ArticleBioinformatics (Oxford, England)2010
ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
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Who cites it
11 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Progenetix oncogenomic resource in 2021.Database : the journal of biological databases and curation · 2021Pooled it
- Homologous recombination deficiency (HRD) testing landscape: clinical applications and technical validation for routine diagnostics.Biomarker research · 2025Review
- Genomic and molecular landscape of homologous recombination deficiency across multiple cancer types.Scientific reports · 2023Article
- Combined clinical and genomic signatures for the prognosis of early stage non-small cell lung cancer based on gene copy number alterations.BMC genomics · 2015Article
- TAFFYS: An Integrated Tool for Comprehensive Analysis of Genomic Aberrations in Tumor Samples.PloS one · 2015Article
- Comprehensive study of tumour single nucleotide polymorphism array data reveals significant driver aberrations and disrupted signalling pathways in human hepatocellular cancer.IET systems biology · 2014Article
- Current analysis platforms and methods for detecting copy number variation.Physiological genomics · 2013Review
- Getting DNA copy numbers without control samples.Algorithms for molecular biology : AMB · 2012Article
- CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation.Bioinformatics (Oxford, England) · 2012Article
- Inference of chromosome-specific copy numbers using population haplotypes.BMC bioinformatics · 2011Article
- Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer.Breast cancer research : BCR · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
motivationCurrent algorithms for estimating DNA copy numbers (CNs) borrow concepts from gene expression analysis methods. However, single nucleotide polymorphism (SNP) arrays have special characteristics that, if taken into account, can improve the overall performance. For example, cross hybridization between alleles occurs in SNP probe pairs. In addition, most of the current CN methods are focused on total CNs, while it has been shown that allele-specific CNs are of paramount importance for some studies. Therefore, we have developed a summarization method that estimates high-quality allele-specific CNs.
resultsThe proposed method estimates the allele-specific DNA CNs for all Affymetrix SNP arrays dealing directly with the cross hybridization between probes within SNP probesets. This algorithm outperforms (or at least it performs as well as) other state-of-the-art algorithms for computing DNA CNs. It better discerns an aberration from a normal state and it also gives more precise allele-specific CNs. AVAILABILITY: The method is available in the open-source R package ACNE, which also includes an add on to the aroma.affymetrix framework (http://www.aroma-project.org/).
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