Which strategy is better for linkage analysis: single-nucleotide polymorphisms or microsatellites? Evaluation by identity-by-state – identity-by-descent transformation affected sib-pair method on GAW14 data

The central issue for Genetic Analysis Workshop 14 (GAW14) is the question, which is the better strategy for linkage analysis, the use of single-nucleotide polymorphisms (SNPs) or microsatellite markers? To answer this question we analyzed the simulated data using Duffy's SIB-PAIR program, which can incorporate parental genotypes, and our identity-by-state – identity-by-descent (IBS-IBD) transformation method of affected sib-pair linkage analysis which uses the matrix transformation between IBS and IBD. The advantages of our method are as follows: the assumption of Hardy-Weinberg equilibrium is not necessary; the parental genotype information maybe all unknown; both IBS and its related IBD transformation can be used in the linkage analysis; the determinant of the IBS-IBD transformation matrix provides a quantitative measure of the quality of the marker in linkage analysis. With the originally distributed simulated data, we found that 1) for microsatellite markers there are virtually no differences in types I and II error rates when parental genotypes were or were not used; 2) on average, a microsatellite marker has more power than a SNP marker does in linkage detection; 3) if parental genotype information is used, SNP markers show lower type I error rates than microsatellite markers; and 4) if parental genotypes are not available, SNP markers show considerable variation in type I error rates for different methods

Analysis of Incomplete Longitudinal Binary Data-A Combined Markov’s Transition and Logistic Model for Non-ignorable Missingness

The problem of incomplete data is a common phenomenon in research that involves the longitudinal design approach. We investigate and develop a likelihood-based approach for incomplete longitudinal binary data using the disposition model when the missing value mechanism is non-ignorable. We combined Markov’s transition and a logistic regression model to build the dropout process and model the response using conditional logistic regression model. By holding the missingness parameter that is weakly identified constant, we analyzed their effects through a sensitivity analysis as the estimation of parameters in MLE for non-ignorable missing data is not generally plausible. An application of our approach to Schizophrenia clinical trial is presented

The home and school environments, physical activity levels, and adiposity indices of school-age children

The home and school environments as well as physical activity may be linked to the development of childhood obesity. We evaluated the home and school environments (HSEs), physical activity levels (PAL), television viewing (TVV) and their associations with adiposity indices of school-age children. This cross-sectional study included children aged 6-12 years and their parents from Tamale, Ghana. HSEs and TVV were assessed using questionnaires. The physical activity questionnaire for children (PAQ-C) was used to assess children’s PALs. Weight, height and waist circumferences were measured using standard tools. About 45% of children lived within a walking distance to parks or outdoor recreation centres. Majority of the parents considered their neighbourhoods to be safe for children to engage in physical activity. Only 27% of the schools had a food and nutrition policy, and more than 70% had a field for outdoor activities. Children watched TV for an average of 1.7 hours/day. Mean physical activity scores was 2.51. The school-age children had mean (SD) BMI-for-age z-scores was -0.23(1.47). Time spent watching TV or playing video games was associated with children’s BMI-for-age z-scores (β=0.48, p=0.043), BMI (β=2.28 p=0.005), and % body fat (β=3.80, p=0.005). Child’s level of activity was negatively associated with waist circumference (β =-0.65, p<0.001). Lack of nutrition policy in schools was common. TVV hours predisposed children to excess weight whiles physical activity decreased the likelihood of being obese.

The home and school environments, physical activity levels, and adiposity indices of school-age children

The home and school environments as well as physical activity may be linked to the development of childhood obesity. We evaluated the home and school environments (HSEs), physical activity levels (PAL), television viewing (TVV) and their associations with adiposity indices of school-age children. This cross-sectional study included children aged 6-12 years and their parents from Tamale, Ghana. HSEs and TVV were assessed using questionnaires. The physical activity questionnaire for children (PAQ-C) was used to assess children’s PALs. Weight, height and waist circumferences were measured using standard tools. About 45% of children lived within a walking distance to parks or outdoor recreation centres. Majority of the parents considered their neighbourhoods to be safe for children to engage in physical activity. Only 27% of the schools had a food and nutrition policy, and more than 70% had a field for outdoor activities. Children watched TV for an average of 1.7 hours/day. Mean physical activity scores was 2.51. The school-age children had mean (SD) BMI-for-age z-scores was -0.23(1.47). Time spent watching TV or playing video games was associated with children’s BMI-for-age z-scores (β=0.48, p=0.043), BMI (β=2.28 p=0.005), and % body fat (β=3.80, p=0.005). Child’s level of activity was negatively associated with waist circumference (β =-0.65, p<0.001). Lack of nutrition policy in schools was common. TVV hours predisposed children to excess weight whiles physical activity decreased the likelihood of being obese.

A study of genetic association with electrophysiological measures related to alcoholism: GAW14 data

Recently, alcohol-related traits have been shown to have a genetic component. Here, we study the association of specific genetic measures in one of the three sets of electrophysiological measures in families with alcoholism distributed as part of the Genetic Analysis Workshop 14 data, the NTTH (non-target case of Visual Oddball experiment for 4 electrode placements) phenotypes: ntth1, ntth2, ntth3, and ntth4. We focused on the analysis of the 786 Affymetrix markers on chromosome 4. Our desire was to find at least a partial answer to the question of whether ntth1, ntth2, ntth3, and ntth4 are separately or jointly genetically controlled, so we studied the principal components that explain most of the covariation of the four quantitative traits. The first principal component, which explains 70% of the covariation, showed association but not genetic linkage to two markers: tsc0272102 and tsc0560854. On the other hand, ntth1 appeared to be the trait driving the variation in the second principal component, which showed association and genetic linkage at markers in four regions: tsc0045058, tsc1213381, tsc0055068, and tsc0051777 at map distances 53.26, 85.42, 89.31, and 172.86, respectively. These results show that the partial answer to our starting question for this brief analysis is that the NTTH phenotypes are not jointly genetically controlled. The component ntth1 displays marked genetic linkage

Genes, age, and alcoholism: analysis of GAW14 data

A genetic analysis of age of onset of alcoholism was performed on the Collaborative Study on the Genetics of Alcoholism data released for Genetic Analysis Workshop 14. Our study illustrates an application of the log-normal age of onset model in our software Genetic Epidemiology Models (GEMs). The phenotype ALDX1 of alcoholism was studied. The analysis strategy was to first find the markers of the Affymetrix SNP dataset with significant association with age of onset, and then to perform linkage analysis on them. ALDX1 revealed strong evidence of linkage for marker tsc0041591 on chromosome 2 and suggestive linkage for marker tsc0894042 on chromosome 3. The largest separation in mean ages of onset of ALDX1 was 19.76 and 24.41 between male smokers who are carriers of the risk allele of tsc0041591 and the non-carriers, respectively. Hence, male smokers who are carriers of marker tsc0041591 on chromosome 2 have an average onset of ALDX1 almost 5 years earlier than non-carriers

Fluorescence measurements of the labile iron pool of sickle erythrocytes

Sickle erythrocytes have increased ferritin and increased molecular iron on the inner membrane leaflet, and we postulated that cytosolic labile iron is also elevated. We used the fluorescent metallosensor, calcein, and a permeant Fe2+ chelator to estimate labile cytoslic Fe2+, and calcein plus an Fe3+ chelator to estimate total cytosolic labile iron (Fe2+ + Fe3+). We measured membrane nonheme iron by its reactivity with ferrozine. As estimated by calcein and Fe2+ chelator, the mean ± SD labile Fe2+ concentration was significantly lower in hemoglobin (Hb) SS (n = 29) than hemoglobin AA (n = 17) erythrocytes (0.56 ± 0.35 μM versus 1.25 ± 0.65 μM; P \u3c .001). In contrast, as estimated by calcein and Fe3+ chelator, total erythrocyte labile iron was similar in hemoglobin SS (n = 12) and hemoglobin AA (n = 10) participants (1.75 ± 0.41 μM versus 2.14 ± 0.93 μM; P = .2). Mean membrane nonheme iron levels were higher in hemoglobin SS cells than hemoglobin AA cells (0.0016 × 10-4 versus 0.0004 × 10-4 fmol/cell; P = .01), but much lower than the mean amounts of total labile iron (1.6-1.8 × 10-4 fmol/cell) or hemoglobin iron (18 000-19 000 × 10-4 fmol/cell). Both membrane iron and total labile iron were much less than the mean amount of iron potentially present in erythrocyte ferritin as calculated from results of other investigators (15 × 10-4 versus 34 × 10-4 fmol/cell in HbAA versus HbSS erythrocytes). We conclude that cytosolic labile iron is not elevated in hemoglobin SS erythrocytes and that elemental membrane iron is present in only trace amounts. © 2003 by The American Society of Hematology

Significant Quantitative Differences in Orexin Neuronal Activation After Pain Assessments in an Animal Model of Sickle Cell Disease

Sickle cell disease is a hemoglobinopathy that causes sickling of red blood cells, resulting in vessel blockage, stroke, anemia, inflammation, and extreme pain. The development and treatment of pain, in particular, neuropathic pain in sickle cell disease patients is poorly understood and impedes our progress toward the development of novel therapies to treat pain associated with sickle cell disease. The orexin/hypocretin system offers a novel approach to treat chronic pain and hyperalgesia. These neuropeptides are synthesized in three regions: perifornical area (PFA), lateral hypothalamus (LH), and dorsomedial hypothalamus (DMH). Data suggest that orexin–A neuropeptide has an analgesic effect on inflammatory pain and may affect mechanisms underlying the maintenance of neuropathic pain. The purpose of this study was to determine whether there are neuronal activation differences in the orexin system as a result of neuropathic pain testing in a mouse model of sickle cell disease. Female transgenic sickle mice that express exclusively (99%) human sickle hemoglobin (HbSS-BERK) and age-/gender-matched controls (HbAA-BERK mice; n = 10/group, 20–30 g) expressing normal human hemoglobin A were habituated to each test protocol and environment before collecting baseline measurements and testing. Four measures were used to assess pain-related behaviors: thermal/heat hyperalgesia, cold hyperalgesia, mechanical hyperalgesia, and deep-tissue hyperalgesia. Hypothalamic brain sections from HbAA-BERK and HbSS-BERK mice were processed to visualize orexin and c-Fos immunoreactivity and quantified. The percentage of double labeled neurons in the PFA was significantly higher than the percentage of double labeled neurons in the LH orexin field of HbAA-BERK mice (*p \u3c 0.05). The percentages of double labeled neurons in PFA and DMH orexin fields are significantly higher than those neurons in the LH of HbSS-BERK mice (*p \u3c 0.05). These data suggest that DMH orexin neurons were preferentially recruited during neuropathic pain testing and a more diverse distribution of orexin neurons may be required to produce analgesia in response to pain in the HbSS-BERK mice. Identifying specific orexin neuronal populations that are integral in neuropathic pain processing will allow us to elucidate mechanisms that provide a more selective, targeted approach in treating of neuropathic pain in sickle cell disease