Reconstruction of clonal trees and tumor composition from multi-sample sequencing data

Clonality inference in multiple tumor samples using phylogeny

(2015) Salem Malikic et al.   BIOINFORMATICS

A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data

(2014) Iman Hajirasouliha et al.   BIOINFORMATICS

Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data

(2014) Layla Oesper et al.   BIOINFORMATICS

Inferring clonal evolution of tumors from single nucleotide somatic mutations

(2014) Wei Jiao et al.   BMC BIOINFORMATICS

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

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

(2014) Marco Gerlinger et al.   NATURE GENETICS

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing

(2014) J. Zhang et al.   SCIENCE

Inferring Clonal Composition from Multiple Sections of a Breast Cancer

(2014) Habil Zare et al.   PLoS Computational Biology

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

(2014) Christopher A. Miller et al.   PLoS Computational Biology

Genome evolution during progression to breast cancer

(2013) D. E. Newburger et al.   GENOME RESEARCH

TrAp: a tree approach for fingerprinting subclonal tumor composition

(2013) Francesco Strino et al.   NUCLEIC ACIDS RESEARCH

THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

(2013) Layla Oesper et al.   GENOME BIOLOGY

Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns

(2012) A. Schuh et al.   BLOOD

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

The clonal and mutational evolution spectrum of primary triple-negative breast cancers

(2012) Sohrab P. Shah et al.   NATURE

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

(2012) Li Ding et al.   NATURE

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE