Formalin-fixed, paraffin-embedded (FFPE) tissue samples represent an invaluable biobank for retrospective cancer research with molecular methods such as real-time PCR and next-generation sequencing (NGS). However, the usage of FFPE material in NGS approaches involves several challenges associated with the limited quantity and quality of DNA. This protocol describes how to purify DNA from FFPE material and how to prepare it for downstream NGS workflows including fragmentation, size selection, and library preparation for Illumina MiSeq/HiSeq sequencing. © 2016 by John Wiley & Sons, Inc.
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High prevalence of reverse transcriptase inhibitors associated resistance mutations among people living with HIV on dolutegravir-based antiretroviral therapy in Francistown, Botswana.
J Antimicrob Chemother
January 2025
Research Laboratory, Botswana Harvard Health Partnership, Gaborone, Botswana.
Objectives: We assessed HIV-1 drug resistance profiles among people living with HIV (PLWH) with detectable viral load (VL) and on dolutegravir-based antiretroviral therapy (ART) in Botswana.
Methods: The study utilised available 100 residual HIV-1 VL samples from unique PLWH in Francistown who had viraemia at-least 6 months after initiating ART in Botswana's national ART program from November 2023 to January 2024. Viraemia was categorized as low-level viraemia (LLV) (VL: 200-999 copies/mL) or virologic failure (VF) (VL ≥1000 copies/mL).
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Department of Clinical Pharmacy, Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
Efforts have been made to leverage technology to accurately identify tumor characteristics and predict how each cancer patient may respond to medications. This involves collecting data from various sources such as genomic data, histological information, functional drug profiling, and drug metabolism using techniques like polymerase chain reaction, sanger sequencing, next-generation sequencing, fluorescence in situ hybridization, immunohistochemistry staining, patient-derived tumor xenograft models, patient-derived organoid models, and therapeutic drug monitoring. The utilization of diverse detection technologies in clinical practice has made "individualized treatment" possible, but the desired level of accuracy has not been fully attained yet.
View Article and Find Full Text PDFPost-transcriptional regulation of the transcriptional apparatus in neuronal development.
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Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States.
Post-transcriptional mechanisms, such as alternative splicing and polyadenylation, are recognized as critical regulatory processes that increase transcriptomic and proteomic diversity. The advent of next-generation sequencing and whole-genome analyses has revealed that numerous transcription and epigenetic regulators, including transcription factors and histone-modifying enzymes, undergo alternative splicing, most notably in the nervous system. Given the complexity of regulatory processes in the brain, it is conceivable that many of these splice variants control different aspects of neuronal development.
View Article and Find Full Text PDFAnalysis of the benefit of anti-PD-1 monotherapy according to NGS-diagnosed genetic alterations in patients with non-small cell lung cancer.
Explor Target Antitumor Ther
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Department of Thoracic Oncology, Georges Pompidou European Hospital, Paris Cité University, AP-HP, CARPEM, 75015 Paris, France.
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View Article and Find Full Text PDFProlonged Severe CD4+ Lymphocytopenia and Hypogammaglobulinemia in Patients With Evans' Syndrome: A Case Report.
Cureus
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Department of Hematology and Oncology, Toyohashi Municipal Hospital, Toyohashi, JPN.
Primary immunodeficiency (PID) is one of the causes of secondary autoimmune hemolytic anemia (AIHA) and Evans' syndrome (ES). Serum immunoglobulins should be tested in patients with AIHA/ES, as common variable immunodeficiency is the most common PID of secondary AIHA/ES. However, it is not fully understood how immunodeficiency is assessed, in addition to serum immunoglobulins.
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