CWAS-Plus: Estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data

Abstract

ABSTRACTVariants in cis-regulatory elements link the noncoding genome to human brain pathology; however, detailed analytic tools for understanding the association between cell-level brain pathology and noncoding variants are lacking. CWAS-Plus, adapted from a Python package for category-wide association testing (CWAS) employs both whole-genome sequencing and user-provided functional data to enhance noncoding variant analysis, with a faster and more efficient execution of the CWAS workflow. Here, we used single-nuclei assay for transposase-accessible chromatin with sequencing to facilitate CWAS-guided noncoding variant analysis at cell-type specific enhancers and promoters. Examining autism spectrum disorder whole-genome sequencing data (n = 7,280), CWAS-Plus identified noncodingde novovariant associations in transcription factor binding sites within conserved loci. Independently, in Alzheimer’s disease whole-genome sequencing data (n = 1,087), CWAS-Plus detected rare noncoding variant associations in microglia-specific regulatory elements. These findings highlight CWAS-Plus’s utility in genomic disorders and scalability for processing large-scale whole-genome sequencing data and in multiple-testing corrections. CWAS-Plus and its user manual are available athttps://github.com/joonan-lab/cwas/andhttps://cwas-plus.readthedocs.io/en/latest/, respectively.KEY POINTSCWAS-Plus efficiently identifies noncoding associations in WGS data, supporting user-friendly categorization and burden enrichment tests.CWAS-Plus integrates various functional datasets, emphasizing cell-type-specific noncoding associations.CWAS-Plus provides a novel approach for multiple testing correction, enhancing the reliability of the results.Autism spectrum disorder risk noncoding variants are identified as enriched with transcription factors, suggesting their role in the pathology.Rare variant analysis with Alzheimer’s disease samples reveals strong association with microglia, supporting the reliability of the results produced by CWAS-Plus.