Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition

Authors: Mitchell R. Vollger^{1 2}, Jonas Korlach³, Kiara C. Eldred⁴, Elliott Swanson¹, Jason G. Underwood³, Yong-Han H. Cheng¹, Jane Ranchalis², Yizi Mao², Elizabeth E. Blue^{2 5 6}, Ulrike Schwarze⁷, Katherine M. Munson¹, Christopher T. Saunders³, Aaron M. Wenger³, Aimee Allworth², Sirisak Chanprasert², Brittney L. Duerden⁸, Ian Glass^{9 6}, Martha Horike-Pyne², Michelle Kim³, Kathleen A. Leppig¹⁰, Ian J. McLaughlin³, Jessica Ogawa¹, Elisabeth A. Rosenthal², Sam Sheppeard², Stephanie M. Sherman², Samuel Strohbehn², Amy L. Yuen¹⁰, University of Washington Center for Mendelian Genomics (UW-CMG), Undiagnosed Diseases Network (UDN), Thomas A. Reh⁴, Peter H. Byers^7,2, Michael J. Bamshad^9,6, Fuki M. Hisama^2,6, Gail P. Jarvik^1,2,6, Yasemin Sancak^1,2, Katrina M. Dipple^9,6 and Andrew B. Stergachis^1,2,6,† 1) University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA 2) University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA 3) PacBio, Menlo Park, CA, USA 4) University of Washington School of Medicine, Department of Biological Structure, Seattle, WA, USA 5) Institute for Public Health Genetics, University of Washington, Seattle, WA, USA 6) Brotman Baty Institute for Precision Medicine, Seattle, WA, USA 7) University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA 8) Mary Bridge/MultiCare, Tacoma, WA, USA 9) University of Washington, Department of Pediatrics, Seattle, WA, USA 10) Genetic Services, Kaiser Permanente Washington, Seattle, Washington, USA 11) Case Western Reserve University, Cleveland, OH 12) University of Washington School of Medicine, Department of Pharmacology, Seattle, WA, USA ↵†) Corresponding author. (e-mail [email protected])

Resolving the molecular basis of a Mendelian condition (MC) remains challenging owing to the diverse mechanisms by which genetic variants cause disease. To address this, we developed a synchronized long-read genome, methylome, epigenome, and transcriptome sequencing approach, which enables accurate single-nucleotide, insertion-deletion, and structural variant calling and diploid de novo genome assembly, and permits the simultaneous elucidation of haplotype-resolved CpG methylation, chromatin accessibility, and full-length transcript information in a single long-read sequencing run. Application of this approach to an Undiagnosed Diseases Network (UDN) participant with a chromosome X;13 balanced translocation of uncertain significance revealed that this translocation disrupted the functioning of four separate genes (NBEA, PDK3, MAB21L1, and RB1) previously associated with single-gene MCs. Notably, the function of each gene was disrupted via a distinct mechanism that required integration of the four ‘omes’ to resolve. These included nonsense-mediated decay, fusion transcript formation, enhancer adoption, transcriptional readthrough silencing, and inappropriate X chromosome inactivation of autosomal genes. Overall, this highlights the utility of synchronized long-read multi-omic profiling for mechanistically resolving complex phenotypes.

Journal: Biorxiv
DOI: 10.1101/2023.09.26.559521
Year: 2023

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