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Using a new analytic approach for genotyping and phenotyping chromosome 9p deletion syndrome

European Journal of Human Genetics (2024)Cite this article

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Abstract

Using a new analytic method (“unique non-overlapping region” (UNOR) analysis), we characterized the genotypes and phenotypes of a large cohort of individuals diagnosed with chromosome 9p deletion syndrome (9PMS) and defined critical genomic regions. We extracted phenotypic information from 48 individuals with 9PMS from medical records and used a guided interview with caregivers to clarify ambiguities. Using high-resolution whole-genome sequencing for breakpoint definition, we aligned deletions and drew virtual breakpoints to obtain UNORs associated with phenotypic characteristics. We next extracted genotype and phenotype data for 57 individuals identified from a systematic review of the 9PMS literature and analyzed these as above. Common phenotypic features included developmental delay/intellectual disability, dysmorphic features, hypotonia, genital defects in XY individuals, psychiatric diagnoses, chronic constipation, atopic disease, vision problems, autism spectrum disorder, gastroesophageal reflux disease, trigonocephaly, congenital heart disease, and neonatal hypoglycemia. Our approach confirmed previous literature reports of an association of FREM1 with trigonocephaly and suggested a possible modifier element for this phenotype. In conclusion, the UNOR approach delineated phenotypic characteristics for 9PMS and confirmed the critical role of FREM1 and a possible long-distance regulatory element in pathogenesis of trigonocephaly that will need to be replicated in future studies.

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Fig. 1: Schematic representation of the delimitation of unique non-overlapping regions (UNORs).
Fig. 2: Flowchart of systematic review results.
Fig. 3: Maximal overlapping regions.
Fig. 4: Unique non-overlapping region (UNOR) analysis per phenotype.

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Data are available for sharing upon request. Limitations to data sharing may include privacy concerns for the individuals included in the study apply for data sharing.

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Acknowledgements

The authors are grateful to the staff of Washington University in Saint Louis and to the Chromosome 9p Minus Network for the critical help in all stages of this project. The authors are also grateful to Dr. Marwan Shinawi for critical insight on methods and findings.

Funding

This study was supported by anonymous charitable donation, as well as by Washington University in Saint Louis.

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Authors and Affiliations

  1. Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, MO, 63110, USA

    Rodrigo Tzovenos Starosta, Nathaniel Jensen, Sophia Couteranis, Rachel Slaugh, Dawn Easterlin, Victoria Tate & Patricia Dickson

  2. Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA

    Eleanor I. Sams, Kostandin Valle, Titilope Akinwe, Tychele N. Turner & Jeffrey Milbrandt

  3. Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA

    Ying-Chen Claire Hou

  4. Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, MO, 63110, USA

    F. Sessions Cole

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  1. Rodrigo Tzovenos Starosta
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Contributions

Conceptualization: RTS, YCCH, TNT, FSC, JM, PD; data curation: RTS, NJ, SC, RS, DE, VT, EIS, KV, TA, YCCH, TNT; formal analysis: RTS, YCCH, TNT, FSC, JM, PD; funding acquisition: TNT, FSC, JM, PD; investigation: RTS, NJ, EIS, KV, TA, YCCH, TNT, PD; methodology: RTS, SC, VT, EIS, KV, TA, TNT, JM, PD; project administration: SC, VT, TNT, FSC, JM, PD; supervision: TNT, FSC, JM, PD; visualization: RTS, EIS, KV, TA, TNT; writing – original draft: RTS, NJ, SC; writing – review and editing: RTS, NJ, SC, RS, DE, YCCH, TNT, FSC, JM, PD.

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Correspondence to Rodrigo Tzovenos Starosta.

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This study was approved by the Washington University in Saint Louis IRB. Informed consent was obtained from all participants or, as applicable, their legal guardians, as required by the IRB. All clinical data were de-identified. This study adheres to the principles outlaid in the Declaration of Helsinki and the Belmont Report.

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Starosta, R.T., Jensen, N., Couteranis, S. et al. Using a new analytic approach for genotyping and phenotyping chromosome 9p deletion syndrome. Eur J Hum Genet (2024). https://doi.org/10.1038/s41431-024-01667-y

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