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000182764 1001_ $$00000-0002-1526-3343$$aJeong, Hyobin$$b0
000182764 245__ $$aFunctional analysis of structural variants in single cells using Strand-seq.
000182764 260__ $$aNew York, NY$$bSpringer Nature$$c2023
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000182764 500__ $$a#LA:B480# / 2023 Jun;41(6):832-844
000182764 520__ $$aSomatic structural variants (SVs) are widespread in cancer, but their impact on disease evolution is understudied due to a lack of methods to directly characterize their functional consequences. We present a computational method, scNOVA, which uses Strand-seq to perform haplotype-aware integration of SV discovery and molecular phenotyping in single cells by using nucleosome occupancy to infer gene expression as a readout. Application to leukemias and cell lines identifies local effects of copy-balanced rearrangements on gene deregulation, and consequences of SVs on aberrant signaling pathways in subclones. We discovered distinct SV subclones with dysregulated Wnt signaling in a chronic lymphocytic leukemia patient. We further uncovered the consequences of subclonal chromothripsis in T cell acute lymphoblastic leukemia, which revealed c-Myb activation, enrichment of a primitive cell state and informed successful targeting of the subclone in cell culture, using a Notch inhibitor. By directly linking SVs to their functional effects, scNOVA enables systematic single-cell multiomic studies of structural variation in heterogeneous cell populations.
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000182764 7001_ $$00000-0002-4805-2366$$aGrimes, Karen$$b1
000182764 7001_ $$aRauwolf, Kerstin K$$b2
000182764 7001_ $$00000-0002-9992-3109$$aBruch, Peter-Martin$$b3
000182764 7001_ $$00000-0001-5773-5620$$aRausch, Tobias$$b4
000182764 7001_ $$aHasenfeld, Patrick$$b5
000182764 7001_ $$aBenito, Eva$$b6
000182764 7001_ $$00000-0002-6973-3531$$aRoider, Tobias$$b7
000182764 7001_ $$aSabarinathan, Radhakrishnan$$b8
000182764 7001_ $$00000-0001-8414-8966$$aPorubsky, David$$b9
000182764 7001_ $$00000-0001-8502-0366$$aHerbst, Sophie A$$b10
000182764 7001_ $$aErarslan-Uysal, Büşra$$b11
000182764 7001_ $$00000-0003-2200-0151$$aJann, Johann-Christoph$$b12
000182764 7001_ $$00000-0002-9376-1030$$aMarschall, Tobias$$b13
000182764 7001_ $$aNowak, Daniel$$b14
000182764 7001_ $$aBourquin, Jean-Pierre$$b15
000182764 7001_ $$00000-0003-1953-0848$$aKulozik, Andreas E$$b16
000182764 7001_ $$0P:(DE-He78)6333b389d0abc96ef7f2f6e049a8f8c4$$aDietrich, Sascha$$b17$$udkfz
000182764 7001_ $$00000-0003-2890-3191$$aBornhauser, Beat$$b18
000182764 7001_ $$00000-0003-3945-0677$$aSanders, Ashley D$$b19
000182764 7001_ $$0P:(DE-He78)372b77c2acf8604690a6a325a4e89287$$aKorbel, Jan$$b20$$eLast author$$udkfz
000182764 773__ $$0PERI:(DE-600)1494943-X$$a10.1038/s41587-022-01551-4$$n6$$p832-844$$tNature biotechnology$$v41$$x0733-222X$$y2023
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