ArticleGenome biology2013
Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 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
48 citing papers in PubMed, 74 citations in OpenAlex.
- Article
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- Integrated transcriptomic and single-cell RNA-seq analysis identifies CLCNKB, KLK1 and PLEKHA4 as key gene of AKI-to-CKD progression.Frontiers in immunology · 2025Article
- Deciphering complex breakage-fusion-bridge genome rearrangements with Ambigram.Nature communications · 2023Article
- Spatial heterogeneity of infiltrating T cells in high-grade serous ovarian cancer revealed by multi-omics analysis.Cell reports. Medicine · 2022Article
- Characterization of somatic structural variations in 528 Chinese individuals with Esophageal squamous cell carcinoma.Nature communications · 2022Article
- Human papillomavirus integration perspective in small cell cervical carcinoma.Nature communications · 2022Article
- A comprehensive benchmarking of WGS-based deletion structural variant callers.Briefings in bioinformatics · 2022Article
- Identification of Copy Number Alterations from Next-Generation Sequencing Data.Advances in experimental medicine and biology · 2022Article
- Pan-Genomic Sequencing Reveals ActionableCancers · 2021Article
- SCYN: single cell CNV profiling method using dynamic programming.BMC genomics · 2021Article
- Comprehensive Study of Germline Mutations and Double-Hit Events in Esophageal Squamous Cell Cancer.Frontiers in oncology · 2021Article
- Oviz-Bio: a web-based platform for interactive cancer genomics data visualization.Nucleic acids research · 2020Article
- Cellular origins and genetic landscape of cutaneous gamma delta T cell lymphomas.Nature communications · 2020Article
- RBV: Read balance validator, a tool for prioritising copy number variations in germline conditions.Scientific reports · 2019Article
- Rectal cancer sub-clones respond differentially to neoadjuvant therapy.Neoplasia (New York, N.Y.) · 2019Article
- Whole-genome sequencing reveals novel tandem-duplication hotspots and a prognostic mutational signature in gastric cancer.Nature communications · 2019Article
- 'Multi-omic' data analysis using O-miner.Briefings in bioinformatics · 2019Article
- Establishment and characterization of new tumor xenografts and cancer cell lines from EBV-positive nasopharyngeal carcinoma.Nature communications · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-genome sequencing of tumor tissue has the potential to provide comprehensive characterization of genomic alterations in tumor samples. We present Patchwork, a new bioinformatic tool for allele-specific copy number analysis using whole-genome sequencing data. Patchwork can be used to determine the copy number of homologous sequences throughout the genome, even in aneuploid samples with moderate sequence coverage and tumor cell content. No prior knowledge of average ploidy or tumor cell content is required. Patchwork is freely available as an R package, installable via R-Forge (http://patchwork.r-forge.r-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.