Common Genomic Alterations
Genomic and epigenetic alterations with relevant molecular profiling have been cataloged for patient-derived xenograft lines in the Mayo Clinic Brain Tumor Patient-Derived Xenograft National Resource.
The PDX National Resource performed cataloging by lesion-specific assays (Sanger sequencing for TERT and IDH1/2 mutations; qMS-PCR for MGMT methylation), by analysis of whole-exome sequencing (mutations and copy number change), or by methylomics (copy number change, G-CIMP).
Variants were annotated using such catalogs as dbSNP, 1000 Genomes and COSMIC. With the exception of TERT and IDH1/2, the mutations are all called from whole-exome sequencing data after appropriate quality filtering, such as strand bias, and base and mapping quality.
Specifically, raw somatic variants were quality filtered based on the allelic and overall depth of coverage (6), fraction of alternative allele (0.1), base quality (20), average mapping quality (20), proximity to homopolymer runs (8), number of zero-mapping-quality reads (10), variant quality (20), strand bias (60), and somatic score (40) if available.