Neuroblastoma somatic mutations enriched in cis-regulatory elements collectively affect genes involved in embryonic development and immune system response
DNA from primary tumor tissues was extracted with MasterPure DNA purification kit (Epicentre) according to manufacturers protocol. DNA quality was monitored on 1% agarose gels. Its purity was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured using Qubit DNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA). A total of 1.0g of DNA per sample was used as input material for library preparation. Sequencing libraries were generated using Truseq Nano DNA HT Sample Preparation Kit (Illumina USA) following manufacturer's recommendations. Genomic DNA was sonicated to a size of 350bp, and then fragments were end-polished, A-tailed, and ligated with the full-length adapter for Illumina sequencing with further PCR amplification. At last, PCR products were purified (AMPure XP system) and libraries were analyzed for size distribution using the DNA Nano 6000 Assay Kit of Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) and quantified using real-time PCR.