FISH 1p/19q Codeletion Testing

Overview

Fluorescence in situ hybridization (FISH) assay used to detect chromosomal codeletion of the short arm of chromosome 1 (1p) and the long arm of chromosome 19 (19q), a defining molecular event in oligodendroglioma. 1p/19q codeletion is a required diagnostic criterion under the WHO 2021 CNS tumor classification for IDH-mutant oligodendrogliomas and is associated with better prognosis and chemosensitivity. The FISH assay uses locus-specific probes flanking the 1p36 and 19q13 regions to detect loss of signal consistent with whole-arm codeletion.

Used by

• Used to assess 1p/19q codeletion status in 39 of 41 anaplastic oligodendroglioma patients enrolled in the MSK HDC-ASCT phase II trial (NCT00588523); 33/39 (85%) were codeleted, identifying the chemotherapy-sensitive majority PMID:28472509.
• NGS (MSK-IMPACT) identified at least one false-positive 1p/19q FISH call in the odg_msk_2017 cohort — a patient classified as codeleted by FISH had a glioblastoma-like NGS signature with no evidence of 1p/19q loss; the authors recommend NGS as a more reliable screening tool than FISH for trials deferring upfront radiotherapy PMID:28472509.

Notes

• FISH detects gross chromosomal loss but does not capture single-nucleotide variants, copy-number neutral events, or the full range of molecular alterations detectable by NGS.
• Interobserver variability in interpreting FISH results for 1p/19q can lead to misclassification, particularly for cases with partial deletions or complex karyotypes.
• Coverage limited to the targeted chromosomal loci; genome-wide copy-number alterations require complementary methods (e.g., SNP arrays, targeted NGS panels, or WES).
• False-positive FISH calls carry clinical consequence when radiotherapy deferral decisions depend on codeletion status.

Sources

• PMID:28472509 — Thomas et al., MSK HDC-ASCT phase II trial in anaplastic oligodendroglioma.

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