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Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants

Alexander A Morgan, Purvesh Khatri, Richard Jones, Minnie M Sarwal, Atul J Butte
2010 BMC Bioinformatics  
Motivated by a need for a deeper understanding of organ transplant rejection, we combine the data from five separate studies to compare acute rejection versus stability after solid organ transplantation  ...  , and use this data to examine approaches to multiplex meta analysis.  ...  Acknowledgements The work was supported by the Lucile Packard Foundation for Children's Health, National Library of Medicine (R01 LM009719 and T15 LM7033), the National Institute of Allergy and Infectious  ... 
doi:10.1186/1471-2105-11-s9-s6 pmid:21044364 pmcid:PMC2967747 fatcat:b3bv2hteqjatnmovv4ww3qgz3u

Donor-Derived Cell-Free DNA to Diagnose Graft Rejection Post-Transplant: Past, Present and Future

Naveen Kumar, Rashmi Rana, Devender Singh Rana, Anurag Gupta, Mohinder Pal Sachdeva
2021 Transplantology  
This review elucidates the evolution, physiology, techniques, limitations, and prospects of dd-cfDNA as a biomarker for post-transplant graft damage and rejection.  ...  Due to its applicability over all transplanted organs irrespective of age, sex, race, ethnicity, and the non-requirement of a donor sample, it emerges as a new gold standard for graft health and rejection  ...  it a late marker for acute rejection [66] .  ... 
doi:10.3390/transplantology2030034 fatcat:my6sdgnwujaa3bjcqhl4gf6uga

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

David Perkins, Meenakshi Verma, Ken J. Park
2011 Seminars in Immunopathology  
mechanistic understanding of the rejection process.  ...  The diagnosis of rejection in kidney transplant patients is based on histologic classification of a graft biopsy.  ...  This illustrated the importance of the statistical approach applied in a multiplex meta-analysis [25] .  ... 
doi:10.1007/s00281-011-0243-2 pmid:21318414 pmcid:PMC3082700 fatcat:thrm2xmd7rhvjfqgt5mexusvry

Gene signatures common to allograft rejection are associated with lymphocytic bronchitis

John R Greenland, Ping Wang, Joshua J Brotman, Rahul Ahuja, Tiffany A Chong, Mary Ellen Kleinhenz, Lorriana E Leard, Jeffrey A Golden, Steven R Hays, Jasleen Kukreja, Jonathan P Singer, Raja Rajalingam (+5 others)
2019 Clinical Transplantation  
The relationships of LB (classified here as Endobronchial or E-grade rejection) to small airway (A- and B-grade) pathologies are unclear.  ...  Differential expression using DESeq2 was used for pathway analysis and to define an LB-associated metagene.  ...  Acknowledgements: We acknowledge the study participants and their families for their generous contributions, and Dr. George Caughey for his mentorship and input into prior versions of this manuscript.  ... 
doi:10.1111/ctr.13515 pmid:30849195 pmcid:PMC6545574 fatcat:45muly6rfva4xnne3drkerryem

An Approach to Fungal Diagnostics in Solid Organ Transplantation

David Gaston, Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut, USA, Marwan Azar, Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
2018 OBM Transplantation  
The approach to diagnosing fungal infections following solid organ transplantation (SOT) is patient-specific.  ...  This review provides a cognitive framework for practitioners aiming to diagnose fungal infections in recipients of SOT, taking into consideration the benefits and limitations of currently available diagnostic  ...  In a Cochrane meta-analysis that included patients with solid organ transplantation, the sensitivity and specificity of PCR for the diagnosis of invasive aspergillosis ranged from 58.0 to 80.5% and 78.5  ... 
doi:10.21926/obm.transplant.1804037 fatcat:roz3an25dvc27ge7mdqx4bqlcq

A Changing Paradigm in Heart Transplantation: An Integrative Approach for Invasive and Non-Invasive Allograft Rejection Monitoring

Alessia Giarraputo, Ilaria Barison, Marny Fedrigo, Jacopo Burrello, Chiara Castellani, Francesco Tona, Tomaso Bottio, Gino Gerosa, Lucio Barile, Annalisa Angelini
2021 Biomolecules  
Cardiac allograft rejection following heart transplantation is challenging to diagnose. Tissue biopsies are the gold standard in monitoring the different types of rejection.  ...  , thus representing an integrated approach for heart transplant patients monitoring.  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/biom11020201 pmid:33535640 fatcat:ojmr6r7y7ranhau6skp2zezvqi

Identifying biomarkers as diagnostic tools in kidney transplantation

Valeria R Mas, Thomas F Mueller, Kellie J Archer, Daniel G Maluf
2011 Expert Review of Molecular Diagnostics  
There is a critical need for biomarkers for early diagnosis, treatment response, and surrogate end point and outcome prediction in organ transplantation, leading to a tailored and individualized treatment  ...  However, there is still no routine application of any of these markers in clinical transplantation.  ...  In a recent publication, the authors combined the data from five separate studies to compare AR versus stability after solid organ transplantation, and used this data to examine approaches to multiplex  ... 
doi:10.1586/erm.10.119 pmid:21405969 pmcid:PMC3116652 fatcat:rivexgj3ojhxdakcaj7wyeuda4

In praise of arrays

Lihua Ying, Minnie Sarwal
2008 Pediatric nephrology (Berlin, West)  
and its applications, as well as the limitations and evolution of microarrays, in the field of organ transplantation.  ...  Methods of applying microarrays to clinical practice 7. Limitations of using microarrays in clinical practice 8. The black-box of microarray data analysis  ...  In the past few years, there has been an increasing number of publications on solid organ transplantation, with particular emphasis on the heart and kidney.  ... 
doi:10.1007/s00467-008-0808-z pmid:18568367 pmcid:PMC2719727 fatcat:f3lebgcy5rh47k7e3ses2ybueq

Landscape of Immune Cells Heterogeneity in Liver Transplantation by Single-Cell RNA Sequencing Analysis

Xinqiang Li, Shipeng Li, Bin Wu, Qingguo Xu, Dahong Teng, Tongwang Yang, Yandong Sun, Yang Zhao, Tianxiang Li, Dan Liu, Shuang Yang, Weihua Gong (+1 others)
2022 Frontiers in Immunology  
Taken together, these findings have gained novel mechanistic insights for understanding the immune landscape in liver transplantation, and it outlines the characteristics of immune cells and provides potential  ...  Rejection is still a critical barrier to the long-term survival of graft after liver transplantation, requiring clinicians to unveil the underlying mechanism of liver transplant rejection.  ...  SL, SY, YZ, and XL contributed to the data management and statistical analyses. JC, SL, and XL wrote the manuscript. All authors contributed to the article and approved the submitted version.  ... 
doi:10.3389/fimmu.2022.890019 fatcat:d7iu47wwbnb25bcr3flcrnl2ei

A urinary Common Rejection Module (uCRM) score for non-invasive kidney transplant monitoring

Tara K. Sigdel, Joshua Y. C. Yang, Oriol Bestard, Andrew Schroeder, Szu-Chuan Hsieh, Juliane M. Liberto, Izabella Damm, Anna C. M. Geraedts, Minnie M. Sarwal, Stanislaw Stepkowski
2019 PLoS ONE  
A Common Rejection Module (CRM) consisting of 11 genes expressed in allograft biopsies was previously reported to serve as a biomarker for acute rejection (AR), correlate with the extent of graft injury  ...  We investigated the use of this gene panel on the urine cell pellet of kidney transplant patients.  ...  Acknowledgments We are grateful for the help from physicians, clinical coordinators, research personnel, patients, and patient families.  ... 
doi:10.1371/journal.pone.0220052 pmid:31365568 pmcid:PMC6668802 fatcat:oabawwdalvfnjh5xsg4s72muya

ABSTRACTS Joint 16th International HLA and Immunogenetics Workshop, 26th European Federation for Immunogenetics Conference and 23rd British Society of Histocompatibility and Immunogenetics Conference, Liverpool, U.K. May 31st - June 3rd, 2012

2012 Tissue Antigens  
The ImmuKnow assay measures the cellular immune function and is aimed at identifying solid organ transplant recipients at risk for acute rejection or infection.  ...  solid organ transplantation.  ...  :01 ( We performed a meta-analysis of the MHC diversity of 25 primate species by extracting DNA sequences available on IPD-MHC Database for catarrhines.  ... 
doi:10.1111/j.1399-0039.2012.01877.x fatcat:q6k6fgfgwbhjdjd6qearg3mlnu

Community-Acquired Respiratory Viruses in Transplant Patients: Diversity, Impact, Unmet Clinical Needs

Michael G. Ison, Hans H. Hirsch
2019 Clinical Microbiology Reviews  
SUMMARY Patients undergoing solid-organ transplantation (SOT) or allogeneic hematopoietic cell transplantation (HCT) are at increased risk for infectious complications.  ...  Here, we review the current knowledge about CARVs in SOT and allogeneic HCT patients to better define the magnitude of this unmet clinical need and to discuss some of the lessons learned from human influenza  ...  ACKNOWLEDGMENTS We are very thankful to Patrick Lane of ScEYEnce Studios for working with us to prepare the graphically enhanced figures.  ... 
doi:10.1128/cmr.00042-19 pmid:31511250 fatcat:ggi6iplx3zcpziuc77yc6friz4

Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients

Marie-Céline Zanella, Samuel Cordey, Laurent Kaiser
2020 Clinical Microbiology Reviews  
SUMMARY Viral primary infections and reactivations are common complications in patients after solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) and are associated with  ...  Beyond the usual well-known viruses that are part of the routine clinical management of transplant recipients, numerous other viral signatures or genomes can be identified in the blood of these patients  ...  We thank Florian Laubscher and Patrick Lane of ScEYEnce Studios for their contribution in designing the figure.  ... 
doi:10.1128/cmr.00027-20 pmid:32847820 fatcat:mj5huvyurbbnlhfprntxuo65ce

If at First You Don't Succeed: Stem-Cell Transplantation for Acute Myeloid Leukemia After First Relapse

Charles A. Schiffer
2013 Journal of Clinical Oncology  
For a detailed description of the disclosure categories, or for more information about ASCO  ...  Although all authors completed the disclosure declaration, the following author(s) and/or an author's immediate family member(s) indicated a financial or other interest that is relevant to the subject  ...  Evens AM, David KA, Helenowski I, et al: Multicenter analysis of 80 solid organ transplantation recipients with post-transplantation lymphoproliferative disease: Outcomes and prognostic factors in the  ... 
doi:10.1200/jco.2012.43.4241 pmid:23439749 fatcat:znxb5vhupffedb77khsjkjxuuq

Clinical severity of rhinovirus/enterovirus compared to other respiratory viruses in children

Sandra A. Asner, Astrid Petrich, Jemila S. Hamid, Dominik Mertz, Susan E. Richardson, Marek Smieja
2014 Influenza and Other Respiratory Viruses  
(HSCT) and solid organ, particularly lung transplant recipients.  ...  One or more of the following immunodeficiency states were included in the latter group: Hematopoietic stem cell transplant (HSCT) (allogeneic and autologous transplants) and solid-organ transplant (SOT  ... 
doi:10.1111/irv.12255 pmid:24801963 pmcid:PMC4181803 fatcat:tj5laoepubcm5fcnfgg6rzswqm
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