PubMed Health⌕ Search

PubMed · 16856945

Multilevel analysis of group-randomized trials with binary outcomes.

Abstract

OBJECTIVES: Many dental studies have assessed the effectiveness of community- or group-based interventions such as community water fluoridation. These cluster trials, of which group-randomized trials (GRTs) are one type, have design and analysis considerations not found in studies with randomization of treatments to individuals (randomized controlled trials, RCTs). The purpose of this paper is to review analytic methods used for the analysis of binary outcomes from cluster trials and to illustrate these concepts and analytical methods using a school-based GRT. METHODS: We examine characteristics of GRTs including intra-class correlation (ICC), their most distinctive feature, and review analytical methods for GRTs including group-level analysis, adjusted chi-square test and multivariable analysis (mixed effect models and generalized estimating equations) for correlated binary data. We consider two- and three-level modeling of data from a cross-sectional cluster design. We apply the concepts reviewed using a GRT designed to determine the effect of incentives on response rates in a school-based dental study. We compare the results of analyses using methods for correlated binary data with those from traditional methods that do not account for ICC. RESULTS: Application of traditional analytic methods to the dental GRT used as an example for this paper led to a substantial overstatement of the effectiveness of the intervention. CONCLUSIONS: Ignoring the ICC among members of the same group in the analysis of public health intervention studies can lead to erroneous conclusions where groups are the unit of assignment. Special consideration is needed in the analysis of data from these cluster trials. Randomization of treatments to groups also should receive more consideration in the design of cluster trials in dental public health.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Hae-Young Kim, John S Preisser, R Gary Rozier, Jayasanker V Valiyaparambil. 2006. Multilevel analysis of group-randomized trials with binary outcomes.. https://doi.org/10.1111/j.1600-0528.2006.00307.x

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

A note on a generalized single step theory for any number of hierarchical genomic matrices.

BACKGROUND: The Single Step algorithm allows combining information from genotyped and un-genotyped individuals, provided they are connected by a pedigree. However, current single step theory is limited to a single list of markers. RESULTS: We present a generalized single step (GSS) method that can accommodate any number of hierarchical molecular datasets (e.g. sequence, high and low density arrays) and pedigree, avoiding imputation. We prove that a similar efficient inversion algorithm exists. The method is recursive, starting with the highest marker density scenario. We illustrate the method with simulation and show that GSS can increase predictive accuracy compared to standard single step. R code is provided so that custom scenarios can be easily compared, either with simulated or real data. CONCLUSION: The method developed generalizes extant single step theory to any number of hierarchical molecular relationship matrices, broadening the scenarios where single step can be applied. A topic of particular interest can be ecology field data or human populations where pedigree is not available, but where samples sequenced and genotyped at different densities can exist. GSS can also be a useful tool to optimize allocation of genotyping and / or sequencing resources.

Algorithms↗

cgDist: Nucleotide-level distance calculation from cgMLST allelic profiles.

Bacterial genomic surveillance requires balancing computational efficiency with genetic resolution for effective cluster investigation. cgMLST distance calculations treat all allelic differences as equivalent units, obscuring nucleotide-level variation. Furthermore, single nucleotide polymorphism-based pipelines provide finer resolution at substantially higher computational cost, which limits their routine deployment in surveillance laboratories. We present cgDist, an algorithm that calculates nucleotide-level distances directly from cgMLST allelic profiles, providing finer resolution than allele-count distances by leveraging within-allele nucleotide variation. The cache architecture stores alignment statistics, enabling distance calculation modes without computation and supporting both dataset-specific and schema-complete cache generation. This design enables incremental surveillance analysis, with performance benefits as laboratories accumulate alignment data. cgDist functions as a precision 'zoom lens' for the investigation of clusters identified through initial cgMLST screening. Rather than restructuring population relationships, this targeted approach concentrates enhanced resolution where it is most informative. The algorithm ensures that cgDist distances are greater than or equal to corresponding cgMLST distances, preserving epidemiological interpretability while adding genetic discrimination. By increasing resolution within identified clusters, cgDist may also support outbreak investigation, a potential application that remains to be evaluated on outbreak-derived data.

Algorithms↗

Theseus: fast and optimal affine-gap sequence-to-graph alignment.

MOTIVATION: Sequence-to-graph alignment is a central problem in bioinformatics, with applications in multiple sequence alignment (MSA) and pangenome analysis, among others. However, current algorithms for optimal affine-gap alignment impose high memory and computational requirements, limiting their scalability to aligning long sequences to complex graphs. Practical solutions partially address this problem using heuristic strategies that ultimately trade off optimality for speed. RESULTS: This work presents Theseus, a novel, fast, and optimal affine-gap sequence-to-graph alignment algorithm. Theseus leverages similarities between genomic sequences to accelerate the alignment computation and reduces the overall memory requirements without compromising optimality. To that end, Theseus processes only a subset of the dynamic programming cells, using a sparse-data strategy that enables efficient sequence-to-graph alignment. Moreover, our algorithm supports optimal affine-gap alignment on arbitrary directed graphs, including those with cycles. We evaluate Theseus on two key problems: MSA and pangenome read mapping. For MSA, we compare it against SPOA, abPOA, and POASTA. Theseus is 1.6× to 17.6× faster than POASTA, and 7.3× faster, on average, than SPOA, both optimal aligners. Compared with abPOA, Theseus ensures optimality and scales to the largest problems. For pangenome read mapping, we benchmark Theseus against the alignment stage of the mapping tool vg map, along with the alignment kernels of SPOA, abPOA, and POASTA. Theseus outperforms the other methods, showing a 1.9× to 16.9× speedup on short reads. Moreover, Theseus is 1.5× to 36.3× faster than vg when aligning against synthetic cyclic graphs. AVAILABILITY AND IMPLEMENTATION: Theseus code and documentation are publicly available at https://github.com/albertjimenezbl/theseus-lib.

Algorithms↗