PMID- 25678190 OWN - NLM STAT- MEDLINE DCOM- 20150505 LR - 20181113 IS - 2210-7762 (Print) VI - 208 IP - 1-2 DP - 2015 Jan-Feb TI - Integration of cytogenomic data for furthering the characterization of pediatric B-cell acute lymphoblastic leukemia: a multi-institution, multi-platform microarray study. PG - 1-18 LID - S2210-7762(14)00247-6 [pii] LID - 10.1016/j.cancergen.2014.11.003 [doi] AB - It is well documented that among subgroups of B-cell acute lymphoblastic leukemia (B-ALL), the genetic profile of the leukemic blasts has significant impact on prognosis and stratification for therapy. Recent studies have documented the power of microarrays to screen genome-wide for copy number aberrations (CNAs) and regions of copy number-neutral loss of heterozygosity (CNLOH) that are not detectable by G-banding or fluorescence in situ hybridization (FISH). These studies have involved application of a single array platform for the respective cases. The present investigation demonstrates the feasibility and usefulness of integrating array results from multiple laboratories (ARUP, The Children's Hospital of Philadelphia, Cincinnati Children's Hospital Medical Center, and University of Minnesota Medical Center) that utilize different array platforms (Affymetrix, Agilent, or Illumina) in their respective clinical settings. A total of 65 patients enrolled on the Children's Oncology Group (COG) study AALL08B1 were identified for study, as cytogenetic and FISH studies had also been performed on these patients, with a central review of those results available for comparison. Microarray data were first analyzed by the individual laboratories with their respective software systems; raw data files were then centrally validated using NEXUS software. The results demonstrated the added value of integrating multi-platform data with cytogenetic and FISH data and highlight novel findings identified by array including the co-occurrence of low and high risk abnormalities not previously reported to coexist within a clone, novel regions of chromosomal amplification, clones characterized by numerous whole chromosome LOH that do not meet criteria for doubling of a near-haploid, and characterization of array profiles associated with an IKZF1 deletion. Each of these findings raises questions that are clinically relevant to risk stratification. CI - Copyright (c) 2015. Published by Elsevier Inc. FAU - Baughn, Linda B AU - Baughn LB AD - Department of Laboratory Medicine and Pathology and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA. FAU - Biegel, Jaclyn A AU - Biegel JA AD - Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. FAU - South, Sarah T AU - South ST AD - ARUP Laboratories, Department of Pathology, University of Utah, Salt Lake City, UT, USA. FAU - Smolarek, Teresa A AU - Smolarek TA AD - Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. FAU - Volkert, Suzanne AU - Volkert S AD - Department of Laboratory Medicine and Pathology and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA. FAU - Carroll, Andrew J AU - Carroll AJ AD - Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA. FAU - Heerema, Nyla A AU - Heerema NA AD - Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA. FAU - Rabin, Karen R AU - Rabin KR AD - Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA. FAU - Zweidler-McKay, Patrick A AU - Zweidler-McKay PA AD - Department of Pediatrics, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA. FAU - Loh, Mignon AU - Loh M AD - Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. FAU - Hirsch, Betsy AU - Hirsch B AD - Department of Laboratory Medicine and Pathology and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA. Electronic address: hirsc003@umn.edu. LA - eng GR - P30 CA77598/CA/NCI NIH HHS/United States GR - P30 CA077598/CA/NCI NIH HHS/United States GR - U10 CA098543/CA/NCI NIH HHS/United States GR - U10 CA180886/CA/NCI NIH HHS/United States GR - U10 CA98543/CA/NCI NIH HHS/United States PT - Journal Article PT - Multicenter Study PT - Research Support, N.I.H., Extramural DEP - 20141121 PL - United States TA - Cancer Genet JT - Cancer genetics JID - 101539150 SB - IM MH - B-Lymphocytes/*metabolism/pathology MH - Child MH - Chromosome Aberrations MH - Chromosome Banding MH - Comparative Genomic Hybridization/*methods MH - Cytogenetic Analysis/*methods MH - DNA Copy Number Variations MH - Female MH - Humans MH - In Situ Hybridization, Fluorescence MH - Karyotyping MH - Loss of Heterozygosity MH - Male MH - Oligonucleotide Array Sequence Analysis MH - Polymorphism, Single Nucleotide MH - Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/diagnosis/*genetics MH - Prognosis MH - Reproducibility of Results MH - Sensitivity and Specificity PMC - PMC5361577 MID - NIHMS771766 OTO - NOTNLM OT - B-ALL OT - ETV6-RUNX1 OT - IKZF1 OT - hypodiploid OT - iAMP21 OT - microarray EDAT- 2015/02/14 06:00 MHDA- 2015/05/06 06:00 PMCR- 2017/03/22 CRDT- 2015/02/14 06:00 PHST- 2014/07/23 00:00 [received] PHST- 2014/11/03 00:00 [revised] PHST- 2014/11/10 00:00 [accepted] PHST- 2015/02/14 06:00 [entrez] PHST- 2015/02/14 06:00 [pubmed] PHST- 2015/05/06 06:00 [medline] PHST- 2017/03/22 00:00 [pmc-release] AID - S2210-7762(14)00247-6 [pii] AID - 10.1016/j.cancergen.2014.11.003 [doi] PST - ppublish SO - Cancer Genet. 2015 Jan-Feb;208(1-2):1-18. doi: 10.1016/j.cancergen.2014.11.003. Epub 2014 Nov 21.