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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 5648-5656 |
| Number of pages | 9 |
| Journal | Clinical Cancer Research |
| Volume | 23 |
| Issue number | 18 |
| DOIs | |
| State | Published - Sep 15 2017 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Oncology
- Cancer Research
Cite this
Development and validation of an ultradeep next-generation sequencing assay for testing of plasma cell-free DNA from patients with advanced cancer. / Janku, Filip; Zhang, Shile; Waters, Jill; Liu, Li; Huang, Helen J.; Subbiah, Vivek; Hong, David S.; Karp, Daniel D.; Fu, Siqing; Cai, Xuyu; Ramzanali, Nishma M.; Madwani, Kiran; Cabrilo, Goran; Andrews, Debra L.; Zhao, Yue; Javle, Milind; Kopetz, E. Scott; Luthra, Rajyalakshmi; Kim, Hyunsung J.; Gnerre, Sante; Satya, Ravi Vijaya; Chuang, Han Yu; Kruglyak, Kristina M.; Toung, Jonathan; Zhao, Chen; Shen, Richard; Heymach, John V.; Meric-Bernstam, Funda; Mills, Gordon; Fan, Jian Bing; Salathia, Neeraj S.
In: Clinical Cancer Research, Vol. 23, No. 18, 15.09.2017, p. 5648-5656.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Development and validation of an ultradeep next-generation sequencing assay for testing of plasma cell-free DNA from patients with advanced cancer
AU - Janku, Filip
AU - Zhang, Shile
AU - Waters, Jill
AU - Liu, Li
AU - Huang, Helen J.
AU - Subbiah, Vivek
AU - Hong, David S.
AU - Karp, Daniel D.
AU - Fu, Siqing
AU - Cai, Xuyu
AU - Ramzanali, Nishma M.
AU - Madwani, Kiran
AU - Cabrilo, Goran
AU - Andrews, Debra L.
AU - Zhao, Yue
AU - Javle, Milind
AU - Kopetz, E. Scott
AU - Luthra, Rajyalakshmi
AU - Kim, Hyunsung J.
AU - Gnerre, Sante
AU - Satya, Ravi Vijaya
AU - Chuang, Han Yu
AU - Kruglyak, Kristina M.
AU - Toung, Jonathan
AU - Zhao, Chen
AU - Shen, Richard
AU - Heymach, John V.
AU - Meric-Bernstam, Funda
AU - Mills, Gordon
AU - Fan, Jian Bing
AU - Salathia, Neeraj S.
PY - 2017/9/15
Y1 - 2017/9/15
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85029517871&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85029517871&partnerID=8YFLogxK
U2 - 10.1158/1078-0432.CCR-17-0291
DO - 10.1158/1078-0432.CCR-17-0291
M3 - Article
C2 - 28536309
AN - SCOPUS:85029517871
VL - 23
SP - 5648
EP - 5656
JO - Clinical Cancer Research
JF - Clinical Cancer Research
SN - 1078-0432
IS - 18
ER -