Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours

Letter OPEN doi:10.1038/nature25795 Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours Xiaotu Ma1*, Yu Liu1*, Yanling Liu1, Ludmil B. Alexandrov2, Michael N. Edmonson1, Charles Gawad1, Xin Zhou1, Yongjin Li1, Michael C. Rusch1, John Easton1, Robert Huether3†, Veronica Gonzalez-Pena4, Mark R. Wilkinson1, Leandro C. Hermida5, Sean Davis6, Edgar Sioson1, Stanley Pounds7, Xueyuan Cao7, Rhonda E. Ries8, Zhaoming Wang1, Xiang Chen1, Li Dong1, Sharon J. Diskin9, Malcolm A. Smith10, Jaime M. Guidry Auvil5, Paul S. Meltzer6, Ching C. Lau11,12, Elizabeth J. Perlman13, John M. Maris9, Soheil Meshinchi8, Stephen P. Hunger9, Daniela S. Gerhard5 & Jinghui Zhang1 Analysis of molecular aberrations across multiple cancer types, known as pan-cancer analysis, identifies commonalities and differences in key biological processes that are dysregulated in cancer cells from diverse lineages. Pan-cancer analyses have been performed for adult1–4 but not paediatric cancers, which commonly occur in developing mesodermic rather than adult epithelial tissues5. Here we present a pan-cancer study of somatic alterations, including single nucleotide variants, small insertions or deletions, structural variations, copy number alterations, gene fusions and internal tandem duplications in 1,699 paediatric leukaemias and solid tumours across six histotypes, with whole-genome, whole-exome and transcriptome sequencing data processed under a uniform analytical framework. We report 142 driver genes in paediatric cancers, of which only 45% match those found in adult pan-cancer studies; copy number alterations and structural variants constituted the majority (62%) of events. Eleven genome-wide mutational signatures were identified, including one attributed to ultravioletlight exposure in eight aneuploid leukaemias. Transcription of the mutant allele was detectable for 34% of protein-coding mutations, and 20% exhibited allele-specific expression. These data provide a comprehensive genomic architecture for paediatric cancers and emphasize the need for paediatric cancer-specific development of precision therapies. Paired tumour and normal samples from 1,699 patients with paediatric cancers enrolled in Children’s Oncology Group clinical trials were analysed, including 689 B-lineage acute lymphoblastic l eukaemias (B-ALL), 267 T-lineage ALLs (T-ALL), 210 acute myeloid leukaemias (AML), 316 neuroblastomas (NBL), 128 Wilms tumours and 89 osteosarcomas (Extended Data Fig. 1a–c). All tumour s pecimens were obtained at initial diagnosis, and 98.5% of patients were 20 years of age or younger (see Methods, Extended Data Fig. 1d). The median somatic mutation rate ranged from 0.17 per million bases (Mb) in AML and Wilms tumours to 0.79 in osteosarcomas (Fig. 1a, b), lower than the 1–10 per Mb found in common adult cancers6. Genome-wide analysis (see Methods) identified 11 mutational signatures (T-1 through T-11; Fig. 1c–e and Supplementary Table 1a–c). Signatures T-1 through T-9 corresponded to known COSMIC signatures7, whereas T-10 and T-11 were novel but enriched in mutations with a low (<0.3) mutant allele fraction (MAF). Signatures T-1 and T-4 (clock-like endogenous mutational processes) were present in all samples and contributed to large proportions of all mutations in T-ALL (97%), AML (63%), B-ALL (36%), and Wilms tumours (28%). T-2 and T-7 (APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like)) were highly enriched in B-ALLs with ETV6-RUNX1 fusions (15-fold and 9-fold enrichment for T-2 and T-7, respectively; Supplementary Table 1e). T-3 (homologous recombination deficiency) was present in many childhood cancers, including osteosarcomas (18 of 19), NBLs (59 of 137), Wilms tumours (28 of 81), and B-ALL (47 of 218). T-8 (8-oxoguanine DNA damage) was present in a small proportion (4.5–12%) of AML, B-ALL, osteosarcoma, and Wilms tumour samples. T-8 was also present in many (36%) NBL samples and was associated with age at diagnosis (Supplementary Table 1d). T-9 (DNA repair deficiency) was present in two B-ALLs, including one (sample PARJSR) with a somatic MSH6 frameshift mutation. T-2, T-3, T-5, T-7, T-8, and T-9 were enriched among the 39 samples with elevated mutation rates in each histotype (Fig. 1d). The T-5 ultraviolet-light (UV)-exposure signature was unexpectedly present in eight B-ALL samples (Extended Data Fig. 2a–c). Although its mutation rate in B-ALL, ranging from 0.06 to 0.72 per Mb, was 100fold lower than the average rate in adult (15.8 per Mb)8 and paediatric (14.4 per Mb)9 skin cancer, T-5 exhibited other features associated with UV-related DNA damage. Specifically, CC>TT dinucleotide mutations were enriched 110-fold in these eight B-ALL samples when compared with other samples (P =  1.07 ×  10−7), which is consistent with pyrimidine dimer formation. Moreover, transcriptional strand bias in T-5 indicated that photodimer formation contributed to cytosine damage. The v alidity of T-5 was further confirmed by analysis of the mutation clonality, cross-platform concordance, genomic distribution and mutation spectrum of each sample (see Methods, Extended Data Fig. 2d–i), indicating that UV exposure or other mutational processes10,11 may contribute to paediatric leukemogenesis. Notably, all T-5 B-ALLs had aneuploid genomes (P =  3 ×  10−5; two-sided binomial test; cohort frequency 24%) without any oncogenic fusions. By analysing the enrichment12,13 of somatic alterations within each histotype or the pan-cancer cohort (see Methods), we identified 142 significantly mutated driver genes (Fig. 2a, Supplementary Table 2, Extended Data Fig. 3a). Somatic alterations in CDKN2A, which were predominantly deletions, occurred at the highest frequency, affecting 1 Computational Biology, St Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA. 2Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, USA. 3Independent Researcher, Chicago, Illinois 60654, USA. 4Oncology, St Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA. 5Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland 20892, USA. 6Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA. 7Department of Biostatistics, St Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA. 8Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. 9Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. 10Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland 20892, USA. 11Division of Hematology-Oncology, Connecticut Children’s Medical Center, Hartford, Connecticut 06106, USA. 12The Ja (...truncated)