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These studies typically assume that blood-derived DNA faithfully reflects an individual\u2019s germline genome. However, this assumption is challenged by somatic mutations arising from processes like clonal hematopoiesis. Although standard bioinformatics pipelines employ variant allele frequency (VAF)-based filtering to mitigate such contamination, the efficacy of these approaches requires systematic evaluation. By systematically analyzing germline genome data from large cohorts through applications of mutational signatures, we revealed critical limitations in current filtering methodologies. We found that the mutational spectrum of rare \u201cgermline\u201d variants is highly similar to that of somatic mutations. Furthermore, we uncovered that these variants show significant associations with phenotypes such as age, sex, and smoking status, established drivers of somatic mutagenesis. Notably, our multivariable regression models estimated that these somatic artifacts contribute to a substantial excess burden, such as 4.73 mutations per megabase (mut\/Mb) in males compared to females, a magnitude exceeding the mutation burden of many cancers. Although the precise absolute size of this contamination may vary depending on specific pathologies and individual environmental exposures, this persistent somatic contamination introduces substantial confounder effects, posing a risk of spurious associations and reverse causality in genetic studies. Our work underscores the urgent reconsideration of two fundamental aspects of genomic research: (1) refinement of variant filtering strategies to better distinguish true germline variants from somatic contaminants, and (2) incorporation of somatic mutagenesis factors as essential covariates in study design. Our findings provide basic guidance for improving the accuracy and interpretability of large-scale genomic studies.<\/jats:p>","DOI":"10.3390\/biology15141204","type":"journal-article","created":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T15:17:52Z","timestamp":1784647072000},"page":"1204","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Evaluating Somatic Mutational Contamination in Large-Scale Germline Genomic Studies"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9427-1754","authenticated-orcid":false,"given":"Xiangwen","family":"Ji","sequence":"first","affiliation":[{"name":"Department of Cardiology and Institute of Vascular Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University Third Hospital, 49 Huayuanbei Road, Beijing 100191, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueke","family":"Bai","sequence":"additional","affiliation":[{"name":"National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6078-3375","authenticated-orcid":false,"given":"Guangda","family":"He","sequence":"additional","affiliation":[{"name":"National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-9586-4104","authenticated-orcid":false,"given":"Kai","family":"Yan","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Medical Genetics, and Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edwin","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Medical Genetics, and Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Da","family":"Tang","sequence":"additional","affiliation":[{"name":"Department of Cardiology and Institute of Vascular Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University Third Hospital, 49 Huayuanbei Road, Beijing 100191, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6374-112X","authenticated-orcid":false,"given":"Liang","family":"Chen","sequence":"additional","affiliation":[{"name":"National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qinghua","family":"Cui","sequence":"additional","affiliation":[{"name":"Department of Cardiology and Institute of Vascular Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University Third Hospital, 49 Huayuanbei Road, Beijing 100191, China"},{"name":"School of Sports Medicine, Wuhan Sports University, No. 461 Luoyu Rd. Hongshan District, Wuhan 430079, China"},{"name":"Department of Biomedical Informatics, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, 38 Xueyuan Rd, Beijing 100191, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1038\/s41586-020-2853-0","article-title":"Exome Sequencing and Characterization of 49,960 Individuals in the UK Biobank","volume":"586","author":"Tachmazidou","year":"2020","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"628","DOI":"10.1038\/s41586-021-04103-z","article-title":"Exome Sequencing and Analysis of 454,787 UK Biobank Participants","volume":"599","author":"Backman","year":"2021","journal-title":"Nature"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1038\/s41586-022-04965-x","article-title":"The Sequences of 150,119 Genomes in the UK Biobank","volume":"607","author":"Halldorsson","year":"2022","journal-title":"Nature"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1832","DOI":"10.1038\/s41588-024-01884-7","article-title":"Genetic Architecture of Telomere Length in 462,666 UK Biobank Whole-Genome Sequences","volume":"56","author":"Burren","year":"2024","journal-title":"Nat. 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