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Non-syndromic forms of OFC are predominantly genetic, with significant variability in prevalence across populations. Understanding the genetic underpinnings of OFCs remains a key public health priority, given the substantial medical and societal burden of these conditions. Recent genome-wide association studies (GWAS) have implicated numerous genetic loci, but challenges remain due to genetic heterogeneity and complex gene-environment interactions. This study aimed to identify sex-specific genetic risk factors for cleft lip with or without cleft palate (CL\/P) through a meta-analysis of whole genome sequencing (WGS) data from 1,922 case-parent trios across eight diverse cohorts. Our approach revealed four SNPs in three distinct regions that showed genome-wide significant sex-specific effects. However, despite each of these SNPs passing standard quality control filters, follow-up analyses showed that these signals most likely were technical artifacts caused by sequencing errors, in particular mis-mapped reads due to sequence similarities with the sex chromo-somes. These findings highlight the necessity for careful scrutiny when studying differences between the sexes in genetic association studies.<\/jats:p>","DOI":"10.64898\/2026.07.07.26357463","type":"posted-content","created":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T03:30:25Z","timestamp":1783654225000},"source":"Crossref","is-referenced-by-count":0,"title":["A study of sex-specific genetic effects underlying risk of orofacial clefts also highlights the potential impact of sequencing errors due to short read mis-mapping"],"prefix":"10.64898","author":[{"given":"Kanika","family":"Kanchan","sequence":"first","affiliation":[{"name":"Genomics and Precision Health Section, Laboratory of Allergic Diseases, The National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zeynep","family":"Erdogan-Yildirim","sequence":"additional","affiliation":[{"name":"Center for Craniofacial and Dental Genetics, Department of 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