ArticleBioinformatics (Oxford, England)2012
CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed.
- Quantifying local malignant adaptation in tissue-specific evolutionary trajectories by harnessing cancer's repeatability at the genetic level.Evolutionary applications · 2019Article
- 'Multi-omic' data analysis using O-miner.Briefings in bioinformatics · 2019Article
- Quantification of within-sample genetic heterogeneity from SNP-array data.Scientific reports · 2017Article
- SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair.Oncogene · 2015Article
- Allelic loss of 9p21.3 is a prognostic factor in 1p/19q codeleted anaplastic gliomas.Neurology · 2015Article
- Clonal status of actionable driver events and the timing of mutational processes in cancer evolution.Science translational medicine · 2015Observational
- Pan-cancer analysis of genomic scar signatures associated with homologous recombination deficiency suggests novel indications for existing cancer drugs.Biomarker research · 2015Article
- Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data.Genome biology · 2014Article
- 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
- Article
- Tumor mutation burden forecasts outcome in ovarian cancer with BRCA1 or BRCA2 mutations.PloS one · 2013Article
- Getting DNA copy numbers without control samples.Algorithms for molecular biology : AMB · 2012Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
summaryCalMaTe calibrates preprocessed allele-specific copy number estimates (ASCNs) from DNA microarrays by controlling for single-nucleotide polymorphism-specific allelic crosstalk. The resulting ASCNs are on average more accurate, which increases the power of segmentation methods for detecting changes between copy number states in tumor studies including copy neutral loss of heterozygosity. CalMaTe applies to any ASCNs regardless of preprocessing method and microarray technology, e.g. Affymetrix and Illumina. AVAILABILITY: The method is available on CRAN (http://cran.r-project.org/) in the open-source R package calmate, which also includes an add-on to the Aroma Project framework (http://www.aroma-project.org/).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.