keyword
https://read.qxmd.com/read/38536168/persistent-cutaneous-lesions-of-darier-disease-and-second-hit-somatic-variants-in-atp2a2-gene
#1
JOURNAL ARTICLE
Lihi Atzmony, Fadia Zagairy, Banan Mawassi, Majd Shehade, Yasmin Tatour, Nada Danial-Farran, Morad Khayat, Nassim Warrour, Roni Dodiuk-Gad, Eran Cohen-Barak
IMPORTANCE: Darier disease (DD) is a rare genetic skin disorder caused by heterozygous variants in the ATP2A2 gene. Clinical manifestations include recurrent hyperkeratotic papules and plaques that occur mainly in seborrheic areas. Although some of the lesions wax and wane in response to environmental factors, others are severe and respond poorly to therapy. OBJECTIVE: To investigate the molecular mechanism underlying the persistency of skin lesions in DD. DESIGN, SETTING, AND PARTICIPANTS: In this case series, DNA was extracted from unaffected skin, transient and persistent lesional skin, and blood from 9 patients with DD...
March 27, 2024: JAMA Dermatology
https://read.qxmd.com/read/38536067/targeted-and-shallow-whole-genome-sequencing-identifies-therapeutic-opportunities-in-p53abn-endometrial-cancers
#2
JOURNAL ARTICLE
Amy Jamieson, Juliana Sobral de Barros, Dawn R Cochrane, J Maxwell Douglas, Sameer Shankar, Branden J Lynch, Samuel Leung, Spencer Martin, Janine Senz, Amy Lum, Yvette Drew, C Blake Gilks, David G Huntsman, Jessica N McAlpine
PURPOSE: Shallow whole genome sequencing (sWGS) can detect copy number (CN) aberrations. In high-grade serous ovarian (HGSOC) sWGS identified CN signatures such as homologous recombination deficiency (HRD) to direct therapy. We applied sWGS with targeted sequencing to p53abn endometrial cancers (ECs) to identify additional prognostic stratification and therapeutic opportunities. EXPERIMENTAL DESIGN: sWGS and targeted panel sequencing was performed on formalin-fixed paraffin-embedded p53abn ECs...
March 27, 2024: Clinical Cancer Research
https://read.qxmd.com/read/38536042/genetic-variation-in-severe-cystic-fibrosis-liver-disease-is-associated-with-novel-mechanisms-for-disease-pathogenesis
#3
JOURNAL ARTICLE
Jaclyn R Stonebraker, Rhonda G Pace, Paul J Gallins, Hong Dang, Melis A Aksit, Anna V Faino, William W Gordon, Sonya MacParland, Michael J Bamshad, Ronald L Gibson, Garry R Cutting, Peter R Durie, Fred A Wright, Yi-Hui Zhou, Scott M Blackman, Wanda K O'Neal, Simon C Ling, Michael R Knowles
BACKGROUND AND AIMS: It is not known why severe cystic fibrosis (CF) liver disease (CFLD) with portal hypertension occurs in only ~7% of people with CF (pwCF). We aimed to identify genetic modifiers for severe CFLD to improve understanding of disease mechanisms. APPROACH AND RESULTS: Whole genome sequencing was available in 4,082 pwCF with pancreatic insufficiency (n=516 with severe CFLD; n=3,566 without CFLD). We tested ~15.9 million SNPs for association with severe CFLD versus no-CFLD, using pre-modulator clinical phenotypes including: 1) genetic variant (SERPINA1; Z-allele) previously associated with severe CFLD; 2) candidate SNPs (n=205) associated with non-CF liver diseases; 3) genome-wide association study (GWAS) of common/rare SNPs; 4) transcriptome-wide association (TWAS); and 5) gene-level and pathway analyses...
March 27, 2024: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://read.qxmd.com/read/38535580/characterization-of-gallibacterium-anatis-isolated-from-pathological-processes-in-domestic-mammals-and-birds-in-the-czech-republic
#4
JOURNAL ARTICLE
Jaroslav Bzdil, Soňa Šlosárková, Petr Fleischer, Monika Zouharová, Ján Matiašovic
Gallibacterium anatis , recognized as a resident and opportunistic pathogen primarily in poultry, underwent investigation in unwell domestic mammals and birds. The study encompassed the mapping and comparison of G. anatis isolates, evaluation of their genetic diversity, and determination of their susceptibility to antimicrobials. A total of 11,908 clinical samples were analyzed using cultivation methods and MALDI-TOF. Whole-genome sequencing was performed on seven calf isolates and six hen isolates. Among mammals, G...
March 7, 2024: Pathogens
https://read.qxmd.com/read/38534782/clinical-genomic-analysis-of-1261-patients-with-ehlers-danlos-syndrome-outlines-an-articulo-autonomic-gene-network-entome
#5
JOURNAL ARTICLE
Golder N Wilson, Vijay S Tonk
Systematic evaluation of 80 history and 40 history findings diagnosed 1261 patients with Ehlers-Danlos syndrome (EDS) by direct or online interaction, and 60 key findings were selected for their relation to clinical mechanisms and/or management. Genomic testing results in 566 of these patients supported EDS relevance by their differences from those in 82 developmental disability patients and by their association with general rather than type-specific EDS findings. The 437 nuclear and 79 mitochondrial DNA changes included 71 impacting joint matrix (49 COL5 ), 39 bone (30 COL1/2/9/11 ), 22 vessel (12 COL3/8VWF) , 43 vessel-heart (17 FBN1 /11 TGFB / BR) , 59 muscle (28 COL6/12 ), 56 neural (16 SCN9A / 10A / 11A ), and 74 autonomic (13 POLG /25porphyria related)...
March 19, 2024: Current Issues in Molecular Biology
https://read.qxmd.com/read/38534716/assessment-of-colistin-heteroresistance-among-multidrug-resistant-klebsiella-pneumoniae-isolated-from-intensive-care-patients-in-europe
#6
JOURNAL ARTICLE
Anouk J M M Braspenning, Sahaya Glingston Rajakani, Adwoa Sey, Mariem El Bounja, Christine Lammens, Youri Glupczynski, Surbhi Malhotra-Kumar
Heteroresistance (HR) to colistin is especially concerning in settings where multi-drug-resistant (MDR) K. pneumoniae are prevalent and empiric use of colistin might lead to treatment failures. This study aimed to assess the frequency of occurrence of colistin HR (CHR) among (MDR) K. pneumoniae ( n = 676) isolated from patients hospitalized in 13 intensive care units (ICUs) in six European countries in a clinical trial assessing the impact of decolonization strategies. All isolates were whole-genome-sequenced and studied for in vitro colistin susceptibility...
March 20, 2024: Antibiotics
https://read.qxmd.com/read/38534348/implementing-whole-genome-sequencing-wgs-in-clinical-practice-advantages-challenges-and-future-perspectives
#7
REVIEW
Petar Brlek, Luka Bulić, Matea Bračić, Petar Projić, Vedrana Škaro, Nidhi Shah, Parth Shah, Dragan Primorac
The integration of whole genome sequencing (WGS) into all aspects of modern medicine represents the next step in the evolution of healthcare. Using this technology, scientists and physicians can observe the entire human genome comprehensively, generating a plethora of new sequencing data. Modern computational analysis entails advanced algorithms for variant detection, as well as complex models for classification. Data science and machine learning play a crucial role in the processing and interpretation of results, using enormous databases and statistics to discover new and support current genotype-phenotype correlations...
March 13, 2024: Cells
https://read.qxmd.com/read/38531075/evaluation-of-5-polymerase-chain-reaction-assays-for-the-detection-of-mpox-virus
#8
JOURNAL ARTICLE
Ramzi Fattouh, Karel Boissinot, Esther Jeong, Andrew B Mendlowitz, Calvin P Sjaarda, Henry Wong, Robert Kozak, Prameet M Sheth, Larissa M Matukas
BACKGROUND: In 2022, the global dissemination of mpox virus (MPXV) outside endemic regions prompted the expansion of diagnostic testing worldwide. This study assesses the performance characteristics of 5 real-time polymerase chain reaction (PCR) assays in detecting MPXV during the 2022 outbreak. METHODS: Clinical specimens collected from patients across Ontario, Canada, were tested on the following assays: RealStar Orthopoxyvirus PCR and FlexStar Monkeypox virus PCR (Altona Diagnostics), Novaplex MPXV (Seegene), VIASURE Monkeypox virus Real Time PCR Reagents (CerTest Biotec), and a laboratory-developed test...
March 26, 2024: Journal of Infectious Diseases
https://read.qxmd.com/read/38529177/epidemiological-investigation-and-pathogenicity-analysis-of-waterfowl-astroviruses-in-some-areas-of-china
#9
JOURNAL ARTICLE
Yang Li, Juan Luo, Jiajing Shang, Fuyou Zhang, Chunran Deng, Yingjie Feng, Ge Meng, Wenming Jiang, Xiaohui Yu, Hualei Liu
Waterfowl astroviruses are mainly duck astroviruses and goose astroviruses, of which duck astroviruses (DAstV-3, -4), goose astroviruses (GoAstV-1, -2) are the four new waterfowl 21 astroviruses in recent years, which can lead to enteritis, viral hepatitis, gout and reduce the growth performance of waterfowl, affecting the healthy development of the waterfowl farming industry. Since no targeted drugs or vaccines on the market, studies on the epidemiology of the virus are necessary for vaccine development. In this study, we collected 1546 waterfowl samples from 13 provinces in China for epidemiological investigation...
2024: Frontiers in Microbiology
https://read.qxmd.com/read/38528912/case-report-novel-sin3a-loss-of-function-variant-as-causative-for-hypogonadotropic-hypogonadism-in-witteveen-kolk-syndrome
#10
Lourdes Correa Brito, Ana Keselman, Florencia Villegas, Paula Scaglia, María Esnaola Azcoiti, Sebastián Castro, Nora Sanguineti, Agustín Izquierdo, Marianela Maier, Ignacio Bergadá, Claudia Arberas, Rodolfo A Rey, María Gabriela Ropelato
Pubertal delay can be due to hypogonadotropic hypogonadism (HH), which may occur in association with anosmia or hyposmia and is known as Kallmann syndrome (OMIM #308700). Recently, hypogonadotropic hypogonadism has been suggested to overlap with Witteveen-Kolk syndrome (WITKOS, OMIM #613406) associated with 15q24 microdeletions encompassing SIN3A . Whether hypogonadotropic hypogonadism is due to haploinsufficiency of SIN3A or any of the other eight genes present in 15q24 is not known. We report the case of a female patient with delayed puberty associated with intellectual disability, behavior problems, dysmorphic facial features, and short stature, at the age of 14 years...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38526879/synergistic-effects-of-ceftazidime-avibactam-combined-with-meropenem-in-a-murine-model-of-infection-with-kpc-producing-klebsiella-pneumoniae
#11
JOURNAL ARTICLE
Mei Zheng, Fu-Hao Li, Juan Liu, Wen-Jie Li, Ruo-Xi Yin, Da-Tong Cai, Diego O Andrey, Si-Lin Zheng, Ana C Gales, Wan-Jiang Zhang, Jian Sun, Xiao-Ping Liao, Yang Yu
OBJECTIVES: The emergence and expansion of carbapenem-resistant Klebsiella pneumoniae infections is a concern due to the lack of 'first-line' antibiotic treatment options. The ceftazidime/avibactam is an important clinical treatment for carbapenem-resistant K. pneumoniae infections but there is an increasing number of cases of treatment failure and drug resistance. Therefore, a potential solution is combination therapies that result in synergistic activity against K. pneumoniae carbapenemase: producing K...
March 25, 2024: Journal of Antimicrobial Chemotherapy
https://read.qxmd.com/read/38526778/donkey-like-kirkovirus-is-associated-with-diarrhea-in-piglets
#12
JOURNAL ARTICLE
Panpan Tong, Zunbao Wang, Yueyi Dang, Lei Zhang, Guangwei Song, Xiaozhen Song, Juanjuan Pan, Ling Kuang, Junhui Li, Gang Lu, Jinxin Xie
Kirkovirus (kirV), a seemingly novel virus family, has been found in horses and donkeys. The study's objectives are to investigate the presence of the virus in swine. In this study, donkey-like kirV was detected in rectal swabs of piglets with diarrhea, and the positive rate was found to be 100% (149/149). However, this virus was detected in only one of 261 clinically healthy piglets, which suggested a strong relationship between the kirV and the diarrheic disease. We obtained the whole-genome sequences of three kirVs (Cj-D5, Cj-D32, and Cj-D43), with a length of 3750 nucleotides (nt) and sharing 99...
March 25, 2024: Virus Genes
https://read.qxmd.com/read/38526086/when-the-trojan-horse-is-unable-to-reach-inside-the-city-investigation-of-the-mechanism-of-resistance-behind-the-first-reported-cefiderocol-resistant-e-coli-in-canada
#13
JOURNAL ARTICLE
Kevin R Barker, Gabriel W Rebick, Ken Fakharuddin, Clayton MacDonald, Michael R Mulvey, Laura F Mataseje
Gram-negative metallo-β-lactamase-producing bacteria can be extremely problematic, especially when found to be extensively drug-resistant (XDR). Cefiderocol is a novel antimicrobial that has been shown to overcome most carbapenemases, with very rare resistance reported to date. Within our institution, two multidrug-resistant and one XDR strains were isolated from a patient who recently emigrated from India. Each isolate underwent whole-genome sequencing to resolve plasmids and determine phylogenetics, strain typing, and mechanisms of resistance...
March 25, 2024: Microbiology Spectrum
https://read.qxmd.com/read/38525876/dysregulation-of-mtor-signaling-mediates-common-neurite-and-migration-defects-in-both-idiopathic-and-16p11-2-deletion-autism-neural-precursor-cells
#14
JOURNAL ARTICLE
Smrithi Prem, Bharati Dev, Cynthia Peng, Monal Mehta, Rohan Alibutud, Robert J Connacher, Madeline St Thomas, Xiaofeng Zhou, Paul Matteson, Jinchuan Xing, James H Millonig, Emanuel DiCicco-Bloom
Autism spectrum disorder (ASD) is defined by common behavioral characteristics, raising the possibility of shared pathogenic mechanisms. Yet, vast clinical and etiological heterogeneity suggests personalized phenotypes. Surprisingly, our iPSC studies find that six individuals from two distinct ASD-subtypes, idiopathic and 16p11.2 deletion, have common reductions in neural precursor cell (NPC) neurite outgrowth and migration even though whole genome sequencing demonstrates no genetic overlap between the datasets...
March 25, 2024: ELife
https://read.qxmd.com/read/38524775/cold-tumour-phenotype-explained-through-whole-genome-sequencing-in-clinical-nasopharyngeal-cancer-a-preliminary-study
#15
JOURNAL ARTICLE
Handoko, Marlinda Adham, Lisnawati Rachmadi, Heri Wibowo, Soehartati A Gondhowiardjo
INTRODUCTION: Nasopharyngeal cancer (NPC) is a complex cancer due to its unique genomic features and association with the Epstein-Barr virus (EBV). Despite therapeutic advancements, NPC prognosis remains poor, necessitating a deeper understanding of its genomics. Here, we present a comprehensive whole genome sequencing (WGS) view of NPC genomics and its correlation with the phenotype. METHODS: This study involved WGS of a clinical NPC biopsy specimen. Sequencing was carried out using a long read sequencer from Oxford Nanopore...
2024: ImmunoTargets and Therapy
https://read.qxmd.com/read/38524570/genotypic-and-phenotypic-mechanisms-underlying-antimicrobial-resistance-and-synergistic-efficacy-of-rifampicin-based-combinations-against-carbapenem-resistant-acinetobacter-baumannii
#16
JOURNAL ARTICLE
Lois Chinwe Nwabor, Arnon Chukamnerd, Ozioma Forstinus Nwabor, Komwit Surachat, Rattanaruji Pomwised, Kongpop Jeenkeawpiam, Sarunyou Chusri
PURPOSE: Carbapenem-resistant Acinetobacter baumannii (CRAB) is an urgent concern to public health. This study focuses on exploring the resistance mechanisms and the in vitro results of using rifampicin in combination with conventional antibiotics for the management of CRAB. METHODS: The synergistic and bactericidal effects of rifampicin with conventional antibiotics were evaluated using chequerboard assay and time-kill assay, while the phenotypic and genotypic characteristics of resistant determinants were performed by efflux pump detection and whole genome sequencing on 29 isolates from ICU patients with underlying health diseases...
March 30, 2024: Heliyon
https://read.qxmd.com/read/38524541/genetic-investigation-in-a-four-generation-chinese-family-with-congenital-fibrosis-of-extraocular-muscles-and-keratoconus
#17
JOURNAL ARTICLE
Qinghong Lin, Xuejun Wang, Xin Zhan, Xiaoliao Peng, Yan Wang, Xingtao Zhou
Here, we have reported the genetic and clinical characteristics of four generations of a family patient from China with congenital fibrosis of extraocular muscles 1 (CFEOM1) and keratoconus (KC). The history of diseases, clinical observations, and blood samples of all family members were collected. A total of 100 healthy participants were recruited as normal controls. The whole exome sequencing of the genomic DNA and polymerase chain reaction were performed on samples obtained from the controls and their family members to verify the gene variants...
March 30, 2024: Heliyon
https://read.qxmd.com/read/38524302/alternative-genome-sequencing-approaches-of-sars-cov-2-using-ion-ampliseq-technology
#18
JOURNAL ARTICLE
Md Shazid Hasan, M Shaminur Rahman, Prosanto Kumar Das, A S M Rubayet Ul Alam, Ovinu Kibria Islam, Hassan M Al-Emran, M Anwar Hossain, Iqbal Kabir Jahid
A thorough understanding of SARS-CoV-2 genetic features is compulsory to track the ongoing pandemic across multiple geographical locations of the world. Thermo Fisher Scientific USA has developed the Ion AmpliSeq SARS-CoV-2 Research Panel for the targeted sequencing of SARS-CoV-2 complete genome with high coverage and lower error rate. In this study an alternative approach of complete genome sequencing has been validated using different commercial sequencing kits to sequence the SARS-CoV-2. Amplification of cDNA with the SARS-CoV-2 primer pool was performed separately using two different master mixes: 2X environmental master mix (EM) and Platinum™ PCR SuperMix High Fidelity master mix (PM) instead of 5X Ion AmpliSeq™ HiFi Mix whereas NEBNext® Fast DNA Library Prep Set for Ion Torrent™ kit was used as an alternative to Ion AmpliSeq Library Kit Plus for other reagents...
June 2024: MethodsX
https://read.qxmd.com/read/38524212/the-first-clinical-validation-of-whole-genome-screening-on-standard-trophectoderm-biopsies-of-preimplantation-embryos
#19
JOURNAL ARTICLE
Yuntao Xia, Maria Katz, Dhruva Chandramohan, Elan Bechor, Benjamin Podgursky, Michael Hoxie, Qinnan Zhang, Willy Chertman, Jessica Kang, Edwina Blue, Justin Chen, Justin Schleede, Nathan R Slotnick, Xiaoli Du, Robert Boostanfar, Eric Urcia, Barry Behr, Jacques Cohen, Noor Siddiqui
OBJECTIVE: To validate the performance of our laboratory-developed whole-genome screening assay within clinical preimplantation genetic testing environments. DESIGN: Perform a laboratory-developed whole-genome assay on both cell lines and trophectoderm biopsies, subsequently employing the next-generation sequencing procedure to reach a sequencing depth of 30X. Adhere to the Genome Analysis Toolkit best practices for accuracy, sensitivity, specificity, and precision calculations by comparing samples with references...
March 2024: F&S reports
https://read.qxmd.com/read/38523846/analysis-of-tumor-mutational-burden-and-mutational-landscape-comparing-whole-exome-sequencing-and-comprehensive-genomic-profiling-in-patients-with-resectable-early-stage-non-small-cell-lung-cancer
#20
JOURNAL ARTICLE
Su-Jin Choi, Jii Bum Lee, Jae Hwan Kim, Min Hee Hong, Byoung Chul Cho, Sun Min Lim
BACKGROUND: Identifying actionable driver mutations via tissue-based comprehensive genomic profiling (CGP) is paramount in treatment decisions for metastatic non-squamous, non-small-cell lung cancer (NSCLC). However, the role of CGP remains elusive in resectable NSCLC. Here, we elucidate the feasibility of CGP in early-stage NSCLC Korean patients and compare the tumor mutational burden (TMB) and mutation landscape using three different platforms. METHODS: All surgically resected NSCLC samples ( N  = 96) were analyzed to assess the concordance in TMB calculation and targetable mutations using whole-exome sequencing (WES) and TruSight Oncology 500 (TSO500)...
2024: Therapeutic Advances in Medical Oncology
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