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 Pockaj, Michael T. Barrett, Idris Tolgay Ocal, Ann E. McCullough, Maria E. Linnaus, James M. Chang, Jennifer H. Yearley, Lakshmanan Annamalai, Karen Anderson

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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; Barrett, Michael T.; Ocal, Idris Tolgay; McCullough, Ann E.; Linnaus, Maria E.; Chang, James M.; Yearley, Jennifer H.; Annamalai, Lakshmanan; Anderson, Karen.

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

    Research output: Contribution to journalArticle

    Chen, Meixuan ; Andreozzi, Mariacarla ; Pockaj, Barbara ; Barrett, Michael T. ; Ocal, Idris Tolgay ; McCullough, Ann E. ; Linnaus, Maria E. ; Chang, James M. ; Yearley, Jennifer H. ; Annamalai, Lakshmanan ; Anderson, Karen. / 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.",
    author = "Meixuan Chen and Mariacarla Andreozzi and Barbara Pockaj and Barrett, {Michael T.} and Ocal, {Idris Tolgay} and McCullough, {Ann E.} and Linnaus, {Maria E.} and Chang, {James M.} and Yearley, {Jennifer H.} and Lakshmanan Annamalai and Karen Anderson",
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    AU - Chen, Meixuan

    AU - Andreozzi, Mariacarla

    AU - Pockaj, Barbara

    AU - Barrett, Michael T.

    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

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