The Ataxia Global Initiative (AGI) is a worldwide multi-stakeholder research platform to systematically enhance trial-readiness in degenerative ataxias. The next-generation sequencing (NGS) working group of the AGI aims to improve methods, platforms, and international standards for ataxia NGS analysis and data sharing, ultimately allowing to increase the number of genetically ataxia patients amenable for natural history and treatment trials. Despite extensive implementation of NGS for ataxia patients in clinical and research settings, the diagnostic gap remains sizeable, as approximately 50% of patients with hereditary ataxia remain genetically undiagnosed. One current shortcoming is the fragmentation of patients and NGS datasets on different analysis platforms and databases around the world. The AGI NGS working group in collaboration with the AGI associated research platforms-CAGC, GENESIS, and RD-Connect GPAP-provides clinicians and scientists access to user-friendly and adaptable interfaces to analyze genome-scale patient data. These platforms also foster collaboration within the ataxia community. These efforts and tools have led to the diagnosis of > 500 ataxia patients and the discovery of > 30 novel ataxia genes. Here, the AGI NGS working group presents their consensus recommendations for NGS data sharing initiatives in the ataxia field, focusing on harmonized NGS variant analysis and standardized clinical and metadata collection, combined with collaborative data and analysis tool sharing across platforms.
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http://dx.doi.org/10.1007/s12311-023-01537-1 | DOI Listing |
J Clin Virol
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Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada. Electronic address:
Background: Next-generation sequencing (NGS) for Hepatitis B virus (HBV) antiviral resistance (AVR) testing is a highly sensitive diagnostic method, able to detect low-level mutant subpopulations. Our clinical virology laboratory previously transitioned from DNA hybridization (INNO-LiPA) to NGS, initially with the GS Junior System and subsequently the MiSeq. The Oxford Nanopore Technology (ONT) sequencing system was evaluated for HBV resistance testing, with regards to sequencing accuracy and turn-around time.
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July 2024
Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110007, India.
Emergence of drug-induced antimicrobial resistance (AMR) forms a crippling health and economic crisis worldwide, causing high mortality from otherwise treatable diseases and infections. Next Generation Sequencing (NGS) has significantly augmented detection of culture independent microbes, potential AMR in pathogens and elucidation of mechanisms underlying it. Here, we review recent findings of AMR evolution in pathogens aided by integrated genomic investigation strategies inclusive of bacteria, virus, fungi and AMR alleles.
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January 2025
Department of Computer Application, National Institute of Technology, Raipur, India. Electronic address:
The emergence of infectious disease and antibiotic resistance in bacteria like Escherichia coli (E. coli) shows the necessity for novel computational techniques for identifying essential genes that contribute to resistance. The task of identifying resistant strains and multi-drug patterns in E.
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January 2025
Department of Pathology and Laboratory Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA; Rutgers Cancer Institute, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.
Collision tumors, characterized by the coexistence of two unique neoplasms in close approximation, are rare and pose diagnostic challenges. This is particularly true when the unique neoplasms are of the same histologic type. Here we report such a case where comprehensive tumor profiling by next generation sequencing (NGS) as well as immunohistochemistry revealed two independent adenocarcinomas comprising what was initially diagnosed as a single adenocarcinoma of the gastroesophageal (GEJ) junction.
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December 2024
Physical Medicine and Rehabilitation, Unidade Local de Saúde de Lisboa Ocidental, Lisbon, PRT.
Chondrodysplasia punctata (CP) is a rare skeletal dysplasia characterized by punctate calcifications in areas of endochondral ossification, with Conradi-Hünermann-Happle syndrome (CDPX2) being the most common form. This study presents a clinical case of a 10-month-old female child, diagnosed with CDPX2 following a referral from a neonatology department of a secondary hospital center to a genetics consultation at a tertiary hospital center in Portugal. Despite normal prenatal monitoring, postnatal evaluations revealed typical manifestations of the syndrome, including nasomaxillary hypoplasia, macrocephaly, and skeletal abnormalities confirmed through imaging.
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