ArticleBioinformatics (Oxford, England)2018
Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Canopy2: Tumor Phylogeny Inference by Bulk DNA and Single-Cell RNA Sequencing.Statistics in biosciences · 2026Article
- Prevalence of germline mutations in cancer susceptibility genes in Chinese patients with renal cell carcinoma.Translational andrology and urology · 2023Article
- Marker-free characterization of full-length transcriptomes of single live circulating tumor cells.Genome research · 2023Article
- Specific gut microbiome signature predicts hepatitis B virus-related hepatocellular carcinoma patients with microvascular invasion.Annals of medicine · 2023Article
- Expression and Significance of Cyclin-Dependent Protein Kinase 6 in Diffuse Large B-Cell Lymphoma.International journal of general medicine · 2022Article
- Hydroxysteroid 17-Beta Dehydrogenase 6 Is a Prognostic Biomarker and Correlates with Immune Infiltrates in Hepatocellular Carcinoma.Digestive diseases and sciences · 2022Article
- Article
- Copy Number Variation Detection by Single-Cell DNA Sequencing with SCOPE.Methods in molecular biology (Clifton, N.J.) · 2022Article
- PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity.BMC bioinformatics · 2021Article
- Potential role of glucosamine-phosphate N-acetyltransferase 1 in the development of lung adenocarcinoma.Aging · 2021Article
- Comprehensive Analysis of Prognostic Value of MEX3A and Its Relationship with Immune Infiltrates in Ovarian Cancer.Journal of immunology research · 2021Article
- Downregulated Expression of CLEC9A as Novel Biomarkers for Lung Adenocarcinoma.Frontiers in oncology · 2021Article
- Overexpression of Taspase 1 Predicts Poor Prognosis in Patients with Hepatocellular Carcinoma.Cancer management and research · 2021Article
- Expression and gene regulation network of TYMS and BCL2L1 in colorectal cancer based on data mining.PeerJ · 2021Article
- SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing.Cell systems · 2020Article
- DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing.Genome biology · 2020Article
- Systemic Expression Analysis Reveals Prognostic Significance of WIPI3 in Hepatocellular Carcinoma.Frontiers in genetics · 2020Article
- Expression and gene regulation network ofAging · 2019Article
- Article
- CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing.Genome biology · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Summary: Copy number variation is an important and abundant source of variation in the human genome, which has been associated with a number of diseases, especially cancer. Massively parallel next-generation sequencing allows copy number profiling with fine resolution. Such efforts, however, have met with mixed successes, with setbacks arising partly from the lack of reliable analytical methods to meet the diverse and unique challenges arising from the myriad experimental designs and study goals in genetic studies. In cancer genomics, detection of somatic copy number changes and profiling of allele-specific copy number (ASCN) are complicated by experimental biases and artifacts as well as normal cell contamination and cancer subclone admixture. Furthermore, careful statistical modeling is warranted to reconstruct tumor phylogeny by both somatic ASCN changes and single nucleotide variants. Here we describe a flexible computational pipeline, MARATHON, which integrates multiple related statistical software for copy number profiling and downstream analyses in disease genetic studies. Availability and implementation: MARATHON is publicly available at https://github.com/yuchaojiang/MARATHON. Supplementary information: Supplementary data are available at Bioinformatics online.
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