Literature DB >> 29927069

Using LICHeE and BAMSE for Reconstructing Cancer Phylogenetic Trees.

Camir Ricketts1,2, Victoria Popic3, Hosein Toosi4, Iman Hajirasouliha2,5.   

Abstract

The reconstruction of cancer phylogeny trees and quantifying the evolution of the disease is a challenging task. LICHeE and BAMSE are two computational tools designed and implemented recently for this purpose. They both utilize estimated variant allele fraction of somatic mutations across multiple samples to infer the most likely cancer phylogenies. This unit provides extensive guidelines for installing and running both LICHeE and BAMSE.
© 2018 by John Wiley & Sons, Inc. © 2018 John Wiley & Sons, Inc.

Entities:  

Keywords:  cancer phylogeny; deep sequencing; next-generation sequencing; somatic variations; tumor heterogeneity

Mesh：

Year:  2018        PMID： 29927069      PMCID： PMC6020047          DOI： 10.1002/cpbi.49

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  13 in total

1.  Evolution and impact of subclonal mutations in chronic lymphocytic leukemia.

Authors:  Dan A Landau; Scott L Carter; Petar Stojanov; Aaron McKenna; Kristen Stevenson; Michael S Lawrence; Carrie Sougnez; Chip Stewart; Andrey Sivachenko; Lili Wang; Youzhong Wan; Wandi Zhang; Sachet A Shukla; Alexander Vartanov; Stacey M Fernandes; Gordon Saksena; Kristian Cibulskis; Bethany Tesar; Stacey Gabriel; Nir Hacohen; Matthew Meyerson; Eric S Lander; Donna Neuberg; Jennifer R Brown; Gad Getz; Catherine J Wu
Journal:  Cell       Date:  2013-02-14       Impact factor: 41.582

2.  SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization.

Authors:  Yi Qiao; Aaron R Quinlan; Amir A Jazaeri; Roeland Gw Verhaak; David A Wheeler; Gabor T Marth
Journal:  Genome Biol       Date:  2014-08-26       Impact factor: 13.583

3.  Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing.

Authors:  Marco Gerlinger; Stuart Horswell; James Larkin; Andrew J Rowan; Max P Salm; Ignacio Varela; Rosalie Fisher; Nicholas McGranahan; Nicholas Matthews; Claudio R Santos; Pierre Martinez; Benjamin Phillimore; Sharmin Begum; Adam Rabinowitz; Bradley Spencer-Dene; Sakshi Gulati; Paul A Bates; Gordon Stamp; Lisa Pickering; Martin Gore; David L Nicol; Steven Hazell; P Andrew Futreal; Aengus Stewart; Charles Swanton
Journal:  Nat Genet       Date:  2014-02-02       Impact factor: 38.330

4.  Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing.

Authors:  Li Ding; Timothy J Ley; David E Larson; Christopher A Miller; Daniel C Koboldt; John S Welch; Julie K Ritchey; Margaret A Young; Tamara Lamprecht; Michael D McLellan; Joshua F McMichael; John W Wallis; Charles Lu; Dong Shen; Christopher C Harris; David J Dooling; Robert S Fulton; Lucinda L Fulton; Ken Chen; Heather Schmidt; Joelle Kalicki-Veizer; Vincent J Magrini; Lisa Cook; Sean D McGrath; Tammi L Vickery; Michael C Wendl; Sharon Heath; Mark A Watson; Daniel C Link; Michael H Tomasson; William D Shannon; Jacqueline E Payton; Shashikant Kulkarni; Peter Westervelt; Matthew J Walter; Timothy A Graubert; Elaine R Mardis; Richard K Wilson; John F DiPersio
Journal:  Nature       Date:  2012-01-11       Impact factor: 49.962

5.  Fast and scalable inference of multi-sample cancer lineages.

Authors:  Victoria Popic; Raheleh Salari; Iman Hajirasouliha; Dorna Kashef-Haghighi; Robert B West; Serafim Batzoglou
Journal:  Genome Biol       Date:  2015-05-06       Impact factor: 13.583

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.  Genomic heterogeneity of multiple synchronous lung cancer.

Authors:  Yu Liu; Jianjun Zhang; Lin Li; Guangliang Yin; Jianhua Zhang; Shan Zheng; Hannah Cheung; Ning Wu; Ning Lu; Xizeng Mao; Longhai Yang; Jiexin Zhang; Li Zhang; Sahil Seth; Huang Chen; Xingzhi Song; Kan Liu; Yongqiang Xie; Lina Zhou; Chuanduo Zhao; Naijun Han; Wenting Chen; Susu Zhang; Longyun Chen; Wenjun Cai; Lin Li; Miaozhong Shen; Ningzhi Xu; Shujun Cheng; Huanming Yang; J Jack Lee; Arlene Correa; Junya Fujimoto; Carmen Behrens; Chi-Wan Chow; William N William; John V Heymach; Waun Ki Hong; Stephen Swisher; Ignacio I Wistuba; Jun Wang; Dongmei Lin; Xiangyang Liu; P Andrew Futreal; Yanning Gao
Journal:  Nat Commun       Date:  2016-10-21       Impact factor: 14.919

8.  Multi-region and single-cell sequencing reveal variable genomic heterogeneity in rectal cancer.

Authors:  Mingshan Liu; Yang Liu; Jiabo Di; Zhe Su; Hong Yang; Beihai Jiang; Zaozao Wang; Meng Zhuang; Fan Bai; Xiangqian Su
Journal:  BMC Cancer       Date:  2017-11-23       Impact factor: 4.430

9.  Genome evolution during progression to breast cancer.

Authors:  Daniel E Newburger; Dorna Kashef-Haghighi; Ziming Weng; Raheleh Salari; Robert T Sweeney; Alayne L Brunner; Shirley X Zhu; Xiangqian Guo; Sushama Varma; Megan L Troxell; Robert B West; Serafim Batzoglou; Arend Sidow
Journal:  Genome Res       Date:  2013-04-08       Impact factor: 9.043

10.  Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling.

Authors:  Ali Bashashati; Gavin Ha; Alicia Tone; Jiarui Ding; Leah M Prentice; Andrew Roth; Jamie Rosner; Karey Shumansky; Steve Kalloger; Janine Senz; Winnie Yang; Melissa McConechy; Nataliya Melnyk; Michael Anglesio; Margaret T Y Luk; Kane Tse; Thomas Zeng; Richard Moore; Yongjun Zhao; Marco A Marra; Blake Gilks; Stephen Yip; David G Huntsman; Jessica N McAlpine; Sohrab P Shah
Journal:  J Pathol       Date:  2013-09       Impact factor: 7.996
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  2 in total

Review 1.  Computational Approaches for the Investigation of Intra-tumor Heterogeneity and Clonal Evolution from Bulk Sequencing Data in Precision Oncology Applications.

Authors:  Alessandro Laganà
Journal:  Adv Exp Med Biol       Date:  2022       Impact factor: 2.622

2.  Implantation metastasis from sigmoid colon cancer to rectal anastomosis proved by whole exome sequencing and lineage inference for cancer heterogeneity and evolution analysis: Case report and literature review.

Authors:  Guan Yu Yu; Xian Hua Gao; Li Jian Xia; De Bin Sun; Tao Liu; Wei Zhang
Journal:  Front Oncol       Date:  2022-09-20       Impact factor: 5.738
  2 in total

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