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CREST maps somatic structural variation in cancer genomes with base-pair resolution |
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| Authors: | Wang Jianmin Mullighan Charles G Easton John Roberts Stefan Heatley Sue L 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 |
| Institution: | Department of Information Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. |
| 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. |
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