Testing quantitative traits for association and linkage in the presence or absence of parental data

Zhu and Elston developed a transmission disequilibrium test for quantitative traits by defining a linear transformation to condition out founder information. The method tests the null hypothesis of no linkage or association and can be applied to general pedigree structures. However, this method requires both genotype and phenotype parental information, which may be difficult to obtain. In this paper, we describe parametric and non-parametric methods to relax this requirement when only nuclear families are sampled. We show that neither method is affected by population stratification in the absence of linkage. The statistical power and validity of the tests are investigated by simulation. A simple simulation method to calculate the power of the nonparametric method is also discussed. In practice, the data may have some families with parental phenotype and genotype information available and some without. We briefly discuss how all the data may be analyzed jointly.     

Linkage and association analysis of angiotensin I-converting enzyme (ACE)-gene polymorphisms with ACE concentration and blood pressure

Considerable effort has been expended to determine whether the gene for angiotensin I-converting enzyme (ACE) confers susceptibility to cardiovascular disease. In this study, we genotyped 13 polymorphisms in the ACE gene in 1,343 Nigerians from 332 families. To localize the genetic effect, we first performed linkage and association analysis of all the markers with ACE concentration. In multipoint variance-component analysis, this region was strongly linked to ACE concentration (maximum LOD score 7.5). Likewise, most of the polymorphisms in the ACE gene were significantly associated with ACE (P<.0013). The two most highly associated polymorphisms, ACE4 and ACE8, accounted for 6% and 19% of the variance in ACE, respectively. A two-locus additive model with an additive x additive interaction of these polymorphisms explained most of the ACE variation associated with this region. We next analyzed the relationship between these two polymorphisms (ACE4 and ACE8) and blood pressure (BP). Although no evidence of linkage was detected, significant association was found for both systolic and diastolic BP when a two-locus additive model developed for ACE concentration was used. Further analyses demonstrated that an epistasis model provided the best fit to the BP variation. In conclusion, we found that the two polymorphisms explaining the greatest variation in ACE concentration are significantly associated with BP, through interaction, in this African population sample. Our study also demonstrates that greater statistical power can be anticipated with association analysis versus linkage, when markers in strong linkage disequilibrium with a trait locus have been identified. Furthermore, allelic interaction may play an important role in the dissection of complex traits such as BP.     

The organization and connections of somatosensory cortex in the brush-tailed possum (Trichosurus vulpecula): evidence for multiple, topographically organized and interconnected representations in an Australian marsupial

Microelectrode mapping techniques were used to determine the organization of somatosensory cortex in the Australian brush-tailed possum (Trichosurus vulpecula). The results of electrophysiological mapping were combined with data on the cyto- and myeloarchitecture, and patterns of corticocortical connections, using sections cut tangential to the pial surface. We found evidence for three topographically organized representations of the body surface that were coextensive with architectonic subdivisions. A large, discontinuous cutaneous representation in anterior parietal cortex was termed the primary somatosensory area (SI). Lateral to SI we found evidence for two further areas, the second somatosensory area (SII) and the parietal ventral area (PV). While neurones in all of these areas were responsive to cutaneous stimulation, those of SI were non-habituating, whereas those in SII and PV often habituated to the stimuli. Moreover, neuronal receptive fields in SII and PV were, in general, larger than those in SI. Neurones in cortex adjacent to the rostral and caudal boundaries of SI, including cortex that interdigitated between the discontinuous SI head and body representations, required stimulation of deep receptors in the periphery to elicit responses. Within the region of cortex containing neurones responsive to stimulation of deep receptors, body parts were represented in a mediolateral progression. Injections of anatomical tracers placed in electrophysiologically identified locations in SI revealed ipsilateral connections with other parts of SI, as well as cortex rostral to, caudal to, and interdigitating between, SI. Injections in SI also resulted in labelling in PV, SII, motor cortex, posterior parietal cortex and perirhinal cortex. The patterns of contralateral projections reflected those of ipsilateral projections, although they were relatively less dense. The present findings support recent observations in other marsupials in which multiple representations of the body surface were described, and suggest that multiple interconnected sensory representations may be a common feature of cortical organization and function in marsupials.     

A whole-genome scan for obstructive sleep apnea and obesity

Obstructive sleep apnea (OSA) is a common, chronic, complex disease associated with serious cardiovascular and neuropsychological sequelae and with substantial social and economic costs. Along with male gender, obesity is the most characteristic feature of OSA in adults. To identify susceptibility loci for OSA, we undertook a 9-cM genome scan in 66 white pedigrees (n=349 subjects) ascertained on the basis of either an affected individual with laboratory-confirmed OSA or a proband who was a neighborhood control individual. Multipoint variance-component linkage analysis was performed for the OSA-associated quantitative phenotypes apnea-hypopnea index (AHI) and body mass index (BMI). Candidate regions on chromosomes 1p (LOD score 1.39), 2p (LOD score 1.64), 12p (LOD score 1.43), and 19p (LOD score 1.40) gave the most evidence for linkage to AHI. BMI was also linked to multiple regions, most significantly to markers on chromosomes 2p (LOD score 3.08), 7p (LOD score 2.53), and 12p (LOD score 3.41). Extended modeling indicated that the evidence for linkage to AHI was effectively removed after adjustment for BMI, with the exception of the candidate regions on chromosomes 2p (adjusted LOD score 1.33) and 19p (adjusted LOD score 1.45). After adjustment for AHI, the primary linkages to BMI remained suggestive but were roughly halved. Our results suggest that there are both shared and unshared genetic factors underlying susceptibility to OSA and obesity and that the interrelationship of OSA and obesity in white individuals may be partially explained by a common causal pathway involving one or more genes regulating both AHI and BMI levels.     

Nonparametric disequilibrium mapping of functional sites using haplotypes of multiple tightly linked single-nucleotide polymorphism markers

As the speed and efficiency of genotyping single-nucleotide polymorphisms (SNPs) increase, using the SNP map, it becomes possible to evaluate the extent to which a common haplotype contributes to the risk of disease. In this study we propose a new procedure for mapping functional sites or regions of a candidate gene of interest using multiple linked SNPs. Based on a case-parent trio family design, we use expectation-maximization (EM) algorithm-derived haplotype frequency estimates of multiple tightly linked SNPs from both unambiguous and ambiguous families to construct a contingency statistic S for linkage disequilibrium (LD) analysis. In the procedure, a moving-window scan for functional SNP sites or regions can cover an unlimited number of loci except for the limitation of computer storage. Within a window, all possible widths of haplotypes are utilized to find the maximum statistic S* for each site (or locus). Furthermore, this method can be applied to regional or genome-wide scanning for determining linkage disequilibrium using SNPs. The sensitivity of the proposed procedure was examined on the simulated data set from the Genetic Analysis Workshop (GAW) 12. Compared with the conventional and generalized TDT methods, our procedure is more flexible and powerful.     

The brownian ratchet and power stroke models for posttranslational protein translocation into the endoplasmic reticulum

A quantitative analysis of experimental data for posttranslational translocation into the endoplasmic reticulum is performed. This analysis reveals that translocation involves a single rate-limiting step, which is postulated to be the release of the signal sequence from the translocation channel. Next, the Brownian ratchet and power stroke models of translocation are compared against the data. The data sets are simultaneously fit using a least-squares criterion, and both models are found to accurately reproduce the experimental results. A likelihood-ratio test reveals that the optimal fit of the Brownian ratchet model, which contains one fewer free parameter, does not differ significantly from that of the power stroke model. Therefore, the data considered here cannot be used to reject this import mechanism. The models are further analyzed using the estimated parameters to make experimentally testable predictions.     

Can one unrestricted meal buffer the effects of previous pre-meal intervals on the feeding behaviour of sheep?

Varying the time since the last meal is one means of manipulating feeding motivation. In order to use this method effectively it is necessary to know whether and the extent to which effects of one pre-meal interval are carried over to affect the behaviour during the following meals. Pre-meal interval (PMI) is defined here for practical purposes, for short meals, as the time between the start of two successive meals. The possibility that one unrestricted meal might buffer the effects of an 8h as opposed to a 4h PMI on aspects of feeding behaviour was studied with eight Scottish Blackface sheep. They were fed on a regime in which they were given access to food until they finished their meal and lay down (this always occurred within 60min) at which time the remaining food was withdrawn. Feeding behaviour was recorded during the meal after these 4 and 8h intervals, as well as during the following meal 4h later.At a meal after a PMI of 8h, compared to 4h, sheep had a higher intake per meal (mean+/-S.T.D. for 8 and 4h PMI, respectively: 604.4+/-78.8 and 430.1+/-100.9g; P<0.001), a longer meal duration (27.1+/-7.5 and 21.8+/-8.1min; P<0.001), and a tendency for a higher intake rate (23.8+/-6.2 and 21.9+/-8.2g/min; P=0.11). During the following meal 4h later these differences were smaller, but intake per meal still tended to be higher (430.8+/-81.5 and 338.5+/-45.6g; P<0.06) for sheep who had previously had the 8h PMI. Meal duration (21.9+/-7.2 and 20.6+/-7.08min; P=0.28) and intake rate (21.2+/-6.1 and 18.7+/-7.2g/min; P=0.13) were no longer different.A single meal after the different PMIs reduced differences in all three aspects of feeding behaviour observed during the subsequent meal, 4h later, but differences in intake per meal were still apparent. It is suggested that an additional meal may overcome the carry-over effect.     

Autosomal recessive cerebellar ataxia with oculomotor apraxia (ataxia-telangiectasia-like syndrome) is linked to chromosome 9q34

Ataxia with oculomotor apraxia (ataxia-telangiectasia-like syndrome [AOA]; MIM 208920) is an autosomal recessive disorder characterized by ataxia, oculomotor apraxia, and choreoathetosis. These neurological features resemble those of ataxia-telangiectasia (AT), but in AOA there are none of the extraneurological features of AT, such as immunodeficiency, neoplasia, chromosomal instability, or sensitivity to ionizing radiation. It is unclear whether these patients have a true disorder of chromosomal instability or a primary neurodegenerative syndrome, and it has not been possible to identify the defective gene in AOA, since the families have been too small for linkage analysis. We have identified a new family with AOA, and we show that the patients have no evidence of chromosomal instability or sensitivity to ionizing radiation, suggesting that AOA in this family is a true primary cerebellar ataxia. We have localized the disease gene, by linkage analysis and homozygosity mapping, to a 15.9-cM interval on chromosome 9q34. This work will ultimately allow the disease gene to be identified and its relevance to other types of autosomal recessive cerebellar ataxias to be determined.     

Models of post-translational protein translocation

Organellar Hsp-70 is required for post-translational translocation into the endoplasmic reticulum and mitochondria. The functional role played by Hsp-70 is unknown. However, two operating principles have been suggested. The power stroke model proposes that Hsp-70 undergoes a conformational change, which pulls the precursor protein through the translocation pore, whereas, in the Brownian ratchet model, the role of Hsp-70 is simply to block backsliding through the pore. A mathematical analysis of both mechanisms is presented and reveals that qualitative differences between the models occur in the behavior of the mean velocity and effective diffusion coefficient as a function of Hsp-70 concentration. An experimental method is proposed for measuring these two quantities that only relies on current experimental techniques.     

Force generation in RNA polymerase.

RNA polymerase (RNAP) is a processive molecular motor capable of generating forces of 25-30 pN, far in excess of any other known ATPase. This force derives from the hydrolysis free energy of nucleotides as they are incorporated into the growing RNA chain. The velocity of procession is limited by the rate of pyrophosphate release. Here we demonstrate how nucleotide triphosphate binding free energy can rectify the diffusion of RNAP, and show that this is sufficient to account for the quantitative features of the measured load-velocity curve. Predictions are made for the effect of changing pyrophosphate and nucleotide concentrations and for the statistical behavior of the system.