Development and validation of a novel clinical fluorescence in situ hybridization assay to detect JAK2 and PD-L1 amplification: A fluorescence in situ hybridization assay for JAK2 and PD-L1 amplification

Meixuan Chen, Mariacarla Andreozzi, Barbara A Pockaj, Michael Barrett, Idris Tolgay Ocal, Ann E. McCullough, Maria E. Linnaus, James M. Chang, Jennifer H. Yearley, Lakshmanan Annamalai, Karen S. Anderson

Research output: Contribution to journalArticle

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Abstract

The amplification of chromosome 9p24.1 encoding PD-L1, PD-L2, and JAK2 has been reported in multiple types of cancer and is associated with poor outcome, upregulation of PD-L1, and activation of the JAK/STAT pathway. We have developed a novel fluorescence in situ hybridization assay which combines 3 probes mapping to 9p24.1 with a commercial chromosome 9 centromere (CEN9) probe for detection of the JAK2/9p24.1 amplification. JAK2 fluorescence in situ hybridization was compared with array-based comparative genomic hybridization in 34 samples of triple negative breast cancer tumor. By array-based comparative genomic hybridization, 15 had 9p24.1 copy-number gain (log2rati<40.3) and 19 were classified as non-gain (log2ratio≤0.3). Copy-number gain was defined as JAK2/CEN9 ratio ≥1.1 or average JAK2 signals≥3.0. Twelve of 15 samples with copy-number gain by array-based comparative genomic hybridization were also detected by fluorescence in situ hybridization. Eighteen of 19 samples classified as copy-number non-gain by array-based comparative genomic hybridization were concordant by array-based comparative genomic hybridization. The sensitivity and specificity of the fluorescence in situ hybridization assay was 80% and 95%, respectively (P=0.02). The sample with the highest level of amplification by array-based comparative genomic hybridization (log2ratio=3.6) also scored highest by fluorescence in situ hybridization (ratio=8.2). There was a correlation between the expression of JAK2 and amplification status (Mean 633 vs 393, P=0.02), and there was a trend of association with PD-L1 RNA expression (Mean 46 vs 22, P=0.11). No significant association was observed between PD-L1 immunohistochemistry expression and copy-number gain status. In summary, the novel array-based comparative genomic hybridization assay for detection of chromosome 9p24.1 strongly correlates with the detection of copy-number gain by array-based comparative genomic hybridization. In triple negative breast cancer, this biomarker may identify a relevant subset of patients for targeted molecular therapies.

Original languageEnglish (US)
Pages (from-to)1516-1526
Number of pages11
JournalModern Pathology
Volume30
Issue number11
DOIs
StatePublished - Nov 1 2017

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Comparative Genomic Hybridization
Fluorescence In Situ Hybridization
Triple Negative Breast Neoplasms
Chromosomes
Molecular Targeted Therapy
Chromosomes, Human, Pair 9
Centromere
Tumor Biomarkers
Up-Regulation
Immunohistochemistry
RNA
Breast Neoplasms
Sensitivity and Specificity

ASJC Scopus subject areas

  • Pathology and Forensic Medicine

Cite this

Development and validation of a novel clinical fluorescence in situ hybridization assay to detect JAK2 and PD-L1 amplification : A fluorescence in situ hybridization assay for JAK2 and PD-L1 amplification. / Chen, Meixuan; Andreozzi, Mariacarla; Pockaj, Barbara A; Barrett, Michael; Ocal, Idris Tolgay; McCullough, Ann E.; Linnaus, Maria E.; Chang, James M.; Yearley, Jennifer H.; Annamalai, Lakshmanan; Anderson, Karen S.

In: Modern Pathology, Vol. 30, No. 11, 01.11.2017, p. 1516-1526.

Research output: Contribution to journalArticle

Chen, Meixuan ; Andreozzi, Mariacarla ; Pockaj, Barbara A ; Barrett, Michael ; Ocal, Idris Tolgay ; McCullough, Ann E. ; Linnaus, Maria E. ; Chang, James M. ; Yearley, Jennifer H. ; Annamalai, Lakshmanan ; Anderson, Karen S. / Development and validation of a novel clinical fluorescence in situ hybridization assay to detect JAK2 and PD-L1 amplification : A fluorescence in situ hybridization assay for JAK2 and PD-L1 amplification. In: Modern Pathology. 2017 ; Vol. 30, No. 11. pp. 1516-1526.
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abstract = "The amplification of chromosome 9p24.1 encoding PD-L1, PD-L2, and JAK2 has been reported in multiple types of cancer and is associated with poor outcome, upregulation of PD-L1, and activation of the JAK/STAT pathway. We have developed a novel fluorescence in situ hybridization assay which combines 3 probes mapping to 9p24.1 with a commercial chromosome 9 centromere (CEN9) probe for detection of the JAK2/9p24.1 amplification. JAK2 fluorescence in situ hybridization was compared with array-based comparative genomic hybridization in 34 samples of triple negative breast cancer tumor. By array-based comparative genomic hybridization, 15 had 9p24.1 copy-number gain (log2rati<40.3) and 19 were classified as non-gain (log2ratio≤0.3). Copy-number gain was defined as JAK2/CEN9 ratio ≥1.1 or average JAK2 signals≥3.0. Twelve of 15 samples with copy-number gain by array-based comparative genomic hybridization were also detected by fluorescence in situ hybridization. Eighteen of 19 samples classified as copy-number non-gain by array-based comparative genomic hybridization were concordant by array-based comparative genomic hybridization. The sensitivity and specificity of the fluorescence in situ hybridization assay was 80{\%} and 95{\%}, respectively (P=0.02). The sample with the highest level of amplification by array-based comparative genomic hybridization (log2ratio=3.6) also scored highest by fluorescence in situ hybridization (ratio=8.2). There was a correlation between the expression of JAK2 and amplification status (Mean 633 vs 393, P=0.02), and there was a trend of association with PD-L1 RNA expression (Mean 46 vs 22, P=0.11). No significant association was observed between PD-L1 immunohistochemistry expression and copy-number gain status. In summary, the novel array-based comparative genomic hybridization assay for detection of chromosome 9p24.1 strongly correlates with the detection of copy-number gain by array-based comparative genomic hybridization. In triple negative breast cancer, this biomarker may identify a relevant subset of patients for targeted molecular therapies.",
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AU - Andreozzi, Mariacarla

AU - Pockaj, Barbara A

AU - Barrett, Michael

AU - Ocal, Idris Tolgay

AU - McCullough, Ann E.

AU - Linnaus, Maria E.

AU - Chang, James M.

AU - Yearley, Jennifer H.

AU - Annamalai, Lakshmanan

AU - Anderson, Karen S.

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N2 - The amplification of chromosome 9p24.1 encoding PD-L1, PD-L2, and JAK2 has been reported in multiple types of cancer and is associated with poor outcome, upregulation of PD-L1, and activation of the JAK/STAT pathway. We have developed a novel fluorescence in situ hybridization assay which combines 3 probes mapping to 9p24.1 with a commercial chromosome 9 centromere (CEN9) probe for detection of the JAK2/9p24.1 amplification. JAK2 fluorescence in situ hybridization was compared with array-based comparative genomic hybridization in 34 samples of triple negative breast cancer tumor. By array-based comparative genomic hybridization, 15 had 9p24.1 copy-number gain (log2rati<40.3) and 19 were classified as non-gain (log2ratio≤0.3). Copy-number gain was defined as JAK2/CEN9 ratio ≥1.1 or average JAK2 signals≥3.0. Twelve of 15 samples with copy-number gain by array-based comparative genomic hybridization were also detected by fluorescence in situ hybridization. Eighteen of 19 samples classified as copy-number non-gain by array-based comparative genomic hybridization were concordant by array-based comparative genomic hybridization. The sensitivity and specificity of the fluorescence in situ hybridization assay was 80% and 95%, respectively (P=0.02). The sample with the highest level of amplification by array-based comparative genomic hybridization (log2ratio=3.6) also scored highest by fluorescence in situ hybridization (ratio=8.2). There was a correlation between the expression of JAK2 and amplification status (Mean 633 vs 393, P=0.02), and there was a trend of association with PD-L1 RNA expression (Mean 46 vs 22, P=0.11). No significant association was observed between PD-L1 immunohistochemistry expression and copy-number gain status. In summary, the novel array-based comparative genomic hybridization assay for detection of chromosome 9p24.1 strongly correlates with the detection of copy-number gain by array-based comparative genomic hybridization. In triple negative breast cancer, this biomarker may identify a relevant subset of patients for targeted molecular therapies.

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