Microarray comparative genomic hybridisation (aCGH) provides an estimate of the relative abundance of genomic DNA (gDNA) taken from comparator and reference organisms by hybridisation to a microarray containing probes that represent sequences from the reference organism. The experimental method is used in a number of biological applications, including the detection of human chromosomal aberrations, and in comparative genomic analysis of bacterial strains, but optimisation of the analysis is desirable in each problem domain.We present a method for analysis of bacterial aCGH data that encodes spatial information from the reference genome in a hidden Markov model. This technique is the first such method to be validated in comparisons of sequenced bacteria that diverge at the strain and at the genus level: Pectobacterium atrosepticum SCRI1043 (Pba1043) and Dickeya dadantii 3937 (Dda3937); and Lactococcus lactis subsp. lactis IL1403 and L. lactis subsp. cremoris MG1363. In all cases our method is found to outperform common and widely used aCGH analysis methods that do not incorporate spatial information. This analysis is applied to comparisons between commercially important plant pathogenic soft-rotting enterobacteria (SRE) Pba1043, P. atrosepticum SCRI1039, P. carotovorum 193, and Dda3937.Our analysis indicates that it should not be assumed that hybridisation strength is a reliable proxy for sequence identity in aCGH experiments, and robustly extends the applicability of aCGH to bacterial comparisons at the genus level. Our results in the SRE further provide evidence for a dynamic, plastic 'accessory' genome, revealing major genomic islands encoding gene products that provide insight into, and may play a direct role in determining, variation amongst the SRE in terms of their environmental survival, host range and aetiology, such as phytotoxin synthesis, multidrug resistance, and nitrogen fixation.
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http://dx.doi.org/10.1371/journal.pcbi.1000473 | DOI Listing |
Mol Diagn Ther
January 2025
Istituto Europeo di Oncologia, IRCCS, Via Adamello 16, 20139, Milan, Italy.
Background: Predicting response to targeted cancer therapies increasingly relies on both simple and complex genetic biomarkers. Comprehensive genomic profiling using high-throughput assays must be evaluated for reproducibility and accuracy compared with existing methods.
Methods: This study is a multicenter evaluation of the Oncomine™ Comprehensive Assay Plus (OCA Plus) Pan-Cancer Research Panel for comprehensive genomic profiling of solid tumors.
Childs Nerv Syst
January 2025
Ph.D. Human Genetics Program, Molecular Biology and Genomics Department, Human Genetics Institute "Dr. Enrique Corona-Rivera", University Center of Health Sciences, University of Guadalajara, Guadalajara, Mexico.
Background: Central nervous system tumors (CNSTs) represent a significant oncological challenge in pediatric populations, particularly in developing regions where access to diagnostic and therapeutic resources is limited.
Methods: This research investigates the epidemiology, histological classifications, and survival outcomes of CNST in a cohort of pediatric patients aged 0 to 19 years within a 25-year retrospective study at the Civil Hospital of Guadalajara, Mexico, from 1999 to 2024.
Results: Data was analyzed from 273 patients who met inclusion criteria, revealing a higher incidence in males (51.
Theor Appl Genet
January 2025
School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China.
A complete set of monosomic alien addition lines of Radish-Brassica oleracea exhibiting extensive variations was generated and well characterized for their chromosome behaviors and phenotypic characteristics. Monosomic alien addition lines (MAALs) are developed through interspecific hybridization, where an alien chromosome from a relative species is introduced into the genome of the recipient plant, serving as valuable genetic resources. In this study, an allotetraploid Raphanobrassica (RRCC, 2n = 36) was created from the interspecific hybridization between radish (Raphanus sativus, RR, 2n = 18) and Brassica oleracea (CC, 2n = 18).
View Article and Find Full Text PDFCell Biol Toxicol
January 2025
Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang , Liaoning Province, China.
NFKB1, a core transcription factor critical in various biological process (BP), is increasingly studied for its role in tumors. This research combines literature reviews, meta-analyses, and bioinformatics to systematically explore NFKB1's involvement in tumor initiation and progression. A unique focus is placed on the NFKB1-94 ATTG promoter polymorphism, highlighting its association with cancer risk across diverse genetic models and ethnic groups, alongside comprehensive analysis of pan-cancer expression patterns and drug sensitivity.
View Article and Find Full Text PDFMayo Clin Proc
January 2025
Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN; Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, MN; Division of Heart Rhythm Services, Department of Cardiovascular Medicine, Windland Smith Rice Genetic Heart Rhythm Clinic, Mayo Clinic, Rochester, MN. Electronic address:
Objective: To test whether an artificial intelligence (AI) deep neural network (DNN)-derived analysis of the 12-lead electrocardiogram (ECG) can distinguish patients with long QT syndrome (LQTS) from those with acquired QT prolongation.
Methods: The study cohort included all patients with genetically confirmed LQTS evaluated in the Windland Smith Rice Genetic Heart Rhythm Clinic and controls from Mayo Clinic's ECG data vault comprising more than 2.5 million patients.
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