Prognostic testing in uveal melanoma by transcriptomic profiling of fine needle biopsy specimens

Michael D. Onken, Lori A. Worley, Rosa M. Dávilla, Devron H. Char, J. William Harbour

Research output: Contribution to journalArticle

61 Citations (Scopus)

Abstract

Many uveal melanoma patients die of metastasis despite ocular treatment. Transcriptomic profiling of enucleated tumors can identify patients at high metastatic risk. Because most uveal melanomas do not require enucleation, a biopsy would be required for this analysis. Here, we establish the feasibility of transcriptomic analysis of uveal melanomas from fine needle aspirates. Transcriptomic profiles were analyzed from postenucleation "mock" needle biopsies and matching tumors from eight enucleated eyes and from fine needle aspirates in 17 uveal melanomas before radiotherapy. Predictive accuracy was assessed using a weighted voting classifier optimized for probe set selection using a minimal redundancy/maximum relevance algorithm. Transcriptomic profiles from mock biopsies were highly similar to those from their matching tumor samples (P < 0.0001). Transcriptomic profiles from fine needle aspirates clustered into two classes with discriminating probe sets that overlapped significantly with those for our published classification (P < 0.00001). No loss of predictive accuracy was identified among eight needle aspirates obtained from a distant location. Thus, it is feasible to obtain RNA of adequate quality and quantity to perform transcriptomic analysis on uveal. melanoma samples obtained by fine needle biopsy This method can be applied to specimens obtained from distant geographic locations and can stratify uveal melanoma patients based on metastatic risk.

Original languageEnglish
Pages (from-to)567-573
Number of pages7
JournalJournal of Molecular Diagnostics
Volume8
Issue number5
DOIs
StatePublished - Nov 1 2006
Externally publishedYes

Fingerprint

Fine Needle Biopsy
Needles
Biopsy
Geographic Locations
Neoplasms
Needle Biopsy
Politics
Melanoma
Radiotherapy
Uveal melanoma
RNA
Neoplasm Metastasis
Therapeutics

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Prognostic testing in uveal melanoma by transcriptomic profiling of fine needle biopsy specimens. / Onken, Michael D.; Worley, Lori A.; Dávilla, Rosa M.; Char, Devron H.; William Harbour, J.

In: Journal of Molecular Diagnostics, Vol. 8, No. 5, 01.11.2006, p. 567-573.

Research output: Contribution to journalArticle

Onken, Michael D. ; Worley, Lori A. ; Dávilla, Rosa M. ; Char, Devron H. ; William Harbour, J. / Prognostic testing in uveal melanoma by transcriptomic profiling of fine needle biopsy specimens. In: Journal of Molecular Diagnostics. 2006 ; Vol. 8, No. 5. pp. 567-573.
@article{08b5f43e6c964a1ebd54152abf3acafe,
title = "Prognostic testing in uveal melanoma by transcriptomic profiling of fine needle biopsy specimens",
abstract = "Many uveal melanoma patients die of metastasis despite ocular treatment. Transcriptomic profiling of enucleated tumors can identify patients at high metastatic risk. Because most uveal melanomas do not require enucleation, a biopsy would be required for this analysis. Here, we establish the feasibility of transcriptomic analysis of uveal melanomas from fine needle aspirates. Transcriptomic profiles were analyzed from postenucleation {"}mock{"} needle biopsies and matching tumors from eight enucleated eyes and from fine needle aspirates in 17 uveal melanomas before radiotherapy. Predictive accuracy was assessed using a weighted voting classifier optimized for probe set selection using a minimal redundancy/maximum relevance algorithm. Transcriptomic profiles from mock biopsies were highly similar to those from their matching tumor samples (P < 0.0001). Transcriptomic profiles from fine needle aspirates clustered into two classes with discriminating probe sets that overlapped significantly with those for our published classification (P < 0.00001). No loss of predictive accuracy was identified among eight needle aspirates obtained from a distant location. Thus, it is feasible to obtain RNA of adequate quality and quantity to perform transcriptomic analysis on uveal. melanoma samples obtained by fine needle biopsy This method can be applied to specimens obtained from distant geographic locations and can stratify uveal melanoma patients based on metastatic risk.",
author = "Onken, {Michael D.} and Worley, {Lori A.} and D{\'a}villa, {Rosa M.} and Char, {Devron H.} and {William Harbour}, J.",
year = "2006",
month = "11",
day = "1",
doi = "10.2353/jmoldx.2006.060077",
language = "English",
volume = "8",
pages = "567--573",
journal = "Journal of Molecular Diagnostics",
issn = "1525-1578",
publisher = "Association of Molecular Pathology",
number = "5",

}

TY - JOUR

T1 - Prognostic testing in uveal melanoma by transcriptomic profiling of fine needle biopsy specimens

AU - Onken, Michael D.

AU - Worley, Lori A.

AU - Dávilla, Rosa M.

AU - Char, Devron H.

AU - William Harbour, J.

PY - 2006/11/1

Y1 - 2006/11/1

N2 - Many uveal melanoma patients die of metastasis despite ocular treatment. Transcriptomic profiling of enucleated tumors can identify patients at high metastatic risk. Because most uveal melanomas do not require enucleation, a biopsy would be required for this analysis. Here, we establish the feasibility of transcriptomic analysis of uveal melanomas from fine needle aspirates. Transcriptomic profiles were analyzed from postenucleation "mock" needle biopsies and matching tumors from eight enucleated eyes and from fine needle aspirates in 17 uveal melanomas before radiotherapy. Predictive accuracy was assessed using a weighted voting classifier optimized for probe set selection using a minimal redundancy/maximum relevance algorithm. Transcriptomic profiles from mock biopsies were highly similar to those from their matching tumor samples (P < 0.0001). Transcriptomic profiles from fine needle aspirates clustered into two classes with discriminating probe sets that overlapped significantly with those for our published classification (P < 0.00001). No loss of predictive accuracy was identified among eight needle aspirates obtained from a distant location. Thus, it is feasible to obtain RNA of adequate quality and quantity to perform transcriptomic analysis on uveal. melanoma samples obtained by fine needle biopsy This method can be applied to specimens obtained from distant geographic locations and can stratify uveal melanoma patients based on metastatic risk.

AB - Many uveal melanoma patients die of metastasis despite ocular treatment. Transcriptomic profiling of enucleated tumors can identify patients at high metastatic risk. Because most uveal melanomas do not require enucleation, a biopsy would be required for this analysis. Here, we establish the feasibility of transcriptomic analysis of uveal melanomas from fine needle aspirates. Transcriptomic profiles were analyzed from postenucleation "mock" needle biopsies and matching tumors from eight enucleated eyes and from fine needle aspirates in 17 uveal melanomas before radiotherapy. Predictive accuracy was assessed using a weighted voting classifier optimized for probe set selection using a minimal redundancy/maximum relevance algorithm. Transcriptomic profiles from mock biopsies were highly similar to those from their matching tumor samples (P < 0.0001). Transcriptomic profiles from fine needle aspirates clustered into two classes with discriminating probe sets that overlapped significantly with those for our published classification (P < 0.00001). No loss of predictive accuracy was identified among eight needle aspirates obtained from a distant location. Thus, it is feasible to obtain RNA of adequate quality and quantity to perform transcriptomic analysis on uveal. melanoma samples obtained by fine needle biopsy This method can be applied to specimens obtained from distant geographic locations and can stratify uveal melanoma patients based on metastatic risk.

UR - http://www.scopus.com/inward/record.url?scp=33751180133&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33751180133&partnerID=8YFLogxK

U2 - 10.2353/jmoldx.2006.060077

DO - 10.2353/jmoldx.2006.060077

M3 - Article

C2 - 17065425

AN - SCOPUS:33751180133

VL - 8

SP - 567

EP - 573

JO - Journal of Molecular Diagnostics

JF - Journal of Molecular Diagnostics

SN - 1525-1578

IS - 5

ER -