Biomedical subjects

Shaw-Hwa Lo

Publications and source records attributed to Shaw-Hwa Lo.

7 recordsLinked to original sources

PubMed2006

Backward genotype-trait association (BGTA)-based dissection of complex traits in case-control designs.

BACKGROUND: The studies of complex traits project new challenges to current methods that evaluate association between genotypes and a specific trait. Consideration of possible interactions among loci leads to overwhelming dimensions that cannot be handled using current statistical methods. METHODS: In this article, we evaluate a multi-marker screening algorithm--the backward genotype-trait association (BGTA) algorithm for case-control designs, which uses unphased multi-locus genotypes. BGTA carries out a global investigation on a candidate marker set and automatically screens out markers carrying diminutive amounts of information regarding the trait in question. To address the 'too many possible genotypes, too few informative chromosomes' dilemma of a genomic-scale study that consists of hundreds to thousands of markers, we further investigate a BGTA-based marker selection procedure, in which the screening algorithm is repeated on a large number of random marker subsets. Results of these screenings are then aggregated into counts that the markers are retained by the BGTA algorithm. Markers with exceptional high counts of returns are selected for further analysis. RESULTS AND CONCLUSION: Evaluated using simulations under several disease models, the proposed methods prove to be more powerful in dealing with epistatic traits. We also demonstrate the proposed methods through an application to a study on the inflammatory bowel disease.

Algorithms↗

PubMed2006

Multilocus linkage analysis of affected sib pairs.

OBJECTIVE: The conventional affected sib pair methods evaluate the linkage information at a locus by considering only marginal information. We describe a multilocus linkage method that uses both the marginal information and information derived from the possible interactions among several disease loci, thereby increasing the significance of loci with modest effects. METHODS: Our method is based on a statistic that quantifies the linkage information contained in a set of markers. By a marker selection-reduction process, we screen a set of polymorphisms and select a few that seem linked to disease. RESULTS: We test our approach on genome scan data for inflammatory bowel disease (InfBD) and on simulated data. On real data we detect 6 of the 8 known InfBD loci; on simulated data we obtain improvements in power of up to 40% compared to a conventional single-locus method. CONCLUSION: Our extensive simulations and the results on real data show that our method is in general more powerful than single-locus methods in detecting disease loci responsible for complex traits. A further advantage of our approach is that it can be extended to make use of both the linkage and the linkage disequilibrium between disease loci and nearby markers.

Genetic Linkage↗

PubMed2005

The clonality of Staphylococcus aureus nasal carriage.

Nasal carriage of Staphylococcus aureus is often a prelude to infection with the same strain. The prevailing assumption has been that colonized individuals carry a single strain. The present study investigated the frequency of simultaneous nasal carriage of multiple strains of S. aureus. Three bacterial colonies from plated samples from colonized subjects were initially compared by pulsed-field gel electrophoresis. Fourteen of 148 S. aureus-positive samples demonstrated at least a difference of a single band; 7 of these 14 samples contained different strains, and 3 of these 7 also belonged to different accessory gene regulator (agr) types. The remaining 7 samples contained clonally related isolates; 3 of these 7 contained pairs that differed by the presence or absence of the staphylococcal chromosomal cassette mec type IV. A mathematical model that we developed predicted that approximately 6.6% of S. aureus-colonized individuals carry >1 strain. The present study demonstrates that carriage of discordant S. aureus strains in individuals with nasal colonization occurs regularly and suggests that the nares are likely sites for horizontal genetic exchange among strains.

Adult↗

PubMed2004

A demonstration and findings of a statistical approach through reanalysis of inflammatory bowel disease data.

We test the backward haplotype transmission association algorithm on genome-scan data previously studied by Rioux et al. [Rioux, J. D., et al. (2000) Am. J. Hum. Genet. 66, 1863-1870]. In their study, multipoint linkage methods were applied to affected sib-pairs with inflammatory bowel disease, and significant linkage evidence points to two susceptibility loci. After we apply our approach to these data with a global search accounting for both joint and marginal effects, very interesting results emerge, many of them intriguing. These results provide compelling support for the application of our approach to other data wherever applicable. Results from this project also make it clear that it is important to reinvestigate available family-based datasets that can be suitably reanalyzed. Given previously collected data in the literature, our approach, with its increased efficiency in using available resources, draws additional crucial information that may lead to novel and surprising results.

Genetic Linkage↗

PubMed2004

Alendronate versus calcitriol for the prevention of bone loss after cardiac transplantation.

BACKGROUND: Osteoporosis is a well-known complication of cardiac transplantation. We conducted a randomized trial comparing alendronate with calcitriol for the prevention of bone loss during the first year after cardiac transplantation. METHODS: A total of 149 patients were randomly assigned to receive either alendronate (10 mg per day) or calcitriol (0.5 microg per day) a mean (+/-SD) of 21+/-11 days after transplantation. Estimates of bone loss and the incidence of fractures among untreated patients were obtained from a reference group of 27 prospectively recruited patients who received cardiac transplants within the same period as the intervention groups. RESULTS: At one year, the bone mineral density at the lumbar spine had decreased by a mean of 0.7 percent in the alendronate group and 1.6 percent in the calcitriol group (P=0.25 for the test of no difference). The bone mineral density at the femoral neck decreased by a mean of 1.7 percent in the alendronate group and 2.1 percent in the calcitriol group (P=0.69). In the reference group, the mean bone mineral density at the lumbar spine decreased by 3.2 percent (P=0.03 for the comparison with the alendronate group; P=0.15 for the comparison with the calcitriol group), and the mean density at the femoral neck decreased by 6.2 percent (P=0.001 for comparisons with both intervention groups). The incidence of vertebral fractures did not differ significantly among the groups (6.8 percent in the alendronate group, 3.6 percent in the calcitriol group, and 13.6 percent in the reference group). Hypercalciuria developed in 27 percent of the patients in the calcitriol group and 7 percent of those in the alendronate group (P=0.01). CONCLUSIONS: The degree of bone loss and the rates of fracture did not differ significantly between the intervention groups. Calcitriol was associated with a higher risk of hypercalciuria. Alendronate-treated patients sustained less bone loss at the spine than those in the reference group, and both intervention groups sustained less bone loss at the hip than the reference group. The requirement for monitoring the serum and urinary calcium levels in calcitriol-treated patients makes alendronate more attractive for the prevention of bone loss early after cardiac transplantation.

Alendronate↗

PubMed2003

A marginal likelihood model for family-based data.

This paper presents a marginal likelihood model for family-based data based upon the transmission of marker alleles from each heterozygous parent to his/her affected children. The proposed model, extending the maximum-likelihood-binomial (MLB) method and the disequilibrium maximum-likelihood-binomial (DMLB) method (Abel et al. 1998; Abel & Müller-Myhsok, 1998; Huang & Jiang, 1999), is adaptive to linkage disequilibrium (LD) and linkage heterogeneity. Compared with other procedures, the likelihood ratio test (LRT) derived from the proposed model enjoys superior qualities. First, simulations indicate that the power of the LRT is greater than that of the TDT or DMLB in all of our studied scenarios. Second, when we applied the LRT and other tests to a Tourette Syndrome data, the result was data favorable to the use of the LRT. Therefore, we recommend the use of the LRT as an additional linkage test wherever applicable, especially when the amount of LD is uncertain.

Alleles↗

PubMed2002

Backward Haplotype Transmission Association (BHTA) algorithm - a fast multiple-marker screening method.

The mapping of complex traits is one of the most important and central areas of human genetics today. Recent attention has been focused on genome scans using a large number of marker loci. Because complex traits are typically caused by multiple genes, the common approaches of mapping them by testing markers one after another fail to capture the substantial information of interactions among disease loci. Here we propose a backward haplotype transmission association (BHTA) algorithm to address this problem. The algorithm can administer a screening on any disease model when case-parent trio data are available. It identifies the important subset of an original larger marker set by eliminating the markers of least significance, one at a time, after a complete evaluation of its importance. In contrast with the existing methods, three major advantages emerge from this approach. First, it can be applied flexibly to arbitrary markers, regardless of their locations. Second, it takes into account haplotype information; it is more powerful in detecting the multifactorial traits in the presence of haplotypic association. Finally, the proposed method can potentially prove to be more efficient in future genomewide scans, in terms of greater accuracy of gene detection and substantially reduced number of tests required in scans. We illustrate the performance of the algorithm with several examples, including one real data set with 31 markers for a study on the Gilles de la Tourette syndrome. Detailed theoretical justifications are also included, which explains why the algorithm is likely to select the 'correct' markers.

Algorithms↗