Genomic profiling of microphthalmia trios reveals novel pathogenic drivers and repetitive element instability.
5 affiliations
- 1Beijing Tongren Eye Center, Beijing key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, No. 1 Dongjiaominxiang, Dongcheng District, Beijing 100730, China.
- 2National Genomics Data Center, China National Center for Bioinformation, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
- 3Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
- 4University of Chinese Academy of Sciences, College of Life Sciences, No. 1 Yanqihu East Rd, Huairou District, Beijing 100049, China.
- 5Beijing Novogene Bioinformatics Technology Co., Ltd., Global Product Center, No. 10A, Jiuxianqiao North Road, Chaoyang District, Beijing 100015, China.
Abstract
Congenital microphthalmos (CMIC) is a rare ocular malformation with marked genetic heterogeneity. To investigate its genomic landscape, we performed whole-genome sequencing of 10 proband-parent trios and integrated analyses of inherited variants, candidate germline de novo variants, and tandem-repeat variation. Following quality, population-frequency, and de novo probability filtering, 45 candidate germline de novo loci involving 37 genes were prioritized, including variants in POMT1, MYH11, and NR4A1. Rare homozygous variants in ANXA9 and SCARA5 showed recessive segregation in their respective families. Integration of gene-expression profiles and published functional evidence highlighted potential biological links to ocular development, calcium homeostasis, iron transport, and cellular stress responses. Repeat analysis further identified prominent repeat-length outlier signals in probands 5, 9, and 10, including a candidate AACCCT repeat-length alteration overlapping the SOX9/SOX9-AS1 locus in proband 10. Collectively, these findings broaden the spectrum of candidate genomic alterations in CMIC and nominate genes and regulatory loci that may contribute to its molecular pathogenesis. Their specific pathogenic roles and functional effects require further validation in independent cohorts and experimental models.
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BibTeX
@article{yang2026genomic,
title = {{Genomic profiling of microphthalmia trios reveals novel pathogenic drivers and repetitive element instability.}},
author = {Li Yang and Congfan Bu and Qianwen Gao and Jingfa Xiao and Zhenglin Du and Dongmei Li},
journal = {Human molecular genetics},
year = {2026},
month = oct,
doi = {10.1093/hmg/ddag111},
url = {https://europepmc.org/article/MED/42949432},
note = {CC BY-NC},
}
RIS
TY - JOUR
TI - Genomic profiling of microphthalmia trios reveals novel pathogenic drivers and repetitive element instability.
AU - Li Yang
AU - Congfan Bu
AU - Qianwen Gao
AU - Jingfa Xiao
AU - Zhenglin Du
AU - Dongmei Li
PY - 2026
DA - 2026/10/01
JO - Human molecular genetics
DO - 10.1093/hmg/ddag111
UR - https://europepmc.org/article/MED/42949432
AB - Congenital microphthalmos (CMIC) is a rare ocular malformation with marked genetic heterogeneity. To investigate its genomic landscape, we performed whole-genome sequencing of 10 proband-parent trios and integrated analyses of inherited variants, candidate germline de novo variants, and tandem-repeat variation. Following quality, population-frequency, and de novo probability filtering, 45 candidate germline de novo loci involving 37 genes were prioritized, including variants in POMT1, MYH11, and NR4A1. Rare homozygous variants in ANXA9 and SCARA5 showed recessive segregation in their respective families. Integration of gene-expression profiles and published functional evidence highlighted potential biological links to ocular development, calcium homeostasis, iron transport, and cellular stress responses. Repeat analysis further identified prominent repeat-length outlier signals in probands 5, 9, and 10, including a candidate AACCCT repeat-length alteration overlapping the SOX9/SOX9-AS1 locus in proband 10. Collectively, these findings broaden the spectrum of candidate genomic alterations in CMIC and nominate genes and regulatory loci that may contribute to its molecular pathogenesis. Their specific pathogenic roles and functional effects require further validation in independent cohorts and experimental models.
SN - 0964-6906
SN - 1460-2083
ER -