@article{3bdd5bcc00fe4716b0a905ad0044c53c,
title = "Development and validation of an ultradeep next-generation sequencing assay for testing of plasma cell-free DNA from patients with advanced cancer",
abstract = "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.",
author = "Filip Janku and Shile Zhang and Jill Waters and Li Liu and Huang, {Helen J.} and Vivek Subbiah and Hong, {David S.} and Karp, {Daniel D.} and Siqing Fu and Xuyu Cai and Ramzanali, {Nishma M.} and Kiran Madwani and Goran Cabrilo and Andrews, {Debra L.} and Yue Zhao and Milind Javle and Kopetz, {E. Scott} and Rajyalakshmi Luthra and Kim, {Hyunsung J.} and Sante Gnerre and Satya, {Ravi Vijaya} and Chuang, {Han Yu} and Kruglyak, {Kristina M.} and Jonathan Toung and Chen Zhao and Richard Shen and Heymach, {John V.} and Funda Meric-Bernstam and Mills, {Gordon B.} and Fan, {Jian Bing} and Salathia, {Neeraj S.}",
note = "Funding Information: This study was supported by the Sidney Kimmel Foundation for Cancer Research (to F. Janku), the Sheikh Khalifa Al Nahyan Ben Zayed Institute for Personalized Cancer Therapy (to F. Janku), the National Center for Advancing Translational Sciences (grant no. UL1 TR000371), and the NIH through MD Anderson's Cancer Center support grant (P30 CA016672). Funding Information: F. Janku reports receiving commercial research grants from Agios, Astellas, BioMed Valley Discoveries, Deciphera, Novartis, Piqur, Roche, Symphogen, and Upsher-Smith Laboratories; holds ownership interest (including patents) in Trovagene; andis aconsultant/advisory board member forDeciphera,Guardant Health, Illumina, and Trovagene. S. Gnerre holds ownership interest (including patents) in Illumina stock. R.V. Satya holds ownership interest (including patents) in Common Stocks of ILMN. F. Meric-Bernstam reports receiving other commercial research support from Aileron, AstraZeneca, Bayer, Calithera, Curis, CytoMx, Debio, Effective Therapeutics, Genentech, Jounce, Novartis, PUMA, Taiho, Verastem, and Zymeworks and is a consultant/advisory board member for Clearlight Diagnostics, Darwin Health, Dialecta, Inflection Biosciences, and Pieris. G.B. Mills reports receiving commercial research grants from Adelson Medical Research Foundation, AstraZeneca, Breast Cancer Research Foundation, Critical Outcome Technologies, Illumina, Karus, Komen Research Foundation, Nanostring, and Takeda/Millennium Pharmaceuticals; reports receiving speakers bureau honoraria from Allostery, AstraZeneca, ImmunoMet, Ionis Pharmaceuticals, Lilly, Medimmune, Novartis, Pfizer, Symphogen, and Tarveda; holds ownership interest (including patents) in Catena Pharmaceuticals, ImmunoMet, Myriad Genetics, PTV Ventures, and Spindletop Ventures; and is a consultant/advisory board member for Adventist Health, Allostery, Astra-Zeneca, Catena Pharmaceuticals, Critical Outcome Technologies, ImmunoMet, Ionis Pharmaceuticals, Lilly, Medimmune, Novartis, Precision Medicine, Pro-vista Diagnostics, Signalchem Lifesciences, Symphogen, Takeda/Millennium Pharmaceuticals, Tarveda, and Tau Therapeutics. No potential conflicts of interest were disclosed by the other authors. Publisher Copyright: {\textcopyright}2017 AACR.",
year = "2017",
month = sep,
day = "15",
doi = "10.1158/1078-0432.CCR-17-0291",
language = "English (US)",
volume = "23",
pages = "5648--5656",
journal = "Clinical Cancer Research",
issn = "1078-0432",
publisher = "American Association for Cancer Research Inc.",
number = "18",
}