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Supplementary Information

Integrated genetic and epigenetic analysis of childhood acute lymphoblastic leukemia

Maria E. Figueroa1, Shann-Ching Chen2, Anna K. Andersson2, Letha A. Phillips2, Yushan Li3,
Jason Sotzen1, Mondira Kundu2, James R. Downing2, Ari Melnick3, and Charles G. Mullighan2

1Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.
2Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA.
3Department of Medicine, Hematology Oncology Division, Weill Cornell Medical College, New York, New York, USA.

Supplementary Table 1: Listing of patient, sample and array characteristics.
Supplementary Table 2: Listing of differentially methylated regions for each subtype of ALL.
Supplementary Table 3: Top networks enriched in each subtype-specific DNA methylation profile.
Supplementary Table 4: Complete listing of correlation data between differentially methylated probe sets and gene expression probe sets in Refseq centric analysis.
Supplementary Table 5: Fisher exact test results showing proportion of hypermethylated genes that are downregulated (5A) or upregulated (5B) and the proportion of downregulated (5A) or upregulated (5B) genes that are hypermethylated.
Supplementary Table 6: Summary of gene set enrichment analyses examining enrichment of hypo- and hypermethylated gene sets in gene expression signatures.
Supplementary Table 7: Relationship between gene methylation and expression by chromosome in hyperdiploid samples..
Supplementary Table 8: Overlap of normal T- v B-cell and leukemic T- v B-cell methylation signatures..
Supplementary Table 9: Genes in the common methylation signature of ALL.
Supplementary Table 10: Genes with recurrent genetic lesions in childhood ALL.
Supplementary Table 11: MassARRAY primers.