Genome-wide DNA Methylation Analysis of FOXP1 in Neuroblastoma

Array-CGH profiles from 159 neuroblastoma tumors were generated using 44 K or 105 K oligonucleotide microarrays as described previously [23 (link), 24 (link)]. The raw data were analyzed by Agilent Genomics Workbench software (v. 7.0; Agilent Technologies, Santa Clara, CA, USA, 2012) [23 (link)]. Array-CGH data are available as a subset at Gene Expression Omnibus (Accession: GSE45480).
FOXP1 promoter methylation analysis was performed by Sequenom Inc. (Hamburg, Germany) as described elsewhere [19 (link), 25 (link)]. Genomic DNA from 47 primary neuroblastoma specimens (high FOXP1 expression, n = 23; low FOXP1 expression, n = 24, as defined by the cutoff value for dichotomization of FOXP1 expression) and the neuroblastoma cell line IMR-32 was used to sequence three selected DNA regions covering 45 CpG units downstream of the FOXP1 start site (Table 1). PCR Primers were designed by using Methprimer (http://www.urogene.org/methprimer/, Additional file 1: Table S1).Table 1

Design statistics of genomic regions analyzed for methylation

Number of DNA samples	48
Number of genomic regions	1
Number of amplicons	3
Number of CpG units	45
Median amplicon length	413 bp (min = 365; max = 435)
Median CpG/amplicon	14 CpG/amplicon (min = 11; max = 20)