Displaying publications 1 - 20 of 27 in total

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  1. Chua EW, Miller AL, Kennedy MA
    Anal Biochem, 2015 May 15;477:115-7.
    PMID: 25766577 DOI: 10.1016/j.ab.2015.02.023
    We compared four brands of microtubes with respect to their suitability for long-range polymerase chain reactions (PCRs). One of the four brands was found to have an inhibitory effect, decreasing PCR yields. The effect was universal across different PCR or enzyme systems. Increased ultraviolet absorbance suggests leaching of unknown chemical species into PCR mixtures. However, this could not be confirmed by high-performance liquid chromatography-mass spectrometry analysis. Nevertheless, our article demonstrates a clear impact of the choice of microtubes on long-range PCR success. Due consideration should be given to the PCR microtubes when determining optimal reaction conditions for long-range PCR.
  2. Chua EW, Harger SP, Kennedy MA
    Front Pharmacol, 2019;10:931.
    PMID: 31507424 DOI: 10.3389/fphar.2019.00931
    We report two cases of metoclopramide-induced acute dystonia in pregnant women and consider the role of genetic variation in the pathogenesis of the adverse effect. By whole-gene sequencing, we found that both women were CYP2D6 poor metabolizers. We theorize that CYP2D6 governs the risk of metoclopramide-related acute dystonia through its role in the synthesis of serotonin, which inhibits the dopamine tone. The effect of CYP2D6 poor metabolism is exaggerated by rises in the estrogen levels during pregnancy, as the hormone augments dopamine sensitivity. Together, the two factors may create a hyper-dopaminergic state that is easily upset by metoclopramide, resulting in acute dystonia.
  3. Chua EW, Maggo S, Kennedy MA
    Methods Mol Biol, 2017;1620:65-74.
    PMID: 28540699 DOI: 10.1007/978-1-4939-7060-5_3
    Polymerase chain reaction (PCR) is an oft-used preparatory technique in amplifying specific DNA regions for downstream analysis. The size of an amplicon was initially limited by errors in nucleotide polymerization and template deterioration during thermal cycling. A variant of PCR, designated long-range PCR, was devised to counter these drawbacks and enable the amplification of large fragments exceeding a few kb. In this chapter we describe a protocol for long-range PCR, which we have adopted to obtain products of 6.6, 7.2, 13, and 20 kb from human genomic DNA samples.
  4. Trutnovsky G, Kamisan Atan I, Martin A, Dietz HP
    BJOG, 2016 Aug;123(9):1551-6.
    PMID: 26435045 DOI: 10.1111/1471-0528.13692
    OBJECTIVE: To analyse the associations between delivery mode and symptoms and signs of pelvic organ prolapse (POP) in a cohort of symptomatic women.

    DESIGN: Retrospective observational study.

    POPULATION: A total of 1258 consecutive women attending a tertiary urogynaecological unit for the investigation of lower urinary tract or pelvic floor disorders between January 2012 and December 2014.

    METHODS: Obstetric history and clinical examination data were obtained from the unit database. Prolapse quantification on imaging was performed using stored four-dimensional translabial ultrasound volume data sets. Women were grouped into four groups according to the most traumatic delivery reported. The presence of symptoms and signs of POP were compared between delivery groups while controlling for potential confounders.

    MAIN OUTCOME MEASURES: Prolapse symptoms, visual analogue score for prolapse bother, International Continence Society Prolapse Quantification System findings and ultrasound findings of anterior, central and posterior compartment descent.

    RESULTS: Nulliparae showed the lowest prevalence of most measures of POP, followed by women exclusively delivered by caesarean section. Highest prevalences were consistently found in women delivered at least once by forceps, although the differences between this group and women delivered by normal vaginal delivery and/or vacuum extraction were significant in three out of eight measures only. Compared with women in the caesarean section group, the adjusted odds ratios for reporting symptoms of prolapse were 2.4 (95% CI 1.30-4.59) and 3.2 (95% CI 1.65-6.12) in the normal vaginal delivery/vacuum extraction group and forceps group, respectively.

    CONCLUSIONS: There is a clear link between vaginal delivery and symptoms and signs of pelvic organ prolapse in urogynaecological patients.

    TWEETABLE ABSTRACT: Compared with caesarean section a history of vaginal delivery more than doubles the risk for POP.

  5. Yahya N, Ebert MA, Bulsara M, House MJ, Kennedy A, Joseph DJ, et al.
    Radiother Oncol, 2015 Nov;117(2):277-82.
    PMID: 26476560 DOI: 10.1016/j.radonc.2015.10.003
    This study aimed to compare urinary dose-symptom correlates after external beam radiotherapy of the prostate using commonly utilised peak-symptom models to multiple-event and event-count models which account for repeated events.
  6. Yahya N, Ebert MA, Bulsara M, House MJ, Kennedy A, Joseph DJ, et al.
    Med Phys, 2016 May;43(5):2040.
    PMID: 27147316 DOI: 10.1118/1.4944738
    Given the paucity of available data concerning radiotherapy-induced urinary toxicity, it is important to ensure derivation of the most robust models with superior predictive performance. This work explores multiple statistical-learning strategies for prediction of urinary symptoms following external beam radiotherapy of the prostate.
  7. Chua EW, Cree SL, Ton KN, Lehnert K, Shepherd P, Helsby N, et al.
    Front Pharmacol, 2016;7:1.
    PMID: 26858644 DOI: 10.3389/fphar.2016.00001
    Whole-exome sequencing (WES) has been widely used for analysis of human genetic diseases, but its value for the pharmacogenomic profiling of individuals is not well studied. Initially, we performed an in-depth evaluation of the accuracy of WES variant calling in the pharmacogenes CYP2D6 and CYP2C19 by comparison with MiSeq(®) amplicon sequencing data (n = 36). This analysis revealed that the concordance rate between WES and MiSeq(®) was high, achieving 99.60% for variants that were called without exceeding the truth-sensitivity threshold (99%), defined during variant quality score recalibration (VQSR). Beyond this threshold, the proportion of discordant calls increased markedly. Subsequently, we expanded our findings beyond CYP2D6 and CYP2C19 to include more genes genotyped by the iPLEX(®) ADME PGx Panel in the subset of twelve samples. WES performed well, agreeing with the genotyping panel in approximately 99% of the selected pass-filter variant calls. Overall, our results have demonstrated WES to be a promising approach for pharmacogenomic profiling, with an estimated error rate of lower than 1%. Quality filters, particularly VQSR, are important for reducing the number of false variants. Future studies may benefit from examining the role of WES in the clinical setting for guiding drug therapy.
  8. Yahya N, Ebert MA, Bulsara M, Haworth A, Kennedy A, Joseph DJ, et al.
    Radiother Oncol, 2015 Jul;116(1):112-8.
    PMID: 26163088 DOI: 10.1016/j.radonc.2015.06.011
    To identify dosimetry, clinical factors and medication intake impacting urinary symptoms after prostate radiotherapy.
  9. Cree SL, Chua EW, Crowther J, Dobson RCJ, Kennedy MA
    Biochimie, 2020 Aug 14.
    PMID: 32805304 DOI: 10.1016/j.biochi.2020.07.022
    Next generation DNA sequencing and analysis of amplicons spanning the pharmacogene CYP2D6 suggested that the Nextera transposase used for fragmenting and providing sequencing priming sites displayed a targeting bias. This manifested as dramatically lower sequencing coverage at sites in the amplicon that appeared likely to form G-quadruplex structures. Since secondary DNA structures such as G-quadruplexes are abundant in the human genome, and are known to interact with many other proteins, we further investigated these sites of low coverage. Our investigation revealed that G-quadruplex structures are formed in vitro within the CYP2D6 pharmacogene at these sites, and G-quadruplexes can interact with the hyperactive Tn5 transposase (EZ-Tn5) with high affinity. These findings indicate that secondary DNA structures such as G-quadruplexes may represent preferential transposon integration sites and provide additional evidence for the role of G-quadruplex structures in transposition or viral integration processes.
  10. Yahya N, Ebert MA, Bulsara M, Kennedy A, Joseph DJ, Denham JW
    Radiother Oncol, 2016 08;120(2):339-45.
    PMID: 27370204 DOI: 10.1016/j.radonc.2016.05.010
    BACKGROUND AND PURPOSE: Most predictive models are not sufficiently validated for prospective use. We performed independent external validation of published predictive models for urinary dysfunctions following radiotherapy of the prostate.

    MATERIALS/METHODS: Multivariable models developed to predict atomised and generalised urinary symptoms, both acute and late, were considered for validation using a dataset representing 754 participants from the TROG 03.04-RADAR trial. Endpoints and features were harmonised to match the predictive models. The overall performance, calibration and discrimination were assessed.

    RESULTS: 14 models from four publications were validated. The discrimination of the predictive models in an independent external validation cohort, measured using the area under the receiver operating characteristic (ROC) curve, ranged from 0.473 to 0.695, generally lower than in internal validation. 4 models had ROC >0.6. Shrinkage was required for all predictive models' coefficients ranging from -0.309 (prediction probability was inverse to observed proportion) to 0.823. Predictive models which include baseline symptoms as a feature produced the highest discrimination. Two models produced a predicted probability of 0 and 1 for all patients.

    CONCLUSIONS: Predictive models vary in performance and transferability illustrating the need for improvements in model development and reporting. Several models showed reasonable potential but efforts should be increased to improve performance. Baseline symptoms should always be considered as potential features for predictive models.

  11. Gan WY, Sulaiman N, Law LS, Zalbahar N, Ahmad Fuzi SF, Wilkes MA
    PMID: 31947907 DOI: 10.3390/ijerph17010348
    Access to food has been determined to be a factor that strongly influences the dietary intake and eating habit of indigenous people (Orang Asli, OA). This study explored food acquisition and the barriers in obtaining traditional and market foods among the Jahai subtribe (within the Negrito ethnic group) via a qualitative approach. Twenty-eight OA (14 males and 14 females) from Gerik, Perak, Malaysia participated in four focus group discussions (FGDs; two male-only and two female-only groups; seven informants in each FGD). Thematic analysis was adopted to analyse the gathered data. The results found that the Jahai applied both modern (buying and receiving food assistance) and traditional (gathering, farming, fishing, and hunting) methods in obtaining food. The barriers they faced in gathering sufficient food supply included low purchasing power, high demand for food, high transport costs, depletion of food supplies in their surroundings, threats from wild animals on the farm and during food searching activities, and food sharing. Food preparation methods practiced by the OA include roasting and grilling, frying, simmering (gulai), and boiling. In conclusion, this study enhances our understanding of the dietary behaviour of the Jahai subtribe and highlights restricted food access among the OA, which demands urgent attention.
  12. Yahya N, Ebert MA, House MJ, Kennedy A, Matthews J, Joseph DJ, et al.
    Int J Radiat Oncol Biol Phys, 2017 02 01;97(2):420-426.
    PMID: 28068247 DOI: 10.1016/j.ijrobp.2016.10.024
    PURPOSE: We assessed the association of the spatial distribution of dose to the bladder surface, described using dose-surface maps, with the risk of urinary dysfunction.

    METHODS AND MATERIALS: The bladder dose-surface maps of 754 participants from the TROG 03.04-RADAR trial were generated from the volumetric data by virtually cutting the bladder at the sagittal slice, intersecting the bladder center-of-mass through to the bladder posterior and projecting the dose information on a 2-dimensional plane. Pixelwise dose comparisons were performed between patients with and without symptoms (dysuria, hematuria, incontinence, and an International Prostate Symptom Score increase of ≥10 [ΔIPSS10]). The results with and without permutation-based multiple-comparison adjustments are reported. The pixelwise multivariate analysis findings (peak-event model for dysuria, hematuria, and ΔIPSS10; event-count model for incontinence), with adjustments for clinical factors, are also reported.

    RESULTS: The associations of the spatially specific dose measures to urinary dysfunction were dependent on the presence of specific symptoms. The doses received by the anteroinferior and, to lesser extent, posterosuperior surface of the bladder had the strongest relationship with the incidence of dysuria, hematuria, and ΔIPSS10, both with and without adjustment for clinical factors. For the doses to the posteroinferior region corresponding to the area of the trigone, the only symptom with significance was incontinence.

    CONCLUSIONS: A spatially variable response of the bladder surface to the dose was found for symptoms of urinary dysfunction. Limiting the dose extending anteriorly might help reduce the risk of urinary dysfunction.

  13. Maggo SD, Chua EW, Chin P, Cree S, Pearson J, Doogue M, et al.
    N Z Med J, 2017 Dec 01;130(1466):62-69.
    PMID: 29197902
    A multitude of factors can affect drug response in individuals. It is now well established that variations in genes, especially those coding for drug metabolising enzymes, can alter the pharmacokinetic and/or pharmacodynamic profile of a drug, impacting on efficacy and often resulting in drug-induced toxicity. The UDRUGS study is an initiative from the Carney Centre for Pharmacogenomics to biobank DNA and store associated clinical data from patients who have suffered rare and/or serious adverse drug reactions (ADRs). The aim is to provide a genetic explanation of drug-induced ADRs using methods ranging from Sanger sequencing to whole exome and whole genome sequencing. Participants for the UDRUGS study are recruited from various sources, mainly via referral through clinicians working in Canterbury District Health Board, but also from district health boards across New Zealand. Participants have also self-referred to us from word-of-mouth communication between participants. We have recruited various ADRs across most drug classes. Where possible, we have conducted genetic analyses in single or a cohort of cases to identify known and novel genetic association(s) to offer an explanation to why the ADR occurred. Any genetic results relevant to the ADR are communicated back to the referring clinician and/or participant. In conclusion, we have developed a programme for studying the genetic basis of severe, rare or unusual ADR cases resulting from pharmacological treatment. Genomic analyses could eventually identify most genetic variants that predispose to ADRs, enabling a priori detection of such variants with high throughput DNA tests.
  14. Kee PS, Karunanathie H, Maggo SDS, Kennedy MA, Chua EW
    Methods Mol Biol, 2023;2967:181-192.
    PMID: 37608112 DOI: 10.1007/978-1-0716-3358-8_15
    Polymerase chain reaction (PCR) is a laboratory technique used to amplify a targeted region of DNA, demarcated by a set of oligonucleotide primers. Long-range PCR is a form of PCR optimized to facilitate the amplification of large fragments. Using the adapted long-range PCR protocol described in this chapter, we were able to generate PCR products of 6.6, 7.2, 13, and 20 kb from human genomic DNA samples. For some of the long PCRs, successful amplification was not possible without the use of PCR enhancers. Thus, we also evaluated the impact of some enhancers on long-range PCR and included the findings as part of this updated chapter.
  15. May IJ, Nowak AK, Francis RJ, Ebert MA, Dhaliwal SS
    J Med Imaging Radiat Oncol, 2024 Feb;68(1):57-66.
    PMID: 37898984 DOI: 10.1111/1754-9485.13592
    INTRODUCTION: Malignant pleural mesothelioma is difficult to prognosticate. F18-Fluorodeoxyglucose positron emission tomography (FDG PET) shows promise for response assessment but is confounded by talc pleurodesis. F18-Fluorothymidine (FLT) PET is an alternative tracer specific for proliferation. We compared the prognostic value of FDG and FLT PET and determined the influence of talc pleurodesis on these parameters.

    METHODS: Overall, 29 prospectively recruited patients had FLT PET, FDG PET and CT-scans performed prior to and post one chemotherapy cycle; 10 had prior talc pleurodesis. Patients were followed for overall survival. CT response was assessed using mRECIST. Radiomic features were extracted using the MiM software platform. Changes in maximum SUV (SUVmax), mean SUV (SUVmean), FDG total lesion glycolysis (TLG), FLT total lesion proliferation (TLP) and metabolic tumour volume (MTV) after one chemotherapy cycle.

    RESULTS: Cox univariate analysis demonstrated FDG PET radiomics were confounded by talc pleurodesis, and that percentage change in FLT MTV was predictive of overall survival. Cox multivariate analysis showed a 10% increase in FLT tumour volume corresponded with 9.5% worsened odds for overall survival (P = 0.028, HR = 1.095, 95% CI [1.010, 1.187]). No other variables were significant on multivariate analysis.

    CONCLUSION: This is the first prospective study showing the statistical significance of FLT PET tumour volumes for measuring mesothelioma treatment response. FLT may be better than FDG for monitoring mesothelioma treatment response, which could help optimise mesothelioma treatment regimes.

  16. Trutnovsky G, Kamisan Atan I, Ulrich D, Martin A, Dietz HP
    Acta Obstet Gynecol Scand, 2016 Dec;95(12):1411-1417.
    PMID: 27622984 DOI: 10.1111/aogs.13018
    INTRODUCTION: The study aimed to analyze the relation between the degree of puborectalis muscle trauma and subjective symptoms and objective findings of pelvic organ prolapse (POP), comparing two continuous scoring systems with a discrete scoring system for translabial ultrasound imaging.

    MATERIAL AND METHODS: In this retrospective observational study the records of patients attending a tertiary urogynecological unit between January 2012 and December 2014 were analyzed. POP assessment included a standardized interview, clinical examination using Pelvic Organ Prolapse Quantification and four-dimensional translabial ultrasound. Puborectalis muscle trauma was assessed with tomographic ultrasound imaging using two continuous scoring systems and a previously established discrete system. Receiver operating characteristics and adjusted odds ratios were used for comparison of scoring systems in predicting symptoms and signs of POP.

    RESULTS: Of 1258 women analyzed, 52.6% complained of prolapse symptoms. On ultrasound imaging, 65.7% of women had sonographically significant POP. Complete avulsion was diagnosed in 25.3% of women, being unilateral in 13.9% and bilateral in 11.4%. A maximum score in the 6-point and the 12-point tomographic ultrasound imaging scale increased the odds for a diagnosis of any significant POP on ultrasound by 4.4 and 4.8 times, respectively, compared with 4.6 times for the discrete diagnosis of bilateral avulsion. For all avulsion scoring systems the relation was strongest for cystocele and uterine prolapse.

    CONCLUSIONS: A continuous avulsion scoring system based on tomographic findings does not provide superior performance for the prediction of subjective symptoms and objective findings of prolapse compared with a discrete diagnostic system of unilateral or bilateral avulsion.

  17. Atieno OM, Opanga S, Martin A, Kurdi A, Godman B
    J Med Econ, 2018 Sep;21(9):878-887.
    PMID: 29860920 DOI: 10.1080/13696998.2018.1484372
    BACKGROUND: Currently the majority of cancer deaths occur in low- and middle-income countries, where there are appreciable funding concerns. In Kenya, most patients currently pay out of pocket for treatment, and those who are insured are generally not covered for the full costs of treatment. This places a considerable burden on households if family members develop cancer. However, the actual cost of cancer treatment in Kenya is unknown. Such an analysis is essential to better allocate resources as Kenya strives towards universal healthcare.

    OBJECTIVES: To evaluate the economic burden of treating cancer patients.

    METHOD: Descriptive cross-sectional cost of illness study in the leading teaching and referral hospital in Kenya, with data collected from the hospital files of sampled adult patients for treatment during 2016.

    RESULTS: In total, 412 patient files were reviewed, of which 63.4% (n = 261) were female and 36.6% (n = 151) male. The cost of cancer care is highly dependent on the modality. Most reviewed patients had surgery, chemotherapy and palliative care. The cost of cancer therapy varied with the type of cancer. Patients on chemotherapy alone cost an average of KES 138,207 (USD 1364.3); while those treated with surgery cost an average of KES 128,207 (1265.6), and those on radiotherapy KES 119,036 (1175.1). Some patients had a combination of all three, costing, on average, KES 333,462 (3291.8) per patient during the year.

    CONCLUSION: The cost of cancer treatment in Kenya depends on the type of cancer, the modality, cost of medicines and the type of inpatient admission. The greatest contributors are currently the cost of medicines and inpatient admissions. This pilot study can inform future initiatives among the government as well as private and public insurance companies to increase available resources, and better allocate available resources, to more effectively treat patients with cancer in Kenya. The authors will be monitoring developments and conducting further research.

  18. Yahya N, Ebert MA, Bulsara M, Haworth A, Kearvell R, Foo K, et al.
    Radiat Oncol, 2014;9:282.
    PMID: 25498565 DOI: 10.1186/s13014-014-0282-7
    To assess the impact of incremental modifications of treatment planning and delivery technique, as well as patient anatomical factors, on late gastrointestinal toxicity using data from the TROG 03.04 RADAR prostate radiotherapy trial.
  19. Baki MM, Menys A, Atkinson D, Bassett P, Morley S, Beale T, et al.
    Eur Radiol, 2017 Feb;27(2):598-606.
    PMID: 27085701 DOI: 10.1007/s00330-016-4341-3
    OBJECTIVE: Determine feasibility of vocal fold (VF) abduction and adduction assessment by cine magnetic resonance imaging (cine-MRI) METHODS: Cine-MRI of the VF was performed on five healthy and nine unilateral VF paralysis (UVFP) participants using an axial gradient echo acquisition with temporal resolution of 0.7 s. VFs were continuously imaged with cine-MRI during a 10-s period of quiet respiration and phonation. Scanning was repeated twice within an individual session and then once again at a 1-week interval. Asymmetry of VF position during phonation (VF phonation asymmetry, VFPa) and respiration (VF respiration asymmetry, VFRa) was determined. Percentage reduction in total glottal area between respiration and phonation (VF abduction potential, VFAP) was derived to measure overall mobility. An un-paired t-test was used to compare differences between groups. Intra-session, inter-session and inter-reader repeatability of the quantitative metrics was evaluated using intraclass correlation coefficient (ICC).

    RESULTS: VF position asymmetry (VFPa and VFRa) was greater (p=0.012; p=0.001) and overall mobility (VFAP) was lower (p=0.008) in UVFP patients compared with healthy participants. ICC of repeatability of all metrics was good, ranged from 0.82 to 0.95 except for the inter-session VFPa (0.44).

    CONCLUSION: Cine-MRI is feasible for assessing VF abduction and adduction. Derived quantitative metrics have good repeatability.

    KEY POINTS: • Cine-MRI is used to assess vocal folds (VFs) mobility: abduction and adduction. • New quantitative metrics are derived from VF position and abduction potential. • Cine-MRI able to depict the difference between normal and abnormal VF mobility. • Cine-MRI derived quantitative metrics have good repeatability.

  20. Ortiz RH, Leon DA, Estevez HO, Martin A, Herrera JL, Romo LF, et al.
    Clin Exp Immunol, 2009 Aug;157(2):271-81.
    PMID: 19604267 DOI: 10.1111/j.1365-2249.2009.03941.x
    Buruli ulcer (BU) is the third most common mycobacterial disease in immunocompetent hosts. BU is caused by Mycobacterium ulcerans, which produces skin ulcers and necrosis at the site of infection. The principal virulence factor of M. ulcerans is a polyketide-derived macrolide named mycolactone, which has cytotoxic and immunosuppressive activities. We determined the severity of inflammation, histopathology and bacillary loads in the subcutaneous footpad tissue of BALB/c mice infected with 11 different M. ulcerans isolates from diverse geographical areas. Strains from Africa (Benin, Ghana, Ivory Coast) induced the highest inflammation, necrosis and bacillary loads, whereas the strains collected from Australia, Asia (Japan, Malaysia, New Guinea), Europe (France) and America (Mexico) induced mild inflammation. Subsequently, animals were infected with the strain that exhibited the highest (Benin) or lowest (Mexico) level of virulence in order to analyse the local immune response generated. The Mexican strain, which does not produce mycolactone, induced a predominantly T helper type 1 (Th1) cytokine profile with constant high expression of the anti-microbial peptides beta defensins 3 and 4, in co-existence with low expression of the anti-inflammatory cytokines interleukin (IL)-10, IL-4 and transforming growth factor (TGF)-beta. The highly virulent strain from Benin which produces mycolactone A/B induced the opposite pattern. Thus, different local immune responses were found depending on the infecting M. ulcerans strain.
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