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PubMed1988

A cladistic analysis of phenotype associations with haplotypes inferred from restriction endonuclease mapping. II. The analysis of natural populations.

Genes that code for products involved in the physiology of a phenotype are logical candidates for explaining interindividual variation in that phenotype. We present a methodology for discovering associations between genetic variation at such candidate loci (assayed through restriction endonuclease mapping) with phenotypic variation at the population level. We confine our analyses to DNA regions in which recombination is very rare. In this case, the genetic variation at the candidate locus can be organized into a cladogram that represents the evolutionary relationships between the observed haplotypes. Any mutation causing a significant phenotypic effect should be imbedded within the same historical structure defined by the cladogram. We showed, in the first paper of this series, how to use the cladogram to define a nested analysis of variance (NANOVA) that was very efficient at detecting and localizing phenotypically important mutations. However, the NANOVA of haplotype effects could only be applied to populations of homozygous genotypes. In this paper, we apply the quantitative genetic concept of average excess to evaluate the phenotypic effect of a haplotype or group of haplotypes stratified and contrasted according to the nested design defined by the cladogram. We also show how a permutational procedure can be used to make statistical inferences about the nested average excess values in populations containing heterozygous as well as homozygous genotypes. We provide two worked examples that investigate associations between genetic variation at or near the Alcohol dehydrogenase (Adh) locus and Adh activity in Drosophila melanogaster, and associations between genetic variation at or near some apolipoprotein loci and various lipid phenotypes in a human population.

Alcohol Dehydrogenase↗
PubMed1993

A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination.

We previously developed an analytical strategy based on cladistic theory to identify subsets of haplotypes that are associated with significant phenotypic deviations. Our initial approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site data to estimate the evolutionary steps that interrelate the observed haplotypes to one another. The cladogram is then used to define a nested statistical design for identifying mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that a mutation responsible for a particular phenotypic effect is embedded within the evolutionary history that is represented by the cladogram. The power of this approach depends on the accuracy of the cladogram in portraying the evolutionary history of the DNA region. This accuracy can be diminished both by recombination and by uncertainty in the estimated cladogram topology. In a previous paper, we presented an algorithm for estimating the set of likely claodgrams and recombination events. In this paper we present an algorithm for defining a nested statistical design under cladogram uncertainty and recombination. Given the nested design, phenotypic associations can be examined using either a nested analysis of variance (for haploids or homozygous strains) or permutation testing (for outcrossed, diploid gene regions). In this paper we also extend this analytical strategy to include categorical phenotypes in addition to quantitative phenotypes. Some worked examples are presented using Drosophila data sets. These examples illustrate that having some recombination may actually enhance the biological inferences that may derived from a cladistic analysis. In particular, recombination can be used to assign a physical localization to a given subregion for mutations responsible for significant phenotypic effects.

Algorithms↗
PubMed1996

Changes in biologic phenotype of human immunodeficiency virus during treatment of patients with didanosine.

Progression to AIDS in patients harboring human immunodeficiency virus type-1 (HIV-1) isolates expressing a syncytium-inducing (SI) phenotype is faster than in those in whom the virus expresses a non-SI (NSI) phenotype. Zidovudine monotherapy does not appear to alter this outcome. To examine the role of didanosine (ddI) monotherapy in phenotype expression, HIV-1 isolates from 73 patients receiving ddI for up to 72 weeks were analyzed. After 12 weeks, the number of isolates expressing an NSI phenotype was 29% higher than at the start of treatment. Patients receiving high-dose ddI (375 mg twice daily) were significantly more likely to express the NSI phenotype at 12 weeks than patients who received low-dose ddI (100 mg twice daily), even after adjustment for phenotype and CD4 cell count at baseline, suggesting that ddI may be selective against the faster-replicating virus. ddI at 375 mg twice daily significantly increases the probability of an NSI phenotype over the short term in patients with advanced HIV disease.

Antiviral Agents↗
PubMed2005

Simple method to determine beta-lactam resistance phenotypes in Pseudomonas aeruginosa using the disc agar diffusion test.

BACKGROUND: Pseudomonas aeruginosa is a major opportunistic bacterial pathogen in nosocomial infections because of the increasing prevalence of resistance to many of the commonly used antibiotics. To ensure optimal efficiency of antibiotic treatment against this species, antibiotic susceptibility tests must be interpreted with caution. Most microbiologists now consider it essential to characterize the antibiotic resistance expressed by isolates. Particular resistance mechanisms may be suspected when the bacterium is resistant to several antibiotics in the same family (for example beta-lactam agents). METHODS: Using the disc agar diffusion test, a simple method was developed to distinguish between the common beta-lactam resistance phenotypes of P. aeruginosa and, consequently, the possible resistance mechanism(s). Over a period of 5 years, we analysed 6300 P. aeruginosa strains isolated from various pathological specimens collected from different wards of Cochin Port-Royal Hospital, and reference and collection strains. Each strain had the wild-type phenotype or an acquired resistance phenotype. Eight anti-pseudomonal beta-lactams (ticarcillin, cefotaxime or moxalactam, cefepime or cefpirome, imipenem, ceftazidime, aztreonam, cefsulodin and ticarcillin + clavulanic acid) were used as phenotypic markers. RESULTS: The following markers were sufficient to distinguish between the wild-type phenotype and the various acquired resistance phenotypes: beta-lactamase synthesis, reduced cell wall permeability and/or increased expression of efflux transporters (active efflux). Detection of resistance phenotypes allows 'interpretive reading' of antibiotic susceptibility tests. CONCLUSIONS: Clearly, improved interpretation of antibiotic susceptibility tests is important for a better appreciation of the effect of antimicrobial agents on bacteria such as P. aeruginosa.

Anti-Bacterial Agents↗
PubMedDate not supplied

Inheritance of a temperature-modified phenotype of the short antennae (sa) mutation in a moth, Ephestia kuehniella (Lepidoptera: Pyralidae).

The autosomal recessive mutation short antennae (sa) causes considerable shortening of antennae in male and female Mediterranean flour moths (Ephestia kuehniella Zeller). However, the sa phenotype can be suppressed by several physical factors, making sa moths indistinguishable from wild-type moths (sa(WT)). This can be done by subjecting larva and pupa to a higher temperature (25 degrees C), to lithium ions, or to an alternate electric field. The first half of pupal development was found to be the sensitive period for the sa(WT) phenotype. The sa(WT) phenotype is stable and cannot be reverted to the original sa type by physical or chemical factors. The sa(WT) phenotype is transmitted to future generations. When crossed with typical sa moths, the sa(WT) phenotype is inherited either as a dominant character if carried by males or a semidominant character if carried by females. We compared proteins of the ejaculate, accessory gland secretions, and spermatophore in sa, sa(WT), and wild-type males and found considerable differences between sperm proteins of sa(WT), sa, and wild-type males. The sa(WT) phenotype influences the mating success of males: sa(WT) males mated successfully with any females, whereas typical sa males were less successful in mating and then mainly with females of the same phenotype.

Animals↗
PubMed2005

The nutritional phenotype in the age of metabolomics.

The concept of the nutritional phenotype is proposed as a defined and integrated set of genetic, proteomic, metabolomic, functional, and behavioral factors that, when measured, form the basis for assessment of human nutritional status. The nutritional phenotype integrates the effects of diet on disease/wellness and is the quantitative indication of the paths by which genes and environment exert their effects on health. Advances in technology and in fundamental biological knowledge make it possible to define and measure the nutritional phenotype accurately in a cross section of individuals with various states of health and disease. This growing base of data and knowledge could serve as a resource for all scientific disciplines involved in human health. Nutritional sciences should be a prime mover in making key decisions that include: what environmental inputs (in addition to diet) are needed; what genes/proteins/metabolites should be measured; what end-point phenotypes should be included; and what informatics tools are available to ask nutritionally relevant questions. Nutrition should be the major discipline establishing how the elements of the nutritional phenotype vary as a function of diet. Nutritional sciences should also be instrumental in linking the elements that are responsive to diet with the functional outcomes in organisms that derive from them. As the first step in this initiative, a prioritized list of genomic, proteomic, and metabolomic as well as functional and behavioral measures that defines a practically useful subset of the nutritional phenotype for use in clinical and epidemiological investigations must be developed. From this list, analytic platforms must then be identified that are capable of delivering highly quantitative data on these endpoints. This conceptualization of a nutritional phenotype provides a concrete form and substance to the recognized future of nutritional sciences as a field addressing diet, integrated metabolism, and health.

Diet↗
PubMed2006

GenomeRNAi: a database for cell-based RNAi phenotypes.

RNA interference (RNAi) has emerged as a powerful tool to generate loss-of-function phenotypes in a variety of organisms. Combined with the sequence information of almost completely annotated genomes, RNAi technologies have opened new avenues to conduct systematic genetic screens for every annotated gene in the genome. As increasing large datasets of RNAi-induced phenotypes become available, an important challenge remains the systematic integration and annotation of functional information. Genome-wide RNAi screens have been performed both in Caenorhabditis elegans and Drosophila for a variety of phenotypes and several RNAi libraries have become available to assess phenotypes for almost every gene in the genome. These screens were performed using different types of assays from visible phenotypes to focused transcriptional readouts and provide a rich data source for functional annotation across different species. The GenomeRNAi database provides access to published RNAi phenotypes obtained from cell-based screens and maps them to their genomic locus, including possible non-specific regions. The database also gives access to sequence information of RNAi probes used in various screens. It can be searched by phenotype, by gene, by RNAi probe or by sequence and is accessible at http://rnai.dkfz.de.

Animals↗
PubMed1982

Establishment of lymphoid cell lines from persons with different P blood group phenotypes and the biosynthesis of the antigenic glycosphingolipids.

Human lymphoid cell lines were established from the peripheral lymphocytes of persons with different P blood group phenotypes by in vitro transformation with EB virus. The glycosphingolipid compositions of these cell lines were examined by TLC. The results show that P1k and P2k phenotype cells lack globoside (P antigen) and that two cell lines established from persons with the p phenotype lack both globoside and CTH (Pk antigen), while both the glycosphingolipids were detected in two cell lines established from persons with usual phenotypes (P1 or P2 phenotype). CTH synthetase activity was detected at decreased levels in two p phenotype cell lines, however, globoside synthetase activities could not be significantly detected in all the P phenotype cells.

Blood Group Antigens↗
PubMed1990

Age dependency of the lactase persistence and lactase restriction phenotypes among children in Sri Lanka and Britain.

All neonates are born with intestinal lactase activity. In most of them the intestinal lactase activity is lost during childhood (lactase restriction phenotype). In a minority of children normal intestinal lactase activity is retained (lactase persistence phenotype). In this study the progression of the lactase restriction phenotypes has been studied in 94 Sri Lankan children by oral lactose loads and 162 British children by intestinal lactase estimation (adult Sri Lankans and British predominantly belong to the lactase restriction and lactase persistence phenotypes, respectively). Lactase was present in infancy at birth in all Sri Lankan children and declined around the age of eight years, the majority (59 per cent) of the 10-15-year-olds belonging to the lactase restriction phenotype. In contrast the majority of the British children (95 per cent of all the British children studied) demonstrated the lactase persistence phenotype. The low prevalence rate of the restriction phenotype found among British children was largely contributed by children of African and Asian origin.

Age Factors↗
PubMed2006

Host Lewis phenotype-dependent Helicobacter pylori Lewis antigen expression in rhesus monkeys.

Both human and H. pylori populations are polymorphic for the expression of Lewis antigens. Using an experimental H. pylori challenge of rhesus monkeys of differing Lewis phenotypes, we aimed to determine whether H. pylori populations adapt their Lewis phenotypes to those of their hosts. After inoculation of four monkeys with a mixture of seven strains identified by RAPD-polymerase chain reaction, H. pylori Lewis expression was followed in 86 isolates obtained over 40 wk. Host Lewis(a/b) secretion status was characterized by immunological assays. Fingerprints of the predominating strain (J166) were identical in all four animals after 40 wk, but its Lewis phenotype had substantial variability in individual hosts. At 40 wk, J166 populations from two Lewis(a-b+) animals predominantly expressed Lewis(y). In contrast, J166 populations had switched to a Lewis(x) dominant phenotype in the two Lewis(a+b-) animals; a frame shift in futC, regulating conversion of Lewis(x) to Lewis(y), accounted for the phenotypic switch. The results indicate that individual cells in H. pylori populations can change Lewis phenotypes during long-term colonization of natural hosts to resemble those of their hosts, providing evidence for host selection for bacterial phenotypes.

Animals↗
PubMed1995

Major injury leads to predominance of the T helper-2 lymphocyte phenotype and diminished interleukin-12 production associated with decreased resistance to infection.

OBJECTIVE: Patients with serious traumatic injury and major burns and an animal model of burn injury were studied to determine the effect of injury on the production of cytokines typical of the T helper-2 lymphocyte phenotype as opposed to the T helper-1 phenotype and on the production of interleukin-12. SUMMARY BACKGROUND DATA: Perturbations of natural and adoptive immunity are related to the increased susceptibility to infection manifested by seriously injured and burn patients. Earlier work has shown that impaired adoptive immunity after injury is characterized by diminished production of interleukin-2 (IL-2), a product of Th lymphocytes. Exposure of naive Th cells to certain antigens and cytokines causes conversion to either the Th-1 or the Th-2 phenotype. Th-1 cells produce IL-2 and interferon-gamma (IFN-tau) and initiate cellular immunity. Th-2 cells secrete interleukin-4 (IL-4) and interleukin-10 (IL-10) and stimulate production of certain antibodies. Conversion to the Th-1 phenotype is facilitated by IL-12, and conversion to the Th-2 phenotype is promoted by IL-4. The authors believed that serious injury might cause conversion of Th cells to the Th-2 as opposed to the Th-1 phenotype rather than generalized Th suppression. METHODS: The authors studied circulating peripheral blood mononuclear cells (PBMC) from 16 major burn and 8 trauma patients on 32 occasions early after injury and from 13 age- and sex-matched healthy individuals for cytokine production after phytohemagglutinin stimulation. Also studied was a mouse model of 20% burn injury known to mimic the immune abnormalities seen in humans with burns. Splenocytes from burn mice, 10 to 12 per group, were studied after activation by concanavalin A or by the bacterial antigen Staphylococcus aureus Cowan strain I for cytokine production and cytokine messenger RNA expression as determined by reverse transcriptase polymerase chain reaction. Burn mice were compared with sham-burn controls and attention was focused on day 10 after burn injury, a time when IL-2 production and resistance to infection are highly suppressed. Finally, burn and sham-burn animals, 20 per group, were treated in vivo with IL-12 (25 ng daily for 5 days) and observed for mortality after septic challenge (cecal ligation and puncture [CLP]) performed on day 10 after injury. RESULTS: Peripheral blood mononuclear cells from burn and trauma patients produced less IFN-tau, the index cytokine of Th-1 cells, than PBMCs from healthy individuals 1 to 14 days after burn injury (SE = 77.6 +/- 16 pg/mL patients vs. 141.3 +/- 35 pg/mL controls, p < 0.05). However, production of IL-4, the index cytokine of Th-2 cells, by patient PBMCs was increased (51.0 +/- 13.0 pg/mL patients vs. 26.9 +/- 2.5 controls, p < 0.05). Splenocytes from mice 10 days after burn injury, when compared with sham-burn controls, showed diminished production of IL-2 (1.04 +/- 0.91 units/mL burns vs. 5.8 +/- 0.55 units/mL controls, p < 0.05) and IFN-tau (1.05 +/- 0.7 units/mL burns vs. 12.0 +/- 8.9 units/mL controls, p < 0.05). However, burn splenocytes produced more IL-4 (2492 +/- 157.0 pg/mL burns vs. 672.0 +/- 22.7 pg/mL controls, p < 0.01) and IL-10 (695.2 +/- 20.8 pg/mL burns vs. 567.0 +/- 16.7 pg/mL controls, p < 0.05). Splenocyte production of IL-12 was also reduced after burn (0.20 +/- 0.035 units/mL) as compared with sham burn (0.46 +/- 0.08 units/mL, p < 0.05). The reduction in IL-2, IFN-tau, and IL-12 production by burn splenocytes was reflected by a tenfold decrease in expression of their respective cytokine mRNAs. In vivo IL-12 treatment of burn animals decreased mortality from CLP on day 10 after injury from 85% to 15% (sham-burn mortality after CLP, 15%, p < 0.05) and increased splenocyte IFN-tau production to supranormal levels. CONCLUSIONS: Serious injury induced diminished production of IL-1 2 and a shift to the Th-2 phenotype with increased production of IL-4 and IL-10, cytokines known to inhibit Th-1 function. The ability of exogenous IL-12 to restore Th-1 cytokine production and resistance to infection suggests a therapeutic role for IL-12 in the immune dysfunction seen after major injury.

Adult↗
PubMed1995

Age-dependent phenotypic switching of mast cells in NGF-transgenic mice.

Effects of overexpression of nerve growth factor (NGF) on mast cell phenotype and numbers were investigated in nasal and oral mucosae and skin of 3- and 6-week-old transgenic mice in which NGF expression in epithelial basal cells was driven by the keratin-14 promoter. Mast cell phenotypes were identified by Alcian blue/safranin and berberine sulfate histochemistry. In the 3-week-old transgenic mice, NGF overexpression had no effect on phenotype except in tongue, where mast cells exhibited mixed or connective tissue phenotypes compared with the mucosal phenotype in the non-transgenic. In 6-week-old transgenic animals, NGF overexpression resulted in the mucosal phenotype in tissues which contained connective tissue or mixed mast cells in non-transgenics. Mast cell hyperplasia occurred at both ages. NGF effects on mast cell phenotype were age-dependent and involve complex microenvironmental interactions.

Age Factors↗
PubMed2001

Comparison of genotyping and phenotyping methods for determining susceptibility of HIV-1 to antiretroviral drugs.

OBJECTIVE(S): To compare antiretroviral resistance susceptibility testing of patient HIV-1 strains using genotype and phenotype methods. DESIGN: Eighteen plasma samples with viral load > 2000 HIV-1 RNA copies/ml were randomly selected for testing by both methods. Disease and treatment data were available for all patients. METHODS: Samples were analysed genotypically using a kit assay (HIV-1 Genotyping Systems, Applied Biosystems), performed by the Clinical Research Laboratory at Macfarlane Burnet Centre for Medical Research. Samples were analysed phenotypically using a rapid phenotypic assay (PhenoSenseTM HIV, ViroLogic), performed by the manufacturer. Results from both methods were interpreted using a defined protocol. Each susceptibility assay was performed and interpreted by individuals unaware of either the clinical data or the results of the other susceptibility assay. Concordance was defined categorically as either the presence of reduced susceptibility (> 2.5-fold change) in the phenotypic assay and resistance associated mutations in the genotypic assay, or the absence of these findings in both assays. RESULTS: Concordance between phenotypic and genotypic susceptibility testing was 81% for nucleoside reverse transcriptase inhibitors, 91% for non-nucleoside reverse transcriptase inhibitors and 90% for protease inhibitors. Complete concordance between phenotype and genotype for all 14 drugs evaluated was observed in three (17%) patient samples. CONCLUSIONS: Phenotypic and genotypic susceptibility appear to provide similar results. However, interpretation of genotypic results can be complicated, and both methods still require clinical validation.

Anti-HIV Agents↗
PubMed1995

A clone of the MOCH-1 glial tumor in culture: multiple phenotypes expressed under different environmental conditions.

The MOCH-1 glial cell line, which was derived from a glioblastoma taken from the brain of a MBP/c-neu transgenic mouse, was used as a model for studying the plastic nature of gliomas in culture. Fifteen MOCH-1 clones were derived and characterized under different growth conditions via Western blot analysis and immunocytochemical staining using a panel of antibodies specific for major myelin markers and glial fibrillary acidic protein. In low serum conditions, the clones resemble immature oligodendrocytes and express only immature oligodendrocyte markers. When placed in serum-free chemically defined medium (CDM), nine clones do not change their phenotypes, while five variably express myelin markers. One clone, 4C8, differentiates into mature, membrane sheet-bearing oligodendrocyte-like cells and expresses major myelin markers in amounts and distributions similar to cultured primary oligodendrocytes. Our data show that 4C8 can reversibly switch from an oligodendrocyte-like phenotype to a reactive astrocyte-like phenotype, depending upon the presence of serum and other factors in different growth media. Our data indicate that serum "pushes" 4C8 into the astrocyte-like phenotype, while serum-free CDM "pushes" 4C8 into the oligodendrocyte-like phenotype. Furthermore, a population of mixed phenotypes results when the astrocyte-like 4C8 cells are placed in serum-free CDM. To our knowledge, this is the first report to show that by altering environment, a "mixed glioma" can arise from a homogeneous population of glial tumor cells. It is therefore possible that glial tumor cells in vivo may be induced to undergo similar phenotypic changes when they are exposed to different environmental signals in the central nervous system.

Animals↗
PubMed1998

Characterization of astroglial versus oligodendroglial phenotypes in glioblastomas by means of quantitative morphonuclear variables generated by computer-assisted microscopy.

The current WHO classification places glioblastomas in the astrocytoma category. However, whether or not glioblastomas also show oligodendroglial differentiation remains a matter of controversy. This study investigates, at the morphonuclear level, the hypothesis that some glioblastomas (GBMs) may also represent the ultimate level of malignancy in the oligodendroglial lineage. Using a series of 164 GBMs, we sought to ascertain whether any of these GBMs exhibited phenotypical characteristics that were more closely related to oligodendroglial lineages than astrocytic lineages. Phenotypical features were quantitatively determined by means of the computer-assisted microscope analysis of Feulgen-stained nuclei, a process that made it possible to quantitatively describe the patterns of the cell nuclei (and, more specifically, of their chromatin) through 16 variables, and the distribution of the nuclear DNA content (DNA ploidy) through 8 variables. The phenotypical characteristics typical of astrocytic and oligodendroglial tumors were analyzed by means of Discriminant Analysis, a statistical multivariate analysis, performed on a series of 65 astrocytic and oligodendroglial tumors. This series consisted of 14 WHO grade II and 19 grade III astrocytomas and 24 WHO grade II and 8 grade III oligodendrogliomas. This multivariate analysis enabled an accurate model to be produced that distinguished between astrocytomas and oligodendrogliomas on the basis of 5 cytometry-generated variables. This model was used to characterize the phenotype of each of the 164 glioblastomas. The results show that of these 164 glioblastomas, 6 (about 3.5%) displayed phenotypes that were very similar to oligodendrogliomas, and 141 displayed phenotypes that were very similar to astrocytomas. The phenotypes of the 17 remaining GBMs were too ambiguous to be categorized as having a pure astrocytic or oligodendroglial lineage.

Adolescent↗
PubMed2000

Genetic polymorphism of CYP2D6 and CYP2C19 metabolism determined by phenotyping Israeli ethnic groups.

Genetic polymorphism of the cytochrome P450 isoenzymes CYP2D6 and CYP2C19 was determined by phenotyping four ethnic groups of the Israeli population. The groups consisted of Ethiopian subjects, Yemenite subjects, and Russian subjects representing first-generation new immigrants and an Israeli Arab group. Dextromethorphan was used as the probe for CYP2D6 activity and mephenytoin was used for CYP2C19 activity. The two drugs were administered simultaneously and urine samples were collected over a period of 8 hours. The CYP2D6 phenotype was determined from the ratio of dextromethorphan conversion to dextrorphan and the CYP2C19 phenotype from the ratio of S-mephenytoin and R-mephenytoin. The used liquid chromatographic method was able to completely separate dextrorphan and dextromethorphan. Fluorescence detection allowed dextromethorphan quantification at 1 ng/mL. Mephenytoin enantiomers were completely separated in high-performance liquid chromatography and the respective fractions were collected and analyzed using a gas chromatography/mass spectrometry system with selective ion monitoring. The prevalence of poor metabolizer phenotype of dextromethorphan (CYP2D6) in the Yemenite (0%) and Ethiopian groups (0%) was significantly different from the prevalence in the Russian (17%) and Israeli Arab (9%) groups. A significant difference was also found in the distribution of the metabolic ratio of the extensive metabolizer phenotype between the Ethiopian group and the Russian and Yemenite groups. No significant difference was found in the prevalence of poor mephenytoin metabolizer phenotype (CYP2C19) between the Yemenite (8%), Ethiopian (6%), Russian (9%), and Israeli Arab (8%) groups. No difference was observed in the distribution of metabolic ratio within the extensive metabolizer phenotype subgroups of the four ethnic groups.

Adult↗
PubMed1997

Meta-analysis of phenotype and genotype of NAT2 deficiency in Chinese populations.

Data on both the incidence of slow acetylator phenotype of probe drugs isoniazid, sulfadimidine or sulfamethazine, caffeine and dapsone in mainland or overseas Chinese, and the distribution of NAT2 genotypes and the frequency of NAT2 alleles in the Chinese populations were summarized and reanalysed using a meta-analysis method. Frequency of the slow acetylator phenotype in 3516 healthy Han Chinese gave an overall mean of approximately 19.9 +/- 4.0%, with the range of the combined data being between 15.8% and 25.5%. In addition, frequencies of the slow acetylator phenotype differ between the different minorities in Chinese populations and the range was between 3.2% and 50.6%, with a mean value of 20.6 +/- 12.9% in a total of 1842 individuals from 17 Chinese minorities. In addition, there was no significant heterogeneity in overseas Chinese between the probe drugs isoniazid and sulfadimidine or sulfamethazine (chi 2 = 5.97, df = 4; p > 0.05), and the mean value of slow acetylator phenotype incidence was 24.5% (119/485; 95% CI: 20.7-28.3%), consistent with that of the native Chinese. As expected, frequency of the slow acetylator genotypes in Chinese populations was 25.4% (112/441; 95% CI: 21.3-29.5%), which was in accordance with that of the slow acetylator phenotype in native or overseas Chinese. For all genotypes, *4/*4 (29.9%, 132/441), *4/*6A (27.4%, 121/441), *4/*7A (12%, 53/441) and *6A/*6A (11.3%, 50/441) occupied 80.6%, but *5A/*7A (0.2%, 1/441), *5A/*5A (1.1%, 5/441) and *7A/*7A (1.8%, 8/441) were not frequently found. From this report, the genotype frequencies of homozygous rapid acetylator, heterozygous rapid acetylator, and homozygous slow acetylator were found to be 0.299 (132/441), 0.447 (197/441) and 0.254 (112/441), respectively. Furthermore, both *4 (52.3%; 95% CI: 49-56%) and *6A (30.5%; 95% CI: 28-34%) were major NAT2 alleles, while *7A (11.2%; 95% CI: 9-13%) and *5A (6%; 95% CI: 4-8%) were uncommonly present. Frequency of the mutant alleles was observed at 0.477 (421/882 alleles). The *7A constituted 23.5% t(99/421) of slow acetylator alleles in Chinese populations, showing that this point mutation exists not only in Oriental or Asiatic, but also in Chinese populations. According to the Hardy-Weinberg equilibrium, in the phenotyped Chinese populations, the mean estimate of predicted allelic frequencies of the genotypes RR, Rr, and rr was 0.294, 0.496, and 0.210 for the Chinese, and the expected frequency of the deficient gene r was 0.458. By comparison, the predicted values are in complete agreement with the observed ones. In conclusion, this meta-analysis determined the accurate population frequencies of phenotype and genotype of the NAT2 genetic deficiency in healthy Chinese subjects.

Arylamine N-Acetyltransferase↗
PubMedDate not supplied

Molecular determination of X inactivation pattern correlates with phenotype in women with a structurally abnormal X chromosome.

PURPOSE: To correlate the X inactivation pattern, as determined by one or more molecular assays, with phenotype in individuals with structurally abnormal X chromosomes. METHODS: We utilized methylation analysis of androgen receptor (AR) and Fragile X (FMR1) genes and expression studies of an XIST polymorphism to assess X inactivation patterns of 28 females with structurally abnormal X chromosomes. Individuals were placed in one of three categories: (1) completely nonrandom inactivation of one X chromosome, (2) preferential or skewed inactivation of one X chromosome, or (3) random inactivation of either X chromosome. RESULTS: In 19 of 21 cases with complete (>97%) skewing of X inactivation, the phenotype was either normal, consistent with a single gene disorder, or consistent with classical Turner syndrome; two cases with completely nonrandom X inactivation had unexplained mental retardation phenotypes. In contrast, six of seven cases that did not exhibit completely nonrandom X inactivation were phenotypically abnormal. Carriers of two balanced translocations, two duplicated Xs, one deleted X, and one 45,X/46,X,r(X) presented with mental retardation and/or multiple congenital anomalies. CONCLUSION: In patients with random or skewed X inactivation, the abnormal phenotype was hypothesized to be due to functional nullisomy or disomy of X-linked genes. Based on these results, we propose that X inactivation studies should be performed on all women with structurally abnormal X chromosomes. This should aid in the understanding of abnormal phenotypes in liveborn individuals with abnormal X chromosomes and may help to predict phenotypes for prenatally detected cases in the future.

Chromosomes, Human, X↗