Inter-platform comparability of microarrays in acute lymphoblastic leukemia

BMC Genomics
Stephanie A MitchellDietrich A Stephan

Abstract

Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy and has been the poster-child for improved therapeutics in cancer, with life time disease-free survival (LTDFS) rates improving from <10% in 1970 to >80% today. There are numerous known genetic prognostic variables in ALL, which include T cell ALL, the hyperdiploid karyotype and the translocations: t(12;21)[TEL-AML1], t(4;11)[MLL-AF4], t(9;22)[BCR-ABL], and t(1;19)[E2A-PBX]. ALL has been studied at the molecular level through expression profiling resulting in un-validated expression correlates of these prognostic indices. To date, the great wealth of expression data, which has been generated in disparate institutions, representing an extremely large cohort of samples has not been combined to validate any of these analyses. The majority of this data has been generated on the Affymetrix platform, potentially making data integration and validation on independent sample sets a possibility. Unfortunately, because the array platform has been evolving over the past several years the arrays themselves have different probe sets, making direct comparisons difficult. To test the comparability between different array platforms, we have accumulated all Affymetrix ALL...Continue Reading

References

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Citations

Jul 29, 2005·BMC Bioinformatics·Antoine VeldhovenGuido Jenster
Oct 1, 2008·Biomarkers in Medicine·Sabine ClassenJoachim L Schultze
Aug 11, 2005·Current Oncology Reports·Joseph M Scandura
Aug 2, 2006·Transfusion Medicine·J Petrik
Sep 20, 2008·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Branimir I SikicNorman J Lacayo
Apr 7, 2009·British Journal of Haematology·Ulrike BacherTorsten Haferlach
Oct 6, 2005·Laboratory Investigation; a Journal of Technical Methods and Pathology·Joerg SchlingemannMeinhard Hahn

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Methods Mentioned

BETA
chips
chip
electrophoresis
cDNA

Software Mentioned

Genecluster2
BLAST
SAM
NetAffx
Microarray Suite

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