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PubMed2005

Evidence for a relationship between genetic variants at the brain-derived neurotrophic factor (BDNF) locus and major depression.

BACKGROUND: Previous genetic studies investigating a possible involvement of variations at the brain derived neurotrophic factor (BDNF) gene locus in major depressive disorder (MDD), bipolar affective disorder (BPAD), and schizophrenia have provided inconsistent results. METHODS: We performed single-marker and haplotype analyses using three BDNF polymorphisms in 2,376 individuals (465 MDD, 281 BPAD, 533 schizophrenia, and 1,097 control subjects). RESULTS: Single-marker analysis did not provide strong evidence for association. Haplotype analysis of marker combination rs988748-(GT)n-rs6265 produced nominally significant associations for all investigated phenotypes (global p values: MDD p = .00006, BPAD p = .0057, schizophrenia p = .016). Association with MDD was the most robust finding and could be replicated in a second German sample of MDD patients and control subjects (p = .0092, uncorrected). Stratification of our schizophrenia sample according to the presence or absence of a lifetime history of depressive symptoms showed that our finding in schizophrenia might be attributable mainly to the presence of depressive symptoms. CONCLUSIONS: Association studies of genetic variants of the BDNF gene with various psychiatric disorders have been published with reports of associations and nonreplications. Our findings suggest that BDNF may be a susceptibility gene for MDD and schizophrenia-in particular, in a subgroup of patients with schizophrenia with a lifetime history of depressive symptoms.

Adult↗
PubMed1986

Biochemical genetic variants in mice selectively bred for sensitivity or resistance to ethanol-induced sedation.

The distribution of biochemical genetic variants was examined among eight inbred strains of mice, which served as contributors to a heterogeneous stock of mice (HS), and in short-sleep (SS) and long-sleep (LS) mice, selectively bred from the HS stock for differential ethanol sensitivity. Fifteen loci for enzymes of alcohol and aldehyde metabolism, as well as 12 other biochemical loci, were investigated. Thirteen of these loci exhibited allelic variation between strains, of which six were separately fixed in the SS and LS mice. Comparisons of genetic similarity coefficients, based upon the distributions of allelic variants for the loci examined, with behavioural sensitivities (sleep-time) to an acute dose of ethanol for the inbred and selected strains of mice, indicated no correlations between these data. This suggests that this collective group of loci are not useful indicators of the genes selectively bred in the SS and LS strains, which are responsible for the differential sensitivities to acute doses of ethanol.

Alcohol Dehydrogenase↗
PubMed1990

Mutations in genetic variants of human serum albumin found in Italy.

A long-term electrophoretic survey of genetic variants of serum albumin has identified an alloalbumin in 589 unrelated individuals in Italy. The alloalbumins were classified electrophoretically into 17 types. The number of unrelated carriers for each type varied from 1 for several variants reported here to 103 for albumin B. The structural change in 8 of these types has previously been determined, and the amino acid substitutions in 3 additional types are reported here. Albumin Varese has a substitution, -2 arginine to histidine (-2 Arg----His), the same as that reported for proalbumin Lille; albumin Torino has the substitution 60 Glu----Lys; and albumin Vibo Valentia has the substitution 82 Glu----Lys. The ability to distinguish so many alloalbumin types by electrophoresis at several pH values indicates that similar substitutions at different sites produce variants with different electrophoretic mobilities. Except for chain terminations in two Italian variants, all the mutations thus far determined for alloalbumins are attributable to a single-base change in the structural gene, and there is a preponderance of transitions and purine mutations. Seven alloalbumins for which the structural change has been established have been ascertained only in Italy. Several of these are clustered in specific geographic regions of Italy, which suggests an origin through a founder individual. Other variants that occur worldwide are nonetheless clustered in geographic regions within Italy. In these cases an independent mutation probably occurred at a hypermutable site such as a CpG dinucleotide.

Amino Acid Sequence↗
PubMed2005

Genetic variants of angiotensin converting enzyme and methylenetetrahydrofolate reductase may act in combination to increase migraine susceptibility.

Migraine, with and without aura (MA and MO), is a prevalent and complex neurovascular disorder that is likely to be influenced by multiple genes some of which may be capable of causing vascular changes leading to disease onset. This study was conducted to determine whether the ACE I/D gene variant is involved in migraine risk and whether this variant might act in combination with the previously implicated MTHFR C677T genetic variant in 270 migraine cases and 270 matched controls. Statistical analysis of the ACE I/D variant indicated no significant difference in allele or genotype frequencies (P > 0.05). However, grouping of genotypes showed a modest, yet significant, over-representation of the DD/ID genotype in the migraine group (88%) compared to controls (81%) (OR of 1.64, 95% CI: 1.00-2.69, P = 0.048). Multivariate analysis, including genotype data for the MTHFR C677T, provided evidence that the MTHFR (TT) and ACE (ID/DD) genotypes act in combination to increase migraine susceptibility (OR = 2.18, 95% CI: 1.15-4.16, P = 0.018). This effect was greatest for the MA subtype where the genotype combination corresponded to an OR of 2.89 (95% CI:1.47-5.72, P = 0.002). In Caucasians, the ACE D allele confers a weak independent risk to migraine susceptibility and also appears to act in combination with the C677T variant in the MTHFR gene to confer a stronger influence on the disease.

Adult↗
PubMedDate not supplied

Impact of a genetic variant in CYP3A4 on risk and clinical presentation of prostate cancer among white and African-American men.

Genes involved in androgen metabolism are strong candidates for having an important role in the pathogenesis of prostate cancer. CYP3A4, a protein in the cytochrome P-450 supergene family, facilitates the oxidative deactivation of testosterone. In previous studies, patients with the G variant of a genetic polymorphism in CYP3A4 had prostate cancers with clinically aggressive characteristics at diagnosis. The association was strongest among elderly men. We investigated whether the CYP3A4 variant was linked with the diagnosis or clinical presentation of prostate cancer in a case control study of a multiethnic urban population. Biologic specimens were genotyped for CYP3A4, and analyzed for the impact of this genotype on risk and tumor characteristics at presentation, controlling for the effect of several cofactors. The CYP3A4 variant was more common among African-Americans than among white men. Race-stratified analyses revealed little association between the CYP3A4 variant and prostate cancer risk among white men but were limited by the small number of white men with the CYP3A4 variant. Of African-American men, while the variant G allele was not associated with prostate cancer that had less aggressive characteristics, it was associated with risk of aggressive prostate cancer when men with the AG genotype (odds ratio = 9.3, 95% confidence interval 1.3-411) or GG genotype (odds ratio = 11.9 95% confidence interval 1.6-533) were compared with those with the AA genotype. The association between the CYP3A4 genotype and aggressive prostate cancer in African-American men is consistent with findings of other studies.

Black or African American↗
PubMed2021

High-impact rare genetic variants in severe schizophrenia.

Extreme phenotype sequencing has led to the identification of high-impact rare genetic variants for many complex disorders but has not been applied to studies of severe schizophrenia. We sequenced 112 individuals with severe, extremely treatment-resistant schizophrenia, 218 individuals with typical schizophrenia, and 4,929 controls. We compared the burden of rare, damaging missense and loss-of-function variants between severe, extremely treatment-resistant schizophrenia, typical schizophrenia, and controls across mutation intolerant genes. Individuals with severe, extremely treatment-resistant schizophrenia had a high burden of rare loss-of-function (odds ratio, 1.91; 95% CI, 1.39 to 2.63; P = 7.8 × 10-5) and damaging missense variants in intolerant genes (odds ratio, 2.90; 95% CI, 2.02 to 4.15; P = 3.2 × 10-9). A total of 48.2% of individuals with severe, extremely treatment-resistant schizophrenia carried at least one rare, damaging missense or loss-of-function variant in intolerant genes compared to 29.8% of typical schizophrenia individuals (odds ratio, 2.18; 95% CI, 1.33 to 3.60; P = 1.6 × 10-3) and 25.4% of controls (odds ratio, 2.74; 95% CI, 1.85 to 4.06; P = 2.9 × 10-7). Restricting to genes previously associated with schizophrenia risk strengthened the enrichment with 8.9% of individuals with severe, extremely treatment-resistant schizophrenia carrying a damaging missense or loss-of-function variant compared to 2.3% of typical schizophrenia (odds ratio, 5.48; 95% CI, 1.52 to 19.74; P = 0.02) and 1.6% of controls (odds ratio, 5.82; 95% CI, 3.00 to 11.28; P = 2.6 × 10-8). These results demonstrate the power of extreme phenotype case selection in psychiatric genetics and an approach to augment schizophrenia gene discovery efforts.

Aged↗
PubMed2003

Ataxia and male sterility (AMS) mouse. A new genetic variant exhibiting degeneration and loss of cerebellar Purkinje cells and spermatic cells.

We describe a novel genetic variant mouse that exhibited ataxia and male sterility, named the AMS mouse. It arose in autoimmune-prone MRL/lpr strain and putative ams mutation showed an autosomal recessive inheritance pattern. Clinical symptoms were first discernible at approximately 21 days of age and consisting of subtle sway of the trunk followed by failure to maintain still posture and appearance of abnormal walk, but no further worsening was noted with advancement of age. The abnormal motor coordination was ascribed to almost complete loss of Purkinje cells of the cerebellum. The cell loss in the Purkinje cell layer began before onset of ataxia and rapidly progressed towards near-complete loss by 6 weeks of age. Another symptom was male sterility due to severe oligozoospermia associated with cellular degeneration during spermatic differentiation in the seminiferous tubules. Thus, the effects of the genetic variation were apparent in two different organs after the development of their basic histological structures, and degeneration and loss of particular cell types in these two tissues produced overt clinical symptoms. Genetic pleiotropism, provided that the nature of genetic variation is of a single gene mutation, is discussed.

Animals↗
PubMed1980

Differences in elimination rates of methylmercury between two genetic variant strains of mice.

This study demonstrates an intraspecies difference in elimination of methylmercury between two genetic variant strains of mice. Following a single non-toxic dose of 203Hg labeled methylmercury (0.5 mg Hg/kg i.p.), the half-time of 203Hg elimination in the CBA/J inbred strain was 7.4 days compared to 3.0 days in the CFW strain. The fecal excretion rate of 203 Hg was the same for both strains, whereas urinary excretion rate was 5-fold higher in the CFW strain than in the CBA/J strain. The higher excretion rate in the CFW strain accounted for significant lowering of mercury concentrations in terminal tissue samples. The mercury burden in the pelt relative to the terminal body burden was similar for the two strains suggesting that elimination via the fur plays no significant role in the difference in overall excretion rate. Intraspecies differences in methylmercury elimination has direct implications for human exposures where a wide variation in kinetics has been observed. This animal model will be useful in studying the mechanism of urinary excretion of methylmercury and provide insight into more effective antidotal procedures.

Animals↗
PubMed1996

Genetic variant near cytosolic phospholipase A2 associated with schizophrenia.

Two studies were undertaken to determine a possible genetic basis for alterations in phospholipid metabolism in schizophrenia. Initial results demonstrated an association in 65 schizophrenics compared with a matched normal control population. A follow-up haplotype relative risk study of 44 triads (mother, father, affected offspring), confirmed the results seen in the association study. Results suggest that a genetic variant near the promotor region of the gene for cytosolic phospholipase A2, the rate-limiting enzyme in the synthesis of prostaglandins from arachindonic acid, is associated with schizophrenia.

Female↗
PubMed1984

Genetic variants found in plasma alpha-amylase and erythrocyte carbonic anhydrase in the musk shrew (Suncus murinus).

Genetic variants of plasma alpha-amylase and erythrocyte carbonic anhydrase in the musk shrew (Suncus murinus) were found by electrophoreses using cellulose acetate plates. It was demonstrated that phenotypic differences of alpha-amylase are controlled by two codominant alleles (Amy-1a and Amy-1b) at a single autosomal locus (Amy-1). The segregation data of the carbonic anhydrase phenotypes in the progeny supported the genetic theory of two codominant alleles (Car-1a and Car-1b) at a single autosomal locus (Car-1). The data suggested that there was no close linkage between the two loci, Amy-1 and Car-1. The Car-1 locus was fixed with one of the two alleles in each of the four lines, i.e. Nag, Oki , Tar and Jak originating from wild animals captured in Nagasaki and Naha and Tarama Island, Okinawa, Japan, and in Jakarta, Indonesia, respectively. Oki and Tar lines still showed segregation of the two alleles at the Amy-1 locus.

Animals↗
PubMed2026

Identifying causal genetic variants for high-altitude adaptation through blood eQTL analysis in plateau populations.

A substantial number of genetic variants have been associated with high-altitude adaptation (HAA), yet most of them are located in non-coding genomic regions, leaving their specific functions and underlying mechanisms largely unknown. In this study, we analyze whole-genome and transcriptome sequencing data from a self-established cohort comprising 61 native highlanders (NHs) and 164 acclimatized newcomers (ANs), identifying 6,586 cis- and 34,203 trans-expression quantitative trait loci (eQTLs), along with 130 cell type-specific eQTLs. By further combining these data with a large East Asia (~30% Tibetan) genome-wide association study (GWAS) cohort, we employ colocalization and causal inference analyses to prioritize 85 cis-eQTLs associated with HAA and identify several novel candidate causal genes, including EXOC8, which is experimentally confirmed to regulate erythroid differentiation. Additionally, network analysis of these causal genes uncovers multiple regulatory pathways, mainly involving energy metabolism, autophagy, ubiquitination and inflammation. Our study offers a comprehensive eQTL map and reveals causal chains of "variant-gene-phenotype" for HAA-related traits, which provides new insights into potential regulatory mechanisms and targets for prevention and treatment of altitude sickness.

Quantitative Trait Loci↗
PubMedDate not supplied

A rapid microbore HPLC method for determination of primary structure of beta-lactoglobulin genetic variants.

A rapid method for determination of the primary structures for beta-lactoglobulin (beta-LG) genetic variants is described. This included rapid microbore HPLC, amino acid analyses, and wherever necessary, direct peptide sequencing. Two novel variants of beta-LG have been identified, bovine beta-LG W and ovine beta-LG C. The proteins were oxidized, digested with trypsin and separated using RP-HPLC. All peptides were recovered in a single run. Peptides with amino acid exchanges were identified by retention time and subjected to amino acid and sequence analyses. Ovine beta-LG C differs from the ovine beta-LG A variant by a single amino acid exchange at position 148 where Arg is replaced by Gln. Bovine beta-LG W differs from bovine beta-LG B by having Leu at position 56 instead of Ile. The method described here is reliable and can be used for mapping of 20-1000 pmol of material.

Amino Acid Sequence↗
PubMed1991

Inflammation-induced changes in expression and glycosylation of genetic variants of alpha 1-acid glycoprotein. Studies with human sera, primary cultures of human hepatocytes and transgenic mice.

The relative occurrence of genetic variants of human alpha 1-acid glycoprotein (AGP) in relation to changes in glycosylation was studied in sera of patients with burn injury, media of cytokine-treated primary cultures of human hepatocytes and Hep 3B cells, and sera of transgenic mice expressing the human AGP-A gene. It is concluded (i) that the glycosylation of AGP was not dependent on its genetic expression and (ii) that both the variants determined by the AGP-A gene as well as by the AGP-B/B' genes are increased after inflammation or treatment with interleukins 1 and 6.

Animals↗
PubMed2003

Differences in clinical manifestations and hematological and serological responses after experimental infection with genetic variants of Anaplasma phagocytophilum in sheep.

Five-month-old lambs were experimentally infected with two 16S rRNA genetic variants of Anaplasma phagocytophilum, variants 1 (GenBank accession no. M73220) and 2 (GenBank accession no. AF336220). Additional sequencing of the groESL heat shock operon gene indicated that these variants differ in three nucleotides at positions 782, 824, and 890. The variants were obtained by blood sampling of A. phagocytophilum-infected lambs from one sheep flock in Norway and were stored at -70 degrees C with 10% dimethyl sulfoxide as a cryoprotectant before being inoculated intravenously into susceptible lambs. The infectious blood contained, per ml, approximately 0.5 x 10(6) neutrophils infected with either of the variants. Six weeks after the primary inoculation, the lambs were challenged with the same infectious dose of the heterologous variant. The results of the study indicate a marked difference in clinical manifestation, neutropenia, antibody response, and cross-protection after experimental infection with the two variants of A. phagocytophilum.

Anaplasma phagocytophilum↗
PubMed2005

Genetic variants of Complex I in multiple sclerosis.

HYPOTHESIS: A mitochondrial mechanism contributes to neurodegeneration in multiple sclerosis (MS). Genetic variants of Complex I genes may influence the nature of tissue response to inflammation in the central nervous system (CNS). BACKGROUND: Complex I is encoded by seven mitochondrial and 38 nuclear genes. Many of the nuclear genes colocalize with regions where full genome scans detected linkage in MS. Previous studies revealed an association between variants of mitochondrial (mt)DNA encoded subunits of Complex I and MS. Biochemical studies suggested a functional involvement of Complex I in the degenerative processes downstream to inflammatory injury in the CNS. METHODS: Patients with all MS phenotypes were included. DNA specimens of affected sib pair, trio and multiplex families were studied. Single nucleotide polymorphisms (SNP) were determined by using the Taqman assay. The association of MS with nuclear DNA encoded alleles and haplotypes of Complex I was tested by the pedigree disequilibrium test (PDT) and by the transmit program in the families. Haplotypes were further investigated by using ldmax (GOLD). The association of mtDNA encoded variants with MS was tested by the Fisher's Exact Test. RESULTS: The previously identified MS-associated mtDNA variants and haplotypes were not increased in mothers as compared to fathers in these families. However, an association of all clinical phenotypes with haplotypes within NDUFS5 (1p34.2-p33), NDUFS7 (19p13) and NDUFA7 (19p13) was detected. The inclusion of families with primary progressive (PP)-MS phenotype did not modify the outcome and, as a subgroup alone, did not have a sufficient size to draw conclusion regarding phenotype specific associations. CONCLUSIONS: SNP haplotypes within Complex I genes are associated with MS. Further studies are needed to refine the identification of disease relevant variants nearby or within these haplotypes. Molecular and functional properties of Complex I subunits may offer novel explanations to better understand the relationship between inflammation and neurodegeneration.

Alleles↗
PubMed2004

Drosophila genetic variants that change cell size and rate of proliferation affect cell communication and hence patterning.

We explore in this paper the role of genetic variants that affect cell size and proliferation in the determination of organ size. We use genetic mosaics of loss or gain of function in six different loci, which promotes smaller or larger than normal cells, associated to either smaller or larger than normal territories. These variants have autonomous effects on patterning and growth in mutant territories. However, there is no correlation between cell size or rate of proliferation on the size of the mutant territory. In addition, these mosaics show non-autonomous effects on surrounding wildtype cells, consisting always in a reduction in number of non-mutant cells. In all mutant conditions the final size (and shape) of the wing is different than normal. The phenotypes of the same variants include higher density of chaetae in the notum. These autonomous and non-autonomous effects suggest that the control of size in the wing is the result of local cell communication defining canonic distances between cells in a positional-values landscape.

Animals↗
PubMed2005

Large-scale identification and characterization of genetic variants in asthma candidate genes.

Asthma is a chronic inflammatory disorder of the airways, and a number of genetic loci are associated with the disease. Candidate gene association studies have been regarded as effective tools to study complex traits. Knowledge of the sequence variation and structure of the candidate genes is required for association studies. Thus, we investigated the genetic variants of 32 asthma candidate genes selected by colocalization of positional and functional candidate genes. We screened all exons and promoter regions of those genes using 12 healthy individuals and 12 asthma patients and identified a total of 418 single nucleotide polymorphisms (SNPs), including 270 known SNPs and 148 novel SNPs. Levels of nucleotide diversity varied from gene to gene (0.72 x 10(-4)-14.53 x 10(-4)), but the average nucleotide diversity between coding SNPs (cSNPs) and noncoding SNPs was roughly equivalent (4.63 x 10(-4) vs 4.69 x 10(-4)). However, nucleotide diversity of cSNPs was strongly correlated to codon degeneracy. Nucleotide diversity was much higher at fourfold degenerate sites than at nondegenerate sites (9.42 x 10(-4) vs 3.14 x 10(-4)). Gene-based haplotype analysis of asthma-associated genes in this study revealed that common haplotypes (frequency >5%) represented 90.5% of chromosomes, and they could be uniquely identified with five or fewer haplotype-tagging SNPs per gene. Therefore, our results may have important implications for the selection of asthma candidate genes and SNP markers for comprehensive association studies using large sample populations.

Asthma↗