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(2) Methods: In total, 595 women with fetal DSMs who underwent prenatal diagnosis were enrolled. We analyzed the diagnostic yields of CMA and ES and evaluated pregnancy outcomes. Copy number variants (CNVs) were classified according to the American College of Medical Genetics and Genomics guidelines. (3) Results: Pathogenic CNVs were detected in 11\/517 (2.12%) fetuses, and variants of unknown significance (VUS) were identified in 69 (13.35%) fetuses using CMA. ES detected 29 pathogenic\/likely pathogenic variants in 23\/143 (16.08%) fetuses and 26\/143 (18.2%) VUS. In those with other ultrasound abnormalities, the detection rate of multiple system structural malformations was 41.2%, followed by skeletal (33.3%), cardiovascular (25.4%), and central nervous system (18.6%) malformations. Of the 391 surviving children, 40 (10.2%) exhibited varying degrees of mental retardation. (4) Conclusion: A correlation exists between DSMs and chromosomal abnormalities. When combined with other systemic abnormalities, the incidence of chromosomal abnormalities increases significantly. Patients with congenital DSM are at risk of developing neurodevelopmental disorders. Combined CMA and ES detection of fetal DSM has good clinical application potential.<\/jats:p>","DOI":"10.3390\/genes14101872","type":"journal-article","created":{"date-parts":[[2023,9,26]],"date-time":"2023-09-26T08:55:01Z","timestamp":1695718501000},"page":"1872","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Chromosome Microarray Analysis and Exome Sequencing: Implementation in Prenatal Diagnosis of Fetuses with Digestive System Malformations"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5405-1255","authenticated-orcid":false,"given":"You","family":"Wang","sequence":"first","affiliation":[{"name":"The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China"},{"name":"Department of Prenatal Diagnostic Center, Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University, Guangzhou 510620, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liyuan","family":"Liu","sequence":"additional","affiliation":[{"name":"The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China"},{"name":"Department of Prenatal Diagnostic Center, Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University, Guangzhou 510620, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fang","family":"Fu","sequence":"additional","affiliation":[{"name":"Department of Prenatal Diagnostic Center, Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University, Guangzhou 510620, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ru","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Prenatal Diagnostic Center, Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University, Guangzhou 510620, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tingying","family":"Lei","sequence":"additional","affiliation":[{"name":"Department of Prenatal Diagnostic Center, Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University, Guangzhou 510620, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8929-7805","authenticated-orcid":false,"given":"Ruibin","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Prenatal Diagnostic Center, Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University, Guangzhou 510620, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongzhi","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Prenatal Diagnostic Center, Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University, Guangzhou 510620, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Can","family":"Liao","sequence":"additional","affiliation":[{"name":"The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China"},{"name":"Department of Prenatal Diagnostic Center, Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University, Guangzhou 510620, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,9,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1046\/j.1469-0705.1995.05030174.x","article-title":"Routine Prenatal Ultrasound Screening for Fetal Abnormalities: 22 Years\u2019 Experience","volume":"5","author":"Carrera","year":"1995","journal-title":"Ultrasound Obstet. 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