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Method: SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data
- Hamim Zafar,
- Nicholas Navin,
- Ken Chen,
- and Luay Nakhleh
Genome Res. November 2019 29: 1847-1859; Published in Advance October 18, 2019, doi:10.1101/gr.243121.118
...framework jointly reconstructs the tumor clones as clusters of single cells as well as their genealogical relationship in the form of a clonal phylogeny. In this process, SiCloneFit accounts for the effects of mutational events (point mutations, LOH, deletion) in the evolutionary history of the tumor via...
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Method: PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data
- Salem Malikic,
- Farid Rashidi Mehrabadi,
- Simone Ciccolella,
- Md. Khaledur Rahman,
- Camir Ricketts,
- Ehsan Haghshenas,
- Daniel Seidman,
- Faraz Hach,
- Iman Hajirasouliha,
- and S. Cenk Sahinalp
Genome Res. November 2019 29: 1860-1877; Published in Advance October 18, 2019, doi:10.1101/gr.234435.118
...in this sample. However, this signal is very likely a consequence of sequencing noise as, for each of the two mutations, there is only a single read supporting the variant allele. In addition, these mutations were not reported in any of the sequenced single cells extracted from the primary tumor.In conclusion...
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Method: Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR
- Marta Puig,
- Jon Lerga-Jaso,
- Carla Giner-Delgado,
- Sarai Pacheco,
- David Izquierdo,
- Alejandra Delprat,
- Magdalena Gayà-Vidal,
- Jack F. Regan,
- George Karlin-Neumann,
- and Mario Cáceres
Genome Res. May 2020 30: 724-735; Published in Advance May 18, 2020, doi:10.1101/gr.255273.119
...-end mapping (PEM) data from large fragments (∼40-kb fosmid clones) (Kidd et al. 2008), are often not able to jump across the breakpoint IRs and determine the inversion orientation. New methods like single-cell sequencing of one DNA strand (Strand-seq) (Sanders et al. 2016; Chaisson et al. 2019) or Bionano...
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Research: Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii
- Frédéric Chaux,
- Nicolas Agier,
- Clotilde Garrido,
- Gilles Fischer,
- Stephan Eberhard,
- and Zhou Xu
Genome Res. September 2023 33: 1582-1598; Published in Advance August 14, 2023, doi:10.1101/gr.278043.123
...-1.Extrachromosomal telomeric DNA molecules, predominantly found as double-stranded or single-stranded circles, are detected in ALT tumors and proposed to be involved in telomere maintenance (Cesare and Reddel 2010). To detect potential circular DNA containing telomere sequences, we performed rolling circle...
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Research: Nucleosome repositioning in chronic lymphocytic leukemia
- Kristan V. Piroeva,
- Charlotte McDonald,
- Charalampos Xanthopoulos,
- Chelsea Fox,
- Christopher T. Clarkson,
- Jan-Philipp Mallm,
- Yevhen Vainshtein,
- Luminita Ruje,
- Lara C. Klett,
- Stephan Stilgenbauer,
- Daniel Mertens,
- Efterpi Kostareli,
- Karsten Rippe,
- and Vladimir B. Teif
Genome Res. October 2023 33: 1649-1661; Published in Advance September 12, 2023, doi:10.1101/gr.277298.122
...of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom; 2Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, United Kingdom; 3German Cancer Research Center (DKFZ) Heidelberg, Single Cell Open Lab, 69120 Heidelberg, Germany; 4...
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