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Full-Text Articles in Life Sciences
Geometric Framework For Evaluating Rare Variant Tests Of Association, Keli Liu, Shannon Fast, Matthew Zawistowski, Nathan L. Tintle
Geometric Framework For Evaluating Rare Variant Tests Of Association, Keli Liu, Shannon Fast, Matthew Zawistowski, Nathan L. Tintle
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The wave of next-generation sequencing data has arrived. However, many questions still remain about how to best analyze sequence data, particularly the contribution of rare genetic variants to human disease. Numerous statistical methods have been proposed to aggregate association signals across multiple rare variant sites in an effort to increase statistical power; however, the precise relation between the tests is often not well understood. We present a geometric representation for rare variant data in which rare allele counts in case and control samples are treated as vectors in Euclidean space. The geometric framework facilitates a rigorous classification of existing rare …
Evaluating Methods For Combining Rare Variant Data In Pathway-Based Tests Of Genetic Association, Ashley Petersen, Alexandra Sitarik, Alexander Luedtke, Scott Powers, Airat Bekmetjev, Nathan L. Tintle
Evaluating Methods For Combining Rare Variant Data In Pathway-Based Tests Of Genetic Association, Ashley Petersen, Alexandra Sitarik, Alexander Luedtke, Scott Powers, Airat Bekmetjev, Nathan L. Tintle
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Analyzing sets of genes in genome-wide association studies is a relatively new approach that aims to capitalize on biological knowledge about the interactions of genes in biological pathways. This approach, called pathway analysis or gene set analysis, has not yet been applied to the analysis of rare variants. Applying pathway analysis to rare variants offers two competing approaches. In the first approach rare variant statistics are used to generate p-values for each gene (e.g., combined multivariate collapsing [CMC] or weighted-sum [WS]) and the gene-level p-values are combined using standard pathway analysis methods (e.g., gene set enrichment analysis or …