Transitioning single-cell genomics into the clinic

[1]  T. Voet,et al.  Methods and applications for single-cell and spatial multi-omics , 2023, Nature Reviews Genetics.

[2]  A. Regev,et al.  Impact of the Human Cell Atlas on medicine , 2022, Nature Medicine.

[3]  Xueda Hu,et al.  Single-cell meta-analyses reveal responses of tumor-reactive CXCL13+ T cells to immune-checkpoint blockade , 2022, Nature Cancer.

[4]  C. Lareau,et al.  Advancing T cell–based cancer therapy with single-cell technologies , 2022, Nature Medicine.

[5]  D. Torrents,et al.  Detection of early seeding of Richter transformation in chronic lymphocytic leukemia , 2022, Nature Medicine.

[6]  J. Park,et al.  Cross-tissue immune cell analysis reveals tissue-specific features in humans , 2022, Science.

[7]  C. V. van Asperen,et al.  Recommendations for reporting results of diagnostic genomic testing , 2022, European Journal of Human Genetics.

[8]  Jin Gu,et al.  Elucidating minimal residual disease of paediatric B-cell acute lymphoblastic leukaemia by single-cell analysis , 2022, Nature Cell Biology.

[9]  G. Eckstein,et al.  Human skin-resident host T cells can persist long term after allogeneic stem cell transplantation and maintain recirculation potential , 2022, Science Immunology.

[10]  D. Landau,et al.  Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation , 2022, bioRxiv.

[11]  H. Grimes,et al.  Why Single-Cell Sequencing Has Promise in MDS , 2021, Frontiers in Oncology.

[12]  M. Berger,et al.  Diverse alterations associated with resistance to KRAS(G12C) inhibition , 2021, Nature.

[13]  K. Döhner,et al.  2021 Update Measurable Residual Disease in Acute Myeloid Leukemia: European LeukemiaNet Working Party Consensus Document. , 2021, Blood.

[14]  C. Leslie,et al.  Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy. , 2021, Cancer cell.

[15]  Martin L. Miller,et al.  Promises and challenges of adoptive T-cell therapies for solid tumours , 2021, British Journal of Cancer.

[16]  Liu Yang,et al.  Hexokinase 2 discerns a novel circulating tumor cell population associated with poor prognosis in lung cancer patients , 2021, Proceedings of the National Academy of Sciences.

[17]  M. Fassan,et al.  The impact of recent next generation sequencing and the need for a new classification in gastric cancer. , 2021, Best practice & research. Clinical gastroenterology.

[18]  F. Solé,et al.  Analysis of Intratumoral Heterogeneity in Myelodysplastic Syndromes with Isolated del(5q) Using a Single Cell Approach , 2021, Cancers.

[19]  G. Coukos,et al.  T-cell repertoire analysis and metrics of diversity and clonality. , 2020, Current opinion in biotechnology.

[20]  H. Ueno,et al.  Shared and distinct roles of T peripheral helper and T follicular helper cells in human diseases , 2020, Cellular & Molecular Immunology.

[21]  J. Derisi,et al.  A pathogenic and clonally expanded B cell transcriptome in active multiple sclerosis , 2020, Proceedings of the National Academy of Sciences.

[22]  John T. Chang,et al.  Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses , 2020, Science Immunology.

[23]  Vladimir Yu Kiselev,et al.  Comparison of visualization tools for single-cell RNAseq data , 2020, NAR genomics and bioinformatics.

[24]  Quan Zou,et al.  Clustering and classification methods for single-cell RNA-sequencing data , 2020, Briefings Bioinform..

[25]  G. Tseng,et al.  Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn's Disease. , 2020, Gastroenterology.

[26]  Johannes G. Reiter,et al.  Single-cell mutational profiling enhances the clinical evaluation of AML MRD. , 2020, Blood advances.

[27]  P. A. Futreal,et al.  Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics , 2020, Nature Communications.

[28]  Timothy J. Peters,et al.  Lymphoma Driver Mutations in the Pathogenic Evolution of an Iconic Human Autoantibody , 2020, Cell.

[29]  J. Vives,et al.  Beyond chimerism analysis: methods for tracking a new generation of cell-based medicines , 2020, Bone Marrow Transplantation.

[30]  H. Kong,et al.  Targeted therapy guided by single-cell transcriptomic analysis in drug-induced hypersensitivity syndrome: a case report , 2020, Nature Medicine.

[31]  P. Klenerman,et al.  Peripheral CD8+ T cell characteristics associated with durable responses to immune checkpoint blockade in patients with metastatic melanoma , 2019, Nature Medicine.

[32]  T. Lassmann,et al.  Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows , 2019, Genome Biology.

[33]  R. Sandberg,et al.  Single-cell RNA counting at allele and isoform resolution using Smart-seq3 , 2019, Nature Biotechnology.

[34]  Matthew D. Young,et al.  Single-cell sequencing reveals clonal expansions of pro-inflammatory synovial CD8 T cells expressing tissue-homing receptors in psoriatic arthritis , 2019, Nature Communications.

[35]  Ricardo J. Miragaia,et al.  scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation , 2019, Genome Biology.

[36]  Hanlee P. Ji,et al.  scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data , 2019, Genome Biology.

[37]  Aviv Regev,et al.  A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors , 2019, Nature Medicine.

[38]  Christopher A. Miller,et al.  A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing , 2019, Nature Communications.

[39]  J. Zehnder,et al.  Clonal Evolution and Changes in Two AML Patients Detected with A Novel Single-Cell DNA Sequencing Platform , 2019, Scientific Reports.

[40]  S. De,et al.  Non-Genetic Intra-Tumor Heterogeneity Is a Major Predictor of Phenotypic Heterogeneity and Ongoing Evolutionary Dynamics in Lung Tumors , 2019, bioRxiv.

[41]  Kieran R. Campbell,et al.  Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses , 2019, bioRxiv.

[42]  N. Stoecklein,et al.  Circulating biomarkers for early detection and clinical management of colorectal cancer. , 2019, Molecular aspects of medicine.

[43]  Paul J. Hoover,et al.  The immune cell landscape in kidneys of patients with lupus nephritis , 2019, Nature Immunology.

[44]  Leonard D. Goldstein,et al.  Massively parallel single-cell B-cell receptor sequencing enables rapid discovery of diverse antigen-reactive antibodies , 2019, Communications Biology.

[45]  Helen M. Moore,et al.  Deleterious effects of formalin-fixation and delays to fixation on RNA and miRNA-Seq profiles , 2019, Scientific Reports.

[46]  Kamil Slowikowski,et al.  Tubular Cell and Keratinocyte Single-cell Transcriptomics Applied to Lupus Nephritis Reveal Type I IFN and Fibrosis Relevant Pathways , 2019, Nature Immunology.

[47]  G. Pinkus,et al.  Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity , 2019, Cell.

[48]  R. Schlenk,et al.  Targeting FLT3 mutations in AML: review of current knowledge and evidence , 2019, Leukemia.

[49]  M. Hemberg,et al.  Challenges in unsupervised clustering of single-cell RNA-seq data , 2019, Nature Reviews Genetics.

[50]  A. Abyzov,et al.  Molecular signatures of multiple myeloma progression through single cell RNA-Seq , 2019, Blood Cancer Journal.

[51]  W. J. Valente,et al.  Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA , 2018, Nature Communications.

[52]  P. A. Futreal,et al.  High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics , 2018, Genome research.

[53]  Boris M. Hartmann,et al.  High-density single cell mRNA sequencing to characterize circulating tumor cells in hepatocellular carcinoma , 2018, Scientific Reports.

[54]  Ambrose J. Carr,et al.  Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment , 2018, Cell.

[55]  K. Metzeler,et al.  Gene mutations and clonal architecture in myelodysplastic syndromes and changes upon progression to acute myeloid leukaemia and under treatment , 2018, British journal of haematology.

[56]  Olaf Wolkenhauer,et al.  Diagnostic Potential of Imaging Flow Cytometry. , 2018, Trends in biotechnology.

[57]  Waseem Asghar,et al.  Circulating tumor cell isolation, culture, and downstream molecular analysis. , 2018, Biotechnology advances.

[58]  Hien Dang,et al.  Single‐cell analysis reveals cancer stem cell heterogeneity in hepatocellular carcinoma , 2018, Hepatology.

[59]  Boxi Kang,et al.  Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing , 2018, Nature Medicine.

[60]  N. Hacohen,et al.  Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry , 2018, bioRxiv.

[61]  J. Reeves,et al.  Clinical activity and molecular correlates of response to atezolizumab alone or in combination with bevacizumab versus sunitinib in renal cell carcinoma , 2018, Nature Medicine.

[62]  Johan Hartman,et al.  Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing , 2018, Cell.

[63]  A. Ferrando,et al.  The subclonal complexity of STIL-TAL1+ T-cell acute lymphoblastic leukaemia , 2018, Leukemia.

[64]  Ruibin Xi,et al.  Diverse modes of clonal evolution in HBV-related hepatocellular carcinoma revealed by single-cell genome sequencing , 2018, Cell Research.

[65]  J. Gartner,et al.  An Efficient Single-Cell RNA-Seq Approach to Identify Neoantigen-Specific T Cell Receptors. , 2018, Molecular therapy : the journal of the American Society of Gene Therapy.

[66]  Xin Zhao,et al.  Single-cell RNA-seq reveals a distinct transcriptome signature of aneuploid hematopoietic cells. , 2017, Blood.

[67]  Leonard D. Goldstein,et al.  Massively parallel nanowell-based single-cell gene expression profiling , 2017, BMC Genomics.

[68]  S. Mustjoki,et al.  Somatic mutations in clonally expanded cytotoxic T lymphocytes in patients with newly diagnosed rheumatoid arthritis , 2017, Nature Communications.

[69]  James A. Eddy,et al.  Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4+ T Cells in Peripheral Blood of Subjects with Type 1 Diabetes , 2017, The Journal of Immunology.

[70]  R. Sandberg,et al.  Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia , 2017, Nature Medicine.

[71]  U. Olsson‐Strömberg,et al.  Single-cell molecular analysis defines therapy response and immunophenotype of stem cell subpopulations in CML. , 2017, Blood.

[72]  L. Penland,et al.  High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis , 2017, bioRxiv.

[73]  I. Amit,et al.  Single-cell transcriptome conservation in cryopreserved cells and tissues , 2016, Genome Biology.

[74]  Kamil Slowikowski,et al.  Pathologically expanded peripheral T helper cell subset drives B cells in rheumatoid arthritis , 2017, Nature.

[75]  James E. Verdone,et al.  Circulating tumour cells as biomarkers of prostate, bladder, and kidney cancer , 2017, Nature Reviews Urology.

[76]  J. González,et al.  Detectable clonal mosaicism in blood as a biomarker of cancer risk in Fanconi anemia. , 2017, Blood Advances.

[77]  Grace X. Y. Zheng,et al.  Massively parallel digital transcriptional profiling of single cells , 2016, Nature Communications.

[78]  O. Elemento,et al.  Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq , 2016, Genome Medicine.

[79]  Tomas W. Fitzgerald,et al.  Detection of structural mosaicism from targeted and whole-genome sequencing data , 2016, bioRxiv.

[80]  D. Cunningham,et al.  Patients’ willingness to participate in clinical trials and their views on aspects of cancer research: results of a prospective patient survey , 2016, Trials.

[81]  J. Lundeberg,et al.  Single cell analysis of cancer cells using an improved RT-MLPA method has potential for cancer diagnosis and monitoring , 2015, Scientific Reports.

[82]  Rona S. Gertner,et al.  Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity , 2015, Cell.

[83]  T. Stahl,et al.  Digital PCR to assess hematopoietic chimerism after allogeneic stem cell transplantation. , 2015, Experimental hematology.

[84]  E. Bonifacio,et al.  High Diversity in the TCR Repertoire of GAD65 Autoantigen-Specific Human CD4+ T Cells , 2015, The Journal of Immunology.

[85]  S. P. Fodor,et al.  Combinatorial labeling of single cells for gene expression cytometry , 2015, Science.

[86]  Ben S. Wittner,et al.  Single-Cell RNA Sequencing Identifies Extracellular Matrix Gene Expression by Pancreatic Circulating Tumor Cells , 2014, Cell reports.

[87]  J. Kendall,et al.  Rapid Phenotypic and Genomic Change in Response to Therapeutic Pressure in Prostate Cancer Inferred by High Content Analysis of Single Circulating Tumor Cells , 2014, PloS one.

[88]  E. Shapiro,et al.  Single cell analysis exposes intratumor heterogeneity and suggests that FLT3-ITD is a late event in leukemogenesis. , 2014, Experimental hematology.

[89]  Shawn M. Gillespie,et al.  Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma , 2014, Science.

[90]  Timothy B Lannin,et al.  Detection of circulating pancreas epithelial cells in patients with pancreatic cystic lesions. , 2014, Gastroenterology.

[91]  Daniel-Christoph Wagner,et al.  Density Gradient Centrifugation Compromises Bone Marrow Mononuclear Cell Yield , 2012, PloS one.

[92]  Rafael López-López,et al.  Molecular Characterization of Circulating Tumor Cells in Human Metastatic Colorectal Cancer , 2012, PloS one.

[93]  J. Troge,et al.  Tumour evolution inferred by single-cell sequencing , 2011, Nature.

[94]  Catalin C. Barbacioru,et al.  mRNA-Seq whole-transcriptome analysis of a single cell , 2009, Nature Methods.

[95]  G. Nossal.  One cell–one antibody: prelude and aftermath , 2007, Nature Immunology.