Clinical and Molecular Features of Acquired Resistance to Immunotherapy in Non-Small Cell Lung Cancer

Basic local alignment search tool.

S. F. Altschul, W. Gish, W. Miller, et al.. (1990). Journal of molecular biology. Cited 92,742 times. https://doi.org/10.1016/S0022-2836(05)80360-2

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger, M. Lohse, B. Usadel. (2014). Bioinformatics. Cited 54,202 times. https://doi.org/10.1093/bioinformatics/btu170

Fast gapped-read alignment with Bowtie 2

Ben Langmead, S. Salzberg. (2012). Nature Methods. Cited 48,549 times. https://doi.org/10.1038/nmeth.1923

limma powers differential expression analyses for RNA-sequencing and microarray studies

Matthew E. Ritchie, B. Phipson, Diabetes-Ling Wu, et al.. (2015). Nucleic Acids Research. Cited 32,121 times. https://doi.org/10.1093/nar/gkv007

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Guangchuang Yu, Li-Gen Wang, Yanyan Han, et al.. (2012). OMICS: A Journal of Integrative Biology. Cited 27,402 times. https://doi.org/10.1089/omi.2011.0118

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang, Tao Liu, Clifford A. Meyer, et al.. (2008). Genome Biology. Cited 16,186 times. https://doi.org/10.1186/gb-2008-9-9-r137

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin, Carrie A. Davis, Felix Schlesinger, et al.. (2013). Bioinformatics. Cited 14,340 times. https://doi.org/10.1093/bioinformatics/bts635

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

Sonja Hänzelmann, R. Castelo, J. Guinney. (2013). BMC Bioinformatics. Cited 11,195 times. https://doi.org/10.1186/1471-2105-14-7

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

M. DePristo, E. Banks, R. Poplin, et al.. (2011). Nature genetics. Cited 10,990 times. https://doi.org/10.1038/ng.806

Twelve years of SAMtools and BCFtools

P. Danecek, J. Bonfield, J. Liddle, et al.. (2020). GigaScience. Cited 10,325 times. https://doi.org/10.1093/gigascience/giab008

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

Pablo Cingolani, A. Platts, Le Lily Wang, et al.. (2012). Fly. Cited 9,823 times. https://doi.org/10.4161/fly.19695

Signatures of mutational processes in human cancer

Ludmil B. Alexandrov, S. Nik-Zainal, D. Wedge, et al.. (2013). Nature. Cited 8,903 times. https://doi.org/10.1038/nature12477

Pembrolizumab versus Chemotherapy for PD-L1-Positive Non-Small-Cell Lung Cancer.

M. Reck, D. Rodríguez-Abreu, A. Robinson, et al.. (2016). The New England journal of medicine. Cited 8,357 times. https://doi.org/10.1056/NEJMOA1606774

The mutational constraint spectrum quantified from variation in 141,456 humans

K. Karczewski, L. Francioli, G. Tiao, et al.. (2020). Nature. Cited 7,870 times. https://doi.org/10.1038/s41586-020-2308-7

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

N. Rizvi, M. Hellmann, A. Snyder, et al.. (2015). Science. Cited 6,463 times. https://doi.org/10.1126/science.aaa1348

Molecular signatures database (MSigDB) 3.0

A. Liberzon, A. Subramanian, Reid Pinchback, et al.. (2011). Bioinformatics. Cited 5,851 times. https://doi.org/10.1093/bioinformatics/btr260

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

Dung T Le, Dung T Le, Jennifer N Durham, et al.. (2017). Science. Cited 5,637 times. https://doi.org/10.1126/science.aan6733

Pembrolizumab plus Chemotherapy in Metastatic Non–Small‐Cell Lung Cancer

L. Gandhi, D. Rodríguez-Abreu, S. Gadgeel, et al.. (2018). The New England Journal of Medicine. Cited 5,192 times. https://doi.org/10.1056/NEJMoa1801005

Robust enumeration of cell subsets from tissue expression profiles

Aaron M. Newman, C. Liu, M. Green, et al.. (2015). Nature methods. Cited 4,788 times. https://doi.org/10.1038/nmeth.3337

Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial

J. Rosenberg, J. Hoffman-Censits, T. Powles, et al.. (2016). The Lancet. Cited 3,249 times. https://doi.org/10.1016/S0140-6736(16)00561-4

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

J. Zaretsky, A. García-Díaz, D. Shin, et al.. (2016). The New England journal of medicine. Cited 2,644 times. https://doi.org/10.1056/NEJMoa1604958

Oncogenic Signaling Pathways in The Cancer Genome Atlas.

F. Sánchez-Vega, Marco Mina, J. Armenia, et al.. (2018). Cell. Cited 2,501 times. https://doi.org/10.1016/j.cell.2018.03.035

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

Yang Liao, G. Smyth, Wei Shi. (2018). Nucleic Acids Research. Cited 2,327 times. https://doi.org/10.1101/377762

Radiation and Dual Checkpoint Blockade Activates Non-Redundant Immune Mechanisms in Cancer

Christina Twyman-Saint Victor, A. Rech, A. Maity, et al.. (2015). Nature. Cited 2,224 times. https://doi.org/10.1038/nature14292

Interferon-gamma: an overview of signals, mechanisms and functions.

K. Schroder, P. Hertzog, T. Ravasi, et al.. (2004). Journal of leukocyte biology. Cited 1,875 times.

The Immune Epitope Database (IEDB): 2018 update

R. Vita, Swapnil Mahajan, James A. Overton, et al.. (2018). Nucleic Acids Research. Cited 1,858 times. https://doi.org/10.1093/nar/gky1006

Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade

Brian C. Miller, Debattama R. Sen, Debattama R. Sen, et al.. (2019). Nature Immunology. Cited 1,588 times. https://doi.org/10.1038/s41590-019-0312-6

COSMIC: the Catalogue Of Somatic Mutations In Cancer

J. Tate, S. Bamford, Harry C Jubb, et al.. (2018). Nucleic Acids Research. Cited 1,576 times. https://doi.org/10.1093/nar/gky1015

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

Moshe Sade-Feldman, Keren Yizhak, Stacey L. Bjorgaard, et al.. (2018). Cell. Cited 1,573 times. https://doi.org/10.1016/j.cell.2018.10.038

Adaptive resistance to therapeutic PD-1 blockade is associated with upregulation of alternative immune checkpoints

S. Koyama, Esra A. Akbay, Yvonne Y. Li, et al.. (2016). Nature Communications. Cited 1,364 times. https://doi.org/10.1038/ncomms10501

Loss of PTEN Promotes Resistance to T Cell-Mediated Immunotherapy.

W. Peng, J. Chen, Chengwen Liu, et al.. (2016). Cancer discovery. Cited 1,287 times. https://doi.org/10.1158/2159-8290.CD-15-0283

Ensembl 2021

Kevin Howe, P. Achuthan, James E. Allen, et al.. (2020). Nucleic Acids Research. Cited 1,267 times. https://doi.org/10.1093/nar/gkaa942

STK11/LKB1 Mutations and PD-1 Inhibitor Resistance in KRAS-Mutant Lung Adenocarcinoma.

F. Skoulidis, M. Goldberg, D. Greenawalt, et al.. (2018). Cancer discovery. Cited 1,236 times. https://doi.org/10.1158/2159-8290.CD-18-0099

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

Jianjun Gao, L. Shi, Hao Zhao, et al.. (2016). Cell. Cited 1,142 times. https://doi.org/10.1016/j.cell.2016.08.069

Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution

N. Mcgranahan, R. Rosenthal, C. Hiley, et al.. (2017). Cell. Cited 1,092 times. https://doi.org/10.1016/j.cell.2017.10.001

Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

Joshua D. Campbell, A. Alexandrov, Jaegil Kim, et al.. (2016). Nature genetics. Cited 1,058 times. https://doi.org/10.1038/ng.3564

Tumor Interferon Signaling Regulates a Multigenic Resistance Program to Immune Checkpoint Blockade

Joseph L. Benci, Bihui Xu, Yu Qiu, et al.. (2016). Cell. Cited 967 times. https://doi.org/10.1016/j.cell.2016.11.022

FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

R. Shen, V. Seshan. (2016). Nucleic Acids Research. Cited 957 times. https://doi.org/10.1093/nar/gkw520

GENCODE 2021

A. Frankish, M. Diekhans, Irwin Jungreis, et al.. (2020). Nucleic Acids Research. Cited 933 times. https://doi.org/10.1093/nar/gkaa1087

PyClone: statistical inference of clonal population structure in cancer

Andrew Roth, J. Khattra, Damian Boon Siew Yap, et al.. (2014). Nature Methods. Cited 917 times. https://doi.org/10.1038/nmeth.2883

Cooperation of Tim-3 and PD-1 in CD8 T-cell exhaustion during chronic viral infection

H. Jin, A. Anderson, W. Tan, et al.. (2010). Proceedings of the National Academy of Sciences. Cited 867 times. https://doi.org/10.1073/pnas.1009731107

Universal Patterns of Selection in Cancer and Somatic Tissues

I. Martincorena, K. Raine, M. Gerstung, et al.. (2017). Cell. Cited 823 times. https://doi.org/10.1016/j.cell.2017.09.042

Resistance to checkpoint blockade therapy through inactivation of antigen presentation

Moshe Sade-Feldman, Yunxin J. Jiao, Jonathan H. Chen, et al.. (2017). Nature Communications. Cited 818 times. https://doi.org/10.1038/s41467-017-01062-w

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

C. Lundegaard, K. Lamberth, M. Harndahl, et al.. (2008). Nucleic Acids Research. Cited 807 times. https://doi.org/10.1093/nar/gkn202

Benchmark and integration of resources for the estimation of human transcription factor activities

Luz Garcia-Alonso, Mahmoud M. Ibrahim, D. Turei, et al.. (2018). Genome Research. Cited 779 times. https://doi.org/10.1101/gr.240663.118

Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer.

V. Anagnostou, Kellie N. Smith, P. Forde, et al.. (2017). Cancer discovery. Cited 741 times. https://doi.org/10.1158/2159-8290.CD-16-0828

Acquired Resistance to Immune Checkpoint Inhibitors.

A. Schoenfeld, M. Hellmann. (2020). Cancer cell. Cited 709 times. https://doi.org/10.1016/j.ccell.2020.03.017

Impaired HLA Class I Antigen Processing and Presentation as a Mechanism of Acquired Resistance to Immune Checkpoint Inhibitors in Lung Cancer.

S. Gettinger, Jungmin Choi, K. Hastings, et al.. (2017). Cancer discovery. Cited 611 times. https://doi.org/10.1158/2159-8290.CD-17-0593

Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures

Y. Şenbabaoğlu, Ron S. Gejman, A. Winer, et al.. (2016). Genome Biology. Cited 586 times. https://doi.org/10.1186/s13059-016-1092-z

A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy

M. Łuksza, N. Riaz, V. Makarov, et al.. (2017). Nature. Cited 573 times. https://doi.org/10.1038/nature24473

Nivolumab with or without ipilimumab treatment for metastatic sarcoma (Alliance A091401): two open-label, non-comparative, randomised, phase 2 trials.

S. D’Angelo, M. Mahoney, B. V. Van Tine, et al.. (2018). The Lancet. Oncology. Cited 564 times. https://doi.org/10.1016/S1470-2045(18)30006-8

Proliferating Transitory T Cells with an Effector-like Transcriptional Signature Emerge from PD-1+ Stem-like CD8+ T Cells during Chronic Infection.

W. Hudson, Julia Gensheimer, M. Hashimoto, et al.. (2019). Immunity. Cited 523 times. https://doi.org/10.1016/j.immuni.2019.11.002

Durvalumab With or Without Tremelimumab vs Standard Chemotherapy in First-line Treatment of Metastatic Non–Small Cell Lung Cancer

N. Rizvi, B. Cho, N. Reinmuth, et al.. (2020). JAMA Oncology. Cited 521 times. https://doi.org/10.1001/jamaoncol.2020.0237

Oncotator: Cancer Variant Annotation Tool

A. Ramos, Lee T Lichtenstein, Manaswi Gupta, et al.. (2015). Human Mutation. Cited 465 times. https://doi.org/10.1002/humu.22771

Neoantigen landscape dynamics during human melanoma–T cell interactions

E. Verdegaal, N. Miranda, Marten Visser, et al.. (2016). Nature. Cited 430 times. https://doi.org/10.1038/nature18945

Loss of PTEN Is Associated with Resistance to Anti‐PD‐1 Checkpoint Blockade Therapy in Metastatic Uterine Leiomyosarcoma

S. George, Diana Miao, G. Demetri, et al.. (2017). Immunity. Cited 423 times. https://doi.org/10.1016/j.immuni.2017.02.001

Opposing Functions of Interferon Coordinate Adaptive and Innate Immune Responses to Cancer Immune Checkpoint Blockade

Joseph L. Benci, Lexus Johnson, R. Choa, et al.. (2019). Cell. Cited 392 times. https://doi.org/10.1016/j.cell.2019.07.019

MATH, a novel measure of intratumor genetic heterogeneity, is high in poor-outcome classes of head and neck squamous cell carcinoma.

E. Mroz, J. Rocco. (2013). Oral oncology. Cited 340 times. https://doi.org/10.1016/j.oraloncology.2012.09.007

Tumor-infiltrating lymphocyte treatment for anti-PD-1-resistant metastatic lung cancer: a phase 1 trial

B. Creelan, chao wang, J. Teer, et al.. (2021). Nature Medicine. Cited 321 times. https://doi.org/10.1038/s41591-021-01462-y

Tumor Mutational Burden as a Predictor of Immunotherapy Response: Is More Always Better?

J. Strickler, B. Hanks, M. Khasraw. (2020). Clinical Cancer Research. Cited 298 times. https://doi.org/10.1158/1078-0432.CCR-20-3054

Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin. (2009). Bioinformatics. Cited 287 times. https://doi.org/10.1093/bioinformatics/btp324

TCR-engineered T cells targeting E7 for patients with metastatic HPV-associated epithelial cancers

N. Nagarsheth, S. Norberg, Andrew Sinkoe, et al.. (2021). Nature Medicine. Cited 262 times. https://doi.org/10.1038/s41591-020-01225-1

Conserved Interferon-γ Signaling Drives Clinical Response to Immune Checkpoint Blockade Therapy in Melanoma.

C. Grasso, C. Grasso, J. Tsoi, et al.. (2020). Cancer cell. Cited 243 times. https://doi.org/10.1016/j.ccell.2020.08.005

Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution

M. Efremova, D. Rieder, V. Klepsch, et al.. (2018). Nature Communications. Cited 243 times. https://doi.org/10.1038/s41467-017-02424-0

Lifileucel, a Tumor-Infiltrating Lymphocyte Therapy, in Metastatic Melanoma

A. Sarnaik, O. Hamid, N. Khushalani, et al.. (2021). Journal of Clinical Oncology. Cited 242 times. https://doi.org/10.1200/JCO.21.00612

PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

A. Deshwar, Shankar Vembu, C. Yung, et al.. (2015). Genome Biology. Cited 210 times. https://doi.org/10.1186/s13059-015-0602-8

APOBEC3B and APOBEC mutational signature as potential predictive markers for immunotherapy response in non-small cell lung cancer

Shixiang Wang, Mingming Jia, Zaoke He, et al.. (2018). Oncogene. Cited 209 times. https://doi.org/10.1038/s41388-018-0245-9

T-Cell Receptor Gene Therapy for Human Papillomavirus–Associated Epithelial Cancers: A First-in-Human, Phase I/II Study

S. Doran, S. Stevanović, S. Adhikary, et al.. (2019). Journal of Clinical Oncology. Cited 178 times. https://doi.org/10.1200/JCO.18.02424

Comparison of the molecular and cellular phenotypes of common mouse syngeneic models with human tumors

Wenyan Zhong, Jeremy S. Myers, F. Wang, et al.. (2020). BMC Genomics. Cited 136 times. https://doi.org/10.1186/s12864-019-6344-3

Unraveling tumor–immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy

A. Jiménez-Sánchez, P. Cybulska, K. Mager, et al.. (2020). Nature Genetics. Cited 133 times. https://doi.org/10.1038/s41588-020-0630-5

Clinical Features and Management of Acquired Resistance to PD‐1 Axis Inhibitors in 26 Patients With Advanced Non–Small Cell Lung Cancer

S. Gettinger, A. Wurtz, S. Goldberg, et al.. (2018). Journal of Thoracic Oncology. Cited 106 times. https://doi.org/10.1016/j.jtho.2018.03.008

Uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data

Kieran R. Campbell, C. Yau. (2018). Nature Communications. Cited 106 times. https://doi.org/10.1038/s41467-018-04696-6

Lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade.

J. Pai, M. Hellmann, J. Sauter, et al.. (2023). Cancer cell. Cited 99 times. https://doi.org/10.1016/j.ccell.2023.03.009

Uncoupling interferon signaling and antigen presentation to overcome immunotherapy resistance due to JAK1 loss in melanoma

A. Kalbasi, Mito Tariveranmoshabad, K. Hakimi, et al.. (2020). Science Translational Medicine. Cited 89 times. https://doi.org/10.1126/scitranslmed.abb0152

Clinical definition of acquired resistance to immunotherapy in patients with metastatic non-small cell lung cancer.

A. Schoenfeld, S. Antonia, M. Awad, et al.. (2021). Annals of oncology : official journal of the European Society for Medical Oncology. Cited 78 times. https://doi.org/10.1016/j.annonc.2021.08.2151

Improved prognosis and increased tumor infiltrating lymphocytes in small cell lung cancer patients with neurologic paraneoplastic syndromes.

W. Iams, E. Shiuan, C. Meador, et al.. (2019). Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer. Cited 51 times. https://doi.org/10.1016/j.jtho.2019.05.042

Melanoma Evolves Complete Immunotherapy Resistance through the Acquisition of a Hypermetabolic Phenotype

A. Jaiswal, Arthur J Liu, Shivanand Pudakalakatti, et al.. (2020). Cancer Immunology Research. Cited 49 times. https://doi.org/10.1158/2326-6066.CIR-19-0005

Checkpoint inhibitors in melanoma and early phase development in solid tumors: what’s the future?

P. Ascierto, G. McArthur. (2017). Journal of Translational Medicine. Cited 38 times. https://doi.org/10.1186/s12967-017-1278-5

Non-small cell to small cell lung cancer on PD-1 inhibitors: two cases on potential histologic transformation

Nadine H Abdallah, M. Nagasaka, E. Abdulfatah, et al.. (2018). Lung Cancer: Targets and Therapy. Cited 36 times. https://doi.org/10.2147/LCTT.S173724

Exceptional responders with invasive mucinous adenocarcinomas: a phase 2 trial of bortezomib in patients with KRAS G12D-mutant lung cancers

A. Drilon, A. Schoenfeld, K. Arbour, et al.. (2019). Cold Spring Harbor Molecular Case Studies. Cited 29 times. https://doi.org/10.1101/mcs.a003665