Contains 29 columns of deidentified clinical data on 266 patients with chronic lymphocytic leukemia (CLL).
data(CLL)Note that there are three distinct objects included in the data
set: clinical, daisydist, and ripDiag.
clinicalA numerical data matrix with 266 rows (patients) amd 29 columns (clinical features). Patients were newly diagnosed with CLL and previously untreated at the time the clinical measurements were recorded.
daisydistA distance matrix, stored as a dist
object, recording pairwise distances between the 266 CLL
patients. Distances were computed using the daisy
function of Kaufmann and Rooseeuw, as implemented in the
cluster R package.
ripDiagThis object is a "Rips diagram". It was produced
by running the the ripsDiag function from the
TDA R package on the daisydist distance matrix.
Kevin R. Coombes krc@silicovore.com, Caitlin E. Coombes ccoombes@stanford.edu, Jake Reed hreed@augusta.edu
Schweighofer CD, Coombes KR, Barron LL, Diao L, Newman RJ, Ferrajoli A, O'Brien S, Wierda WG, Luthra R, Medeiros LJ, Keating MJ, Abruzzo LV. A two-gene signature, SKI and SLAMF1, predicts time-to-treatment in previously untreated patients with chronic lymphocytic leukemia. PLoS One. 2011;6(12):e28277. doi: 10.1371/journal.pone.0028277.
Duzkale H, Schweighofer CD, Coombes KR, Barron LL, Ferrajoli A, O'Brien S, Wierda WG, Pfeifer J, Majewski T, Czerniak BA, Jorgensen JL, Medeiros LJ, Freireich EJ, Keating MJ, Abruzzo LV. LDOC1 mRNA is differentially expressed in chronic lymphocytic leukemia and predicts overall survival in untreated patients. Blood. 2011 Apr 14;117(15):4076-84. doi: 10.1182/blood-2010-09-304881.
Schweighofer CD, Coombes KR, Majewski T, Barron LL, Lerner S, Sargent RL, O'Brien S, Ferrajoli A, Wierda WG, Czerniak BA, Medeiros LJ, Keating MJ, Abruzzo LV. Genomic variation by whole-genome SNP mapping arrays predicts time-to-event outcome in patients with chronic lymphocytic leukemia: a comparison of CLL and HapMap genotypes. J Mol Diagn. 2013 Mar;15(2):196-209. doi: 10.1016/j.jmoldx.2012.09.006.
Herling CD, Coombes KR, Benner A, Bloehdorn J, Barron LL, Abrams ZB, Majewski T, Bondaruk JE, Bahlo J, Fischer K, Hallek M, Stilgenbauer S, Czerniak BA, Oakes CC, Ferrajoli A, Keating MJ, Abruzzo LV. Time-to-progression after front-line fludarabine, cyclophosphamide, and rituximab chemoimmunotherapy for chronic lymphocytic leukaemia: a retrospective, multicohort study. Lancet Oncol. 2019 Nov;20(11):1576-1586. doi: 10.1016/S1470-2045(19)30503-0.
Coombes CE, Abrams ZB, Li S, Abruzzo LV, Coombes KR. Unsupervised machine learning and prognostic factors of survival in chronic lymphocytic leukemia. J Am Med Inform Assoc. 2020 Jul 1;27(7):1019-1027. doi: 10.1093/jamia/ocaa060.