Huntsman DG, McAlpine JN, Aparicio S,
Shah SP (2014) TITAN: inference of copy
number architectures, in clonal cell popula-
tions from tumor whole-genome sequence
data. Genome Res 24(11):1881–1893.
https://doi.org/10.1101/gr.180281.114
- Strino F, Parisi F, Micsinai M, Kluger Y
(2013) TrAp: a tree approach for fingerprint-
ing subclonal tumor composition. Nucleic
Acids Res 41(17). https://doi.org/10.
1093/nar/gkt641 - El-Kebir M, Oesper L, Acheson-Field H,
Raphael BJ (2015) Reconstruction of clonal
trees and tumor composition from multi-sam-
ple sequencing data. Bioinformatics 31
(12):62–70.https://doi.org/10.1093/bioin
formatics/btv261 - Qiao Y, Quinlan AR, Jazaeri AA, Verhaak
RGW, Wheeler DA, Marth GT (2014) Sub-
cloneSeeker: a computational framework for
reconstructing tumor clone structure for can-
cer variant interpretation and prioritization.
Genome Biol 15(8). https://doi.org/10.
1186/S13059-014-0443-X - Deshwar AG, Vembu S, Yung CK, Jang GH,
Stein L, Morris Q (2015) PhyloWGS: recon-
structing subclonal composition and evolu-
tion from whole-genome sequencing of
tumors. Genome Biol 16.https://doi.org/
10.1186/s13059-015-0602-8 - Malikic S, McPherson AW, Donmez N, Sahi-
nalp CS (2015) Clonality inference in multi-
ple tumor samples using phylogeny.
Bioinformatics 31(9):1349–1356. https://
doi.org/10.1093/bioinformatics/btv003 - Davis A, Navin NE (2016) Computing tumor
trees from single cells. Genome Biol 17.
https://doi.org/10.1186/S13059-016-
0987-Z
- Potter NE, Ermini L, Papaemmanuil E, Caz-
zaniga G, Vijayaraghavan G, Titley I, Ford A,
Campbell P, Kearney L, Greaves M (2013)
Single-cell mutational profiling and clonal
phylogeny in cancer. Genome Res 23
(12):2115–2125.https://doi.org/10.1101/
gr.159913.113 - Salehi S, Steif A, Roth A, Aparicio S, Bou-
chard-Cote A, Shah SP (2017) ddClone:
joint statistical inference of clonal populations
from single cell and bulk tumour sequencing
data. Genome Biol 18.https://doi.org/10.
1186/s13059-017-1169-3 - Miller CA, White BS, Dees ND, Griffith M,
Welch JS, Griffith OL, Vij R, Tomasson MH,
Graubert TA, Walter MJ, Ellis MJ, Schierding
W, DiPersio JF, Ley TJ, Mardis ER, Wilson
RK, Ding L (2014) SciClone: inferring clonal
architecture and tracking the spatial and tem-
poral patterns of tumor evolution. PLoS
Comput Biol 10(8). https://doi.org/10.
1371/journal.pcbi.1003665 - Ernst J, Kellis M (2015) Large-scale imputa-
tion of epigenomic datasets for systematic
annotation of diverse human tissues. Nat Bio-
technol 33(4):364–U374.https://doi.org/
10.1038/nbt.3157 - Stevens M, Cheng JB, Li DF, Xie MC, Hong
CB, Maire CL, Ligon KL, Hirst M, Marra
MA, Costello JF, Wang T (2013) Estimating
absolute methylation levels at single-CpG res-
olution from methylation enrichment and
restriction enzyme sequencing methods.
Genome Res 23(9):1541–1553.https://doi.
org/10.1101/gr.152231.112
374 Yungang Xu and Xiaobo Zhou