Detection of KIAA1549-BRAF fusion transcripts in formalin-fixed paraffin-embedded pediatric low-grade gliomas

Yongji Tian, Benjamin E. Rich, Natalie Vena, Justin M. Craig, Laura E. MacConaill, Veena Rajaram, Stewart Goldman, Hala Taha, Madeha Mahmoud, Memet Ozek, Aydin Sav, Janina A. Longtine, Neal I. Lindeman, Levi A. Garraway, Azra H. Ligon, Charles D. Stiles, Sandro Santagata, Jennifer A. Chan, Mark W. Kieran, Keith L. Ligon

Research output: Contribution to journalArticle

51 Citations (Scopus)

Abstract

Alterations of BRAF are the most common known genetic aberrations in pediatric gliomas. They frequently are found in pilocytic astrocytomas, where genomic duplications involving BRAF and the poorly characterized gene KIAA1549 create fusion proteins with constitutive B-Raf kinase activity. BRAF V600E point mutations are less common and generally occur in nonpilocytic tumors. The development of BRAF inhibitors as drugs has created an urgent need for robust clinical assays to identify activating lesions in BRAF. KIAA1549-BRAF fusion transcripts have been detected in frozen tissue, however, methods for FFPE tissue have not been reported. We developed a panel of FFPE-compatible quantitative RT-PCR assays for the most common KIAA1549-BRAF fusion transcripts. Application of these assays to a collection of 51 low-grade pediatric gliomas showed 97% sensitivity and 91% specificity compared with fluorescence in situ hybridization or array comparative genomic hybridization. In parallel, we assayed samples for the presence of the BRAF V600E mutation by PCR pyrosequencing. The data further support previous observations that these two alterations of the BRAF, KIAA1549 fusions and V600E point mutations, are associated primarily with pilocytic astrocytomas and nonpilocytic gliomas, respectively. These results show that fusion transcripts and mutations can be detected reliably in standard FFPE specimens and may be useful for incorporation into future studies of pediatric gliomas in basic science or clinical trials.

Original languageEnglish (US)
Pages (from-to)669-677
Number of pages9
JournalJournal of Molecular Diagnostics
Volume13
Issue number6
DOIs
StatePublished - Nov 2011

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Glioma
Paraffin
Formaldehyde
Pediatrics
Astrocytoma
Point Mutation
Proto-Oncogene Proteins B-raf
Polymerase Chain Reaction
Mutation
Comparative Genomic Hybridization
Fluorescence In Situ Hybridization
Clinical Trials
Sensitivity and Specificity
Pharmaceutical Preparations
Genes
Neoplasms
Proteins

ASJC Scopus subject areas

  • Molecular Medicine
  • Pathology and Forensic Medicine

Cite this

Detection of KIAA1549-BRAF fusion transcripts in formalin-fixed paraffin-embedded pediatric low-grade gliomas. / Tian, Yongji; Rich, Benjamin E.; Vena, Natalie; Craig, Justin M.; MacConaill, Laura E.; Rajaram, Veena; Goldman, Stewart; Taha, Hala; Mahmoud, Madeha; Ozek, Memet; Sav, Aydin; Longtine, Janina A.; Lindeman, Neal I.; Garraway, Levi A.; Ligon, Azra H.; Stiles, Charles D.; Santagata, Sandro; Chan, Jennifer A.; Kieran, Mark W.; Ligon, Keith L.

In: Journal of Molecular Diagnostics, Vol. 13, No. 6, 11.2011, p. 669-677.

Research output: Contribution to journalArticle

Tian, Y, Rich, BE, Vena, N, Craig, JM, MacConaill, LE, Rajaram, V, Goldman, S, Taha, H, Mahmoud, M, Ozek, M, Sav, A, Longtine, JA, Lindeman, NI, Garraway, LA, Ligon, AH, Stiles, CD, Santagata, S, Chan, JA, Kieran, MW & Ligon, KL 2011, 'Detection of KIAA1549-BRAF fusion transcripts in formalin-fixed paraffin-embedded pediatric low-grade gliomas', Journal of Molecular Diagnostics, vol. 13, no. 6, pp. 669-677. https://doi.org/10.1016/j.jmoldx.2011.07.002
Tian, Yongji ; Rich, Benjamin E. ; Vena, Natalie ; Craig, Justin M. ; MacConaill, Laura E. ; Rajaram, Veena ; Goldman, Stewart ; Taha, Hala ; Mahmoud, Madeha ; Ozek, Memet ; Sav, Aydin ; Longtine, Janina A. ; Lindeman, Neal I. ; Garraway, Levi A. ; Ligon, Azra H. ; Stiles, Charles D. ; Santagata, Sandro ; Chan, Jennifer A. ; Kieran, Mark W. ; Ligon, Keith L. / Detection of KIAA1549-BRAF fusion transcripts in formalin-fixed paraffin-embedded pediatric low-grade gliomas. In: Journal of Molecular Diagnostics. 2011 ; Vol. 13, No. 6. pp. 669-677.
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AU - Vena, Natalie

AU - Craig, Justin M.

AU - MacConaill, Laura E.

AU - Rajaram, Veena

AU - Goldman, Stewart

AU - Taha, Hala

AU - Mahmoud, Madeha

AU - Ozek, Memet

AU - Sav, Aydin

AU - Longtine, Janina A.

AU - Lindeman, Neal I.

AU - Garraway, Levi A.

AU - Ligon, Azra H.

AU - Stiles, Charles D.

AU - Santagata, Sandro

AU - Chan, Jennifer A.

AU - Kieran, Mark W.

AU - Ligon, Keith L.

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