Genetics and Molecular Pathology Research Group
Research Group Head
The Genetics and Molecular Pathology research group is interested in the genetic and epigenetic basis for cancer in childhood and uses genomics tools to investigate cancer in both familial settings and in the context of cancer predisposition syndromes. The group is also interested in genomic imprinting, the process that controls gene dosage from the parental chromosomes in early development by epigenetic mechanisms.
Our group also offers molecular diagnostic testing for paediatric cancer predisposition syndromes as well as a range of tumours.
Molecular Diagnostic Testing Service
Service Leader: Associate Professor Elizabeth Algar
The Molecular Diagnostic group offers a range of constitutional and somatic clinical genetic tests relevant to cancer predisposition and cancer diagnosis and treatment. A NATA accredited facility, the group is recognised as a national reference centre for these diseases, and is continually expanding to accommodate new biomarker tests relevant to both adult and paediatric cancer.
Accredited genetic diagnostic tests performed in the Genetics and Molecular Pathology Group:
Beckwith Wiedemann syndrome – 11p15 methylation and CDKN1C screen
Russell Silver syndrome – 11p15 methylation and UPD7
Schwannomatosis – SMARCB1
Malignant rhabdoid tumour – SMARCB1
Wilms tumour – WT1 and 11p15 methylation, 1p/16q loss of heterozygosity
Sarcomas – EWS-FLI1, EWS-ERG1, PAX3-FKHR, PAX7-FKHR, ASPSCR1-TFE3.
Pilocytic Astrocytoma – BRAF-KIAA fusion
Brain tumours – 1p/19q deletion testing
B-cell Acute lymphoblastic leukaemia – IKAROS, molecular fusions of ETV6-RUNX1, E2A-PBX1, MLL-AF4, MLL-AF9, MLL-ENL1, MLL-AF10.
Acute myeloid leukaemia – WT1 expression and WT1 mutation
Chronic myeloid leukaemia – BCR-ABL
T cell Acute lymphoblastic leukaemia – NUP214-ABL1
Myeloproliferative disorders – JAK2 exon 14 V617F and JAK2 exon 12
Single exon mutation screens – As requested
Research NGS Gene Panels-Germline cancer predisposition (paediatric cancers) and somatic mutations in lung, colorectal, pancreatic and brain cancer.
Methylation profiling in paediatric brain cancer—Research testing of signature methylation profiles in medulloblastoma for sub-group classification.
The group is also able to undertake nucleic acids extraction services from a range of tissues for clinical trials (blood, bone marrow, tumour tissue including FFPE sections, buccal swabs) and can also perform specialized molecular testing.
Gene panels for Paediatric Cancer
The group has an active translational research program focused on the identification of new mutations in children with cancer and cancer predisposition, including the ascertainment of epimutations affecting imprinted genes. Genomic imprinting is a process through which it is possible to control gene dosage from the parental chromosomes in early development by epigenetic modification of locus control regions (lcrs). Several genes imprinted are important in childhood cancer with accumulating evidence that disruption to the imprinting process is a critical step in the initiation of certain childhood cancers. A focus of our current research is on identifying the genetic factors that control and disrupt the imprinting process.
The Genetics and Molecular Pathology group is developing specialized gene panels and SNP/GCH arrays for paediatric cancer screening. These are unique in their inclusion of regions of imprinting control. Once validated, we predict translation of the panels to the domain of clinical testing will reveal important clinical information about constitutional cancer predisposition.
Rare incurable paediatric tumours
The Genetics and Molecular Pathology group has an ongoing research interest into the biology of rare paediatric tumours. In collaboration with researchers from the Developmental and Cancer Biology group, this research aims to increase understanding of the biology of malignant rhabdoid tumour (MRT) and diffuse intrinsic pontine glioma (DIPG). MRT is an incurable tumor affecting the kidney and brain and affects children in infancy. In MRT, a single gene SMARCB1 is the target for inactivating mutations. We have previously hypothesized that MRT may be uniquely sensitive to epigenetic therapies and demonstrated this in MRT cell lines with histone deacetylase inhibitors (HDACi). Changes in histone acetylation in the promoters of downstream genes also seen following restoration of SMARCB1 accompany HDACi treatment providing a powerful rationale for further investigation of HDACi as a therapeutic for MRT. The group is also investigating the hypothesis that SMARCB1 plays a role in the post-transcriptional modification of downstream gene expression through effects on RNA splicing. Work on DIPG aims to investigate the epigenetic landscape in tumours, evaluate the specific role of Histone H3.3 mutations, and in vitro responses to epigenetic therapies.