Integration of cytogenomic data for furthering the characterization of pediatric B-cell acute lymphoblastic leukemia: A multi-institution, multi-platform microarray study

Linda B. Baughn, Jaclyn A. Biegel, Sarah T. South, Teresa A. Smolarek, Suzanne Volkert, Andrew J. Carroll, Nyla A. Heerema, Karen R. Rabin, Patrick A. Zweidler-McKay, Mignon Loh, Betsy Hirsch

Research output: Contribution to journalArticlepeer-review

29 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)1-18
Number of pages18
JournalCancer Genetics
Issue number1-2
StatePublished - Jan 1 2015

Bibliographical note

Funding Information:
This work was supported in part by grants to the Children's Oncology Group U10 CA98543 (Chair's grant) and to NIH / NCI P30 (CA77598) University of Minnesota Comprehensive Cancer Center: Cytogenomics Shared Resource Core Facility. K.R.R. is a St. Baldrick's Foundation scholar. We thank Donna Wilmoth and Laura Tooke for technical assistance.

Publisher Copyright:
© 2015 Published by Elsevier Inc.


  • B-ALL
  • ETV6-RUNX1
  • Hypodiploid
  • IAMP21
  • IKZF1
  • Microarray


Dive into the research topics of 'Integration of cytogenomic data for furthering the characterization of pediatric B-cell acute lymphoblastic leukemia: A multi-institution, multi-platform microarray study'. Together they form a unique fingerprint.

Cite this