Estimation of copy number aberrations: Comparison of exome sequencing data with SNP microarrays identifies homozygous deletions of 19q13.2 and CIC in neuroblastoma

International Journal of Oncology
Susanne FranssonT Martinsson

Abstract

In the pediatric cancer neuroblastoma, analysis of recurrent chromosomal aberrations such as loss of chromosome 1p, 11q, gain of 17q and MYCN amplification are used for patient stratification and subsequent therapy decision making. Different analysis techniques have been used for detection of segmental abnormalities, including fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH)-microarrays and multiplex ligation-dependent probe amplification (MLPA). However, as next-generation sequencing becomes available for clinical use, this technique could also be used for assessment of copy number alterations simultaneously with mutational analysis. In this study we compare genomic profiles generated through exome sequencing data with profiles generated from high resolution Affymetrix single nucleotide polymorphism (SNP) microarrays on 30 neuroblastoma tumors of different stages. Normalized coverage reads for tumors were calculated using Control-FREEC software and visualized through a web based Shiny application, prior to comparison with corresponding SNP-microarray data. The two methods show high-level agreement for breakpoints and copy number of larger segmental aberrations and numerical aneuploidies. Howev...Continue Reading

References

Sep 9, 2006·Science·Tobias SjöblomVictor E Velculescu
Dec 3, 2008·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Susan L CohnUNKNOWN INRG Task Force
Jan 28, 2009·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Isabelle Janoueix-LeroseyOlivier Delattre
Feb 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·Helena CarénTommy Martinsson
Feb 18, 2011·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Inge M AmbrosPeter F Ambros
Aug 11, 2011·Bioinformatics·Jarupon Fah SathirapongsasutiStanley F Nelson
Apr 25, 2012·Journal of Cell Science·Gerardo JiménezZe'ev Paroush
May 16, 2012·Genome Research·Niklas KrummEvan E Eichler
Jan 4, 2013·PloS One·Rafael Valdés-MasXose S Puente
Jan 22, 2013·Nature Genetics·Trevor J PughJohn M Maris

❮ Previous
Next ❯

Citations

Sep 18, 2018·Expert Review of Molecular Diagnostics·Jayne Y Hehir-KwaPatrick Kemmeren
Apr 18, 2017·G3 : Genes - Genomes - Genetics·Inge SeimLisa K Chopin
Jul 11, 2019·The American Journal of Surgical Pathology·Rose ChamiPaul S Thorner
Nov 22, 2016·Nature Genetics·Ross A OkimotoTrever G Bivona
Jun 17, 2018·Cold Spring Harbor Molecular Case Studies·Jikui GuanBengt Hallberg

❮ Previous
Next ❯

Related Concepts

Related Feeds

Cancer Genomics (Keystone)

Cancer genomics approaches employ high-throughput technologies to identify the complete catalog of somatic alterations that characterize the genome, transcriptome and epigenome of cohorts of tumor samples. Discover the latest research using such technologies in this feed.