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PubMed2005

Genome-wide associations of gene expression variation in humans.

The exploration of quantitative variation in human populations has become one of the major priorities for medical genetics. The successful identification of variants that contribute to complex traits is highly dependent on reliable assays and genetic maps. We have performed a genome-wide quantitative trait analysis of 630 genes in 60 unrelated Utah residents with ancestry from Northern and Western Europe using the publicly available phase I data of the International HapMap project. The genes are located in regions of the human genome with elevated functional annotation and disease interest including the ENCODE regions spanning 1% of the genome, Chromosome 21 and Chromosome 20q12-13.2. We apply three different methods of multiple test correction, including Bonferroni, false discovery rate, and permutations. For the 374 expressed genes, we find many regions with statistically significant association of single nucleotide polymorphisms (SNPs) with expression variation in lymphoblastoid cell lines after correcting for multiple tests. Based on our analyses, the signal proximal (cis-) to the genes of interest is more abundant and more stable than distal and trans across statistical methodologies. Our results suggest that regulatory polymorphism is widespread in the human genome and show that the 5-kb (phase I) HapMap has sufficient density to enable linkage disequilibrium mapping in humans. Such studies will significantly enhance our ability to annotate the non-coding part of the genome and interpret functional variation. In addition, we demonstrate that the HapMap cell lines themselves may serve as a useful resource for quantitative measurements at the cellular level.

Chromosome Mapping↗
PubMed2006

Integrating genetic and network analysis to characterize genes related to mouse weight.

Systems biology approaches that are based on the genetics of gene expression have been fruitful in identifying genetic regulatory loci related to complex traits. We use microarray and genetic marker data from an F2 mouse intercross to examine the large-scale organization of the gene co-expression network in liver, and annotate several gene modules in terms of 22 physiological traits. We identify chromosomal loci (referred to as module quantitative trait loci, mQTL) that perturb the modules and describe a novel approach that integrates network properties with genetic marker information to model gene/trait relationships. Specifically, using the mQTL and the intramodular connectivity of a body weight-related module, we describe which factors determine the relationship between gene expression profiles and weight. Our approach results in the identification of genetic targets that influence gene modules (pathways) that are related to the clinical phenotypes of interest.

Animals↗
PubMed2006

Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome.

Significant interest has emerged in mapping genetic susceptibility for complex traits through whole-genome association studies. These studies rely on the extent of association, i.e., linkage disequilibrium (LD), between single nucleotide polymorphisms (SNPs) across the human genome. LD describes the nonrandom association between SNP pairs and can be used as a metric when designing maximally informative panels of SNPs for association studies in human populations. Using data from the 1.58 million SNPs genotyped by Perlegen, we explored the allele frequency dependence of the LD statistic r(2) both empirically and theoretically. We show that average r(2) values between SNPs unmatched for allele frequency are always limited to much less than 1 (theoretical approximately 0.46 to 0.57 for this dataset). Frequency matching of SNP pairs provides a more sensitive measure for assessing the average decay of LD and generates average r(2) values across nearly the entire informative range (from 0 to 0.89 through 0.95). Additionally, we analyzed the extent of perfect LD (r(2) = 1.0) using frequency-matched SNPs and found significant differences in the extent of LD in genic regions versus intergenic regions. The SNP pairs exhibiting perfect LD showed a significant bias for derived, nonancestral alleles, providing evidence for positive natural selection in the human genome.

Animals↗
PubMed2006

Quantitative genomics of aggressive behavior in Drosophila melanogaster.

Aggressive behavior is important for animal survival and reproduction, and excessive aggression is an enormous social and economic burden for human society. Although the role of biogenic amines in modulating aggressive behavior is well characterized, other genetic mechanisms affecting this complex behavior remain elusive. Here, we developed an assay to rapidly quantify aggressive behavior in Drosophila melanogaster, and generated replicate selection lines with divergent levels of aggression. The realized heritability of aggressive behavior was approximately 0.10, and the phenotypic response to selection specifically affected aggression. We used whole-genome expression analysis to identify 1,539 probe sets with different expression levels between the selection lines when pooled across replicates, at a false discovery rate of 0.001. We quantified the aggressive behavior of 19 mutations in candidate genes that were generated in a common co-isogenic background, and identified 15 novel genes affecting aggressive behavior. Expression profiling of genetically divergent lines is an effective strategy for identifying genes affecting complex traits.

Aggression↗
PubMed2006

Multicapillary electrophoresis analysis of single-nucleotide sequence variations in the deoxycytidine kinase gene.

BACKGROUND: Investigation of the genetic background of complex traits is the focus of recent interest, as several common diseases or the individual response to treatments of various illnesses have not yet been explored. These studies require the development and implementation of reliable and large-scale genotyping methods. In this report, we introduce an efficient technique based on PCR-restriction fragment length sequence variation technique for the analysis of the -360CG and -201CT single-nucleotide sequence variations in the deoxycytidine kinase gene. METHODS: A multicapillary gel electrophoresis instrument was used for the size determination of the generated DNA fragments. A healthy Hungarian population of 100 individuals was investigated to determine allele and genotype frequencies for the 2 sequence variations of interest. RESULTS: We found that the occurrence of the minor allele is rather low, i.e., the frequency of both the -360G and -201T variants is 1%. CONCLUSIONS: Our technique can readily facilitate the analysis of these important sequence variations in other ethnic groups to clarify the role of these sequence variations in conjunction with arabinosylcytosine treatment in acute myeloid leukemia.

Deoxycytidine Kinase↗
PubMed2005

Problems with using sum scores for estimating variance components: contamination and measurement noninvariance.

Twin studies of complex traits, such as behavior or psychiatric diagnoses, frequently involve univariate analysis of a sum score derived from multiple items. In this article, we show that absence of measurement invariance across zygosity can bias estimates of genetic and environmental components of variance. Specifically, if the item responses are considered as multiple indicators of a latent factor, and the aim is to partition the variance in the latent factor, then the factor loadings relating the items to the factor should be equal for monozygotic (MZ) and dizygotic (DZ) twins. While it seems unlikely, a priori, that these loadings should differ as a function of zygosity, certain special measurement situations are cause for concern. Ratings by parents, or self-ratings of phenotypes which are more easily observed in others than via introspection, may be tainted by the co-twin's phenotype to a greater extent in MZ than DZ pairs. We also show that the analysis of sum scores typically biases both MZ and DZ correlations compared to the true latent trait correlation. These two sources of bias are quantified for a range of values and are shown to be especially acute for sum scores based on binary items. Solutions to these problems include formal tests for measurement invariance across zygosity prior to analysis of the sum or scale scores, and multivariate genetic analysis at the individual item or symptom level.

Humans↗
PubMed2006

Empirical evaluation of the genetic similarity of samples from twin registries in Australia and the Netherlands using 359 STRP markers.

One way to achieve the large sample sizes required for genetic studies of complex traits is to combine samples collected by different groups. It is not often clear, however, whether this practice is reasonable from a genetic perspective. To assess the comparability of samples from the Australian and the Netherlands twin studies, we estimated Fst (the proportion of total genetic variability attributable to genetic differences between cohorts) based on 359 short tandem repeat polymorphisms in 1068 individuals. Fst was estimated to be 0.30% between the Australian and the Netherlands cohorts, a smaller value than between many European groups. We conclude that it is reasonable to combine the Australian and the Netherlands samples for joint genetic analyses.

Australia↗
PubMed2005

Atherosclerosis: from genetic polymorphisms to system genetics.

It is generally considered that the genetics of atherosclerosis and its complications involves a large number of genes with common alleles having weak effects on disease risk but possibly interacting with each other and with non-genetic factors. In such a complex system, absence of marginal effects (effects of polymorphisms considered one at a time) is insufficient to exclude the implication of a polymorphism on disease risk. Investigating polymorphisms and even genes one by one is no longer appropriate. It is necessary to focus on biological systems and integrate the contribution of genetic as well as non-genetic factors and their interactions. Hopefully, system genetics will ultimately improve our understanding of the genetic architecture of complex traits.

Animals↗
PubMed2002

A rat linkage map based on BC x LEW intercross.

A genetic linkage map consisting of 258 polymorphic loci has been constructed on the basis of an F2 intercross between the BC/CpbU and LEW/OlaHsd inbred rat strains. When compared to previously published maps a discrepancy was found for rat chromosome 7. The map spans a sex-averaged genetic length of 1790 cM and has an average marker spacing of 7.7 cM. It was estimated that this genetic map is linked to about 90% of the DNA in the rat genome. Because LEW/OlaHsd and BC/CpbU strains differ for dietary cholesterol susceptibility and hepatic copper content, the map is considered to be a valuable tool for studying the genetic background of these complex traits.

Animals↗
PubMed1998

Genetic models for non insulin dependent diabetes mellitus in rodents.

Efforts to identify human genes with major effects on insulin resistance and type II diabetes have yet to be successful because of the technical difficulties associated with the analysis of complex traits in humans. Animal models, particularly the rodent models with their well developed genetic tools, and their genetic similarity to humans, offer an alternate approach to access genes important in the etiology of diabetes. This approach is validated by the remarkable progress that has been made in the identification and characterization of the genes mutated in five monogenic mouse models of obesity. Identification of these genes has led to new insights into the etiology of obesity and provided promising targets for therapeutic intervention. Arguably, genetic animal models could do the same for our understanding of diabetes. In this brief review, we introduce rodent models of type II diabetes and report on the state of their genetic analyses.

Animals↗
PubMedDate not supplied

Transcriptomics and proteomics: tools for optimising phytoremediation activities.

Negligent industrial development has greatly contributed to environmental pollution through the contamination of water and soil by xenobiotic organic chemicals Remedial strategies to deal with chemical pollution require reliable methods to identify and monitor contamination, as well as effective procedures to attenuate or to eliminate the pollutant. In the food chain, plants are ideally placed as early bio-indicators of environmental pollution as they experience and respond to environmental toxicants sooner than organisms at higher trophic levels. Furthermore, some plants are capable of detoxifying anthropogenic chemicals by metabolic transformation and could prove useful for the remediation of contaminated water and soil: so-called phytoremediation. So far research technologies aimed at developing plants for bio-indication/bio-monitoring and for remediation have largely relied on standardised chemical and biochemical procedures to evaluate phytotoxicity, metabolic fate and persistence of organic pollutants in plants. The next stage in the evolution of these plant-based technologies is the improvement and optimisation of any innate phytoremediation activities identified in selected plants. In general, uptake followed by metabolism and compartmentation is responsible for the detoxification of organic xenobiotics in plants. These are complex cellular systems that may be organised in well-defined pathways and are often controlled by large families of genes. In order to elucidate complex traits such as detoxification, an emerging idea is to make use of global approaches such as the new "omic" technologies to identify molecular changes in plant tissues exposed to specific organic xenobiotics. From expression profiles at the messenger RNA level, transcriptomics permit the identification of function-related gene clusters and at the protein level proteomics provide information on where, when and at what level specific proteins accumulate. We conclude that these global approaches may be a useful way of widening screening capability to identify appropriate molecular markers that can be used to improve detoxification activity.

Arabidopsis↗
PubMed2001

The relative power of SNPs and haplotype as genetic markers for association tests.

Identifying the polymorphisms that contribute to disease predisposition and drug response is a major goal of the post-genome era. Single nucleotide polymorphisms (SNPs) in disease-related genes are often used as candidates in the search for causative variations. Association tests based on haplotypes have also been suggested and, at times, have provided greater statistical power than tests based on the underlying SNPs. Here we review the statistical model traditionally used to describe association studies for complex traits and derive novel results for the relative power of SNP-based and haplotype-based tests of association. In the model, a set of independent SNP-based variations, some of which contribute to a measured phenotype, may be used as markers directly or may be organised into haplotype markers. Provided that the marker set includes all the causative SNPs, we find a simple rule for the relative power of SNP and haplotype markers: SNP-based tests have greater power when the number of causative SNPs (a subset of the total set of SNPs) is smaller than the total number of haplotypes. Furthermore, we find that regression tests for the simple main effect of each haplotype are generally more powerful than ANOVA tests applied to haplotype pairs. A review of recent literature supports our findings.

Analysis of Variance↗
PubMed2002

Murine pharmacogenomics: using the mouse to understand the genetics of drug therapy.

Pharmacogenomics seeks to understand the genetic basis of interindividual differences in drug disposition and effects. Differential drug response is likely to most often be a complex trait, in which multiple genes contribute with varying strengths to the therapeutic phenotype. Due to technical and economic limitations, pharmacogenomic studies in humans are mainly limited to a small number of candidate genes with relatively major influences on drug response. This review discusses the problems involved in mapping genes underlying drug response in humans and highlights the theoretical and applied uses of mouse genetics to address these important issues.

Animals↗
PubMed2006

AAV-mediated gene transfer for retinal diseases.

Vectors based on the adeno-associated virus (rAAV) are able to transduce the retina of animal models, including non-human primates, for a long-term period, safely and at sustained levels. The ability of the various rAAV serotypes to transduce retinal target cells has been exploited to successfully transfer genes to photoreceptors, retinal pigment epithelium and the inner retina, which are affected in many inherited and non-inherited blinding diseases. rAAV-mediated, constitutive and regulated gene expression at therapeutic levels has been achieved in the retina of animal models, thus providing proof-of-principle of gene therapy efficacy and safety in models of dominant and recessive retinal disorders. In addition, gene transfer of molecules with either neurotrophic or antiangiogenic properties provides useful alternatives to the classic gene replacement for treatment of both mendelian and complex traits affecting the retina. Years of successful rAAV-mediated gene transfer to the retina have resulted in restoration of vision in dogs affected with congenital blindness. This has paved the way to the first attempts at treating inherited retinal diseases in humans with rAAV. Although the results of rAAV clinical trials for non-retinal diseases give a warning that the outcome of viral-mediated gene transfer in humans may be different from that predicted based on results in other species, the immune privilege of the retina combined with the versatility of rAAV serotypes may ultimately provide the first successful treatment of human inherited diseases using rAAV.

Adenoviridae↗
PubMed2007

Adiposity, estradiol, and genetic variants of steroid-metabolizing enzymes as determinants of bone mineral density.

OBJECTIVES: Bone mineral density (BMD) is a complex trait resulting from the interplay of genetic and acquired factors. The objective of this study was to explore the influence of several anthropometric, lifestyle, genetic, and hormonal factors on BMD and analyze the possible differences in men and women. METHODS: We studied 572 individuals over 50 years of age (381 postmenopausal women and 191 men). Lumbar spine and femoral neck BMD were measured by dual energy x-ray absorptiometry. The free estrogen index (FEI) was calculated as the ratio of serum estradiol to sex hormone binding globulin in 241 individuals. Three polymorphisms in the genes coding for 17-hydroxylase/liase, sulfotransferase, and 5alpha-reductase were studied in DNA isolated from blood cells. RESULTS: Body mass index was strongly correlated to spine and femoral BMD both in women and in men (r = 0.32-0.49; P < 0.001). FEI was also independently correlated with spine BMD in both sexes (r = 0.23 and 0.34, P < 0.01), and with femoral neck in women (r = 0.30). Women with G alleles of the sulfotransferase gene tended to have higher spine BMD than those with C alleles (P = 0.025). No other genotype-related differences in BMD were found. CONCLUSIONS: In conclusion, the results of this study point toward body weight and estradiol levels as major factors determining BMD both in women and in men. A common polymorphism of the sulfotransferase gene also appears to be associated to spine BMD in women.

3-Oxo-5-alpha-Steroid 4-Dehydrogenase↗
PubMed2004

A microsatellite genetic linkage map for Xiphophorus.

Interspecies hybrids between distinct species of the genus Xiphophorus are often used in varied research investigations to identify genomic regions associated with the inheritance of complex traits. There are 24 described Xiphophorus species and a greater number of pedigreed strains; thus, the number of potential interspecies hybrid cross combinations is quite large. Previously, select Xiphophorus experimental crosses have been shown to exhibit differing characteristics between parental species and among the hybrid fishes derived from crossing them, such as widely differing susceptibilities to chemical or physical agents. For instance, genomic regions harboring tumor suppressor and oncogenes have been identified via linkage association of these loci with a small set of established genetic markers. The power of this experimental strategy is related to the number of genetic markers available in the Xiphophorus interspecies cross of interest. Thus, we have undertaken the task of expanding the suite of easily scored markers by characterization of Xiphophorus microsatellite sequences. Using a cross between Xiphophorus maculatus and X. andersi, we report a linkage map predominantly composed of microsatellite markers. All 24 acrocentric chromosome sets of Xiphophorus are represented in the assembled linkage map with an average intergenomic distance of 7.5 cM. Since both male and female F1 hybrids were used to produce backcross progeny, these recombination rates were compared between "male" and "female" maps. Although several genomic regions exhibit differences in map length, male- and female-derived maps are similar. Thus Xiphophorus, in contrast to zebrafish, Danio rerio, and several other vertebrate species, does not show sex-specific differences in recombination. The microsatellite markers we report can be easily adapted to any Xiphophorus interspecies and some intraspecies crosses, and thus provide a means to directly compare results derived from independent experiments.

Animals↗
PubMed2004

Phenotypic variation resulting from a deficiency of epidermal growth factor receptor in mice is caused by extensive genetic heterogeneity that can be genetically and molecularly partitioned.

The timing of lethality caused by homozygosity for a null allele of the epidermal growth factor receptor (Egfrtm1Mag) in mice is strongly dependent on genetic background. Initial attempts to genetically map background modifiers using Swiss-derived, outbred CD-1 mice were unsuccessful. To investigate the genetic architecture contributing to survival of Egfrtm1Mag homozygous embryos, the genetic variability segregating within the outbred population was partitioned by surveying viability of Egfrtm1Mag mutants using intercrosses between 129S6/SvEvTAC-Egfrtm1Mag and nine Swiss-derived, inbred strains: ALR/LtJ, ALS/LtJ, APN, APS, ICR/HaRos, NOD/LtJ, NON/LtJ, SJL/J, and SWR/J. The observations showed that these strains support varying levels of survival of Egfrtm1Mag homozygous embryos, suggesting that genetic heterogeneity within the CD-1 stock contributed to the original lack of Egfrtm1Mag modifier detection. Similar to the Swiss-derived intercrosses, nine congenic strains, derived from 129S6/SvEvTAC, AKR/J, APN, BALB/cJ, BTBR-T+ tf/tf, C3H/HeJ, C57BL/6J, DBA/2J, and FVB/NJ inbred backgrounds, also supported varying levels of survival of Egfrtm1Mag mutants. By intercrossing the congenic lines to create hybrid F1 embryos, different genetic backgrounds were found to have complementary modifiers. Analysis of the congenic lines argues against heterosis of outbred backgrounds contributing to Egfrtm1Mag phenotypic variability. A detailed analysis of the crosses suggests that modifiers function at three distinct stages of development. One class of modifiers supports survival of Egfrtm1Mag homozygous embryos to mid-gestation, another class supports development through the mid-gestation transition from yolk-sac to placental-derived nutrient sources, and a third class supports survival through later stages of gestation. Data from microarray analysis using RNA from wild-type and Egfrtm1Mag mutant placentas support the existence of extensive genetic heterogeneity and suggest that it can be molecularly partitioned. This method should be generally useful to partition heterogeneity contributing to other complex traits.

Animals↗
PubMed2004

Evidence for nucleolus organizer regions as the units of regulation in nucleolar dominance in Arabidopsis thaliana interecotype hybrids.

Nucleolar dominance describes the silencing of one parent's ribosomal RNA (rRNA) genes in a genetic hybrid. In Arabidopsis thaliana, rRNA genes are clustered in two nucleolus organizer regions, NOR2 and NOR4. In F(8) recombinant inbreds (RI) of the A. thaliana ecotypes Ler and Cvi, lines that display strong nucleolar dominance inherited a specific combination of NORs, Cvi NOR4 and Ler NOR2. These lines express almost all rRNA from Cvi NOR4. The reciprocal NOR genotype, Ler NOR4/Cvi NOR2, allowed for expression of rRNA genes from both NORs. Collectively, these data reveal that neither Cvi rRNA genes nor NOR4 are always dominant. Furthermore, strong nucleolar dominance does not occur in every RI line inheriting Cvi NOR4 and Ler NOR2, indicating stochastic effects or the involvement of other genes segregating in the RI mapping population. A partial explanation is provided by an unlinked locus, identified by QTL analysis, that displays an epistatic interaction with the NORs and affects the relative expression of NOR4 vs. NOR2. Collectively, the data indicate that nucleolar dominance is a complex trait in which NORs, rather than individual rRNA genes, are the likely units of regulation.

Arabidopsis↗