ArticlePloS one2018
AMYCNE: Confident copy number assessment using whole genome sequencing data.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- High-coverage ancient genomes reveal divergent population histories and prehistoric starch-related genetic variation in Japan.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Genetic variation and molecular profiling of congenital malformations of the female genital tract based on whole-genome sequencing.World journal of pediatrics : WJP · 2024Article
- Case report: Second report of neuromuscular syndrome caused by biallelic variants inFrontiers in genetics · 2024Article
- GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads.Scientific reports · 2023Article
- JAX-CNV: A Whole-genome Sequencing-based Algorithm for Copy Number Detection at Clinical Grade Level.Genomics, proteomics & bioinformatics · 2022Article
- Impact of salivary and pancreatic amylase gene copy numbers on diabetes, obesity, and functional profiles of microbiome in Northern Japanese population.Scientific reports · 2022Article
- Prenatal diagnosis of 21 fetuses with balanced chromosomal abnormalities (BCAs) using whole-genome sequencing.Frontiers in genetics · 2022Article
- Ethnic-specific association of amylase gene copy number with adiposity traits in a large Middle Eastern biobank.NPJ genomic medicine · 2021Article
- MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data.BMC medical genomics · 2020Article
- Hierarchical discovery of large-scale and focal copy number alterations in low-coverage cancer genomes.BMC bioinformatics · 2020Article
- From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability.Genome medicine · 2019Article
- Copy number determination of the gene for the human pancreatic polypeptide receptor NPY4R using read depth analysis and droplet digital PCR.BMC biotechnology · 2019Article
- Complete sequencing of the SMN2 gene in SMA patients detects SMN gene deletion junctions and variants in SMN2 that modify the SMA phenotype.Human genetics · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
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Abstract
Copy number variations (CNVs) within the human genome have been linked to a diversity of inherited diseases and phenotypic traits. The currently used methodology to measure copy numbers has limited resolution and/or precision, especially for regions with more than 4 copies. Whole genome sequencing (WGS) offers an alternative data source to allow for the detection and characterization of the copy number across different genomic regions in a single experiment. A plethora of tools have been developed to utilize WGS data for CNV detection. None of these tools are designed specifically to accurately estimate copy numbers of complex regions in a small cohort or clinical setting. Herein, we present AMYCNE (automatic modeling functionality for copy number estimation), a CNV analysis tool using WGS data. AMYCNE is multifunctional and performs copy number estimation of complex regions, annotation of VCF files, and CNV detection on individual samples. The performance of AMYCNE was evaluated using AMY1A ddPCR measurements from 86 unrelated individuals. In addition, we validated the accuracy of AMYCNE copy number predictions on two additional genes (FCGR3A and FCGR3B) using datasets available through the 1000 genomes consortium. Finally, we simulated levels of mosaic loss and gain of chromosome X and used this dataset for benchmarking AMYCNE. The results show a high concordance between AMYCNE and ddPCR, validating the use of AMYCNE to measure tandem AMY1 repeats with high accuracy. This opens up new possibilities for the use of WGS for accurate copy number determination of other complex regions in the genome in small cohorts or single individuals.
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