Browsing by Author "Jackson C"

Now showing 1 - 4 of 4
  • Thumbnail Image
    Item
    Barriers and facilitators to colorectal cancer diagnosis in New Zealand: a qualitative study
    (BioMed Central Ltd, 2020-10-01) Blackmore T; Norman K; Kidd J; Cassim S; Chepulis L; Keenan R; Firth M; Jackson C; Stokes T; Weller D; Emery J; Lawrenson R
    Background New Zealand (NZ) has high rates of colorectal cancer but low rates of early diagnosis. Due to a lack of understanding of the pre-diagnostic experience from the patient’s perspective, it is necessary to investigate potential patient and health system factors that contribute to longer diagnostic intervals. Previous qualitative studies have discussed delays using The Model of Pathways to Treatment, but this has not been explored in the NZ context. This study aimed to understand the patient experience and perception of their general practitioner (GP) through the diagnostic process in the Waikato region of NZ. In particular, we sought to investigate potential barriers and facilitators that contribute to longer diagnostic intervals. Methods Ethical approval for this study was granted by the New Zealand Health and Disability Ethics Committee. Twenty-eight participants, diagnosed with colorectal cancer, were interviewed about their experience. Semi-structured interviews were audio recorded, transcribed verbatim and analysed thematically using The Model of Pathways to Treatment framework (intervals: appraisal, help-seeking, diagnostic). Results Participant appraisal of symptoms was a barrier to prompt diagnosis, particularly if symptoms were normalised, intermittent, or isolated in occurrence. Successful self-management techniques also resulted in delayed help-seeking. However if symptoms worsened, disruption to work and daily routines were important facilitators to seeking a GP consultation. Participants positively appraised GPs if they showed good technical competence and were proactive in investigating symptoms. Negative GP appraisals were associated with a lack of physical examinations and misdiagnosis, and left participants feeling dehumanised during the diagnostic process. However high levels of GP interpersonal competence could override poor technical competence, resulting in an overall positive experience, even if the cancer was diagnosed at an advanced stage. Māori participants often appraised symptoms inclusive of their sociocultural environment and considered the impact of their symptoms in relation to family. Conclusions The findings of this study highlight the importance of tailored colorectal cancer symptom communication in health campaigns, and indicate the significance of the interpersonal competence aspect of GP-patient interactions. These findings suggest that interpersonal competence be overtly displayed in all GP interactions to ensure a higher likelihood of a positive experience for the patient.
  • Thumbnail Image
    Item
    Lessons from COVID-19 for behavioural and communication interventions to enhance vaccine uptake
    (Springer Nature Limited, 2023-11-24) Lewandowsky S; Schmid P; Habersaat KB; Nielsen SM; Seale H; Betsch C; Böhm R; Geiger M; Craig B; Sunstein C; Sah S; MacDonald NE; Dubé E; Fancourt D; Larson HJ; Jackson C; Mazhnaya A; Dutta M; Fountoulakis KN; Kachkachishvili I; Soveri A; Caserotti M; Őri D; de Girolamo G; Rodriguez-Blazquez C; Falcón M; Romay-Barja M; Forjaz MJ; Blomquist SE; Appelqvist E; Temkina A; Lieberoth A; Harvey TS; Holford D; Fasce A; Van Damme P; Danchin M
    The Covid pandemic has yielded new insights into psychological vaccine acceptance factors. This knowledge serves as a basis for behavioral and communication interventions that can increase vaccination readiness for other diseases.
  • Thumbnail Image
    Item
    New targets acquired: Improving locus recovery from the Angiosperms353 probe set
    (Botanical Society of America, 14/06/2021) McLay T; Birch J; Gunn B; Ning W; Tate J; Nauheimer L; Joyce E; Simpson L; Schmidt-Lebuhn A; Baker W; Forest F; Jackson C
    PREMISE: Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost-efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 6–18 taxa per locus. Consequently, reads sequenced from on-target DNA molecules may fail to map to references, resulting in fewer on-target reads for assembly, and reducing locus recovery. METHODS: We expanded the Angiosperms353 target file, incorporating sequences from 566 transcriptomes to produce a ‘mega353’ target file, with each locus represented by 17–373 taxa. This mega353 file is a drop-in replacement for the original Angiosperms353 file in HybPiper analyses. We provide tools to subsample the file based on user-selected taxon groups, and to incorporate other transcriptome or protein-coding gene data sets. RESULTS: Compared to the default Angiosperms353 file, the mega353 file increased the percentage of on-target reads by an average of 32%, increased locus recovery at 75% length by 49%, and increased the total length of the concatenated loci by 29%. DISCUSSION: Increasing the phylogenetic density of the target reference file results in improved recovery of target capture loci. The mega353 file and associated scripts are available at: https://github.com/chrisjackson-pellicle/NewTargets.
  • Thumbnail Image
    Item
    Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer
    (Springer Nature in partnership with the Center of Excellence in Genomic Medicine Research at King Abdulaziz University, 2018-07-20) Lawrence B; Blenkiron C; Parker K; Tsai P; Fitzgerald S; Shields P; Robb T; Yeong ML; Kramer N; James S; Black M; Fan V; Poonawala N; Yap P; Coats E; Woodhouse B; Ramsaroop R; Yozu M; Robinson B; Henare K; Koea J; Johnston P; Carroll R; Connor S; Morrin H; Elston M; Jackson C; Reid P; Windsor J; MacCormick A; Babor R; Bartlett A; Damianovich D; Knowlton N; Grimmond S; Findlay M; Print C
    Pancreatic neuroendocrine tumors (pNETs) are uncommon cancers arising from pancreatic islet cells. Here we report the analysis of gene mutation, copy number, and RNA expression of 57 sporadic well-differentiated pNETs. pNET genomes are dominated by aneuploidy, leading to concordant changes in RNA expression at the level of whole chromosomes and chromosome segments. We observed two distinct patterns of somatic pNET aneuploidy that are associated with tumor pathology and patient prognosis. Approximately 26% of the patients in this series had pNETs with genomes characterized by recurrent loss of heterozygosity (LoH) of 10 specific chromosomes, accompanied by bi-allelic MEN1 inactivation and generally poor clinical outcome. Another ~40% of patients had pNETs that lacked this recurrent LoH pattern but had chromosome 11 LoH, bi-allelic MEN1 inactivation, and universally good clinical outcome. The somatic aneuploidy allowed pathogenic germline variants (e.g., ATM) to be expressed unopposed, with RNA expression patterns showing inactivation of downstream tumor suppressor pathways. No prognostic associations were found with tumor morphology, single gene mutation, or expression of RNAs reflecting the activity of immune, differentiation, proliferative or tumor suppressor pathways. In pNETs, single gene mutations appear to be less important than aneuploidy, with MEN1 the only statistically significant recurrently mutated driver gene. In addition, only one pNET in the series had clearly actionable single nucleotide variants (SNVs) (in PTEN and FLCN) confirmed by corroborating RNA expression changes. The two clinically relevant patterns of LoH described here define a novel oncogenic mechanism and a plausible route to genomic precision oncology for this tumor type.