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

Xiaotu Ma, Yu Liu, Yanling Liu, Ludmil B. Alexandrov, Michael N. Edmonson, Charles Gawad, Xin Zhou, Yongjin Li, Michael C. Rusch, Easton John, Robert Huether, Veronica Gonzalez-Pena, Mark R. Wilkinson, Leandro C. Hermida, Sean Davis, Edgar Sioson, Stanley Pounds, Xueyuan Cao, Rhonda E. Ries, Zhaoming Wang & 13 others Xiang Chen, Li Dong, Sharon J. Diskin, Malcolm A. Smith, Jaime M.Guidry Auvi, Paul S. Meltzer, Ching C. Lau, Elizabeth J. Perlman, John M. Maris, Soheil Meshinchi, Stephen P. Hunger, Daniela S. Gerhard, Jinghui Zhang

Research output: Contribution to journalArticle

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Abstract

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 adult but not paediatric cancers, which commonly occur in developing mesodermic rather than adult epithelial tissues. 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 ultraviolet-light 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.

Original languageEnglish (US)
Pages (from-to)371-376
Number of pages6
JournalNature
Volume555
Issue number7696
DOIs
StatePublished - Mar 15 2018

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Gene Expression Profiling
Leukemia
Genome
Pediatrics
Neoplasms
Alleles
Exome
Biological Phenomena
Gene Fusion
Aneuploidy
Cell Lineage
Ultraviolet Rays
Transcriptome
Epithelium
Nucleotides
Mutation

All Science Journal Classification (ASJC) codes

  • General

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Ma, X., Liu, Y., Liu, Y., Alexandrov, L. B., Edmonson, M. N., Gawad, C., ... Zhang, J. (2018). Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours. Nature, 555(7696), 371-376. https://doi.org/10.1038/nature25795

Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours. / Ma, Xiaotu; Liu, Yu; Liu, Yanling; Alexandrov, Ludmil B.; Edmonson, Michael N.; Gawad, Charles; Zhou, Xin; Li, Yongjin; Rusch, Michael C.; John, Easton; Huether, Robert; Gonzalez-Pena, Veronica; Wilkinson, Mark R.; Hermida, Leandro C.; Davis, Sean; Sioson, Edgar; Pounds, Stanley; Cao, Xueyuan; Ries, Rhonda E.; Wang, Zhaoming; Chen, Xiang; Dong, Li; Diskin, Sharon J.; Smith, Malcolm A.; Auvi, Jaime M.Guidry; Meltzer, Paul S.; Lau, Ching C.; Perlman, Elizabeth J.; Maris, John M.; Meshinchi, Soheil; Hunger, Stephen P.; Gerhard, Daniela S.; Zhang, Jinghui.

In: Nature, Vol. 555, No. 7696, 15.03.2018, p. 371-376.

Research output: Contribution to journalArticle

Ma, X, Liu, Y, Liu, Y, Alexandrov, LB, Edmonson, MN, Gawad, C, Zhou, X, Li, Y, Rusch, MC, John, E, Huether, R, Gonzalez-Pena, V, Wilkinson, MR, Hermida, LC, Davis, S, Sioson, E, Pounds, S, Cao, X, Ries, RE, Wang, Z, Chen, X, Dong, L, Diskin, SJ, Smith, MA, Auvi, JMG, Meltzer, PS, Lau, CC, Perlman, EJ, Maris, JM, Meshinchi, S, Hunger, SP, Gerhard, DS & Zhang, J 2018, 'Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours', Nature, vol. 555, no. 7696, pp. 371-376. https://doi.org/10.1038/nature25795
Ma X, Liu Y, Liu Y, Alexandrov LB, Edmonson MN, Gawad C et al. Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours. Nature. 2018 Mar 15;555(7696):371-376. https://doi.org/10.1038/nature25795
Ma, Xiaotu ; Liu, Yu ; Liu, Yanling ; Alexandrov, Ludmil B. ; Edmonson, Michael N. ; Gawad, Charles ; Zhou, Xin ; Li, Yongjin ; Rusch, Michael C. ; John, Easton ; Huether, Robert ; Gonzalez-Pena, Veronica ; Wilkinson, Mark R. ; Hermida, Leandro C. ; Davis, Sean ; Sioson, Edgar ; Pounds, Stanley ; Cao, Xueyuan ; Ries, Rhonda E. ; Wang, Zhaoming ; Chen, Xiang ; Dong, Li ; Diskin, Sharon J. ; Smith, Malcolm A. ; Auvi, Jaime M.Guidry ; Meltzer, Paul S. ; Lau, Ching C. ; Perlman, Elizabeth J. ; Maris, John M. ; Meshinchi, Soheil ; Hunger, Stephen P. ; Gerhard, Daniela S. ; Zhang, Jinghui. / Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours. In: Nature. 2018 ; Vol. 555, No. 7696. pp. 371-376.
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AU - Zhou, Xin

AU - Li, Yongjin

AU - Rusch, Michael C.

AU - John, Easton

AU - Huether, Robert

AU - Gonzalez-Pena, Veronica

AU - Wilkinson, Mark R.

AU - Hermida, Leandro C.

AU - Davis, Sean

AU - Sioson, Edgar

AU - Pounds, Stanley

AU - Cao, Xueyuan

AU - Ries, Rhonda E.

AU - Wang, Zhaoming

AU - Chen, Xiang

AU - Dong, Li

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AU - Smith, Malcolm A.

AU - Auvi, Jaime M.Guidry

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AU - Maris, John M.

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AU - Zhang, Jinghui

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N2 - 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 adult but not paediatric cancers, which commonly occur in developing mesodermic rather than adult epithelial tissues. 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 ultraviolet-light 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.

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