Linkage mapping of a complex trait in the New York population of the GAW14 simulated dataset: a multivariate phenotype approach
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: 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: Deciphering the genetic architecture of a multivariate phenotype.
abstract: A heritable multivariate quantitative phenotype comprises several correlated component phenotypes that are usually pleiotropically controlled by a set of major loci and environmental factors. One approach to decipher the genetic architecture of a multivariate phenotype, in particular to map the underlying loci, is to reduce the dimensionality of the data by means of a data reduction technique, such as principal component analysis. The extracted principal components are then analyzed in conjunction with marker data to map the underlying loci. We have examined the efficiency of this approach with and without taking into account the correlation structure of the multivariate phenotype when extracting principal components. We have assumed that genome-wide scan data on sibpairs are available for low-density (widely spaced) and high-density markers. Using extensive simulations, based on three models of the multivariate phenotype, we have shown that although ignoring the correlation structure of the multivariate phenotype does not have any serious impact on the efficiency of mapping the underlying trait loci in wide marker intervals, there is a significant adverse effect of this practice for fine-mapping. We, therefore, recommend that the correlation structure of the multivariate phenotype be carefully examined to decide on the strategy of extracting principal components for deciphering the genetic architecture of the multivariate phenotype.

title: A nonparametric regression-based linkage scan of rheumatoid factor-IgM using sib-pair squared sums and differences
abstract: Parametric linkage methods for quantitative trait locus mapping require explicit specification of the probability model of the quantitative trait and hence can lead to misleading linkage inferences when the model assumptions are not valid. Ghosh and Majumder developed a nonparametric regression method based on kernel-smoothing for linkage mapping of quantitative trait locus using squared differences in trait values of independent sib pairs, which is relatively more robust than parametric methods with respect to violations in distributional assumptions. In this study, we modify the above mentioned nonparametric regression method by considering local linear polynomials instead of the Nadaraya-Watson estimator and squared sums of sib-pair trait values in addition to squared differences to perform a genome-wide scan of rheumatoid factor-IgM levels on sib pairs in the Genetic Analysis Workshop 15 simulated data set. We obtain significant evidence of linkage very close to the quantitative trait locus controlling for RF-IgM. We find that the simultaneous use of squared differences and squared sums increases the power to detect linkage compared to using only squared differences. However, because of all the sib pairs are selected for rheumatoid arthritis, there is reduced variance of RF-IgM values, and empirical power to detect linkage is not very high. We also compare the performance of our method with two linear regression approaches: the classical Haseman-Elston method using squared sib-pair trait differences and its extension proposed by Elston et al. using mean-corrected sib-pair cross-products. We find that the proposed nonparametric method yields more power than the linear regression approaches.

title: Linkage analyses of rheumatoid arthritis and related quantitative phenotypes: the GAW15 experience.
abstract: The group that formed on the theme of linkage analyses of rheumatoid arthritis RA and related phenotypes (Group 10) in the Genetic Analysis Workshop 15 comprised 18 sets of investigators. Two data sets were available: one was a real set provided by the North American Rheumatoid Arthritis Consortium and collaborators in Canada, France (European Consortium Of Rheumatoid Arthritis Families) and the UK; the other was a simulated data set modelled after the real data set. Whereas a majority of the investigators analyzed the RA affection status as a binary phenotype, a few contributions considered data on correlated quantitative traits such as anti-cyclic citrullinated peptide and rheumatoid factor-immunoglobulin M. The different investigators applied a wide spectrum of linkage methods. As expected, most methods could identify the human leukocyfeantigen region on chromosome 6 as a major genetic factor for RA. In addition, some novel chromosomal regions provided significant evidence of linkage in multiple contributions in the group. In this report, we discuss the different strategies explored by the different investigators with the common goal of improving the power to detect linkage.

title: How Do Homozygous Parents Affect TDT as a Test for Association?
abstract: The traditional transmission disequilibrium test (TDT) (Spielman et al., 1993) is a powerful test for association only in the presence of linkage. Since allele transmissions from homozygous parents do not carry any information on linkage, the TDT statistic uses data only on heterozygous parents. However, homozygous parents carry information on association between alleles at a marker locus and a disease locus. In this article, we explore whether inclusion of homozygous parents increases the power to detect association. The resultant test statistic follows a χ2 distribution with 2 degrees of freedom. Monte-Carlo simulations are included to compare the performance of this test with the traditional TDT under different disease models.

title: Evidence for a new rotavirus subgroup in India.
abstract: Monoclonal antibodies specific for rotavirus subgroup 1 (SG1) and subgroup 2 (SG2) were used to analyse by enzyme immunoassay (EIA) the subgroups of human rotavirus isolates obtained from three different parts of India during the period September 1985 to July 1987. We identified one isolate which failed to react with either SG1 or SG2 specific monoclonal antibodies, although it reacted well with a monoclonal antibody specific for group A rotaviruses. This finding suggests that it belongs to a new rotavirus subgroup. Further, another isolate was found to belong to SG1 although it had a 'long' electropherotype.

title: Molecular characterization of full-length genomic segment 2 of a bovine picobirnavirus (PBV) strain: evidence for high genetic diversity with genogroup I PBVs.
abstract: We report here the molecular characterization of a bovine genogroup I picobirnavirus strain RUBV-P detected from a 1-month-old diarrhoeic calf in eastern India. Sequence comparisons and phylogenetic analysis of a short stretch of gene segment 2 of RUBV-P revealed low nucleotide identities (51.2-64.9%) with and distant genetic relatedness to other genogroup I picobirnaviruses. The complete gene segment 2 sequence of RUBV-P was obtained by the single primer amplification method with modifications. Gene segment 2 of RUBV-P was 1758 bp long, encoded a predicted protein of 554 aa and exhibited low nucleotide (58.1-58.8%) and amino acid (51.3-55.4%) identities with genogroup I human strains Hy005102 and 1-CHN-97. The 5'- and 3'-end nucleotide sequences, and the three motifs of RNA-dependent RNA polymerases of double-stranded RNA viruses, were conserved among these strains. Our findings suggested that bovine strain RUBV-P might be distinct from genogroup I picobirnaviruses of humans and other animals.

title: Intestinal entry of prions.
abstract: Variant Creutzfeldt-Jakob disease is thought to be caused by infected prion protein via ingestion of contaminated beef. After ingestion of infected prion proteins, uptake by small intestine may be by either M-cell dependent or M-cell independent routes. A receptor for prion protein, laminin receptor precursor is expressed on the brush border of small intestinal epithelium in 40 % of subjects. The cellular prion protein expressed on the enteric nervous system might serve as the target for conversion to infectious prion protein and a route for spread to the central nervous system.

title: Regeneration of lower and upper jaws in urodeles is differentially affected by retinoic acid.
abstract: The vitamin A derivative retinoic acid (RA) is a powerful teratogen which can induce severe craniofacial and limb malformations if administered at certain stages of gestation. In addition this compound has been shown to affect patterning in regenerating systems. A classical example is the induction of supernumerary structures along the proximodistal axis of the regenerating amphibian limb. We have investigated the effect of RA on other regenerating systems, the amphibian lower and upper jaws, both in developing and adult animals. We report here that RA does not induce formation of extra structures either in the lower or in the upper jaw of adult newts under experimental conditions where duplications of the regenerating limb occur. However, RA selectively induces severe malformations in the upper jaw regenerate that resemble those induced in avian and mammalian embryos. Analysis of the expression of the newt retinoic acid receptors RAR alpha and delta in upper and lower jaws showed that RAR alpha was expressed at a significant level in the wound epidermis, but not in blastemal cells, whereas no RAR delta could be detected in the regenerate either by in situ hybridization or by using an anti-RAR delta antibody. Therefore, unlike in the limb, in jaws RAR delta is not up-regulated following amputation, and this difference in expression may be causally related to the different effects induced by RA on jaws and limbs. In order to establish whether retinoids affected regeneration of developing jaws in a similar fashion, their effects were studied in animals whose jaws had been amputated at different developmental stages. Under the experimental conditions used overall growth retardation and head defects were observed in the majority of embryos which had been amputated and treated with retinol palmitate (RP) between stages 26-28 and 38-39. In contrast, patterning of upper jaw regenerates in larvae amputated at stage 26-28 and 38-39. In contrast, patterning of upper jaw regenerates in larvae amputated at stage 45 was not significantly affected by the treatment, although the early phase of regeneration was slower than in controls. The different responses to retinoids of regenerating facial structures in embryos, larvae and adults will be discussed.

title: Fluorescent Probing of Protein Bovine Serum Albumin Stability and Denaturation Using Polarity Sensitive Spectral Response of a Charge Transfer Probe
abstract: The polarity sensitive photo-induced intra-molecular charge transfer (ICT) fluorescence probe (E)-3-(4-methylamino-phenyl)-acrylic acid ethyl ester (MAPAEE) has been used to study the model protein Bovine Serum Albumin (BSA) in its native and thermal and urea induced denatured states. The interaction between BSA and the regular surfactant Sodium Dodecyl Sulphate (SDS) as well as the biologically relevant steroid-based amphiphile Sodium Deoxycholate (NaDC) has also been very keenly followed using this ICT probe. The variation of micellar properties of both SDS and NaDC with increasing ionic strengths and in presence of the chaotrope urea has also been well documemted by the same probe. Steady-state spectroscopy, FRET, and fluorescence anisotropy measurements have been used to gain better insight into these processes and the molecule MAPAEE to be a full-bodied fluorescent probe for studying such intricate biological systems, their properties and interactions.