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

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. However, several smaller gene containing deletions that could not readily be detected through the SNP-microarray analyses were identified through exome profiling, most likely due to difference between spatial distribution of microarray probes and targeted regions of the exome capture. These smaller aberrations included focal ATRX deletion in two tumors and three cases of novel deletions in chromosomal region 19q13.2 causing homozygous loss of multiple genes including the CIC (Capicua) gene. In conclusion, genomic profiles generated from normalized coverage of exome sequencing show concordance with SNP microarray generated genomic profiles. Exome sequencing is therefore a useful diagnostic tool for copy number variant (CNV) detection in neuroblastoma tumors, especially considering the combination with mutational screening. This enables detection of theranostic targets such as ALK and ATRX together with detection of significant segmental aneuploidies, such as 2p-gain, 17q-gain, 11q-deletion as well as MYCN amplification.

Inactivation of Capicua drives cancer metastasis

“…We then employed the previously published Shiny application (https://malinost.shinyapps.io/CNPupload) to visualize Control-FREEC profiles 11 . The Shiny program uploaded the ratios from the Control-FREEC file and allowed direct visualization through R based chromosome plots.…”

Whole-Genome Sequence of the Metastatic PC3 and LNCaP Human Prostate Cancer Cell Lines

“…Recent WGS data also suggests that CIC is lost in PC3 cells (Iorio et al 2016). Homozygous deletions of CIC have been reported in neuroblastoma (Nagaishi et al 2014; Fransson et al 2016), and a homozygous deletion of CIC in a subpopulation of H1975 human nonsmall cell lung cancer cell line xenografts rendered them highly metastatic (Okimoto et al 2017). We interrogated 75 cBioPortal data sets from diverse tumors, confirming that one or two copies of CIC are lost in many cancer types (see Supplemental Material, Figure S1).…”

TFCP2 Genetic Polymorphism Is Associated with Predisposition to and Transplant Prognosis of Hepatocellular Carcinoma

“…Additionally, TFCP2 has also been identified as an important determinant of multiple cancers [23, 24]. Polymorphisms in genes, including exons, introns, and untranslated regions, have been shown to affect the processing of mRNAs as well as their regulatory effects and expressions, thus affecting the development and prognosis of different cancers [25, 26]. No studies have specifically addressed the role of TFCP2 polymorphisms in HCC so far.…”