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PubMed2006

Epigenetics of complex diseases: from general theory to laboratory experiments.

Despite significant effort, understanding the causes and mechanisms of complex non-Mendelian diseases remains a key challenge. Although numerous molecular genetic linkage and association studies have been conducted in order to explain the heritable predisposition to complex diseases, the resulting data are quite often inconsistent and even controversial. In a similar way, identification of environmental factors causal to a disease is difficult. In this article, a new interpretation of the paradigm of "genes plus environment" is presented in which the emphasis is shifted to epigenetic misregulation as a major etiopathogenic factor. Epigenetic mechanisms are consistent with various non-Mendelian irregularities of complex diseases, such as the existence of clinically indistinguishable sporadic and familial cases, sexual dimorphism, relatively late age of onset and peaks of susceptibility to some diseases, discordance of monozygotic twins and major fluctuations on the course of disease severity. It is also suggested that a substantial portion of phenotypic variance that traditionally has been attributed to environmental effects may result from stochastic epigenetic events in the cell. It is argued that epigenetic strategies, when applied in parallel with the traditional genetic ones, may significantly advance the discovery of etiopathogenic mechanisms of complex diseases. The second part of this chapter is dedicated to a review of laboratory methods for DNA methylation analysis, which may be useful in the study of complex diseases. In this context, epigenetic microarray technologies are emphasized, as it is evident that such technologies will significantly advance epigenetic analyses in complex diseases.

Age Factors↗
PubMed2006

The impact of data quality on the identification of complex disease genes: experience from the Family Blood Pressure Program.

The application of genome-wide linkage scans to uncover susceptibility loci for complex diseases offers great promise for the risk assessment, treatment, and understanding of these diseases. However, for most published studies, linkage signals are typically modest and vary considerably from one study to another. The multicenter Family Blood Pressure Program has analyzed genome-wide linkage scans of over 12 000 individuals. Based on this experience, we developed a protocol for large linkage studies that reduces two sources of data error: pedigree structure and marker genotyping errors. We then used the linkage signals, before and after data cleaning, to illustrate the impact of missing and erroneous data. A comprehensive error-checking protocol is an important part of complex disease linkage studies and enhances gene mapping. The lack of significant and reproducible linkage findings across studies is, in part, due to data quality.

Blood Pressure↗
PubMed1971

Acute immune complex disease in rabbits. The role of complement and of a leukocyte-dependent release of vasoactive amines from platelets.

By depletion of C3 from rabbits undergoing acute experimental immune complex disease with an anticomplementary factor in cobra venom, it has been possible to demonstrate that deposition of the complexes in arteries and glomeruli does not require the complement components reacting after C2. Immunological reactions, in which platelets release their vasoactive amines, have been examined in rabbits undergoing immune complex disease. A correlation was obtained between the presence of a complement-independent reaction which required blood leukocytes, antigen and platelets, the deposition of immune complexes, and the induction of glomerulonephritis. C3 depletion did, however, have a marked alleviating effect on the severity of the arterial lesions. Neutrophil accumulation and the subsequent necrotizing arteritis were prevented. In contrast, the character and severity of the glomerulonephritis was not altered by depletion of later-acting complement components.

Animals↗
PubMed1989

Clonidine-induced immune complex disease.

We report upon a 46-year-old woman, who developed immune complex disease after treatment with clonidine for one year. The diagnosis was verified with histological demonstration of IgG and IgM complexes as well as complement C1q, C3c and C4 between muscle fibres and at the dermo-epidermal junctions. The patient's symptoms abated and the abnormal results of blood tests reverted to normal following cessation of clonidine therapy.

Clonidine↗
PubMed1994

Predictors of survival in patients with AIDS and disseminated Mycobacterium avium complex disease.

Patients with AIDS and disseminated Mycobacterium avium complex disease (DMAC), as defined by the presence of a positive blood culture for MAC, were studied retrospectively to define the natural history of DMAC. All patients had fevers, severe anemia (hematocrit < 26%), or both. Eighty-seven (76%) had signs, symptoms, or laboratory findings related to the gastrointestinal tract, but no distinct syndrome was identified. Sixty-nine patients received antimycobacterial therapy; assignment to therapy was not randomized. In a proportional hazards analysis, shorter survival was associated with higher initial level of mycobacteremia (relative risk [RR], 1.86; 95% confidence interval [CI], 1.49-2.31; P < .001), while administration of antimycobacterial chemotherapy (RR, 0.42; 95% CI, 0.26-0.70; P < .001) and antiretroviral therapy (RR, 0.40; 95% CI, 0.22-0.73; P < .01) had protective effects. Thus, the initial level of mycobacteremia of patients with DMAC may have prognostic value, and administration of antimycobacterial and antiretroviral agents may be associated with prolonged survival.

AIDS-Related Opportunistic Infections↗
PubMed1982

Dietary fat affects immune response, production of antiviral factors, and immune complex disease in NZB/NZW mice.

Autoimmune-prone (NZB x NZW)F1 (B/W) mice fed three nearly isocaloric diets with varied fat content showed a marked difference in their spontaneous development of immune complex disease and their immune response. Those animals received the diets high in either unsaturated or saturated fats had more severe immune complex nephritis and died earlier than mice on the low-fat diet. Endogenous production of the mouse xenotropic virus was unaffected by dietary fats, but the serum lipoproteins associated with antiviral activity were increased to levels as high as 1:600,000 in the B/W mice on the high-fat diets. These lipoproteins may be partially responsible for the decreased mitogenic response of spleen cells from mice fed the two high-fat diets. The mice receiving a diet high in saturated fats produced substantially higher titers of natural thymocytotoxic autoantibody, an IgM class of antibody, than did the mice maintained either on the high-unsaturated-fat or low-fat diet. In contrast, the mice receiving the diet high in unsaturated fats made significantly greater levels of antibodies to double-stranded DNA, an IgG, than did the mice kept on the two other diets. These results suggest that the type of fat in the diet could affect the serum level of different immunoglobulin classes. The data provide further evidence that the amount of dietary lipids alone can influence cellular and humoral immune responses and the spontaneous development of immune complex disease.

Animals↗
PubMedDate not supplied

A renaissance of "biochemical genetics"? SNPs, haplotypes, function, and complex diseases.

We have made remarkable progress in understanding the molecular bases of many Mendelian diseases over the past 2-3 decades. The current interest in discovering the molecular basis of complex diseases uses either linkage or candidate gene approaches. The latter often uses case/control (or case/cohort) study designs. We believe it is critically important to have a thorough understanding of SNP (single nucleotide) and haplotype function in such endeavors. Functionally neutral SNPs and haplotypes are probably best suited for linkage studies (far away from the locus of interest). Functionally relevant SNPs and haplotypes seem best suited for candidate gene approaches. The need for functional data may result in a renaissance of biochemical genetics with a new twist in the genomic era. We propose that the functional characterization of SNPs and haplotypes be advanced with great vigor for those genes with defined assayable phenotypes. These systematic investigations will involve classical biochemistry, modern genetics, and genomics and will probably also draw on newer technologies such as microarrays. In short, a renaissance of biochemical genetics will advance our understanding of complex diseases.

3-Oxo-5-alpha-Steroid 4-Dehydrogenase↗
PubMed2003

Multipoint linkage disequilibrium mapping for complex diseases.

Linkage disequilibrium (LD) or association studies using case-parent trios have become a common approach to locate unobserved susceptibility genes underlying complex diseases. With the availability of ever more dense marker maps, how to utilize the information carried by multiple markers simultaneously remains challenging. Recently, Liang et al. ([2001a] Am. J. Hum. Genet. 68: 937-950) proposed a multipoint LD method to estimate the location of a susceptibility gene within a framework map along with its sampling uncertainty. Two important features of this method are that 1) it uses all trios whether parents are heterozygous for a given marker or not, and 2) it provides a single test statistic for the null hypothesis of no linkage or no LD to the region, avoiding the multiple testing problem encountered when performing individual transmission disequilibrium tests (TDT) for each marker individually. In this paper, we discuss how this method can be expanded to address important issues pertaining to complex diseases in a unified fashion. These issues include, among others, gene-gene and gene-environment interactions, genetic heterogeneity, phenotypic refinement, and paternal vs. maternal transmission. We applied this method to asthmatic case-parent trios from the Collaborative Study on the Genetics of Asthma (CSGA), and found that the previous evidence for linkage and LD in a 13.6 cM region of chromosome 11 can be attributed to maternal transmission, while there was no evidence of excess paternal transmission. Furthermore, such discrepancy in preferential transmission was most evident among probands with early onset age (6 years old or younger).

Algorithms↗
PubMed2003

Geminivirus disease complexes: an emerging threat.

Small circular single-stranded DNA satellites have recently been isolated from plants infected with whitefly-transmitted monopartite begomoviruses. The satellites, named DNA beta, depend on the helper viruses for their proliferation and, in turn, are required for helper virus accumulation and symptom expression. They are highly diverse yet retain an overall conserved structure with respect to potential coding regions and regulatory elements. The begomovirus-satellite disease complexes are associated with economically important diseases, and have been isolated from vegetable and fibre crops, ornamental plants and weeds throughout Africa and Asia. Their widespread distribution and diversity, coupled to the global movement of plant material and the dissemination of the whitefly vector, suggests that these disease complexes pose a serious threat to tropical and sub-tropical agro-ecosystems worldwide.

Africa↗
PubMed2001

Lack of replication of association findings in complex disease: an analysis of 15 polymorphisms in prior candidate genes for sporadic Alzheimer's disease.

There is considerable enthusiasm for the prospect of using common polymorphisms (primarily single nucleotide polymorphisms; SNPs) in candidate genes to unravel the genetics of complex disease. This approach has generated a number of findings of loci which are significantly associated with sporadic Alzheimer's disease (AD). In the present study, a total of 15 genes of interest were chosen from among the previously published reports of significant association in AD. Genotyping was performed on polymorphisms within those genes (14 SNPs and one deletion) using Dynamic Allele Specific Hybridization (DASH) in 204 Swedish patients with sporadic late-onset AD and 186 Swedish control subjects. The genes chosen for analysis were; low-density lipoprotein receptor-related protein (LRP1), angiotensin converting enzyme (DCP1), alpha-2-macroglobulin (A2M), bleomycin hydrolase (BLMH), dihydrolipoyl S-succinyltransferase (DLST), tumour necrosis factor receptor superfamily member 6 (TNFRSF6), nitric oxide synthase (NOS3), presenilin 1 (PSEN1), presenilin 2 (PSEN2), butyrylcholinesterase (BCHE), Fe65 (APBB1), oestrogen receptor alpha (ESR1), cathepsin D (CTSD), methylenetetrahydrofolate reductase (MTHFR), and interleukin 1A (IL1A). We found no strong evidence of association for any of these loci with AD in this population. While the possibility exists that the genes analysed are involved in AD (ie they have weak effects and/or are population specific), results reinforce the need for extensive replication studies if we are to be successful in defining true risk factors in complex diseases.

Alleles↗
PubMed2003

Measuring and using admixture to study the genetics of complex diseases.

Admixture is an important evolutionary force that can and should be used in efforts to apply genomic data and technology to the study of complex disease genetics. Admixture linkage disequilibrium (ALD) is created by the process of admixture and, in recently admixed populations, extends for substantial distances (of the order of 10 to 20 cM). The amount of ALD generated depends on the level of admixture, ancestry information content of markers and the admixture dynamics of the population, and thus influences admixture mapping (AM). The authors discuss different models of admixture and how these can have an impact on the success of AM studies. Selection of markers is important, since markers informative for parental population ancestry are required and these are uncommon. Rarely does the process of admixture result in a population that is uniform for individual admixture levels, but instead there is substantial population stratification. This stratification can be understood as variation in individual admixtures and can be both a source of statistical power for ancestry--phenotype correlation studies as well as a confounder in causing false-positives in gene association studies. Methods to detect and control for stratification in case/control and AM studies are reviewed, along with recent studies showing individual ancestry--phenotype correlations. Using skin pigmentation as a model phenotype, implications of AM in complex disease gene mapping studies are discussed. Finally, the article discusses some limitations of this approach that should be considered when designing an effective AM study.

Black or African American↗
PubMed2005

High resolution T association tests of complex diseases based on family data.

This paper proposes family based Hotelling's T(2) tests for high resolution linkage disequilibrium (LD) mapping or association studies of complex diseases. Assume that genotype data of multiple markers or haplotype blocks are available for a sample of nuclear families, in which some offspring are affected. Paired Hotelling's T(2) test statistics are proposed for a high resolution association study using parents as controls for affected offspring, based on two coding methods: haplotype/allele coding and genotype coding. The paired Hotelling's T(2) tests take not only the correlation between the haplotype blocks or markers into account, but also take the correlation within each parent-offspring pair into account. The method extends two sample Hotelling's T(2) test statistics for population case control association studies, which are not valid for family data due to correlation of genetic data among family members. The validity of the proposed method is justified by rigorous mathematical and statistical proof under the large sample theory. The non-centrality parameter approximations of the test statistics are calculated for power and sample size calculations. From power comparison and type I error calculations, it is shown that the test statistic based on haplotype/allele coding is advantageous over the test statistic of genotype coding. Analysis using multiple markers may provide higher power than single marker analysis. If only one marker is utilized the power of the test statistic based on haplotype/allele coding is nearly identical to that of 1-TDT. Moreover, a permutation procedure is provided for data analysis. The method is applied to data from a German asthma family study. The results based on the paired Hotelling's T(2) statistic tests confirm the previous findings. However, the paired Hotelling's T(2) tests produce much smaller P-values than those of the previous study. The permutation tests produce similar results to those of the previous study; moreover, additional marker combinations are shown to be significant by permutation tests. The proposed paired Hotelling's T(2) statistic tests are potentially powerful in mapping complex diseases. A SAS Macro, Hotel_fam.sas, has been written to implement the method for data analysis.

Asthma↗
PubMed2006

Relationship between clinical efficacy of treatment of pulmonary Mycobacterium avium complex disease and drug-sensitivity testing of Mycobacterium avium complex isolates.

We prospectively investigated the relationship between the clinical efficacy of treatment of pulmonary Mycobacterium avium complex (MAC) disease and drug-sensitivity testing of MAC isolates for antituberculous drugs, new quinolone antibiotics, and clarithromycin (CAM). Fifty-two patients who satisfied the diagnostic criteria of the American Thoracic Society (ATS) and who received treatment between April 1998 and December 2005, using combined therapy of rifampicin (RFP), ethambutol (EB), streptomycin (SM), and CAM, were enrolled in this study. The causative microorganisms isolated were Mycobacterium avium in 30 patients and M. intracellulare in 22 patients. Although separation of the two strains showed drug sensitivity testing to have slightly better minimal inhibitory concentrations (MIC) for M. intracellulare than for M. avium, there were no significant differences in the sputum eradication rate or clinical improvement between the two strains. The MICs of various antibiotics for the isolated MAC strains were as follows: RFP, 0.125-8 microg/ml; CAM, 0.25-16 microg/ml; SM, 2-128< or =microg/ml; EB, 128< or = microg/ml; levofloxacin (LVFX), 1-32 microg/ml; sparfloxacin (SPFX), 0.5-16 microg/ml; and gatifloxacin (GFLX), 0.25-8 microg/ml. The isolated MAC strains showed the same excellent drug sensitivity test results for RFP, new quinolones, and CAM, but they showed resistant drug-sensitivity results for EB and SM. Regarding the relationship between clinical efficacy and the MICs of RFP, EB, CAM, and SM, there was a good relationship only for CAM. Although the ATS has not yet recommended routine drug susceptibility testing of CAM, we believe that drug susceptibility testing of CAM should be performed before the initial treatment is undertaken for pulmonary MAC disease.

Anti-Bacterial Agents↗
PubMed2003

Familiality in simple and complex disease.

Establishing the existence of a genetic contribution to disease is the first step in identifying the underlying gene defect(s). This can present a considerable challenge, particularly in diseases where the genetic contribution is complex in nature. Clinically well-characterized cohorts and large inter-institutional collaborations will be required to identify genes involved in complex disease.

Family↗
PubMed2003

A practice approach for identifying previously unsuspected environmental contributors to systemic lupus erythematosus and other complex diseases.

Existing medical records and health surveys provide insights into potential environmental contributors to complex chronic diseases. Those recognizable risks (e.g., workplace exposures and behaviors including smoking) do not, however, exhaust the domain of potential environmental contributors. Qualitative ethnographic investigation can be used to generate statistically testable hypotheses about environmental contributors to complex disease that otherwise would not be recognized as such. Consequently, we can empirically specify lifestyle beliefs and behaviors usually summarized by proxy identities such as race, ethnicity, gender, class, and culture. The investigation of potential environmental contributors to complex diseases may be particularly useful in confirming or disconfirming suggestive or established linkages and for indicating the kind of gene-environment interaction that may be involved.

Environmental Exposure↗
PubMed2006

Individual single tube genotyping and DNA pooling by allele-specific PCR to uncover associations of polymorphisms with complex diseases.

BACKGROUND: The genotyping for the study of the SNPs in different complex diseases require a great number of patients. In this sense, the determination of allele frequencies and genotypes requires a rapid and economical procedure. METHODS: The genotype has been carried out by allele-specific PCR in single tube with the discrimination of the products of PCR by its T(m). For this purpose a GC tail was added to 5' extreme of the specific primer. The allele frequencies were also calculated by DNA pooling and QRT-PCR using allele-specific primers. RESULTS: The use of the genotyping in single tube through allele-specific PCR and melting curves has led us to the accurate genotype of three polymorphisms of vdr (cdx-2), osteoprotegerin (A-163G) and ppar-gamma (C-681G) genes in 225 postmenopausal women to be associated to osteoporosis. Only the cdx-2 polymorphism was associated with a reduced bone mineral density (BMD). These data were similar to those obtained when the allele frequencies were calculated using QRT-PCR in DNA pools. CONCLUSIONS: Individual genotyping with allele-specific PCR in single tube and melting curve analysis is a fast, trustworthy and economic method to study any SNP. We propose the following approach to determine the possible association of SNPs with complex and multifactorial diseases like osteoporosis, in which hundreds of individuals should be analyzed: construct control and problem groups, make DNA pools, and calculate pooled allelic frequencies. Genotyping each individual further permits to determine the genotypic distribution when differences in allelic frequencies are observed, thus allowing more complex statistical analyses (including other variables like age, weight, etc.).

CDX2 Transcription Factor↗