Utility of Next-Generation Sequencing compared to FISH for Detection of High-Risk Lesions in Bile Duct Brushings in Patients with Primary Sclerosing Cholangitis

In recent years, next generation sequencing (NGS) technology has been widely used for the discovery of novel human papillomavirus (HPV) genotypes, variant characterization and genotyping. Here, we compared the analytical performance of NGS with a commercial PCR-based assay (Anyplex II HPV28) in cervical samples of 744 women. Overall, HPV positivity was 50.2% by the Anyplex and 45.5% by the NGS. With the NGS, we detected 25 genotypes covered by Anyplex and 41 additional genotypes. Agreement between the two methods for HPV positivity was 80.8% (kappa = 0.616) and 84.8% (kappa = 0.652) for 28 HPV genotypes and 14 high-risk genotypes, respectively. We recovered and characterized 243 complete HPV genomes from 153 samples spanning 40 different genotypes. According to phylogenetic analysis and pairwise distance, we identified novel lineages and sublineages of four high-risk and 16 low-risk genotypes. In total, 17 novel lineages and 14 novel sublineages were proposed, including novel lineages of HPV45, HPV52, HPV66 and a novel sublineage of HPV59. Our study provides important genomic insights on HPV types and lineages, where few complete genomes were publicly available.

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A14 Estimating time since HIV infection using next-generation sequencing data: A unique tool to help understand HIV prevention among high-risk young women in Ukraine

Virus Evolution ◽

10.1093/ve/vez002.013 ◽

2019 ◽

Vol 5 (Supplement_1) ◽

Author(s):

Francois Cholette ◽

Christina Daniuk ◽

Emma Lee ◽

Rupert Capina ◽

Eve Cheuk ◽

...

Keyword(s):

Next Generation Sequencing ◽

High Risk ◽

Hiv Prevention ◽

Hiv Infection ◽

Sex Work ◽

Young Women ◽

Casual Sex ◽

Transactional Sex ◽

Next Generation ◽

Generation Sequencing

Abstract The transitions study examines HIV risk among adolescent girls and young women through their sexual life course from first sex, to past and current engagement in casual sex, transactional sex, and, for some, formal sex work (FSW). Understanding the timing of HIV infection and the circumstances around early infection in young females is critical to HIV prevention interventions. We inferred time since HIV infection using next-generation sequencing (NGS) of the HIV pol gene isolated from cross-sectional samples among high-risk young women in Dnipro, Ukraine. Dried blood spots were collected on Whatman 903 cards from young women aged 14–24 engaged in casual sex (n = 894), transactional sex (n = 464), and FSW (n = 452). The HIV pol gene was sequenced using an in-house NGS HIV drug resistance mutation genotyping assay. Time since HIV infection was inferred using an online tool as described by Puller et al. (2017) freely available at https://hiv.biozentrum.unibas.ch/ETI/. The mean estimated time since HIV infection (ETI) for participants engaged in casual sex, transactional sex, and FSW is 1.98, 1.84, and 3.01 years, respectively. ETI was used to determine the duration of HIV infection for each participant and compared to the number of sexually active years prior to FSW. Among FSW, 61 per cent of participants were infected with HIV prior to entry into sex work. In general, ETI from NGS data suggests that FSWs were infected with HIV before entry into FSW. Expansion of targeted prevention programs beyond FSW could play an important role in mitigating HIV transmission at the population level.

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Next-Generation Sequencing Informing Therapeutic Decisions and Personalized Approaches

American Society of Clinical Oncology Educational Book ◽

10.1200/edbk_159017 ◽

2016 ◽

pp. e442-e448 ◽

Cited By ~ 3

Author(s):

Raphael Szalat ◽

Nikhil C. Munshi

Keyword(s):

Next Generation Sequencing ◽

High Risk ◽

Proteasome Inhibitors ◽

Next Generation ◽

Current State ◽

Therapeutic Decisions ◽

High Risk Disease ◽

Risk Patients ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Multiple myeloma is a heterogeneous disease featured by different molecular subtypes. In the last decade, new therapeutics including second- and third-generation proteasome inhibitors and immunomodulatory agents, monoclonal antibodies, and other novel targeted agents have completely transformed the outcome of the disease. The task ahead is to develop strategies to identify effective combinations and sequences of agents that can exploit the genetic make-up of myeloma cells to improve efficacy. Moreover, a subgroup of high-risk patients who experience early disease relapse and shorter survival also requires early identification and specific intervention. Next-generation sequencing (NGS) technologies now allow us to accomplish some of these goals. As described here, besides improving our understanding of the disease, it is beginning to influence our clinical decisions and therapeutic choices. In this article, we describe the current state-of-the-art role of NGS in myeloma from identifying high-risk disease, to drug selection, and, ultimately, to guide personalized therapy.

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