Please use this identifier to cite or link to this item: https://doi.org/10.1371/journal.pone.0046152
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dc.titleLong Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons
dc.contributor.authorYao, F.
dc.contributor.authorAriyaratne, P.N.
dc.contributor.authorHillmer, A.M.
dc.contributor.authorLee, W.H.
dc.contributor.authorLi, G.
dc.contributor.authorTeo, A.S.M.
dc.contributor.authorWoo, X.Y.
dc.contributor.authorZhang, Z.
dc.contributor.authorChen, J.P.
dc.contributor.authorPoh, W.T.
dc.contributor.authorZawack, K.F.B.
dc.contributor.authorChan, C.S.
dc.contributor.authorLeong, S.T.
dc.contributor.authorNeo, S.C.
dc.contributor.authorChoi, P.S.D.
dc.contributor.authorGao, S.
dc.contributor.authorNagarajan, N.
dc.contributor.authorThoreau, H.
dc.contributor.authorShahab, A.
dc.contributor.authorRuan, X.
dc.contributor.authorCacheux-Rataboul, V.
dc.contributor.authorWei, C.-L.
dc.contributor.authorBourque, G.
dc.contributor.authorSung, W.-K.
dc.contributor.authorLiu, E.T.
dc.contributor.authorRuan, Y.
dc.date.accessioned2014-11-26T07:45:51Z
dc.date.available2014-11-26T07:45:51Z
dc.date.issued2012-09-28
dc.identifier.citationYao, F., Ariyaratne, P.N., Hillmer, A.M., Lee, W.H., Li, G., Teo, A.S.M., Woo, X.Y., Zhang, Z., Chen, J.P., Poh, W.T., Zawack, K.F.B., Chan, C.S., Leong, S.T., Neo, S.C., Choi, P.S.D., Gao, S., Nagarajan, N., Thoreau, H., Shahab, A., Ruan, X., Cacheux-Rataboul, V., Wei, C.-L., Bourque, G., Sung, W.-K., Liu, E.T., Ruan, Y. (2012-09-28). Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS ONE 7 (9) : -. ScholarBank@NUS Repository. https://doi.org/10.1371/journal.pone.0046152
dc.identifier.issn19326203
dc.identifier.urihttp://scholarbank.nus.edu.sg/handle/10635/109441
dc.description.abstractStructural variations (SVs) contribute significantly to the variability of the human genome and extensive genomic rearrangements are a hallmark of cancer. While genomic DNA paired-end-tag (DNA-PET) sequencing is an attractive approach to identify genomic SVs, the current application of PET sequencing with short insert size DNA can be insufficient for the comprehensive mapping of SVs in low complexity and repeat-rich genomic regions. We employed a recently developed procedure to generate PET sequencing data using large DNA inserts of 10-20 kb and compared their characteristics with short insert (1 kb) libraries for their ability to identify SVs. Our results suggest that although short insert libraries bear an advantage in identifying small deletions, they do not provide significantly better breakpoint resolution. In contrast, large inserts are superior to short inserts in providing higher physical genome coverage for the same sequencing cost and achieve greater sensitivity, in practice, for the identification of several classes of SVs, such as copy number neutral and complex events. Furthermore, our results confirm that large insert libraries allow for the identification of SVs within repetitive sequences, which cannot be spanned by short inserts. This provides a key advantage in studying rearrangements in cancer, and we show how it can be used in a fusion-point-guided-concatenation algorithm to study focally amplified regions in cancer. © 2012 Yao et al.
dc.description.urihttp://libproxy1.nus.edu.sg/login?url=http://dx.doi.org/10.1371/journal.pone.0046152
dc.sourceScopus
dc.typeArticle
dc.contributor.departmentBIOCHEMISTRY
dc.description.doi10.1371/journal.pone.0046152
dc.description.sourcetitlePLoS ONE
dc.description.volume7
dc.description.issue9
dc.description.page-
dc.identifier.isiut000309973900099
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