ArticlePloS one2013
CEQer: a graphical tool for copy number and allelic imbalance detection from whole-exome sequencing data.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed.
- Recurrent somatic mutations of FAT family cadherins induce an aggressive phenotype and poor prognosis in anaplastic large cell lymphoma.British journal of cancer · 2024Article
- Late relapse of chronic myeloid leukemia after allogeneic bone marrow transplantation points to KANSARL (KANSL1::ARL17A) alteration: a case report with insights on the molecular landscape.Annals of hematology · 2024Article
- Idiopathic erythrocytosis: a germline disease?Clinical and experimental medicine · 2024Article
- Integrated Genomic, Functional, and Prognostic Characterization of Atypical Chronic Myeloid Leukemia.HemaSphere · 2020Article
- ETNK1 mutations induce a mutator phenotype that can be reverted with phosphoethanolamine.Nature communications · 2020Article
- Article
- OncoScore: a novel, Internet-based tool to assess the oncogenic potential of genes.Scientific reports · 2017Article
- Preimplantation genetic diagnosis/screening by comprehensive molecular testing.Reproductive medicine and biology · 2016Review
- Intragenic duplication in the PKHD1 gene in autosomal recessive polycystic kidney disease.BMC medical genetics · 2015Article
- Exome sequencing identifies frequent mutation of MLL2 in non-small cell lung carcinoma from Chinese patients.Scientific reports · 2014Article
- YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens.Genome medicine · 2014Article
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Authors and funding
11 authors.
Funding
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Abstract
Copy number alterations (CNA) are common events occurring in leukaemias and solid tumors. Comparative Genome Hybridization (CGH) is actually the gold standard technique to analyze CNAs; however, CGH analysis requires dedicated instruments and is able to perform only low resolution Loss of Heterozygosity (LOH) analyses. Here we present CEQer (Comparative Exome Quantification analyzer), a new graphical, event-driven tool for CNA/allelic-imbalance (AI) coupled analysis of exome sequencing data. By using case-control matched exome data, CEQer performs a comparative digital exonic quantification to generate CNA data and couples this information with exome-wide LOH and allelic imbalance detection. This data is used to build mixed statistical/heuristic models allowing the identification of CNA/AI events. To test our tool, we initially used in silico generated data, then we performed whole-exome sequencing from 20 leukemic specimens and corresponding matched controls and we analyzed the results using CEQer. Taken globally, these analyses showed that the combined use of comparative digital exon quantification and LOH/AI allows generating very accurate CNA data. Therefore, we propose CEQer as an efficient, robust and user-friendly graphical tool for the identification of CNA/AI in the context of whole-exome sequencing data.
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