Application of multiplex ligation-dependent probe amplification (MLPA) and low pass whole genome sequencing (LP-WGS) to the classification / characterisation of low grade glioneuronal tumours

Jason Dyke; Leslie Calapre; Aaron Beasley; Elin Gray; Richard Allcock; Jacqueline Bentel

doi:10.1016/j.prp.2021.153724

Application of multiplex ligation-dependent probe amplification (MLPA) and low pass whole genome sequencing (LP-WGS) to the classification / characterisation of low grade glioneuronal tumours

Pathol Res Pract. 2022 Jan:229:153724. doi: 10.1016/j.prp.2021.153724. Epub 2021 Nov 29.

Authors

Jason Dyke¹, Leslie Calapre², Aaron Beasley³, Elin Gray⁴, Richard Allcock⁵, Jacqueline Bentel⁶

Affiliations

¹ PathWest Neuropathology, Royal Perth Hospital, Perth, WA, Australia; School of Medicine and Pharmacology, University of Western Australia, Crawley, WA, Australia. Electronic address: [email protected].
² School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.
³ School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia; Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia.
⁴ School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia; Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia; Lions Eye Institute, Nedlands, WA, Australia.
⁵ Pathology & Laboratory Medicine, University of Western Australia, Crawley, WA, Australia.
⁶ PathWest Neuropathology, Royal Perth Hospital, Perth, WA, Australia; PathWest Anatomical Pathology, Fiona Stanley Hospital, Murdoch, WA, Australia.

PMID: 34942511
DOI: 10.1016/j.prp.2021.153724

Abstract

Aims: Glioneuronal tumours, although rare, are an important cause of treatment-resistant epilepsy. Differential diagnosis of glioneuronal tumour subtypes is complicated by their variable histological appearance and the lack of pathognomonic histological or molecular biomarkers. In this study we have applied techniques available in a diagnostic laboratory setting to characterise molecular and cytogenetic abnormalities in a single institution cohort of glioneuronal tumours.

Methods: A cohort of 29 glioneuronal tumours that included 21 gangliogliomas and 5 dysembryoplastic neuroepithelial tumours (DNETs) was analysed using low pass whole genome sequencing (WGS) and 2 multiplex ligation-dependent probe amplification (MLPA) central nervous system (CNS) tumour probesets.

Results: Low pass WGS identified chromosomal or subchromosomal alterations in 15 specimens. The most common chromosomal alterations were gains of chromosome 7 (n = 8) and chromosome 16 (n = 3). The BRAF^V600E mutation was detected by MLPA in 9/21 (42.9%) gangliogliomas and 2/2 pleomorphic xanthoastrocytomas (PXAs). Chromosome 7 gains detected by WGS were reflected in MLPAs by overall gains of chromosome 7 gene probes, including those for BRAF, KIAA1549 and EGFR, while an internal BRAF/MKRN1 duplication was detected in a single ganglioglioma. Homozygous CDKN2A/B loss was detected by MLPA in 3 gangliogliomas, with p16 immunohistochemistry supporting these results.

Conclusions: The combination of low pass WGS and MLPA identifies multiple, diverse genetic and chromosomal alterations in glioneuronal tumours, irrespective of histological tumour grade.

Keywords: Ganglioglioma; Glioneuronal tumour; MLPA; Whole genome sequencing.

MeSH terms

Adolescent
Adult
Aged
Brain Neoplasms / classification
Brain Neoplasms / genetics*
Brain Neoplasms / pathology
Child
Child, Preschool
Female
Ganglioglioma / classification
Ganglioglioma / genetics*
Ganglioglioma / pathology
Glioma / classification
Glioma / genetics*
Glioma / pathology
Humans
Infant
Male
Middle Aged
Multiplex Polymerase Chain Reaction*
Neoplasm Grading
Whole Genome Sequencing
Young Adult