Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures

Tobias Rausch; Rene Snajder; Adrien Leger; Milena Simovic; Mădălina Giurgiu; Laura Villacorta; Anton G Henssen; Stefan Fröhling; Oliver Stegle; Ewan Birney; Marc Jan Bonder; Aurelie Ernst; Jan O Korbel

doi:10.1016/j.xgen.2023.100281

Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures

Cell Genom. 2023 Mar 22;3(4):100281. doi: 10.1016/j.xgen.2023.100281. eCollection 2023 Apr 12.

Authors

Tobias Rausch^{1

2}, Rene Snajder^{3

4

5}, Adrien Leger⁶, Milena Simovic⁷, Mădălina Giurgiu^{8

9}, Laura Villacorta², Anton G Henssen^{10

8

11}, Stefan Fröhling^{12

13

14}, Oliver Stegle^{1

3

15}, Ewan Birney⁶, Marc Jan Bonder³, Aurelie Ernst⁷, Jan O Korbel^{1

6

16}

Affiliations

¹ European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
² European Molecular Biology Laboratory (EMBL), GeneCore, Heidelberg, Germany.
³ Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
⁴ Faculty for Biosciences, Heidelberg University, Heidelberg, Germany.
⁵ HIDSS4Health, Helmholtz Information and Data Science School for Health, Heidelberg, Germany.
⁶ European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
⁷ Group "Genome Instability in Tumors," German Cancer Research Center (DKFZ), Heidelberg, Germany.
⁸ Experimental and Clinical Research Center (ECRC) of the Max Delbrück Center (MDC) and Charité-Universitätsmedizin, Berlin, Germany.
⁹ Freie Universität Berlin, Berlin, Germany.
¹⁰ Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin, Berlin, Germany.
¹¹ German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
¹² National Center for Tumor Diseases (NCT), Heidelberg, Germany.
¹³ German Cancer Research Center (DKFZ), Heidelberg, Germany.
¹⁴ German Cancer Consortium (DKTK), Heidelberg, Germany.
¹⁵ Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
¹⁶ Bridging Research Division on Mechanisms of Genomic Variation and Data Science, DKFZ, Heidelberg, Germany.

Abstract

Cancer genomes harbor a broad spectrum of structural variants (SVs) driving tumorigenesis, a relevant subset of which escape discovery using short-read sequencing. We employed Oxford Nanopore Technologies (ONT) long-read sequencing in a paired diagnostic and post-therapy medulloblastoma to unravel the haplotype-resolved somatic genetic and epigenetic landscape. We assembled complex rearrangements, including a 1.55-Mbp chromothripsis event, and we uncover a complex SV pattern termed templated insertion (TI) thread, characterized by short (mostly <1 kb) insertions showing prevalent self-concatenation into highly amplified structures of up to 50 kbp in size. TI threads occur in 3% of cancers, with a prevalence up to 74% in liposarcoma, and frequent colocalization with chromothripsis. We also perform long-read-based methylome profiling and discover allele-specific methylation (ASM) effects, complex rearrangements exhibiting differential methylation, and differential promoter methylation in cancer-driver genes. Our study shows the advantage of long-read sequencing in the discovery and characterization of complex somatic rearrangements.

Keywords: Nanopore methylation calling; cancer genomics; chromothripsis; complex rearrangements; epigenetic signatures; long read sequencing; templated insertions.