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Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction

Alexander A Morgan, Vasilios J Pyrgos, Kari C Nadeau, Peter R Williamson, Atul Janardhan Butte
2012 JAMIA Journal of the American Medical Informatics Association  
Objective We demonstrate a genome-wide method for the integration of many studies of gene expression of phenotypically similar disease processes, a method of multiplex meta-analysis.  ...  Our method may be extended to other disease processes, using RNA levels to prioritize genes likely to contain disease associated DNA variants.  ...  Acknowledgments Special thanks to Rong Chen and Alex Skrenchuk for the development of database resources.  ... 
doi:10.1136/amiajnl-2011-000657 pmid:22319178 pmcid:PMC3277634 fatcat:dhebtuhnjfavhj6zfxdrvbifgq

SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery

Siwen Hu-Lieskovan, Srabani Bhaumik, Kavita Dhodapkar, Jean-Charles J B Grivel, Sumati Gupta, Brent A Hanks, Sylvia Janetzki, Thomas O Kleen, Yoshinobu Koguchi, Amanda W Lund, Cristina Maccalli, Yolanda D Mahnke (+5 others)
2020 Journal for ImmunoTherapy of Cancer  
particular the development and approval of immune checkpoint inhibitors, engineered cellular therapies, and tumor vaccines to unleash antitumor immune activity.  ...  These durable responses have been noted in tumor types that were not previously considered immunotherapy-sensitive, suggesting that all patients with cancer may have the potential to benefit from immunotherapy  ...  They have identified the epigenetic processes associated with dysfunctional immune cells and surface biomarkers to identify reprogrammable T cells. ► Chromatin states define tumour-specific T cell dysfunction  ... 
doi:10.1136/jitc-2020-000705 pmid:33268350 fatcat:iuqgiddv4ra63bz7ge3rq2ppk4

Genome-wide association study in frontal fibrosing alopecia identifies four susceptibility loci including HLA-B*07:02

Christos Tziotzios, Christos Petridis, Nick Dand, Chrysanthi Ainali, Jake R. Saklatvala, Venu Pullabhatla, Alexandros Onoufriadis, Rashida Pramanik, David Baudry, Sang Hyuck Lee, Kristie Wood, Lu Liu (+62 others)
2019 Nature Communications  
We undertake genome-wide association studies in females from a UK cohort, comprising 844 cases and 3,760 controls, a Spanish cohort of 172 cases and 385 controls, and perform statistical meta-analysis.  ...  Transcriptomic analysis of affected scalp tissue highlights overrepresentation of transcripts encoding components of innate and adaptive immune response pathways.  ...  We are thankful to Prof Kathryn Lewis, Dr. Raquel Iniesta, Dr. Ken Hanscombe and Dr. Leo Bottolo for their input and advice with the statistical analysis aspects of the metabolomic exploration.  ... 
doi:10.1038/s41467-019-09117-w pmid:30850646 pmcid:PMC6408457 fatcat:v2pkria2gjfltaou6jy5g6g4di

Autism risk factors: genes, environment, and gene-environment interactions

Pauline Chaste, Marion Leboyer
2012 Dialogues in Clinical Neuroscience  
One aspect of this search that has been neglected so far is the study of interactions between genes and environmental factors.  ...  The identification of specific alleles contributing to the autism spectrum has supplied important pieces for the autism puzzle.  ...  of common variants in autism, a recent analysis of genetic variations associated with ASD suggests that common and rare C l i n i c a l r e s e a r c h variants contribute to ASD by perturbation of common  ... 
pmid:23226953 pmcid:PMC3513682 fatcat:quomgjutbjenblrp5wq5vou5la

Molecular Dysregulation in Autism Spectrum Disorder

Pritmohinder S. Gill, Jeffery L. Clothier, Aravindhan Veerapandiyan, Harsh Dweep, Patricia A. Porter-Gill, G. Bradley Schaefer
2021 Journal of Personalized Medicine  
Advances in genomic analysis have contributed to numerous candidate genes for the risk of ASD, where rare mutations and s common variants contribute to its susceptibility.  ...  non-coding RNAs and CRISPR/Cas9 models.  ...  Gene-based association analysis on primary ASD meta-analysis using MAGMA identified the top associated genes KIZ and XRN2 (Chr 20), MFHAS1, XKR6, MSRA, and SOX7 (Chr 8).  ... 
doi:10.3390/jpm11090848 pmid:34575625 fatcat:7z7li3qltvgsvotzhyf4ibmrxu

Advances of genomic science and systems biology in renal transplantation: a review

David Perkins, Meenakshi Verma, Ken J. Park
2011 Seminars in Immunopathology  
To develop the most appropriate molecular criteria, there have been studies by multiple groups applying omics technologies in attempts to identify biomarkers of rejection.  ...  In this review, we discuss studies using genome-wide data sets of the transcriptome and proteome to investigate acute rejection, chronic allograft dysfunction, and tolerance.  ...  In a multiplex meta-analysis designed to identify the core immune response genes as defined by the Molecular Signatures Database [24] , a comparative analysis of five studies of AR from kidney, lung,  ... 
doi:10.1007/s00281-011-0243-2 pmid:21318414 pmcid:PMC3082700 fatcat:thrm2xmd7rhvjfqgt5mexusvry

90PMolecular feature and clinical use development of gene expression profile "TP53 signature" in early stage breast cancer

S. Yamaguchi, S. Takahashi, T. Nomizu, Y. Kakugawa, T. Ishida, S. Kato, C. Ishioka
2017 Annals of Oncology  
As with BRCA, the acquisition of additional mutations predicted to restore at least some PALB2 function and thus potentially confer resistance to therapies dependent on HRD, can be observed in tumors such  ...  Conclusions: In addition to the commonly sequenced genes BRCA1/2, PALB2 mutation can lead to homologous recombination deficiency.  ...  To identify potential driver alterations enriched in MSI-H tumors, variants in regions likely to be affected by polymerase slippage were excluded.  ... 
doi:10.1093/annonc/mdx363.006 fatcat:ifholazkkbc7dk3jmbsafpq5xe

Identification of a Sjögren's syndrome susceptibility locus at OAS1 that influences isoform switching, protein expression, and responsiveness to type I interferons

He Li, Tove Ragna Reksten, John A. Ice, Jennifer A. Kelly, Indra Adrianto, Astrid Rasmussen, Shaofeng Wang, Bo He, Kiely M. Grundahl, Stuart B. Glenn, Corinne Miceli-Richard, Simon Bowman (+53 others)
2017 PLoS Genetics  
Acknowledgments We are grateful to all the individuals with Sjögren's syndrome and those serving as healthy controls who participated in this study.  ...  We would like to thank the following individuals for their help in the collection and ascertainment of the samples used in this study: Erin We would also like to thank Jared Ning for the ongoing assistance  ...  Therefore, we identified a variant associated with both SS susceptibility and gene expression in the IFN signature gene OAS1.  ... 
doi:10.1371/journal.pgen.1006820 pmid:28640813 pmcid:PMC5501660 fatcat:m4nhejcw25aq5jwyarlekg3uce

EBV infection determines the immune hallmarks of plasmablastic lymphoma

Pauline Gravelle, Sarah Péricart, Marie Tosolini, Bettina Fabiani, Paul Coppo, Nadia Amara, Alexandra Traverse-Gléhen, Nathalie Van Acker, Pierre Brousset, Jean-Jacques Fournie, Camille Laurent
2018 Oncoimmunology  
Unsupervised hierarchical clustering analysis of PBL samples revealed they segregate according to their tumor EBV-status.  ...  Moreover, EBV+ PBL displays abundant leucocyte infiltrates and T-cell activation signatures, together with high expression levels of mRNA and protein markers of immune escape.  ...  Conflict-of-interest disclosure The authors declare no conflict of interest.  ... 
doi:10.1080/2162402x.2018.1486950 pmid:30288350 pmcid:PMC6169584 fatcat:7os4rb6y4fgdxbmkwrqd7gdoqa

Genetic architecture, epigenetic influence and environment exposure in the pathogenesis of Autism

Li Yu, YiMing Wu, Bai-Lin Wu
2015 Science China Life Sciences  
and gastrointestinal microbiota are two prominent ones. autism spectrum disorder, genetic architecture, genomic disorder, gene mutation, copy number variants, single nucleotide variants, genetic pathways  ...  , epigenetic influence, DNA methylation, chromatin remodeling, long non-coding RNAs, environment exposure, immune dysregulation, gastrointestinal microbiota Citation: Yu L, Wu YM, Wu BL.  ...  Meta-analysis identified three single-nucleotide polymorphisms and related haplotypes; all were mapped to a previously reported linkage region (1p13.2) with autism [26] .  ... 
doi:10.1007/s11427-015-4941-1 pmid:26490976 fatcat:erjhekqbsralhhinx5ykc6k6we

Beyond Single-Nucleotide Polymorphisms

Nuala J. Meyer
2014 Clinics in Chest Medicine  
As future GWAS are published, new candidates will undoubtedly emerge and meta-analysis will be possible to harness the power of multiple populations.  ...  This article summarizes the contributions of high throughput genomic, proteomic, metabolomic, and gene expression investigations to our understanding of inherited or acquired risk for acute respiratory  ...  that gene variants associated with ARDS may be specific to ARDS risk factor. 54 In the first published human genome-wide association study (GWAS) for ARDS susceptibility, Christie and colleagues identified  ... 
doi:10.1016/j.ccm.2014.08.006 pmid:25453417 pmcid:PMC5629971 fatcat:pehfkke25za7tib4zoziwxaq6q

The Meta-Genome of Sepsis: Host Genetics, Pathogens and the Acute Immune Response

John H. Boyd, James A. Russell, Chris D. Fjell
2014 Journal of Innate Immunity  
The pathogen is discussed with particular emphasis upon the modern era of microbiome analysis and nucleic acid diagnostics.  ...  Finally, we discuss the host clinical and immune responses and present new data to suggest that the immune response is the key to understanding sepsis and improving a death rate of nearly 30%.  ...  Acknowledgements Support for this study was obtained through SONRIS CIHR Network grant, Heart and Stroke Foundation, and the National Sanitorium Association.  ... 
doi:10.1159/000358835 pmid:24525633 pmcid:PMC6741586 fatcat:4ulmyzigkfagnggpip4oqqovyi

SAGES 2018, Symposium on Advances in Genomics, Epidemiology and Statistics 2018, Philadelphia, PA, USA, June 1, 2018: Abstracts

2018 Human Heredity  
We expect that screening for deleterious variants in the subset of candidate genes involved in cognition may be useful to identifying genetic factors contributing to expression of phenotype differences  ...  and GTEx eQTL data from 44 tissues to identify target genes regulated by variants overlapping enhancers in matching tissue categories.  ...  Capabilities to Predict Gene Expression Levels and Prioritize Variant-Based Associations Using Datasets with Varied Population Background QC Software for Analysis of Sequence Data in Family-Based Studies  ... 
doi:10.1159/000490340 pmid:29852479 fatcat:c24yw4b2vngd5hnvf2nluajrfa

Discovery and application of immune biomarkers for hematological malignancies

Dimitrios Zafeiris, Jayakumar Vadakekolathu, Sarah Wagner, Alan Graham Pockley, Graham Roy Ball, Sergio Rutella
2017 Expert Review of Molecular Diagnostics  
Moreover, the analysis of multidimensional, clinically annotated data sets obtained from public repositories such as Array Express, TCGA and GEO is crucial to identify immune biomarkers, to inform the  ...  Although high-throughput transcriptomic and proteomic approaches are being employed to interrogate immune surveillance and escape mechanisms in patients with solid tumours, and to identify actionable targets  ...  Importantly, immune-related gene signatures, and not tumour-related gene expression patterns, have been identified as being the main parameters associated with dissemination of CRC to distant metastases  ... 
doi:10.1080/14737159.2017.1381560 pmid:28927305 fatcat:w6xgbthnm5gyjcbeouh4bx4rja

Identification of aberrant innate and adaptive immunity based on changes in global gene expression in the blood of adults with autism spectrum disorder

Fumie Horiuchi, Yuta Yoshino, Hiroshi Kumon, Rie Hosokawa, Kiwamu Nakachi, Kentaro Kawabe, Jun-ichi Iga, Shu-ichi Ueno
2021 Journal of Neuroinflammation  
A previous meta-analysis of seven microarray studies and one RNA sequencing (RNA-seq) study using the blood of children with ASD identified dysregulation of gene expressions relevant to the immune system  ...  Conclusions The dysregulated gene expressions confirmed in the blood of adults with ASD were relevant to the dysfunction of innate and adaptive immunity.  ...  Acknowledgments We would like to thank Ms. Chiemi Onishi for the technical assistance. We also wish to thank Dr. Naohito Tokunaga for the technical advice on RNAsequencing.  ... 
doi:10.1186/s12974-021-02154-7 pmid:33931079 pmcid:PMC8086363 fatcat:5fxoxx3rlfey5pyuuh444ji7ye
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