Servicenavigation

Detailseite

Zurück

Projekt Druckansicht

Identifizierung struktureller genomischer Veränderungen im Neuroblastom mittels “linked-read whole-genome sequencing“

Fachliche Zuordnung Kinder- und Jugendmedizin
Bioinformatik und Theoretische Biologie
Hämatologie, Onkologie
Förderung Förderung von 2020 bis 2023
Projektkennung Deutsche Forschungsgemeinschaft (DFG) - Projektnummer 433152224
 
Erstellungsjahr 2024

Zusammenfassung der Projektergebnisse

The pathogenetic relevance of structural alterations in high-risk neuroblastoma has been underestimated in the past. We therefore hypothesized that novel insights into the genetic etiology of high-risk neuroblastoma would provide the basis for establishing biomarker-guided personalized treatment strategies in the future. By generating sequencing data of 118 samples of 71 patients, including both high- and low/intermediate-risk cases, we created a larger and more diverse Linked-Read sequencing cohort than originally planned. Over the course of the project, we integrated computational analysis of Linked-read WGS data into our in-house pipeline, and also incorporated copy number calling and RNA-seq information of the same patients. Comparison to matched conventional WGS data of the same patients demonstrated an increased alignment accuracy when using the Linked-read sequencing information, which allows for more sensitive and precise rearrangement calling, especially in low-complexity regions. We detected deletions, inversions, tandem duplications and translocations larger than 1.500 bp in all cases (median, 20-25 rearrangements per case). Similar to point mutations, rearrangements were of high diversity and low recurrency in neuroblastoma. While only part of the rearrangements immediately affected genes, we found a profound effect on gene expression in some cases. Known alterations, e.g., amplification of the oncogene MYCN or copy number gains and losses at chromosomes 11q and 17q, were detected, and complex amplifications on chromosome 12 were reconstructed in great detail. We used the power of Linked-read sequencing for in-depth analysis of such complex structural alterations, which we termed seismic amplification, in two liposarcoma cell lines. We demonstrated that these events follow an evolutionary process that reaches an equilibrium state with excessively amplified oncogenes, and which then persists over the course of the disease. Similarly, structural rearrangements detected in longitudinal patient samples in our present cohort, though less complex, mostly persisted over time. The development and evaluation of the Linked-read sequencing analysis pipeline was hampered and protracted by the discontinuation of this technology by 10x Genomics, and a subsequent paucity of – often premature – published work by other groups. However, this left us with one of the largest Linked-read sequencing databases to date, and our work and future publications of results will provide analysis strategies to others. Recently, companies such as Sage Science with its Transposase Enzyme Linked Long-Read Sequencing (TELL-Seq) emerged, which likely will reinvigorate the technology of Linked-Read sequencing as a promising alternative to long-read sequencing. In future analyses of this project, we will investigate the molecular effects of genomic rearrangements on gene expression patterns and chromatin structure in detail, and we will validate potentially relevant structural alterations by FISH analysis. We will particularly focus on the temporal development of genomic rearrangements in longitudinal samples to gain insights into the evolution of structural variations in the neuroblastoma’s genome over the course of disease. We are currently also examining whole-exome sequencing data of longitudinal samples from the same patients, which we plan to integrate with information on structural alterations from Linked-Read sequencing. Finally, we aim to assess the potential effect of genes affected by potentially relevant genomic rearrangements on the clinical phenotype in experimental systems to gain insights into the key alterations that drive malignant transformation of this malignancy.

Projektbezogene Publikationen (Auswahl)

 
 

Zusatzinformationen

© 2026 DFG Kontakt / Impressum / Datenschutz

Textvergrößerung und Kontrastanpassung