Broad, hybrid capture-based next generation sequencing of circulating tumor DNA identified actionable genetic alterations in advanced cancer with treatment resistance.

2015 ◽  
Vol 33 (15_suppl) ◽  
pp. e22078-e22078
Author(s):  
Xiaochun Zhang ◽  
Helei Hou ◽  
Lihua Deng ◽  
Chuantao Zhang ◽  
Xiaofeng Cheng ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Advanced Cancer ◽  
Treatment Resistance ◽  
Circulating Tumor Dna ◽  
Genetic Alterations ◽  
Next Generation ◽  
Hybrid Capture ◽  
Tumor Dna ◽  
Generation Sequencing

scholarly journals Design and Testing of a Custom Melanoma Next Generation Sequencing Panel for Analysis of Circulating Tumor DNA

Cancers ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 2228 ◽  
Author(s):  
Russell J. Diefenbach ◽  
Jenny H. Lee ◽  
Alexander M. Menzies ◽  
Matteo S. Carlino ◽  
Georgina V. Long ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Stage Iv ◽  
Treatment Resistance ◽  
Circulating Tumor Dna ◽  
Stage Iii ◽  
Next Generation ◽  
Input Quantity ◽  
Melanoma Patients ◽  
Tumor Dna ◽  
Generation Sequencing

Detection of melanoma-associated mutations using circulating tumor DNA (ctDNA) from plasma is a potential alternative to using genomic DNA from invasive tissue biopsies. In this study, we developed a custom melanoma next-generation sequencing (NGS) panel which includes 123 amplicons in 30 genes covering driver and targetable mutations and alterations associated with treatment resistance. Analysis of a cohort of 74 stage III and IV treatment-naïve melanoma patients revealed that sensitivity of ctDNA detection was influenced by the amount of circulating-free DNA (cfDNA) input and stage of melanoma. At the recommended cfDNA input quantity of 20 ng (available in 28/74 patients), at least one cancer-associated mutation was detected in the ctDNA of 84% of stage IV patients and 47% of stage III patients with a limit of detection for mutant allele frequency (MAF) of 0.2%. This custom melanoma panel showed significant correlation with droplet digital PCR (ddPCR) and provided a more comprehensive melanoma mutation profile. Our custom panel could be further optimized by replacing amplicons spanning the TERT promoter, which did not perform well due to the high GC content. To increase the detection rate to 90% of stage IV melanoma and decrease the sensitivity to 0.1% MAF, we recommend increasing the volume of plasma to 8 mL to achieve minimal recommended cfDNA input and the refinement of poorly performing amplicons. Our panel can also be expanded to include new targetable and treatment resistance mutations to improve the tracking of treatment response and resistance in melanoma patients treated with systemic drug therapies.

Correlation of genomic alterations between tumor tissue and circulating tumor DNA by next-generation sequencing

2018 ◽  
Vol 144 (11) ◽  
pp. 2167-2175 ◽  
Author(s):  
Ya-Sian Chang ◽  
Hsin-Yuan Fang ◽  
Yao-Ching Hung ◽  
Tao-Wei Ke ◽  
Chieh-Min Chang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Tumor Tissue ◽  
Circulating Tumor Dna ◽  
Next Generation ◽  
Genomic Alterations ◽  
Tumor Dna ◽  
Generation Sequencing
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