10.5061/DRYAD.866T1G1P1
Kuhner, Mary
0000-0002-6986-3870
University of Washington
Smith, Lucian
0000-0001-7002-6386
University of Washington
Newick trees for "Within-patient phylogenetic reconstruction reveals
early events in Barrett's Esophagus"
Dryad
dataset
2020
cancer phylogenetics
cancer phylogenetics
National Cancer Institute
https://ror.org/040gcmg81
PO1 CA91955
National Cancer Institute
https://ror.org/040gcmg81
P30 CA015704
2020-09-10T00:00:00Z
2020-09-10T00:00:00Z
en
12329 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Newick format within-patient phylogenetic trees for a Barrett's
Esophagus WGS dataset
Phylogenies were generated using the method described in the associated
paper. After September 30, 2020, the underlying whole-genome data will be
archived at
http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001912.v1.p1 and can be retrieved from that site.
Each file represents one patient and is named by the ID used in the study.
Each file contains one or more Newick trees; when multiple trees are
present, they represent putative independent origins of Barrett's
Esophagus. Branch lengths are proportional to inferred number of
mutations. Root branches have lengths which represent mutations found in
all Barrett's samples but not in a blood or gastric control from the
same patient. Note that some Newick-reading software will discard these
root lengths. Filenames containing "_all" are trees for extended
data sets with two additional samples from a third time point. The
filename for the same patient ID without "_all" contains trees
for only the samples from the first two time points. Tip names in the
trees are sample IDs from the study. When a single sample is inferred to
contain two or more lineages, they are suffixed with "-1",
"-2" etc.