Cold and heterogeneous T cell repertoire is associated with copy number aberrations and loss of immune genes in small-cell lung cancer

Multifactorial deep learning reveals pan-cancer genomic tumor clusters with distinct immunogenomic landscape and response to immunotherapy

(2020) Feng Xie et al.   CLINICAL CANCER RESEARCH

Comprehensive T cell repertoire characterization of non-small cell lung cancer

(2020) Alexandre Reuben et al.   Nature Communications

PyClone-VI: scalable inference of clonal population structures using whole genome data

(2020) Sierra Gillis et al.   BMC BIOINFORMATICS

Neoantigen-directed immune escape in lung cancer evolution

(2019) Rachel Rosenthal et al.   NATURE

Cooperation between Constitutive and Inducible Chemokines Enables T Cell Engraftment and Immune Attack in Solid Tumors

(2019) Denarda Dangaj et al.   CANCER CELL

Reduced CTL motility and activity in avascular tumor areas

(2019) Yoav Manaster et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Combination of TMB and CNA stratifies prognostic and predictive responses to immunotherapy across metastatic cancer

(2019) Li Liu et al.   CLINICAL CANCER RESEARCH

Durvalumab plus platinum–etoposide versus platinum–etoposide in first-line treatment of extensive-stage small-cell lung cancer (CASPIAN): a randomised, controlled, open-label, phase 3 trial

(2019) Luis Paz-Ares et al.   LANCET

Tumor Mutational Burden and Efficacy of Nivolumab Monotherapy and in Combination with Ipilimumab in Small-Cell Lung Cancer

(2018) Matthew D. Hellmann et al.   CANCER CELL

Multiregion gene expression profiling reveals heterogeneity in molecular subtypes and immunotherapy response signatures in lung cancer

(2018) Won-Chul Lee et al.   MODERN PATHOLOGY

Multi-omics analysis reveals neoantigen-independent immune cell infiltration in copy-number driven cancers

(2018) Daniel J. McGrail et al.   Nature Communications

Abstract 213: Exome sequencing of paired primary and relapsed small cell lung cancers reveals increased copy number aberration complexity to be associated with disease relapse

(2018) Marcelo V. Negrao et al.   CANCER RESEARCH

The role of immune microenvironment in small-cell lung cancer: Distribution of PD-L1 expression and prognostic role of FOXP3-positive tumour infiltrating lymphocytes

(2018) L. Bonanno et al.   EUROPEAN JOURNAL OF CANCER

First-Line Atezolizumab plus Chemotherapy in Extensive-Stage Small-Cell Lung Cancer

(2018) Leora Horn et al.   NEW ENGLAND JOURNAL OF MEDICINE

Circulating tumor DNA analysis depicts subclonal architecture and genomic evolution of small cell lung cancer

(2018) Jingying Nong et al.   Nature Communications

Recurrent WNT pathway alterations are frequent in relapsed small cell lung cancer

(2018) Alex H. Wagner et al.   Nature Communications

Prospects of targeted and immune therapies in SCLC

(2018) Lizza E. L. Hendriks et al.   Expert Review of Anticancer Therapy

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

Tracking the Evolution of Non–Small-Cell Lung Cancer

(2017) Mariam Jamal-Hanjani et al.   NEW ENGLAND JOURNAL OF MEDICINE

Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy

(2017) Teresa Davoli et al.   SCIENCE

TCR Repertoire Intratumor Heterogeneity in Localized Lung Adenocarcinomas: An Association with Predicted Neoantigen Heterogeneity and Postsurgical Recurrence

(2017) Alexandre Reuben et al.   Cancer Discovery

DNA methylation intratumor heterogeneity in localized lung adenocarcinomas

(2017) Kelly Quek et al.   Oncotarget

Small Cell Lung Cancer

(2017) Gregory P. Kalemkerian et al.   Journal of the National Comprehensive Cancer Network

Loss of IFN-γ Pathway Genes in Tumor Cells as a Mechanism of Resistance to Anti-CTLA-4 Therapy

(2016) Jianjun Gao et al.   CELL

T-Cell Transfer Therapy Targeting Mutant KRAS in Cancer

(2016) Eric Tran et al.   NEW ENGLAND JOURNAL OF MEDICINE

Mutations Associated with Acquired Resistance to PD-1 Blockade in Melanoma

(2016) Jesse M. Zaretsky et al.   NEW ENGLAND JOURNAL OF MEDICINE

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

(2016) N. McGranahan et al.   SCIENCE

Targeting of cancer neoantigens with donor-derived T cell receptor repertoires

(2016) E. Stronen et al.   SCIENCE

Loss of heterozygosity: what is it good for?

(2015) Georgina L. Ryland et al.   BMC Medical Genomics

Comprehensive genomic profiles of small cell lung cancer

(2015) Julie George et al.   NATURE

Neoantigens in cancer immunotherapy

(2015) T. N. Schumacher et al.   SCIENCE

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

(2014) F. Favero et al.   ANNALS OF ONCOLOGY

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

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

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Whole chromosome instability resulting from the synergistic effects of pRB and p53 inactivation

(2013) A L Manning et al.   ONCOGENE

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

(2013) Kosuke Yoshihara et al.   Nature Communications

Using synthetic templates to design an unbiased multiplex PCR assay

(2013) Christopher S. Carlson et al.   Nature Communications

Deciphering Signatures of Mutational Processes Operative in Human Cancer

(2013) Ludmil B. Alexandrov et al.   Cell Reports

Marginating Dendritic Cells of the Tumor Microenvironment Cross-Present Tumor Antigens and Stably Engage Tumor-Specific T Cells

(2012) John J. Engelhardt et al.   CANCER CELL

Matrix architecture defines the preferential localization and migration of T cells into the stroma of human lung tumors

(2012) Hélène Salmon et al.   JOURNAL OF CLINICAL INVESTIGATION

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

Bringing the genomic landscape of small-cell lung cancer into focus

(2012) M Catherine Pietanza et al.   NATURE GENETICS

Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer

(2012) Charles M Rudin et al.   NATURE GENETICS

Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer

(2012) Martin Peifer et al.   NATURE GENETICS

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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

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

(2011) Jarupon Fah Sathirapongsasuti et al.   BIOINFORMATICS

Ultra-sensitive detection of rare T cell clones

(2011) Harlan Robins et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Small-cell lung cancer

(2011) Jan P van Meerbeeck et al.   LANCET

Comprehensive assessment of T-cell receptor  -chain diversity in    T cells

(2009) H. S. Robins et al.   BLOOD

Fitness and its role in evolutionary genetics

(2009) H. Allen Orr   NATURE REVIEWS GENETICS

Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers

(2008) C. Lundegaard et al.   BIOINFORMATICS

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