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Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features

By Jessica X. Chong, Joon-Ho Yu, Peter Lorentzen, Karen M. Park, Seema M Jamal, Holly K Tabor, Anita Rauch, Margarita Sifuentes Saenz, Eugen Boltshauser, Karynne E Patterson, Deborah A. Nickerson, University of Washington Center for Mendelian Genomics, Michael J. Bamshad

Posted 03 Oct 2015
bioRxiv DOI: 10.1101/028241 (published DOI: 10.1038/gim.2015.161)

Purpose: The pace of Mendelian gene discovery is slowed by the "n-of-1 problem" - the difficulty of establishing causality of a putatively pathogenic variant in a single person or family. Identification of an unrelated person with an overlapping phenotype and suspected pathogenic variant in the same gene can overcome this barrier but is often impeded by lack of a convenient or widely-available way to share data on candidate variants / genes among families, clinicians and researchers. Methods: Social networking among families, clinicians and researchers was used to identify three children with variants of unknown significance in KDM1A and similar phenotypes. Results: De novo variants in KDM1A underlie a new syndrome characterized by developmental delay and distinctive facial features. Conclusion: Social networking is a potentially powerful strategy to discover genes for rare Mendelian conditions, particularly those with non-specific phenotypic features. To facilitate the efforts of families to share phenotypic and genomic information with each other, clinicians, and researchers, we developed the Repository for Mendelian Genomics Family Portal (RMD-FP). Design and development of a web-based tool, MyGene2, that enables families, clinicians and researchers to search for gene matches based on analysis of phenotype and exome data deposited into the RMD-FP is underway.

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