Chromosome 3 status in uveal melanoma: A comparison of fluorescence in situ hybridization and single-nucleotide polymorphism array

Arun D. Singh, Mary E. Aronow, Yang Sun, Gurkan Bebek, Yogen Saunthararajah, Lynn R. Schoenfield, Charles V. Biscotti, Raymond R. Tubbs, Pierre L. Triozzi, Charis Eng

Research output: Contribution to journalArticle

Abstract

PURPOSE. To compare fluorescence in situ hybridization (FISH) using a centromeric probe for chromosome 3 (CEP3) and 3p26 locus-specific probe with single-nucleotide polymorphism array (SNP-A) analysis in the detection of high-risk uveal melanoma. METHODS. Fifty cases of uveal melanoma (28 males, 22 females) treated by enucleation between 2004 and 2010 were analyzed. Fresh tissue was used for FISH and SNP-A analysis. FISH was performed using a CEP3 and a 3p26 locus-specific probe. Tumor size, location, and clinical outcome were recorded during the 7-year study period (median follow-up: 35.5 months; mean: 38.5 months). The sensitivity, specificity, positive predictive value, and negative predictive value were calculated. RESULTS. Monosomy 3 was detected by FISH-CEP3 in 27 tumors (54%), FISH-3p26 deletion was found in 30 (60%), and SNP-A analysis identified 31 (62%) of the tumors with monosomy 3. Due to technical failures, FISH and SNP-A were noninterpretable in one case (2%) and two cases (4%), respectively. In both cases of SNP-A failure, tumors were positive for FISH 3p26 deletion and in a single case of FISH failure, monosomy 3 was found using SNP-A. No statistically significant differences were observed in any of the sensitivity or specificity measures. CONCLUSIONS. For prediction of survival at 36 months, FISH CEP3, FISH 3p26, and SNP-A were comparable. A combination of prognostication techniques should be used in an unlikely event of technical failure (2%-4%).

Original languageEnglish (US)
Pages (from-to)3331-3339
Number of pages9
JournalInvestigative Ophthalmology and Visual Science
Volume53
Issue number7
DOIs
StatePublished - Jun 2012
Externally publishedYes

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Chromosomes, Human, Pair 3
Fluorescence In Situ Hybridization
Single Nucleotide Polymorphism
Monosomy
Neoplasms
Uveal melanoma
Sensitivity and Specificity

ASJC Scopus subject areas

  • Ophthalmology
  • Sensory Systems
  • Cellular and Molecular Neuroscience

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Chromosome 3 status in uveal melanoma : A comparison of fluorescence in situ hybridization and single-nucleotide polymorphism array. / Singh, Arun D.; Aronow, Mary E.; Sun, Yang; Bebek, Gurkan; Saunthararajah, Yogen; Schoenfield, Lynn R.; Biscotti, Charles V.; Tubbs, Raymond R.; Triozzi, Pierre L.; Eng, Charis.

In: Investigative Ophthalmology and Visual Science, Vol. 53, No. 7, 06.2012, p. 3331-3339.

Research output: Contribution to journalArticle

Singh, AD, Aronow, ME, Sun, Y, Bebek, G, Saunthararajah, Y, Schoenfield, LR, Biscotti, CV, Tubbs, RR, Triozzi, PL & Eng, C 2012, 'Chromosome 3 status in uveal melanoma: A comparison of fluorescence in situ hybridization and single-nucleotide polymorphism array', Investigative Ophthalmology and Visual Science, vol. 53, no. 7, pp. 3331-3339. https://doi.org/10.1167/iovs.11-9027
Singh, Arun D. ; Aronow, Mary E. ; Sun, Yang ; Bebek, Gurkan ; Saunthararajah, Yogen ; Schoenfield, Lynn R. ; Biscotti, Charles V. ; Tubbs, Raymond R. ; Triozzi, Pierre L. ; Eng, Charis. / Chromosome 3 status in uveal melanoma : A comparison of fluorescence in situ hybridization and single-nucleotide polymorphism array. In: Investigative Ophthalmology and Visual Science. 2012 ; Vol. 53, No. 7. pp. 3331-3339.
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abstract = "PURPOSE. To compare fluorescence in situ hybridization (FISH) using a centromeric probe for chromosome 3 (CEP3) and 3p26 locus-specific probe with single-nucleotide polymorphism array (SNP-A) analysis in the detection of high-risk uveal melanoma. METHODS. Fifty cases of uveal melanoma (28 males, 22 females) treated by enucleation between 2004 and 2010 were analyzed. Fresh tissue was used for FISH and SNP-A analysis. FISH was performed using a CEP3 and a 3p26 locus-specific probe. Tumor size, location, and clinical outcome were recorded during the 7-year study period (median follow-up: 35.5 months; mean: 38.5 months). The sensitivity, specificity, positive predictive value, and negative predictive value were calculated. RESULTS. Monosomy 3 was detected by FISH-CEP3 in 27 tumors (54{\%}), FISH-3p26 deletion was found in 30 (60{\%}), and SNP-A analysis identified 31 (62{\%}) of the tumors with monosomy 3. Due to technical failures, FISH and SNP-A were noninterpretable in one case (2{\%}) and two cases (4{\%}), respectively. In both cases of SNP-A failure, tumors were positive for FISH 3p26 deletion and in a single case of FISH failure, monosomy 3 was found using SNP-A. No statistically significant differences were observed in any of the sensitivity or specificity measures. CONCLUSIONS. For prediction of survival at 36 months, FISH CEP3, FISH 3p26, and SNP-A were comparable. A combination of prognostication techniques should be used in an unlikely event of technical failure (2{\%}-4{\%}).",
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TY - JOUR

T1 - Chromosome 3 status in uveal melanoma

T2 - A comparison of fluorescence in situ hybridization and single-nucleotide polymorphism array

AU - Singh, Arun D.

AU - Aronow, Mary E.

AU - Sun, Yang

AU - Bebek, Gurkan

AU - Saunthararajah, Yogen

AU - Schoenfield, Lynn R.

AU - Biscotti, Charles V.

AU - Tubbs, Raymond R.

AU - Triozzi, Pierre L.

AU - Eng, Charis

PY - 2012/6

Y1 - 2012/6

N2 - PURPOSE. To compare fluorescence in situ hybridization (FISH) using a centromeric probe for chromosome 3 (CEP3) and 3p26 locus-specific probe with single-nucleotide polymorphism array (SNP-A) analysis in the detection of high-risk uveal melanoma. METHODS. Fifty cases of uveal melanoma (28 males, 22 females) treated by enucleation between 2004 and 2010 were analyzed. Fresh tissue was used for FISH and SNP-A analysis. FISH was performed using a CEP3 and a 3p26 locus-specific probe. Tumor size, location, and clinical outcome were recorded during the 7-year study period (median follow-up: 35.5 months; mean: 38.5 months). The sensitivity, specificity, positive predictive value, and negative predictive value were calculated. RESULTS. Monosomy 3 was detected by FISH-CEP3 in 27 tumors (54%), FISH-3p26 deletion was found in 30 (60%), and SNP-A analysis identified 31 (62%) of the tumors with monosomy 3. Due to technical failures, FISH and SNP-A were noninterpretable in one case (2%) and two cases (4%), respectively. In both cases of SNP-A failure, tumors were positive for FISH 3p26 deletion and in a single case of FISH failure, monosomy 3 was found using SNP-A. No statistically significant differences were observed in any of the sensitivity or specificity measures. CONCLUSIONS. For prediction of survival at 36 months, FISH CEP3, FISH 3p26, and SNP-A were comparable. A combination of prognostication techniques should be used in an unlikely event of technical failure (2%-4%).

AB - PURPOSE. To compare fluorescence in situ hybridization (FISH) using a centromeric probe for chromosome 3 (CEP3) and 3p26 locus-specific probe with single-nucleotide polymorphism array (SNP-A) analysis in the detection of high-risk uveal melanoma. METHODS. Fifty cases of uveal melanoma (28 males, 22 females) treated by enucleation between 2004 and 2010 were analyzed. Fresh tissue was used for FISH and SNP-A analysis. FISH was performed using a CEP3 and a 3p26 locus-specific probe. Tumor size, location, and clinical outcome were recorded during the 7-year study period (median follow-up: 35.5 months; mean: 38.5 months). The sensitivity, specificity, positive predictive value, and negative predictive value were calculated. RESULTS. Monosomy 3 was detected by FISH-CEP3 in 27 tumors (54%), FISH-3p26 deletion was found in 30 (60%), and SNP-A analysis identified 31 (62%) of the tumors with monosomy 3. Due to technical failures, FISH and SNP-A were noninterpretable in one case (2%) and two cases (4%), respectively. In both cases of SNP-A failure, tumors were positive for FISH 3p26 deletion and in a single case of FISH failure, monosomy 3 was found using SNP-A. No statistically significant differences were observed in any of the sensitivity or specificity measures. CONCLUSIONS. For prediction of survival at 36 months, FISH CEP3, FISH 3p26, and SNP-A were comparable. A combination of prognostication techniques should be used in an unlikely event of technical failure (2%-4%).

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U2 - 10.1167/iovs.11-9027

DO - 10.1167/iovs.11-9027

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JO - Investigative Ophthalmology and Visual Science

JF - Investigative Ophthalmology and Visual Science

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