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Newick trees for "Within-patient phylogenetic reconstruction reveals early events in Barrett's Esophagus"

Citation

Kuhner, Mary; Smith, Lucian (2020), Newick trees for "Within-patient phylogenetic reconstruction reveals early events in Barrett's Esophagus", Dryad, Dataset, https://doi.org/10.5061/dryad.866t1g1p1

Abstract

Newick format within-patient phylogenetic trees for a Barrett's Esophagus WGS dataset

Methods

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.

Usage Notes

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.

Funding

National Institutes of Health, Award: PO1 CA91955

National Institutes of Health, Award: P30 CA015704