Application of NGS Technology in Understanding the Pathology of Autoimmune Diseases

Commensal microbiota regulates skin barrier function and repair via signaling through the aryl hydrocarbon receptor

(2021) Aayushi Uberoi et al.   Cell Host & Microbe

Influence of immunomodulatory drugs on the gut microbiota

(2021) Inessa Cohen et al.   Translational Research

Global miRNA and mRNA expression profiles identify miRNA‐26a‐2‐3p‐dependent repression of IFN signature in systemic sclerosis human monocytes

(2020) Marzena Ciechomska et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

European Society for Immunodeficiencies (ESID) and European Reference Network on Rare Primary Immunodeficiency, Autoinflammatory and Autoimmune Diseases (ERN RITA) Complement Guideline: Deficiencies, Diagnosis, and Management

(2020) Nicholas Brodszki et al.   JOURNAL OF CLINICAL IMMUNOLOGY

A high-resolution HLA imputation system for the Taiwanese population: a study of the Taiwan Biobank

(2020) Yu-Han Huang et al.   PHARMACOGENOMICS JOURNAL

The Serum Cell-Free microRNA Expression Profile in MCTD, SLE, SSc, and RA Patients

(2020) Barbara Stypinska et al.   Journal of Clinical Medicine

Genetic heterogeneity of pediatric systemic lupus erythematosus with lymphoproliferation

(2020) Guomin Li et al.   MEDICINE

In Human Autoimmunity, a Substantial Component of the B Cell Repertoire Consists of Polyclonal, Barely Mutated IgG+ve B Cells

(2020) Graeme J. M. Cowan et al.   Frontiers in Immunology

Clinical utility of next generation sequencing based HLA typing for disease association and pharmacogenetic testing

(2020) Tracie Profaizer et al.   HUMAN IMMUNOLOGY

Upregulation of miR-941 in Circulating CD14+ Monocytes Enhances Osteoclast Activation via WNT16 Inhibition in Patients with Psoriatic Arthritis

(2020) Shang-Hung Lin et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Discovery of a Novel Multi-Strains Probiotic Formulation with Improved Efficacy toward Intestinal Inflammation

(2020) Michele Biagioli et al.   Nutrients

Microbiome definition re-visited: old concepts and new challenges

(2020) Gabriele Berg et al.   Microbiome

Epigenetic Regulations of AhR in the Aspect of Immunomodulation

(2020) Anna Wajda et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Activation of aryl hydrocarbon receptor in Langerhans cells by a microbial metabolite of tryptophan negatively regulates skin inflammation

(2020) Xiaochun Liu et al.   JOURNAL OF DERMATOLOGICAL SCIENCE

Serum a proliferation-inducing ligand and MicroRNA-223 are associated with rheumatoid arthritis: diagnostic and prognostic implications

(2020) Mohamed Taha et al.   MOLECULAR MEDICINE

Differential mitochondrial genome in patients with Rheumatoid Arthritis

(2020) Kumar Sagar Jaiswal et al.   AUTOIMMUNITY

Novel Pathogenic Variants of the AIRE Gene in Two Autoimmune Polyendocrine Syndrome Type I Cases with Atypical Presentation: Role of the NGS in Diagnostic Pathway and Review of the Literature

(2020) Luigia Cinque et al.   Biomedicines

Assessing the utilization of high-resolution two-field HLA typing in solid organ transplantation

(2019) Yanping Huang et al.   AMERICAN JOURNAL OF TRANSPLANTATION

An estimate of the total number of true human miRNAs

(2019) Julia Alles et al.   NUCLEIC ACIDS RESEARCH

Genetic and phenotypic landscape of the major histocompatibilty complex region in the Japanese population

(2019) Jun Hirata et al.   NATURE GENETICS

Whole-genome sequencing identifies complex contributions to genetic risk by variants in genes causing monogenic systemic lupus erythematosus

(2019) Jonas Carlsson Almlöf et al.   HUMAN GENETICS

MicroRNA expression studies: challenge of selecting reliable reference controls for data normalization

(2019) Soheil Madadi et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Correlation of microRNA expression profile with clinical response to tumor necrosis factor inhibitor in treating rheumatoid arthritis patients: A prospective cohort study

(2019) Yaqiong Liu et al.   JOURNAL OF CLINICAL LABORATORY ANALYSIS

TARgeting the cutaneous microbiota in atopic dermatitis by coal tar via AHR-dependent induction of antimicrobial peptides.

(2019) Jos P.H. Smits et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

The immune cell landscape in kidneys of patients with lupus nephritis

(2019) Arnon Arazi et al.   NATURE IMMUNOLOGY

Circulating microRNA-23b as a new biomarker for rheumatoid arthritis

(2019) Xi Liu et al.   GENE

Hsa_circ_0000479 as a Novel Diagnostic Biomarker of Systemic Lupus Erythematosus

(2019) Gangqiang Guo et al.   Frontiers in Immunology

The role of AhR in transcriptional regulation of immune cell development and function

(2019) Prashant Trikha et al.   BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER

Circulating serum miR-223-3p and miR-16-5p as possible biomarkers of early rheumatoid arthritis

(2018) Marina Dunaeva et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

Regulation of the Immune Response by the Aryl Hydrocarbon Receptor

(2018) Cristina Gutiérrez-Vázquez et al.   IMMUNITY

HLA-DRB1 Shared Epitope Alleles and Disease Activity Are Correlated with Reduced T Cell Receptor Repertoire Diversity in CD4+ T Cells in Rheumatoid Arthritis

(2018) Keiichi Sakurai et al.   JOURNAL OF RHEUMATOLOGY

Whole Exome Sequencing in Early-onset Systemic Lupus Erythematosus

(2018) Ezgi Deniz Batu et al.   JOURNAL OF RHEUMATOLOGY

Whole‑genome sequencing of a monozygotic twin discordant for systemic lupus erythematosus

(2018) Fei Chen et al.   Molecular Medicine Reports

Next generation sequencing identifies miRNA-based biomarker panel for lupus nephritis

(2018) Yu-Jih Su et al.   Oncotarget

Whole Exome Sequencing of Patients from Multicase Families with Systemic Lupus Erythematosus Identifies Multiple Rare Variants

(2018) Angélica M. Delgado-Vega et al.   Scientific Reports

MicroRNA-132, miR-146a, and miR-155 as potential biomarkers of methotrexate response in patients with rheumatoid arthritis

(2018) Ankita Singh et al.   CLINICAL RHEUMATOLOGY

A tryptophan metabolite of the skin microbiota attenuates inflammation in patients with atopic dermatitis through the aryl hydrocarbon receptor

(2018) Jinlei Yu et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Deep intronic mutations and human disease

(2017) Rita Vaz-Drago et al.   HUMAN GENETICS

MicroRNA-146a governs fibroblast activation and joint pathology in arthritis

(2017) Victoria Saferding et al.   JOURNAL OF AUTOIMMUNITY

miR-146b Probably Assists miRNA-146a in the Suppression of Keratinocyte Proliferation and Inflammatory Responses in Psoriasis

(2017) Helen Hermann et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Performing Skin Microbiome Research: A Method to the Madness

(2017) Heidi H. Kong et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Antigen-specific regulatory T-cell responses to intestinal microbiota

(2017) E V Russler-Germain et al.   Mucosal Immunology

Mutational profile of rare variants in inflammasome-related genes in Behçet disease: A Next Generation Sequencing approach

(2017) Sergio Burillo-Sanz et al.   Scientific Reports

Discovery of T Cell Receptor β Motifs Specific to HLA-B27-Positive Ankylosing Spondylitis by Deep Repertoire Sequence Analysis

(2017) Malek Faham et al.   Arthritis & Rheumatology

MicroRNA expression profiles identify disease-specific alterations in systemic lupus erythematosus and primary Sjögren's syndrome

(2017) Ji-Qing Chen et al.   PLoS One

Clinical impact of a targeted next-generation sequencing gene panel for autoinflammation and vasculitis

(2017) Ebun Omoyinmi et al.   PLoS One

Prediction and Prevention of Autoimmune Disease in the 21st Century: A Review and Preview

(2016) Noel R. Rose   AMERICAN JOURNAL OF EPIDEMIOLOGY

Aryl hydrocarbon receptor is required for optimal B‐cell proliferation

(2016) Matteo Villa et al.   EMBO JOURNAL

Cross-Disease Transcriptomics: Unique IL-17A Signaling in Psoriasis Lesions and an Autoimmune PBMC Signature

(2016) William R. Swindell et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

AHR Function in Lymphocytes: Emerging Concepts

(2016) Liang Zhou   TRENDS IN IMMUNOLOGY

Epidemiology of Mixed Connective Tissue Disease, 1985-2014: A Population-Based Study

(2016) Patompong Ungprasert et al.   ARTHRITIS CARE & RESEARCH

AHR Activation Is Protective against Colitis Driven by T Cells in Humanized Mice

(2016) Jeremy A. Goettel et al.   Cell Reports

Brief Report: First Identification of Intrafamilial Recurrence of Blau Syndrome due to GonosomalNOD2Mosaicism

(2016) Anna Mensa-Vilaro et al.   Arthritis & Rheumatology

HLA genotyping in the clinical laboratory: comparison of next-generation sequencing methods

(2016) T. Profaizer et al.   HLA

Next-generation sequencing and its initial applications for molecular diagnosis of systemic auto-inflammatory diseases

(2015) Marta Rusmini et al.   ANNALS OF THE RHEUMATIC DISEASES

Laser capture microdissection followed by next-generation sequencing identifies disease-related microRNAs in psoriatic skin that reflect systemic microRNA changes in psoriasis

(2015) Marianne B. Løvendorf et al.   EXPERIMENTAL DERMATOLOGY

Detecting copy-number variations in whole-exome sequencing data using the eXome Hidden Markov Model: an ‘exome-first’ approach

(2015) Satoko Miyatake et al.   JOURNAL OF HUMAN GENETICS

Additive and interaction effects at three amino acid positions in HLA-DQ and HLA-DR molecules drive type 1 diabetes risk

(2015) Xinli Hu et al.   NATURE GENETICS

Longitudinal analysis of peripheral blood T cell receptor diversity in patients with systemic lupus erythematosus by next-generation sequencing

(2015) Dharma R Thapa et al.   ARTHRITIS RESEARCH & THERAPY

Circulating miRNAs as potential biomarkers of therapy effectiveness in rheumatoid arthritis patients treated with anti-TNFα

(2015) Carmen Castro-Villegas et al.   ARTHRITIS RESEARCH & THERAPY

Challenges in Using Circulating miRNAs as Cancer Biomarkers

(2015) Paola Tiberio et al.   Biomed Research International

Association of Valine and Leucine at HLA-DRB1 Position 11 With Radiographic Progression in Rheumatoid Arthritis, Independent of the Shared Epitope Alleles but Not Independent of Anti-Citrullinated Protein Antibodies

(2015) H. W. van Steenbergen et al.   Arthritis & Rheumatology

Applications of Next-generation Sequencing in Systemic Autoimmune Diseases

(2015) Yiyangzi Ma et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Pregnancy-Induced Changes in Systemic Gene Expression among Healthy Women and Women with Rheumatoid Arthritis

(2015) Anuradha Mittal et al.   PLoS One

The TNFRSF1B rs1061622 polymorphism (p.M196R) is associated with biological drug outcome in Psoriasis patients

(2014) Leire González-Lara et al.   ARCHIVES OF DERMATOLOGICAL RESEARCH

Role of the Microbiota in Immunity and Inflammation

(2014) Yasmine Belkaid et al.   CELL

An Evaluation of Copy Number Variation Detection Tools from Whole-Exome Sequencing Data

(2014) Renjie Tan et al.   HUMAN MUTATION

Identification of a probiotic bacteria-derived activator of the aryl hydrocarbon receptor that inhibits colitis

(2014) Suguru Fukumoto et al.   IMMUNOLOGY AND CELL BIOLOGY

Circulating miRNA-125b Is a Potential Biomarker Predicting Response to Rituximab in Rheumatoid Arthritis

(2014) Isabelle Duroux-Richard et al.   MEDIATORS OF INFLAMMATION

RNA-seq analysis of synovial fibroblasts in human rheumatoid arthritis

(2014) XIUHUI WANG et al.   Molecular Medicine Reports

DNA methylation and miRNA—key roles in systemic autoimmunity

(2014) Bruce C. Richardson et al.   Nature Reviews Rheumatology

HLA-B27 and Human β2-Microglobulin Affect the Gut Microbiota of Transgenic Rats

(2014) Phoebe Lin et al.   PLoS One

Interferon gene expression signature in rheumatoid arthritis neutrophils correlates with a good response to TNFi therapy

(2014) Helen L. Wright et al.   RHEUMATOLOGY

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Single Cell Genomics: Advances and Future Perspectives

(2014) Iain C. Macaulay et al.   PLoS Genetics

Brief Report: Identification of a Pathogenic Variant in TREX1 in Early-Onset Cerebral Systemic Lupus Erythematosus by Whole-Exome Sequencing

(2014) Julia I. Ellyard et al.   Arthritis & Rheumatology

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

(2014) Sylvie Sanschagrin et al.   Jove-Journal of Visualized Experiments

What is next generation sequencing?

(2013) Sam Behjati et al.   Archives of Disease in Childhood-Education and Practice Edition

Transcriptional Regulation and Its Misregulation in Disease

(2013) Tong Ihn Lee et al.   CELL

Identification of novel markers in rheumatoid arthritis through integrated analysis of DNA methylation and microRNA expression

(2013) Lorenzo de la Rica et al.   JOURNAL OF AUTOIMMUNITY

Exome sequencing identifies novel rheumatoid arthritis-susceptible variants in the BTNL2

(2013) Shigeki Mitsunaga et al.   JOURNAL OF HUMAN GENETICS

Use of antibiotics in the treatment of Crohn’s disease

(2013) Maria Lia Scribano   WORLD JOURNAL OF GASTROENTEROLOGY

The role of antimicrobials in Crohn’s disease

(2013) Pramodini B Kale-Pradhan et al.   Expert Review of Gastroenterology & Hepatology

Helicobacter pylori and autoimmune diseases

(2012) Carolina Faria et al.   BIOMEDICINE & PHARMACOTHERAPY

Analyzing the cancer methylome through targeted bisulfite sequencing

(2012) Eun-Joon Lee et al.   CANCER LETTERS

Exome versus transcriptome sequencing in identifying coding region variants

(2012) Chee-Seng Ku et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis

(2012) Soumya Raychaudhuri et al.   NATURE GENETICS

Dissecting negative regulation of Toll-like receptor signaling

(2012) Takeshi Kondo et al.   TRENDS IN IMMUNOLOGY

RNA-seq analysis of synovial fibroblasts brings new insights into rheumatoid arthritis

(2012) Daniel P Heruth et al.   Cell and Bioscience

Landscape of Next-Generation Sequencing Technologies

(2011) Thomas P. Niedringhaus et al.   ANALYTICAL CHEMISTRY

Therapeutic Targeting of the Interleukin-6 Receptor

(2011) Toshio Tanaka et al.   Annual Review of Pharmacology and Toxicology

Aryl Hydrocarbon Receptor-Induced Signals Up-regulate IL-22 Production and Inhibit Inflammation in the Gastrointestinal Tract

(2011) Ivan Monteleone et al.   GASTROENTEROLOGY

Inflammatory Cytokines in Systemic Lupus Erythematosus

(2011) Kim Ohl et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

TGF- /Smad3 Signaling Promotes Renal Fibrosis by Inhibiting miR-29

(2011) W. Qin et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

Tartrate-resistant acid phosphatase deficiency causes a bone dysplasia with autoimmunity and a type I interferon expression signature

(2011) Tracy A Briggs et al.   NATURE GENETICS

Activation of Aryl Hydrocarbon Receptor (AhR) Leads to Reciprocal Epigenetic Regulation of FoxP3 and IL-17 Expression and Amelioration of Experimental Colitis

(2011) Narendra P. Singh et al.   PLoS One

The genomic binding sites of a noncoding RNA

(2011) M. D. Simon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toll-like receptor driven B cell activation in the induction of systemic autoimmunity

(2011) Nathaniel M. Green et al.   SEMINARS IN IMMUNOLOGY

International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data

(2011) J. Zhang et al.   Database-The Journal of Biological Databases and Curation

Inhibition and Role of let-7d in Idiopathic Pulmonary Fibrosis

(2010) Kusum V. Pandit et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

(2010) K. Atarashi et al.   SCIENCE

Diversity in the contribution of interleukin-10 to T-cell-mediated immune regulation

(2009) Craig L. Maynard et al.   IMMUNOLOGICAL REVIEWS

The U1-snRNP complex: structural properties relating to autoimmune pathogenesis in rheumatic diseases

(2009) Nicole H. Kattah et al.   IMMUNOLOGICAL REVIEWS

TGF-β activates Akt kinase through a microRNA-dependent amplifying circuit targeting PTEN

(2009) Mitsuo Kato et al.   NATURE CELL BIOLOGY

Partial sequencing of a single DNA molecule with a scanning tunnelling microscope

(2009) Hiroyuki Tanaka et al.   Nature Nanotechnology

Specific Microbiota Direct the Differentiation of IL-17-Producing T-Helper Cells in the Mucosa of the Small Intestine

(2008) Ivaylo I. Ivanov et al.   Cell Host & Microbe

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

(2008) J. R. Sanford et al.   GENOME RESEARCH

Shifting the imbalance from Th1/Th2 to Th17/treg: The changing rheumatoid arthritis paradigm

(2008) Marie-Christophe Boissier et al.   JOINT BONE SPINE

SMAD proteins control DROSHA-mediated microRNA maturation

(2008) Brandi N. Davis et al.   NATURE

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Transforming growth factor- -regulated miR-24 promotes skeletal muscle differentiation

(2008) Q. Sun et al.   NUCLEIC ACIDS RESEARCH