ArticleBMC bioinformatics2010
TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Genetic imputation of kidney transcriptome, proteome and multi-omics illuminates new blood pressure and hypertension targets.Nature communications · 2024Article
- A Unique Panel of Patient-Derived Cutaneous Squamous Cell Carcinoma Cell Lines Provides a Preclinical Pathway for Therapeutic Testing.International journal of molecular sciences · 2019Article
- Gene Co-expression Network and Copy Number Variation Analyses Identify Transcription Factors Associated With Multiple Myeloma Progression.Frontiers in genetics · 2019Article
- Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus.Plant biotechnology journal · 2017Article
- A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data.PloS one · 2017Article
- The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE".PLoS medicine · 2016Article
- Abundant copy-number loss of CYCLOPS and STOP genes in gastric adenocarcinoma.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2016Article
- SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair.Oncogene · 2015Article
- Performance evaluation of DNA copy number segmentation methods.Briefings in bioinformatics · 2015Article
- Pan-cancer analysis of genomic scar signatures associated with homologous recombination deficiency suggests novel indications for existing cancer drugs.Biomarker research · 2015Article
- MPAgenomics: an R package for multi-patient analysis of genomic markers.BMC bioinformatics · 2014Article
- PRC2 is recurrently inactivated through EED or SUZ12 loss in malignant peripheral nerve sheath tumors.Nature genetics · 2014Article
- MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes.Genome biology · 2014Article
- AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data.Bioinformatics (Oxford, England) · 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
- Exome sequencing identifies distinct mutational patterns in liver fluke-related and non-infection-related bile duct cancers.Nature genetics · 2013Article
- PAIR: paired allelic log-intensity-ratio-based normalization method for SNP-CGH arrays.Bioinformatics (Oxford, England) · 2013Article
- Tumor mutation burden forecasts outcome in ovarian cancer with BRCA1 or BRCA2 mutations.PloS one · 2013Article
- Fast detection of de novo copy number variants from SNP arrays for case-parent trios.BMC bioinformatics · 2012Article
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3 authors.
Funding
Abstract
backgroundHigh-throughput genotyping microarrays assess both total DNA copy number and allelic composition, which makes them a tool of choice for copy number studies in cancer, including total copy number and loss of heterozygosity (LOH) analyses. Even after state of the art preprocessing methods, allelic signal estimates from genotyping arrays still suffer from systematic effects that make them difficult to use effectively for such downstream analyses.
resultsWe propose a method, TumorBoost, for normalizing allelic estimates of one tumor sample based on estimates from a single matched normal. The method applies to any paired tumor-normal estimates from any microarray-based technology, combined with any preprocessing method. We demonstrate that it increases the signal-to-noise ratio of allelic signals, making it significantly easier to detect allelic imbalances.
conclusionsTumorBoost increases the power to detect somatic copy-number events (including copy-neutral LOH) in the tumor from allelic signals of Affymetrix or Illumina origin. We also conclude that high-precision allelic estimates can be obtained from a single pair of tumor-normal hybridizations, if TumorBoost is combined with single-array preprocessing methods such as (allele-specific) CRMA v2 for Affymetrix or BeadStudio's (proprietary) XY-normalization method for Illumina. A bounded-memory implementation is available in the open-source and cross-platform R package aroma.cn, which is part of the Aroma Project (http://www.aroma-project.org/).
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