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Method: Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer
- Eva K.F. Chan,
- Daniel L. Cameron,
- Desiree C. Petersen,
- Ruth J. Lyons,
- Benedetta F. Baldi,
- Anthony T. Papenfuss,
- David M. Thomas,
- and Vanessa M. Hayes
Genome Res. May 2018 28: 726-738; Published in Advance April 4, 2018, doi:10.1101/gr.227975.117
...AK, Buczkowicz P, Jiang Y, Yu M, Hawkins C, Brudno M. 2017. Identification of complex genomic rearrangements in cancers using CouGaR. Genome Res 27: 107–117. ↵Garsed DW, Marshall OJ, Corbin VDA, Hsu A, Di Stefano L, Schröder J, Li J, Feng ZP, Kim BW, Kowarsky...
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Method: Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples
- Sergey Aganezov and
- Benjamin J. Raphael
Genome Res. September 2020 30: 1274-1290; Published in Advance September 4, 2020, doi:10.1101/gr.256701.119
...be inferred from DNA sequencing technologies whose read lengths are shorter than the length of rearrangements.RCK solves the following Cancer Karyotype Reconstruction Problem: given allele-specific segment copy numbers and a list of novel adjacencies (i.e., pairs of genomic loci that are measured as adjacent...

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