Frequency of false-positive FISH 1p/19q codeletion in adult diffuse astrocytic gliomas

Abstract

Background: Oligodendroglioma is genetically defined by concomitant IDH (IDH1/IDH2) mutation and whole-arm 1p/19q codeletion. Codeletion of 1p/19q traditionally evaluated by fluorescence in situ hybridization (FISH) cannot distinguish partial from whole-arm 1p/19q codeletion. Partial 1p/19q codeletion called positive by FISH is diagnostically a "false-positive" result. Chromosomal microarray (CMA) discriminates partial from whole-arm 1p/19q codeletion. Herein, we aimed to estimate the frequency of partial 1p/19q codeletion that would lead to a false-positive FISH result.

Methods: FISH 1p/19q codeletion test probe coordinates were mapped onto Oncoscan CMA data to determine the rate of partial 1p/19q codeletion predicted to be positive by FISH. Diffuse astrocytic gliomas with available CMA data (2015-2018) were evaluated and classified based on IDH1-R132H/ATRX/p53 immunohistochemistry, IDH/TERT promoter targeted sequencing, and/or CMA according to classification updates. Predicted false-positive cases were verified by FISH whenever possible.

Results: The overall estimated false-positive FISH 1p/19q codeletion rate was 3.6% (8/223). Predicted false positives were verified by FISH in 6 (of 8) cases. False-positive rates did not differ significantly (P = .49) between IDH-mutant (4.6%; 4/86) and IDH-wildtype (2.9%; 4/137) tumors. IDH-wildtype false positives were all WHO grade IV, whereas IDH-mutant false positives spanned WHO grades II-IV. Testing for 1p/19q codeletion would not have been indicated for most false positives based on current classification recommendations.

Conclusion: Selective 1p/19q codeletion testing and cautious interpretation for conflicting FISH and histopathological findings are recommended to avoid potential misdiagnosis.

Keywords: WHO; astrocytoma; cIMPACT; chromosomal microarray; oligodendroglioma.

Figure 1.

Case 1: False-positive IDH-wildtype glioblastoma. (A) Chromosomal microarray weighted log2 ratio and B-allele frequency traces show partial-arm deletion of 1p and 19q, which includes the areas spanning the FISH probes (indicated by arrows). (B and C) False-positive FISH results show a single red target signal and 2 green control signals for chromosome 1 and a relative loss of red to green signals for chromosome 19, indicating 1p deletion and relative 19q loss, respectively. (D) H&E showing astrocytic morphology with elongated nuclei and necrosis, consistent with a morphological diagnosis of glioblastoma. (E) IDH1-R132H immunostain is negative (sequencing for IDH1/IDH2 was also negative), (F) ATRX immunostain shows retained protein expression, and (G) p53 immunostain is consistent with protein overexpression in tumor cells. Scale bars, 50 µm.

Figure 2.

Case 6: False-positive IDH-mutant low-grade infiltrating glioma. (A) Chromosomal microarray weighted log2 ratio and B-allele frequency traces show whole-arm deletion of 1p and partial-arm deletion of 19q, which includes the areas spanning the FISH probes (indicated by arrows). (B and C) False-positive FISH results show a relative loss of red to green signals for chromosomes 1 and 19, indicating relative 1p/19q loss in the context of additional copies of chromosomes 1 and 19. (D) H&E showing tumor cells with round to oval nuclei, regular nuclear contours, and perinuclear halos, a morphology that was considered somewhat ambiguous and not definitive for a morphological diagnosis of astrocytoma or oligodendroglioma. (E) IDH1-R132H immunostain is positive, (F) ATRX immunostain shows loss of protein expression, and (G) p53 immunostain shows protein overexpression only in scattered tumor cells. Scale bars, 50 µm.