Abstract 4868: Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations within a wide spectrum of genetic heterogeneity
Authors: Pugh Trevor J. , Cho Yoon-Jae , Archer Tenley , Weeraratne Dilhan , Jones David T. W. , Jaeger Natalie , Auclair Daniel , Cibulskis Kristian , Lawrence Michael S. , Ramos Alex H. , Shefler Erica , Sivachenko Andrey , Tamayo Pablo , Mesirov Jill P. , Gabriel Stacey B. , Getz Gad , Pfister Stefan M. , Lichter Peter , Meyerson Matthew , Pomeroy Scott L. 
Published: August 2012

Abstract
Medulloblastoma is a pediatric brain tumor with poor overall survival and adverse long-term effects from current surgical and radiation treatments. Our group has recently used expression and copy number analysis to define six medulloblastoma subtypes, c1-c6. To assess whether these subgroups contain somatic mutations that encode potential therapeutic or diagnostic targets, we performed whole exome hybrid capture and Illumina sequencing of 94 tumor/normal pairs. For each sample, we sequenced 193,094 exons from 18,863 genes to 126X average coverage. Tumors contained a median 5 silent and 11 non-silent candidate mutations, corresponding to 0.34 non-silent mutations per megabase, a low mutation rate consistent with other pediatric tumors. Overall, 16 genes were mutated at statistically significant frequency and several clustered within subtypes. Eleven tumors harbored mutually-exclusive, likely loss-of-function missense mutations within the helicase domains of candidate oncogene DDX3X (n=7) or SMARCA4 (n=4). These mutations were found in five of seven c6 tumors (3 DDX3X, 2 SMARCA4) of which four had known beta-catenin mutations. Two SMARCA4 mutations were identical and two affected adjacent residues. None of the DDX3X mutations were recurrent, however several are proximal when mapped to a tertiary protein model. To confirm these variants, we are performing deep sequencing of these genes using multiplex PCR (Fluidigm) followed by single-molecule real-time sequencing (PacBio). We are also characterizing the functional effect of DDX3X and SMARCA4 mutations alone and in combination with beta-catenin mutations in medulloblastoma cell lines. Other genes with subtype-associated, loss-of-function mutations include DULLARD in 2 of 9 c1 tumors, PTCH1 in 5 of 16 c3 tumors, and MLL2 in 2 of 3 tumors without any copy number alterations as well as a c1 tumor and two c3 tumors. Several genes are mutated across subtypes, notably tumor suppressors TP53 (n=3), GPS2 (n=3) and SOCS4 (n=2). 19 chromatin remodeling genes including cancer genes BRCA2, KDM5/6A, CREBBP, EP300, BRD4, and MLL3/4 are mutated across 17 tumors from all subtypes. While we have uncovered several subtype-associated mutations, 88% of mutated genes are only altered in a single tumor. This analysis demonstrates the diversity of somatic mutation in medulloblastoma, even within copy number subtypes. To better understand infrequently mutated genes, we will attempt to assemble them into commonly altered gene sets and pathways. We also intend to investigate potentially pathogenic germline variations in each case.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4868. doi:1538-7445.AM2012-4868