Development and Validation of an Ultradeep Next-Generation Sequencing Assay for Testing of Plasma Cell-Free DNA from Patients with Advanced Cancer
| Autor: | John V. Heymach, E. Scott Kopetz, Jill Waters, Chen Zhao, Jian-Bing Fan, Xuyu Cai, Hyunsung John Kim, Sante Gnerre, Vivek Subbiah, Yue Zhao, Milind Javle, Kiran Madwani, Daniel D. Karp, Han-Yu Chuang, Filip Janku, Kristina M. Kruglyak, Shile Zhang, Neeraj Salathia, Funda Meric-Bernstam, David S. Hong, Ravi Vijaya Satya, Siqing Fu, Gordon B. Mills, Debra L. Andrews, Jonathan Toung, Li Liu, Helen J. Huang, Rajyalakshmi Luthra, Richard Shen, Nishma M. Ramzanali, Goran Cabrilo |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Adult Male Cancer Research Biology Plasma cell Free dna Sensitivity and Specificity DNA sequencing Article Circulating Tumor DNA 03 medical and health sciences 0302 clinical medicine Neoplasms medicine Biomarkers Tumor Humans Genetic Testing Genetic testing Aged Aged 80 and over medicine.diagnostic_test Cancer High-Throughput Nucleotide Sequencing Reproducibility of Results Middle Aged medicine.disease Prognosis Advanced cancer Molecular biology Mutational analysis 030104 developmental biology medicine.anatomical_structure Oncology 030220 oncology & carcinogenesis Mutation Cancer research Mutation testing Female |
| Zdroj: | Clinical cancer research : an official journal of the American Association for Cancer Research. 23(18) |
| ISSN: | 1557-3265 |
| Popis: | Purpose: Tumor-derived cell-free DNA (cfDNA) in plasma can be used for molecular testing and provide an attractive alternative to tumor tissue. Commonly used PCR-based technologies can test for limited number of alterations at the time. Therefore, novel ultrasensitive technologies capable of testing for a broad spectrum of molecular alterations are needed to further personalized cancer therapy. Experimental Design: We developed a highly sensitive ultradeep next-generation sequencing (NGS) assay using reagents from TruSeqNano library preparation and NexteraRapid Capture target enrichment kits to generate plasma cfDNA sequencing libraries for mutational analysis in 61 cancer-related genes using common bioinformatics tools. The results were retrospectively compared with molecular testing of archival primary or metastatic tumor tissue obtained at different points of clinical care. Results: In a study of 55 patients with advanced cancer, the ultradeep NGS assay detected 82% (complete detection) to 87% (complete and partial detection) of the aberrations identified in discordantly collected corresponding archival tumor tissue. Patients with a low variant allele frequency (VAF) of mutant cfDNA survived longer than those with a high VAF did (P = 0.018). In patients undergoing systemic therapy, radiological response was positively associated with changes in cfDNA VAF (P = 0.02), and compared with unchanged/increased mutant cfDNA VAF, decreased cfDNA VAF was associated with longer time to treatment failure (TTF; P = 0.03). Conclusions: Ultradeep NGS assay has good sensitivity compared with conventional clinical mutation testing of archival specimens. A high VAF in mutant cfDNA corresponded with shorter survival. Changes in VAF of mutated cfDNA were associated with TTF. Clin Cancer Res; 23(18); 5648–56. ©2017 AACR. |
| Databáze: | OpenAIRE |
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