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Functional validation of variants of unknown significance using CRISPR gene editing and transcriptomics: A Kleefstra syndrome case studyThere are an estimated > 400 million people living with a rare disease globally, with genetic variants the cause of approximately 80% of cases. Next Generation Sequencing (NGS) rapidly identifies genetic variants however they are often of unknown significance.
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Tricho-hepatic-enteric syndrome (THES) without intractable diarrhoeaWe report an 8 year old girl who was diagnosed with THES by the Undiagnosed Disease Program-WA with compound heterozygous pathogenic variants in SKIV2L
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An integrated expression atlas of miRNAs and their promoters in human and mouseWe provided a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA.
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Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture MicrodissectionThis study provides an initial insight into the TFs of cerebellar granule cells that might be important for development
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Mapping mammalian cell-type-specific transcriptional regulatory networks using KD-CAGE and ChIP-seq data in the TC-YIK cell line.Examining the overlap between genes perturbed in the KD-CAGE experiments and genes with a ChIP-seq peak within 50 kb of their promoter, we identified direct...
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Cellular and molecular changes to cortical neurons following low intensity repetitive magnetic stimulation at different frequenciesA systematic comparison of the cellular and molecular changes in neurons in vitro induced by low intensity magnetic stimulation at different frequencies.
The aim of the Computational Biology team is to understand how individual bases in our genome predispose, alter and interact in normal and disease contexts.
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CD4+ T cells drive an inflammatory, TNF-α/IFN-rich tumor microenvironment responsive to chemotherapyWhile chemotherapy remains the first-line treatment for many cancers, it is still unclear what distinguishes responders from non-responders. Here, we characterize the chemotherapy-responsive tumor microenvironment in mice, using RNA sequencing on tumors before and after cyclophosphamide, and compare the gene expression profiles of responders with progressors.
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Identifying SETBP1 haploinsufficiency molecular pathways to improve patient diagnosis using induced pluripotent stem cells and neural disease modellingSETBP1 Haploinsufficiency Disorder (SETBD) is characterised by mild to moderate intellectual disability, speech and language impairment, mild motor developmental delay, behavioural issues, hypotonia, mild facial dysmorphisms, and vision impairment. Despite a clear link between SETBP1 mutations and neurodevelopmental disorders the precise role of SETBP1 in neural development remains elusive.
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An expanded phenotype centric benchmark of variant prioritisation toolsIdentifying the causal variant for diagnosis of genetic diseases is challenging when using next-generation sequencing approaches and variant prioritization tools can assist in this task. These tools provide in silico predictions of variant pathogenicity, however they are agnostic to the disease under study. We previously performed a disease-specific benchmark of 24 such tools to assess how they perform in different disease contexts.