The President’s Prize 2024

Tuesday, 7th May, 11am – via Zoom Webinar

The Academy continues with it’s award scheme for graduates in the degree courses in Biomedical Science from TU Dublin, ATU and MTU/UCC. Each year the colleges are requested to nominate their two students who have excelled in the research project component of their final exams. This year, the nominated students will present their research findings live via Zoom webinar. The President’s Prize is awarded to the student who presents a project judged to be the winner by a panel of selected members and other professionals.

The winning student is presented with the President’s Prize medal and will represent Ireland at the European Professionals in BioMedical Science (EPBS) Conference, competing with other European graduates  for the Martin Nickolson Award.

The Academy would like to invite you to The Presidents Prize.

The event organiser is Bernadette Jackson. Ber will open proceedings at 11am.
Via the Zoom link:

Meeting ID: 889 6286 6261       Passcode: 527835

Bernadette Jackson
Point of Care Manager
Naas General Hospital


Evaluation of the Sysmex XN Automated Haematopoietic Progenitor Cell Count as a Surrogate Marker for Flow Cytometric CD34+ Cell Count in Autologous Peripheral Blood Stem Cell Transplants

1,2 Chong, C., 1 Lyons, M, 1Murray, F., 2 Hooban, B.
1Haematology Department, University Hospital Galway, Galway.
2Atlantic Technological University

Enumeration of peripheral blood stem cells (PBSCs) is essential for determining the optimal timing to initiate the apheresis harvesting process in order to successfully harvest a sufficient harvest yield for autologous peripheral blood stem cell transplantations (PBSCT).The current method, relying on flow cytometric CD34+ cell counts, is technically demanding and time-consuming. This study evaluates the Sysmex XN-HPC parameter, a fully automated method based on cell membrane lipid composition, aiming to optimise the current PBSCT apheresis workflow.

Materials & Methods:
Within- and between-run precision, repeatability, sample stability and selectivity of the Sysmex XN-HPC parameter were evaluated using XN-CHECKTM IQC and patient samples. Pre-apheresis samples (n=28) from 12 autologous PBSCT patients were analysed simultaneously by flow cytometric CD34+ counts and the Sysmex XN-HPC. The statistical analysis included Wilcoxon’s signed-rank test, Spearman’s correlation test, Passing-Bablok regression and Bland-Altman difference plots. Diagnostic accuracy for XN-HPC predicting CD34+ cell counts ≥20 cells/µL was assessed using receiver operating characteristic (ROC) analysis.

The XN-HPC showed high precision (CV=7%), acceptable repeatability (CV=20.7%), and stability for at least 24 hours. The paired measurements between XN-HPC and CD34+ showed no statistical differences, with good correlation (rho=0.719; slope=1.32). The mean Bland-Altman difference was 10.8 cells/µL, with wide 95% limit of agreement (-54.8 to 76.3 cells/µL). An XN-HPC positive cut-off (>78/µL) demonstrated 100% specificity and positive predictive value for identifying target CD34+ cell count of ≥20/µL, thus serving as a reliable marker for initiating apheresis. Conversely, the XN-HPC negative cut-off (≤9/µL) showed 100% sensitivity and negative predictive value for CD34+ cell counts <20/µL, indicating its potential to identify cases requiring delayed apheresis.

XN-HPC emerges as a viable surrogate for CD34+ cell counts in pre-apheresis samples. Integrating XN-HPC cut-off values into PBSCT protocols could significantly improve workflow efficiency. Further validation with larger patient cohorts is necessary to validate its applicability.

Cindy graduated with first-class honours in BSc (Hons) in Medical Science from Atlantic Technological University (ATU) and was awarded the President’s Prize from the Institute of Biomedical Science (IBMS). Her final research project was completed at Galway University Hospital (GUH), where she now works as a Medical Scientist in the Haematology Department.

Previously, her research project was presented at the Haematology Association of Ireland (HAI) annual conference, where she received the Laboratory Early Career Recognition Award. Additionally, Cindy presented her research findings at the annual Sysmex User Symposium, where her research poster was honoured with the Professor Sam Machin Award 2024.

Dedicated to expanding her expertise in haematology, Cindy is currently immersed in ongoing training under the guidance of an exceptional team at GUH, while actively seeking further opportunities to engage in research and advance her knowledge within the field.

Development of a Polymerase Chain Reaction Quantification Assay for Base Editing engineered Virus-like Particle Preparations.

James Patrick Costello (MTU)

Abstract: Base editing engineered virus-like particles (BE-eVLPs) enable safe and efficient delivery of editing machinery (base editors) that allows for the precise editing of genomic DNA (deoxyribonucleic acid) and represent a potential mechanism to correct the genome sequence source of many genetic diseases. An assay capable of defining the relationship between BE-eVLPs dosage and editing efficiency is essential for the development of dose-response curves, ensuring data derived from testing can be replicated and compared. A quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay was developed to quantify BE-eVLPs accurately. Two distinct BE-eVLP preparations were to be to be quantitated. One was designed to edit a control HEK3 locus sequence and the other to edit a G542X cystic fibrosis (CF) mutation respectively. Both BE-eVLPs were adenine base editors (ABEs) capable of catalysing deamination of exposed target bases following binding by nickase Cas9 (nCas9) joined sgRNA (single guide ribonucleic acid) to the target locus. The sgRNA component of the BE-eVLPs is the only source of nucleic acid to act as a target for a qRT-PCR assay and consists of a custom-designed short crRNA sequence conjoined to a scaffold tracrRNA sequence that guides the nCas9 to the target sequence to be edited. A qRT-PCR assay amplifying the shared tracrRNA component of the BE-eVLPs was designed, tested, and optimised. Quantification of both the HEK3 and G542X BE-eVLPs was achieved. This is an important advance in enabling the plotting of dosage response curves, ensuring data derived from BE-EVLP testing can be replicated and compared.

Evaluation of the Allplex SARS-CoV-2 Variant I and II Assay for the Identification and Differentiation of SARS-CoV-2 Variants of Concern and their Implementation as a Routine Surveillance Tool

Katie Newe
School of Biological Health and Sport Sciences
Technological University Dublin
City Campus

The outbreak of Coronavirus disease 2019 (COVID-19) presented an unprecedented threat to public health worldwide since the early stages of 2020. The causative organism SARS-CoV-2 soon began to evolve and mutate causing the emergence and spread of numerous SARS-CoV-2 variants. Surveillance of such variants is vital for the control and monitoring of the global pandemic. This study provides the first comprehensive data set on the molecular epidemiology of COVID-19 in our institution and has demonstrated that RT-PCR assays such as the Allplex SARS-CoV-2 Variant I Assay and the Allplex SARS-CoV-2 Variant II Assay can identify and differentiate between VOC in SARS-CoV-2 positive samples.
When compared to the national surveillance data, the genotyping PCR assay have demonstrated similar trends for the VOC circulating in Ireland throughout 2021 and 2022. This study has shown such assays provide a quick and cost-effective method of monitoring circulating variants and could be used as a second line diagnostic tool in the surveillance and monitoring of these variants at a local level.

Katie graduated from TU Dublin in 2023 with degree in Biomedical Science. In final year Katie majored in Microbiology and Transfusion. Katie is currently working as a medical scientist in the Transfusion/Haematology department in Connolly Hospital, Blanchardstown.

The Introduction of a HSP70, Glutamine Synthetase and Glypican 3 Panel for the Diagnosis of Hepatocellular Carcinoma

Daniya Rose Sony
Supervisors: Danielle Scally, Galway University Hospital and Joan O’ Keeffe, Atlantic Technological University, Galway.

Introduction: Hepatocellular carcinoma (HCC) is one of the leading causes of cancer associated deaths worldwide. Histological diagnosis of HCC can be challenging at both ends of HCC differentiation and often requires the help of immunohistochemical markers. The existing individual markers in Galway University Hospital (GUH) are not specific for HCC diagnosis. This results in suspected HCC cases being referred to St. Vincent’s University Hospital in Dublin where the HSP70, Glutamine Synthetase (GS) and Glypican 3 (GPC3) antibody panel is carried out for accurate diagnosis.
The aims of this study was to validate the HSP70, GS and GPC3 antibody panel Ventana BenchMark Ultra in GUH which will enable diagnosis of suspected HCC in GUH itself. The second aim of this study was to identify the ability of the panel in differentiating HCC from liver metastasis of non-liver primary tumours.
Methods: HSP70 and GS antibody optimisation was performed on the Ventana BenchMark Ultra staining platform. 34 liver biopsy samples were tested: 14 HCC and 20 non-HCC tumours to evaluate the panels ability in differentiating HCC from liver metastases of non-hepatic primary tumours. The ability of this antibody panel in accurately identifying HCC tumours was assessed based on staining intensity and positivity. Results were analysed using the Fishers exact test (p-value of <0.05 was considered significant). Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy were calculated for each individual marker and for the antibody panel as a whole in detecting HCC. Diagnostic criteria for HCC is established as positive staining in at least two out of three biomarkers.
Results: In contrast to using HSP70, GS and GPC3 as individual markers, the antibody panel exhibited markedly enhanced sensitivity (92.9%) while retaining specificity (90%). Furthermore, improvements were also seen to the PPV, NPV and accuracy.
Conclusion: It is the opinion of this study that the HSP70, GS and GPC3 antibody panel should be introduced into the routine immunohistochemistry laboratory for the identification of HCC.
Since conducting this study, the antibody panel has been implemented in GUH.

Daniya studied Medical Science in Atlantic Technological University, Galway, specialising in Haematology, Transfusion and Cellular Pathology in her final year and graduated with First-Class Honours. Presently, she is working as a Medical Scientist in the Histology Department at Galway University Hospital where she also completed this project.

Validation of pan-TRK IHC and correlation with PCR and NGS testing

Moya Rowan (TU Dublin)

Neurotrophic Tyrosine Receptor Kinase (NTRK) genes are a novel area of research. The NTRK genes have important roles in normal physiological processes, particularly in neural development and neural cell differentiation and proliferation. Fusion gene formation is the most common aberration of the NTRK gene. A translocation occurs which results in the 3’ end of the NTRK kinase domain fusing with the 5’ end of a partner gene. This rearrangement results in the translation of a mutated Tropomyosin Receptor Kinase (TRK) receptor which can be activated, independent of whether a ligand is bound or not.

In recent years, NTRK gene fusions have been investigated and deemed to be actionable biomarkers for therapy in many different cancer types. NTRK fusions are expressed in rare tumours at a high frequency and in common tumour types at a low frequency. Examples include secretory breast carcinoma, infantile fibrosarcoma, lung carcinoma and gastric carcinoma. The Food and Drugs Administration (FDA) has approved TRK inhibitory therapies such as Larotrectinib and Entrectinib, which have proven highly effective in the treatment of patients harbouring NTRK fusions. There are a number of methods available to detect NTRK fusions such as immunohistochemistry (IHC), reverse transcription polymerase chain reaction (RT-PCR) and Next-Generation Sequencing (NGS). Detecting NTRK fusions in tumours, offers patients an alternative and targeted last-line therapy option, especially for those with metastatic or late-stage disease.

In this study, the VENTANA pan-TRK (EPR17341) assay was validated. 29 patient samples were investigated for TRK fusion protein expression via the pan-TRK Immunohistochemistry (IHC) method. Four equivocal false positive results were identified using this method.
Reflex testing via the Idylla GeneFusion RT-PCR-based Assay was performed on 19 patient samples, of which 16 valid results were obtained. NTRK fusion genes were not detected in 13 patient samples. An indeterminate result was obtained for NTRK3 in three patient samples. The Idylla GeneFusion Assay had a 29% failure rate.

In conclusion, NTRK fusion genes were not detected in the patient cohort investigated (n=29). This study highlights the rarity of NTRK fusions. Further studies are required to optimise the Idylla GeneFusion assay as it is currently a research use-only (RUO) based method. Pan-TRK IHC may be useful as a screening tool, followed by preliminary confirmation via the Idylla
GeneFusion assay. However, NTRK fusion status must be confirmed via NGS testing such as the Oncomine Focus Assay, so that patients can avail of TRK inhibitory therapy. The validated pan-TRK IHC method was implemented into use in the Mater Misericordiae University Hospital as a screening method in the NTRK fusion testing algorithm.

Moya graduated with a First-Class Honours degree in Medical Science from Technological University Dublin in 2023. She was awarded the Student Excellence Award from the School of Biological, Health, and Sports Science along with the Serosep Gold Medal Award 2023, which was based on her academic achievements and final year results. Moya is currently working in the Blood Transfusion laboratory in St. James Hospital.

An Investigation into D-Glutamate Resistance and adaptive mechanisms in Escherichia Coli Strains.

Sive Anne O’Mahony (MTU)

Although D-amino acids are important structural components of the bacterial peptidoglycan layer, it is interesting to observe the inhibition of certain strains of bacteria grown in their presence. Bacteria display a unique ability to overcome this toxic effect via activation of certain molecular pathways which modulate gene expression and influence genetic processes This inhibitory effect is observed when Escherichia coli is grown in the presence of D-Glu. This study aims to investigate the mechanism of bacterial growth inhibition, looking at aspects such as the uniformity of inhibition between species and media types, and the effect of varying D-Glu concentrations on bacterial growth. An investigation of the inhibitory effects of other D-amino acids on bacterial growth and an evolutionary analysis were conducted to study the adaptive mechanisms of E. coli in an inhibitory environment. Increase in growth rate indicated the presence of D-Glu mutants. These mutants developed a certain adaptive response and were no longer compromised by the toxic D-Glu environment. Further studies may involve detecting underlying genetic mechanisms responsible for conferring tolerance in the mutant population, such as whole genome sequencing. Identification of these molecular changes display E. coli’s ability to activate certain regulatory channels in response to an unfavourable environment.

Sive graduated from UCC/MTU in October 2023 with a first class honours degree in Biomedical Science. Sive is currently undertaking her clinical laboratory placement in University Hospital Waterford