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

Jianmin Wang; Charles G. Mullighan; John Easton; Stefan Roberts; Sue L. 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; Jinghui Zhang

doi:10.1038/nmeth.1628

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

Jianmin Wang, Charles G. Mullighan, John Easton, Stefan Roberts, Sue L. 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. DowningJinghui Zhang

Research output: Contribution to journal › Article › peer-review

393 Scopus citations

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.

Original language	English (US)
Pages (from-to)	652-654
Number of pages	3
Journal	Nature Methods
Volume	8
Issue number	8
DOIs	https://doi.org/10.1038/nmeth.1628
State	Published - Aug 2011
Externally published	Yes

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/nmeth.1628

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Wang, J., Mullighan, C. G., Easton, J., Roberts, S., Heatley, S. L., Ma, J., Rusch, M. C., Chen, K., Harris, C. C., Ding, L., Holmfeldt, L., Payne-Turner, D., Fan, X., Wei, L., Zhao, D., Obenauer, J. C., Naeve, C., Mardis, E. R., Wilson, R. K., ... 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, J, Mullighan, CG, Easton, J, Roberts, S, Heatley, SL, 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

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title = "CREST maps somatic structural variation in cancer genomes with base-pair resolution",

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.",

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

note = "Funding Information: This study was supported by St. Jude Children{\textquoteright}s Research Hospital–Washington University Pediatric Cancer Genome Project, Cancer Center support grant P30 CA021765 from the US National Cancer Institute and the American Lebanese Syrian Associated Charities of St. Jude Children{\textquoteright}s Research Hospital. We thank K. Ye for stimulating discussion on the analysis of the COLO-829 cell line. C.G.M. is supported as a Pew Scholar in the Biomedical Sciences. S.L.H. was supported by a Haematology Society of Australasia Travelling Fellowship.",

year = "2011",

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doi = "10.1038/nmeth.1628",

language = "English (US)",

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T1 - CREST maps somatic structural variation in cancer genomes with base-pair resolution

AU - Wang, Jianmin

AU - Mullighan, Charles G.

AU - Easton, John

AU - Roberts, Stefan

AU - Heatley, Sue L.

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

N1 - Funding Information: This study was supported by St. Jude Children’s Research Hospital–Washington University Pediatric Cancer Genome Project, Cancer Center support grant P30 CA021765 from the US National Cancer Institute and the American Lebanese Syrian Associated Charities of St. Jude Children’s Research Hospital. We thank K. Ye for stimulating discussion on the analysis of the COLO-829 cell line. C.G.M. is supported as a Pew Scholar in the Biomedical Sciences. S.L.H. was supported by a Haematology Society of Australasia Travelling Fellowship.

PY - 2011/8

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

Abstract

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