scholarly journals P1.01-016 Next-Generation Sequencing Shows Mechanisms of Intrinsic Resistance in ALK-Positive NSCLC Patients Treated with Crizotinib

2017 ◽  
Vol 12 (11) ◽  
pp. S1898-S1899
Author(s):  
B. Solomon ◽  
J. Soria ◽  
F. Blackhall ◽  
A. Shaw ◽  
D.R. Camidge ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Intrinsic Resistance ◽  
Alk Positive ◽  
Nsclc Patients ◽  
Generation Sequencing

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 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.

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.

Next-generation sequencing for tumor mutation quantification using liquid biopsies

2020 ◽  
Vol 58 (2) ◽  
pp. 306-313 ◽  
Author(s):  
Mariano Provencio ◽  
Clara Pérez-Barrios ◽  
Miguel Barquin ◽  
Virginia Calvo ◽  
Fabio Franco ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Next Generation Sequencing ◽  
Correlation Coefficient ◽  
Resistance Mutation ◽  
Response To Treatment ◽  
Clinical Samples ◽  
Next Generation ◽  
Liquid Biopsies ◽  
Nsclc Patients ◽  
Generation Sequencing

AbstractBackgroundNon-small cell lung cancer (NSCLC) patients benefit from targeted therapies both in first- and second-line treatment. Nevertheless, molecular profiling of lung cancer tumors after first disease progression is seldom performed. The analysis of circulating tumor DNA (ctDNA) enables not only non-invasive biomarker testing but also monitoring tumor response to treatment. Digital PCR (dPCR), although a robust approach, only enables the analysis of a limited number of mutations. Next-generation sequencing (NGS), on the other hand, enables the analysis of significantly greater numbers of mutations.MethodsA total of 54 circulating free DNA (cfDNA) samples from 52 NSCLC patients and two healthy donors were analyzed by NGS using the Oncomine™ Lung cfDNA Assay kit and dPCR.ResultsLin’s concordance correlation coefficient and Pearson’s correlation coefficient between mutant allele frequencies (MAFs) assessed by NGS and dPCR revealed a positive and linear relationship between the two data sets (ρc = 0.986; 95% confidence interval [CI] = 0.975–0.991; r = 0.987; p < 0.0001, respectively), indicating an excellent concordance between both measurements. Similarly, the agreement between NGS and dPCR for the detection of the resistance mutation p.T790M was almost perfect (K = 0.81; 95% CI = 0.62–0.99), with an excellent correlation in terms of MAFs (ρc = 0.991; 95% CI = 0.981–0.992 and Pearson’s r = 0.998; p < 0.0001). Importantly, cfDNA sequencing was successful using as low as 10 ng cfDNA input.ConclusionsMAFs assessed by NGS were highly correlated with MAFs assessed by dPCR, demonstrating that NGS is a robust technique for ctDNA quantification using clinical samples, thereby allowing for dynamic genomic surveillance in the era of precision medicine.

scholarly journals PTEN Loss-of-Function Alterations Are Associated With Intrinsic Resistance to BRAF Inhibitors in Metastatic Melanoma

2017 ◽  
pp. 1-15 ◽  
Author(s):  
Federica Catalanotti ◽  
Donavan T. Cheng ◽  
Alexander N. Shoushtari ◽  
Douglas B. Johnson ◽  
Katherine S. Panageas ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Tumor Regression ◽  
Braf Inhibitor ◽  
Molecular Signature ◽  
Braf Inhibitors ◽  
Next Generation ◽  
Loss Of Function ◽  
Intrinsic Resistance ◽  
Braf Mutant ◽  
Generation Sequencing

Purpose The clinical use of BRAF inhibitors in patients with melanoma is limited by intrinsic and acquired resistance. We asked whether next-generation sequencing of pretreatment tumors could identify coaltered genes that predict for intrinsic resistance to BRAF inhibitor therapy in patients with melanoma as a prelude to rational combination strategies. Patients and Methods We analyzed 66 tumors from patients with metastatic BRAF-mutant melanoma collected before treatment with BRAF inhibitors. Tumors were analyzed for > 250 cancer-associated genes using a capture-based next-generation sequencing platform. Antitumor responses were correlated with clinical features and genomic profiles with the goal of identifying a molecular signature predictive of intrinsic resistance to RAF pathway inhibition. Results Among the 66 patients analyzed, 11 received a combination of BRAF and MEK inhibitors for the treatment of melanoma. Among the 55 patients treated with BRAF inhibitor monotherapy, objective responses, as assessed by Response Evaluation Criteria in Solid Tumors (RECIST), were observed in 30 patients (55%), with five (9%) achieving a complete response. We identified a significant association between alterations in PTEN that would be predicted to result in loss of function and reduced progression-free survival, overall survival, and response grade, a metric that combines tumor regression and duration of treatment response. Patients with melanoma who achieved an excellent response grade were more likely to have an elevated BRAF-mutant allele fraction. Conclusion These results provide a rationale for cotargeting BRAF and the PI3K/AKT pathway in patients with BRAF-mutant melanoma when tumors have concurrent loss-of-function mutations in PTEN. Future studies should explore whether gain of the mutant BRAF allele and/or loss of the wild-type allele is a predictive marker of BRAFi sensitivity.

miRNA profiling in resectable NSCLC by multiplex next-generation sequencing.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 7060-7060
Author(s):  
Sandra Gallach ◽  
Eloisa Jantus-Lewintre ◽  
David Montaner ◽  
Marta Usó ◽  
Elena Sanmartin ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Mirna Expression ◽  
Early Stage ◽  
Normal Lung ◽  
Next Generation ◽  
Early Stage Nsclc ◽  
Nsclc Patients ◽  
Generation Sequencing ◽  
Independent Cohort

7060 Background: Early-stage NSCLC has a relapse rate around 40% within 5 years. With the advent of microRNA (miRNA), which seems to regulate many genes critical for tumorigenesis, there is a growing interest in the characterization of miRNAome in NSCLC specimens and to correlate them with prognosis. Next generation sequencing is a useful tool to study the miRNA content of solid tumors. Here, we applied high-throughput SOLiD transcriptome sequencing to study miRNAs expression in a cohort of early-stage NSCLC patients (tumor vs normal lung). Methods: RNA was isolated from frozen lung specimens (tumor and normal lung) from resectable NSCLC patients (n=35). Samples with a RIN ≥ 7 were analyzed and enriched in the miRNA fraction. miRNAs were sequencing using a bar-code multiplex SOLiD protocol. Data normalization was carried out by rescaling all data according to their counts. Readings were mapped against mature and no-mature miRNAs using miRBase. Statistical analysis was performed with CLCbio software and considered significant when p-adj<0.005. Results: Using the SOLiD high throughput sequencing, we performed a systemic miRNA expression profiling analysis of paired samples (tumor vs normal lung). A total of 1268 miRNAs (mature and no-mature) have been detected in at least one sample. The differential expression between normal and tumor samples shown that 6 miRNAs (miR-193b, miR-182, miR-96, miR-148a, miR-299, miR-590) were upregulated and 7 (miR-145, miR-133a, miR-218, miR-125a, miR-30a, miR-126 and miR-139) were down-regulated significantly in tumor samples compared with normal lung tissues. We are performing studies using qRT-PCR in an independent cohort to further validate these findings. Conclusions: The deep sequencing technology used for differential miRNA expression is useful and novel. The use of barcoding allows multiplexing and lowers cost per sample. Several miRNAs were differentially expressed between tumor and normal tissue, but this point needs to be further validated in an independent cohort. Supported by grants TRA09-0132 (MICINN) and RD06/0020/1024 (ISCIII).

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