ORCID Profile
0000-0001-7472-6128
Current Organisation
Peter MacCallum Cancer Centre
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Publisher: Springer Science and Business Media LLC
Date: 15-04-2013
DOI: 10.1038/SREP01659
Publisher: Springer Science and Business Media LLC
Date: 18-06-1999
Abstract: The validation of multiplex solid-phase fluorescent minisequencing of mitochondrial DNA (mtDNA) for use in forensic casework is presented. Validation included testing of the reliability and species specificity of the technique, analysis of mixed body fluid s les, analysis of s les and substrate controls from previous cases and somatic stability of mtDNA. Animal, bacterial and fungal species extracts were examined and the test did not show cross-reactivity with other species. Hair, blood, saliva, faeces and semen or vaginal s les were tested from five male and five female in iduals. For all the s les tested, heteroplasmy was observed only at position 302/309.1. Body fluid mixtures (blood:saliva, semen:saliva, faeces:semen, vaginal:semen) and DNA:DNA mixtures were examined. In total, 189 mixtures were analysed of which one resulted in a hybrid profile consisting of peaks from each of the two donors. The semen fraction of the semen:saliva and vaginal:semen mixtures appeared to be concentrated in the supernatant fraction of the extract thus highlighting the need to extract both the pellet and supernatant fractions of a stain. Control s les, crime stains and their substrate controls from previous cases were examined. Of the 12 loci typed by minisequencing, 11 could be verified by comparison to results from the sequencing method currently in use for casework and no discrepancies were observed between the two. MtDNA minisequencing was found to be a reliable and reproducible technique and its rapid and discriminating nature make it particularly suitable as a screening technique.
Publisher: American Society of Hematology
Date: 26-02-2008
DOI: 10.1182/BLOOD-2008-06-161422
Abstract: Down syndrome (DS) persons are born with various hematopoietic abnormalities, ranging from relatively benign, such as neutrophilia and macrocytosis, to a more severe transient myeloproliferative disorder (TMD). In most cases, these abnormalities resolve in the first few months to years of life. However, sometimes the TMD represents a premalignant disease that develops into acute megakaryocytic leukemia (AMKL), usually in association with acquired GATA1 mutations. To gain insight into the mechanisms responsible for these abnormalities, we analyzed the hematopoietic development of the Ts1Cje mouse model of DS. Our analyses identified defects in mature blood cells, including macrocytosis and anemia, as well as abnormalities in fetal liver and bone marrow stem and progenitor cell function. Despite these defects, the Ts1Cje mice do not develop disease resembling either TMD or AMKL, and this was not altered by a loss of function allele of Gata1. Thus, loss of Gata1 and partial trisomy of chromosome 21 orthologs, when combined, do not appear to be sufficient to induce TMD or AMKL-like phenotypes in mice.
Publisher: Informa UK Limited
Date: 22-02-2019
Publisher: Oxford University Press (OUP)
Date: 06-08-2011
Abstract: Nrgn and Camk2n1 are highly expressed in the brain and play an important role in synaptic long-term potentiation via regulation of Ca(2+)/calmodulin-dependent protein kinase II. We have shown that the gene loci for these 2 proteins are actively transcribed in the adult cerebral cortex and feature multiple overlapping transcripts in both the sense and antisense orientations with alternative polyadenylation. These transcripts were upregulated in the adult compared with embryonic and P1.5 mouse cerebral cortices, and transcripts with different 3' untranslated region lengths showed differing expression profiles. In situ hybridization (ISH) analysis revealed spatiotemporal regulation of the Nrgn and Camk2n1 sense and natural antisense transcripts (NATs) throughout cerebral corticogenesis. In addition, we also demonstrated that the expression of these transcripts was organ-specific. Both Nrgn and Camk2n1 sense and NATs were also upregulated in differentiating P19 teratocarcinoma cells. RNA fluorescent ISH analysis confirmed the capability of these NATs to form double-stranded RNA aggregates with the sense transcripts in the cytoplasm of cells obtained from the brain. We propose that the differential regulation of multiple sense and novel overlapping NATs at the Nrgn and Camk2n1 loci will increase the ersity of posttranscriptional regulation, resulting in cell- and time-specific regulation of their gene products during cerebral corticogenesis and function.
Publisher: Elsevier BV
Date: 04-2022
Publisher: Elsevier BV
Date: 12-2014
Publisher: Springer Science and Business Media LLC
Date: 13-02-2019
Publisher: Elsevier BV
Date: 10-2022
DOI: 10.1016/J.PATHOL.2022.02.010
Abstract: Droplet digital PCR (ddPCR) has been demonstrated in many research studies to be a sensitive method in the analysis of circulating tumour DNA (ctDNA) for identifying mutations and tracking disease. The transition of ddPCR into the diagnostic setting requires a number of critical steps including the assessment of accuracy and precision and ultimately implementation into clinical use. Here we present the clinical validation of ddPCR for the detection of BRAF mutations (V600E and V600K) from plasma. We describe the performance characteristics assessed including the limit of blank, limit of detection, ruggedness, accuracy, precision and the effect of the matrix. Overall, each assay could achieve a limit of detection of 0.5% variant allele fraction and was highly accurate, with 100% concordance of results obtained from routine diagnostic testing of formalin fixed tumour s les or reference controls (n=36 for BRAF V600E and n=30 for BRAF V600K). Inter-laboratory reproducibility across 12 plasma s les for each assay was also assessed and results were 100% concordant. Overall, we report the successful validation and translation of a ddPCR assay into clinical routine practice.
Publisher: Elsevier BV
Date: 10-2022
DOI: 10.1016/J.EJSO.2022.06.014
Abstract: Stratification of patients with colorectal peritoneal metastases (CRPM) using RAS/BRAF mutational status may refine patient selection for cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC). This study aimed to analyse the association of RAS/BRAF status and their variants, with clinicopathological variables and survival outcomes in patients who have undergone CRS ± HIPEC. A single centre, peritonectomy database was interrogated for patients with CRPM who underwent peritonectomy procedures between 2010 and 2020. During the study period, 174 patients were included. Molecular status was obtained on 169 patients, with 68 (40.5%) KRAS, 25 (14.8%) BRAF and 6 (3.6%) NRAS mutations detected. Patients with BRAF mutations were more likely to be mismatch repair deficient (dMMR) (BRAF 20%, KRAS 4.4%, wild type 8.6%, p = 0.015). Most common BRAF and KRAS variants were, V600E (80%) and G12D (39.7%), respectively. BRAF V600E was independently associated with worse overall (median: 28 months, multivariate: HR 2.29, p = 0.026) and disease-free survival (median: 8 months, multivariate: HR 1.8, p = 0.047). KRAS G12V was a strong prognostic factor associated with disease-free survival (median: 9 months, HR 2.63, p = 0.016). dMMR patients (14/161, 8.7%) exhibited worse median overall survival compared to those with proficient MMR (dMMR 27 months, pMMR 29 months p = 0.025). This study highlights the importance of molecular analysis in CRPM stratification. BRAF V600E mutations predict poor outcomes post CRS and HIPEC and may help refine patient selection for this procedure. Molecular analysis should be performed preoperatively to characterise prognosis and guide perioperative therapeutic options.
Publisher: Springer Science and Business Media LLC
Date: 24-04-2013
Abstract: The JAK2 V617F mutation is the most frequent somatic change in myeloproliferative neoplasms, making it an important tumour-specific marker for diagnostic purposes and for the detection of minimal residual disease. Sensitive quantitative assays are required for both applications, particularly for the monitoring of minimal residual disease, which requires not only high sensitivity but also very high specificity. We developed a highly sensitive probe-free quantitative mutant-allele detection method, Quantitative Threefold Allele-Specific PCR (QuanTAS-PCR), that is performed in a closed-tube system, thus eliminating the manipulation of PCR products. QuantTAS-PCR uses a threefold approach to ensure allele-specific lification of the mutant sequence: (i) a mutant allele-specific primer, (ii) a 3′dideoxy blocker to suppress false-positive lification from the wild-type template and (iii) a PCR specificity enhancer, also to suppress false-positive lification from the wild-type template. Mutant alleles were quantified relative to exon 9 of JAK2 . We showed that the addition of the 3′dideoxy blocker suppressed but did not eliminate false-positive lification from the wild-type template. However, the addition of the PCR specificity enhancer near eliminated false-positive lification from the wild-type allele. Further discrimination between true and false positives was enabled by using the quantification cycle (Cq) value of a single mutant template as a cut-off point, thus enabling robust distinction between true and false positives. As 10,000 JAK2 templates were used per replicate, the assay had a sensitivity of 1/10 -4 per replicate. Greater sensitivity could be reached by increasing the number of replicates analysed. Variation in replicates when low mutant-allele templates were present necessitated the use of a statistics-based approach to estimate the load of mutant JAK2 copies. QuanTAS-PCR showed comparable quantitative results when validated against a commercial assay. QuanTAS-PCR is a simple, cost-efficient, closed-tube method for JAK2 V617F mutation quantification that can detect very low levels of the mutant allele, thus enabling analysis of minimal residual disease. The approach can be extended to the detection of other recurrent single nucleotide somatic changes in cancer.
Publisher: Public Library of Science (PLoS)
Date: 16-07-2010
Publisher: Public Library of Science (PLoS)
Date: 10-02-2011
Publisher: IMR Press
Date: 2007
DOI: 10.2741/2291
Abstract: The Ts65Dn mouse is the most widely investigated segmentally trisomic mouse model of Down syndrome. Quantitative PCR based methods are the preferred way of detecting the trisomic segment for genotyping purposes. However, identification of a 1.5 fold difference in target DNA is at the limit of detection of most quantitative PCR based methods, and in practice this can lead to difficulties in assigning genotypes. We report a 100% accurate multiplex ligation-dependent probe lification (MLPA) assay for genotyping the Ts65Dn mouse that is also applicable to all other segmentally trisomic mouse models of Down syndrome.
Publisher: Elsevier BV
Date: 06-2012
Publisher: Springer Science and Business Media LLC
Date: 2009
Publisher: American Geophysical Union (AGU)
Date: 05-2019
DOI: 10.1029/2019JC015071
Publisher: Springer Science and Business Media LLC
Date: 2014
Publisher: Ferrata Storti Foundation (Haematologica)
Date: 12-2011
Publisher: Cold Spring Harbor Laboratory
Date: 14-10-2021
DOI: 10.1101/MCS.A006133
Abstract: Nevus sebaceous syndrome (NSS) is a rare, multisystem neurocutaneous disorder, characterized by a congenital nevus, and may include brain malformations such as hemimegalencephaly or focal cortical dysplasia, ocular, and skeletal features. It has been associated with several eponyms including Schimmelpenning and Jadassohn. The isolated skin lesion, nevus sebaceous, is associated with postzygotic variants in HRAS or KRAS in all in iduals studied. The RAS proteins encode a family of GTPases that form part of the RAS/MAPK signaling pathway, which is critical for cell cycle regulation and differentiation during development. We studied an in idual with nevus sebaceous syndrome with an extensive nevus sebaceous, epilepsy, intellectual disability, and hippoc al sclerosis without pathological evidence of a brain malformation. We used high-depth gene panel sequencing and droplet digital polymerase chain reaction (PCR) to detect and quantify RAS/MAPK gene variants in nevus sebaceous and temporal lobe tissue collected during plastic and epilepsy surgery, respectively. A mosaic KRAS c.34G T p.(Gly12Cys) variant, also known as G12C, was detected in nevus sebaceous tissue at 25% variant allele fraction (VAF), at the residue most commonly substituted in KRAS . Targeted droplet digital PCR validated the variant and quantified the mosaicism in other tissues. The variant was detected at 33% in temporal lobe tissue but was absent from blood and healthy skin. We provide molecular confirmation of the clinical diagnosis of NSS. Our data extends the histopathological spectrum of KRAS G12C mosaicism beyond nevus sebaceous to involve brain tissue and, more specifically, hippoc al sclerosis.
No related grants have been discovered for Chelsee Hewitt.