Figure 2. ATRTs Comprise Three Epigenetic Subgroups with Distinct Clinical Profiles and Genotypes.
(A and B) ATRTs were classified by unsupervised consensus hierarchical (HCL) and non-negative matrix factorization (NMF) cluster analyses of 450k methylation array (A) or Illumina HT12 gene expression array data (B). Adjusted Rand Index indicates concordance in methylation and gene expression clusters. Most stable tumor grouping indicated by highest cophenetic coefficient (Coph. Coef; k = 3) with 250 genes and 10,000 methylation probes are shown.
(C) Clinical, molecular, and genotypic features of 177 primary ATRTs. Tumor subgroups determined by methylation or gene expression are indicated by red (group 1), blue (group 2A), green (group 2B) or gray (group not available) bars; clinical (tumor location, patient age, metastatic status), global patterns of CNAs (chromosomal or subchromosomal/focal), and type of SMARCB1 alterations in individual tumors are indicated. Clinical or molecular features with significant subgroup correlation are indicated in red. SMARCB1 alterations were classified as focal (point mutations, small indels, intergenic deletions) or broad (intragenic events, large deletions).
(D) Tumor location, median age, and age distribution in ATRT subgroups. Boxplot middle represents median, box boundaries represent first and third quartiles, and whiskers represent 10th and 90th percentiles.
See also Figures S2, S3, and Table S6.