Literature DB >> 35510362

Efficient Algorithms Unlock Understanding of Clonal Evolution in Cancer.

Christopher A Miller1.   

Abstract

In this issue of Blood Cancer Discovery, Wintersinger and colleagues present a new algorithm for quickly and accurately inferring clonal phylogenies from heterogeneous tumors sampled at many timepoints and/or many sites. When coupled with serial sequencing of tumors, this advance promises to increase our understanding of the clonal dynamics that shape tumor evolution and response to therapy. See related article by Wintersinger et al., p. 208 (9). ©2022 American Association for Cancer Research.

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Year:  2022        PMID： 35510362      PMCID： PMC9245365          DOI： 10.1158/2643-3230.BCD-22-0036

Source DB:  PubMed          Journal:  Blood Cancer Discov        ISSN： 2643-3230


  10 in total

1.  CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples.

Authors:  Matthew A Myers; Gryte Satas; Benjamin J Raphael
Journal:  Cell Syst       Date:  2019-06-19       Impact factor: 10.304

2.  PyClone: statistical inference of clonal population structure in cancer.

Authors:  Andrew Roth; Jaswinder Khattra; Damian Yap; Adrian Wan; Emma Laks; Justina Biele; Gavin Ha; Samuel Aparicio; Alexandre Bouchard-Côté; Sohrab P Shah
Journal:  Nat Methods       Date:  2014-03-16       Impact factor: 28.547

3.  Reconstructing Complex Cancer Evolutionary Histories from Multiple Bulk DNA Samples Using Pairtree.

Authors:  Jeff A Wintersinger; Stephanie M Dobson; Ethan Kulman; Lincoln D Stein; John E Dick; Quaid Morris
Journal:  Blood Cancer Discov       Date:  2022-05-05

4.  Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing.

Authors:  Yuchao Jiang; Yu Qiu; Andy J Minn; Nancy R Zhang
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-29       Impact factor: 11.205

5.  Subclonal diversification of primary breast cancer revealed by multiregion sequencing.

Authors:  Lucy R Yates; Moritz Gerstung; Stian Knappskog; Christine Desmedt; Gunes Gundem; Peter Van Loo; Turid Aas; Ludmil B Alexandrov; Denis Larsimont; Helen Davies; Yilong Li; Young Seok Ju; Manasa Ramakrishna; Hans Kristian Haugland; Peer Kaare Lilleng; Serena Nik-Zainal; Stuart McLaren; Adam Butler; Sancha Martin; Dominic Glodzik; Andrew Menzies; Keiran Raine; Jonathan Hinton; David Jones; Laura J Mudie; Bing Jiang; Delphine Vincent; April Greene-Colozzi; Pierre-Yves Adnet; Aquila Fatima; Marion Maetens; Michail Ignatiadis; Michael R Stratton; Christos Sotiriou; Andrea L Richardson; Per Eystein Lønning; David C Wedge; Peter J Campbell
Journal:  Nat Med       Date:  2015-06-22       Impact factor: 53.440

6.  Inferring clonal evolution of tumors from single nucleotide somatic mutations.

Authors:  Wei Jiao; Shankar Vembu; Amit G Deshwar; Lincoln Stein; Quaid Morris
Journal:  BMC Bioinformatics       Date:  2014-02-01       Impact factor: 3.169

7.  Clonal evolution in myelodysplastic syndromes.

Authors:  Pedro da Silva-Coelho; Leonie I Kroeze; Kenichi Yoshida; Theresia N Koorenhof-Scheele; Ruth Knops; Louis T van de Locht; Aniek O de Graaf; Marion Massop; Sarah Sandmann; Martin Dugas; Marian J Stevens-Kroef; Jaroslav Cermak; Yuichi Shiraishi; Kenichi Chiba; Hiroko Tanaka; Satoru Miyano; Theo de Witte; Nicole M A Blijlevens; Petra Muus; Gerwin Huls; Bert A van der Reijden; Seishi Ogawa; Joop H Jansen
Journal:  Nat Commun       Date:  2017-04-21       Impact factor: 14.919

8.  The clonal evolution of metastatic colorectal cancer.

Authors:  Ha X Dang; Bradley A Krasnick; Brian S White; Julie G Grossman; Matthew S Strand; Jin Zhang; Christopher R Cabanski; Christopher A Miller; Robert S Fulton; S Peter Goedegebuure; Catrina C Fronick; Malachi Griffith; David E Larson; Brian D Goetz; Jason R Walker; William G Hawkins; Steven M Strasberg; David C Linehan; Kian H Lim; A Craig Lockhart; Elaine R Mardis; Richard K Wilson; Timothy J Ley; Christopher A Maher; Ryan C Fields
Journal:  Sci Adv       Date:  2020-06-10       Impact factor: 14.136

9.  Biallelic mutations in cancer genomes reveal local mutational determinants.

Authors:  Jonas Demeulemeester; Stefan C Dentro; Moritz Gerstung; Peter Van Loo
Journal:  Nat Genet       Date:  2022-02-10       Impact factor: 38.330

10.  SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution.

Authors:  Christopher A Miller; Brian S White; Nathan D Dees; Malachi Griffith; John S Welch; Obi L Griffith; Ravi Vij; Michael H Tomasson; Timothy A Graubert; Matthew J Walter; Matthew J Ellis; William Schierding; John F DiPersio; Timothy J Ley; Elaine R Mardis; Richard K Wilson; Li Ding
Journal:  PLoS Comput Biol       Date:  2014-08-07       Impact factor: 4.475
  10 in total

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