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Allelic association and disease mapping.

The application of allelic association to map genes for complex traits, particularly using high-density maps of single nucleotide polymorphisms in candidate regions, is an area of very active research. Here we present some aspects of the methodology and applications to both major gene mapping, which illustrates the effectiveness of the method, and oligogenes, where methods are still in flux and for which there have been relatively few successes to date. Several important considerations emerge, including the selection of the optimal metric for measuring association and the importance of modelling the decline in association with distance given the variability in association in a candidate region. The Malecot model of association with distance is shown to have a resolution of greater than 50 kilobases but the available evidence suggests that considerably higher resolution might be achieved with dense single nucleotide polymorphism (SNP) maps.

Alleles↗

Microtubule-associated proteins (MAPs) regulate cAMP signalling through exchange protein directly activated by cAMP (EPAC).

cAMP is an essential signalling molecule whose concentration in cells is regulated by a wide range of hormones. A large number of diseases, including cancer and asthma, are linked to improper regulation of the cAMP signalling system, and manipulation of cAMP levels by pharmaceutical agents has proven therapeutic benefit. The action of cAMP in cells is mediated through the signalling enzymes PKA (protein kinase A) and EPAC (exchange protein directly activated by cAMP). The study of the function of these proteins is essential to understand the role of cAMP in controlling disease. We have found that EPAC interacts with an ancillary protein, called LC2 (light chain 2), and this interaction enhances EPAC's ability to activate its substrate protein, Rap1 GTPase. This is an important finding because Rap1 is involved in the control of cell migration and cell shape, functions that are disrupted in diseases like cancer. LC2 appears to enhance EPAC activity towards Rap1 by increasing the ability of EPAC to interact with cAMP, so that EPAC activation occurs at lower concentrations of cAMP. The design of inhibitors that disrupt or enhance EPAC1-LC2 interaction may therefore form the basis of future therapeutics for diseases where cAMP signalling through Rap1 is improperly regulated.

Acetylcysteine↗

Informativeness of genetic markers for inference of ancestry.

Inference of individual ancestry is useful in various applications, such as admixture mapping and structured-association mapping. Using information-theoretic principles, we introduce a general measure, the informativeness for assignment (I(n)), applicable to any number of potential source populations, for determining the amount of information that multiallelic markers provide about individual ancestry. In a worldwide human microsatellite data set, we identify markers of highest informativeness for inference of regional ancestry and for inference of population ancestry within regions; these markers, which are listed in online-only tables in our article, can be useful both in testing for and in controlling the influence of ancestry on case-control genetic association studies. Markers that are informative in one collection of source populations are generally informative in others. Informativeness of random dinucleotides, the most informative class of microsatellites, is five to eight times that of random single-nucleotide polymorphisms (SNPs), but 2%-12% of SNPs have higher informativeness than the median for dinucleotides. Our results can aid in decisions about the type, quantity, and specific choice of markers for use in studies of ancestry.

Algorithms↗

Demography, recombination hotspot intensity, and the block structure of linkage disequilibrium.

BACKGROUND: Effective gene mapping based on genetic association data will require detailed knowledge of patterns of linkage disequilibrium (LD) in human populations. It has been recently suggested that linkage disequilibrium in humans may be organized in a block-like structure, with islands of high LD separated by regions of rapid breakdown of LD due to recombination hotspots. The experimental data to date, however, are limited, and fundamental questions remain about the implications of recombination rate heterogeneity. Here, we use computer simulations to evaluate how such heterogeneity influences patterns of LD, and we develop formal criteria to assess whether the patterns are functionally block like in the context of association mapping. RESULTS: Our analyses suggest that, even in models of extreme recombination rate heterogeneity, some human populations will have a functionally block-like structure to the pattern of LD, but others will not, depending on their precise demographic histories. In fact, for many models, we find that, following an LD-generating event, populations may move through discrete phases that can be functionally described as pre-block, block, and post-block. An analysis of observed and expected patterns of LD surrounding hotspots within the MHC Class II region confirms these theoretical expectations. CONCLUSIONS: Even if highly punctuated patterns of recombination are the rule, patterns of LD are still likely to show differences among populations and among genomic regions that are of practical importance in the design of genetic association studies. The notion that the average extent of LD is a useful concept for the design of association studies must be abandoned in light of the experimental and theoretical evidence.

Demography↗

Sodium nitroprusside-induced mitochondrial apoptotic events in insulin-secreting RINm5F cells are associated with MAP kinases activation.

Exposure of insulin-secreting RINm5F cells to the chemical nitric oxide donor sodium nitroprusside (SNP) resulted in apoptotic cell death, as detected by cytochrome c release from mitochondria and caspase 3 activation. SNP exposure also leads to phosphorylation and activation of enzymes involved in cellular response to stress such as signal-regulated kinase 2 (ERK2) and c-Jun NH(2)-terminal kinase 46 (JNK46). Both cytochrome c release and caspase 3 activation were abrogated in cells exposed to MEK and p38 inhibitors. Treatment of cells with the NO donors SNP, DETA-NO, GEA 5024, and SNAP resulted in phosphorylation of the antiapoptotic protein Bcl-2, which was resistant to blockade of MEK, p38, and JNK pathways and sensitive to phosphoinositide 3-kinase (PI3K) inhibition. In addition, transient transfection of cells with the wild-type PI3K gamma gene mimics the increased rate of Bcl-2 phosphorylation detected in NO-treated cells. The generation of phosphoinositides seems to participate in the process since Bcl-2 phosphorylation was not observed in cells overexpressing lipid-kinase-deficient PI3Kgamma. The potential of SNP toxicity directly from NO was supported by our finding that the NO scavenger carboxy-PTIO prevented cell death. We found no evidence to support the contention that oxygen radicals generated during cellular SNP metabolism mediate cell toxicity in RINm5F cells, since neither addition of catalase/superoxide dismutase nor transfection with superoxide dismutase prevented SNP-induced cell death. Thus, we propose that exposure to apoptotic concentrations of NO triggers ERK- and p38-dependent cytochrome c release, caspase 3 activation, and PI3K-dependent Bcl-2 phosphorylation.

Animals↗

Fifty years of genetic epidemiology, with special reference to Japan.

Genetic epidemiology deals with etiology, distribution, and control of disease in groups of relatives and with inherited causes of disease in populations. It took its first steps before its recognition as a discipline, and did not reach its present scope until the Human Genome Project succeeded. The intimate relationship between genetics and epidemiology was discussed by Neel and Schull (1954), just a year after Watson and Crick reported the DNA double helix, and 2 years before human cytogenetics and the Japan Society of Human Genetics were founded. It is convenient to divide the next half-century into three phases. The first of these (1956-1979) was before DNA polymorphisms were typed, and so the focus was on segregation and linkage of major genes, cytogenetics, population studies, and biochemical genetics. The next phase (1980-2001) progressively identified DNA polymorphisms and their application to complex inheritance. The last phase began with a reliable sequence of the human genome (2002), followed by exploration of genomic diversity. Linkage continues to be useful to study recombination and to map major genes, but association mapping gives much greater resolution and enables studies of complex inheritance. The generation now entering human genetics will have collaborative opportunities undreamed of a few years ago, without the independence that led to great advances during the past half-century.

Epidemiology↗

The oral-facial-digital syndrome type 1 (OFD1), a cause of polycystic kidney disease and associated malformations, maps to Xp22.2-Xp22.3.

Key features of the oral-facial-digital syndrome type 1 (OFD1) include malformations of the face, oral cavity and digits. In addition, the clinical phenotype often includes mental retardation and renal functional impairment. Approximately 75% of cases of OFD1 are sporadic, and the condition occurs almost exclusively in females. In familial cases, the most likely mode of inheritance is considered to be X-linked dominant with prenatal lethality in affected males. Therefore, the OFD1 gene product appears to have widespread importance in organogenesis and is essential for fetal survival. We have studied two kindreds in which the clinical course was dominated by polycystic kidney disease requiring dialysis and transplantation. Using polymorphic chromosome markers spaced at approximately 10 cM intervals along the X chromosome, we mapped the disease to a region on the short arm of the X chromosome (Xp22.2-Xp22.3) spanning 19.8 cM and flanked by crossovers with the markers DXS996 and DX7S105. There was a maximum lod score of 3.32 in an 'affecteds only' analysis using a marker within the KAL gene (theta = 0.0 ), thereby confirming the location of the gene for OFD1 on the X chromosome. The remainder of the X chromosome was excluded by recombinants in affected individuals. The importance of our findings includes the definitive assignment of this male-lethal disease to the X chromosome and the mapping of a further locus for a human polycystic kidney disease. Furthermore, this mapping study suggests a possible mouse model for OFD1 as the X-linked dominant Xpl mutant, in which polydactyly and renal cystic disease occurs, maps to the homologous region of the mouse X chromosome.

Chromosome Aberrations↗

Self-association and mapping of interaction domains of helper component-proteinase of potato A potyvirus.

Potyviral helper component-proteinase (HC-Pro) is a multifunctional protein involved in aphid transmission, long-distance movement, polyprotein processing, genome amplification and symptom expression. It has been proposed that the active form of HC-Pro is a dimer and that coat protein (CP)-HC-Pro interaction is required for aphid transmission. To test these proposed interactions between CP and HC-Pro of potato A potyvirus (PVA), the yeast two-hybrid system was used. HC-Pro was shown to interact with itself in vivo in yeast cells, as did CP. Taken together with previous observations, we conclude that the functional HC-Pro is a homodimer. Deletion analysis showed that a 24 aa domain in the N-terminal half and the C-terminal proteinase part of HC-Pro were required for the interaction between HC-Pro molecules. No interactions were found between HC-Pro and CP using the genes of aphid-transmissible as well as aphid non-transmissible strains of PVA.

Animals↗

Structure and phosphorylation of microtubule-associated protein 2 (MAP 2).

Chymotryptic fragments of microtubule-associated protein 2 (MAP 2) containing the portion of the molecule responsible for promoting microtubule assembly were identified. These assembly-promoting fragments displaced intact MAP 2, but not MAP 1, from assembled microtubules. This indicates that the association of MAP 2 with the microtubule surface is reversible. Both the assembly-promoting fragments and fragments representing the portion of the MAP 2 molecule observed as a projection on the microtubule surface were found to contain sites for endogenous cyclic AMP-dependent phosphorylation. The projection fragments were capable of endogenous phosphorylation even after their physical separation from microtubules. This suggests an intimate association of a kinase activity with the projections. Detailed analysis of the properties of the chymotryptic fragments of MAP 2 has led to a map of the molecule showing the major sites of proteolytic attack and the sites of phosphorylation.

Animals↗

Event-related potential maps depend on prestimulus brain electric microstate map.

The brain functional microstate immediately before each of about 3000 identical tone stimuli was classified using extracted reference-free descriptors (locations of maximal and minimal potential) of the landscape of the brain's momentary electric field, in 8 volunteers. Six prestimulus microstate map classes occurred more than 30 times in each subject, and were clustered into two map class types (totals of 242 and 283 cases, respectively, on the average per subject). Event-related potential (ERP) map series were averaged for each subject and prestimulus map class. Map descriptors were extracted from the ERP maps at times of maximal Global Field Power during the component time windows N100, P200 and P330. Discriminant functions were estimated; for the maps of N100 and P330, the discriminant scores differed significantly between the maps associated with the two prestimulus map class types (paired t-tests, df = 7, p = .014 and p = .005, respectively). The dominant axis of the poststimulus class type II ERP maps deviated clockwise from that of the type I ERP maps in all components. We conclude that subtle changes in the brain's spontaneous momentary functional microstate (as classified by spatial descriptors of a single map) influence event-related information processing by the brain, following common rules over subjects.

Adult↗

Improved bidirectional retrieval of sparse patterns stored by Hebbian learning.

The Willshaw model is asymptotically the most efficient neural associative memory (NAM), but its finite version is hampered by high retrieval errors. Iterative retrieval has been proposed in a large number of different models to improve performance in auto-association tasks. In this paper, bidirectional retrieval for the hetero-associative memory task is considered: we define information efficiency as a general performance measure for bidirectional associative memory (BAM) and determine its asymptotic bound for the bidirectional Willshaw model. For the finite Willshaw model, an efficient new bidirectional retrieval strategy is proposed, the appropriate combinatorial model analysis is derived, and implications of the proposed sparse BAM for applications and brain theory are discussed. The distribution of the dendritic sum in the finite Willshaw model given by Buckingham and Willshaw [Buckingham, J., & Willshaw, D. (1992). Performance characteristics of associative nets. Network, 3, 407-414] allows no fast numerical evaluation. We derive a combinatorial formula with a highly reduced evaluation time that is used in the improved error analysis of the basic model and for estimation of the retrieval error in the naive model extension, where bidirectional retrieval is employed in the hetero-associative Willshaw model. The analysis rules out the naive BAM extension as a promising improvement. A new bidirectional retrieval algorithm - called crosswise bidirectional (CB) retrieval - is presented. The cross talk error is significantly reduced without employing more complex learning procedures or dummy augmentation in the pattern coding, as proposed in other refined BAM models [Wang, Y. F., Cruz, J. B., & Mulligan, J. H. (1990). Two coding strategies for bidirectional associative memory. IEEE Trans. Neural Networks, 1(1), 81-92; Leung, C.-S., Chan, L.-W., & Lai, E. (1995). Stability, capacity and statistical dynamics of second-order bidirectional associative memory. IEEE Trans. Syst. Man Cybern., 25(10), 1414-1424]. The improved performance of CB retrieval is shown by a combinatorial analysis of the first step and by simulation experiments: it allows very efficient hetero-associative mapping, as well as auto-associative completion for sparse patterns - the experimentally achieved information efficiency is close to the asymptotic bound. The different retrieval methods in the hetero-associative Willshaw matrix are discussed as Boolean linear optimization problems. The improved BAM model opens interesting new perspectives, for instance, in information retrieval it allows efficient data access providing segmentation of ambiguous user input, relevance feedback and relevance ranking. Finally, we discuss BAM models as functional models for reciprocal cortico-cortical pathways, and the implication of this for a more flexible version of Hebbian cell-assemblies.

Journal Article↗

A map of the human genome in linkage disequilibrium units.

Two genetic maps with additive distances contribute information about recombination patterns, recombinogenic sequences, and discovery of genes affecting a particular phenotype. Recombination is measured in morgans (w) over a single generation in a linkage map but may cover thousands of generations in a linkage disequilibrium (LD) map measured in LD units (LDU). We used a subset of single nucleotide polymorphisms from the HapMap Project to create a genome-wide map in LDU. Recombination accounts for 96.8% of the LDU variance in chromosome arms and 92.4% in their deciles. However, deeper analysis shows that LDU/w, an estimate of the effective bottleneck time (t), is significantly variable among chromosome arms because (i) the linkage map is approximated from the Haldane function, then adjusted toward the Kosambi function that is more accurate but still exaggerates w for all chromosomes, especially shorter ones; (ii) the non-pseudoautosomal region of the X chromosome is subject to hemizygous selection; and (iii) at resolution less than approximately 40,000 markers per w, there are indeterminacies (holes) in the LD map reflecting intervals of very high recombination. Selection and stochastic variation in small regions must have effects, which remain to be investigated by comparisons among populations. These considerations suggest an optimal strategy to eliminate holes quickly, greatly enhance the resolution of sex-specific linkage maps, and maximize the gain in association mapping by using LD maps.

Chromosome Mapping↗