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Article: Genome-wide transposon screening and quantitative insertion site sequencing for cancer gene discovery in mice

TitleGenome-wide transposon screening and quantitative insertion site sequencing for cancer gene discovery in mice
Authors
Issue Date2017
Citation
Nature Protocols, 2017, v. 12, n. 2, p. 289-309 How to Cite?
AbstractTransposon-mediated forward genetics screening in mice has emerged as a powerful tool for cancer gene discovery. It pinpoints cancer drivers that are difficult to find with other approaches, thus complementing the sequencing-based census of human cancer genes. We describe here a large series of mouse lines for insertional mutagenesis that are compatible with two transposon systems, PiggyBac and Sleeping Beauty, and give guidance on the use of different engineered transposon variants for constitutive or tissue-specific cancer gene discovery screening. We also describe a method for semiquantitative transposon insertion site sequencing (QiSeq). The QiSeq library preparation protocol exploits acoustic DNA fragmentation to reduce bias inherent to widely used restriction-digestion-based approaches for ligation-mediated insertion site amplification. Extensive multiplexing in combination with next-generation sequencing allows affordable ultra-deep transposon insertion site recovery in high-throughput formats within 1 week. Finally, we describe principles of data analysis and interpretation for obtaining insights into cancer gene function and genetic tumor evolution.
Persistent Identifierhttp://hdl.handle.net/10722/249154
ISSN
2017 Impact Factor: 12.423
2015 SCImago Journal Rankings: 9.039
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorFriedrich, Mathias J.-
dc.contributor.authorRad, Lena-
dc.contributor.authorBronner, Iraad F.-
dc.contributor.authorStrong, Alexander-
dc.contributor.authorWang, Wei-
dc.contributor.authorWeber, Julia-
dc.contributor.authorMayho, Matthew-
dc.contributor.authorPonstingl, Hannes-
dc.contributor.authorEngleitner, Thomas-
dc.contributor.authorGrove, Carolyn-
dc.contributor.authorPfaus, Anja-
dc.contributor.authorSaur, Dieter-
dc.contributor.authorCadiñanos, Juan-
dc.contributor.authorQuail, Michael A.-
dc.contributor.authorVassiliou, George S.-
dc.contributor.authorLiu, Pentao-
dc.contributor.authorBradley, Allan-
dc.contributor.authorRad, Roland-
dc.date.accessioned2017-10-27T05:59:14Z-
dc.date.available2017-10-27T05:59:14Z-
dc.date.issued2017-
dc.identifier.citationNature Protocols, 2017, v. 12, n. 2, p. 289-309-
dc.identifier.issn1754-2189-
dc.identifier.urihttp://hdl.handle.net/10722/249154-
dc.description.abstractTransposon-mediated forward genetics screening in mice has emerged as a powerful tool for cancer gene discovery. It pinpoints cancer drivers that are difficult to find with other approaches, thus complementing the sequencing-based census of human cancer genes. We describe here a large series of mouse lines for insertional mutagenesis that are compatible with two transposon systems, PiggyBac and Sleeping Beauty, and give guidance on the use of different engineered transposon variants for constitutive or tissue-specific cancer gene discovery screening. We also describe a method for semiquantitative transposon insertion site sequencing (QiSeq). The QiSeq library preparation protocol exploits acoustic DNA fragmentation to reduce bias inherent to widely used restriction-digestion-based approaches for ligation-mediated insertion site amplification. Extensive multiplexing in combination with next-generation sequencing allows affordable ultra-deep transposon insertion site recovery in high-throughput formats within 1 week. Finally, we describe principles of data analysis and interpretation for obtaining insights into cancer gene function and genetic tumor evolution.-
dc.languageeng-
dc.relation.ispartofNature Protocols-
dc.titleGenome-wide transposon screening and quantitative insertion site sequencing for cancer gene discovery in mice-
dc.typeArticle-
dc.description.natureLink_to_subscribed_fulltext-
dc.identifier.doi10.1038/nprot.2016.164-
dc.identifier.pmid28079877-
dc.identifier.scopuseid_2-s2.0-85010930897-
dc.identifier.volume12-
dc.identifier.issue2-
dc.identifier.spage289-
dc.identifier.epage309-
dc.identifier.eissn1750-2799-
dc.identifier.isiWOS:000394187000007-

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