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https://www.readbyqxmd.com/read/30333179/impact-of-dna-sequencing-and-analysis-methods-on-16s-rrna-gene-bacterial-community-analysis-of-dairy-products
#1
Zhengyao Xue, Mary E Kable, Maria L Marco
DNA sequencing and analysis methods were compared for 16S rRNA V4 PCR amplicon and genomic DNA (gDNA) mock communities encompassing nine bacterial species commonly found in milk and dairy products. The two communities comprised strain-specific DNA that was pooled before (gDNA) or after (PCR amplicon) the PCR step. The communities were sequenced on the Illumina MiSeq and Ion Torrent PGM platforms and then analyzed using the QIIME 1 (UCLUST) and Divisive Amplicon Denoising Algorithm 2 (DADA2) analysis pipelines with taxonomic comparisons to the Greengenes and Ribosomal Database Project (RDP) databases...
October 17, 2018: MSphere
https://www.readbyqxmd.com/read/30185233/high-resolution-isr-amplicon-sequencing-reveals-personalized-oral-microbiome
#2
Chiranjit Mukherjee, Clifford J Beall, Ann L Griffen, Eugene J Leys
BACKGROUND: Sequencing of the 16S rRNA gene has been the standard for studying the composition of microbial communities. While it allows identification of bacteria at the level of species, this method does not usually provide sufficient information to resolve communities at the sub-species level. Species-level resolution is not adequate for studies of transmission or stability or for exploring subspecies variation in disease association. Strain level analysis using whole metagenome shotgun sequencing has significant limitations that can make it unsuitable for large-scale studies...
September 5, 2018: Microbiome
https://www.readbyqxmd.com/read/30139808/ada2-deficiency-mimicking-idiopathic-multicentric-castleman-disease
#3
Erika Van Nieuwenhove, Stephanie Humblet-Baron, Lien Van Eyck, Lien De Somer, James Dooley, Thomas Tousseyn, Michael Hershfield, Adrian Liston, Carine Wouters
Multicentric Castleman disease (MCD) is a rare entity that, unlike unicentric Castleman disease, involves generalized polyclonal lymphoproliferation, systemic inflammation, and multiple-organ system failure resulting from proinflammatory hypercytokinemia, including, in particular, interleukin-6. A subset of MCD is caused by human herpesvirus-8 (HHV-8), although the etiology for HHV-8-negative, idiopathic MCD (iMCD) cases is unknown at present. Recently, a consensus was reached on the diagnostic criteria for iMCD to aid in diagnosis, recognize mimics, and initiate prompt treatment...
September 2018: Pediatrics
https://www.readbyqxmd.com/read/30123705/denoising-the-denoisers-an-independent-evaluation-of-microbiome-sequence-error-correction-approaches
#4
Jacob T Nearing, Gavin M Douglas, André M Comeau, Morgan G I Langille
High-depth sequencing of universal marker genes such as the 16S rRNA gene is a common strategy to profile microbial communities. Traditionally, sequence reads are clustered into operational taxonomic units (OTUs) at a defined identity threshold to avoid sequencing errors generating spurious taxonomic units. However, there have been numerous bioinformatic packages recently released that attempt to correct sequencing errors to determine real biological sequences at single nucleotide resolution by generating amplicon sequence variants (ASVs)...
2018: PeerJ
https://www.readbyqxmd.com/read/30099592/a-retrospective-study-comparing-the-phenotype-and-outcomes-of-patients-with-polyarteritis-nodosa-between-uk-and-turkish-cohorts
#5
Omer Karadag, Abdulsamet Erden, Yelda Bilginer, Seerapani Gopaluni, Alper Sari, Berkan Armagan, Ihsan Ertenli, Seza Ozen, David Jayne
There is a need for better definition of polyarteritis nodosa (PAN) subphenotypes and the influence of ethnicity and geography. This study is aimed to study the demographic and clinical features of PAN cohorts from the UK and Turkey (TR) and to compare and contrast disease characteristics. A retrospective survey of databases from two vasculitis centres between 1990 and 2016 for PAN patients fulfilling the EMEA Vasculitis Classification algorithm. All paediatric-onset adult patients met the Ankara 2008 (EULAR/PReS endorsed) criteria for childhood PAN...
October 2018: Rheumatology International
https://www.readbyqxmd.com/read/30047330/vasculitis-decade-in-review
#6
Selcan Demir, Hafize Emine Sonmez, Seza OZen
In the last decade we have come to better understand and manage the vasculitides. Classification of vasculitides has been revised. Genome- wide association studies and linkage analyses have been undertaken in hope of better understanding the pathogenesis of vasculitides. Comprehensive genetic studies have highlighted new pathways that may guide us in more targeted therapies. Description of the monogenic forms of vasculitis, such as deficiency of adenosine deaminase type 2 (DADA2), haploinsufficiency of A20 (HA20), have introduced a new perspective to vasculopathies, and introduced alternative treatments for these diseases...
July 25, 2018: Current Rheumatology Reviews
https://www.readbyqxmd.com/read/29963054/deficiency-of-adenosine-deaminase-2-in-adult-siblings-many-years-of-a-misdiagnosed-disease-with-severe-consequences
#7
Jason Michael Springer, Selina A Gierer, Hong Jiang, David Kleiner, Natalie Deuitch, Amanda K Ombrello, Peter C Grayson, Ivona Aksentijevich
Objective: Describe the clinical characteristics and histopathology findings in a family with two siblings affected with deficiency of adenosine deaminase 2 (DADA2). Both patients presented in childhood with polyarthritis and developed significant neurological and gastrointestinal features of DADA2 in ear, including variable degrees of immunologic and hematologic manifestations. Methods: Adenosine Deaminase 2 (ADA2; also known as cat eye syndrome chromosome region, candidate 1 gene; CECR1) exon sequencing and serum ADA2 levels were performed to confirm the diagnosis of DADA2...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29951947/deficiency-of-adenosine-deaminase-2-dada2-updates-on-the-phenotype-genetics-pathogenesis-and-treatment
#8
REVIEW
Isabelle Meyts, Ivona Aksentijevich
Deficiency of ADA2 (DADA2) is the first molecularly described monogenic vasculitis syndrome. DADA2 is caused by biallelic hypomorphic mutations in the ADA2 gene that encodes the adenosine deaminase 2 (ADA2) protein. Over 60 disease-associated mutations have been identified in all domains of ADA2 affecting the catalytic activity, protein dimerization, and secretion. Vasculopathy ranging from livedo reticularis to polyarteritis nodosa (PAN) and life-threatening ischemic and/or hemorrhagic stroke dominate the clinical features of DADA2...
July 2018: Journal of Clinical Immunology
https://www.readbyqxmd.com/read/29913178/deficiency-of-adenosine-deaminase-2-special-focus-on-central-nervous-system-imaging
#9
Elif Bulut, Abdulsamet Erden, Omer Karadag, Kader Karli Oguz, Seza Ozen
PURPOSE: To increase the knowledge of central nervous system (CNS) imaging features in deficiency of adenosine deaminase 2 (DADA2) by examining magnetic resonance imaging (MRI) studies of a relatively large number of patients. METHODS: We retrospectively examined neuroimages of 12 patients (7 male, 5 female) diagnosed with DADA2. The mean age of the patients at the time of initial brain MRI was 16.7±10.2 years. Seven patients (58.3%) fulfilled the classification criteria of polyarteritis nodosa...
June 18, 2018: Journal of Neuroradiology. Journal de Neuroradiologie
https://www.readbyqxmd.com/read/29681619/a-decision-tree-for-the-genetic-diagnosis-of-deficiency-of-adenosine-deaminase-2-dada2-a-french-reference-centres-experience
#10
Mélanie Rama, Claire Duflos, Isabelle Melki, Didier Bessis, Axelle Bonhomme, Hélène Martin, Diane Doummar, Stéphanie Valence, Diana Rodriguez, Emilie Carme, David Genevieve, Ketil Heimdal, Antonella Insalaco, Nathalie Franck, Viviane Queyrel-Moranne, Nathalie Tieulie, Jonathan London, Florence Uettwiller, Sophie Georgin-Lavialle, Alexandre Belot, Isabelle Koné-Paut, Véronique Hentgen, Guilaine Boursier, Isabelle Touitou, Guillaume Sarrabay
Deficiency of adenosine deaminase 2 (DADA2) is a recently described autoinflammatory disorder. Genetic analysis is required to confirm the diagnosis. We aimed to describe the identifying symptoms and genotypes of patients referred to our reference centres and to improve the indications for genetic testing. DNA from 66 patients with clinically suspected DADA2 were sequenced by Sanger or next-generation sequencing. Detailed epidemiological, clinical and biological features were collected by use of a questionnaire and were compared between patients with and without genetic confirmation of DADA2...
July 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29608151/guided-protocol-for-fecal-microbial-characterization-by-16s-rrna-amplicon-sequencing
#11
Ayelet Di Segni, Tzipi Braun, Marina BenShoshan, Sarit Farage Barhom, Efrat Glick Saar, Karen Cesarkas, James E Squires, Nathan Keller, Yael Haberman
The human intestinal microbiome plays a central role in protecting cells from injury, in processing energy and nutrients, and in promoting immunity. Deviations from what is considered a healthy microbiota composition (dysbiosis) may impair vital functions leading to pathologic conditions. Recent and ongoing research efforts have been directed toward the characterization of associations between microbial composition and human health and disease. Advances in high-throughput sequencing technologies enable characterization of the gut microbial composition...
March 19, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29564582/novel-mutation-in-cecr1-leads-to-deficiency-of-ada2-with-associated-neutropenia
#12
Funda Erol Cipe, Cigdem Aydogmus, Nina K Serwas, Gonca Keskindemirci, Kaan Boztuğ
PURPOSE: Adenosine deaminase 2 (ADA2) have been reported to cause vasculitic diseases and immunodeficiency recently. Patients present with stroke episodes and rashes mimicking polyarteritis nodosa (PAN). We report a patient who has been followed up with severe neutropenia and found an unexpectedly revealed novel mutation in CECR1 affecting ADA2. METHODS: We reviewed medical records and clinical history of the patient. No mutations in other known neutropenia genes such as ELA, G6PC3, HAX1, AP3B1, LAMTOR2, VPS13B, VPS45, GFI1, JAGN1, or WAS could be detected...
April 2018: Journal of Clinical Immunology
https://www.readbyqxmd.com/read/29330190/influence-of-pig-farming-on-the-human-s-nasal-microbiota-the-key-role-of-the-airborne-microbial-communities
#13
Julia G Kraemer, Alban Ramette, Suzanne Aebi, Anne Oppliger, Markus Hilty
It has been hypothesized that the environment can influence the composition of the nasal microbiota. However, the direct influence of pig farming on the anterior and posterior nasal microbiota is unknown. Using a cross-sectional design, pig farms (n=28) were visited in 2014-2015 and nasal swabs from 43 pig farmers and 56 pigs as well as 27 air samples taken in the vicinity of pig enclosure were collected. As controls, nasal swabs from 17 cow farmers and 26 non-animal exposed individuals were also included. Analyses of the microbiota were performed based on 16S rRNA amplicon sequencing and the DADA2 pipeline to define sequence variants (SVs)...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29273180/-multiple-facets-of-ada2-deficiency-vasculitis-auto-inflammatory-disease-and-immunodeficiency-a-literature-review-of-135-cases-from-literature
#14
A Fayand, G Sarrabay, A Belot, V Hentgen, I Kone-Paut, G Grateau, I Melki, S Georgin-Lavialle
Deficiency of adenosine deaminase 2 (DADA2) is a recently described auto-inflammatory disorder. It is an autosomal recessive inherited disease, caused by mutations in the ADA2 gene (formerly known as CECR1) encoding ADA2 enzyme. Besides its role in the purine metabolism, it has been postulated that ADA2 may act as a growth factor for endothelial cells and in the differenciation of monocytes. Thus, deficiency of ADA2 would lead to endothelial damage and a skewing of monocytes into M1 pro-inflammatory macrophage, causing DADA2 manifestations...
April 2018: La Revue de Médecine Interne
https://www.readbyqxmd.com/read/29271561/deficiency-of-ada2-mimicking-autoimmune-lymphoproliferative-syndrome-in-the-absence-of-livedo-reticularis-and-vasculitis
#15
Abdulrahman Alsultan, Enas Basher, Jubran Alqanatish, Reem Mohammed, Majid Alfadhel
Adenosine deaminase-2 (ADA2) deficiency (DADA2) is associated with early onset polyarteritis nodosa and vasculopathy. Classic presentation includes livedo reticularis, vasculitis, and stroke. However, the phenotype and disease severity are variable. We present a 5-year-old female who presented with features that mimicked autoimmune lymphoproliferative syndrome (ALPS) in the absence of classic features of DADA2. Exome sequencing identified a novel homozygous splicing variant in ADA2 c.882-2A > G. Patient responded to anti- tumor necrosis factor medication and is in complete remission...
April 2018: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/29238339/comparing-the-healthy-nose-and-nasopharynx-microbiota-reveals-continuity-as-well-as-niche-specificity
#16
Ilke De Boeck, Stijn Wittouck, Sander Wuyts, Eline F M Oerlemans, Marianne F L van den Broek, Dieter Vandenheuvel, Olivier Vanderveken, Sarah Lebeer
To improve our understanding of upper respiratory tract (URT) diseases and the underlying microbial pathogenesis, a better characterization of the healthy URT microbiome is crucial. In this first large-scale study, we obtained more insight in the URT microbiome of healthy adults. Hereto, we collected paired nasal and nasopharyngeal swabs from 100 healthy participants in a citizen-science project. High-throughput 16S rRNA gene V4 amplicon sequencing was performed and samples were processed using the Divisive Amplicon Denoising Algorithm 2 (DADA2) algorithm...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29051624/autoinflammation-stem-cell-transplantation-for-dada2
#17
Joanna Collison
No abstract text is available yet for this article.
December 2017: Nature Reviews. Rheumatology
https://www.readbyqxmd.com/read/29032440/vasculitis-and-vasculitis-like-manifestations-in-monogenic-autoinflammatory-syndromes
#18
REVIEW
Avinash Jain, Durga Prasanna Misra, Aman Sharma, Anupam Wakhlu, Vikas Agarwal, Vir Singh Negi
Monogenic autoinflammatory syndromes are a rare group of disorders characterized by periodic episodes of systemic inflammation of endogenous origin. Sometimes, these diseases may present with features akin to vasculitis. We conducted a literature review on such vasculitic manifestations in described monogenic autoinflammatory syndromes utilizing the Online Mendelian Inheritance in Man (OMIM), Medline, and Scopus databases. Our search identified that Familial Mediterranean fever (FMF) can manifest with features of either small, medium, large, or variable-vessel vasculitis...
January 2018: Rheumatology International
https://www.readbyqxmd.com/read/28983775/deficiency-of-adenosine-deaminase-2-dada2-an-inherited-cause-of-polyarteritis-nodosa-and-a-mimic-of-other-systemic-rheumatologic-disorders
#19
REVIEW
Hasan Hashem, Susan J Kelly, Nancy J Ganson, Michael S Hershfield
PURPOSE OF REVIEW: A new autoinflammatory disease, deficiency of adenosine deaminase 2 (DADA2), caused by mutations in the CECR1 gene, was first reported in 2014. This review aims to update progress in defining, treating, and understanding this multi-faceted disorder. RECENT FINDINGS: DADA2 was first described in patients with systemic inflammation, mild immune deficiency, and vasculopathy manifested as recurrent stroke or polyarteritis nodosa (PAN). More than 125 patients have now been reported, and the phenotype has expanded to include children and adults presenting primarily with pure red cell aplasia (PRCA), or with antibody deficiency...
October 5, 2017: Current Rheumatology Reports
https://www.readbyqxmd.com/read/28974505/hematopoietic-stem-cell-transplantation-rescues-the-hematological-immunological-and-vascular-phenotype-in-dada2
#20
MULTICENTER STUDY
Hasan Hashem, Ashish R Kumar, Ingo Müller, Florian Babor, Robbert Bredius, Jignesh Dalal, Amy P Hsu, Steven M Holland, Dennis D Hickstein, Stephen Jolles, Robert Krance, Ghadir Sasa, Mervi Taskinen, Minna Koskenvuo, Janna Saarela, Joris van Montfrans, Keith Wilson, Barbara Bosch, Leen Moens, Michael Hershfield, Isabelle Meyts
Deficiency of adenosine deaminase 2 (DADA2) is caused by biallelic deleterious mutations in CECR1 DADA2 results in variable autoinflammation and vasculopathy (recurrent fevers, livedo reticularis, polyarteritis nodosa, lacunar ischemic strokes, and intracranial hemorrhages), immunodeficiency and bone marrow failure. Tumor necrosis factor-α blockade is the treatment of choice for the autoinflammation and vascular manifestations. Hematopoietic stem cell transplantation (HSCT) represents a potential definitive treatment...
December 14, 2017: Blood
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