title: Concordance of copy number alterations using a common analytic pipeline for genome-wide analysis of Illumina and Affymetrix genotyping data: a report from the Children's Oncology Group.
abstract: Copy number alterations (CNAs) are a hallmark of pediatric cancer 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 children with de novo acute myeloid leukemia between two experimental platforms: Affymetrix SNP 6.0 array and Illumina OmniQuad 2.5 BeadChip. Forty-five paired tumor-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 tumors (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 tumor 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.
authors.affiliation: Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. Electronic address: vujkovicm@email.chop.edu.
authors.forename: Marijana
authors.initials: M
authors.lastname: Vujkovic
authors.affiliation: Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
authors.forename: Edward F
authors.initials: EF
authors.lastname: Attiyeh
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
authors.forename: Rhonda E
authors.initials: RE
authors.lastname: Ries
authors.affiliation: Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
authors.forename: Michelle
authors.initials: M
authors.lastname: Horn
authors.affiliation: Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
authors.forename: Elizabeth K
authors.initials: EK
authors.lastname: Goodman
authors.affiliation: Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
authors.forename: Yang
authors.initials: Y
authors.lastname: Ding
authors.affiliation: University Medical Centre, Ljubljana, Slovenia.
authors.forename: Marko
authors.initials: M
authors.lastname: Kavcic
authors.affiliation: Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
authors.forename: Todd A
authors.initials: TA
authors.lastname: Alonzo
authors.affiliation: Children's Oncology Group, Monrovia, CA, USA.
authors.forename: Robert B
authors.initials: RB
authors.lastname: Gerbing
authors.affiliation: University of Minnesota, Minneapolis, MN, USA.
authors.forename: Betsy
authors.initials: B
authors.lastname: Hirsch
authors.affiliation: Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
authors.forename: Susana
authors.initials: S
authors.lastname: Raimondi
authors.affiliation: Division of Hematology/Oncology/Bone Marrow Transplantation, Children's Mercy Hospitals and Clinics, Kansas City, MO, USA.
authors.forename: Alan S
authors.initials: AS
authors.lastname: Gamis
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
authors.forename: Soheil
authors.initials: S
authors.lastname: Meshinchi
authors.affiliation: Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Aplenc
mesh_terms: D000208:Acute Disease; D056915:DNA Copy Number Variations; D005260:Female; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D007951:Leukemia, Myeloid / Q000235:genetics*; D019656:Loss of Heterozygosity; D008297:Male; D046228:Microarray Analysis / Q000379:methods; D020641:Polymorphism, Single Nucleotide
keywords: Pediatrics; SNP array; acute myeloid leukemia; copy number alterations