UNASSIGNED: In the @entity5 , analysis of recurrent @entity2008 such as @entity393 , 11q, gain of 17q and @entity4180 amplification are used for @entity1 stratification and subsequent therapy decision making. Different analysis techniques have been used for detection of @entity1347 , 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 @entity5 of different stages. Normalized coverage reads for @entity5 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 @entity2007 . 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 @entity8171 deletion in two @entity5 and three cases of novel deletions in chromosomal region 19q13.2 causing homozygous loss of multiple genes including the @entity69010 ( @entity69010 ) 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 ( @entity471 ) detection in @entity5 , especially considering the combination with mutational screening. This enables detection of theranostic targets such as @entity7041 and @entity8171 together with detection of significant segmental @entity2007 , such as 2p-gain, 17q-gain, 11q-deletion as well as @entity4180 amplification.

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

@entity1 :: ('9606', 'Species') :: ['patient'] @entity7041 :: ('238', 'Gene') :: ['ALK'] @entity2007 :: ('MESH:D000782', 'Disease') :: ['aneuploidies'] @entity8171 :: ('546', 'Gene') :: ['ATRX'] @entity5 :: ('MESH:D009369', 'Disease') :: ['tumors', 'neuroblastoma tumors', 'pediatric cancer neuroblastoma'] @entity1347 :: ('MESH:C537775', 'Disease') :: ['segmental abnormalities'] @entity4180 :: ('4613', 'Gene') :: ['MYCN'] @entity471 :: ('12143', 'Species') :: ['CNV'] @entity2008 :: ('MESH:D002869', 'Disease') :: ['chromosomal aberrations'] @entity393 :: ('MESH:D034381', 'Disease') :: ['loss of chromosome 1p'] @entity69010 :: ('23152', 'Gene') :: ['Capicua', 'CIC']
@entity69010 :: (23152,Gene) :: ['CIC']
