AbstractCopy number variants (CNVs) are the gain or loss of DNA segments in the genome that can vary in dosage and length. CNVs comprise a large proportion of variation in human genomes and impact health conditions. To detect rare CNV association, kernel-based methods have been shown to be a powerful tool because their flexibility in modeling the aggregate CNV effects, their ability to capture effects from different CNV features, and their ability to accommodate effect heterogeneity. To perform a kernel association test, a CNV locus needs to be defined so that locus-specific effects can be retained during aggregation. However, CNV loci are arbitrarily defined and different locus definitions can lead to different performance depending on the underlying effect patterns. In this work, we develop a new kernel-based test called CONCUR (i.e., Copy Number profile Curve-based association test) that is free from a definition of locus and evaluates CNV-phenotype association by comparing individuals’ copy number profiles across the genomic regions. CONCUR is built on the proposed concepts of “copy number profile curves” to describe the CNV profile of an individual, and the “common area under the curve (cAUC) kernel” to model the multi-feature CNV effects. Compared to existing methods, CONCUR captures the effects of CNV dosage and length, accounts for the continuous nature of copy number values, and accommodates between- and within-locus etiological heterogeneities without the need to define artificial CNV loci as required in current kernel methods. In a variety of simulation settings, CONCUR shows comparable and improved power over existing approaches. Real data analyses suggest that CONCUR is well powered to detect CNV effects in gene pathways associated with phenotypes using data from the Swedish Schizophrenia Study and the Taiwan Biobank.Author summaryCopy number variants comprise a large proportion of variation in human genomes. Large rare CNVs, especially those disrupting genes or changing the dosages of genes, can carry relatively strong risks for neurodevelopmental and neuropsychiatric disorders. Kernel-based association methods have been developed for the analysis of rare CNVs and shown to be a valuable tool. Kernel methods model the collective effect of rare CNVs using flexible kernel functions that capture the characteristics of CNVs and measure CNV similarity of individual pairs. Typically kernels are created by summarizing similarity within an artificially defined “CNV locus” and then collapsing across all loci. In this work, we propose a new kernel-based test, CONCUR, that is based on the CNV location information contained in standard processing of the variants and removes the need for any arbitrarily defined CNV loci. CONCUR quantifies similarity between individual pairs as the common area under their copy number profile curves and is designed to detect CNV dosage, length and dosage-length interaction effects. In simulation studies and real data analysis, we demonstrate the ability of CONCUR test to detect CNV effects under diverse CNV architectures with power and robustness over existing methods.
A fast variational algorithm to detect the clonal copy number substructure of tumors from single-cell data
