Key Points• Complete genome sequence analysis of 40 DLBCL tumors and 13 cell lines reveals novel somatic point mutations, rearrangements, and fusions. • Recurrence of mutations in genes involved in B-cell homing were identified in germinal center B-cell DLBCLs.Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous cancer composed of at least 2 molecular subtypes that differ in gene expression and distribution of mutations. Recently, application of genome/exome sequencing and RNAseq to DLBCL has revealed numerous genes that are recurrent targets of somatic point mutation in this disease. Here we provide a whole-genome-sequencing-based perspective of DLBCL mutational complexity by characterizing 40 de novo DLBCL cases and 13 DLBCL cell lines and combining these data with DNA copy number analysis and RNA-seq from an extended cohort of 96 cases. Our analysis identified widespread genomic rearrangements including evidence for chromothripsis as well as the presence of known and novel fusion transcripts. We uncovered new gene targets of recurrent somatic point mutations and genes that are targeted by focal somatic deletions in this disease. We highlight the recurrence of germinal center B-cell-restricted mutations affecting genes that encode the S1P receptor and 2 small GTPases (GNA13 and GNAI2) that together converge on regulation of B-cell homing. We further analyzed our data to approximate the relative temporal order in which some recurrent mutations were acquired and demonstrate that ongoing acquisition of mutations and intratumoral clonal heterogeneity are common features of DLBCL. This study further improves our understanding of the processes and pathways involved in lymphomagenesis, and some of the pathways mutated here may indicate new avenues for therapeutic intervention. (Blood. 2013;122(7):1256-1265 Introduction Diffuse large B-cell lymphoma (DLBCL) is an aggressive nonHodgkin lymphoma (NHL) with at least 2 molecular subtypes that demonstrate distinct clinical outcomes and gene expression profiles. Because these cancers derive from mature B cells, the mutations that arise in DLBCLs can result from somatic hypermutation that targets a small number of genes, 1 as well as structural rearrangements that arise from double-strand breaks that can be initiated by the B-cell recombination apparatus. In recent years, multiple groups have used massively parallel sequencing (genome/ exome sequencing and RNA-seq) to ascertain the full set of genes targeted by somatic single-nucleotide variants (SNVs) in this disease.2-5 On the basis of these and earlier studies, 6 it is now known that the 2 molecular subtypes also harbor distinct repertoires of somatic copy number alterations (CNAs) and SNVs. In particular, mutations affecting genes involved in B-cell receptor signaling and nuclear factor kB are common in the activated B-cell variety, 7 whereas those affecting certain genes with roles in histone modification may be more common in the germinal center B-cell (GCB) subtype. 2,8,9 These studies have confirmed t...

Next-generation sequencing has allowed identification of millions of somatic mutations and epigenetic changes in cancer cells. A key challenge in interpreting cancer genomes and epigenomes is distinguishing which genetic and epigenetic changes are drivers of cancer development. Frequency-based and function-based approaches have been developed to identify candidate drivers; we discuss the advantages and drawbacks of these methods as well as their latest refinements. We focus particularly on identification of the types of drivers most likely to be missed, such as genes affected by copy number alterations, mutations in noncoding regions, dysregulation of microRNA, epigenetic changes, and mutations in chromatin modifiers.

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