Linkage mapping of beta 2 EEG waves via non-parametric regression.
Parametric linkage methods for analyzing quantitative trait loci are sensitive to violations in trait distributional assumptions. Non-parametric methods are relatively more robust. In this article, we modify the non-parametric regression procedure proposed by Ghosh and Majumder [2000: Am J Hum Genet 66:1046-1061] to map Beta 2 EEG waves using genome-wide data generated in the COGA project. Significant linkage findings are obtained on chromosomes 1, 4, 5, and 15 with findings at multiple regions on chromosomes 4 and 15. We analyze the data both with and without incorporating alcoholism as a covariate. We also test for epistatic interactions between regions of the genome exhibiting significant linkage with the EEG phenotypes and find evidence of epistatic interactions between a region each on chromosome 1 and chromosome 4 with one region on chromosome 15. While regressing out the effect of alcoholism does not affect the linkage findings, the epistatic interactions become statistically insignificant.

title: A quantile-based method for association mapping of quantitative phenotypes: an application to rheumatoid arthritis phenotypes
abstract: Genetic association of population-based quantitative trait data has traditionally been analyzed using analysis of variance (ANOVA). However, violations of certain statistical assumptions may lead to false-positive association results. In this study, we have explored model-free alternatives to ANOVA using correlations between allele frequencies in the different quantile intervals of the quantitative trait and the quantile values. We performed genome-wide association scans on anti-cyclic citrullinated peptide and rheumatoid factor-immunoglobulin M, two quantitative traits correlated with rheumatoid arthritis, using the data provided in Genetic Analysis Workshop 16. Both the quantitative traits exhibited significant evidence of association on Chromosome 6, although not in the human leukocyte antigen region which is known to harbor a major gene predisposing to rheumatoid arthritis. We found that while a majority of the significant findings using the asymptotic thresholds of ANOVA was not validated using permutations, a relatively higher proportion of the significant findings using the asymptotic cut-offs of the correlation statistic were validated using permutations.

title: A novel non-parametric regression reveals linkage on chromosome 4 for the number of externalizing symptoms in sib-pairs.
abstract: In this report, we present results of a genome-wide linkage scan using as a phenotype the number of externalizing symptoms associated with alcohol use disorders. Subjects were collected by the Collaborative Study on the Genetics of Alcoholism project from families in which at least three first degree relatives were affected by alcohol dependence. We use a novel non-parametric regression method based on kernel smoothing for our analysis. We report a statistically significant linkage close to the ADH gene cluster on Chromosome 4. We also obtain evidence for epistatic interaction between a region on Chromosome 1 and one on Chromosome 15. Although alcoholism as a covariate does not have any effect on the linkage scan, it has an effect on the epistatic interaction.

title: Integrating sibship data for mapping quantitative trait loci.
abstract: Sibship methods have been shown to be more powerful than traditional sib-pair methods in mapping quantative trait loci. We propose a statistical procedure which integrates data on sibships into a so-called 'contrast function', a natural extension of the classical squared sib-pair trait difference proposed by Haseman & Elston (1972). We also develop a combined mean and contrast function which provides more information on linkage compared to the contrast function. Our method is extended to multiple, epistatically interacting trait loci. Monte-Carlo simulations are included to compare the efficiencies of the proposed procedures with some currently used methods. An application of our proposed method is presented using data on alcohol dependence.

title: Linkage mapping of a complex trait in the New York population of the GAW14 simulated dataset: a multivariate phenotype approach
abstract: Multivariate phenotypes underlie complex traits. Thus, instead of using the end-point trait, it may be statistically more powerful to use a multivariate phenotype correlated to the end-point trait for detecting linkage. In this study, we develop a reverse regression method to analyze linkage of Kofendrerd Personality Disorder affection status in the New York population of the Genetic Analysis Workshop 14 (GAW14) simulated dataset. When we used the multivariate phenotype, we obtained significant evidence of linkage near four of the six putative loci in at least 25% of the replicates. On the other hand, the linkage analysis based on Kofendrerd Personality Disorder status as a phenotype produced significant findings only near two of the loci and in a smaller proportion of replicates.

title: Identifying rare variants from exome scans: the GAW17 experience
abstract: Genetic Analysis Workshop 17 (GAW17) provided a platform for evaluating existing statistical genetic methods and for developing novel methods to analyze rare variants that modulate complex traits. In this article, we present an overview of the 1000 Genomes Project exome data and simulated phenotype data that were distributed to GAW17 participants for analyses, the different issues addressed by the participants, and the process of preparation of manuscripts resulting from the discussions during the workshop.

title: Ipsilateral cortical connections of area 6 in the cat cerebral cortex.
abstract: Many motor areas have been identified within cytoarchitectonic area 6 of the cerebral cortex in primates. To provide a better understanding of the motor functions of area 6 in the cat, the ipsilateral cortical connections of the different cytoarchitectonic subdivisions of area 6 (areas 6a alpha, 6a beta, 6a gamma, and 6iffu) were studied by the use of fluorescent retrograde tracers. Tracer injections, made in the forelimb and face regions of areas 6a alpha and 6a gamma, were guided by data from intracortical microstimulation (ICMS). ICMS did not evoke movements from areas 6a beta and 6iffu. Retrogradely labeled neurons were enumerated in cytoarchitectonically identified areas in the frontal and parietal lobes to show that the subdivisions of area 6 are strongly interconnected except for areas 6a gamma and 6a beta. There are considerable differences in the pattern of connections of the area 6 subdivisions with area 4 and with prefrontal, cingulate, and parietal cortices. Area 4 gamma projects strongly to area 6a gamma but not to the other subdivisions. Areas 4 delta, 4fu, and 4sfu project strongly to 6a alpha and 6iffu but relatively weakly to area 6a beta. Prefrontal areas project strongly to area 6a beta and 6iffu, moderately to 6a alpha, but weakly to area 6a gamma. Cingulate areas project strongly to area 6iffu and moderately to areas 6a alpha and 6a beta but do not project to area 6a gamma. Parietal projections from primary and second somatosensory cortex were directed to area 6a gamma, whereas areas 5, 7, and insula were found to project to all the subdivisions of area 6. These findings support earlier suggestions that secondary motor areas may be located in areas 6a alpha and 6a gamma (Ghosh [1997] ). Features of the pattern of cortical connections of area 6 common to the cat and primates suggest that their motor areas in the frontal lobe are organized in a similar manner.

title: Airway obstruction in lungs obtained from an asthmatic donor complicating heart-lung transplantation.

title: Hypertrophic cardiomyopathy with preexcitation: insights from noninvasive electrocardiographic imaging (ECGI) and catheter mapping.
abstract: Hypertrophic Cardiomyopathy and Preexcitation.



Fasciculoventricular pathway has been described as an unusual variant of preexcitation. Electrocardiographic imaging (ECGI) is a novel imaging modality for noninvasive electroanatomic mapping of epicardial activation and repolarization.



We present a case of an 18-year-old male with hypertrophic cardiomyopathy (HCM) and an electrocardiogram (ECG)-based diagnosis of Wolff-Parkinson-White (WPW) syndrome, who underwent a noninvasive ECGI study to image ventricular activation, followed by an electrophysiology study (EPS). The ECGI electroanatomic isochrone map showed early activation of the epicardial aspect of the atrioventricular (A-V) groove and an aberrant posterior-base-to-apex progression of activation in the left ventricular (LV) epicardium. The EPS showed a likely fasciculoventricular pathway (FVP) without any inducible tachycardia.



While FVP has been described before, this is the first report of detailed quantitative three-dimensional characterization of electrical activation sequence of a heart with this type of preexcitation, using a novel noninvasive imaging modality (ECGI). In spite of abnormal ventricular activation, the EPS demonstrated that the FVP is not capable of supporting reentrant supraventricular tachycardia or rapidly conducted atrial fibrillation.

title: Comparative diagnostic potentiality of ELISA and dot-ELISA in prepatent diagnosis of experimental Fasciola gigantica infection in cattle.
abstract: A glycoprotein (27 kDa) was isolated from crude somatic antigen of Fasciola gigantica by two steps affinity chromatography and was used in early detection of experimental fasciolosis in cattle by indirect ELISA and in dot-ELISA formats. Although, anti-27 kDa antibodies could be detected after 3 weeks post infection (WPI) by dot - ELISA which was one week later than indirect ELISA. The test, dot-ELISA, was more convenient in field application. By the test (dot-ELISA) the infection could be equally detected in animals infected with 100, 200 and 300 metacercariae of F. gigantica with high sensitivity. Further, the antigen (27 kDa) was not found to react with goat sera infected with Paramphistomum epiclitum, which are giving strong reaction to homologous immature and mature fluke antigens of P. epiclitum.

title: Interactions of Escherichia coli thioredoxin, the processivity factor, with bacteriophage T7 DNA polymerase and helicase.
abstract: Escherichia coli thioredoxin binds to a unique flexible loop of 71 amino acid residues, designated the thioredoxin binding domain (TBD), located in the thumb subdomain of bacteriophage T7 gene 5 DNA polymerase. The initial designation of thioredoxin as a processivity factor was premature. Rather it remodels the TBD for interaction with DNA and the other replication proteins. The binding of thioredoxin exposes a number of basic residues on the TBD that lie over the duplex region of the primer-template and increases the processivity of nucleotide polymerization. Two small solvent-exposed loops (loops A and B) located within TBD electrostatically interact with the acidic C-terminal tail of T7 gene 4 helicase-primase, an interaction that is enhanced by the binding of thioredoxin. Several basic residues on the surface of thioredoxin in the polymerase-thioredoxin complex lie in close proximity to the TBD. One of these residues, lysine 36, is located proximal to loop A. The substitution of glutamate for lysine has a dramatic effect on the binding of gene 4 helicase to a DNA polymerase-thioredoxin complex lacking charges on loop B; binding is decreased 15-fold relative to that observed with wild-type thioredoxin. This defective interaction impairs the ability of T7 DNA polymerase-thioredoxin together with T7 helicase to mediate strand displacement synthesis. This is the first demonstration that thioredoxin interacts with replication proteins other than T7 DNA polymerase.