The power of the transmission disequilibrium test (TDT) with both case-parent and control-parent trios

The transmission disequilibrium test (TDT) customarily uses affected children and their parents (often case-parent trios, TDTD). Control-parent trios are necessary to guard against spurious significant results due to segregation distortion but are not generally utilized in the identification of disease susceptibility loci (DSL). Controls are often easy to recruit and the TDT can easily be extended to include control-parent trios into the analyses with unrelated case-parent trios. We present an extension of the TDT (TDTDC) that incorporates unrelated cases and controls and their parents into a single analysis. We develop a simple and accurate analytical method for computing the statistical power of various TDT (e.g. the TDTD, TDTDC, TDTDC and TDTC that employ control-parent trios only) under any genetic model. We investigated the power of these TDT, and particularly compared the relative power of the TDTD and TDTDC. We found that the TDTDC is almost always more powerful than the TDTC and TDTD. The relative power of the TDTDC and TDTD depends largely upon a number of parameters identified in the study. This study provides a basis for efficient use of control-parent trios in DSL identification.     

Linkage and association of proinflammatory cytokines genes <Emphasis Type=Italic>IL-6, IFNG</Emphasis> and <Emphasis Type=Italic>TNF</Emphasis> with multiple sclerosis

Proinflammatory cytokines interleukin-6 (IL-6), interferon-γ (IFNg) and tumor necrosis factor (TNF) play an important role in the pathogenesis of multiple sclerosis. Based on the published data concerning the effects of the SNPs G(−308)A of TNF, A(+874)T of IFNG, and G(−174)C of IL-6 on the production of these cytokines, we investigated the relation of these polymorphisms with multiple sclerosis. Linkage and association of alleles of these genes with multiple sclerosis were analyzed by transmission disequilibrium test. In a group of 104 nuclear families of Russian ethnicity, the TNF*(−308)A allele was more frequently transmitted from healthy heterozygous parents to affected children (p = 0.01). Linkage/association of IFNG and IL-6 alleles with multiple sclerosis was not detected. Thus, the data obtained indicate that TNF is involved in susceptibility to multiple sclerosis in Russians.     

Assessment of the levels of nitric oxide (NO) and cytokines (IL-5, IL-6, IL-13, TNF, IFN-gamma) in giardiosis

The current study aims to determine the involvement of cellular responses in combating Giardia intestinalis invasion. The study group consisted of 44 women and 18 men, aged 18-72 years, infected with G. intestinalis. The diagnosis was established based on laboratory investigations (examination of stool, choloscopy, GSA-65). Blood for analysis was collected before antiparasitic treatment and two weeks after treatment termination. The control group consisted of 22 women and 18 men aged 20-45 years. The serum concentrations of IL-5, IL-6, IL-13, TNF, IFN-g were assayed using a set of Quantikine human. The concentrations of NO in the serum were determined using a set of Total Nitric Oxide Assay. Patients infected with G. intestinalis showed a statistically significant increase in the levels of NO, IFN-g and IL-13. Even the antiparasitic treatment applied did not reduce the levels of these parameters and only caused a rise in IL-6. Our study showed a lack of acute inflammatory state in the course of G. intestinalis infection.     

A sibship test for linkage in the presence of association: the sib transmission/disequilibrium test.

Linkage analysis with genetic markers has been successful in the localization of genes for many monogenic human diseases. In studies of complex diseases, however, tests that rely on linkage disequilibrium (the simultaneous presence of linkage and association) are often more powerful than those that rely on linkage alone. This advantage is illustrated by the transmission/disequilibrium test (TDT). The TDT requires data (marker genotypes) for affected individuals and their parents; for some diseases, however, data from parents may be difficult or impossible to obtain. In this article, we describe a method, called the "sib TDT" (or "S-TDT"), that overcomes this problem by use of marker data from unaffected sibs instead of from parents, thus allowing application of the principle of the TDT to sibships without parental data. In a single collection of families, there might be some that can be analyzed only by the TDT and others that are suitable for analysis by the S-TDT. We show how all the data may be used jointly in one overall TDT-type procedure that tests for linkage in the presence of association. These extensions of the TDT will be valuable for the study of diseases of late onset, such as non-insulin-dependent diabetes, cardiovascular diseases, and other diseases associated with aging.     

Selection of genetic markers for association analyses,using linkage disequilibrium and haplotypes

The genotyping of closely spaced single-nucleotide polymorphism (SNP) markers frequently yields highly correlated data, owing to extensive linkage disequilibrium (LD) between markers. The extent of LD varies widely across the genome and drives the number of frequent haplotypes observed in small regions. Several studies have illustrated the possibility that LD or haplotype data could be used to select a subset of SNPs that optimize the information retained in a genomic region while reducing the genotyping effort and simplifying the analysis. We propose a method based on the spectral decomposition of the matrices of pairwise LD between markers, and we select markers on the basis of their contributions to the total genetic variation. We also modify Clayton's "haplotype tagging SNP" selection method, which utilizes haplotype information. For both methods, we propose sliding window-based algorithms that allow the methods to be applied to large chromosomal regions. Our procedures require genotype information about a small number of individuals for an initial set of SNPs and selection of an optimum subset of SNPs that could be efficiently genotyped on larger numbers of samples while retaining most of the genetic variation in samples. We identify suitable parameter combinations for the procedures, and we show that a sample size of 50-100 individuals achieves consistent results in studies of simulated data sets in linkage equilibrium and LD. When applied to experimental data sets, both procedures were similarly effective at reducing the genotyping requirement while maintaining the genetic information content throughout the regions. We also show that haplotype-association results that Hosking et al. obtained near CYP2D6 were almost identical before and after marker selection.     

Relationship between circulating interleukin-10 (IL-10) with interleukin-6 (IL-6) type cytokines (IL-6, interleukin-11 (IL-11), oncostatin M (OSM)) and soluble interleukin-6 (IL-6) receptor (sIL-6R) in patients with multiple myeloma

We investigated the serum concentration of the interleukin-10 (IL-10), along with cytokines of interleukin-6 (IL-6) family (IL-6, IL-11 and oncostatin M - OSM), as well as soluble receptor for IL-6 (sIL-6R), in 121 patients with multiple myeloma (MM) and 28 healthy subjects. We studied the interactions between IL-10 and other cytokines, and the receptor. The correlation between IL-10 and some clinical and laboratory parameters associated with the disease activity were also analysed. The IL-10 was detectable in all patients with multiple myeloma and in all controls. The IL-10 concentration was significantly increased in myeloma patients compared with healthy persons (mean - 7.09 and 2.1 pg/ml, respectively) (p = 0.008). The level of IL-10 correlated positively with the advanced stage of disease estimated according to the Salmon and Durie classification (I versus III stage - p = 0.03). Higher values of IL-10 were found in patients with the light chain disease, hypercalcaemia, and correlated with the elevated concentrations of C-reactive protein (CRP). IL-6 was detected in 117 of the 121 patients and in all controls. The concentration of IL-6 was statistically increased in MM patients compared with control group (mean - 16.06 and 4.49 pg/ml, respectively) (p = 0.01). We found a positive correlation between IL-10 and IL-6 serum levels in MM patients. The relationship, expressed as Spearman's rank sum coefficient (rho = 0.249, p = 0.006) was significant. IL-11 was detected in 26 of the 121 MM patients and in 3 of the 28 healthy subjects at the mean concentration of 1.2 and 0.6 pg/ml respectively (p > 0.05). OSM was at detectable levels in 51 of the 121 patients and in only 4 of the 28 controls (mean - 3.84 and 0.1 pg/ml, p = 0. 002). The correlation between IL-10 and IL-11 levels in MM patients was not significant, but there was a strong statistical correlation between IL-10 and OSM concentrations (rho= 0.327, p = 0.0002). The serum concentration of sIL-6R was measurable in all patients and all controls (mean - 66.00 and 39.57 ng/ml respectively), but the difference between these groups was not significant. We found significant, positive correlation between the levels of IL-10 and sIL-6R (rho= 0.233, p = 0.01). In conclusion, we state that the serum concentrations of IL-10, IL-6, OSM and sIL-6R in MM patients may be a useful markers for the evaluation of the disease activity.     

Nucleotide diversity and linkage disequilibrium of adaptive significant genes in Larix (Pinaceae)

Russian Journal of Genetics - Nucleotide polymorphism in genes potentially responsible for the adaptation to the latitudinal gradient of climate was investigated in the Siberian larch (Larix...     

Genetic diversity, linkage disequilibrium, and association mapping analyses of peach (Prunus persica) landraces in China

The genetic diversity, population structure, and linkage disequilibrium (LD) of peaches are greatly important in genome-wide association mapping. In the current study, 104 peach landrace accessions from six Chinese geographical regions were evaluated for fruit and phenological period. The accessions were genotyped with 53 genome-wide simple sequence repeat (SSR) markers. All SSR markers were highly polymorphic across the accessions, and a total of 340 alleles were detected, including 59 private alleles. Of the six regions studied, the northern part of China as well as the middle and lower reaches of the Changjiang River were found to be the most highly diverse genetically. Based on population structure analysis, the peaches were divided into five groups, which well agreed with the geographical distribution. Of the SSR pairs in these accessions, 18.07% (P?<?0.05) were in LD. The mean r ² value for all intrachromosomal loci pairs was 0.0149, and LD decayed at 6.01?cM. The general linear model was used to calculate the genome-wide marker-trait associations of 10 complex traits. The traits include flesh color around the stone, red pigment in the flesh, flesh texture, flesh adhesion, flesh firmness, fruit weight, chilling requirement, flowering time, ripening time, and fruit development period. These traits were estimated by analyzing the 104 landraces. Many of the associated markers were located in regions where quantitative trait loci (QTLs) were previously identified. Peach association mapping is an effective approach for identifying QTLs and may be an alternative to QTL mapping based on crosses between different lines.     

The effects of genotype-dependent recombination, and transmission asymmetry, on linkage disequilibrium

A recent sperm-typing study by Jeffreys and Neumann suggested that recombination rates in different individuals at the DNA2 recombination hotspot appeared to be highly dependent on their genotype at a particular A/G SNP, FG11. Specifically, individuals who carried at least one copy of the A allele at this SNP exhibited rates of crossover considerably higher than those of individuals with no copies. Further, recombinant sperm from heterozygous individuals showed a preferential tendency to carry the G allele. We consider the effects of these phenomena on patterns of linkage disequilibrium and find them to be more subtle than might have been expected. In particular, our analysis suggests that, perhaps surprisingly, patterns of LD among chromosomes carrying the "hot" allele (in this case, A) will typically be similar to those among chromosomes carrying the "cold" allele (G).     

Simultaneous fine mapping of multiple closely linked quantitative trait Loci using combined linkage disequilibrium and linkage with a general pedigree

Within a small region (e.g., <10 cM), there can be multiple quantitative trait loci (QTL) underlying phenotypes of a trait. Simultaneous fine mapping of closely linked QTL needs an efficient tool to remove confounded shade effects among QTL within such a small region. We propose a variance component method using combined linkage disequilibrium (LD) and linkage information and a reversible jump Markov chain Monte Carlo (MCMC) sampling for model selection. QTL identity-by-descent (IBD) coefficients between individuals are estimated by a hybrid MCMC combining the random walk and the meiosis Gibbs sampler. These coefficients are used in a mixed linear model and an empirical Bayesian procedure combines residual maximum likelihood (REML) to estimate QTL effects and a reversible jump MCMC that samples the number of QTL and the posterior QTL intensities across the tested region. Note that two MCMC processes are used, i.e., an (internal) MCMC for IBD estimation and an (external) MCMC for model selection. In a simulation study, the use of the multiple-QTL model clearly removes the shade effects between three closely linked QTL located at 1.125, 3.875, and 7.875 cM across the region of 10 cM, using 40 markers at 0.25-cM intervals. It is shown that the use of combined LD and linkage information gives much more useful information compared to using linkage information alone for both single- and multiple-QTL analyses. When using a lower marker density (11 markers at 1-cM intervals), the signal of the second QTL can disappear. Extreme values of past effective size (resulting in extreme levels of LD) decrease the mapping accuracy.     

Interleukin (IL)-1 gene polymorphisms: relevance of disease severity associated alleles with IL-1beta and IL-1ra production in multiple sclerosis

BACKGROUND: Multiple sclerosis (MS) is an autoimmune disorder, with a considerable genetic influence on susceptibility and disease course. Cytokines play an important role in MS pathophysiology, and genes encoding various cytokines are logical candidates to assess possible associations with MS susceptibility and disease course. We previously reported an association of a combination of polymorphisms in the interleukin (IL)-1B and IL-1 receptor antagonist (IL-1RN) genes (i.e. IL-1RN allele 2+/IL-1B(+3959)allele 2-) with disease severity in MS. Extending this observation, we investigated whether IL-1beta and IL-1ra production differed depending on carriership of this gene combination. METHODS: Twenty MS patients and 20 controls were selected based upon carriership of the specific combination. In whole blood, in vitro IL-1beta and IL-1ra production was determined by enzyme-linked immunosorbent-assay after 6 and 24 h of stimulation with lipopolysaccharide. RESULTS: Carriers of the specific combination produced more IL-1ra, especially in MS patients, although not significantly. IL-1ra production was significantly higher in individuals homozygous for IL-1RN allele 2. In patients, Il-1ra production was higher and IL-1beta production lower compared with controls. In primary progressive patients, the IL-1beta /IL-1ra ratio was significantly lower than in relapsing-remitting patients. CONCLUSION: Our results suggest higher in vitro IL-1ra production in carriers of IL-1RN allele 2, with an indication of an allelic dose-effect relationship.     

Expectation maximization algorithm based haplotype relative risk (EM-HRR): test of linkage disequilibrium using incomplete case-parents trios

The Haplotype Relative Risk (HRR) was first proposed [Falk et al., Ann Hum Genet 1987] to test for Linkage Disequilibrium (LD) between a marker and a putative disease locus using case-parent trios. Spurious association does not appear in such family-based studies under population admixture. In this paper, we extend the HRR to accommodate incomplete trios via the Expectation-Maximization (EM) algorithm [Dempster et al., J R Stat Soc Ser B, 1977]. In addition to triads and dyads (parent-offspring pair), the EM-HRR easily incorporates individuals with no parental genotype information available, which is excluded from the one parent Transmission/Disequilibrium Test (1-TDT) [Sun et al., Am J Epidemiol 1999]. Due to the data structure of EM-HRR, transmitted alleles are always available regardless of the number of missing parental genotypes. As a result of having a larger sample size, computer simulations reveal that the EM-HRR is more powerful in detecting LD than the 1-TDT in a population under Hardy-Weinberg Equilibirum (HWE). If admixture is not extreme, the EM-HRR remains more powerful. When a large degree of admixture exists, the EM-HRR performs better the 1-TDT when the association is strong, though not as well when the association is weak. We illustrate the proposed method with an application to the Framingham Heart Study.     

Enhancement of IL-6 receptor beta chain (gp130) expression by IL-6, IL-1 and TNF in human epithelial cells.

Analysis of the IL-6 Receptor beta chain (gp130) mRNA expression on the two human epithelial cell lines UAC and Hep3B reveals that it is enhanced by IL-6, IL-1 and TNF treatment. In the case of UAC cells, TNF action might be mediated by IL-6. For Hep3B cells, TNF seems to exert a direct effect on gp130, as no IL-6 expression is detected after stimulation by this cytokine. On the same cells, increase of the binding of an anti-gp130 monoclonal antibody was observed after treatment by TNF, which denotes the effective appearance of new gp130 molecules on the cell surface. All this cytokines seem to act selectively on the beta chain of the IL-6 receptor. This probably reflects the importance for some cells to have gp130 represented on their membrane in inflammatory contexts.     

Complex inheritance of ABCR mutations in Stargardt disease: linkage disequilibrium, complex alleles, and pseudodominance

Stargardt disease is a recessively transmitted disease caused by mutations in the ABCR gene. Linkage disequilibrium has recently been reported between a polymorphism, 2828 A, and a common Western European founder mutation, 2588 C. Here, we confirm this linkage disequilibrium in a North American population. We also describe two complex alleles involving the 2828 A and 2588 C alterations and suggest a possible order of clinical severity of mutations identified in trans to the complex alleles. Finally, we report pseudodominance of Stargardt disease in a family with the 2588 C mutation, further supporting a high frequency of carriers for ABCR mutations in our population.     

Analysis of the HLA-ABC linkage disequilibrium: Decreasing strength of gametic association with increasing map distance

Summary 1242 HLA-ABC haplotypes of the North German population (Hamburg) as deduced by family analyses are described. They are in perfect agreement with recently published data by Mayr (1977) from Austria (Vienna) in all parameters tested: frequency of the single HLA-alleles, haplotype distribution and linkage disequilibrium values. Gametic association studies revealed that 69.4% of the B and C genes (map distance 0.2 cM) 36.9% of the A and C genes (0.6 cM), but only 23.2% of the A and B genes (0.8 cM) were significantly more often combined than expected due to their frequencies. From these findings it seems likely that the linkage disequilibrium within the MHC is rather due to a short evolutionary period than to selective forces. Some observations as to the most common European haplotype A1,B8 are discussed.     

Analysis of the MTHFR gene linkage disequilibrium structure and association of polymorphic gene variants with coronary atherosclerosis

Analysis of the genome-specific linkage disequilibrium patterns in certain populations is a highly promising approach to the identification of functional variants that underlie susceptibility to complex diseases. In the present study, the linkage disequilibrium patterns of the methylenetetrahydrofolate reductase gene (MTHFR) were examined in a group of patients with coronary atherosclerosis (coronary artery disease, CAD) and in a control sample from the Russian population. It was demonstrated that in the samples from one population, which were differentiated by the presence or absence of CAD, the MTHFR linkage disequilibrium patterns had similar features. Association of the MTHFR rs7533315 and rs2066462 polymorphisms with CAD was demonstrated. In addition, the evolution of the haplotypes and their role in the formation of CAD in the Russian population was reconstructed. The data on the association between genetic variability in the MTHFR locus and pathogenetically important indices of lipid metabolism were obtained. The high informativeness of the haplotype approach in case-control tests for associations with CAD was demonstrated.