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Updated: Jun 1, 2026

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
CREST maps somatic structural variation in cancer genomes with base-pair resolution
Jianmin Wang1, Charles G Mullighan, John Easton
1Department of Information Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
We created a new algorithm called CREST to precisely map genetic structural variations using sequencing data. This tool accurately identified 160 new variations in leukemia and melanoma samples.
Area of Science:
- Genomics
- Bioinformatics
- Cancer Research
Background:
- Structural variations (SVs) are crucial in cancer development.
- Accurate detection of SVs at nucleotide resolution is challenging.
Purpose of the Study:
- To introduce CREST, a novel algorithm for nucleotide-level mapping of structural variations.
- To assess CREST's performance in identifying somatic SVs in cancer genomes.
Main Methods:
- Developed the 'clipping reveals structure' (CREST) algorithm.
- Utilized next-generation sequencing reads with partial alignments to a reference genome.
- Applied CREST to whole-genome sequencing data from T-ALL and melanoma cell lines.
Main Results:
- Identified 160 somatic structural variations.
- Achieved experimental validation exceeding 80% accuracy.
- Demonstrated high predictive accuracy of the CREST algorithm.
Conclusions:
- CREST enables direct mapping of structural variations at nucleotide resolution.
- The algorithm shows high accuracy and potential for cancer genomics research.
- CREST is a valuable tool for identifying genetic alterations in diseases.
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