ArticleBMC bioinformatics2015
Quantitative analysis of differences in copy numbers using read depth obtained from PCR-enriched samples and controls.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Article
- Deep genomic characterization highlights complexities and prognostic markers of pediatric acute myeloid leukemia.Communications biology · 2023Article
- Molecular and cytogenetic characterization of myelodysplastic syndromes in cell-free DNA.Blood advances · 2022Article
- Clinical and mutational profiles of adult medulloblastoma groups.Acta neuropathologica communications · 2020Article
- Investigating appropriate molecular and chemical methods for ingredient identity testing of plant-based protein powder dietary supplements.Scientific reports · 2019Article
- Article
- Article
- Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma.Cancer discovery · 2017Article
- Molecular characterization of circulating colorectal tumor cells defines genetic signatures for individualized cancer care.Oncotarget · 2017Article
- Clinical impact of targeted amplicon sequencing for meningioma as a practical clinical-sequencing system.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2016Article
Corrections and comments
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Authors and funding
3 authors.
Funding
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Abstract
backgroundNext-generation sequencing (NGS) is rapidly becoming common practice in clinical diagnostics and cancer research. In addition to the detection of single nucleotide variants (SNVs), information on copy number variants (CNVs) is of great interest. Several algorithms exist to detect CNVs by analyzing whole genome sequencing data or data from samples enriched by hybridization-capture. PCR-enriched amplicon-sequencing data have special characteristics that have been taken into account by only one publicly available algorithm so far.
resultsWe describe a new algorithm named quandico to detect copy number differences based on NGS data generated following PCR-enrichment. A weighted t-test statistic was applied to calculate probabilities (p-values) of copy number changes. We assessed the performance of the method using sequencing reads generated from reference DNA with known CNVs, and we were able to detect these variants with 98.6% sensitivity and 98.5% specificity which is significantly better than another recently described method for amplicon sequencing. The source code (R-package) of quandico is licensed under the GPLv3 and it is available at https://github.com/reineckef/quandico .
conclusionWe demonstrated that our new algorithm is suitable to call copy number changes using data from PCR-enriched samples with high sensitivity and specificity even for single copy differences.
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