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

By Jianmin Wang, C. Mullighan, J. Easton, S. Roberts, Jing Ma, M. Rusch, Ken Chen, C. Harris, Li Ding, S. Heatley and 11 more. Nature Methods, 2011

505 citations recorded by the source corpus.

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.

Subfields: Cancer Research, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/72d6bc79070e0f0582e65db0167e27c0c2211c61

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Citations in the corpus

Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia (2012, methodology): “We used multiple complementary analysis pipelines, including deFuse (McPherson et al., 2011), Mosaik (Marth, 2010), CREST (Wang et al., 2011), CONSERTING (Zhang et al., 2012), and Trans-ABySS (Robertson et al., 2010) to identify rearrangements, structural variations, and sequence mutations.”
Recurrent Somatic Structural Variations Contribute to Tumorigenesis in Pediatric Osteosarcoma (2014, unknown): “Structural variations including the 5 deletions in ATRX were detected using the CREST algorithm (Wang et al., 2011) and CONSERTING algorithm.”
Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma (2017, methodology): “Detection and annotation of structural variations BWA-MEM alignments from each tumor-normal pair were analyzed by CREST (Clipping REveals STructure) (60) and PTRfinder (61).”
LUMPY: a probabilistic framework for structural variant discovery (2012, methodology): “In contrast, although other tools such as GASVPro [4], DELLY [3], CNVer [7], CREST [6] and Genome STRiP [5] also exploit multiple SV detection signals, to our knowledge they first use one signal (that is, read-pair) to drive discovery and then refine and/or genotype candidates with a second signal (”
GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly (2017, unknown): “Assembly of reads obtained from clusters of SC reads (e.g., CREST [Wang et al. 2011]) or OEA read pairs (e.g., NovelSeq [Hajirasouliha et al. 2010]) has been used to form break-end contigs, which extend out and span the breakpoint from each side.”
DELLY: structural variant discovery by integrated paired-end and split-read analysis (2012, methodology): “Availability: DELLY is available at www.korbel.embl.de/software.html Contact: tobias.rausch@embl.de”