Detection of cancer DNA in plasma of patients with early-stage breast cancer

Julia A Beaver; Danijela Jelovac; Sasidharan Balukrishna; Rory Cochran; Sarah Croessmann; Daniel J Zabransky; Hong Yuen Wong; Patricia Valda Toro; Justin Cidado; Brian G Blair; David Chu; Timothy Burns; Michaela J Higgins; Vered Stearns; Lisa Jacobs; Mehran Habibi; Julie Lange; Paula J Hurley; Josh Lauring; Dustin VanDenBerg; Jill Kessler; Stacie Jeter; Michael L Samuels; Dianna Maar; Leslie Cope; Ashley Cimino-Mathews; Pedram Argani; Antonio C Wolff; Ben H Park

doi:10.1158/1078-0432.CCR-13-2933

Detection of cancer DNA in plasma of patients with early-stage breast cancer

Julia A Beaver, Danijela Jelovac, Sasidharan Balukrishna, Rory Cochran, Sarah Croessmann, Daniel J Zabransky, Hong Yuen Wong, Patricia Valda Toro, Justin Cidado, Brian G Blair, David Chu, Timothy Burns, Michaela J Higgins, Vered Stearns, Lisa Jacobs, Mehran Habibi, Julie Lange, Paula J Hurley, Josh Lauring, Dustin VanDenBergJill Kessler, Stacie Jeter, Michael L Samuels, Dianna Maar, Leslie Cope, Ashley Cimino-Mathews, Pedram Argani, Antonio C Wolff, Ben H Park

Research output: Contribution to journal › Article › peer-review

Abstract

PURPOSE: Detecting circulating plasma tumor DNA (ptDNA) in patients with early-stage cancer has the potential to change how oncologists recommend systemic therapies for solid tumors after surgery. Droplet digital polymerase chain reaction (ddPCR) is a novel sensitive and specific platform for mutation detection.

EXPERIMENTAL DESIGN: In this prospective study, primary breast tumors and matched pre- and postsurgery blood samples were collected from patients with early-stage breast cancer (n = 29). Tumors (n = 30) were analyzed by Sanger sequencing for common PIK3CA mutations, and DNA from these tumors and matched plasma were then analyzed for PIK3CA mutations using ddPCR.

RESULTS: Sequencing of tumors identified seven PIK3CA exon 20 mutations (H1047R) and three exon 9 mutations (E545K). Analysis of tumors by ddPCR confirmed these mutations and identified five additional mutations. Presurgery plasma samples (n = 29) were then analyzed for PIK3CA mutations using ddPCR. Of the 15 PIK3CA mutations detected in tumors by ddPCR, 14 of the corresponding mutations were detected in presurgical ptDNA, whereas no mutations were found in plasma from patients with PIK3CA wild-type tumors (sensitivity 93.3%, specificity 100%). Ten patients with mutation-positive ptDNA presurgery had ddPCR analysis of postsurgery plasma, with five patients having detectable ptDNA postsurgery.

CONCLUSIONS: This prospective study demonstrates accurate mutation detection in tumor tissues using ddPCR, and that ptDNA can be detected in blood before and after surgery in patients with early-stage breast cancer. Future studies can now address whether ptDNA detected after surgery identifies patients at risk for recurrence, which could guide chemotherapy decisions for individual patients.

Original language	English
Pages (from-to)	2643-2650
Number of pages	8
Journal	Clinical cancer research : an official journal of the American Association for Cancer Research
Volume	20
Issue number	10
DOIs	https://doi.org/10.1158/1078-0432.CCR-13-2933
State	Published - May 15 2014
Externally published	Yes

Keywords

Adult
Aged
Breast Neoplasms/diagnosis
Class I Phosphatidylinositol 3-Kinases
DNA Mutational Analysis/methods
DNA, Neoplasm/blood
Exons/genetics
Female
Humans
Middle Aged
Mutation
Neoplasm Staging
Phosphatidylinositol 3-Kinases/genetics
Polymerase Chain Reaction/methods
Postoperative Period
Preoperative Period
Prospective Studies
Reproducibility of Results
Sensitivity and Specificity

Access to Document

10.1158/1078-0432.CCR-13-2933

Cite this

Beaver, J. A., Jelovac, D., Balukrishna, S., Cochran, R., Croessmann, S., Zabransky, D. J., Wong, H. Y., Toro, P. V., Cidado, J., Blair, B. G., Chu, D., Burns, T., Higgins, M. J., Stearns, V., Jacobs, L., Habibi, M., Lange, J., Hurley, P. J., Lauring, J., ... Park, B. H. (2014). Detection of cancer DNA in plasma of patients with early-stage breast cancer. Clinical cancer research : an official journal of the American Association for Cancer Research, 20(10), 2643-2650. https://doi.org/10.1158/1078-0432.CCR-13-2933

Beaver, JA, Jelovac, D, Balukrishna, S, Cochran, R, Croessmann, S, Zabransky, DJ, Wong, HY, Toro, PV, Cidado, J, Blair, BG, Chu, D, Burns, T, Higgins, MJ, Stearns, V, Jacobs, L, Habibi, M, Lange, J, Hurley, PJ, Lauring, J, VanDenBerg, D, Kessler, J, Jeter, S, Samuels, ML, Maar, D, Cope, L, Cimino-Mathews, A, Argani, P, Wolff, AC & Park, BH 2014, 'Detection of cancer DNA in plasma of patients with early-stage breast cancer', Clinical cancer research : an official journal of the American Association for Cancer Research, vol. 20, no. 10, pp. 2643-2650. https://doi.org/10.1158/1078-0432.CCR-13-2933

@article{a06fb7bcee434965a75470dde679a295,

title = "Detection of cancer DNA in plasma of patients with early-stage breast cancer",

abstract = "PURPOSE: Detecting circulating plasma tumor DNA (ptDNA) in patients with early-stage cancer has the potential to change how oncologists recommend systemic therapies for solid tumors after surgery. Droplet digital polymerase chain reaction (ddPCR) is a novel sensitive and specific platform for mutation detection.EXPERIMENTAL DESIGN: In this prospective study, primary breast tumors and matched pre- and postsurgery blood samples were collected from patients with early-stage breast cancer (n = 29). Tumors (n = 30) were analyzed by Sanger sequencing for common PIK3CA mutations, and DNA from these tumors and matched plasma were then analyzed for PIK3CA mutations using ddPCR.RESULTS: Sequencing of tumors identified seven PIK3CA exon 20 mutations (H1047R) and three exon 9 mutations (E545K). Analysis of tumors by ddPCR confirmed these mutations and identified five additional mutations. Presurgery plasma samples (n = 29) were then analyzed for PIK3CA mutations using ddPCR. Of the 15 PIK3CA mutations detected in tumors by ddPCR, 14 of the corresponding mutations were detected in presurgical ptDNA, whereas no mutations were found in plasma from patients with PIK3CA wild-type tumors (sensitivity 93.3\%, specificity 100\%). Ten patients with mutation-positive ptDNA presurgery had ddPCR analysis of postsurgery plasma, with five patients having detectable ptDNA postsurgery.CONCLUSIONS: This prospective study demonstrates accurate mutation detection in tumor tissues using ddPCR, and that ptDNA can be detected in blood before and after surgery in patients with early-stage breast cancer. Future studies can now address whether ptDNA detected after surgery identifies patients at risk for recurrence, which could guide chemotherapy decisions for individual patients.",

keywords = "Adult, Aged, Breast Neoplasms/diagnosis, Class I Phosphatidylinositol 3-Kinases, DNA Mutational Analysis/methods, DNA, Neoplasm/blood, Exons/genetics, Female, Humans, Middle Aged, Mutation, Neoplasm Staging, Phosphatidylinositol 3-Kinases/genetics, Polymerase Chain Reaction/methods, Postoperative Period, Preoperative Period, Prospective Studies, Reproducibility of Results, Sensitivity and Specificity",

author = "Beaver, \{Julia A\} and Danijela Jelovac and Sasidharan Balukrishna and Rory Cochran and Sarah Croessmann and Zabransky, \{Daniel J\} and Wong, \{Hong Yuen\} and Toro, \{Patricia Valda\} and Justin Cidado and Blair, \{Brian G\} and David Chu and Timothy Burns and Higgins, \{Michaela J\} and Vered Stearns and Lisa Jacobs and Mehran Habibi and Julie Lange and Hurley, \{Paula J\} and Josh Lauring and Dustin VanDenBerg and Jill Kessler and Stacie Jeter and Samuels, \{Michael L\} and Dianna Maar and Leslie Cope and Ashley Cimino-Mathews and Pedram Argani and Wolff, \{Antonio C\} and Park, \{Ben H\}",

note = "{\textcopyright}2014 American Association for Cancer Research.",

year = "2014",

month = may,

day = "15",

doi = "10.1158/1078-0432.CCR-13-2933",

language = "English",

volume = "20",

pages = "2643--2650",

journal = "Clinical cancer research : an official journal of the American Association for Cancer Research",

issn = "1078-0432",

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TY - JOUR

T1 - Detection of cancer DNA in plasma of patients with early-stage breast cancer

AU - Beaver, Julia A

AU - Jelovac, Danijela

AU - Balukrishna, Sasidharan

AU - Cochran, Rory

AU - Croessmann, Sarah

AU - Zabransky, Daniel J

AU - Wong, Hong Yuen

AU - Toro, Patricia Valda

AU - Cidado, Justin

AU - Blair, Brian G

AU - Chu, David

AU - Burns, Timothy

AU - Higgins, Michaela J

AU - Stearns, Vered

AU - Jacobs, Lisa

AU - Habibi, Mehran

AU - Lange, Julie

AU - Hurley, Paula J

AU - Lauring, Josh

AU - VanDenBerg, Dustin

AU - Kessler, Jill

AU - Jeter, Stacie

AU - Samuels, Michael L

AU - Maar, Dianna

AU - Cope, Leslie

AU - Cimino-Mathews, Ashley

AU - Argani, Pedram

AU - Wolff, Antonio C

AU - Park, Ben H

PY - 2014/5/15

Y1 - 2014/5/15

N2 - PURPOSE: Detecting circulating plasma tumor DNA (ptDNA) in patients with early-stage cancer has the potential to change how oncologists recommend systemic therapies for solid tumors after surgery. Droplet digital polymerase chain reaction (ddPCR) is a novel sensitive and specific platform for mutation detection.EXPERIMENTAL DESIGN: In this prospective study, primary breast tumors and matched pre- and postsurgery blood samples were collected from patients with early-stage breast cancer (n = 29). Tumors (n = 30) were analyzed by Sanger sequencing for common PIK3CA mutations, and DNA from these tumors and matched plasma were then analyzed for PIK3CA mutations using ddPCR.RESULTS: Sequencing of tumors identified seven PIK3CA exon 20 mutations (H1047R) and three exon 9 mutations (E545K). Analysis of tumors by ddPCR confirmed these mutations and identified five additional mutations. Presurgery plasma samples (n = 29) were then analyzed for PIK3CA mutations using ddPCR. Of the 15 PIK3CA mutations detected in tumors by ddPCR, 14 of the corresponding mutations were detected in presurgical ptDNA, whereas no mutations were found in plasma from patients with PIK3CA wild-type tumors (sensitivity 93.3%, specificity 100%). Ten patients with mutation-positive ptDNA presurgery had ddPCR analysis of postsurgery plasma, with five patients having detectable ptDNA postsurgery.CONCLUSIONS: This prospective study demonstrates accurate mutation detection in tumor tissues using ddPCR, and that ptDNA can be detected in blood before and after surgery in patients with early-stage breast cancer. Future studies can now address whether ptDNA detected after surgery identifies patients at risk for recurrence, which could guide chemotherapy decisions for individual patients.

AB - PURPOSE: Detecting circulating plasma tumor DNA (ptDNA) in patients with early-stage cancer has the potential to change how oncologists recommend systemic therapies for solid tumors after surgery. Droplet digital polymerase chain reaction (ddPCR) is a novel sensitive and specific platform for mutation detection.EXPERIMENTAL DESIGN: In this prospective study, primary breast tumors and matched pre- and postsurgery blood samples were collected from patients with early-stage breast cancer (n = 29). Tumors (n = 30) were analyzed by Sanger sequencing for common PIK3CA mutations, and DNA from these tumors and matched plasma were then analyzed for PIK3CA mutations using ddPCR.RESULTS: Sequencing of tumors identified seven PIK3CA exon 20 mutations (H1047R) and three exon 9 mutations (E545K). Analysis of tumors by ddPCR confirmed these mutations and identified five additional mutations. Presurgery plasma samples (n = 29) were then analyzed for PIK3CA mutations using ddPCR. Of the 15 PIK3CA mutations detected in tumors by ddPCR, 14 of the corresponding mutations were detected in presurgical ptDNA, whereas no mutations were found in plasma from patients with PIK3CA wild-type tumors (sensitivity 93.3%, specificity 100%). Ten patients with mutation-positive ptDNA presurgery had ddPCR analysis of postsurgery plasma, with five patients having detectable ptDNA postsurgery.CONCLUSIONS: This prospective study demonstrates accurate mutation detection in tumor tissues using ddPCR, and that ptDNA can be detected in blood before and after surgery in patients with early-stage breast cancer. Future studies can now address whether ptDNA detected after surgery identifies patients at risk for recurrence, which could guide chemotherapy decisions for individual patients.

KW - Adult

KW - Aged

KW - Breast Neoplasms/diagnosis

KW - Class I Phosphatidylinositol 3-Kinases

KW - DNA Mutational Analysis/methods

KW - DNA, Neoplasm/blood

KW - Exons/genetics

KW - Female

KW - Humans

KW - Middle Aged

KW - Mutation

KW - Neoplasm Staging

KW - Phosphatidylinositol 3-Kinases/genetics

KW - Polymerase Chain Reaction/methods

KW - Postoperative Period

KW - Preoperative Period

KW - Prospective Studies

KW - Reproducibility of Results

KW - Sensitivity and Specificity

U2 - 10.1158/1078-0432.CCR-13-2933

DO - 10.1158/1078-0432.CCR-13-2933

M3 - Article

C2 - 24504125

SN - 1078-0432

VL - 20

SP - 2643

EP - 2650

JO - Clinical cancer research : an official journal of the American Association for Cancer Research

JF - Clinical cancer research : an official journal of the American Association for Cancer Research

IS - 10

ER -