ArticleGenome biology2017
SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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
19 citing papers in PubMed.
- Analysis of Pre- and Posttreatment Tissues from the SWOG S0800 Trial Reveals an Effect of Neoadjuvant Chemotherapy on the Breast Cancer Genome.Clinical cancer research : an official journal of the American Association for Cancer Research · 2020Trial
- Integrated Analysis of RNA and DNA from the Phase III Trial CALGB 40601 Identifies Predictors of Response to Trastuzumab-Based Neoadjuvant Chemotherapy in HER2-Positive Breast Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2018Trial
- LCCC 1025: a phase II study of everolimus, trastuzumab, and vinorelbine to treat progressive HER2-positive breast cancer brain metastases.Breast cancer research and treatment · 2018Trial
- Disease burden and conditioning regimens in ASCT1221, a randomized phase II trial in children with juvenile myelomonocytic leukemia: A Children's Oncology Group study.Pediatric blood & cancer · 2018Trial
- Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer.The Journal of clinical investigation · 2018Trial
- Mutation divergence over space in tumour expansion.Journal of the Royal Society, Interface · 2023Article
- Dermokine mutations contribute to epithelial-mesenchymal transition and advanced melanoma through ERK/MAPK pathways.PloS one · 2023Article
- Integrated DNA and RNA Sequencing Reveals Drivers of Endocrine Resistance in Estrogen Receptor-Positive Breast Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2022Article
- Identification of Copy Number Alterations from Next-Generation Sequencing Data.Advances in experimental medicine and biology · 2022Article
- UNMASC: tumor-only variant calling with unmatched normal controls.NAR cancer · 2021Article
- Quantifying smoking exposure, genomic correlates, and related risk of treatment failure in p16+ squamous cell carcinoma of the oropharynx.Laryngoscope investigative otolaryngology · 2021Article
- Article
- Correlation of alterations in theLaryngoscope investigative otolaryngology · 2021Article
- Genome‑wide copy number analysis of circulating tumor cells in breast cancer patients with liver metastasis.Oncology reports · 2020Article
- A systematic evaluation of copy number alterations detection methods on real SNP array and deep sequencing data.BMC bioinformatics · 2019Article
- Genomic evolution of cancer models: perils and opportunities.Nature reviews. Cancer · 2019Review
- Identification of Jun loss promotes resistance to histone deacetylase inhibitor entinostat through Myc signaling in luminal breast cancer.Genome medicine · 2018Article
- Single-Cell Genomic Analysis in Plants.Genes · 2018Review
- Using single-cell multiple omics approaches to resolve tumor heterogeneity.Clinical and translational medicine · 2017Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Changes in the quantity of genetic material, known as somatic copy number alterations (CNAs), can drive tumorigenesis. Many methods exist for assessing CNAs using microarrays, but considerable technical issues limit current CNA calling based upon DNA sequencing. We present SynthEx, a novel tool for detecting CNAs from whole exome and genome sequencing. SynthEx utilizes a "synthetic-normal" strategy to overcome technical and financial issues. In terms of accuracy and precision, SynthEx is highly comparable to array-based methods and outperforms sequencing-based CNA detection tools. SynthEx robustly identifies CNAs using sequencing data without the additional costs associated with matched normal specimens.
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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.