Download Distinct effects of 11q aberrations on neuroblastoma with

Supplementaries
Supplementary table 1: Characteristics of patients and tumour samples of the four clinicogenetic subgroups normal_fav (A), normal_unfav (B), del11q_fav (C) and del11q_unfav (D).
Indicated are the stage of disease according to INSS, the age at diagnosis (days), the
genomic MYCN, 1p, 11q and 3p status according to FISH results (1, not amplified; n, not
deleted; del, deletion; im, imbalance; n.d., not determined), the histological assessment
according to Shimada (F, favourable; UF, unfavourable; n.d., not determined), the risk
estimation according to the criteria of the German Neuroblastoma Trial NB2004 (LR, low risk;
IR, intermediate risk; HR, high risk), the gene expression-based classification according to
PAM by either cross validation (CV) or prediction (test set; LR, low risk; HR, high risk), the
initial cytotoxic treatment, the current status of the patient (0, no event; 1, death of disease;
2, relapse or progression), the event-free and overall survival (EFS and OS; days), the
treatment protocol according to which the patients were treated, and the neuroblastoma
screening status (n, not screened; TP, true positive; FN, false negative). (*) indicates tumour
samples used for promoter methylation analyses.
Supplementary table 2: Genomic sequences amplified for methylation analysis of promoter
regions. Indicated are the amplicon and gene name, the UCSC annotation template and the
genomic sequence template, the oligonucleotide sequences used as primers, the strand
direction, the target nucleotide sequence and sequence length, the number of CpG units
within each amplified sequence, the chromosome, and the target start site and end on the
chromosome.
Supplementary table 3: Genes differentially expressed between clinico-genetic subgroups
as determined by SAM: normal_fav vs. normal_unfav (A); del11q_fav vs. del11q_unfav (B);
normal_fav vs. del11q_fav (C); normal_unfav vs. del11q_unfav (D); normal_fav vs.
del11q_unfav (E); normal_unfav vs. del11q_fav (F). Indicated are the probe ID, the gene
1
symbol and gene description, the chromosomal location of the gene, the fold-change of
expression between the subgroups under investigation, the SAM q-value, the false discovery
rate (FDR), and the direction of regulation between the respective subgroups. “Up” and
“down” refer to the average gene expression level in the second group of each comparison;
e.g., 598 genes are significantly up-regulated in the normal_unfav subgroup in comparison to
the normal_fav subgroup in supplementary table 3A.
Supplementary table 4: Overlap of genes differentially expressed between distinct
neuroblastoma subgroups: Overlap of transcripts with differential expression in normal_fav
vs. normal_unfav and 11_fav vs. del11q_unfav neuroblastoma (A); overlap of transcripts with
differential expression in normal_fav vs. del11q_unfav and 11_fav vs. del11q_unfav
neuroblastoma (B); overlap of transcripts with differential expression in normal_fav vs.
del11q_unfav and normal_unfav vs. del11q_unfav neuroblastoma (C). Indicated are the
probe ID, the gene symbol and gene description, the chromosomal location of the gene, the
fold-change of expression between the subgroups under investigation, and the direction of
regulation between the respective subgroups as described in legend to supplementary table
3.
Supplementary table 5: Whole genome aCGH analysis of neuroblastoma subgroups
del11q_fav, del11q_unfav, normal_fav and normal_unfav. Aberrations of ≥2 Mb are
indicated. CNA at 11q are given in bold; CNA at 11q of tumour NB062 is given in parenthesis
since only a weak signal could be detected in this case.
Supplementary table 6: Genes selected for promoter methylation analysis: Genes downregulated in del11q_unfav tumours in comparison to normal_unfav tumours (A); genes downregulated in del11q_unfav tumours in comparison to del11q_fav tumours (B). Indicated are
the probe ID, the gene symbol and NCBI Reference Sequence ID, the fold-change and
2
direction of expression relating to del11q_unfav tumours, as well as the cytogenetic and
genomic location of the gene.
Supplementary figure 1: Overlap of genes differentially expressed between normal_fav vs.
normal_unfav and del11q_fav vs. del11q_unfav (A), del11q_unfav vs. normal_fav and
del11q_unfav vs. del11q_fav (B) as well as between del11q_unfav vs. normal_fav and
del11q_unfav vs. normal_unfav (C).
3