedded normal tissue adjacent to breast cancer.

Genetic polymorphism analysis for disease risk is widely used in epidemiology studies; blood or oral cavity cells are the most widely used source of DNA. However, these types of samples are not always available, particularly for studies that were conducted years ago. An alternative potential source of patient DNA exists in the form of paraffin-embedded normal tissue adjacent to tumor samples, which are collected and stored routinely for clinical use. The use of such samples can be conceptually problematic, however, due to the presence of field cancerization in the surrounding normal tissue, with the possible presence of chromosomal loss. Specifically, loss of heterozygosity (LOH) might bias the genotyping results and cause genotype misclassification. However, field cancerization and LOH might not be an issue because LOH is not easily found unless there is careful microdissection of only tumor cells (leaving stromal, inflammatory and fat cells), for example, laser-capture microdissection. In this study, we set out to determine the degree of genotype misclassification from normal tissues adjacent to tumors, if any, by comparing these results with blood genotyping. We examined samples from 106 subjects with breast cancer, analyzing five different genotypes selected from regions commonly known to have LOH in breast cancer. These genotypes were methylenetetrahydrofolate reductase (MTHFR), oxoguanosine glycosylase 1 (hOGG1), dopamine beta-hydroxylase (DBH), dopamine receptor D2 (DRD2) and NAD(P)H dehydrogenase quinone 1 (NQO1), conducted by using real-time PCR and TaqMan genotyping analyses. We found that among these five genotypes and 106 comparisons, there was a 100% concordance for genotyping from normal tissue adjacent to tumor and from blood. Our findings indicate that the use of adjacent normal tissues provides accurate genotyping results with high specificity. Although this study only used breast tumor samples, and may be applicable only to breast cancer studies, we expect the results to be applicable to other types of cancers also.

Biopsy↗
PubMed2003

Genotyping error detection through tightly linked markers.

The identification of genotyping errors is an important issue in mapping complex disease genes. Although it is common practice to genotype multiple markers in a candidate region in genetic studies, the potential benefit of jointly analyzing multiple markers to detect genotyping errors has not been investigated. In this article, we discuss genotyping error detections for a set of tightly linked markers in nuclear families, and the objective is to identify families likely to have genotyping errors at one or more markers. We make use of the fact that recombination is a very unlikely event among these markers. We first show that, with family trios, no extra information can be gained by jointly analyzing markers if no phase information is available, and error detection rates are usually low if Mendelian consistency is used as the only standard for checking errors. However, for nuclear families with more than one child, error detection rates can be greatly increased with the consideration of more markers. Error detection rates also increase with the number of children in each family. Because families displaying Mendelian consistency may still have genotyping errors, we calculate the probability that a family displaying Mendelian consistency has correct genotypes. These probabilities can help identify families that, although showing Mendelian consistency, may have genotyping errors. In addition, we examine the benefit of available haplotype frequencies in the general population on genotyping error detections. We show that both error detection rates and the probability that an observed family displaying Mendelian consistency has correct genotypes can be greatly increased when such additional information is available.

Family↗
PubMed2003

Comparative evaluation of three computerized algorithms for prediction of antiretroviral susceptibility from HIV type 1 genotype.

OBJECTIVES: To compare three methods for using HIV-1 genotype to predict antiretroviral drug susceptibility. METHODS: We applied three genotypic interpretation algorithms to 478 reverse transcriptase (RT) and 410 protease sequences for which phenotypic data were available. Sequences were obtained from clinical practice and from published sequences in the Stanford HIV-1 RT and Protease Sequence Database. The genotypic interpretation algorithms included: Stanford HIVdb program (HIVdb), the Visible Genetics/Bayer Diagnostics Guidelines 6.0 (VGI) and a genotypic interpretation program (AntiRetroScan, ARS) developed at the University of Siena, Italy. Genotypic interpretations were normalized to a three-level output: susceptible, intermediate and resistant. Discordances were defined as differences between genotype and phenotype for the same virus isolate. Discordances for which an isolate was considered susceptible by one test but resistant by another test were considered major discordances. RESULTS: The frequency of major discordances between genotype and phenotype was 10.6, 13.7 and 15.7% for ARS, VGI and HIVdb, respectively (P < 0.0001 for ARS versus HIVdb and for ARS versus VGI; P = 0.002 for VGI versus HIVdb). The correlation between genotype and phenotype was highest for non-nucleoside RT inhibitors and lowest for nucleoside RT inhibitors. Half of the major discordances involved stavudine, didanosine and zalcitabine. The concordance among the three genotypic algorithms was high, with weighted Kappa values ranging between 0.76 and 0.84 for the pairwise comparisons between each of the algorithms. CONCLUSIONS: Genotype interpretation algorithms correctly predict phenotype in 85-90% of cases, but the rate of concordance is not uniformly distributed among different drugs. These data provide insight into the potential additional benefit derived from phenotyping.

Algorithms↗
PubMed2004

Influence of hepatitis B virus genotypes on the response to antiviral therapies.

Hepatitis B virus (HBV) has been classified into eight genotypes (A-H) based on genome sequence divergence. Genotypes of HBV have distinct geographical distributions, and two genotypes account for most HBV worldwide. Hepatitis B e antigen expression lasts longer and liver disease is more severe with graver outcomes in carriers of genotype C than B in Asia. Accumulating lines of evidence indicate a better response to interferon and lamivudine in patients with chronic hepatitis B who are infected with genotype B rather than C. The therapeutic response may differ, however, in patients infected with HBV of the same genotype. For example, the response to lamivudine is poorer in patients infected with subtype Ba, which contains a recombination with genotype C, than in those with subtype Bj without such a recombination. Influence of genotypes on therapeutic response needs to be examined in patients infected with the other genotypes, particularly in those with genotype A or D infection.

Animals↗
PubMed1996

Glutathione S-transferase and N-acetyltransferase genotypes and asbestos-associated pulmonary disorders.

BACKGROUND: Humans vary in their ability to metabolize endogenous and exogenous compounds. Glutathione S-transferases (GSTs) and N-acetyltransferases (NATs) are enzymes involved in the detoxification of hazardous agents. The GSTM1 and GSTT1 genes exhibit null (i.e., deletion) polymorphisms; in specific individuals, homozygous deletion (i.e., both copies lost) of these genes can be detected. Polymorphism of the NAT2 gene results in slow and fast acetylators of potentially toxic substances. The GSTM1-null and the NAT2 slow-acetylator genotypes have been associated with increased risks for the development of environmentally induced cancers. PURPOSE: We assessed whether homozygous GSTM1-null or GSTT1-null genotypes or the NAT2 slow-acetylator genotype were associated with increased risks for the development of malignant and nonmalignant asbestos-related pulmonary disorders in a cohort of Finnish construction workers. METHODS: The study population consisted of 145 asbestos insulators who were classified as having been exposed to high levels of asbestos; 69 of these individuals had no pulmonary disorders (control subjects), and 76 had either malignant mesothelioma (n = 24) or nonmalignant pulmonary disorders, such as asbestosis and/or pleural plaques (n = 52). Lymphocyte DNA and the polymerase chain reaction were used to determine the GSTM1, GSTT1, and NAT2 genotypes of the study subjects. Odds ratios (ORs) and 95% confidence intervals (CIs) estimating the relative risks of disease associated with specific genotypes were calculated from 2 x 2 tables by use of Fisher's exact method. RESULTS: Risks for the development of asbestos-related pulmonary disorders were not affected significantly by homozygous deletion of the GSTM1 or GSTT1 genes. However, the risk of developing both malignant and nonmalignant pulmonary disorders for individuals with a NAT2 slow-acetylator genotype was more than twice that observed for those with a NAT2 fast-acetylator genotype (OR = 2.3; 95% CI = 1.1-4.7); the risk of developing malignant mesothelioma for NAT2 slow acetylators was increased almost fourfold (OR = 3.8; 95% CI = 1.2-14.3). Individuals who lacked the GSTM1 gene and possessed a NAT2 slow-acetylator genotype had a risk of developing malignant and nonmalignant pulmonary disorders that was approximately fivefold greater than that observed for those who had the GSTM1 gene and a NAT2 fast-acetylator genotype (OR = 5.1; 95% CI = 1.6-17.6); these individuals had a fourfold increased risk of developing nonmalignant pulmonary disorders (OR = 4.1; 95% CI = 1.1-17.2) and an eightfold increased risk of developing malignant mesothelioma (OR = 7.8; 95% CI = 1.4-78.7) when compared with the same reference group. CONCLUSIONS: Individuals with homozygous deletion of the GSTM1 gene and a NAT2 slow-acetylator genotype who are exposed to high levels of asbestos appear to have enhanced susceptibility to asbestos-related pulmonary disorders.

Acetylation↗
PubMed2005

Hepatitis B virus genotype and DNA level and hepatocellular carcinoma: a prospective study in men.

BACKGROUND: Although chronic infection with hepatitis B virus (HBV) has been established as a cause of hepatocellular carcinoma (HCC), the roles of viral load and HBV genotype remain unclear. METHODS: From 1988 through 1992, baseline blood samples were collected from 4841 Taiwanese men who were HBV carriers but had not been diagnosed with HCC. We used real-time polymerase chain reaction assays of plasma DNA samples to quantify HBV DNA levels (a measure of viral load) and determine HBV genotypes for 154 case patients who were diagnosed with HCC during 14 years of follow-up and 316 control subjects. Unconditional logistic regression was used to assess odds ratios (ORs) of HCC for HBV-related factors. All statistical tests were two-sided. RESULTS: The risk of HCC increased with increasing HBV viral load (adjusted OR for the highest versus the lowest quintile of HBV DNA copies/mL = 7.26, 95% confidence interval [CI] = 3.54 to 14.89; P(trend)<.001). Genotype C HBV was associated with an increased risk of HCC compared with other HBV genotypes (adjusted OR = 5.11, 95% CI = 3.20 to 8.18). Both viral load and genotype were positively associated with HCC within 10-year age categories among subjects aged 30 years old to older than 60 years. Genotype C HBV was associated with increased viral load, and associations of HBV genotype and viral load with HCC risk were additive. The adjusted OR of HCC for those carrying genotype C HBV and with viral load in the highest quintile was 26.49 (95% CI = 10.41 to 67.42) compared with HBV carriers with other HBV genotypes and viral load in the lowest two quintiles. CONCLUSIONS: Measurements of HBV viral load and genotype may help to define which male HBV carriers aged 30 years or older are at high risk for HCC.

Adult↗
PubMed2006

Evaluation of slower-growing broiler genotypes grown with and without outdoor access: sensory attributes.

Consumer interest in organic and natural poultry production is growing. An experiment was conducted to assess the impact of genotype and outdoor access on sensory attributes of broiler meat. One slow-growing genotype (S), 2 medium-growing genotypes (M1 and M2), and a commercial fast-growing genotype (F) were raised (straight-run) for 81, 67, or 53 d, respectively. The placement dates were staggered to achieve a similar final BW, and each genotype was processed on the same day. Each genotype was assigned to 3 pens of 24 birds each, and all birds were raised in indoor floor pens in a naturally ventilated facility. The S and F genotypes were also assigned to 2 floor pens with outdoor access (during daylight hours) containing 36 birds each. All birds were provided with the same starter, grower, and finisher feeds, and birds were commercially processed. Breast and thigh meat were evaluated for sensory attributes and acceptability by a consumer panel. The M1 and M2 breasts were more tender than other indoor genotypes (P < 0.05); however, all treatments scored "slightly to moderately tender." The thigh meat of the M2 birds was more flavorful than that of S birds (P < 0.05), and the flavor of the S thigh meat was less liked than other indoor genotypes (P < 0.05). Outdoor access did not impact flavor. These data indicate that differences in sensory attributes may exist among genotypes with different growth rates and reared with or without outdoor access.

Animal Husbandry↗
PubMed2000

Genotypic variation in physiological and growth responses of Populus tremuloides to elevated atmospheric CO2 concentration.

Physiological and biomass responses of six genotypes of Populus tremuloides Michx., grown in ambient t (357 micromol mol(-1)) or twice ambient (707 micromol mol(-1)) CO2 concentration ([CO2]) and in low-N or high-N soils, were studied in 1995 and 1996 in northern Lower Michigan, USA. There was a significant CO2 x genotype interaction in photosynthetic responses. Net CO2 assimilation (A) was significantly enhanced by elevated [CO2] for five genotypes in high-N soil and for four genotypes in low-N soil. Enhancement of A by elevated [CO2] ranged from 14 to 68%. Genotypes also differed in their biomass responses to elevated [CO2], but biomass responses were poorly correlated with A responses. There was a correlation between magnitude of A enhancement by elevated [CO2] and stomatal sensitivity to CO2. Genotypes with low stomatal sensitivity to CO2 had a significantly higher A at elevated [CO2] than at ambient [CO2], but elevated [CO2] did not affect the ratio of intercellular [CO2] to leaf surface [CO2]. Stomatal conductance and A of different genotypes responded differentially to recovery from drought stress. Photosynthetic quantum yield and light compensation point were unaffected by elevated [CO2]. We conclude that P. tremuloides genotypes will respond differentially to rising atmospheric [CO2], with the degree of response dependent on other abiotic factors, such as soil N and water availability. The observed genotypic variation in growth could result in altered genotypic representation within natural populations and could affect the composition and structure of plant communities in a higher [CO2] environment in the future.

Biomass↗
PubMed1998

MT-2 tropism and CCR-5 genotype strongly influence disease progression in HIV-1-infected individuals.

BACKGROUND: The beta-chemokine receptor CCR-5 is the coreceptor for cellular entry by non-syncytium-inducing (NSI) HIV-1 strains that dominate early in infection. A 32 base-pair deletion (delta32) in the CCR-5 gene renders this coreceptor non-functional. Heterozygosity for this deletion [delta32/wild-type (wt)] is associated with slow disease progression. The purpose of this study was to document the combined impact on HIV-1 disease progression of the CCR-5 genotype and the biological phenotype of HIV-1. METHODS: In a cross-sectional study of 258 HIV-1-infected Swedish individuals, the CCR-5 genotype (wt/wt or delta32/wt) was determined by polymerase chain reaction and the biological phenotype [NSI or syncytium-inducing (SI)] of virus isolates was determined in the MT-2 cell assay. Clinical status, HIV-1 RNA levels in plasma, CD4+ lymphocyte counts, and rate of CD4+ lymphocyte decline, based on retrospective analysis of CD4+ lymphocyte counts, were also recorded. None of the individuals were treated with protease inhibitors. RESULTS: The prevalence of the delta32/wt genotype was 23%. Subjects with the delta32/wt CCR-5 genotype more often carried SI virus than subjects with the wt/wt genotype (49 versus 35%; P=0.067), but there were no differences between the two groups in prevalence of AIDS, viral load, CD4+ lymphocyte count or CD4+ slope. NSI virus isolates were found in 159 (62%) out of 258 individuals. Individuals with NSI had lower prevalence of AIDS (39 versus 19%; P < 0.01), higher CD4+ lymphocyte counts (289+/-188 x 10(6)/l versus 153+/-162 x 10(6)/l; P=0.001), lower viral loads (median, 4.45 log10 versus 4.91 log10 copies/ml; P < 0.01) and a lower prevalence of the delta32/wt genotype (19 versus 29%; P=0.067) compared with individuals with SI virus. When the material was further subdivided, subjects with the delta32/wt genotype and SI virus had the highest prevalence of AIDS (P < 0.001), lowest CD4+ lymphocyte count (P=0.0001) and highest viral load (P=0.023) whereas the opposite was true for subjects with the delta32/wt genotype and NSI virus. A significantly higher proportion of subjects with NSI virus with delta32/wt and wt/wt CCR-5 genotype had been immunized with recombinant gp160. CONCLUSION: In summary, the delta32/wt CCR-5 genotype has a protective effect against HIV-1 disease progression that appears to be limited to individuals carrying HIV-1 variants with NSI phenotype. Immunization with recombinant gp160 tended to reduce the frequency of SI phenotypes.

AIDS Vaccines↗
PubMed2002

Association of physical activity and bone: influence of vitamin D receptor genotype.

PURPOSE: The aim of the study was to investigate the interaction between leisure physical activity and a BsmI polymorphism at the vitamin D receptor (VDR) gene on the modulation of bone mineral density (BMD). METHODS: We studied 575 unrelated healthy postmenopausal women. Lumbar spine and femoral neck BMD were measured by dual-energy x-ray absorptiometry (DXA), and results were expressed as age-and-weight-adjusted (Z-score). VDR BsmI genotype was determined by polymerase reaction chain on peripheral blood leukocytes. RESULTS: Overall, no significant association was found between the level of leisure physical activity or VDR genotypes and adjusted BMD at both bone sites. However, in active women, there was a trend for an association between VDR genotypes and adjusted BMD at the lumbar spine. Active women, who exercised three times or more a week, carrying the "bb" genotype had a lower BMD at the lumbar spine than active women carrying "BB" genotype (ANOVA; P = 0.04). No significant difference in crude or adjusted BMD at both bone sites was found between VDR genotypes in sedentary or moderately active women. Furthermore, classification of women according to the median-age of the sample (63.1 yr) revealed a significant interaction between the level of leisure physical activity and VDR genotype on adjusted lumbar spine BMD in the older active postmenopausal women (N = 137). Older active women carrying the "bb" genotype showed a lower adjusted BMD at the lumbar spine compared with active women carrying the "BB" genotype (P = 0.007). CONCLUSION: These results suggested that gene-environment interactions such as leisure physical activity and VDR genotype may play a role in maintaining the BMD at the lumbar spine in active postmenopausal women, especially in older active women.

Adult↗
PubMed1998

Association of cytomegalovirus genotype with graft rejection after liver transplantation.

BACKGROUND: The envelope glycoprotein gB of human cytomegalovirus (CMV) occurs as one of four main genotypes. Some previous studies have proposed a relationship of CMV gB genotype to the frequency of symptomatic infection and to clinical outcomes in both transplant and human immunodeficiency virus-infected populations. Our aim was to define the distribution of CMV gB genotypes and the impact on acute cellular rejection and graft/patient survival after orthotopic liver transplantation (OLT). METHODS: Between October 1988 and December 1996, 325 patients underwent cyclosporine-based OLT at our center. CMV infection was surveyed prospectively and defined as viral isolation from blood or urine; 53 (16%) patients had detectable CMV. Isolates were genotyped by polymerase chain reaction amplification and restriction digest analysis. RESULTS: The distribution of CMV genotypes was: gB1, 19 (36%) patients; gB2, 15 (28%) patients; gB3, 13 (24%) patients; and gB4, 4 (8%) patients. Two patients (4%) had mixed infection (1 + 3, 1 + 4). Age, preOLT diagnosis, use of ganciclovir prophylaxis, basal immunosuppression, mean number of HLA donor/recipient mismatches, and United Network of Organ Sharing status were comparable among patients with different genotypes. Patients with gBl had a significantly higher mean number of acute rejection episodes (1.52+0.30 vs. 0.67+0.22; P=0.027). However, there was no difference in rejection severity, including OKT3 usage or FK506 conversion, or development of chronic rejection among patients with different genotypes. The gB genotype did not affect the development of symptomatic or tissue-invasive CMV disease, detected in 15 patients. Actuarial rates of patient (odds ratio [OR] 3.0; confidence interval [CI] 1.49-6.0) and graft (OR 2.57; CI 1.25-5.22) survival were significantly diminished in the group with CMV infection versus those without CMV (P<0.0001 for both), but there was no association with CMV genotype. CONCLUSIONS: (1) Patients with CMV infection had significantly reduced patient and graft survival rates at 1 and 5 years after OLT as compared with OLT recipients without CMV infection. (2) CMV genotype gB1 was associated with a higher mean number of acute rejection episodes.

Adult↗