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Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ERBB receptors in breast cancer cellsThe analysis of CAGE (Cap Analysis of Gene Expression) time-courses has been applied to examine the dynamics of enhancer and promoter by sequentially...
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CAGE-defined promoter regions of the genes implicated in Rett SyndromeA comprehensive picture of the regulatory regions of the three genes involved in Rett Syndrome
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Personalised analytics for rare disease diagnosticsHere we focus on the problem of prioritising variants with respect to the observed disease phenotype
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Tumour draining lymph node-generated CD8 T cells play a role in controlling lung metastases after a primary tumour is removed but not when adjuvant immunotherapy is usedSurgical resection of cancer remains the frontline therapy for millions of patients annually, but post-operative recurrence is common, with a relapse rate of around 45% for non-small cell lung cancer. The tumour draining lymph nodes (dLN) are resected at the time of surgery for staging purposes, and this cannot be a null event for patient survival and future response to immune checkpoint blockade treatment. This project investigates cancer surgery, lymphadenectomy, onset of metastatic disease, and response to immunotherapy in a novel model that closely reflects the clinical setting. In a murine metastatic lung cancer model, primary subcutaneous tumours were resected with associated dLNs remaining intact, completely resected or partially resected.
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A phenotype centric benchmark of variant prioritisation toolsWe hypothesised that the performance of variant prioriisation tools may vary by disease phenotype.
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Pushing the boundaries of rare disease diagnostics with the help of the first Undiagnosed HackathonTimo Lassmann BSc (Hons) MSc PhD Feilman Fellow; Head, Precision Health Research and Head, Computational Biology timo.lassmann@thekids.org.au
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What’s in a name?In WA, 60,000 kids live with a rare disease, and of those about half do not have a diagnosis. At The Kids, researchers are leading the charge in developing a method to identify genetic variations, so that kids like Charlotte can get answers.
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CRISPR-Cas9-generated PTCHD1 2489T>G stem cells recapitulate patient phenotype when undergoing neural inductionAn estimated 3.5%-5.9% of the global population live with rare diseases, and approximately 80% of these diseases have a genetic cause. Rare genetic diseases are difficult to diagnose, with some affected individuals experiencing diagnostic delays of 5-30 years. Next-generation sequencing has improved clinical diagnostic rates to 33%-48%. In a majority of cases, novel variants potentially causing the disease are discovered.
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SAMStat 2: quality control for next generation sequencing dataSAMStat is an efficient program to extract quality control metrics from fastq and SAM/BAM files. A distinguishing feature is that it displays sequence composition, base quality composition and mapping error profiles split by mapping quality. This allows users to rapidly identify reasons for poor mapping including the presence of untrimmed adapters or poor sequencing quality at individual read positions.
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Gateways to the FANTOM5 promoter level mammalian expression atlasThe FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE.