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PubMedDate not supplied

Sequence diversity and haplotype structure at the human CYP3A cluster.

The four members of the human CYP3A subfamily play important roles in the clearance of xenobiotics, hormones, and environmental compounds. Many SNPs at the CYP3A locus have been characterized, with several showing large allele frequency differences across populations. In addition to the effects of CYP3A SNPs on drug metabolism, recent studies have highlighted the potential for CYP3A variation in susceptibility to several common phenotypes, including hypertension and cancer. We previously showed that the CYP3A4 and CYP3A5 genes have a strong haplotype structure at varying frequencies across ethnic groups. Here, we extend our re-sequencing survey to the remaining CYP3A genes in the same cluster, CYP3A7 and CYP3A43. Our study identified a large number of SNPs in coding and conserved noncoding sequences, several of which are common. The combined data set allows us to investigate patterns of sequence variation and linkage disequilibrium at the entire CYP3A locus for use in future association studies.

Black or African American↗
PubMed2003

The future of psychiatric genetics.

Geneticists have been predicting that advances in their discipline will revolutionize the understanding of human disease and behavior. While there has been considerable progress in disorders showing simple, Mendelian patterns of inheritance, expectations have yet to be fulfilled for disorders and traits showing complex inheritance. In this article, we consider the difficulties that complex diseases pose to genetic research, discuss progress and make suggestions regarding future directions.

Animals↗
PubMed2003

Genomewide distribution of high-frequency, completely mismatching SNP haplotype pairs observed to be common across human populations.

Knowledge of human haplotype structure has important implications for strategies of disease-gene mapping and for understanding human evolutionary history. Many attributes of SNPs and haplotypes appear to exhibit highly nonrandom behavior, suggesting past operation of selection or other nonneutral forces. We report the exceptional abundance of a particular haplotype pattern in which two high-frequency haplotypes have different alleles at every SNP site (hence the name "yin yang haplotypes"). Analysis of common haplotypes in 62 random genomic loci and 85 gene coding regions in humans shows that the proportion of the genome spanned by yin yang haplotypes is 75%-85%. Population data of 28 genomic loci in Drosophila melanogaster reveal a similar pattern. The high recurrence (>/=85%) of these haplotype patterns in four distinct human populations suggests that the yin yang haplotypes are likely to predate the African diaspora. The pattern initially appeared to suggest deep population splitting or maintenance of ancient lineages by selection; however, coalescent simulation reveals that the yin yang phenomenon can be explained by strictly neutral evolution in a well-mixed population.

Algorithms↗
PubMed1996

Identification of new TAP2 alleles in gorilla: evolution of the locus within hominoids.

Transporters associated with antigen processing molecules (TAP1 and TAP2) mediate the transfer of cytosolic peptides into the lumen of the endoplasmic reticulum for association with newly synthesized class I molecules of the major histocompatibility complex. Previous molecular and functional analyses of rat and human TAP2 homologues indicated major differences in gene diversification patterns and selectivity of peptides transported. Therefore, in this study, we analyzed the alleles of the gorilla TAP2 locus to determine whether the pattern of diversification resembled that in either of those two species. Sequence analysis of the TAP2 cDNAs from gorilla Epstein-Barr virus-transformed B-cell lines revealed four alleles with a genetic distance of less than 1%. The nucleotide substitutions distinguishing the alleles are confined to the 3' half of the coding region and occur individually or within two small clusters of variability. Diversification of the locus appears to have resulted from point substitutions and recombinational events. Evolutionary-rate estimates for the TAP2 gene in gorilla and human closely approximate those observed for other hominoid genes. The amino acid polymorphisms within the gorilla molecules are distinct from those in the human homologues. The absence of ancestral polymorphisms suggests that gorilla and human TAP2 genes have not evolved in a trans-species fashion but rather have diversified since the divergence of the lineages.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2003

Expression analysis of the human adducin gene family and evidence of ADD2 beta4 multiple splicing variants.

Adducin is a cytoskeleton heterodimeric protein. Its subunits are encoded by three related genes (ADD1, ADD2, and ADD3) which show alternative spliced variants. Adducin polymorphisms are involved in blood pressure regulation in humans and rats. We have analyzed mRNA distribution of ADD gene family in human tissues and cells with Real-Time TaqMan RT-PCR. Whereas ADD1 is ubiquitously distributed, ADD3 is more expressed in kidney medulla and cortex than in fetal kidney, while in adult liver it is less abundant than in fetal liver. ADD2 beta1 and beta4 variants show the same pattern of distribution with the highest expression in brain, fetal liver, and kidney. Conventional RT-PCR identified new beta4 variants. Beta4a is characterized by an in-frame insertion of 21 nucleotides upstream exon 15 predicting a 7 amino acids longer protein with a similar C-terminus region. It is coexpressed with beta1 and beta4 in several tissues. Fetal kidney shows further beta4b, beta4c and beta4d variants containing internal exon deletions that enormously modify the predicted NH(2) and central regions. Our findings could help one to understand the functional role of adducin variants in specific tissues and cells.

Amino Acid Sequence↗
PubMed2005

Haplotypes in the gene encoding protein kinase c-beta (PRKCB1) on chromosome 16 are associated with autism.

Autism is a developmental disorder characterized by impairments in social interaction and communication associated with repetitive patterns of interest or behavior. Autism is highly influenced by genetic factors. Genome-wide linkage and candidate gene association approaches have been used to try and identify autism genes. A few loci have repeatedly been reported linked to autism. Several groups reported evidence for linkage to a region on chromosome 16p. We have applied a direct physical identity-by-descent (IBD) mapping approach to perform a high-density (0.85 megabases) genome-wide linkage scan in 116 families from the AGRE collection. Our results confirm linkage to a region on chromosome 16p with autism. High-resolution single-nucleotide polymorphism (SNP) genotyping and analysis of this region show that haplotypes in the protein kinase c-beta gene are strongly associated with autism. An independent replication of the association in a second set of 167 trio families with autism confirmed our initial findings. Overall, our data provide evidence that the PRKCB1 gene on chromosome 16p may be involved in the etiology of autism.

Autistic Disorder↗
PubMed1999

Positive selection drives the evolution of the Acp29AB accessory gland protein in Drosophila.

Nucleotide sequence variation at the Acp29AB gene region has been surveyed in Drosophila melanogaster from Spain (12 lines), Ivory Coast (14 lines), and Malawi (13 lines) and in one line of D. simulans. The approximately 1.7-kb region studied encompasses the Acp29AB gene that codes for a male accessory gland protein and its flanking regions. Seventy-seven nucleotide and 8 length polymorphisms were detected. Nonsynonymous polymorphism was an order of magnitude lower than synonymous polymorphism, but still high relative to other non-sex-related genes. In D. melanogaster variation at this region revealed no major genetic differentiation between East and West African populations, while differentiation was highly significant between the European and the two African populations. Comparison of polymorphism and divergence at synonymous and nonsynonymous sites showed an excess of fixed nonsynonymous changes, which indicates that the evolution of the Acp29AB protein has been driven by directional selection at least after the split of the D. melanogaster and D. simulans lineages. The pattern of variation in extant populations of D. melanogaster favors a scenario where the fixation of advantageous replacement substitutions occurred in the early stages of speciation and balancing selection is maintaining variation in this species.

Amino Acid Sequence↗
PubMed2004

Molecular study of vancomycin-resistant enterococci isolated from humans and from food in a cattle-rearing area of France.

OBJECTIVES: Study possible links between vancomycin-resistant enterococci strains isolated from human stool samples and from pork or poultry food products. METHODS: One hundred and eleven vancomycin-resistant enterococci strains (15 VanA and 96 VanC) were isolated from human stool samples and from pork or poultry food products. Characterization of the Tn1546-like element of the 15 VanA strains was realized by restriction analysis of PCR products and polymorphism study. The 96 strains of VanC phenotype (75 Enterococcus gallinarum and 21 Enterococcus casseliflavus) were analysed by pulsed-field gel electrophoresis (PFGE). RESULTS: In the study described here, polymorphism of the Tn1546-like element enabled the establishment of five groups. Groups III, IV and V were found only in human strains. Groups I and II were found to occur in strains isolated from humans and from food, suggesting a possible transfer of the Tn1546-like element. The isolates from Group I harboured the whole Tn1546 element. In Group II, the five strains possessed a novel Tn1546-like element, characterized by a single-nucleotide difference in the vanX gene and a deletion upstream from the nucleotide 164. Analysis by PFGE of the 75 E. gallinarum strains revealed 20 different patterns. One pattern was shared by isolates from pork food and human samples. None of the 21 E. casseliflavus strains tested was found to share similar PFGE patterns. CONCLUSIONS: Results tend to support the possible transfer of the Tn1546-like element between strains of VanA phenotype. Concerning VanC phenotype strains, the transfer was not demonstrated.

Agriculture↗
PubMed2005

In silico simulation of fingerprinting techniques based on double endonuclease digestion of genomic DNA.

UNLABELLED: We have developed an online generic tool for simulation of fingerprinting techniques based on the double endonuclease digestion of DNA. This tool allows modelling and modifications of already existing techniques, as well as new theoretical approaches not yet tried in the lab. It allows the use of any combination of recognition patterns and discrimination of end types yielded by restriction with non palindromic recognition sizes. Re-creation of experimental conditions in silico saves time and reduces laboratory costs. This tool allows simulation of Amplified Fragment Length Polymorphism (AFLP-PCR), Subtracted Restriction Fingerprinting (SRF), and additional novel fingerprinting techniques. Simulation may be performed against custom sequences uploaded to the server, or against all sequenced bacterial genomes. Different endonuclease types may be selected from a list, or a recognition sequence may be introduced in the form. After double digestion of DNA, four fragment types are yielded, and the program allows their customised selection. Selective nucleotides may be used in the experiment. Scripts for specific simulation of AFLP-PCR and SRF techniques are available, and both include a suggestion tool for the selection of endonucleases. This is the first program available for the simulation of SRF fingerprinting. AVAILABILITY: This free online tool is available at http://www.in-silico.com/DDF/.

DNA↗
PubMed2004

[Analysis of the angiotensinogen gene T174M polymorphism in populations of the Volga-Ural region].

The method of polymerase chain reaction was used to analyze T174M polymorphism at the angiotensinogen (AGT) gene in a number of populations of the Volga-Ural region, belonging to Finno-Ugric (Komi-Permyaks, Maris, Mordovians, and Udmurts), Turkic (Chuvashes, Tatars, and Bashkirs), and Eastern-Slavic (Russians) ethnic groups. Population-specific patterns of the polymorphic alleles and genotypes frequency distribution were established. Comparison of the results with the literature data on the AGT gene polymorphism in different world populations provided identification of specific trends in the changes of genotype frequency of the AGT gene depending on the ethnicity of the populations.

Angiotensinogen↗
PubMed2003

Maternal alleles acquiring paternal methylation patterns in biparental complete hydatidiform moles.

We previously mapped a maternal locus responsible for biparental complete hydatidiform moles (BiCHMs) to 19q13.4. The two index patients had a total of 14 molar pregnancies, eight abortions at various developmental stages, and one 16-year-old healthy offspring. We suggested that the defective gene deregulates the expression of imprinted genes. Here, we report the methylation status of four imprinted genes in two BiCHMs from the two sisters, the 16-year-old normal offspring, and two sporadic BiCHMs from unrelated patients. Using two bisulfite-based methods, we demonstrate a general trend of abnormal hypomethylation at the paternally expressed genes, PEG3 and SNRPN, and hypermethylation at the maternally expressed genes, NESP55 and H19, in two to four BiCHMs. Using single nucleotide polymorphisms, we provide the first evidence that SNRPN, NESP55 and H19 are abnormally methylated on the maternal alleles in BiCHMs. We show, in the BiCHMs from the two sisters, that the abnormally methylated H19 allele is inherited from either the maternal grandmother or the maternal grandfather. These data suggest that the abnormal methylation in BiCHMs is not due to an error in erasing the parental imprinting marks but rather in the re-establishment of the new maternal marks during oogenesis or their postzygotic maintenance. The defective 19q13.4 locus may have led to the development of variable degrees of 'faulty' paternal marks on the maternal chromosomes.

Adolescent↗
PubMed2000

Use of denaturing gradient gel electrophoresis for human polyomavirus JC sequence analysis.

Five genotypes of human polyomavirus JC (JCV) have been detected so far by nucleotide sequencing and by restriction fragment length polymorphism analysis. These genotypes are the result of geographically based virus evolution. However, interesting aspects of genotyping could involve both pathogenetic and diagnostic aspects. The product from amplification of JCV sequences, found in urine from 12 healthy individuals from different countries, have been analysed by denaturing gradient gel electrophoresis (DGGE) and by nucleotide sequencing. The aim of this study was to assess if the DGGE analysis could be used to study the variability of the JCV genome. The target sequence of this study was 233 bp long, within the gene coding for the VP1, known to contain several type-determining sites. Four DGGE patterns have been observed among our strains. Five strains, from African individuals, were of type 3 and exhibited the same electrophoretic pattern, clearly distinguishable from that of the type 1 strains detected in the urine from 6 European individuals. Five type 1 strains shared a similar DGGE pattern, slightly different from that of the sixth. A different pattern characterised as a type 2 strain was detected in the urine from a Peruvian individual. These results suggest that DGGE analysis could be used as a screening assay for choosing strains for nucleotide sequencing. The analysis of a fragment larger than the one used in this study could allow the identification of more types and subtypes.

Adolescent↗
PubMed2000

High-throughput detection of unknown mutations by using multiplexed capillary electrophoresis with poly(vinylpyrrolidone) solution.

Single-nucleotide polymorphism detection has been the focus of much attention recently. Although many methods have been reported, low-cost, high-throughput, and high-detection-rate methods are still in demand. We present a fast and reliable mutation detection scheme based on temperature-gradient capillary electrophoresis. A large temperature gradient (10 degrees C) was applied with a precision of 0.02 degrees C and a temperature ramp of 0.7 degrees C/min. Multiple unlabeled samples from PCR were injected and analyzed. Ethidium bromide was used as the intercalating dye for laser-induced fluorescence detection. Mutations can be recognized by comparing the electrophoretic patterns of the heteroduplex with that of a homoduplex reference without prior knowledge of the exact type of mutation present. Mutations in all five test samples were successfully detected with high confidence. This scheme is demonstrated in 96-capillary array electrophoresis for screening single-point polymorphism in large numbers of samples prior to full sequencing of only the positive samples to identify the nature of the mutation.

DNA↗
PubMed1990

HLA-DQ beta sequence polymorphism and genetic susceptibility to IDDM.

The analysis of HLA-DQ beta nucleotide sequence polymorphism in insulin-dependent diabetes mellitus (IDDM) patients and control subjects suggests a role for the DQ beta-chain in genetic susceptibility. Sequence determination and oligonucleotide hybridization was carried out on enzymatically amplified DNA from various HLA-DR-typed individuals, including the rare class of DR2+ patients. In the analysis of DQ beta variation in DR4, DRw6, and DR2 haplotypes, a correlation was observed between the presence of the negatively charged residue Asp at position 57 and low susceptibility and the presence of an Ala (DR4), Val (DRw6), or Ser (DR2) and higher susceptibility. However, important exceptions to this pattern have been identified in the analysis of heterozygous DR1/4 IDDM patients. In these individuals, susceptibility appears to correlate with specific DR beta l alleles (Dw4) on the DR4 haplotype, rather than with the DQ beta allele (DQB3.2) that contains Ala at position 57. The DQ beta alleles found in some Chinese IDDM patients also proved discordant with the position-57 correlations. Thus, although there is a general correlation between the residue at position 57 of the DQ beta-chain and IDDM susceptibility, these data do not support the notion that Asp 57 confers complete resistance or protection to IDDM. In general, these results suggest that IDDM susceptibility is conferred by specific combinations of DQ beta and DR beta sequences.

Alleles↗
PubMed1989

A study of the relatedness of Mycobacterium leprae isolates using restriction fragment length polymorphism analysis.

The inability to cultivate Mycobacterium leprae in vitro has severely hampered comprehensive phenotypic analysis of individual isolates, leaving unanswered the question of the relatedness of these isolates. Since the nucleotide sequence of a bacterial chromosome is its "genetic fingerprint", we have employed the use of restriction fragment length polymorphism (RFLP) analysis of chromosomal DNA of M. leprae isolates to assess the relatedness among these isolates. DNA of M. leprae was harvested from infected armadillo tissue originally inoculated with bacilli from lepromatous lesions of human patients from geographically distinct regions of the world. Restriction endonuclease (EcoRI, PstI, and PvuI) digests of chromosomal DNA were analysed using DNA probes encoding all or part of the 28-kDa, 65-kDa and 70-kDa proteins of M. leprae. Comparison of the resultant autoradiographs showed that the RFLP patterns were all identical indicating that these isolates contained no polymorphism with respect to the restriction endonuclease sites analysed. These results indicated that the M. leprae isolates tested in this study were indistinguishable at the genotypic level, suggesting the possibility of homogeneity among members of the species, M. leprae.

Animals↗
PubMed2004

Sequence polymorphism of the predicted human metapneumovirus G glycoprotein.

The putative G glycoprotein genes of 25 human metapneumovirus (hMPV) field isolates obtained during five consecutive epidemic seasons (1997 to 2002) were sequenced. Sequence alignments identified two major genetic groups, designated groups 1 and 2, and two minor genetic clusters within each major group, designated subgroups A and B. Extensive nucleotide and deduced amino acid sequence variability was observed, consisting of high rates of nucleotide substitutions, use of alternative transcription-termination codons and insertions that retained the reading frame. Deduced amino acid sequences showed the greatest variability, with most differences located in the extracellular domain of the protein: nucleotide and amino acid sequence identities for the entire open reading frame ranged from 52 to 58 % and 31 to 35 %, respectively, between the two major groups. Like the closely related avian pneumovirus and human and bovine respiratory syncytial viruses, the predicted G protein of hMPV shared the basic features of a type II mucin-like glycosylated protein. However, differences from these related viruses were also observed, e.g. lack of conserved cysteine clusters as seen in human respiratory syncytial virus and avian pneumovirus. The displacement of genetic groups of hMPV observed during the study period suggests that potential antigenic differences in the G glycoprotein, which have evolved in response to immune-mediated pressure, may influence the circulation patterns of hMPV strains.

Adolescent↗
PubMed2005

[Diabetes and mitochondrial cytopathies: pathological studies].

Maternal diabetes associated with neural deafness is designated as MIDD (maternal inherited diabetes and deafness); it is linked to a A3243G tRNA leucine gene mutation. The disease course is progressive and involvement of other systems is frequent. In most cases, macular pattern dystrophy is present. Muscular lesions are characteristic of mitochondrial myopathies. Mitochondrial abnormalities have also been observed in pancreas, heart, kidney, smooth muscle of the digestive tract with variable heteroplasmy levels. MIDD may present as a single syndrome or is part of MELAS or Kearns-Sayre syndrome.

Deafness↗
PubMed2006

DRD4 and DAT1 polymorphisms modulate human gamma band responses.

Gamma oscillations (30-80 Hz) have been demonstrated to be important for perceptual and cognitive processes. Animal and in vitro studies have revealed possible underlying generation mechanisms of the gamma rhythm. However, little is known about the neurochemical modulation of these oscillations during human cognition. Schizophrenia and Attention Deficit Hyperactivity Disorder, which lead to failure of attentional modulation and working memory, introduce significant changes in gamma responses and have significant associations with genetic polymorphisms of dopamine receptor D4 (DRD4), dopamine transporter (DAT), and catechol-O-methyltransferase (COMT). Therefore, the presence of direct relations between these polymorphisms and gamma oscillations was investigated in human subjects using an auditory target detection paradigm. The 7-repeat isoform of the DRD4 polymorphism that produces a subsensitive variant of the D4 receptor enhanced the auditory evoked and induced gamma responses to both standard and target stimuli. The 10/10 genotype of the DAT1 polymorphism, which reduces DAT expression and hence yields an increase in extracellular dopamine, specifically enhanced evoked gamma responses to target stimuli. The COMT polymorphism did not significantly change gamma responses. It seems plausible to assume that the modulation pattern of the evoked gamma response by DRD4 polymorphism relates to reduced inhibition via the D4 receptor, whereas the DAT1 effect is related to the target detection mechanism probably mediated by the D1 receptor.

Adaptation, Physiological↗