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PubMed1997

Genetics of complex disease: approaches, problems, and solutions.

Complex or multifactorial diseases are defined as diseases that are ultimately determined by a number of genetic and environmental factors. Although there are many technologies and strategies that can be used to detect genetic factors influencing complex diseases, these technologies and strategies have inherent limitations. In fact, the very name "complex disease" suggests that the results from relevant studies will not be simple to decipher. Ultimately, both the detection and precise characterization of a factor's contribution to a complex disease are difficult undertakings, because the effect of any one factor may be obscured or confounded by other factors. However, the genetic dissection of complex diseases can be greatly facilitated by paying heed to two very basic distinctions. The first distinction is between complexity at the level of individuals and complexity at the level of populations. The second distinction is between the two sequentially pursued components of gene discovery paradigms: gene identification and gene effect characterization. Although genetic epidemiology, as a research field, is oriented to both components of gene discovery for complex diseases, it is suited to gene effect characterization at the population level more than anything else. This paper reviews the origins of the genetic basis of complex traits, as well as the problems plaguing genetic epidemiologic analysis strategies, with the hope of showing how greater attention to these distinctions, as well as a greater integration of relevant knowledge, can alleviate confusion and shape future investigations. In addition, a new discipline, "phenomics" or "phenometrics," could be initiated that would complement genomic research as presently performed.

Chromosome Mapping↗
PubMed2005

The role of metallothionein in the pathogenesis of acute lung injury.

Often fatal, acute lung injury has a complicated etiology. Previous studies from our laboratory in mice have demonstrated that survival during acute lung injury is a complex trait governed by multiple loci. We also found that the increase in metallothionein (MT) is one of the greatest noted in transcriptome-wide analyses of gene expression. To assess the role of MT in nickel-induced acute lung injury, the survival of Mt-transgenic, Mt1/2(+/+), and Mt1/2(-/-) mice was compared. Pulmonary inflammation and global gene expression were compared in Mt1/2(+/+) and Mt1/2(-/-) mice. Gene-targeted Mt1/2(-/-) mice were more susceptible than Mt1/2(+/+) mice to nickel-induced inflammation, surfactant-associated protein B transcript loss, and lethality. Similarly, Mt-transgenic mice exhibited increased survival. MAPPFinder analyses also noted significant decreases in genes involved in protein processing (e.g., ubiquitination, folding), which were greater in Mt1/2(-/-) mice as compared with Mt1/2(+/+) mice early in the progression of acute lung injury, possibly due to a zinc-mediated transcript destabilization. In contrast, transcript levels of genes associated with the inflammatory response, extracellular matrix regulation, and coagulation/fibrinolysis were increased more in Mt1/2(-/-) mice as compared with Mt1/2(+/+) mice late in the development of acute lung injury. Thus, MT ultimately improves survival in the progression of acute lung injury in mice. Transcriptome-wide analysis suggests that this survival may be mediated through changes in the destabilization of transcripts associated with protein processing, the subsequent augmentation of transcripts controlling inflammation, extracellular matrix regulation, coagulation/fibrinolysis, and disruption of surfactant homeostasis.

Animals↗
PubMed2004

Sequence variants in the transforming growth beta-induced factor (TGIF) gene are not associated with high myopia.

PURPOSE: High myopia is a common complex-trait eye disorder, with implications for blindness due to increased risk of retinal detachment, macular degeneration, premature cataracts, and glaucoma. Mapping studies have identified at least four loci for nonsyndromic autosomal dominant high myopia at 18p11.31, 12q22-q23, 17q21-q23, and 7q36. The smallest haplotyped interval for these loci is that of the MYP2 locus on 18p11.31. Recently, the transforming growth beta-induced factor (TGIF) gene was reported to be a candidate gene for MYP2-associated high myopia in single-nucleotide polymorphism studies. The purpose of this study was to determine whether DNA sequence variants in the human TGIF gene are causally related to MYP2-associated high myopia. METHODS: The protein coding regions and intron-exon boundaries of the human TGIF gene were sequenced using genomic DNA samples from MYP2 individuals (affected, unaffected) and external control subjects. The TGIF model used was the April 20, 2003, human genome National Center for Biotechnology Information (NCBI) build 33, which has 10 exons and encodes eight transcript variants. Polymorphic sequence changes were compared to those in the previous report. Reverse-transcription polymerase chain reaction (RT-PCR) was performed to validate TGIF gene expression in ocular tissues. RESULTS: A total of 21 polymorphisms of TGIF were found by direct sequencing: 3 were missense, 2 were silent, 10 were not translated, 4 were intronic, and 2 were homozygous deletions. The 3 missense allelic variants were localized to exon 10 at positions 236C-->T(Pro-->Leu), 244C-->T(Pro-->Ser), and 245C-->T(Pro-->Leu). Silent mutations were observed in exon 10 at positions 177A-->G, 333C-->T. Ten polymorphisms were novel. No sequence alterations were exclusively associated with the affected disease phenotype. RT-PCR results confirmed expression of TGIF in RNA samples derived from human sclera, cornea, optic nerve, and retina. CONCLUSIONS: TGIF is a known candidate gene for MYP2-associated high myopia, based on its mapped location within the MYP2 interval. Mutation analysis of the encoded TGIF gene for MYP2 autosomal dominant high myopia did not identify sequence alterations associated with the disease phenotype. Further studies of MYP2 candidate genes are needed to determine the gene that causes of this potentially blinding disorder.

DNA Mutational Analysis↗
PubMed2006

Association of the Y402H polymorphism in complement factor H gene and neovascular age-related macular degeneration in Chinese patients.

PURPOSE: Age-related macular degeneration (AMD), with its complex traits and multiple risk factors, is the leading cause of blindness in the elderly. A strong association between a coding variant, Y402H, in the complement factor H gene (CFH) and AMD has been recently identified in white patients. This study was conducted to investigate the association between the Y402H polymorphism in CFH and neovascular AMD in Chinese patients. METHODS: One hundred sixty-three Chinese patients with neovascular AMD and 232 age-matched healthy controls were enrolled in the study. Genomic DNA from white blood cells was extracted. The Y402H polymorphism in CFH, with the substitution of T to C at nucleotide position 1277 in exon 9, was determined by polymerase chain reaction-restriction fragment length polymorphism analysis. The association between the genetic polymorphism and the disease was examined by chi(2) test and logistic regression. RESULTS: The frequency of the risk allele, 1277C, was 11.3% in AMD patients compared with 2.8% in controls (P < 0.00001). Genotype frequency differed significantly between the two groups (1277TT 81.0%, 1277TC 15.3%, and 1277CC 3.7% in the AMD group; 1277TT 94.4%, 1277TC 5.6%, and 1277CC 0% in the control group; P < 0.0001). The 1277C allele significantly increased the risk for neovascular AMD and had an odds ratio of 4.4 (95% confidence interval [95% CI], 2.3-8.5; P < 0.00001). CONCLUSIONS: The allele frequency of Y402H polymorphism in CFH has an ethnic variation, with much lower 1277C frequency in Chinese than in white patients. Despite this, the polymorphism is significantly associated with neovascular AMD in the Chinese population.

Aged↗
PubMed1995

A variant of human paraoxonase/arylesterase (HUMPONA) gene is a risk factor for coronary artery disease.

Coronary artery disease (CAD) is a complex trait caused by a number of genetic and environmental factors. Recently, paraoxonase/arylesterase (PONA) enzyme has been implicated in the pathogenesis of atherosclerosis. There is a 10-40-fold variability in the activity of this enzyme among individuals. This variability is due to the presence of an A/G polymorphism in the coding region of the gene (HUMPONA). The A and G alleles code for glutamine (A genotype) and arginine (B genotype), respectively. Individuals with A genotype have a lower enzymatic activity than those with B genotype. We determined the HUMPONA genotypes and alleles in 223 patients with angiographically documented CAD and in 247 individuals in the general population. The distribution of genotypes were in Hardy-Weinberg equilibrium in patients and in controls. Genotypes A and B were present in 120 (49%) and 28 (11%) individuals in controls and in 68 (30%) and 40 (18%) patients with CAD, respectively (chi squared= 16.5, P= 0.0003). The frequency of the A allele was 0.69 in controls and 0.56 in patients (OR= 1.7, P= 0.0001). There were no differences in the distribution of HUMPONA genotypes in the subgroups of patients with restenosis, myocardial infarction, or any of the conventional risk factors for CAD as compared with corresponding subgroups. In summary, variants of the HUMPONA gene are involved in predisposition to coronary atherosclerosis.

Adult↗
PubMed2005

Hypertension from targeted ablation of chromogranin A can be rescued by the human ortholog.

The secretory prohormone chromogranin A (CHGA) is overexpressed in essential hypertension, a complex trait with genetic predisposition, while its catecholamine release-inhibitory fragment catestatin is diminished, and low catestatin predicts augmented adrenergic pressor responses. These findings from studies on humans suggest a mechanism whereby diminished catestatin might increase the risk for hypertension. We generated Chga and humanized mice through transgenic insertion of a human CHGA haplotype in order to probe CHGA and catestatin in vivo. Chga mice displayed extreme phenotypic changes, including: (a) decreased chromaffin granule size and number; (b) elevated BP; (c) loss of diurnal BP variation; (d) increased left ventricular mass and cavity dimensions; (e) decreased adrenal catecholamine, neuropeptide Y (Npy), and ATP contents; (f) increased catecholamine/ATP ratio in the chromaffin granule; and (g) increased plasma catecholamine and Npy levels. Rescue of elevated BP to normalcy was achieved by either exogenous catestatin replacement or humanization of Chga mice. Loss of the physiological "brake" catestatin in Chga mice coupled with dysregulation of transmitter storage and release may act in concert to alter autonomic control of the circulation in vivo, eventuating in hypertension.

Animals↗
PubMedDate not supplied

Is clinical radiosensitivity a complex genetically controlled event?

New insights into molecular mechanisms responsible for cellular radiation response are coming from recent basic radiobiological studies. Preliminary data supporting the concept of clinical radiosensitivity as a complex genetically controlled event are available, and it seems reasonable to hypothesize that genes encoding for proteins implicated in known radiation-induced pathways, such as DNA repair, could influence normal tissue and tumor response to radiotherapy. Such genes could be considered as candidates for experimental studies and as targets for innovative therapies. Variants that could influence individual radiosensitivity have been recently identified, and specific Single Nucleotide Polymorphisms have been associated to the development of different radiation effects on normal tissues. Allelic architecture of complex traits able to modify phenotypes is difficult to be established, and different grades of interaction between common or rare genetic determinants may be present and should be considered. Many different experimental strategies could be investigated in the future, such as analysis of multiple genes in large irradiated patient cohorts strictly observed for radiation effects or identification of new candidate genes, with the aim of identifying factors that could be employed in predictive testing and individualization of radiation therapy on a genetic basis.

Alleles↗
PubMed1999

Genetic susceptibility to neurodevelopmental disorders.

A large body of evidence suggests that genetic factors influence liability to many common neurodevelopmental disorders. Examples include Tourette syndrome, attention-deficit hyperactivity disorder, autism, and dyslexia. Characterization of the genetic component of susceptibility to these conditions at a molecular level should improve classification, elucidate fundamental neurobiologic mechanisms of disease, and suggest novel approaches to treatment. Susceptibility loci for complex traits could be identified by detecting linkage to a well-mapped genetic marker or by detecting association with a putative high-risk allele at a candidate locus. This article reviews the principles underlying these complementary approaches, and notes recent progress in specific conditions. As the molecular epidemiology of susceptibility to common neurodevelopmental disorders emerges, it might be increasingly possible to identify "high-risk" and "low-risk" genotypes. Clinicians should understand the nature of this kind of information in order to appreciate its power as well as its limitations.

Attention Deficit Disorder with Hyperactivity↗
PubMed2006

Early environmental exposure and the development of lupus.

Systemic lupus erythematosus (SLE) is a complex trait with evidence of polygenic inheritance influenced by environmental factors. However, the precise underlying causes of SLE remain unclear. A number of environmental exposures have been associated with lupus or related autoimmune phenomena. Evidence suggests that some environmental exposures need to be present many years before the onset of SLE. Both SLE and rheumatoid arthritis (RA) can occur in very young children and this supports the possibility that important environmental factors must be present during or before this time. In addition, the immune pathology, including autoantibody production, in adult lupus may begin years before clinical disease. There is also evidence that the developing immune system demonstrates developmental plasticity and can be permanently altered or 'programmed' by the early environment. We describe how early life environmental influences including infectious exposure may lead to autoantibody production in later life thus beginning the journey that leads to autoimmune diseases such as lupus in susceptible individuals.

Arthritis, Rheumatoid↗
PubMed2005

Parkinson's disease risk factors: genetic, environmental, or both?

Perhaps one of the most important questions posed by the neurobiology of aging concerns the pathogenic mechanisms in Parkinson's disease (PD). Recently, it was suggested that exposure to pesticides could be the main cause of PD. Another study reported that the environmental endotoxin, lipopolysaccaride produced by Salmonella minnesota, might be a risk factor for PD. An alternative explanation is the genetic component, which has been suggested to be an important risk factor. Epidemiological studies have identified a positive family history of Parkinson as one of the most important risk factors for the disease. However, these studies neither examined nor reviewed the medical records of the family members. The twin study stated that the major factors in the etiology of PD are non-genetic. Meanwhile, epidemiological studies from China have shown that the prevalence of PD is much lower than in the Caucasian population, explained by the low frequency of cytochrome P-450 CYP2D6 debrisoquine hydroxylase gene polymorphism. The etiology of idiopathic PD is still a question for scientists, and calls for further research, especially with the growing proportion of elderly and the rising incidence of PD worldwide. Future research for PD risk factors should consider that multiple interactions occur in PD, resulting in a complex trait, which includes genetic, acquired, and environmental components.

Environment↗
PubMed2002

A genetic and genomic analysis identifies a cluster of genes associated with hematopoietic cell turnover.

Hematopoietic stem cells from different strains of mice vary widely with respect to their cell cycle activity. In the present study we used complementary genetic and genomic approaches to identify molecular pathways affecting this complex trait. We identified a major quantitative trait locus (QTL) associated with variation in cell proliferation in C57BL/6 and DBA/2 mice to a 10 centimorgan (cM) region on chromosome 11. A congenic mouse model confirmed that a genomic interval on chromosome 11 in isolation confers the proliferation phenotype. To detect candidate genes we performed subtractive hybridizations and gene arrays using cDNA from highly enriched stem cells from parental strains. Intriguingly, a disproportionate number of differentially expressed genes mapped to chromosome 11 and, more specifically, these transcripts occurred in 3 distinct clusters. The largest cluster colocalized exactly with the cell cycling QTL. Such clustering suggested the involvement of genetic variation that affects higher-order chromosomal organization. This hypothesis was reinforced by the fact that differentially expressed genes mapped to recombination "coldspots," as a consequence of which clustered genes are collectively inherited. These findings suggest the functional interdependence of these closely linked genes. Our data are consistent with the hypothesis that this isolated cell cycle QTL does not result from a mutation in a single gene but rather is a consequence of variable expression of a collection of highly linked genes.

Animals↗
PubMed2006

PDA: Pooled DNA analyzer.

BACKGROUND: Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity. Genotyping large numbers of SNPs individually is performed routinely but is cost prohibitive for large-scale genetic studies. DNA pooling is a reliable and cost-saving alternative genotyping method. However, no software has been developed for complete pooled-DNA analyses, including data standardization, allele frequency estimation, and single/multipoint DNA pooling association tests. This motivated the development of the software, 'PDA' (Pooled DNA Analyzer), to analyze pooled DNA data. RESULTS: We develop the software, PDA, for the analysis of pooled-DNA data. PDA is originally implemented with the MATLAB language, but it can also be executed on a Windows system without installing the MATLAB. PDA provides estimates of the coefficient of preferential amplification and allele frequency. PDA considers an extended single-point association test, which can compare allele frequencies between two DNA pools constructed under different experimental conditions. Moreover, PDA also provides novel chromosome-wide multipoint association tests based on p-value combinations and a sliding-window concept. This new multipoint testing procedure overcomes a computational bottleneck of conventional haplotype-oriented multipoint methods in DNA pooling analyses and can handle data sets having a large pool size and/or large numbers of polymorphic markers. All of the PDA functions are illustrated in the four bona fide examples. CONCLUSION: PDA is simple to operate and does not require that users have a strong statistical background. The software is available at http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm.

Algorithms↗
PubMed2003

Genome-wide linkage analysis of systolic blood pressure slope using the Genetic Analysis Workshop 13 data sets.

Systolic blood pressure (SBP) is an age-dependent complex trait for which both environmental and genetic factors may play a role in explaining variability among individuals. We performed a genome-wide scan of the rate of change in SBP over time on the Framingham Heart Study data and one randomly selected replicate of the simulated data from the Genetic Analysis Workshop 13. We used a variance-component model to carry out linkage analysis and a Markov chain Monte Carlo-based multiple imputation approach to recover missing information. Furthermore, we adopted two selection strategies along with the multiple imputation to deal with subjects taking antihypertensive treatment. The simulated data were used to compare these two strategies, to explore the effectiveness of the multiple imputation in recovering varying degrees of missing information, and its impact on linkage analysis results. For the Framingham data, the marker with the highest LOD score for SBP slope was found on chromosome 7. Interestingly, we found that SBP slopes were not heritable in males but were for females; the marker with the highest LOD score was found on chromosome 18. Using the simulated data, we found that handling treated subjects using the multiple imputation improved the linkage results. We conclude that multiple imputation is a promising approach in recovering missing information in longitudinal genetic studies and hence in improving subsequent linkage analyses.

Age Factors↗
PubMed2004

A new set of BXD recombinant inbred lines from advanced intercross populations in mice.

BACKGROUND: Recombinant inbred (RI) strains are an important resource for mapping complex traits in many species. While large RI panels are available for Arabidopsis, maize, C. elegans, and Drosophila, mouse RI panels typically consist of fewer than 30 lines. This is a severe constraint on the power and precision of mapping efforts and greatly hampers analysis of epistatic interactions. RESULTS: In order to address these limitations and to provide the community with a more effective collaborative RI mapping panel we generated new BXD RI strains from two independent advanced intercrosses (AI) between C57BL/6J (B6) and DBA/2J (D2) progenitor strains. Progeny were intercrossed for 9 to 14 generations before initiating inbreeding, which is still ongoing for some strains. Since this AI base population is highly recombinant, the 46 advanced recombinant inbred (ARI) strains incorporate approximately twice as many recombinations as standard RI strains, a fraction of which are inevitably shared by descent. When combined with the existing BXD RI strains, the merged BXD strain set triples the number of previously available unique recombinations and quadruples the total number of recombinations in the BXD background. CONCLUSION: The combined BXD strain set is the largest mouse RI mapping panel. It is a powerful tool for collaborative analysis of quantitative traits and gene function that will be especially useful to study variation in transcriptome and proteome data sets under multiple environments. Additional strains also extend the value of the extensive phenotypic characterization of the previously available strains. A final advantage of expanding the BXD strain set is that both progenitors have been sequenced, and approximately 1.8 million SNPs have been characterized. This provides unprecedented power in screening candidate genes and can reduce the effective length of QTL intervals. It also makes it possible to reverse standard mapping strategies and to explore downstream effects of known sequence variants.

Animals↗
PubMed2005

A genome-wide linkage and association study using COGA data.

BACKGROUND: Genome-wide association will soon be available to use as an adjunct to traditional linkage analysis. We studied alcoholism in 119 families collected by the Collaborative Study on the Genetics of Alcoholism and made available in Genetic Analysis Workshop 14, using genome-wide linkage and association analyses. METHODS: Genome-wide linkage analysis was first performed using microsatellite markers and a region with the strongest linkage evidence was further analyzed using single-nucleotide polymorphisms (SNPs). Family based genome-wide association test was also conducted using the SNPs. RESULTS: Nonparametric linkage analysis revealed weak linkage evidence on chromosome 7, and association analysis identified SNP tsc0515272 on chromosome 3 as significantly associated with alcoholism. CONCLUSION: Linkage analysis may require large sample sizes and high quality genotyping and marker maps to adequately improve power, while association analysis could hold more promise in efforts to identify variants responsible for complex traits.

Alcoholism↗
PubMed2005

Construction of endophenotypes for complex diseases in the presence of heterogeneity.

Endophenotypes such as behavior disorders have been increasingly adopted in genetic studies for complex traits. For efficient gene mapping, it is essential that an endophenotype is associated with the disease of interest and is inheritable or co-segregating within families. In this study, we proposed a strategy to construct endophenotypes to analyze the Genetic Analysis Workshop 14 simulated dataset. Initially, generalized estimating equation models were employed to identify phenotypes that were correlated to the disease (affected status) in combination with the family structures in data. Endophenotypes were then constructed with consideration of heterogeneity as functions of the identified phenotypes. Genome scans on the constructed endophenotypes were carried out using family-based association analysis. For comparison, genome scans were also performed with the original affected status. The family-based association analysis using the endophenotypes correctly identified the same susceptible gene in about 80 of the 100 replicates.

Chromosomes, Human, Pair 3↗
PubMed2005

Comparison of single-nucleotide polymorphisms and microsatellites in inference of population structure.

Single-nucleotide polymorphisms (SNPs) are a class of attractive genetic markers for population genetic studies and for identifying genetic variations underlying complex traits. However, the usefulness and efficiency of SNPs in comparison to microsatellites in different scientific contexts, e.g., population structure inference or association analysis, still must be systematically evaluated through large empirical studies. In this article, we use the Collaborative Studies on Genetics of Alcoholism (COGA) data from Genetic Analysis Workshop 14 (GAW14) to compare the performance of microsatellites and SNPs in the whole human genome in the context of population structure inference. A total of 328 microsatellites and 15,840 SNPs are used to infer population structure in 236 unrelated individuals. We find that, on average, the informativeness of random microsatellites is four to twelve times that of random SNPs for various population comparisons, which is consistent with previous studies. Our results also indicate that for the combined set of microsatellites and SNPs, SNPs constitute the majority among the most informative markers and the use of these SNPs leads to better inference of population structure than the use of microsatellites. We also find that the inclusion of less informative markers may add noise and worsen the results.

Genetic Loci↗
PubMed2005

Haplotype sharing correlation of alcohol dependence on chromosomes 1-6 in 93 nuclear families.

Haplotype data contain signatures of ancestral alleles and increased information for mapping genes associated with complex traits. The motivation of this paper is to test the feasibility of a recently developed haplotype reconstruction algorithm and to perform haplotype-sharing correlation (HSC) analysis in nuclear families using data provided by the Genetic Analysis Workshop 14 and the Collaborative Study of the Genetics of Alcoholism. As an exemplary analysis, haplotype data on chromosomes 1-6 were reconstructed from genotype data in 93 nuclear families by minimizing both the recombinants in within-family haplotypes and the tree distance in between-family haplotypes. HSC analysis was performed using the best set of reconstructed haplotypes, and chromosome-wide significance was evaluated using a permutation procedure. Three markers were found to have significant haplotype associations with DSM-IV alcohol dependence that exceeded the 0.05 level of chromosome-wide significance: marker rs895941 at 36.7 cM on chromosome 3 (p = 0.03), marker rs1631833 at 109.1 cM on chromosome 4 (p = 0.008), and marker rs953887 at 74.2 cM on chromosome 6 (p = 0.02). These results indicated the usefulness of HSC analysis and provided further evidence on chromosome regions associated with alcohol dependence.

Alcoholism↗