BACKGROUND: Lower grade gliomas (LGG) are infiltrative brain tumors that include astrocytomas, oligodendrogliomas and oligoastrocytomas, grades II and III. LGGs almost always progress, typically to glioblastoma (GBM, grade IV), and are uniformly fatal. The Cancer Genome Atlas (TCGA) is conducting a comprehensive molecular analysis of LGG, incorporating genetic and genomic alterations, DNA methylation profiles, and RNA and proteomic signatures. The rich, integrated clinical data of TCGA provides an outstanding platform to uncover biomarkers of therapy response and outcome. METHODS: We analyzed 289 lower grade gliomas for exome sequence to uncover somatic mutations; DNA copy number alterations; RNA sequencing for expression and gene fusion; DNA methlyation; microRNA expression; and protein level and phosphorylation. Supervised and unsupervised clustering was performed to segregate LGGs into robust molecular categories. RESULTS: Among 289 LGGs, exome sequencing identified 19 significantly mutated genes, including IDH1, TP53, ATRX, CIC, FUBP1, NOTCH1, PIK3CA, NF1, PIK3R1, ARID1A, PTEN, SMARCA4 and EGFR. Frequent arm-level deletions were 1p, 19q, 13q, 9p, 10q, 10p, 4q and 4p; arm-level gains included 7q, 7p, 19p and 11q. There were 15 significant genomic amplifications, among which were 7p11.2 (EGFR), 12q14.1 (CDK4), 1q32.1 (MDM4), 8q24.21 (MYC), 12p13.32 (CCND2) and 4q12 (PDGFR). Among 28 deletions were 9p21.3 (CDKN2A, CDKN2B), 19q13.42 (TFPT, ZNF331), 2q37.3, 10q26.2 (FGFR2, DUX4) and 14q24.3 (TSHR, GPHN).Global analysis of DNA methylation identified 5 stable clusters, with one showing substantial hypomethylation. Gene expression profiling identified 4 stable clusters. On integrative analysis, IDH1/2 wt LGGs had features of “pre-GBM”: they formed distinct hypomethylation and gene expression clusters; had molecular alterations typical of GBM, such as EGFR amplifications, PTEN mutations, CDKN2A loss and RTK gene fusions; were mostly grade III astrocytomas; and had short survivals. IDH1/2 mutant LGGs were hypermethylated. One subgroup was enriched for 1p/19q co-deletion, CIC and FUBP mutations, and oligodendrogliomas. Another subset was enriched for TP53 and ATRX mutations and astrocytomas. These groups clustered separately on gene expression analysis. A fourth gene expression cluster had elements of these two IDH1/2 mutant subgroups and the longest survival. A cluster-of-cluster analysis of mRNA, copy number, miRNA and methylation analyses reinforced the clear separation of three molecular classes of LGG based on the status of IDH1/2 and 1p/19q. CONCLUSIONS: These data illustrate a potential stratification of LGGs that emphasizes molecular characteristics. IDH wt LGG have molecular alterations and clinical behavior similar to GBMs, whereas IDH mutant LGGs segregate based on 1p/19q status. SECONDARY CATEGORY: Tumor Biology.