ArticleBMC genomics2014
Sequencing methods and datasets to improve functional interpretation of sleeping beauty mutagenesis screens.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 24 citations in OpenAlex.
- Identification of genes that promote PI3K pathway activation and prostate tumour formation.Oncogene · 2024Article
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- Understanding cancer drug resistance withiScience · 2023Article
- Transmicron: accurate prediction of insertion probabilities improves detection of cancer driver genes from transposon mutagenesis screens.Nucleic acids research · 2023Article
- A Genetic Screen to Identify Gain- and Loss-of-Function Modifications that Enhance T-cell Infiltration into Tumors.Cancer immunology research · 2020Article
- CRISPR and transposon in vivo screens for cancer drivers and therapeutic targets.Genome biology · 2020Review
- Src-Dependent DBL Family Members Drive Resistance to Vemurafenib in Human Melanoma.Cancer research · 2019Article
- Affinities of Terminal Inverted Repeats to DNA Binding Domain of Transposase Affect the Transposition Activity of BambooInternational journal of molecular sciences · 2019Article
- A simplified transposon mutagenesis method to perform phenotypic forward genetic screens in cultured cells.BMC genomics · 2019Article
- Liver Cancer Gene Discovery Using Gene Targeting, Sleeping Beauty, and CRISPR/Cas9.Seminars in liver disease · 2019Review
- Sleeping Beauty Mouse Models of Cancer: Microenvironmental Influences on Cancer Genetics.Frontiers in oncology · 2019Review
- Advances in functional genetic screening with transposons and CRISPR/Cas9 to illuminate cancer biology.Current opinion in genetics & development · 2018Review
- A Forward Genetic Screen Targeting the Endothelium Reveals a Regulatory Role for the Lipid Kinase Pi4ka in Myelo- and Erythropoiesis.Cell reports · 2018Article
- RNA sequencing of Sleeping Beauty transposon-induced tumors detects transposon-RNA fusions in forward genetic cancer screens.Genome research · 2016Article
- The utility of transposon mutagenesis for cancer studies in the era of genome editing.Genome biology · 2015Review
- A Hybrid Adenoviral Vector System Achieves Efficient Long-Term Gene Expression in the Liver via piggyBac Transposition.Human gene therapy · 2015Article
- Sleeping Beauty transposon insertional mutagenesis based mouse models for cancer gene discovery.Current opinion in genetics & development · 2015Review
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
backgroundAnimal models of cancer are useful to generate complementary datasets for comparison to human tumor data. Insertional mutagenesis screens, such as those utilizing the Sleeping Beauty (SB) transposon system, provide a model that recapitulates the spontaneous development and progression of human disease. This approach has been widely used to model a variety of cancers in mice. Comprehensive mutation profiles are generated for individual tumors through amplification of transposon insertion sites followed by high-throughput sequencing. Subsequent statistical analyses identify common insertion sites (CISs), which are predicted to be functionally involved in tumorigenesis. Current methods utilized for SB insertion site analysis have some significant limitations. For one, they do not account for transposon footprints - a class of mutation generated following transposon remobilization. Existing methods also discard quantitative sequence data due to uncertainty regarding the extent to which it accurately reflects mutation abundance within a heterogeneous tumor. Additionally, computational analyses generally assume that all potential insertion sites have an equal probability of being detected under non-selective conditions, an assumption without sufficient relevant data. The goal of our study was to address these potential confounding factors in order to enhance functional interpretation of insertion site data from tumors.
resultsWe describe here a novel method to detect footprints generated by transposon remobilization, which revealed minimal evidence of positive selection in tumors. We also present extensive characterization data demonstrating an ability to reproducibly assign semi-quantitative information to individual insertion sites within a tumor sample. Finally, we identify apparent biases for detection of inserted transposons in several genomic regions that may lead to the identification of false positive CISs.
conclusionThe information we provide can be used to refine analyses of data from insertional mutagenesis screens, improving functional interpretation of results and facilitating the identification of genes important in cancer development and progression.
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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.