ArticleNucleic acids research2009
Integrated study of copy number states and genotype calls using high-density SNP arrays.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers, 1 of them a synthesis that pooled it.
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Who cites it
77 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Neural Cell Models of Specific Reading Disabilities: Identification of Cellular and Transcriptome Alterations.Genes, brain, and behavior · 2026Article
- MarkerMatch: a proximity-based probe-matching algorithm for joint analysis of copy-number variants from different genotyping arrays.Bioinformatics (Oxford, England) · 2026Article
- Pivotal role of biallelic frequency analysis in identifying copy number alterations using genome-wide methods in tumors with a high level of aneuploidy.Journal of applied genetics · 2026Article
- The hidden Markov model and its applications in bioinformatics analysis.Genes & diseases · 2026Review
- Homologous recombination deficiency (HRD) testing landscape: clinical applications and technical validation for routine diagnostics.Biomarker research · 2025Review
- High level of aneuploidy and recurrent loss of chromosome 11 as relevant features of somatotroph pituitary tumors.Journal of translational medicine · 2024Article
- A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data.Nature communications · 2023Article
- Progress in Methods for Copy Number Variation Profiling.International journal of molecular sciences · 2022Review
- Article
- Set-Wise Differential Interaction Between Copy Number Alterations and Gene Expressions of Lower-Grade Glioma Reveals Prognosis-Associated Pathways.Entropy (Basel, Switzerland) · 2020Article
- Technologies for Pharmacogenomics: A Review.Genes · 2020Review
- NTHL1 biallelic mutations seldom cause colorectal cancer, serrated polyposis or a multi-tumor phenotype, in absence of colorectal adenomas.Scientific reports · 2019Article
- DBS: a fast and informative segmentation algorithm for DNA copy number analysis.BMC bioinformatics · 2019Article
- ShinyCNV: a Shiny/R application to view and annotate DNA copy number variations.Bioinformatics (Oxford, England) · 2019Article
- SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling.Genome biology · 2017Article
- FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing.Nucleic acids research · 2016Article
- Statistical Methods in Integrative Genomics.Annual review of statistics and its application · 2016Article
- A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data.PloS one · 2016Article
- argyle: An R Package for Analysis of Illumina Genotyping Arrays.G3 (Bethesda, Md.) · 2015Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
We propose a statistical framework, named genoCN, to simultaneously dissect copy number states and genotypes using high-density SNP (single nucleotide polymorphism) arrays. There are at least two types of genomic DNA copy number differences: copy number variations (CNVs) and copy number aberrations (CNAs). While CNVs are naturally occurring and inheritable, CNAs are acquired somatic alterations most often observed in tumor tissues only. CNVs tend to be short and more sparsely located in the genome compared with CNAs. GenoCN consists of two components, genoCNV and genoCNA, designed for CNV and CNA studies, respectively. In contrast to most existing methods, genoCN is more flexible in that the model parameters are estimated from the data instead of being decided a priori. GenoCNA also incorporates two important strategies for CNA studies. First, the effects of tissue contamination are explicitly modeled. Second, if SNP arrays are performed for both tumor and normal tissues of one individual, the genotype calls from normal tissue are used to study CNAs in tumor tissue. We evaluated genoCN by applications to 162 HapMap individuals and a brain tumor (glioblastoma) dataset and showed that our method can successfully identify both types of copy number differences and produce high-quality genotype calls.
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Registered trials
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