ArticleBMC bioinformatics2007
A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- An efficient method to handle the 'large p, small n' problem for genomewide association studies using Haseman-Elston regression.Journal of genetics · 2016Article
- Copynumber: Efficient algorithms for single- and multi-track copy number segmentation.BMC genomics · 2012Article
- DNA polymerase β variant Ile260Met generates global gene expression changes related to cellular transformation.Mutagenesis · 2012Article
- O-miner: an integrative platform for automated analysis and mining of -omics data.Nucleic acids research · 2012Article
- ROCS: receiver operating characteristic surface for class-skewed high-throughput data.PloS one · 2012Article
- CNV-WebStore: online CNV analysis, storage and interpretation.BMC bioinformatics · 2011Article
- A multi-sample based method for identifying common CNVs in normal human genomic structure using high-resolution aCGH data.PloS one · 2011Article
- A bayesian analysis for identifying DNA copy number variations using a compound poisson process.EURASIP journal on bioinformatics & systems biology · 2010Article
- Cancer gene discovery in mouse and man.Biochimica et biophysica acta · 2009Review
- Integrated study of copy number states and genotype calls using high-density SNP arrays.Nucleic acids research · 2009Article
- Article
- A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets.Nucleic acids research · 2009Article
- RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions.Bioinformatics (Oxford, England) · 2009Article
- Article
- ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data.PloS one · 2007Article
- Hierarchical clustering of high-throughput expression data based on general dependences.IEEE/ACM transactions on computational biology and bioinformaticsArticle
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9 authors.
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Abstract
backgroundDNA copy number aberration (CNA) is one of the key characteristics of cancer cells. Recent studies demonstrated the feasibility of utilizing high density single nucleotide polymorphism (SNP) genotyping arrays to detect CNA. Compared with the two-color array-based comparative genomic hybridization (array-CGH), the SNP arrays offer much higher probe density and lower signal-to-noise ratio at the single SNP level. To accurately identify small segments of CNA from SNP array data, segmentation methods that are sensitive to CNA while resistant to noise are required.
resultsWe have developed a highly sensitive algorithm for the edge detection of copy number data which is especially suitable for the SNP array-based copy number data. The method consists of an over-sensitive edge-detection step and a test-based forward-backward edge selection step.
conclusionUsing simulations constructed from real experimental data, the method shows high sensitivity and specificity in detecting small copy number changes in focused regions. The method is implemented in an R package FASeg, which includes data processing and visualization utilities, as well as libraries for processing Affymetrix SNP array data.
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