scholarly journals 1584. Development and Dynamics of Cytomegalovirus UL97 Ganciclovir Resistance Mutations in Transplant Recipients Detected by Next-generation Sequencing

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S495-S496
Author(s):  
Isabelle Paula Lodding ◽  
Mette Jørgensen ◽  
Marc Bennedbæk ◽  
Nikolai Kirkby ◽  
Klaudia Naegele ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Transplant Recipients ◽  
Next Generation ◽  
Resistance Mutations ◽  
Ganciclovir Resistance ◽  
Generation Sequencing

scholarly journals Development and Dynamics of Cytomegalovirus UL97 Ganciclovir Resistance Mutations in Transplant Recipients Detected by Next Generation Sequencing

2021 ◽  
Author(s):  
Isabelle P Lodding ◽  
Mette Jørgensen ◽  
Marc Bennedbæk ◽  
Nikolai Kirkby ◽  
Klaudia Naegele ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Illumina Miseq ◽  
Primary Prophylaxis ◽  
Solid Organ ◽  
Next Generation ◽  
Induced Mutations ◽  
Resistance Mutations ◽  
Hematopoietic Stem ◽  
Ganciclovir Resistance ◽  
Generation Sequencing

Abstract Background (Val)ganciclovir resistance mutations in CMV UL97 (UL97-GCV-R) complicate anti-CMV therapy in recipients of solid organ and hematopoietic stem-cell transplants but comprehensive data on prevalence, emergence, and outcome are scarce. Methods Using next generation sequencing (NGS) (Illumina MiSeq platform), we analysed UL97-GCV-R in patients with available plasma samples and refractory CMV replication/DNAemia (n=87) containing viral loads ≥910 IU/mL. 21 patients with CMV DNAemia resolving under antiviral therapy were analysed as controls. Detected mutations were considered induced and of potential clinical significance if they increased by ≥10% compared to the first detected frequency, or if they had a maximum frequency ≥25%. Results 19/87 (21.8%) with refractory CMV replication had >1 UL97-GCV-R detected by NGS, in comparison to 0/21 of the controls (p=0.02). One third of the recipients had 2 or more induced UL97-GCV-R mutations. The most frequently induced mutations affected codons 595 (42% (8/19)), 594 (32% (6/19)) and 603 (32% (6/19)). C592G was present in all episodes of both cases and controls at frequencies <15%, but never induced. UL97-GCV-R tended to be more frequent in donor/recipient CMV IgG mismatch or following failure to complete primary prophylaxis, and many developed invasive CMV disease. Conclusion UL97-GCV-R is common among transplant patients with refractory CMV replication. Early testing by NGS allows for identification of major mutations at codons 595, 594 and 603, and exclude a major role of C592G in ganciclovir resistance. Large prospective studies on UL97-GCV-R are warranted.

scholarly journals HIV Drug Resistance Mutations Detection by Next-Generation Sequencing during Antiretroviral Therapy Interruption in China

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 264
Author(s):  
Miaomiao Li ◽  
Shujia Liang ◽  
Chao Zhou ◽  
Min Chen ◽  
Shu Liang ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Next Generation Sequencing ◽  
Antiretroviral Therapy ◽  
Detection Threshold ◽  
Next Generation ◽  
Resistance Mutations ◽  
Hiv Drug Resistance ◽  
Drug Resistance Mutations ◽  
Therapy Interruption ◽  
Generation Sequencing

Patients with antiretroviral therapy interruption have a high risk of virological failure when re-initiating antiretroviral therapy (ART), especially those with HIV drug resistance. Next-generation sequencing may provide close scrutiny on their minority drug resistance variant. A cross-sectional study was conducted in patients with ART interruption in five regions in China in 2016. Through Sanger and next-generation sequencing in parallel, HIV drug resistance was genotyped on their plasma samples. Rates of HIV drug resistance were compared by the McNemar tests. In total, 174 patients were included in this study, with a median 12 (interquartile range (IQR), 6–24) months of ART interruption. Most (86.2%) of them had received efavirenz (EFV)/nevirapine (NVP)-based first-line therapy for a median 16 (IQR, 7–26) months before ART interruption. Sixty-one (35.1%) patients had CRF07_BC HIV-1 strains, 58 (33.3%) CRF08_BC and 35 (20.1%) CRF01_AE. Thirty-four (19.5%) of the 174 patients were detected to harbor HIV drug-resistant variants on Sanger sequencing. Thirty-six (20.7%), 37 (21.3%), 42 (24.1%), 79 (45.4%) and 139 (79.9) patients were identified to have HIV drug resistance by next-generation sequencing at 20% (v.s. Sanger, p = 0.317), 10% (v.s. Sanger, p = 0.180), 5% (v.s. Sanger, p = 0.011), 2% (v.s. Sanger, p < 0.001) and 1% (v.s. Sanger, p < 0.001) of detection thresholds, respectively. K65R was the most common minority mutation, of 95.1% (58/61) and 93.1% (54/58) in CRF07_BC and CRF08_BC, respectively, when compared with 5.7% (2/35) in CRF01_AE (p < 0.001). In 49 patients that followed-up a median 10 months later, HIV drug resistance mutations at >20% frequency such as K103N, M184VI and P225H still existed, but with decreased frequencies. The prevalence of HIV drug resistance in ART interruption was higher than 15% in the survey. Next-generation sequencing was able to detect more minority drug resistance variants than Sanger. There was a sharp increase in minority drug resistance variants when the detection threshold was below 5%.

scholarly journals P1.03-15 Non-Invasive Detection of Secondary Resistance Mutations in ALK-Positive NSCLC Patients by Next-Generation Sequencing

2019 ◽  
Vol 14 (10) ◽  
pp. S423
Author(s):  
E. Sánchez Herrero ◽  
M. Barquin ◽  
V. Calvo De Juan ◽  
M. Auglyte ◽  
R. Garcia Campelo ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Resistance Mutations ◽  
Secondary Resistance ◽  
Non Invasive ◽  
Alk Positive ◽  
Nsclc Patients ◽  
Generation Sequencing

scholarly journals Improved Detection by Next-Generation Sequencing of Pyrazinamide Resistance in Mycobacterium tuberculosis Isolates

2015 ◽  
Vol 53 (12) ◽  
pp. 3779-3783 ◽  
Author(s):  
Nontuthuko E. Maningi ◽  
Luke T. Daum ◽  
John D. Rodriguez ◽  
Matsie Mphahlele ◽  
Remco P. H. Peters ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Next Generation Sequencing ◽  
Sanger Sequencing ◽  
Detection Sensitivity ◽  
Next Generation ◽  
Resistance Mutations ◽  
Coding Region ◽  
Content Type ◽  
Mdr Tb ◽  
Generation Sequencing

The technical limitations of common tests used for detecting pyrazinamide (PZA) resistance inMycobacterium tuberculosisisolates pose challenges for comprehensive and accurate descriptions of drug resistance in patients with multidrug-resistant tuberculosis (MDR-TB). In this study, a 606-bp fragment (comprising thepncAcoding region plus the promoter) was sequenced using Ion Torrent next-generation sequencing (NGS) to detect associated PZA resistance mutations in 88 recultured MDR-TB isolates from an archived series collected in 2001. These 88 isolates were previously Sanger sequenced, with 55 (61%) designated as carrying the wild-typepncAgene and 33 (37%) showing mutations. PZA susceptibility of the isolates was also determined using the Bactec 460 TB system and the Wayne test. In this study, isolates were recultured and susceptibility testing was performed in Bactec 960 MGIT. Concordance between NGS and MGIT results was 93% (n= 88), and concordance values between the Bactec 460, the Wayne test, orpncAgene Sanger sequencing and NGS results were 82% (n= 88), 83% (n= 88), and 89% (n= 88), respectively. NGS confirmed the majority ofpncAmutations detected by Sanger sequencing but revealed several new and mixed-strain mutations that resolved discordancy in other phenotypic results. Importantly, in 53% (18/34) of these isolates,pncAmutations were located in the 151 to 360 region and warrant further exploration. In these isolates, with their known resistance to rifampin, NGS ofpncAimproved PZA resistance detection sensitivity to 97% and specificity to 94% using NGS as the gold standard and helped to resolve discordant results from conventional methodologies.

scholarly journals Identification of Mechanisms of Resistance to ALK Inhibitors. Next-generation sequencing-based liquid biopsy profiling: A step towards personalized treatment.

2020 ◽  
Author(s):  
Estela Sánchez-Herrero ◽  
Roberto Serna-Blasco ◽  
Vadym Ivanchuk ◽  
Rosario García-Campelo ◽  
Manuel Dómine ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Disease Progression ◽  
Line Treatment ◽  
Next Generation ◽  
Resistance Mutations ◽  
Primary Resistance ◽  
Alk Inhibitors ◽  
Alk Positive ◽  
Nsclc Patients ◽  
Generation Sequencing

Abstract Background: Despite impressive and durable responses, patients treated with ALK inhibitors (ALK-Is) ultimately progress. We investigated potential resistance mechanisms in a series of ALK-positive non-small cell lung cancer (NSCLC) patients progressing on different types of ALK-Is.Methods: 26 plasma and 2 cerebrospinal fluid samples collected upon disease progression to an ALK-I, from 24 advanced ALK-positive NSCLC patients, were analyzed by next-generation sequencing (NGS). A tool to retrieve variants at the ALK locus was developed. Results: 61 somatic mutations were detected in 14 genes: TP53, ALK, PIK3CA, SMAD4, MAP2K1 (MEK1) FGFR2, FGFR3, BRAF, EGFR, IDH2, MYC, MET, CCND3 and CCND1. Overall, We identified at least one mutation in ALK locus in 10 (38.5%) plasma samples, being the G1269A and G1202R mutations the most prevalent among patients progressing to first- and second-generation ALK-I treatment, respectively. An exon 19 deletion in EGFR was identified in a patient showing primary resistance to ALK-I. Likewise, the G466V mutation in BRAF and the F129L mutation in MAP2K1 (MEK1) were identified as the underlying mechanism of resistance in three patients who gained no or little benefit from second-line treatment with an ALK-I. Putative ALK-I resistance mutations were also found in PIK3CA and IDH2. Finally, a c-MYC gain, along with a loss of CCND1 and a FGFR3, were detected in a patient progressing on a first-line treatment with crizotinib. Conclusions: NGS analysis of liquid biopsies upon disease progression identified putative ALK-I resistance mutations in most cases, being a valuable approach to devise therapeutic strategies upon ALK-I failure.

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