title: Illumina MiSeq paired end sequencing; Targeted sequencing of 42 primary medulloblastoma samples using Illumina TruSight Tumor 15 assay
design: Targeted sequencing of 42 primary medulloblastoma samples using Illumina TruSight Tumor 15 assay
library_construction_protocol: Tumor tissue was obtained from N=49 untreated primary medulloblastomas at diagnosis from three Dutch university medical centers (University Medical Center Groningen, Radboud University Medical Center Nijmegen, and VU University Medical Center Amsterdam) by surgical resection. Immediately following surgical resection, tissue samples were snap frozen in liquid nitrogen and stored at -80°C until further processing. Tumor material was histologically evaluated by an experienced neuropathologist and examined for tumor content. Samples were excluded from analysis when tumor content was below 70%. Informed consent and local Medical Ethical Committee approval was granted for use of the patient material. The IARC TP53 database version R18 was consulted for the molecular interpretation of TP53 variants (www.p53.iarc.fr). Total DNA was isolated using the Qiagen Allprep DNA/RNA/Protein mini kit (Qiagen) following the manufacturer's protocol. DNA concentration was determined using the QuBit fluorometric quantitation assay (Thermo Fisher).  The CAP-compliant clinically validated TruSight Tumor 15 assay kit was performed as per supplier's instruction with 10 ng DNA input.
attributes.tag: Experimental Factor: clinical information
attributes.value: TP53 variant subgroup 3