Tumor Touch Imprints As Source for Whole Genome Analysis of Neuroblastoma Tumors

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2016 Aug 26

PMID 27560999

Citations 3

Authors

Clemens Brunner

Bettina Brunner-Herglotz

Andrea Ziegler

Christian Frech

Gabriele Amann

Ruth Ladenstein

Inge M Ambros

Peter F Ambros

Affiliations

Soon will be listed here.

Abstract

Introduction: Tumor touch imprints (TTIs) are routinely used for the molecular diagnosis of neuroblastomas by interphase fluorescence in-situ hybridization (I-FISH). However, in order to facilitate a comprehensive, up-to-date molecular diagnosis of neuroblastomas and to identify new markers to refine risk and therapy stratification methods, whole genome approaches are needed. We examined the applicability of an ultra-high density SNP array platform that identifies copy number changes of varying sizes down to a few exons for the detection of genomic changes in tumor DNA extracted from TTIs.

Material And Methods: DNAs were extracted from TTIs of 46 neuroblastoma and 4 other pediatric tumors. The DNAs were analyzed on the Cytoscan HD SNP array platform to evaluate numerical and structural genomic aberrations. The quality of the data obtained from TTIs was compared to that from randomly chosen fresh or fresh frozen solid tumors (n = 212) and I-FISH validation was performed.

Results: SNP array profiles were obtained from 48 (out of 50) TTI DNAs of which 47 showed genomic aberrations. The high marker density allowed for single gene analysis, e.g. loss of nine exons in the ATRX gene and the visualization of chromothripsis. Data quality was comparable to fresh or fresh frozen tumor SNP profiles. SNP array results were confirmed by I-FISH.

Conclusion: TTIs are an excellent source for SNP array processing with the advantage of simple handling, distribution and storage of tumor tissue on glass slides. The minimal amount of tumor tissue needed to analyze whole genomes makes TTIs an economic surrogate source in the molecular diagnostic work up of tumor samples.

Citing Articles

Application of the FISH method and high-density SNP arrays to assess genetic changes in neuroblastoma-research by one institute.

Winnicka D, Skowera P, Stelmach M, Styka B, Lejman M Acta Biochim Pol. 2024; 71:12821.

PMID: 39049899 PMC: 11267511. DOI: 10.3389/abp.2024.12821.

Mutational spectrum of ATRX aberrations in neuroblastoma and associated patient and tumor characteristics.

van Gerven M, Bozsaky E, Matser Y, Vosseberg J, Taschner-Mandl S, Koster J Cancer Sci. 2022; 113(6):2167-2178.

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An annotated fluorescence image dataset for training nuclear segmentation methods.

Kromp F, Bozsaky E, Rifatbegovic F, Fischer L, Ambros M, Berneder M Sci Data. 2020; 7(1):262.

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