scholarly journals Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights

2021 ◽  
Author(s):  
Dorottya Nagy-Szakal ◽  
Mara Couto-Rodriguez ◽  
Heather L. Wells ◽  
Joseph E. Barrows ◽  
Marilyne Debieu ◽  
...  
Keyword(s):  
Genetic Variant ◽  
Viral Metagenomics ◽  
Research Use ◽  
The Novel ◽  
Emerging Pathogens ◽  
Hybrid Capture ◽  
Hybridization Capture ◽  
Variant Discovery ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

This is the first FDA emergency-use-authorized hybridization capture-based next-generation sequencing (NGS) assay to detect the SARS-CoV-2 genome. Viral metagenomics and the novel hybrid capture NGS-based assay, along with its research-use-only analysis, can provide important genetic insights into SARS-CoV-2 and other emerging pathogens and improve surveillance and early detection, potentially preventing or mitigating new outbreaks.

scholarly journals Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights

2021 ◽  
Author(s):  
Dorottya Nagy-Szakal ◽  
Mara Couto-Rodriguez ◽  
Heather L. Wells ◽  
Joseph E. Barrows ◽  
Marilyne Debieu ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Limit Of Detection ◽  
Viral Evolution ◽  
Viral Fitness ◽  
Pcr Assay ◽  
Hybridization Capture ◽  
Variant Discovery ◽  
Powerful Approach ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The emergence of novel SARS-CoV-2 genetic variants that may alter viral fitness highlights the urgency of widespread next-generation sequencing (NGS) surveillance. To profile genetic variants, we developed and clinically validated a hybridization capture SARS-CoV-2 NGS assay, integrating novel methods for panel design using dsDNA biotin-labeled probes, and built accompanying software. The positive and negative percent agreement were defined in comparison to an orthogonal RT-PCR assay (PPA and NPA: both 96.7%). The limit of detection was established to be 800 copies/ml with an average fold-enrichment of 46,791x. We identified novel 107 mutations, including 24 in the functionally-important spike protein. Further, we profiled the full nasopharyngeal microbiome using metagenomics and found overrepresentation of 7 taxa and macrolide resistance in SARS-CoV-2-positive patients. This hybrid capture NGS assay, coupled with optimized software, is a powerful approach to detect and comprehensively map SARS-CoV-2 genetic variants for tracking viral evolution and guiding vaccine updates.

scholarly journals Different Methods in HPV Genotyping of Anogenital and Oropharyngeal Lesions: Comparison between VisionArray® Technology, Next Generation Sequencing, and Hybrid Capture Assay

2021 ◽  
Vol 2 (1) ◽  
pp. 29-41
Author(s):  
Giorgia Acquaviva ◽  
Michela Visani ◽  
Viviana Sanza ◽  
Antonio De Leo ◽  
Thais Maloberti ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Turnaround Time ◽  
Hpv Infection ◽  
Human Papillomaviruses ◽  
Next Generation ◽  
Hybrid Capture ◽  
Capture Assay ◽  
Anogenital Area ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

(1) Background: Human papillomaviruses (HPVs) are known to be related to the development of about 5% of all human cancers. The clinical relevance of HPV infection has been deeply investigated in carcinomas of the oropharyngeal area, uterine cervix, and anogenital area. To date, several different methods have been used for detecting HPV infection. The aim of the present study was to compare three different methods for the diagnosis of the presence of the HPV genome. (2) Methods: A total of 50 samples were analyzed. Twenty-five of them were tested using both next generation sequencing (NGS) and VisionArray® technology, the other 25 were tested using Hybrid Capture (HC) II assay and VisionArray® technology. (3) Results: A substantial agreement was obtained using NGS and VisionArray® (κ = 0.802), as well as between HC II and VisionArray® (κ = 0.606). In both analyses, the concordance increased if only high risk HPVs I(HR-HPVs) were considered as “positive”. (4) Conclusions: Our data highlighted the importance of technical choice in HPV characterization, which should be guided by the clinical aims, costs, starting material, and turnaround time for results.

scholarly journals Clinical results and importance of next-generation sequencing (NGS) in detecting targeted mutations in the treatment of metastatic Lung Cancer: Single center initial results

2019 ◽  
Vol 6 (12) ◽  
pp. 327-332
Author(s):  
Cem Mirili ◽  
Çiğdem Kahraman ◽  
Ali Yılmaz ◽  
Mehmet Bilici ◽  
Salim Başol Tekin ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Next Generation Sequencing ◽  
Genetic Variants ◽  
Genetic Variant ◽  
Clinical Results ◽  
Clinical Effects ◽  
Next Generation ◽  
Variant Analysis ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Objective:  In Lung cancer (LC), which is one of the most deadly cancers, longer survival has been achieved with targeted agents. For this reason, it is important to find the patients who are suitable for targeted therapies. Next-generation sequencing (NGS) is a method that allows multiple genetic variants to be detected simultaneously by performing massive parallel DNA sequencing at the same time. We wanted to reveal the clinical effects and benefits of genetic variant analysis with NGS for our patients. Material and Methods: Patients with stage 4 non-squamous and not otherwise specified (NOS) Non-small cell LC who underwent genetic variant analysis with NGS were included in the study, retrospectively. Results: Total of the 51 patients, 41 (80.4%) were male and the median age was 64 (35-85) years. According to TNM, 21 (41.2%) patients were stage 4A, 30 (58.8%) patients were stage 4B and 39 (76.5%) patients had adenocarcinoma and 12 (23.5%) had NOS histology. NGS analyzes were performed in median 14 days (8-43) and determined 24 pathogenic variants in 17 (%25) patients: 9EGFR (%17,6), 6PIKC3A (%11,7), 5KRAS (%9,8), 2PTEN (%3,9), 1BRAF (%1,9), 1MET (%1,6) (7 of them concomitantly). Cytotoxic chemotherapy was recommended in 41, anti-EGFR agents in 8 (afatinib in 4, erlotinib in 4 patients) patients and anti-BRAF+MEK inhibitor agent (dabrafenib+trametinib) in 1 patient. Conclusion: With the NGS, in just two weeks, both target and resistance genetic variants of our patients were detected at the same time and individualized treatments were applied. In this way, both time and cost were saved.

scholarly journals Genetic and Antigenetic Characterization of the Novel Kotalahti Bat Lyssavirus (KBLV)

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 69
Author(s):  
Sten Calvelage ◽  
Niina Tammiranta ◽  
Tiina Nokireki ◽  
Tuija Gadd ◽  
Elisa Eggerbauer ◽  
...  
Keyword(s):  
Novel Species ◽  
Reservoir Host ◽  
The Novel ◽  
Ion Torrent ◽  
Sequence Analyses ◽  
Cross Neutralization ◽  
Next Generation Sequencing Ngs ◽  
Demarcation Criteria ◽  
Generation Sequencing

There is a growing diversity of bat-associated lyssaviruses in the Old World. In August 2017, a dead Brandt’s bat (Myotis brandtii) tested positive for rabies and based on partial sequence analysis, the novel Kotalahti bat lyssavirus (KBLV) was identified. Because the bat was in an autolyzed state, isolation of KBLV was neither successful after three consecutive cell passages on cells nor in mice. Next generation sequencing (NGS) was applied using Ion Torrent ™ S5 technology coupled with target enrichment via hybridization-based capture (myBaits®) was used to sequence 99% of the genome, comprising of 11,878 nucleotides (nt). KBLV is most closely related to EBLV-2 (78.7% identity), followed by KHUV (79.0%) and BBLV (77.6%), supporting the assignment as phylogroup I lyssavirus. Interestingly, all of these lyssaviruses were also isolated from bat species of the genus Myotis, thus supporting that M. brandtii is likely the reservoir host. All information on antigenic and genetic divergence fulfil the species demarcation criteria by ICTV, so that we recommend KBLV as a novel species within the Lyssavirus genus. Next to sequence analyses, assignment to phylogroup I was functionally corroborated by cross-neutralization of G-deleted RABV, pseudotyped with KBLV-G by sera from RABV vaccinated humans. This suggests that conventional RABV vaccines also confer protection against the novel KBLV.

A 975-mW Fully Integrated Genetic Variant Discovery System-on-Chip in 28 nm for Next-Generation Sequencing

2021 ◽  
Vol 56 (1) ◽  
pp. 123-135
Author(s):  
Yi-Chung Wu ◽  
Yen-Lung Chen ◽  
Chung-Hsuan Yang ◽  
Chao-Hsi Lee ◽  
Chao-Yang Yu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Variant ◽  
System On Chip ◽  
Next Generation ◽  
Fully Integrated ◽  
Variant Discovery ◽  
Discovery System ◽  
On Chip ◽  
Generation Sequencing ◽  
28 Nm

scholarly journals Feasibility of comprehensive genotyping specimens from radial endobronchial ultrasonography and electromagnetic navigation bronchoscopy

2021 ◽  
pp. 00942-2020
Author(s):  
Maxime Robin ◽  
Laurent Mhanna ◽  
Leonor Chaltiel ◽  
Gavin Plat ◽  
Valentin Héluain ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Sampling Method ◽  
Small Samples ◽  
Molecular Testing ◽  
Electromagnetic Navigation ◽  
Hybrid Capture ◽  
Endobronchial Ultrasonography ◽  
Peripheral Lung ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

IntroductionMini-invasive bronchoscopic techniques (such as radial endobronchial ultrasonography (rEBUS) and electromagnetic navigation (EMN)) have been developed to reach the peripheral lung but result in small samples. The feasibility of an adequate molecular testing from these specimens has been very little studied.MethodsWe retrospectively reviewed EMN and rEBUS procedures performed in patients diagnosed with lung cancer in our institution in 2017 and 2018. We analysed the sensitivity for rEBUS and EMN and each sampling method, and the feasibility of a comprehensive molecular testing.Results317 rEBUS and 14 EMN were performed. Median sizes of tumors were 16 and 32 mm for EMN and rEBUS, respectively. Overall sensitivity for rEBUS and EMN was 84.3%. Cytology was found to be complementary with biopsies, with 13.3% of cancer diagnosed on cytology while biopsies were negative. Complication rate was 2.4% (pneumothorax 1.5%, mild hemoptysis 0.9%). Genotyping (immunohistochemistry (IHC) for ROS1 and ALK followed by FISH if positive and hybrid capture next-generation sequencing (NGS) covering 48-genes), when ordered (n=188), was feasible in 69.1% (EGFR 17.7%, KRAS 31.7%, BRAF 4.8%, ALK 1.2%, MET 3.1%, HER2 0.8%). PD-L1 expression, when ordered (n=232), could be analysed in 94% of cases. 56.9% (33/58) of patients for whom genotyping was not feasible underwent a second sampling (12 pretreatment, 21 at progression), allowing for the detection of 6 actionable genotypes (5 EGFR, 1 MET).ConclusionrEBUS and EMN are sensitive and safe procedures that result in limited samples, often not suitable for genotyping, highlighting the importance to integrate liquid biopsy in routine.

scholarly journals Nephroplex: a kidney-focused NGS panel highlights the challenges of PKD1 sequencing and identifies a founder BBS4 mutation

2021 ◽  
Author(s):  
Miriam Zacchia ◽  
Francesca Del Vecchio Blanco ◽  
Francesco Trepiccione ◽  
Giancarlo Blasio ◽  
Annalaura Torella ◽  
...  
Keyword(s):  
Kidney Diseases ◽  
Regression Line ◽  
Geographical Area ◽  
Renal Diseases ◽  
The Novel ◽  
Similar Frequency ◽  
Bardet Biedl Syndrome ◽  
Autosomal Dominant Polycystic Kidney ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background Genetic testing of patients with inherited kidney diseases has emerged as a tool of clinical utility by improving the patients’ diagnosis, prognosis, surveillance and therapy. Methods The present study applied a Next Generation Sequencing (NGS)-based panel, named NephroPlex, testing 115 genes causing renal diseases, to 119 individuals, including 107 probands and 12 relatives. Thirty-five (poly)cystic and 72 non (poly)cystic individuals were enrolled. The latter subgroup of patients included Bardet-Biedl syndrome (BBS) patients, as major components. Results Disease-causing mutations were identified in 51.5 and 40% of polycystic and non-polycystic individuals, respectively. Autosomal dominant polycystic kidney disease (ADPKD) patients with truncating PKD1 variants showed a trend towards a greater slope of the age-estimated glomerular filtration rate (eGFR) regression line than patients with (i) missense variants, (ii) any PKD2 mutations and (iii) no detected mutations, according to previous findings. The analysis of BBS individuals showed a similar frequency of BBS4,9,10 and 12 mutations. Of note, all BBS4-mutated patients harbored the novel c.332+1G>GTT variant, which was absent in public databases, however, in our internal database, an additional heterozygote carrier was found. All BBS4-mutated individuals originated from the same geographical area encompassing the coastal provinces of Naples. Discussion In conclusion, these findings indicate the potential for a genetic panel to provide useful information at both clinical and epidemiological levels. Graphic abstract

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