CREST maps somatic structural variation in cancer genomes with base-pair resolution

Jianmin Wang, Charles G. Mullighan, John Easton, Stefan Roberts, Susan Heatley, Jing Ma, Michael C. Rusch, Ken Chen, Christopher C. Harris, Li Ding, Linda Holmfeldt, Debbie Payne-Turner, Xian Fan, Lei Wei, David Zhao, John C. Obenauer, Clayton Naeve, Elaine R. Mardis, Richard K. Wilson, James R. Downing & 1 others Jinghui Zhang

Research output: Contribution to journalArticle

294 Citations (Scopus)

Abstract

We developed 'clipping reveals structure' (CREST), an algorithm that uses next-generation sequencing reads with partial alignments to a reference genome to directly map structural variations at the nucleotide level of resolution. Application of CREST to whole-genome sequencing data from five pediatric T-lineage acute lymphoblastic leukemias (T-ALLs) and a human melanoma cell line, COLO-829, identified 160 somatic structural variations. Experimental validation exceeded 80%, demonstrating that CREST had a high predictive accuracy.

LanguageEnglish
Pages652-654
Number of pages3
JournalNature Methods
Volume8
Issue number8
DOIs
Publication statusPublished - 1 Aug 2011

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Wang, J., Mullighan, C. G., Easton, J., Roberts, S., Heatley, S., Ma, J., ... Zhang, J. (2011). CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nature Methods, 8(8), 652-654. https://doi.org/10.1038/nmeth.1628
Wang, Jianmin ; Mullighan, Charles G. ; Easton, John ; Roberts, Stefan ; Heatley, Susan ; Ma, Jing ; Rusch, Michael C. ; Chen, Ken ; Harris, Christopher C. ; Ding, Li ; Holmfeldt, Linda ; Payne-Turner, Debbie ; Fan, Xian ; Wei, Lei ; Zhao, David ; Obenauer, John C. ; Naeve, Clayton ; Mardis, Elaine R. ; Wilson, Richard K. ; Downing, James R. ; Zhang, Jinghui. / CREST maps somatic structural variation in cancer genomes with base-pair resolution. In: Nature Methods. 2011 ; Vol. 8, No. 8. pp. 652-654.
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Wang, J, Mullighan, CG, Easton, J, Roberts, S, Heatley, S, Ma, J, Rusch, MC, Chen, K, Harris, CC, Ding, L, Holmfeldt, L, Payne-Turner, D, Fan, X, Wei, L, Zhao, D, Obenauer, JC, Naeve, C, Mardis, ER, Wilson, RK, Downing, JR & Zhang, J 2011, 'CREST maps somatic structural variation in cancer genomes with base-pair resolution', Nature Methods, vol. 8, no. 8, pp. 652-654. https://doi.org/10.1038/nmeth.1628

CREST maps somatic structural variation in cancer genomes with base-pair resolution. / Wang, Jianmin; Mullighan, Charles G.; Easton, John; Roberts, Stefan; Heatley, Susan; Ma, Jing; Rusch, Michael C.; Chen, Ken; Harris, Christopher C.; Ding, Li; Holmfeldt, Linda; Payne-Turner, Debbie; Fan, Xian; Wei, Lei; Zhao, David; Obenauer, John C.; Naeve, Clayton; Mardis, Elaine R.; Wilson, Richard K.; Downing, James R.; Zhang, Jinghui.

In: Nature Methods, Vol. 8, No. 8, 01.08.2011, p. 652-654.

Research output: Contribution to journalArticle

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AU - Mullighan, Charles G.

AU - Easton, John

AU - Roberts, Stefan

AU - Heatley, Susan

AU - Ma, Jing

AU - Rusch, Michael C.

AU - Chen, Ken

AU - Harris, Christopher C.

AU - Ding, Li

AU - Holmfeldt, Linda

AU - Payne-Turner, Debbie

AU - Fan, Xian

AU - Wei, Lei

AU - Zhao, David

AU - Obenauer, John C.

AU - Naeve, Clayton

AU - Mardis, Elaine R.

AU - Wilson, Richard K.

AU - Downing, James R.

AU - Zhang, Jinghui

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