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ItemRuns of homozygosity in killer whale genomes provide a global record of demographic histories.Foote, AD ; Hooper, R ; Alexander, A ; Baird, RW ; Baker, CS ; Ballance, L ; Barlow, J ; Brownlow, A ; Collins, T ; Constantine, R ; Dalla Rosa, L ; Davison, NJ ; Durban, JW ; Esteban, R ; Excoffier, L ; Martin, SLF ; Forney, KA ; Gerrodette, T ; Gilbert, MTP ; Guinet, C ; Hanson, MB ; Li, S ; Martin, MD ; Robertson, KM ; Samarra, FIP ; de Stephanis, R ; Tavares, SB ; Tixier, P ; Totterdell, JA ; Wade, P ; Wolf, JBW ; Fan, G ; Zhang, Y ; Morin, PA (Wiley, 2021-12)Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global data set of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstructed demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We found a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1 Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations, and populations of known conservation concern. These include a Scottish killer whale, for which 37.8% of the autosomes were comprised of ROH >1.5 Mb in length. The fate of this population, in which only two adult males have been sighted in the past five years, and zero fecundity over the last two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.
ItemNo Preview AvailableChallenges in data linkage - experiences from an upper gastrointestinal cancer data linkage studyKhan, N ; Ioannou, L ; Pilgrim, C ; Earnest, A ; Maharaj, A ; Croagh, D ; Liew, D ; Atwood, D ; Holland, J ; Philip, J ; Emery, J ; Ijzerman, M ; Brown, W ; Zalcberg, J ; Evans, S (OXFORD UNIV PRESS, 2021-09-01)IntroductionNearly one quarter of a million Australian workers experience a work injury annually and make a benefit claim through one of the nation’s eleven workers’ compensation (WC) systems. The total cost to Australian society has most recently been estimated at $61.8 billion or 4.1% of GDP. The disaggregation of legislative responsibility between jurisdictions has contributed to a lack of common data standards, and thus minimal understanding of the efficiency or effectiveness of service provision in the Australian WC sector. Objectives and ApproachThis project developed a new multi-jurisdictional work disability database including detailed information on work disability duration, health and social care service provision. Service level payment data contained in structured WC insurance claims datasets held by five large WC jurisdictions with >60% coverage of the Australian labour force was collected for all cases of work-related low back pain, fractures and limb soft tissue disease over between 2010 and 2015. Database development involved creation and coding of harmonised service-level indicators for individual episodes of healthcare provision and weekly periods of wage replacement. ResultsA total of 253,000 cases and 10.7 million service episodes are included in the database. Initial exploratory analyses focused on the frequency, prevalence, timing, intensity and continuity of General Practitioner (GP) services to each of the injury groups. Regression modelling examined occupational, injury, demographic and jurisdictional factors affecting GP service use outcomes. As anticipated, service patterns varied by injury type, age, gender and occupational group. Significant differences in service use between WC jurisdictions were observed. Conclusion / ImplicationsThis exploratory study demonstrates the feasibility of developing a population-based service level database for monitoring health service delivery to injured Australian workers. Future studies will examine the impact of jurisdictional policy differences on service delivery, and the relationship between service delivery and outcomes such as disability duration.
ItemHandling uncertainty using features from pathology: Opportunities in primary care data for developing high risk cancer survival methodsRistanoski, G ; Emery, J ; Martinez Gutierrez, J ; McCarthy, D ; Aickelin, U (ACM, 2021)More than 144 000 Australians were diagnosed with cancer in 2019. Diagnosing cancer in primary care is challenging due to the non-specific nature of cancer symptoms and its low prevalence. Understanding the epidemiology of cancer symptoms and patterns of presentation in patient's medical history from primary care data could be important to improve earlier detection and cancer outcomes. As past medical data about a patient can be incomplete, irregular or missing, this creates additional challenges when attempting to use the patient's history for any new diagnosis. Our research aims to investigate the opportunities in a patient's pathology history available to a GP, initially focused on the results within the frequently ordered full blood count to determine relevance to a future high-risk cancer prognosis, and treatment outcome. We investigated how past pathology test results can lead to deriving features that can be used to predict cancer outcomes, with emphasis on patients at risk of not surviving the cancer within 2-year period. This initial work focuses on patients with lung cancer, although the methodology can be applied to other types of cancer and other data within the medical record. Our findings indicate that even in cases of incomplete or obscure patient history, hematological measures can be useful in generating features relevant for predicting cancer risk and survival. The results strongly indicate to add the use of pathology test data for potential high-risk cancer diagnosis, and utilize additional pathology metrics or other primary care datasets even more for similar purposes.
ItemThe use of organ donor blood in liver transplantationTang, GT ; Shaylor, R ; Hui, V ; Przybylowski, G ; Jones, RM ; Starkey, G ; Perini, MV ; Wang, B-Z ; Zantomio, D ; Hogan, C ; Fink, MA (WILEY, 2021-09-16)BACKGROUND: Blood removed from organs during deceased donor organ procurement is routinely discarded but is a potential resource for donor-specific transfusion (DST) in subsequent liver transplantation (LT). This study retrospectively analyses the impact of DST on intraoperative bank blood product usage, long-term graft, and patient survival, as well as frequency of rejection post-LT. METHODS: A total of 992 adult LT performed from 1993 to 2018 in a single quaternary center were included. Intraoperative blood product usage, patient, and graft survival, as well as acute and chronic rejection were assessed in patients who received blood retrieved from the organ donor, the "donor blood" (DB) group (n = 437) and patients who did not, the "no donor blood" (NDB) group (n = 555). RESULTS: Processing of DB ensured safe levels of potassium, magnesium, and insulin. There were fewer units of bank red blood cells transfusion required in the DB group compared to NDB group (2 vs. 4 units, P = .01). Graft survival was significantly superior in the DB group (10-year survival 75% vs. 69%, respectively, P = .04) but DST was not an independent predictor of graft survival. There was no significant difference in patient survival or rejection between the groups. There was no difference in treated, biopsy-proven rejection between the two groups. CONCLUSIONS: This is the first large-cohort study assessing long-term outcomes of intraoperative DST in LT. The collection of organ donor blood and subsequent use in LT recipients appeared feasible with appropriate quality checks ensuring safety. DST resulted in a reduction in the use of packed red blood cells. There was no difference in the rate of rejection or graft or patient survival.