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At least 577 records · Page 32Linked to original sources
PubMed2006

Genomewide scan and fine mapping of quantitative trait loci for intraocular pressure on 5q and 14q in West Africans.

PURPOSE: High intraocular pressure (IOP) is a major risk factor for glaucoma, one of the leading causes of blindness worldwide. Because it has been demonstrated that African populations are at increased risk for glaucoma, the authors investigated the genetic basis of IOP in a sample of West Africans with type 2 diabetes (T2D) from Ghana and Nigeria. METHODS: Genomewide linkage analysis was conducted for loci linked to IOP (measured by applanation tonometry) in 244 affected sibling pairs with T2D using 372 autosomal short-tandem repeat markers at an average spacing of 9 cM. RESULTS: Multipoint variance components linkage analyses revealed suggestive linkage on chromosome 5 (5q22) with a logarithm of odds (LOD) score of 2.50 (nominal P = 0.0003; empiric P = 0.0004) and on chromosome 14 (14q22) with an LOD score of 2.95 (nominal P = 0.0001; empiric P = 0.0003). Fine mapping at a marker density of 2 cM in the 5q region confirmed the linkage signal, with an increase in peak LOD score to 4.91. CONCLUSIONS: The strong signal on chromosome 5 lies in the region in which a novel gene, WDR36, in the GLC1G locus was recently identified as causative for adult-onset primary open-angle glaucoma and provides additional evidence that chromosome 5 contains susceptibility loci for glaucoma in multiple human populations. The evidence provided in this study is particularly important given the evolutionary history of these West African populations and the recent ancestral relationship to African Americans-a population with one of the highest rates of diabetes and associated complications (including glaucoma) in the world.

Chromosome Mapping↗
PubMed2003

Using haplotype blocks to map human complex trait loci.

Understanding of linkage disequilibrium (LD) in human populations could facilitate the discovery of genes that influence complex human diseases. The "HapMap" project is now underway to characterize patterns of LD in the human genome. A pilot study showed "haplotype blocks" in 51 regions scattered throughout the genome. These intriguing results raise important questions about the nature of recombination, and highlight practical issues of marker collection, the influence of statistical modelling on apparent block structure, and the levels of genotyping necessary for studies of common diseases. Knowledge of local disequilibrium patterns may help identify common polymorphisms involved in complex disease, but completely new analytical methods and experimental designs will be required to identify important rare variants.

Chromosome Mapping↗
PubMed1998

Mapping of quantitative trait loci for body weight on chromosomes 1 and 4 in the rat.

Quantitative trait loci (QTLs) affecting body weight were investigated in the backcross population derived from diabetic BB/OK and spontaneously hypertensive rat (SHR). The F1 hybrids were backcrossed onto BB/OK rats, and QTL analysis was performed with the resulting backcross population on chromosomes 1, 3, 4, 10, 13 and 18. According to the stringent threshold for a lod score of 3.0, markers on chromosomes 1 and 4 were found to be linked with body weight. The QTL with a peak lod score (3.3) on chromosome 1 for a male population was located within the region flanked by loci Igf2 and D1Mgh12. On chromosome 4, linkage between the body weight and the region around the Npy locus was observed (lod score 3.1). The existence of the QTL on chromosome 4 affecting body weight was confirmed by congenic BB.LL rats, carrying chromosomal region of SHR (D4Mit6-Npy-Spr) on the genetic background of the BB/OK rat.

Animals↗
PubMed2004

Mapping of quantitative trait loci for growth and carcass traits in commercial sheep populations.

Quantitative trait loci analyses were applied to data from Suffolk and Texel commercial sheep flocks in the United Kingdom. The populations comprised 489 Suffolk animals in three half-sib families and 903 Texel animals in nine half-sib families. Phenotypic data comprised measurements of live weight at 8 and 20 wk of age and ultrasonically measured fat and muscle depth at 20 wk. Lambs and their sires were genotyped across candidate regions on chromosomes 1, 2, 3, 4, 5, 6, 11, 18, and 20. Data were analyzed at the breed level, at the family level, and across extended families when families were genetically related. The breed-level analyses revealed a suggestive QTL on chromosome 1 in the Suffolk breed, between markers BM8246 and McM130, affecting muscle depth, although the effect was only significant in one of the three Suffolk families. A two-QTL analysis suggested that this effect may be due to two adjacent QTL acting in coupling. In total, 24 suggestive QTL were identified from individual family analyses. The most significant QTL affected fat depth and was segregating in a Texel family on chromosome 2, with an effect of 0.62 mm. The QTL was located around marker ILSTS030, 26 cM distal to myostatin. Two of the Suffolk and two of the Texel sires were related, and a three-generation analysis was applied across these two extended families. Seven suggestive QTL were identified in this analysis, including one that had not been detected in the individual family analysis. The most significant QTL, which affected muscle depth, was located on chromosome 18 near the callipyge and Carwell loci. Based on the phenotypic effect and location of the QTL, the data suggest that a locus similar to the Carwell locus may be segregating in the United Kingdom Texel population.

Adipose Tissue↗
PubMed1996

Interval mapping of quantitative trait loci controlling humoral immunity to exogenous antigens: evidence that non-MHC immune response genes may also influence susceptibility to autoimmunity.

IgG Ab titers elicited to bovine rhodopsin in CFA differ 8- to 10-fold between H2s identical inbred strains A.SW/snJ (high responder) and SJL/snJ (low responder). This variation in IgG Ab titer resulted from a dramatic difference in the rise in Ab titer occurring during the maturation of the T-dependent humoral immune response. To determine the positions of non-MHC genes controlling this quantitative variation in T-dependent humoral immune responsiveness, 206 reciprocal (A.SW/snJ x SJL/snJ)F2 female progeny were immunized and assayed for anti-rhodopsin responsiveness. The genomes of these progeny were screened with 115 polymorphic simple sequence repeat markers covering >90% of the mouse genome. interval mapping analysis localized the positions of these non-MHC immune response genes to genomic intervals on chromosomes 1, 5, and 13. Interestingly, these three intervals coincide exactly with three intervals recently shown to contain genes contributing to susceptibility to systemic lupus erythematosus and/or the production of autoimmune anti-dsDNA Abs. These results suggest that some genes affecting levels of humoral immune responsiveness to exogenous Ag may also play a role in genetic susceptibility to humoral autoimmune diseases. Analyses of the modes of inheritance demonstrated that high responder alleles were inherited from both parental genomes, indicative of epistatic interactions among genes influencing humoral immune responsiveness.

Animals↗
PubMed1999

Detection and mapping of quantitative trait loci for haloperidol-induced catalepsy in a C57BL/6J x DBA/2J F2 intercross.

A genomewide scan was conducted to detect quantitative trait loci (QTLs) for haloperidol-induced catalepsy in a C57BL/6J (B6) x DBA/2J (D2) F2 intercross (N = 678). Significant QTLs (LOD, > 4.3) were detected on chromosomes 1 and 9. The relative position of the QTL on chromosome 1 is similar to open-field activity QTLs previously identified by Flint et al. (1995) and Gershenfeld et al. (1997). Given the broad confidence intervals for these QTLs, such associations must be viewed cautiously. However, these data are consistent with the report of Kline et al. (1998), who found a significant genetic associations between catalepsy and open-field activity. The QTL interval on chromosome 9 stretched from approximately 25 to 55 cM; this region contains numerous candidate genes, including Drd2, Ncam, Acat1, and Htr1b. The data also suggest the presence of a second QTL on chromosome 9 (LOD, > 3.5) in the proximal region of the chromosome. Potential candidate genes in this region include Penk2 and Gria4. Overall, these data support our previous observation (Kanes et al., 1996) that for the B6 x D2 genotypes, one or more polymorphisms on chromosome 9 are associated with the variance in haloperidol response.

Animals↗
PubMed2003

The mapping of quantitative trait loci underlying strain differences in locomotor activity between 129S6 and C57BL/6J mice.

Performance in the open field and rotarod paradigms, two common assessments of locomotor function, have been demonstrated to be strain dependent in mice. In this study, eight significant quantitative trait loci (QTL) for behavior phenotypes in either the open field or rotarod paradigms were identified between the 129S6 (129/SvEvTac) and C57BL/6J strains. These strains were chosen for comparison because of their frequent use in the generation of mutant mice from gene-targeted, embryonic stem cells. Two of the QTLs for horizontal distance traveled are located on Chromosomes (Chrs) 1 and 12 and closely replicate the findings of other groups using different strains of mice. Rotarod performance was influenced in an oppositional manner by two separate QTLs on Chr 1 and 2. Additionally, examination of several different aspects of behavior in the open field revealed significant QTLs for average speed (Chr 12), duration (Chrs 2, 16, and 18), time spent in motion (Chr 16), vertical movements (rearing) (Chrs 6 and 12), and vertical time (rearing time) (Chrs 6 and 12). Our finding of independent QTLs for these topographic components of open field activity supports the idea that they are separate and distinct from total horizontal distance traveled and should be studied independently. The QTLs described in this study, in combination with our panel of polymorphic chromosomal markers for 129S6 and C57BL/6J strains, will be useful in assessing the potential epistatic effects of parental strain background on the phenotypes of genetically modified mice.

Animals↗
PubMed1996

Chromosomal mapping of quantitative trait loci contributing to stroke in a rat model of complex human disease.

Stroke is a complex disorder with a poorly understood multifactorial and polygenic aetiology. We used the stroke-prone spontaneously hypertensive rat (SHRSP) as a model organism, mated it with the stroke-resistant spontaneously hypertensive rat (SHR) and performed a genome-wide screen in the resultant F2 cohort where latency until stroke, but not hypertension (a major confounder) segregated. We identified three major quantitative trait loci, STR1-3, with lod scores of 7.4, 4.7 and 3.0, respectively, that account for 28% of the overall phenotypic variance. STR2 colocalizes with the genes encoding atrial and brain natriuretic factor, peptides with important vasoactive properties. Our results demonstrate the existence of primary, blood pressure-independent genetic factors predisposing to a complex form of stroke.

Animals↗
PubMed1997

Strategies for mapping heterogeneous recessive traits by allele-sharing methods.

We investigate strategies for detecting linkage of recessive and partially recessive traits, using sibling pairs and inbred individuals. We assume that a genomewide search is being conducted and that locus heterogeneity of the trait is likely. For sibling pairs, we evaluate the efficiency of different statistics under the assumption that one does not know the true degree of recessiveness of the trait. We recommend a sibling-pair statistic that is a linear compromise between two previously suggested statistics. We also compare the power of sibling pairs to that of more distant relatives, such as cousins. For inbred individuals, we evaluate the power of offspring of different types of matings and compare them to sibling pairs. Over a broad range of trait etiologies, sibling pairs are more powerful than inbred individuals, but for traits caused by very rare alleles, particularly in the case of heterogeneity, inbred individuals can be much more powerful. The models we develop can also be used to examine specific situations other than those we look at. We present this analysis in the idealized context of a dense set of highly polymorphic markers. In general, incorporation of real-world complexities makes inbred individuals, particularly offspring of distant relatives, look slightly less useful than our results imply.

Chromosome Mapping↗
PubMed1994

Monte Carlo likelihood in the genetic mapping of complex traits.

Many of the likelihoods arising in the analysis of complex genetic traits, particularly in linkage analysis, are computationally infeasible. Where exact likelihoods cannot be computed, Monte Carlo estimates of likelihoods may provide a satisfactory alternative. Although simulation on pedigrees is straightforward, simulation conditional upon observed phenotypic data is not. However, recent advances in Markov chain Monte Carlo methods have provided a method well suited to this problem. From realizations of underlying genes, simulated under a genetic model, conditional upon observed data, a Monte Carlo estimate of this likelihood surface can be formed. Various sampler and model modifications are needed to enhance the statistical efficiency of the Monte Carlo estimator; as these methods become increasingly developed, this approach becomes a useful tool in resolving the genes contributing to the phenotypes associated with genetically complex diseases.

Algorithms↗
PubMed2004

A cross-genomic approach for systematic mapping of phenotypic traits to genes.

We present a computational method for de novo identification of gene function using only cross-organismal distribution of phenotypic traits. Our approach assumes that proteins necessary for a set of phenotypic traits are preferentially conserved among organisms that share those traits. This method combines organism-to-phenotype associations,along with phylogenetic profiles,to identify proteins that have high propensities for the query phenotype; it does not require the use of any functional annotations for any proteins. We first present the statistical foundations of this approach and then apply it to a range of phenotypes to assess how its performance depends on the frequency and specificity of the phenotype. Our analysis shows that statistically significant associations are possible as long as the phenotype is neither extremely rare nor extremely common; results on the flagella,pili, thermophily,and respiratory tract tropism phenotypes suggest that reliable associations can be inferred when the phenotype does not arise from many alternate mechanisms.

Bacterial Proteins↗
PubMed2002

Interval mapping of QTLs controlling some morphological traits in pea.

A linkage map of pea was constructed based on a 104 RIL population derived from the cross combination Wt10245 x Wt11238. The map, which consisted of 204 morphological, isozyme, AFLP, ISSR, STS, CAPS and RAPD markers, was used for interval mapping of the QTLs controlling the stem length and internode number of pea. In the characterization of a given QTL, we included an identification of its position with reference to the flanking markers, an estimation of the part of variance explained by it, and a determination of gene action. Six QTLs per trait were identified as demonstrating linkage to ten intervals on five linkage groups. As many as seven QTLs influencing the analysed traits were mapped on linkage group II, indicating the important role of this region of the pea genome in plant height control.

Chromosome Mapping↗
PubMed2003

Cost-effective designs for linkage disequilibrium mapping of complex traits.

The current development of densely spaced collections of single nucleotide polymorphisms (SNPs) will lead to genomewide association studies for a wide range of diseases in many different populations. Determinations of the appropriate number of SNPs to genotype involve a balancing of power and cost. Several variables are important in these determinations. We show that there are different combinations of sample size and marker density that can be expected to achieve the same power. Within certain bounds, investigators can choose between designs with more subjects and fewer markers or those with more markers and fewer subjects. Which designs are more cost-effective depends on the cost of phenotyping versus the cost of genotyping. We show that, under the assumption of a set cost for genotyping, one can calculate a "threshold cost" for phenotyping; when phenotyping costs per subject are less than this threshold, designs with more subjects will be more cost-effective than designs with more markers. This framework for determining a cost-effective study will aid in the planning of studies, especially if there are choices to be made with respect to phenotyping methods or study populations.

Chromosome Mapping↗
PubMed1995

Restriction fragment length polymorphism mapping of quantitative trait loci for malaria parasite susceptibility in the mosquito Aedes aegypti.

Susceptibility of the mosquito Aedes aegypti to the malarial parasite Plasmodium gallinaceum was investigated as a quantitative trait using restriction fragment length polymorphisms (RFLP). Two F2 populations of mosquitoes were independently prepared from pairwise matings between a highly susceptible and a refractory strain of A. aegypti. RFLP were tested for association with oocyst development on the mosquito midgut. Two putative quantitative trait loci (QTL) were identified that significantly affect susceptibility. One QTL, pgs[2,LF98], is located on chromosome 2 and accounted for 65 and 49% of the observed phenotypic variance in the two populations, respectively. A second QTL, pgs[3,MalI], is located on chromosome 3 and accounted for 14 and 10% of the observed phenotypic variance in the two populations, respectively. Both QTL exhibit a partial dominance effect on susceptibility, wherein the dominance effect is derived from the refractory parent. No indication of epistasis between these QTL was detected. Evidence suggests that either a tightly linked cluster of independent genes or a single locus affecting susceptibility to various mosquito-borne parasites and pathogens has evolved near the LF98 locus; in addition to P. gallinaceum susceptibility, this general genome region has previously been implicated in susceptibility to the filarial nematode Brugia malayi and the yellow fever virus.

Aedes↗
PubMed1992

Maximum likelihood mapping of quantitative trait loci using full-sib families.

A maximum likelihood method is presented for the detection of quantitative trait loci (QTL) using flanking markers in full-sib families. This method incorporates a random component for common family effects due to additional QTL or the environment. Simulated data have been used to investigate this method. With a fixed total number of full sibs power of detection decreased substantially with decreasing family size. Increasing the number of alleles at the marker loci (i.e., polymorphism information content) and decreasing the interval size about the QTL increased power. Flanking markers were more powerful than single markers. In testing for a linked QTL the test must be made against a model which allows for between family variation (i.e., including an unlinked QTL or a between family variance component) or the test statistic may be grossly inflated. Mean parameter estimates were close to the simulated values in all situations when fitting the full model (including a linked QTL and common family effect). If the common family component was omitted the QTL effect was overestimated in data in which additional genetic variance was simulated and when compared with an unlinked QTL model there was reduced power. The test statistic curves, reflecting the likelihood of the QTL at each position along the chromosome, have discontinuities at the markers caused by adjacent pairs of markers providing different amounts of information. This must be accounted for when using flanking markers to search for a QTL in an outbred population.

Animals↗
PubMed2004

Statistical tests for admixture mapping with case-control and cases-only data.

Admixture mapping is a promising new tool for discovering genes that contribute to complex traits. This mapping approach uses samples from recently admixed populations to detect susceptibility loci at which the risk alleles have different frequencies in the original contributing populations. Although the idea for admixture mapping has been around for more than a decade, the genomic tools are only now becoming available to make this a feasible and attractive option for complex-trait mapping. In this article, we describe new statistical methods for analyzing multipoint data from admixture-mapping studies to detect "ancestry association." The new test statistics do not assume a particular disease model; instead, they are based simply on the extent to which the sample's ancestry proportions at a locus deviate from the genome average. Our power calculations show that, for loci at which the underlying risk-allele frequencies are substantially different in the ancestral populations, the power of admixture mapping can be comparable to that of association mapping but with a far smaller number of markers. We also show that, although "ancestry informative markers" (AIMs) are superior to random single-nucleotide polymorphisms (SNPs), random SNPs can perform quite well when AIMs are not available. Hence, researchers who study admixed populations in which AIMs are not available can perform admixture mapping with the use of modestly higher densities of random markers. Software to perform the gene-mapping calculations, "MALDsoft," is freely available on the Pritchard Lab Web site.

Chromosome Mapping↗
PubMed1999

Linkage of low-density lipoprotein size to the lipoprotein lipase gene in heterozygous lipoprotein lipase deficiency.

Small low-density lipoprotein (LDL) particles are a genetically influenced coronary disease risk factor. Lipoprotein lipase (LpL) is a rate-limiting enzyme in the formation of LDL particles. The current study examined genetic linkage of LDL particle size to the LpL gene in five families with structural mutations in the LpL gene. LDL particle size was smaller among the heterozygous subjects, compared with controls. Among heterozygous subjects, 44% were classified as affected by LDL subclass phenotype B, compared with 8% of normal family members. Plasma triglyceride levels were significantly higher, and high-density lipoprotein cholesterol (HDL-C) levels were lower, in heterozygous subjects, compared with normal subjects, after age and sex adjustment. A highly significant LOD score of 6.24 at straight theta=0 was obtained for linkage of LDL particle size to the LpL gene, after adjustment of LDL particle size for within-genotype variance resulting from triglyceride and HDL-C. Failure to adjust for this variance led to only a modest positive LOD score of 1.54 at straight theta=0. Classifying small LDL particles as a qualitative trait (LDL subclass phenotype B) provided only suggestive evidence for linkage to the LpL gene (LOD=1. 65 at straight theta=0). Thus, use of the quantitative trait adjusted for within-genotype variance, resulting from physiologic covariates, was crucial for detection of significant evidence of linkage in this study. These results indicate that heterozygous LpL deficiency may be one cause of small LDL particles and may provide a potential mechanism for the increase in coronary disease seen in heterozygous LpL deficiency. This study also demonstrates a successful strategy of genotypic specific adjustment of complex traits in mapping a quantitative trait locus.

Adolescent↗