UNASSIGNED: Copy number alterations (CNAs) are a hallmark of pediatric @entity5 genomes. An increasing number of research groups use multiple platforms and software packages to detect and analyze CNAs. However, different platforms have experimental and analysis-specific biases that may yield different results. We sought to estimate the concordance of CNAs in @entity1 with de novo @entity3052 between two experimental platforms: Affymetrix SNP 6.0 array and Illumina OmniQuad 2.5 BeadChip. Forty-five @entity5 -remission samples were genotyped on both platforms, and CNAs were estimated from total signal intensity and allelic contrast values using the allele-specific copy number analysis of @entity5 (ASCAT) algorithm. The two platforms were comparable in detection of CNAs, each missing only two segments from a total of 42 CNAs (4.6%).  Overall, there was an interplatform agreement of 96% for allele-specific @entity5 profiles. However, poor quality samples with low signal/noise ratios showed a high rate of false-positive segments independent of the genotyping platform. These results demonstrate that a common analytic pipeline can be utilized for SNP array data from these two platforms. The customized programming template for the preprocessing, data integration, and analysis is publicly available at https://github.com/AplenCHOP/affyLumCNA.

Concordance of copy number alterations using a common analytic pipeline for genome-wide analysis of Illumina and Affymetrix genotyping data: a report from the XXXX 's Oncology Group.

@entity5 :: ('MESH:D009369', 'Disease') :: ['tumor', 'paired tumor', 'cancer', 'tumors'] @entity1 :: ('9606', 'Species') :: ['children'] @entity3052 :: ('MESH:D015470', 'Disease') :: ['acute myeloid leukemia']
@entity1 :: (9606,Species) :: ['Children']
