Interest of next-generation sequencing in BCG-treated high-risk bladder cancer

2018 ◽  
Vol 28 (6) ◽  
pp. 344-350 ◽  
Author(s):  
C. Jungels ◽  
N. Martinez Chanza ◽  
S. Albisinni ◽  
M. Mercier ◽  
N. d’Haene ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Next Generation Sequencing ◽  
High Risk ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Characterization and Diversity of 243 Complete Human Papillomavirus Genomes in Cervical Swabs Using Next Generation Sequencing

Viruses ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1437
Author(s):  
Ardashel Latsuzbaia ◽  
Anke Wienecke-Baldacchino ◽  
Jessica Tapp ◽  
Marc Arbyn ◽  
Irma Karabegović ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Next Generation Sequencing ◽  
High Risk ◽  
Pairwise Distance ◽  
Next Generation ◽  
Hpv Genotypes ◽  
Complete Genomes ◽  
Hpv Types ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

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.

scholarly journals 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

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.

RNAseq in addition to next generation sequencing in advanced genitourinary cancers reveals transcriptomic silencing of DNA mutations: Implications for resistance to targeted therapeutics.

2019 ◽  
Vol 37 (7_suppl) ◽  
pp. 583-583 ◽  
Author(s):  
Jacob J. Adashek ◽  
Shumei Kato ◽  
Rahul Parulkar ◽  
Christopher Szeto ◽  
Sandeep K. Reddy ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Bladder Cancer ◽  
Next Generation Sequencing ◽  
Kidney Cancer ◽  
Next Generation ◽  
Dna And Rna ◽  
Number Of Patients ◽  
Study Results ◽  
Dna Alterations ◽  
Generation Sequencing

583 Background: Next generation sequencing (NGS) for advanced tumors is becoming more routine. However, not all patients respond to precision matched treatments. We hypothesized that one potential reason for treatment failure with targeted therapy could be discrepancies between DNA alterations and RNA expression. Methods: Tumor samples from patients with metastatic kidney, bladder, and prostate cancer were analyzed by whole exome or whole genome NGS and RNA sequencing (CLIA-certified laboratory; NantOmics LLC, Santa Cruz, CA). Only known pathogenic driver alterations were analyzed in the current study. Results: Of 45 patients, 10 had kidney cancer, 18 had bladder cancer; and 17 had prostate cancer. Median age was 66 years (range, 28 - 86). The most commonly altered genes were TP53 (35.6% [16/45]), PIK3CA (15.6% [7/45]), FGFR3 (11.1% [5/45]), ALK (8.9% [4/45]), and ATM (8.9% [4/45]). In total, 86 pathogenic DNA alterations were identified; 17 of these (19.8%) were not observed at the RNA level. Among 45 patients, 31.1% (14/45) had ≥1 DNA alteration that was not expressed at the RNA level. Discordance between DNA and RNA was seen in 40% of patients with kidney cancer (4/10), 28% of patients with bladder cancer (5/18), and 29% with prostate cancer (5/17). Examples of genes that had pathogenic DNA alterations not seen at the RNA level included ALK (four discordant cases), KDR (three discordant cases) and GNAS (one discordant case). On the other hand, alterations involving certain genes showed 100% concordance between DNA and RNA: TP53 [N = 16], PIK3CA [N = 7], and FGFR3 [N = 5]). Conclusions: A significant number of patients with genitourinary tumors had DNA alterations that are silenced at the RNA level (19.8%). Transcriptomic silencing merits additional investigation as a mechanism that could mediate resistance to therapeutics targeted at cognate alterations.

Next-Generation Sequencing Informing Therapeutic Decisions and Personalized Approaches

2016 ◽  
pp. e442-e448 ◽  
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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