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CWAS-Plus, adapted from a Python package for category-wide association testing (CWAS), enhances noncoding variant analysis by integrating both whole-genome sequencing (WGS) and user-provided functional data. With simplified parameter settings and an efficient multiple testing correction method, CWAS-Plus conducts the CWAS workflow 50 times faster than CWAS, making it more accessible and user-friendly for researchers. Here, we used a 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 WGS data (n\u2009=\u20097280), CWAS-Plus identified noncoding de novo variant associations in transcription factor binding sites within conserved loci. Independently, in Alzheimer\u2019s disease WGS data (n\u2009=\u20091087), CWAS-Plus detected rare noncoding variant associations in microglia-specific regulatory elements. These findings highlight CWAS-Plus\u2019s utility in genomic disorders and scalability for processing large-scale WGS data and in multiple-testing corrections. CWAS-Plus and its user manual are available at https:\/\/github.com\/joonan-lab\/cwas\/ and https:\/\/cwas-plus.readthedocs.io\/en\/latest\/, respectively.<\/jats:p>","DOI":"10.1093\/bib\/bbae323","type":"journal-article","created":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T17:32:59Z","timestamp":1718731979000},"source":"Crossref","is-referenced-by-count":16,"title":["CWAS-Plus: estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data"],"prefix":"10.1093","volume":"25","author":[{"given":"Yujin","family":"Kim","sequence":"first","affiliation":[{"name":"Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-ku, Seoul 02841 , Republic of Korea"},{"name":"L-HOPE Program for Community-Based Total Learning Health Systems, Korea University , 145 Anam-ro, Seongbuk-ku, Seoul 02841 , Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minwoo","family":"Jeong","sequence":"additional","affiliation":[{"name":"School of Biosystem and Biomedical Science, College of Health Science, Korea University , 145 Anam-ro, Seongbuk-ku, Seoul 02841 , Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"In Gyeong","family":"Koh","sequence":"additional","affiliation":[{"name":"Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-ku, Seoul 02841 , Republic of Korea"},{"name":"L-HOPE Program for Community-Based Total Learning Health Systems, Korea University , 145 Anam-ro, Seongbuk-ku, Seoul 02841 , Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chanhee","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-ku, Seoul 02841 , Republic of Korea"},{"name":"L-HOPE Program for Community-Based Total Learning Health Systems, Korea University , 145 Anam-ro, Seongbuk-ku, Seoul 02841 , Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyeji","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-ku, Seoul 02841 , Republic of Korea"},{"name":"L-HOPE Program for Community-Based Total Learning Health Systems, Korea University , 145 Anam-ro, Seongbuk-ku, Seoul 02841 , Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jae Hyun","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-ku, Seoul 02841 , Republic of Korea"},{"name":"L-HOPE Program for Community-Based Total Learning Health Systems, Korea University , 145 Anam-ro, Seongbuk-ku, Seoul 02841 , Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9677-6599","authenticated-orcid":false,"given":"Ronald","family":"Yurko","sequence":"additional","affiliation":[{"name":"Department of Statistics and Data Science, Carnegie Mellon University , 5000 Forbes Avenue, Squirrel Hill North, Pittsburgh, PA 15213 , United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Il Bin","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Psychiatry , CHA Gangnam Medical Center, , 566 Nonhyon-ro, Gangnam-gu, Seoul 06135 , Republic of Korea"},{"name":"CHA University School of Medicine , CHA Gangnam Medical Center, , 566 Nonhyon-ro, Gangnam-gu, Seoul 06135 , Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeongbin","family":"Park","sequence":"additional","affiliation":[{"name":"School of Biomedical Convergence Engineering, Pusan National University , 49 Busandaehak-ro, Mulgeum-eup, Yangsan-si, Gyeongsangnam-do, 50612 , Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donna M","family":"Werling","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, University of Wisconsin-Madison , 425-g Henry Mall, Madison, WI 53706 , Unite States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephan J","family":"Sanders","sequence":"additional","affiliation":[{"name":"Department of Paediatrics, Institute of Developmental and Regenerative Medicine, University of Oxford , Old Road Campus, Roosevelt Dr, Headington, Oxford OX3 7TY , United Kingdom"},{"name":"Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California , 1651 4th Street, San Francisco, CA 94158 , United 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