Minimally invasive real-time detection of actionable mutations in patients with metastatic solid tumors using fine-needle and liquid biopsies

Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Philip C. Zuzarte, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Malcolm J. Moore, Amit M. Oza, Eitan Amir, John D. McPherson, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. SiuAaron R. Hansen

Research output: Contribution to journalArticle

Abstract

Purpose Fine-needle biopsy (FNB) and liquid biopsy are minimally invasive methods of tumor sampling that provide feasible means to assess tumor genotypes in real time. However, more data are needed to establish the strength of these methods by benchmarking against the current gold standard methods, core-needle biopsy (CNB) or surgical excision of the tumor. Patients and Methods Eligible patients with advanced solid tumors were prospectively recruited. We performed mutation profiling using matched tumor DNA obtained by CNB, FNB and liquid biopsy, and matrix-assisted laser desorption/ionization time-offlight custom mass-spectrometry or targeted next-generation DNA sequencing. The actionability of detected mutations was determined using the OncoKB Web tool. Agreement between mutations detected in CNBs, FNBs, and circulating tumor DNA (ctDNA) was examined. Results Forty-one patients underwent tumor biopsy. Thirty CNBs (73%) and 34 FNBs (83%) had sufficient tumor and DNA for mutation profiling. Median DNA yield from CNB and FNB were 775 ng (interquartile range, 240 to 347 4ng) and 649 ng (interquartile range, 180 to1350 ng), respectively. Of 29 CNB/FNB pairs available for comparison, actionable mutation results were concordant in 28 (96%). Six of nine actionable mutations (67%) that were found by CNB, FNB, or both were detectable in ctDNA. Two additional actionable mutations were found exclusively in ctDNA. Conclusion Optimally processed FNB and liquid biopsy can be used routinely for tumor mutation profiling to identify actionable mutations.

Original languageEnglish (US)
JournalJCO Precision Oncology
Volume2
DOIs
StatePublished - Jan 1 2018

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Fine Needle Biopsy
Mutation
Large-Core Needle Biopsy
Neoplasms
DNA
Biopsy
Benchmarking
DNA Fingerprinting
DNA Sequence Analysis
Mass Spectrometry
Lasers
Genotype

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

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Minimally invasive real-time detection of actionable mutations in patients with metastatic solid tumors using fine-needle and liquid biopsies. / Aung, Kyaw L.; Bedard, Philippe L.; Yu, Celeste; Boerner, Scott L.; Zuzarte, Philip C.; Ghai, Sangeet; Berman, Hal K.; Serra, Stefano; Giesler, Amanda; Ahmed, Lailah; Joshua, Anthony M.; Moore, Malcolm J.; Oza, Amit M.; Amir, Eitan; McPherson, John D.; Zhang, Tong; Sukhai, Mahadeo A.; Stockley, Tracy L.; Kamel-Reid, Suzanne; Siu, Lillian L.; Hansen, Aaron R.

In: JCO Precision Oncology, Vol. 2, 01.01.2018.

Research output: Contribution to journalArticle

Aung, KL, Bedard, PL, Yu, C, Boerner, SL, Zuzarte, PC, Ghai, S, Berman, HK, Serra, S, Giesler, A, Ahmed, L, Joshua, AM, Moore, MJ, Oza, AM, Amir, E, McPherson, JD, Zhang, T, Sukhai, MA, Stockley, TL, Kamel-Reid, S, Siu, LL & Hansen, AR 2018, 'Minimally invasive real-time detection of actionable mutations in patients with metastatic solid tumors using fine-needle and liquid biopsies', JCO Precision Oncology, vol. 2. https://doi.org/10.1200/PO.17.00248
Aung, Kyaw L. ; Bedard, Philippe L. ; Yu, Celeste ; Boerner, Scott L. ; Zuzarte, Philip C. ; Ghai, Sangeet ; Berman, Hal K. ; Serra, Stefano ; Giesler, Amanda ; Ahmed, Lailah ; Joshua, Anthony M. ; Moore, Malcolm J. ; Oza, Amit M. ; Amir, Eitan ; McPherson, John D. ; Zhang, Tong ; Sukhai, Mahadeo A. ; Stockley, Tracy L. ; Kamel-Reid, Suzanne ; Siu, Lillian L. ; Hansen, Aaron R. / Minimally invasive real-time detection of actionable mutations in patients with metastatic solid tumors using fine-needle and liquid biopsies. In: JCO Precision Oncology. 2018 ; Vol. 2.
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abstract = "Purpose Fine-needle biopsy (FNB) and liquid biopsy are minimally invasive methods of tumor sampling that provide feasible means to assess tumor genotypes in real time. However, more data are needed to establish the strength of these methods by benchmarking against the current gold standard methods, core-needle biopsy (CNB) or surgical excision of the tumor. Patients and Methods Eligible patients with advanced solid tumors were prospectively recruited. We performed mutation profiling using matched tumor DNA obtained by CNB, FNB and liquid biopsy, and matrix-assisted laser desorption/ionization time-offlight custom mass-spectrometry or targeted next-generation DNA sequencing. The actionability of detected mutations was determined using the OncoKB Web tool. Agreement between mutations detected in CNBs, FNBs, and circulating tumor DNA (ctDNA) was examined. Results Forty-one patients underwent tumor biopsy. Thirty CNBs (73{\%}) and 34 FNBs (83{\%}) had sufficient tumor and DNA for mutation profiling. Median DNA yield from CNB and FNB were 775 ng (interquartile range, 240 to 347 4ng) and 649 ng (interquartile range, 180 to1350 ng), respectively. Of 29 CNB/FNB pairs available for comparison, actionable mutation results were concordant in 28 (96{\%}). Six of nine actionable mutations (67{\%}) that were found by CNB, FNB, or both were detectable in ctDNA. Two additional actionable mutations were found exclusively in ctDNA. Conclusion Optimally processed FNB and liquid biopsy can be used routinely for tumor mutation profiling to identify actionable mutations.",
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T1 - Minimally invasive real-time detection of actionable mutations in patients with metastatic solid tumors using fine-needle and liquid biopsies

AU - Aung, Kyaw L.

AU - Bedard, Philippe L.

AU - Yu, Celeste

AU - Boerner, Scott L.

AU - Zuzarte, Philip C.

AU - Ghai, Sangeet

AU - Berman, Hal K.

AU - Serra, Stefano

AU - Giesler, Amanda

AU - Ahmed, Lailah

AU - Joshua, Anthony M.

AU - Moore, Malcolm J.

AU - Oza, Amit M.

AU - Amir, Eitan

AU - McPherson, John D.

AU - Zhang, Tong

AU - Sukhai, Mahadeo A.

AU - Stockley, Tracy L.

AU - Kamel-Reid, Suzanne

AU - Siu, Lillian L.

AU - Hansen, Aaron R.

PY - 2018/1/1

Y1 - 2018/1/1

N2 - Purpose Fine-needle biopsy (FNB) and liquid biopsy are minimally invasive methods of tumor sampling that provide feasible means to assess tumor genotypes in real time. However, more data are needed to establish the strength of these methods by benchmarking against the current gold standard methods, core-needle biopsy (CNB) or surgical excision of the tumor. Patients and Methods Eligible patients with advanced solid tumors were prospectively recruited. We performed mutation profiling using matched tumor DNA obtained by CNB, FNB and liquid biopsy, and matrix-assisted laser desorption/ionization time-offlight custom mass-spectrometry or targeted next-generation DNA sequencing. The actionability of detected mutations was determined using the OncoKB Web tool. Agreement between mutations detected in CNBs, FNBs, and circulating tumor DNA (ctDNA) was examined. Results Forty-one patients underwent tumor biopsy. Thirty CNBs (73%) and 34 FNBs (83%) had sufficient tumor and DNA for mutation profiling. Median DNA yield from CNB and FNB were 775 ng (interquartile range, 240 to 347 4ng) and 649 ng (interquartile range, 180 to1350 ng), respectively. Of 29 CNB/FNB pairs available for comparison, actionable mutation results were concordant in 28 (96%). Six of nine actionable mutations (67%) that were found by CNB, FNB, or both were detectable in ctDNA. Two additional actionable mutations were found exclusively in ctDNA. Conclusion Optimally processed FNB and liquid biopsy can be used routinely for tumor mutation profiling to identify actionable mutations.

AB - Purpose Fine-needle biopsy (FNB) and liquid biopsy are minimally invasive methods of tumor sampling that provide feasible means to assess tumor genotypes in real time. However, more data are needed to establish the strength of these methods by benchmarking against the current gold standard methods, core-needle biopsy (CNB) or surgical excision of the tumor. Patients and Methods Eligible patients with advanced solid tumors were prospectively recruited. We performed mutation profiling using matched tumor DNA obtained by CNB, FNB and liquid biopsy, and matrix-assisted laser desorption/ionization time-offlight custom mass-spectrometry or targeted next-generation DNA sequencing. The actionability of detected mutations was determined using the OncoKB Web tool. Agreement between mutations detected in CNBs, FNBs, and circulating tumor DNA (ctDNA) was examined. Results Forty-one patients underwent tumor biopsy. Thirty CNBs (73%) and 34 FNBs (83%) had sufficient tumor and DNA for mutation profiling. Median DNA yield from CNB and FNB were 775 ng (interquartile range, 240 to 347 4ng) and 649 ng (interquartile range, 180 to1350 ng), respectively. Of 29 CNB/FNB pairs available for comparison, actionable mutation results were concordant in 28 (96%). Six of nine actionable mutations (67%) that were found by CNB, FNB, or both were detectable in ctDNA. Two additional actionable mutations were found exclusively in ctDNA. Conclusion Optimally processed FNB and liquid biopsy can be used routinely for tumor mutation profiling to identify actionable mutations.

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