The Ligamp TP53 assay for detection of minimal residual disease in head and neck squamous cell carcinoma surgical margins

M. Luana Poeta, Judith Manola, David Goldenberg, Arlene Forastiere, Joseph A. Califano, John A. Ridge, W. Jarrard Goodwin, Daniel Kenady, John Saunders, William Westra, David Sidransky, Wayne M. Koch

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

Purpose: Detect tumor-related DNA using LigAmp in histologically clear margins and associate results with clinical outcome. Experimental Design: Patients with head and neck cancer were registered for molecular analysis of surgical margins. Adequacy of resection was ensured using histologic margin analysis. Further margins were then harvested and DNA extracted. TP53 mutations in tumor were determined using Affymetrix p53 GeneChip. Margins were analyzed by Ligamp in comparison with standard curves for quantification of mutant DNA. Ligation used two oligonucleotides to isolate DNA targeting the mutation. Ligated DNA was amplified using real-time PCR. The quantity of mutation in the margin was determined as percent of mutant species relative to plasmid and relative to tumor. Cutpoints were identified and defined groups were evaluated for local failure-free, cancer-specific, and overall survival. Study margins were examined for presence of tumor by light microscopy. Results: Tissue from 95 patients with common mutations was analyzed. Fifteen experienced local recurrence. Cutpoints of 0.15% for mutant species relative to plasmid and 0.5% for mutant species relative to tumor were chosen as most selective of recurrent cases. LigAmp had slightly better area under the receiver operator characteristic curve (P = 0.09) than light microscopy correctly predicting 9 of 15 recurrent tumors. There were 6 false negative cases and 26 false positive results. No statistically significant distinctions were observed in cancer-specific or overall survival in this limited cohort. Conclusions: Ligamp provides quantifiable, sensitive detection of mutant DNA in histologically normal margins. Detection of mutant species in margins may identify patients at risk of local recurrence.

Original languageEnglish
Pages (from-to)7658-7665
Number of pages8
JournalClinical Cancer Research
Volume15
Issue number24
DOIs
StatePublished - Dec 15 2009

Fingerprint

Residual Neoplasm
DNA
Neoplasms
Mutation
Microscopy
Plasmids
Light
Recurrence
Survival
Carcinoma, squamous cell of head and neck
Margins of Excision
Head and Neck Neoplasms
Oligonucleotides
Ligation
Real-Time Polymerase Chain Reaction
Research Design

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

Poeta, M. L., Manola, J., Goldenberg, D., Forastiere, A., Califano, J. A., Ridge, J. A., ... Koch, W. M. (2009). The Ligamp TP53 assay for detection of minimal residual disease in head and neck squamous cell carcinoma surgical margins. Clinical Cancer Research, 15(24), 7658-7665. https://doi.org/10.1158/1078-0432.CCR-09-1433

The Ligamp TP53 assay for detection of minimal residual disease in head and neck squamous cell carcinoma surgical margins. / Poeta, M. Luana; Manola, Judith; Goldenberg, David; Forastiere, Arlene; Califano, Joseph A.; Ridge, John A.; Goodwin, W. Jarrard; Kenady, Daniel; Saunders, John; Westra, William; Sidransky, David; Koch, Wayne M.

In: Clinical Cancer Research, Vol. 15, No. 24, 15.12.2009, p. 7658-7665.

Research output: Contribution to journalArticle

Poeta, ML, Manola, J, Goldenberg, D, Forastiere, A, Califano, JA, Ridge, JA, Goodwin, WJ, Kenady, D, Saunders, J, Westra, W, Sidransky, D & Koch, WM 2009, 'The Ligamp TP53 assay for detection of minimal residual disease in head and neck squamous cell carcinoma surgical margins', Clinical Cancer Research, vol. 15, no. 24, pp. 7658-7665. https://doi.org/10.1158/1078-0432.CCR-09-1433
Poeta, M. Luana ; Manola, Judith ; Goldenberg, David ; Forastiere, Arlene ; Califano, Joseph A. ; Ridge, John A. ; Goodwin, W. Jarrard ; Kenady, Daniel ; Saunders, John ; Westra, William ; Sidransky, David ; Koch, Wayne M. / The Ligamp TP53 assay for detection of minimal residual disease in head and neck squamous cell carcinoma surgical margins. In: Clinical Cancer Research. 2009 ; Vol. 15, No. 24. pp. 7658-7665.
@article{147b7fe0f31643dd9e884698cc9f7d4c,
title = "The Ligamp TP53 assay for detection of minimal residual disease in head and neck squamous cell carcinoma surgical margins",
abstract = "Purpose: Detect tumor-related DNA using LigAmp in histologically clear margins and associate results with clinical outcome. Experimental Design: Patients with head and neck cancer were registered for molecular analysis of surgical margins. Adequacy of resection was ensured using histologic margin analysis. Further margins were then harvested and DNA extracted. TP53 mutations in tumor were determined using Affymetrix p53 GeneChip. Margins were analyzed by Ligamp in comparison with standard curves for quantification of mutant DNA. Ligation used two oligonucleotides to isolate DNA targeting the mutation. Ligated DNA was amplified using real-time PCR. The quantity of mutation in the margin was determined as percent of mutant species relative to plasmid and relative to tumor. Cutpoints were identified and defined groups were evaluated for local failure-free, cancer-specific, and overall survival. Study margins were examined for presence of tumor by light microscopy. Results: Tissue from 95 patients with common mutations was analyzed. Fifteen experienced local recurrence. Cutpoints of 0.15{\%} for mutant species relative to plasmid and 0.5{\%} for mutant species relative to tumor were chosen as most selective of recurrent cases. LigAmp had slightly better area under the receiver operator characteristic curve (P = 0.09) than light microscopy correctly predicting 9 of 15 recurrent tumors. There were 6 false negative cases and 26 false positive results. No statistically significant distinctions were observed in cancer-specific or overall survival in this limited cohort. Conclusions: Ligamp provides quantifiable, sensitive detection of mutant DNA in histologically normal margins. Detection of mutant species in margins may identify patients at risk of local recurrence.",
author = "Poeta, {M. Luana} and Judith Manola and David Goldenberg and Arlene Forastiere and Califano, {Joseph A.} and Ridge, {John A.} and Goodwin, {W. Jarrard} and Daniel Kenady and John Saunders and William Westra and David Sidransky and Koch, {Wayne M.}",
year = "2009",
month = "12",
day = "15",
doi = "10.1158/1078-0432.CCR-09-1433",
language = "English",
volume = "15",
pages = "7658--7665",
journal = "Clinical Cancer Research",
issn = "1078-0432",
publisher = "American Association for Cancer Research Inc.",
number = "24",

}

TY - JOUR

T1 - The Ligamp TP53 assay for detection of minimal residual disease in head and neck squamous cell carcinoma surgical margins

AU - Poeta, M. Luana

AU - Manola, Judith

AU - Goldenberg, David

AU - Forastiere, Arlene

AU - Califano, Joseph A.

AU - Ridge, John A.

AU - Goodwin, W. Jarrard

AU - Kenady, Daniel

AU - Saunders, John

AU - Westra, William

AU - Sidransky, David

AU - Koch, Wayne M.

PY - 2009/12/15

Y1 - 2009/12/15

N2 - Purpose: Detect tumor-related DNA using LigAmp in histologically clear margins and associate results with clinical outcome. Experimental Design: Patients with head and neck cancer were registered for molecular analysis of surgical margins. Adequacy of resection was ensured using histologic margin analysis. Further margins were then harvested and DNA extracted. TP53 mutations in tumor were determined using Affymetrix p53 GeneChip. Margins were analyzed by Ligamp in comparison with standard curves for quantification of mutant DNA. Ligation used two oligonucleotides to isolate DNA targeting the mutation. Ligated DNA was amplified using real-time PCR. The quantity of mutation in the margin was determined as percent of mutant species relative to plasmid and relative to tumor. Cutpoints were identified and defined groups were evaluated for local failure-free, cancer-specific, and overall survival. Study margins were examined for presence of tumor by light microscopy. Results: Tissue from 95 patients with common mutations was analyzed. Fifteen experienced local recurrence. Cutpoints of 0.15% for mutant species relative to plasmid and 0.5% for mutant species relative to tumor were chosen as most selective of recurrent cases. LigAmp had slightly better area under the receiver operator characteristic curve (P = 0.09) than light microscopy correctly predicting 9 of 15 recurrent tumors. There were 6 false negative cases and 26 false positive results. No statistically significant distinctions were observed in cancer-specific or overall survival in this limited cohort. Conclusions: Ligamp provides quantifiable, sensitive detection of mutant DNA in histologically normal margins. Detection of mutant species in margins may identify patients at risk of local recurrence.

AB - Purpose: Detect tumor-related DNA using LigAmp in histologically clear margins and associate results with clinical outcome. Experimental Design: Patients with head and neck cancer were registered for molecular analysis of surgical margins. Adequacy of resection was ensured using histologic margin analysis. Further margins were then harvested and DNA extracted. TP53 mutations in tumor were determined using Affymetrix p53 GeneChip. Margins were analyzed by Ligamp in comparison with standard curves for quantification of mutant DNA. Ligation used two oligonucleotides to isolate DNA targeting the mutation. Ligated DNA was amplified using real-time PCR. The quantity of mutation in the margin was determined as percent of mutant species relative to plasmid and relative to tumor. Cutpoints were identified and defined groups were evaluated for local failure-free, cancer-specific, and overall survival. Study margins were examined for presence of tumor by light microscopy. Results: Tissue from 95 patients with common mutations was analyzed. Fifteen experienced local recurrence. Cutpoints of 0.15% for mutant species relative to plasmid and 0.5% for mutant species relative to tumor were chosen as most selective of recurrent cases. LigAmp had slightly better area under the receiver operator characteristic curve (P = 0.09) than light microscopy correctly predicting 9 of 15 recurrent tumors. There were 6 false negative cases and 26 false positive results. No statistically significant distinctions were observed in cancer-specific or overall survival in this limited cohort. Conclusions: Ligamp provides quantifiable, sensitive detection of mutant DNA in histologically normal margins. Detection of mutant species in margins may identify patients at risk of local recurrence.

UR - http://www.scopus.com/inward/record.url?scp=73349118750&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=73349118750&partnerID=8YFLogxK

U2 - 10.1158/1078-0432.CCR-09-1433

DO - 10.1158/1078-0432.CCR-09-1433

M3 - Article

AN - SCOPUS:73349118750

VL - 15

SP - 7658

EP - 7665

JO - Clinical Cancer Research

JF - Clinical Cancer Research

SN - 1078-0432

IS - 24

ER -