Karin S. Kassahn
A5057342873- Cancer Genomics and Diagnostics
- Genomics and Rare Diseases
- Pancreatic and Hepatic Oncology Research
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- RNA Research and Splicing
- Genomic variations and chromosomal abnormalities
- Genetic factors in colorectal cancer
- Genomics and Chromatin Dynamics
- Evolution and Genetic Dynamics
- Chromosomal and Genetic Variations
- Cancer-related molecular mechanisms research
- Bioinformatics and Genomic Networks
- Mitochondrial Function and Pathology
- Aquaculture disease management and microbiota
- RNA and protein synthesis mechanisms
- BRCA gene mutations in cancer
- Gene expression and cancer classification
- Nutrition, Genetics, and Disease
- Physiological and biochemical adaptations
- Lung Cancer Treatments and Mutations
- Prenatal Screening and Diagnostics
- Acute Myeloid Leukemia Research
- Autopsy Techniques and Outcomes
South Australia Pathology
2014-2024
The University of Adelaide
2003-2024
The University of Queensland
2010-2023
University of South Australia
2016-2021
South Australian Health and Medical Research Institute
2021
Royal Adelaide Hospital
2021
Royal Brisbane and Women's Hospital
2021
Women's and Children's Hospital
2014-2018
Centre for Cancer Biology
2016
The University of Melbourne
2015
The Protein Interaction Network Analysis (PINA) platform is a comprehensive web resource, which includes database of unified protein–protein interaction data integrated from six manually curated public databases, and set built-in tools for network construction, filtering, analysis visualization. second version PINA enhances its utility studies protein interactions at level, by including multiple collections modules identified different clustering approaches the whole ('interactome') model...
Abstract Background Variants of microRNAs (miRNAs), called isomiRs, are commonly reported in deep-sequencing studies; however, the functional significance these variants remains controversial. Observational studies show that isomiR patterns non-random, hinting molecules could be regulated and therefore functional, although no conclusive biological role has been demonstrated for molecules. Results To assess relevance we have performed ultra-deep miRNA-seq on ten adult human tissues, created...
The importance of epigenetic modifications such as DNA methylation in tumorigenesis is increasingly being appreciated. To define the genome-wide pattern pancreatic ductal adenocarcinomas (PDAC), we captured profiles 167 untreated resected PDACs and compared them to a panel 29 adjacent nontransformed pancreata using high-density arrays. A total 11,634 CpG sites associated with 3,522 genes were significantly differentially methylated (DM) PDAC capable segregating from non-malignant pancreas,...
Pancreatic cancer is one of the most deadly cancers affecting Western world. Because disease highly metastatic and difficult to diagnosis until late stages, 5-y survival rate around 5%. The identification molecular drivers critical for furthering our understanding development improved diagnostic tools therapeutics. We have conducted a mutagenic screen using Sleeping Beauty ( SB ) in mice identify new candidate genes pancreatic cancer. By combining with an oncogenic Kras allele, we observed...
Critically ill infants and children with rare diseases need equitable access to rapid accurate diagnosis direct clinical management. Over 2 years, the Acute Care Genomics program provided whole-genome sequencing 290 families whose critically were admitted hospitals throughout Australia suspected genetic conditions. The average time result was 2.9 d diagnostic yield 47%. We performed additional bioinformatic analyses transcriptome in all patients who remained undiagnosed. Long-read functional...
ABSTRACT Recent advances in molecular biology and the use of DNA microarrays for gene expression profiling are providing new insights into animal stress response, particularly effects on regulation. However, interpretation complex transcriptional changes that occur during still poses many challenges because relationship between at level other levels biological organisation is not well understood. To confront these challenges, a conceptual model linking physiological responses to would be...
Our understanding of the importance transcriptional regulation for biological function is continuously improving. We still know, however, comparatively little about how environmentally induced stress affects gene expression in vertebrates, and consistency responses to different types environmental stress. In this study, we used a multi-stressor approach identify components common response as well unique exposed individuals coral reef fish Pomacentrus moluccensis hypoxic, hyposmotic, cold...
The significance of whole-genome duplications (WGD) for vertebrate evolution remains controversial, in part because the mechanisms by which WGD contributed to functional or speciation are still incompletely characterized. Fish genomes provide an ideal context examine consequences WGD, teleost lineage experienced additional soon after divergence from tetrapods and five available comparative analysis. Here we present integrated approach characterize these post-duplication based on genome-scale...
Abstract Background Proteins of the mammalian PYHIN (IFI200/HIN-200) family are involved in defence against infection through recognition foreign DNA. The member absent melanoma 2 (AIM2) binds cytosolic DNA via its HIN domain and initiates inflammasome formation pyrin domain. AIM2 lies within a cluster related genes, many which uncharacterised mouse. To better understand evolution, orthology function these we have documented range genes present representative species, undertaken phylogenetic...
Pancreatic cancer is one of the most lethal and molecularly diverse malignancies. Repurposing therapeutics that target specific molecular mechanisms in different disease types offers potential for rapid improvements outcome. Although HER2 amplification occurs pancreatic cancer, it inadequately characterized to exploit anti-HER2 therapies.HER2 was detected further analyzed using multiple genomic sequencing approaches. Standardized reference laboratory assays defined a large cohort patients (n...
Abstract Treatment options for patients with brain metastases ( BMs ) have limited efficacy and the mortality rate is virtually 100%. Targeted therapy critically under‐utilized, our understanding of mechanisms underpinning metastatic outgrowth in limited. To address these deficiencies, we investigated genomic transcriptomic landscapes 36 from breast, lung, melanoma oesophageal cancers, using DNA copy‐number analysis exome‐ RNA ‐sequencing. The key findings were as follows. (a) Identification...
Pancreatic ductal adenocarcinoma (PDAC) can be divided into transcriptomic subtypes with two broad lineages referred to as classical (pancreatic) and squamous. We find that these are driven by distinct metabolic phenotypes. Loss of genes drive endodermal lineage specification, HNF4A GATA6, switch profiles from predominantly squamous, glycogen synthase kinase 3 beta (GSK3β) a key regulator glycolysis. Pharmacological inhibition GSK3β results in selective sensitivity the squamous subtype;...
Abstract Pregnancy loss and perinatal death are devastating events for families. We assessed ‘genomic autopsy’ as an adjunct to standard autopsy 200 families who had experienced fetal or newborn death, providing a definitive candidate genetic diagnosis in 105 Our cohort provides evidence of severe atypical utero presentations known disorders identifies novel phenotypes disease genes. Inheritance 42% diagnoses were either autosomal recessive (30.8%), X-linked (3.8%) dominant (excluding de...
Tumour cellularity, the relative proportion of tumour and normal cells in a sample, affects sensitivity mutation detection, copy number analysis, cancer gene expression methylation profiling. cellularity is traditionally estimated by pathological review sectioned specimens; however this method both subjective prone to error due heterogeneity within lesions differences between sample viewed during tissue used for research purposes. In paper we describe statistical model estimate from SNP...
Abstract Coral reef fishes are expected to experience rising sea surface temperatures due climate change. How well tropical will respond these increased and which genes important in the response elevated is not known. Microarray technology provides a powerful tool for gene discovery studies, but development of microarrays individual species can be expensive time‐consuming. In this study, we tested suitability Danio rerio oligonucleotide microarray application with few genomic resources,...
Human-induced environmental changes have been linked directly with loss of biodiversity. Coral reefs, which severely impacted by anthropogenic activities over the last few decades, exemplify this global problem and provide an opportunity to develop research addressing key knowledge gaps through 'omics'-based approaches. While many stressors, e.g. warming, ocean acidification, overfishing coastal development identified, there is urgent need understand how corals function at a basic level in...
The return of research results (RoR) remains a complex and well-debated issue. Despite the debate, actual data related to experience giving individual back, impact these may have on clinical care health outcomes, is sorely lacking. Through work Australian Pancreatic Cancer Genome Initiative (APGI) we: (1) delineate pathway back patient where actionable were identified; (2) report utilisation returned. Using this experience, we discuss barriers opportunities associated with comprehensive...