Implementing personalized cancer genomics in clinical trials

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data

(2013) Wenlong Jia et al.   GENOME BIOLOGY

Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues

(2012) Levi Waldron et al.   BMC CANCER

Intratumor Heterogeneity: Evolution through Space and Time

(2012) C. Swanton   CANCER RESEARCH

The Origin and Evolution of Mutations in Acute Myeloid Leukemia

(2012) John S. Welch et al.   CELL

Resistance to BRAF Inhibition in BRAF-Mutant Colon Cancer Can Be Overcome with PI3K Inhibition or Demethylating Agents

(2012) M. Mao et al.   CLINICAL CANCER RESEARCH

Making Personalized Cancer Medicine a Reality: Challenges and Opportunities in the Development of Biomarkers and Companion Diagnostics

(2012) D. R. Parkinson et al.   CLINICAL CANCER RESEARCH

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

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

ROS1 Rearrangements Define a Unique Molecular Class of Lung Cancers

(2012) Kristin Bergethon et al.   JOURNAL OF CLINICAL ONCOLOGY

Combining Highly Multiplexed PCR with Semiconductor-Based Sequencing for Rapid Cancer Genotyping

(2012) Carol Beadling et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

A Patient With BRAF V600E Lung Adenocarcinoma Responding to Vemurafenib

(2012) Oliver Gautschi et al.   Journal of Thoracic Oncology

Combinations of BRAF, MEK, and PI3K/mTOR Inhibitors Overcome Acquired Resistance to the BRAF Inhibitor GSK2118436 Dabrafenib, Mediated by NRAS or MEK Mutations

(2012) J. G. Greger et al.   MOLECULAR CANCER THERAPEUTICS

Unresponsiveness of colon cancer to BRAF(V600E) inhibition through feedback activation of EGFR

(2012) Anirudh Prahallad et al.   NATURE

Sequence analysis of mutations and translocations across breast cancer subtypes

(2012) Shantanu Banerji et al.   NATURE

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

(2012) Li Ding et al.   NATURE

Assuring the quality of next-generation sequencing in clinical laboratory practice

(2012) Amy S Gargis et al.   NATURE BIOTECHNOLOGY

Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies

(2012) Doron Lipson et al.   NATURE MEDICINE

BRAF Inhibition in Refractory Hairy-Cell Leukemia

(2012) Sascha Dietrich et al.   NEW ENGLAND JOURNAL OF MEDICINE

Combined BRAF and MEK Inhibition in Melanoma with BRAF V600 Mutations

(2012) Keith T. Flaherty et al.   NEW ENGLAND JOURNAL OF MEDICINE

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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

New dream team for melanoma therapy

(2012) Meenhard Herlyn   Pigment Cell & Melanoma Research

Paired Tumor and Normal Whole Genome Sequencing of Metastatic Olfactory Neuroblastoma

(2012) Glen J. Weiss et al.   PLoS One

Designs and challenges for personalized medicine studies in oncology: focus on the SHIVA trial

(2012) Christophe Le Tourneau et al.   Targeted Oncology

Cancer of the ampulla of Vater: analysis of the whole genome sequence exposes a potential therapeutic vulnerability

(2012) Michael J Demeure et al.   Genome Medicine

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

(2011) Jarupon Fah Sathirapongsasuti et al.   BIOINFORMATICS

Targeted high throughput sequencing in clinical cancer Settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity

(2011) Martin Kerick et al.   BMC Medical Genomics

“Stand up to cancer” focuses on accelerating promising research

(2011) Carrie Printz   CANCER

Reciprocal Feedback Regulation of PI3K and Androgen Receptor Signaling in PTEN-Deficient Prostate Cancer

(2011) Brett S. Carver et al.   CANCER CELL

Activating mutations of TOR (target of rapamycin)

(2011) Molly Hardt et al.   GENES TO CELLS

Androgen Receptor Rediscovered: The New Biology and Targeting the Androgen Receptor Therapeutically

(2011) Charles J. Ryan et al.   JOURNAL OF CLINICAL ONCOLOGY

A decade’s perspective on DNA sequencing technology

(2011) Elaine R. Mardis   NATURE

The ethical use of mandatory research biopsies

(2011) Erin M. Olson et al.   Nature Reviews Clinical Oncology

Role of randomized phase III trials in an era of effective targeted therapies

(2011) Manish R. Sharma et al.   Nature Reviews Clinical Oncology

Janus kinase inhibitors for the treatment of myeloproliferative neoplasias and beyond

(2011) Alfonso Quintás-Cardama et al.   NATURE REVIEWS DRUG DISCOVERY

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

(2011) Gregory M. Cooper et al.   NATURE REVIEWS GENETICS

High Throughput Interrogation of Somatic Mutations in High Grade Serous Cancer of the Ovary

(2011) Ursula A. Matulonis et al.   PLoS One

Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study

(2011) S. Roychowdhury et al.   Science Translational Medicine

High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by Targeted, Massively Parallel Sequencing

(2011) Nikhil Wagle et al.   Cancer Discovery

High Frequency of PIK3R1 and PIK3R2 Mutations in Endometrial Cancer Elucidates a Novel Mechanism for Regulation of PTEN Protein Stability

(2011) Lydia W.T. Cheung et al.   Cancer Discovery

Clinical trials for predictive medicine: new challenges and paradigms

(2010) Richard Simon   Clinical Trials

Rapid targeted mutational analysis of human tumours: a clinical platform to guide personalized cancer medicine

(2010) Dora Dias-Santagata et al.   EMBO Molecular Medicine

Big science: The cancer genome challenge

(2010) Heidi Ledford   NATURE

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

Anaplastic Lymphoma Kinase Inhibition in Non–Small-Cell Lung Cancer

(2010) Eunice L. Kwak et al.   NEW ENGLAND JOURNAL OF MEDICINE

CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge

(2010) Jessica Ahmed et al.   NUCLEIC ACIDS RESEARCH

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Single amino-acid changes that confer constitutive activation of mTOR are discovered in human cancer

(2010) T Sato et al.   ONCOGENE

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Cell cycle kinases as therapeutic targets for cancer

(2009) Silvia Lapenna et al.   NATURE REVIEWS DRUG DISCOVERY

Clinical trial designs for evaluating the medical utility of prognostic and predictive biomarkers in oncology

(2009) Richard Simon   Personalized Medicine

Profiling Critical Cancer Gene Mutations in Clinical Tumor Samples

(2009) Laura E. MacConaill et al.   PLoS One

PTEN and the PI3-Kinase Pathway in Cancer

(2008) Nader Chalhoub et al.   Annual Review of Pathology-Mechanisms of Disease

Targeting the MDM2-p53 Interaction for Cancer Therapy

(2008) S. Shangary et al.   CLINICAL CANCER RESEARCH

Oncogenic mutations of ALK kinase in neuroblastoma

(2008) Yuyan Chen et al.   NATURE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS