Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells

AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data

(2014) Lei Bao et al.   BIOINFORMATICS

Functional Heterogeneity of Genetically Defined Subclones in Acute Myeloid Leukemia

(2014) Jeffery M. Klco et al.   CANCER CELL

Patient-Derived Xenografts from Non-Small Cell Lung Cancer Brain Metastases Are Valuable Translational Platforms for the Development of Personalized Targeted Therapy

(2014) H. W. Lee et al.   CLINICAL CANCER RESEARCH

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution

(2014) Peter Eirew et al.   NATURE

Novel somatic and germline mutations in intracranial germ cell tumours

(2014) Linghua Wang et al.   NATURE

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Tracking Genomic Cancer Evolution for Precision Medicine: The Lung TRACERx Study

(2014) Mariam Jamal-Hanjani et al.   PLOS BIOLOGY

Reliable Identification of Genomic Variants from RNA-Seq Data

(2013) Robert Piskol et al.   AMERICAN JOURNAL OF HUMAN GENETICS

High-Throughput Screening (HTS) of Anticancer Drug Efficacy on a Micropillar/Microwell Chip Platform

(2013) Dong Woo Lee et al.   ANALYTICAL CHEMISTRY

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

High intratumor genetic heterogeneity is related to worse outcome in patients with head and neck squamous cell carcinoma

(2013) Edmund A. Mroz et al.   CANCER

Basic Mechanisms of Therapeutic Resistance to Radiation and Chemotherapy in Lung Cancer

(2013) Henning Willers et al.   CANCER JOURNAL

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

(2013) Ali Bashashati et al.   JOURNAL OF PATHOLOGY

Molecular Testing Guideline for Selection of Lung Cancer Patients for EGFR and ALK Tyrosine Kinase Inhibitors: Guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology

(2013) Neal I. Lindeman et al.   Journal of Thoracic Oncology

The causes and consequences of genetic heterogeneity in cancer evolution

(2013) Rebecca A. Burrell et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer

(2013) Sarah-Jane Dawson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

Patient-Specific Orthotopic Glioblastoma Xenograft Models Recapitulate the Histopathology and Biology of Human Glioblastomas In Situ

(2013) Kyeung Min Joo et al.   Cell Reports

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers

(2013) Qingguo Wang et al.   Genome Medicine

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Clonal competition with alternating dominance in multiple myeloma

(2012) J. J. Keats et al.   BLOOD

Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor

(2012) Xun Xu et al.   CELL

Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm

(2012) Yong Hou et al.   CELL

Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing

(2012) Marcin Imielinski et al.   CELL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Selumetinib plus docetaxel for KRAS-mutant advanced non-small-cell lung cancer: a randomised, multicentre, placebo-controlled, phase 2 study

(2012) Pasi A Jänne et al.   LANCET ONCOLOGY

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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

Variable Clonal Repopulation Dynamics Influence Chemotherapy Response in Colorectal Cancer

(2012) A. Kreso et al.   SCIENCE

Impact of KRAS and EGFR Gene Mutations on Recurrence and Survival in Patients with Surgically Resected Lung Adenocarcinomas

(2011) Makoto Sonobe et al.   ANNALS OF SURGICAL ONCOLOGY

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV

(2011) Jarupon Fah Sathirapongsasuti et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

The International Epidemiology of Lung Cancer: Geographical Distribution and Secular Trends

(2010) Danny R. Youlden et al.   Journal of Thoracic Oncology

Genome remodelling in a basal-like breast cancer metastasis and xenograft

(2010) Li Ding et al.   NATURE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Inferring tumor progression from genomic heterogeneity

(2009) N. Navin et al.   GENOME RESEARCH

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer

(2009) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

MicroRNA Signature Predicts Survival and Relapse in Lung Cancer

(2008) Sung-Liang Yu et al.   CANCER CELL

Lung Cancer with Epidermal Growth Factor Receptor Exon 20 Mutations Is Associated with Poor Gefitinib Treatment Response

(2008) J.-Y. Wu et al.   CLINICAL CANCER RESEARCH

Prediction of Recurrence-Free Survival in Postoperative Non-Small Cell Lung Cancer Patients by Using an Integrated Model of Clinical Information and Gene Expression

(2008) E.-S. Lee et al.   CLINICAL CANCER RESEARCH

Clinical and biological implications of CD133-positive and CD133-negative cells in glioblastomas

(2008) Kyeung Min Joo et al.   LABORATORY INVESTIGATION

Somatic mutations affect key pathways in lung adenocarcinoma

(2008) Li Ding et al.   NATURE

Effective use of PI3K and MEK inhibitors to treat mutant Kras G12D and PIK3CA H1047R murine lung cancers

(2008) Jeffrey A Engelman et al.   NATURE MEDICINE