Centrifuged supernatants from FNA provide a liquid biopsy option for clinical next-generation sequencing of thyroid nodules

Wenrui Ye, Brette Hannigan, Stephanie Zalles, Meenakshi Mehrotra, Bedia A. Barkoh, Michelle Dianne Williams, Maria E Cabanillas, Beth S Edeiken-Monroe, Peter C Hu, Dzifa Duose, Ignacio Ivan Wistuba, L Jeffrey Medeiros, John Stewart, Rajyalakshmi Luthra, Sinchita Roy Chowdhuri

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Background: Molecular testing is recommended as an adjunct to improve the preoperative diagnosis of fine-needle aspiration (FNA) of thyroid nodules. Centrifuged supernatants from FNA samples, which are typically discarded, have recently emerged as a novel liquid-based biopsy for molecular testing. This study evaluates the use of thyroid FNA supernatants for detecting clinically relevant mutations. Methods: Supernatants from thyroid FNA samples (n = 156) were evaluated. A 50-gene next-generation sequencing (NGS) assay was used, and mutation analysis results from a subset of samples were further compared with those of paired FNA smears and/or cell blocks. Results: All 156 samples yielded adequate DNA (median, 135 ng; range, 11-3180 ng), and 129 of these samples (83%) were successfully sequenced by NGS. The most frequently detected somatic mutations included BRAF and RAS mutations, which were followed by RET, TP53, PTEN, CDKN2A, and PIK3CA mutations. Eleven of 31 cases with an indeterminate cytologic diagnosis and 9 of 12 cases that were suspicious for malignancy had somatic mutations, including the BRAF V600E mutation, which is highly definitive for papillary thyroid carcinoma (PTC). Seven of the 9 indeterminate and suspicious cases with the BRAF V600E mutation had surgical follow-up, and they were all confirmed to be PTC. A comparison of the mutation profiles derived from supernatants with those of paired smears and/or cell blocks in a small subset of cases (n = 8) showed 100% concordance. Conclusions: This study provides evidence that FNA supernatants can be used as a surrogate for thyroid molecular testing to improve diagnostic accuracy in indeterminate nodules, provide prognostic/predictive information, and improve overall patient management.

Original languageEnglish (US)
Pages (from-to)146-160
Number of pages15
JournalCancer Cytopathology
Volume127
Issue number3
DOIs
StatePublished - Mar 1 2019

Fingerprint

Thyroid Nodule
Fine Needle Biopsy
Biopsy
Mutation
Thyroid Gland
DNA

Keywords

  • centrifugation
  • cytopathology
  • droplet digital polymerase chain reaction
  • fine-needle aspiration
  • liquid biopsy
  • molecular
  • mutation profiling
  • next-generation sequencing
  • supernatant
  • thyroid

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

@article{a39a33566d804a3985f3dbe60931869b,
title = "Centrifuged supernatants from FNA provide a liquid biopsy option for clinical next-generation sequencing of thyroid nodules",
abstract = "Background: Molecular testing is recommended as an adjunct to improve the preoperative diagnosis of fine-needle aspiration (FNA) of thyroid nodules. Centrifuged supernatants from FNA samples, which are typically discarded, have recently emerged as a novel liquid-based biopsy for molecular testing. This study evaluates the use of thyroid FNA supernatants for detecting clinically relevant mutations. Methods: Supernatants from thyroid FNA samples (n = 156) were evaluated. A 50-gene next-generation sequencing (NGS) assay was used, and mutation analysis results from a subset of samples were further compared with those of paired FNA smears and/or cell blocks. Results: All 156 samples yielded adequate DNA (median, 135 ng; range, 11-3180 ng), and 129 of these samples (83{\%}) were successfully sequenced by NGS. The most frequently detected somatic mutations included BRAF and RAS mutations, which were followed by RET, TP53, PTEN, CDKN2A, and PIK3CA mutations. Eleven of 31 cases with an indeterminate cytologic diagnosis and 9 of 12 cases that were suspicious for malignancy had somatic mutations, including the BRAF V600E mutation, which is highly definitive for papillary thyroid carcinoma (PTC). Seven of the 9 indeterminate and suspicious cases with the BRAF V600E mutation had surgical follow-up, and they were all confirmed to be PTC. A comparison of the mutation profiles derived from supernatants with those of paired smears and/or cell blocks in a small subset of cases (n = 8) showed 100{\%} concordance. Conclusions: This study provides evidence that FNA supernatants can be used as a surrogate for thyroid molecular testing to improve diagnostic accuracy in indeterminate nodules, provide prognostic/predictive information, and improve overall patient management.",
keywords = "centrifugation, cytopathology, droplet digital polymerase chain reaction, fine-needle aspiration, liquid biopsy, molecular, mutation profiling, next-generation sequencing, supernatant, thyroid",
author = "Wenrui Ye and Brette Hannigan and Stephanie Zalles and Meenakshi Mehrotra and Barkoh, {Bedia A.} and Williams, {Michelle Dianne} and Cabanillas, {Maria E} and Edeiken-Monroe, {Beth S} and Hu, {Peter C} and Dzifa Duose and Wistuba, {Ignacio Ivan} and Medeiros, {L Jeffrey} and John Stewart and Rajyalakshmi Luthra and {Roy Chowdhuri}, Sinchita",
year = "2019",
month = "3",
day = "1",
doi = "10.1002/cncy.22098",
language = "English (US)",
volume = "127",
pages = "146--160",
journal = "Cancer cytopathology",
issn = "1934-662X",
publisher = "Wiley-Blackwell",
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TY - JOUR

T1 - Centrifuged supernatants from FNA provide a liquid biopsy option for clinical next-generation sequencing of thyroid nodules

AU - Ye, Wenrui

AU - Hannigan, Brette

AU - Zalles, Stephanie

AU - Mehrotra, Meenakshi

AU - Barkoh, Bedia A.

AU - Williams, Michelle Dianne

AU - Cabanillas, Maria E

AU - Edeiken-Monroe, Beth S

AU - Hu, Peter C

AU - Duose, Dzifa

AU - Wistuba, Ignacio Ivan

AU - Medeiros, L Jeffrey

AU - Stewart, John

AU - Luthra, Rajyalakshmi

AU - Roy Chowdhuri, Sinchita

PY - 2019/3/1

Y1 - 2019/3/1

N2 - Background: Molecular testing is recommended as an adjunct to improve the preoperative diagnosis of fine-needle aspiration (FNA) of thyroid nodules. Centrifuged supernatants from FNA samples, which are typically discarded, have recently emerged as a novel liquid-based biopsy for molecular testing. This study evaluates the use of thyroid FNA supernatants for detecting clinically relevant mutations. Methods: Supernatants from thyroid FNA samples (n = 156) were evaluated. A 50-gene next-generation sequencing (NGS) assay was used, and mutation analysis results from a subset of samples were further compared with those of paired FNA smears and/or cell blocks. Results: All 156 samples yielded adequate DNA (median, 135 ng; range, 11-3180 ng), and 129 of these samples (83%) were successfully sequenced by NGS. The most frequently detected somatic mutations included BRAF and RAS mutations, which were followed by RET, TP53, PTEN, CDKN2A, and PIK3CA mutations. Eleven of 31 cases with an indeterminate cytologic diagnosis and 9 of 12 cases that were suspicious for malignancy had somatic mutations, including the BRAF V600E mutation, which is highly definitive for papillary thyroid carcinoma (PTC). Seven of the 9 indeterminate and suspicious cases with the BRAF V600E mutation had surgical follow-up, and they were all confirmed to be PTC. A comparison of the mutation profiles derived from supernatants with those of paired smears and/or cell blocks in a small subset of cases (n = 8) showed 100% concordance. Conclusions: This study provides evidence that FNA supernatants can be used as a surrogate for thyroid molecular testing to improve diagnostic accuracy in indeterminate nodules, provide prognostic/predictive information, and improve overall patient management.

AB - Background: Molecular testing is recommended as an adjunct to improve the preoperative diagnosis of fine-needle aspiration (FNA) of thyroid nodules. Centrifuged supernatants from FNA samples, which are typically discarded, have recently emerged as a novel liquid-based biopsy for molecular testing. This study evaluates the use of thyroid FNA supernatants for detecting clinically relevant mutations. Methods: Supernatants from thyroid FNA samples (n = 156) were evaluated. A 50-gene next-generation sequencing (NGS) assay was used, and mutation analysis results from a subset of samples were further compared with those of paired FNA smears and/or cell blocks. Results: All 156 samples yielded adequate DNA (median, 135 ng; range, 11-3180 ng), and 129 of these samples (83%) were successfully sequenced by NGS. The most frequently detected somatic mutations included BRAF and RAS mutations, which were followed by RET, TP53, PTEN, CDKN2A, and PIK3CA mutations. Eleven of 31 cases with an indeterminate cytologic diagnosis and 9 of 12 cases that were suspicious for malignancy had somatic mutations, including the BRAF V600E mutation, which is highly definitive for papillary thyroid carcinoma (PTC). Seven of the 9 indeterminate and suspicious cases with the BRAF V600E mutation had surgical follow-up, and they were all confirmed to be PTC. A comparison of the mutation profiles derived from supernatants with those of paired smears and/or cell blocks in a small subset of cases (n = 8) showed 100% concordance. Conclusions: This study provides evidence that FNA supernatants can be used as a surrogate for thyroid molecular testing to improve diagnostic accuracy in indeterminate nodules, provide prognostic/predictive information, and improve overall patient management.

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KW - droplet digital polymerase chain reaction

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KW - mutation profiling

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KW - thyroid

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