The emerging clinical relevance of genomics in cancer medicine

Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing

(2017) Diana Mandelker et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Basket Trials in Oncology: A Trade-Off Between Complexity and Efficiency

(2017) Kristen M. Cunanan et al.   JOURNAL OF CLINICAL ONCOLOGY

AKT Inhibition in Solid Tumors With AKT1 Mutations

(2017) David M. Hyman et al.   JOURNAL OF CLINICAL ONCOLOGY

Guidelines for Validation of Next-Generation Sequencing–Based Oncology Panels

(2017) Lawrence J. Jennings et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Analytical Validation of the Next-Generation Sequencing Assay for a Nationwide Signal-Finding Clinical Trial

(2017) Chih-Jian Lih et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer

(2017) Ugur Sahin et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

(2017) Malachi Griffith et al.   NATURE GENETICS

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients

(2017) Ahmet Zehir et al.   NATURE MEDICINE

DNA sequencing technologies: 2006–2016

(2017) Elaine R Mardis   Nature Protocols

Olaparib for Metastatic Breast Cancer in Patients with a Germline BRCA Mutation

(2017) Mark Robson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade

(2017) Dung T. Le et al.   SCIENCE

Direct detection of early-stage cancers using circulating tumor DNA

(2017) Jillian Phallen et al.   Science Translational Medicine

Early Detection of Molecular Residual Disease in Localized Lung Cancer by Circulating Tumor DNA Profiling

(2017) Aadel A. Chaudhuri et al.   Cancer Discovery

AACR Project GENIE: Powering Precision Medicine through an International Consortium

(2017)   Cancer Discovery

Lost in translation: returning germline genetic results in genome-scale cancer research

(2017) Amber L. Johns et al.   Genome Medicine

Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis

(2017) Alexandra Snyder et al.   PLOS MEDICINE

Identification of Factors Affecting the Success of Next-Generation Sequencing Testing in Solid Tumors

(2016) Rashmi S. Goswami et al.   AMERICAN JOURNAL OF CLINICAL PATHOLOGY

Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V’DJer

(2016) Lisle E. Mose et al.   BIOINFORMATICS

Cancer Therapy Directed by Comprehensive Genomic Profiling: A Single Center Study

(2016) Jennifer J. Wheler et al.   CANCER RESEARCH

Oncologists’ and cancer patients’ views on whole-exome sequencing and incidental findings: results from the CanSeq study

(2016) Stacy W. Gray et al.   GENETICS IN MEDICINE

The BATTLE-2 Study: A Biomarker-Integrated Targeted Therapy Study in Previously Treated Patients With Advanced Non–Small-Cell Lung Cancer

(2016) Vassiliki Papadimitrakopoulou et al.   JOURNAL OF CLINICAL ONCOLOGY

Highly Accurate Sequencing of Full-Length Immune Repertoire Amplicons Using Tn5-Enabled and Molecular Identifier–Guided Amplicon Assembly

(2016) Charles Cole et al.   JOURNAL OF IMMUNOLOGY

Pan-Specific Prediction of Peptide–MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity

(2016) Michael Rasmussen et al.   JOURNAL OF IMMUNOLOGY

Precision Oncology: The UC San Diego Moores Cancer Center PREDICT Experience

(2016) M. Schwaederle et al.   MOLECULAR CANCER THERAPEUTICS

Integrated digital error suppression for improved detection of circulating tumor DNA

(2016) Aaron M Newman et al.   NATURE BIOTECHNOLOGY

Landscape of tumor-infiltrating T cell repertoire of human cancers

(2016) Bo Li et al.   NATURE GENETICS

Classification and characterization of microsatellite instability across 18 cancer types

(2016) Ronald J Hause et al.   NATURE MEDICINE

Facilitating a culture of responsible and effective sharing of cancer genome data

(2016) Lillian L Siu et al.   NATURE MEDICINE

Circulating tumor DNA analysis detects minimal residual disease and predicts recurrence in patients with stage II colon cancer

(2016) Jeanne Tie et al.   Science Translational Medicine

Panel's "Moonshot" Goals Released

(2016)   Cancer Discovery

Clinical Applications of Circulating Tumor Cells and Circulating Tumor DNA as Liquid Biopsy

(2016) C. Alix-Panabieres et al.   Cancer Discovery

The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine

(2016) Andrea Garofalo et al.   Genome Medicine

Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations

(2016) Jennifer A. Oberg et al.   Genome Medicine

Molecular profiling of advanced solid tumors and patient outcomes with genotype-matched clinical trials: the Princess Margaret IMPACT/COMPACT trial

(2016) Tracy L. Stockley et al.   Genome Medicine

pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens

(2016) Jasreet Hundal et al.   Genome Medicine

Germline Variants in Targeted Tumor Sequencing Using Matched Normal DNA

(2016) Kasmintan A. Schrader et al.   JAMA Oncology

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

ALCHEMIST Trials: A Golden Opportunity to Transform Outcomes in Early-Stage Non-Small Cell Lung Cancer

(2015) R. Govindan et al.   CLINICAL CANCER RESEARCH

Lung Master Protocol (Lung-MAP)--A Biomarker-Driven Protocol for Accelerating Development of Therapies for Squamous Cell Lung Cancer: SWOG S1400

(2015) R. S. Herbst et al.   CLINICAL CANCER RESEARCH

Pathogenic and likely pathogenic variant prevalence among the first 10,000 patients referred for next-generation cancer panel testing

(2015) Lisa R. Susswein et al.   GENETICS IN MEDICINE

The distribution ofBRAFgene fusions in solid tumors and response to targeted therapy

(2015) Jeffrey S. Ross et al.   INTERNATIONAL JOURNAL OF CANCER

Noninvasive Prenatal Testing and Incidental Detection of Occult Maternal Malignancies

(2015) Diana W. Bianchi et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Feasibility of Large-Scale Genomic Testing to Facilitate Enrollment Onto Genomically Matched Clinical Trials

(2015) Funda Meric-Bernstam et al.   JOURNAL OF CLINICAL ONCOLOGY

Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT)

(2015) Donavan T. Cheng et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Cancer Driver Log (CanDL)

(2015) Senthilkumar Damodaran et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

A Decision Support Framework for Genomically Informed Investigational Cancer Therapy

(2015) Funda Meric-Bernstam et al.   JNCI-Journal of the National Cancer Institute

Pilot Trial of Selecting Molecularly Guided Therapy for Patients with Non-V600 BRAF-Mutant Metastatic Melanoma: Experience of the SU2C/MRA Melanoma Dream Team

(2015) P. M. LoRusso et al.   MOLECULAR CANCER THERAPEUTICS

On the Road to Precision Cancer Medicine: Analysis of Genomic Biomarker Actionability in 439 Patients

(2015) M. Schwaederle et al.   MOLECULAR CANCER THERAPEUTICS

Identification of major factors associated with failed clinical molecular oncology testing performed by next generation sequencing (NGS)

(2015) Hussam Al-Kateb et al.   Molecular Oncology

Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Improved Overall Survival in Melanoma with Combined Dabrafenib and Trametinib

(2015) Caroline Robert et al.   NEW ENGLAND JOURNAL OF MEDICINE

AZD9291 in EGFR Inhibitor–Resistant Non–Small-Cell Lung Cancer

(2015) Pasi A. Jänne et al.   NEW ENGLAND JOURNAL OF MEDICINE

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

(2015) Dung T. Le et al.   NEW ENGLAND JOURNAL OF MEDICINE

Germline Mutations in Predisposition Genes in Pediatric Cancer

(2015) Jinghui Zhang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Vemurafenib in Multiple Nonmelanoma Cancers with BRAF V600 Mutations

(2015) David M. Hyman et al.   NEW ENGLAND JOURNAL OF MEDICINE

ClinVar: public archive of interpretations of clinically relevant variants

(2015) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma

(2015) E. M. Van Allen et al.   SCIENCE

A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells

(2015) B. M. Carreno et al.   SCIENCE

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

Personalized genomic analyses for cancer mutation discovery and interpretation

(2015) Siân Jones et al.   Science Translational Medicine

Response to MET Inhibitors in Patients with Stage IV Lung Adenocarcinomas Harboring MET Mutations Causing Exon 14 Skipping

(2015) P. K. Paik et al.   Cancer Discovery

Activation of MET via Diverse Exon 14 Splicing Alterations Occurs in Multiple Tumor Types and Confers Clinical Sensitivity to MET Inhibitors

(2015) G. M. Frampton et al.   Cancer Discovery

Next-generation sequencing to guide cancer therapy

(2015) Jeffrey Gagan et al.   Genome Medicine

A Decision Support Framework for Genomically Informed Investigational Cancer Therapy

(2015) Funda Meric-Bernstam et al.   JNCI-Journal of the National Cancer Institute

Optimizing Cancer Genome Sequencing and Analysis

(2015) Malachi Griffith et al.   Cell Systems

Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response

(2015) Himisha Beltran et al.   JAMA Oncology

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

Sequence Artifacts in DNA from Formalin-Fixed Tissues: Causes and Strategies for Minimization

(2014) H. Do et al.   CLINICAL CHEMISTRY

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

Convergent loss of PTEN leads to clinical resistance to a PI(3)Kα inhibitor

(2014) Dejan Juric et al.   NATURE

Age-related mutations associated with clonal hematopoietic expansion and malignancies

(2014) Mingchao Xie et al.   NATURE MEDICINE

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine

(2014) Eliezer M Van Allen et al.   NATURE MEDICINE

Detecting ultralow-frequency mutations by Duplex Sequencing

(2014) Scott R Kennedy et al.   Nature Protocols

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

(2014) Alexandra Snyder et al.   NEW ENGLAND JOURNAL OF MEDICINE

Crizotinib in ROS1-Rearranged Non–Small-Cell Lung Cancer

(2014) Alice T. Shaw et al.   NEW ENGLAND JOURNAL OF MEDICINE

Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence

(2014) Giulio Genovese et al.   NEW ENGLAND JOURNAL OF MEDICINE

Age-Related Clonal Hematopoiesis Associated with Adverse Outcomes

(2014) Siddhartha Jaiswal et al.   NEW ENGLAND JOURNAL OF MEDICINE

Combined Vemurafenib and Cobimetinib in BRAF-Mutated Melanoma

(2014) James Larkin et al.   NEW ENGLAND JOURNAL OF MEDICINE

Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies

(2014) C. Bettegowda et al.   Science Translational Medicine

The landscape of kinase fusions in cancer

(2014) Nicolas Stransky et al.   Nature Communications

Lessons from the Cancer Genome

(2013) Levi A. Garraway et al.   CELL

Immunosequencing: applications of immune repertoire deep sequencing

(2013) Harlan Robins   CURRENT OPINION IN IMMUNOLOGY

ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing

(2013) Robert C. Green et al.   GENETICS IN MEDICINE

Tumor Exome Analysis Reveals Neoantigen-Specific T-Cell Reactivity in an Ipilimumab-Responsive Melanoma

(2013) Nienke van Rooij et al.   JOURNAL OF CLINICAL ONCOLOGY

Clinical Validation of a Next-Generation Sequencing Screen for Mutational Hotspots in 46 Cancer-Related Genes

(2013) Rajesh R. Singh et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Validation of a Next-Generation Sequencing Assay for Clinical Molecular Oncology

(2013) Catherine E. Cottrell et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

(2013) Garrett M Frampton et al.   NATURE BIOTECHNOLOGY

ESR1 ligand-binding domain mutations in hormone-resistant breast cancer

(2013) Weiyi Toy et al.   NATURE GENETICS

Activating ESR1 mutations in hormone-resistant metastatic breast cancer

(2013) Dan R Robinson et al.   NATURE GENETICS

Acquired Resistance and Clonal Evolution in Melanoma during BRAF Inhibitor Therapy

(2013) H. Shi et al.   Cancer Discovery

The Genetic Landscape of Clinical Resistance to RAF Inhibition in Metastatic Melanoma

(2013) E. M. Van Allen et al.   Cancer Discovery

The Pediatric Cancer Genome Project

(2012) James R Downing et al.   NATURE GENETICS

Ponatinib in Refractory Philadelphia Chromosome–Positive Leukemias

(2012) Jorge E. Cortes et al.   NEW ENGLAND JOURNAL OF MEDICINE

Circumventing Cancer Drug Resistance in the Era of Personalized Medicine

(2012) Levi A. Garraway et al.   Cancer Discovery

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Derivation of HLA types from shotgun sequence datasets

(2012) René L Warren et al.   Genome Medicine

Dissecting Therapeutic Resistance to RAF Inhibition in Melanoma by Tumor Genomic Profiling

(2011) Nikhil Wagle et al.   JOURNAL OF CLINICAL ONCOLOGY

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation

(2011) Paul B. Chapman et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

Effects of KRAS, BRAF, NRAS, and PIK3CA mutations on the efficacy of cetuximab plus chemotherapy in chemotherapy-refractory metastatic colorectal cancer: a retrospective consortium analysis

(2010) Wendy De Roock et al.   LANCET ONCOLOGY

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

Nilotinib versus Imatinib for Newly Diagnosed Chronic Myeloid Leukemia

(2010) Giuseppe Saglio et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

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

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Gefitinib or Carboplatin–Paclitaxel in Pulmonary Adenocarcinoma

(2009) Tony S. Mok et al.   NEW ENGLAND JOURNAL OF MEDICINE

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts

(2009) Joshua Z Levin et al.   GENOME BIOLOGY

Epitope Landscape in Breast and Colorectal Cancer

(2008) N. H. Segal et al.   CANCER RESEARCH

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Circulating mutant DNA to assess tumor dynamics

(2008) Frank Diehl et al.   NATURE MEDICINE

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11

(2008) Claus Lundegaard et al.   NUCLEIC ACIDS RESEARCH

Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan

(2008) Morten Nielsen et al.   PLoS Computational Biology