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.

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

Parallel VENTANA IHC and RT-PCR of ALK status in non-small cell lung cancer and response to crizotinib.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 11623-11623 ◽  
Author(s):  
Chunwei Xu ◽  
Wen-xian Wang ◽  
Meiyu Fang ◽  
Yan-ping Chen ◽  
Yu Chen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Advanced Nsclc ◽  
Rapid Screening ◽  
Next Generation ◽  
Rt Pcr ◽  
Alk Rearrangement ◽  
Curative Effect ◽  
Alk Positive ◽  
Nsclc Patients ◽  
Generation Sequencing

11623 Background: Advanced NSCLC patients who harbor (ALK) rearrangement were sensitive to crizotinib. However, not all ALK-positive patients benefit equally from crizotinib. A method for determining ALK rearrangement is RT-PCR, the Chinese FDA has approved RT-PCR to detect ALK rearrangement. In this regard, VENTANA IHC is a standard method to identify ALK protein overexpression in NSCLC. However, up to now, it is still largely unknown about the response to crizotinib for Chinese NSCLC patients having ALK overexpress detected by VENTANA IHC. To better clarify the clinical implication of VENTANA IHC to detect ALK rearrangement, we compared the curative effect and survival by the two methods in advanced NSCLC patients and analysis VENTNA IHC and RT-PCR inconsistent cases. Methods: A total of 1720 patients with NSCLC who had their ALK rearrangement detected by IHC and/or RT-PCR were included in this analysis. And we compared the efficacy and survival of patients with ALK positive detected by IHC and RT-PCR. We used next-generation sequencing (NGS) to detect patients whom two methods were not consistent. Results: 187/1720 patients were identified as ALK-positive by IHC and/or RT-PCR and 66 patient received crizotinib. We identified 172/1674 patients had ALK positive by IHC method, 41/322 patients had ALK rearrangements by RT-PCR method. And 29/276 patients with ALK positive were simultaneously analyzed by IHC and RT-PCR. The overall response rates (ORR) were 65.90% by IHC and 55.88% by RT-PCR, respectively. And the disease control rates (DCR) were 86.36% by IHC and 76.47% by RT-PCR. The median PFS of IHC was 8.5 months and RT-PCR was 9.2 months Targeted next-generation sequencing in the special type: Among 6 cases of 17 cases ALK positive patients were inconsistent by IHC and RT-PCR performed with NGS, 4 cases were identified to have EML4-ALK fusions, and 2 cases were KCL1-ALK(ND) and FBXO36-ALK (PFS 21.2 months). Conclusions: VENTANA IHC is a reliable and rapid screening tool in routine pathologic laboratories for the identification of suitable candidates for targeted therapy. It has a moderate sensitivity and a slightly higher curative effect, and some VENTANA IHC positive but RT-PCR negative cases may benefit from crizotinib.

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 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
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