Preventing adverse events during paediatric cancer treatment: protocol for a multi-site hybrid randomised controlled trial of catheter lock solutions (the CLOCK trial).

INTRODUCTION: Central venous access devices (CVADs) are commonly used for the treatment of paediatric cancer patients. Catheter locking is a routine intervention that prevents CVAD-associated adverse events, such as infection, occlusion and thrombosis. While laboratory and clinical data are promising, tetra-EDTA (T-EDTA) has yet to be rigorously evaluated or introduced in cancer care as a catheter lock. METHODS AND ANALYSIS: This is a protocol for a two-arm, superiority type 1 hybrid effectiveness-implementation randomised controlled trial conducted at seven hospitals across Australia and New Zealand. Randomisation will be in a 3:2 ratio between the saline (heparinised saline and normal saline) and T-EDTA groups, with randomly varied blocks of size 10 or 20 and stratification by (1) healthcare facility; (2) CVAD type and (3) duration of dwell since insertion. Within the saline group, there will be a random allocation between normal and heparin saline. Participants can be re-recruited and randomised on insertion of a new CVAD. Primary outcome for effectiveness will be a composite of CVAD-associated bloodstream infections (CABSI), CVAD-associated thrombosis or CVAD occlusion during CVAD dwell or at removal. Secondary outcomes will include CABSI, CVAD-associated-thrombosis, CVAD failure, incidental asymptomatic CVAD-associated-thrombosis, other adverse events, health-related quality of life, healthcare costs and mortality. To achieve 90% power (alpha=0.05) for the primary outcome, data from 720 recruitments are required. A mixed-methods approach will be employed to explore implementation contexts from the perspective of clinicians and healthcare purchasers. ETHICS AND DISSEMINATION: Ethics approval has been provided by Children's Health Queensland Hospital and Health Service Human Research Ethics Committee (HREC) (HREC/22/QCHQ/81744) and the University of Queensland HREC (2022/HE000196) with subsequent governance approval at all sites. Informed consent is required from the substitute decision-maker or legal guardian prior to participation. In addition, consent may also be obtained from mature minors, depending on the legislative requirements of the study site. The primary trial and substudies will be written by the investigators and published in peer-reviewed journals. The findings will also be disseminated through local health and clinical trial networks by investigators and presented at conferences. TRIAL REGISTRATION NUMBER: ACTRN12622000499785.

Precision-guided treatment in high-risk pediatric cancers.

Recent research showed that precision medicine can identify new treatment strategies for patients with childhood cancers. However, it is unclear which patients will benefit most from precision-guided treatment (PGT). Here we report consecutive data from 384 patients with high-risk pediatric cancer (with an expected cure rate of less than 30%) who had at least 18 months of follow-up on the ZERO Childhood Cancer Precision Medicine Program PRecISion Medicine for Children with Cancer (PRISM) trial. A total of 256 (67%) patients received PGT recommendations and 110 (29%) received a recommended treatment. PGT resulted in a 36% objective response rate and improved 2-year progression-free survival compared with standard of care (26% versus 12%; P = 0.049) or targeted agents not guided by molecular findings (26% versus 5.2%; P = 0.003). PGT based on tier 1 evidence, PGT targeting fusions or commenced before disease progression had the greatest clinical benefit. Our data show that PGT informed by comprehensive molecular profiling significantly improves outcomes for children with high-risk cancers. ClinicalTrials.gov registration: NCT03336931.

Radiologic Manifestations of Mycobacterium chimaera Infection After Open Heart Surgery.

PURPOSE: The objective of this study is to identify and detail the radiologic manifestations of surgical site and disseminated Mycobacterium chimaera (MC) infection. The aim is to facilitate early identification and diagnosis of MC, considering its indolent nature and the challenges involved in clinically and pathologically establishing the diagnosis. PATIENTS AND METHODS: This was a retrospective cohort study reviewing computed tomography (CT), positron emission tomography (PET)/CT, and magnetic resonance imaging examinations in patients over the age of 18 years with a history of open heart surgery and a clinical or pathologic diagnosis of MC. Two radiology residents, a fellowship-trained nuclear medicine radiologist, and a fellowship-trained cardiothoracic radiologist performed consensus reads to determine the imaging findings seen in MC infection. RESULTS: Twenty-five patients were included. Localized, surgical site infection was more common than disseminated disease. Typical CT findings included peristernal soft tissue thickening, sinus tracts often extending to the cutaneous surface, slowly enlarging fluid collections, and sternal osteolysis. PET/CT findings demonstrated hypermetabolic activity in nearly all patients localized to sites of infection. Imaging findings for disseminated infection included hepatosplenomegaly, lymphadenopathy, involvement of the central nervous system, discitis/osteomyelitis, and distant abscesses. CONCLUSIONS: Imaging plays a vital role in suggesting possible surgical sites and disseminated MC infection acquired from open heart surgery. Radiologists must keep a high index of suspicion given the indolent nature and subtle imaging change over time. PET/CT is most useful in diagnosis and helps in differentiating between a sterile postoperative fluid collection or scarring and active MC infection and helps provide a target for debridement.

Point of Care Ultrasound Identification and Aspiration of a Neck Lymph Node.

The tissue diagnosis and staging of all types of lung cancer is foundational for prognosis and establishing the optimal treatment plan. In order to appropriately stage lung cancer, the highest stage should be established using the 8th edition TNM criteria, where tumor size (T), nodal involvement (N), and metastasis (M) are all taken into account. Establishing a tissue diagnosis may involve the use of CT guided biopsy, navigational bronchoscopy, endobronchial biopsy, EBUS, percutaneous lymph node biopsy and/or excisional biopsy of supraclavicular nodes. It is recommended to proceed with the method that is considered least invasive and provides the highest staging. We present a case of recurrent lung adenocarcinoma diagnosed with real time ultrasound-guided fine needle aspiration of a neck lymph node.

Invasive fungal disease in children with solid tumors: An Australian multicenter 10-year review.

Invasive fungal disease (IFD) occurs less frequently during treatment for solid compared to hematological malignancies in children, and risk groups are poorly defined. Retrospective national multicenter cohort data (2004-2013) were analyzed to document prevalence, clinical characteristics, and microbiology of IFD. Amongst 2067 children treated for solid malignancy, IFD prevalence was 1.9% overall and 1.4% for proven/probable IFD. Of all IFD episodes, 42.5% occurred in patients with neuroblastoma (prevalence 7.0%). Candida species comprised 54.8% of implicated pathogens in proven/probable IFD. In children with solid tumors, IFD is rare, and predominantly caused by yeasts.Routine prophylaxis may not be warranted.

Exploring NK cell receptor dynamics in paediatric leukaemias: implications for immunotherapy and prognosis.

Objectives: Immunotherapies targeting natural killer (NK) cell receptors have shown promise against leukaemia. Unfortunately, cancer immunosuppressive mechanisms that alter NK cell phenotype prevent such approaches from being successful. The study utilises advanced cytometry to examine how cancer immunosuppressive pathways affect NK cell phenotypic changes in clinical samples. Methods: In this study, we conducted a high-dimensional examination of the cell surface expression of 16 NK cell receptors in paediatric patients with acute myeloid leukaemia and acute lymphoblastic leukaemia, as well as in samples of non-age matched adult peripheral blood (APB) and umbilical cord blood (UCB). An unsupervised analysis was carried out in order to identify NK cell populations present in paediatric leukaemias. Results: We observed that leukaemia NK cells clustered together with UCB NK cells and expressed relatively higher levels of the NKG2A receptor compared to APB NK cells. In addition, CD56dimCD16+CD57- NK cells lacking NKG2A expression were mainly absent in paediatric leukaemia patients. However, CD56br NK cell populations expressing high levels of NKG2A were highly represented in paediatric leukaemia patients. NKG2A expression on leukaemia NK cells was found to be positively correlated with the expression of its ligand, suggesting that the NKG2A-HLA-E interaction may play a role in modifying NK cell responses to leukaemia cells. Conclusion: We provide an in-depth analysis of NK cell populations in paediatric leukaemia patients. These results support the development of immunotherapies targeting immunosuppressive receptors, such as NKG2A, to enhance innate immunity against paediatric leukaemia.

Nurse-led approach to standardising the management of iron-deficiency anaemia, achieving the 2-week cancer pathway targets and reducing hospital admissions: practicalities and learnings from a success story.

The most significant and common cause of anaemia is iron deficiency, which occurs when iron absorption cannot meet the body's demands due to growth, pregnancy, poor nutrition, malabsorption or blood loss. It is estimated that in the UK 11% of the adult population have iron-deficiency anaemia (IDA) and investigation is essential to exclude significant pathology as the underlying cause. It has been shown that IDA is responsible for 57 000 hospital admissions in the UK, and at least 10% of gastroenterology referrals per annum. IDA is a major red flag symptom for gastrointestinal cancer. At the Royal Liverpool University Hospital, a dedicated nurse-led IDA service was developed in 2005 to help alleviate the clinical pressures created by the two week suspected cancer referral pathway. With the success of this service, investigation and management of IDA has been extended to referrals from accident and emergency, with the aim of reducing hospital admissions and to investigating and optimising iron replacement therapy in preoperative patients. Delivering this as a nurse consultant-led service was proposed by the gastroenterology medical team who felt that, as a clinical problem with well established, published investigative algorithms, IDA would be suitable for management in a dedicated nurse-led clinic. This article will focus on the strategies employed to achieve sufficient resources and clinic capacity to run this service effectively, develop strong nurse education and training, and the development of agreed investigation pathways. A robust results review process, with rapid management of abnormal results, was established with timely discharge for those patients with normal results. Optimisation of iron replacement therapy and verification of sustained haematological response was prioritised as this was identified as being poorly managed across all specialties. A process for ongoing audit of results was included to show the success of the service and highlight areas for redesign. Here, we demonstrate the effectiveness of our nurse-led IDA service and suggest it as the basis for other IDA services in the UK and beyond.

PARC: a phase I/II study evaluating the safety and activity of pegylated recombinant human arginase BCT-100 in relapsed/refractory cancers of children and young adults.

Background: The survival for many children with relapsed/refractory cancers remains poor despite advances in therapies. Arginine metabolism plays a key role in the pathophysiology of a number of pediatric cancers. We report the first in child study of a recombinant human arginase, BCT-100, in children with relapsed/refractory hematological, solid or CNS cancers. Procedure: PARC was a single arm, Phase I/II, international, open label study. BCT-100 was given intravenously over one hour at weekly intervals. The Phase I section utilized a modified 3 + 3 design where escalation/de-escalation was based on both the safety profile and the complete depletion of arginine (defined as adequate arginine depletion; AAD <8µM arginine in the blood after 4 doses of BCT-100). The Phase II section was designed to further evaluate the clinical activity of BCT-100 at the pediatric RP2D determined in the Phase I section, by recruitment of patients with pediatric cancers into 4 individual groups. A primary evaluation of response was conducted at eight weeks with patients continuing to receive treatment until disease progression or unacceptable toxicity. Results: 49 children were recruited globally. The Phase I cohort of the trial established the Recommended Phase II Dose of 1600U/kg iv weekly in children, matching that of adults. BCT-100 was very well tolerated. No responses defined as a CR, CRi or PR were seen in any cohort within the defined 8 week primary evaluation period. However a number of these relapsed/refractory patients experienced prolonged radiological SD. Conclusion: Arginine depletion is a clinically safe and achievable strategy in children with cancer. The RP2D of BCT-100 in children with relapsed/refractory cancers is established at 1600U/kg intravenously weekly and can lead to sustained disease stability in this hard to treat population. Clinical trial registration: EudraCT, 2017-002762-44; ISRCTN, 21727048; and ClinicalTrials.gov, NCT03455140.

Outcomes of Thumb Metacarpophalangeal Joint Arthrodesis Using the XMCP Intramedullary Interlocking Device.

Purpose: The intramedullary interlocking device for metacarpophalangeal (MCP) joint arthrodesis (XMCP, Extremity Medical, Parsippany, NJ) has been shown to promote union at a precise angle, provide strong fixation without the need for prolonged immobilization, and lower the incidence of hardware irritation and revision surgery. In this study, we evaluated the clinical outcomes of patients undergoing MCP joint arthrodesis with the XMCP system using a retrospective chart review, patient reported outcomes, and radiographic analysis. Methods: A retrospective chart review and phone survey was conducted on 57 patients (58 cases) from a single institution between 2017 and 2022. The primary outcome was patient satisfaction, including pre- and postoperative Numeric Rating Scale (NRS) pain scores, Disabilities of Arm Shoulder and Hand (QuickDASH) outcomes, perceived grip strength, and willingness to undergo the procedure again. Secondary outcomes included the need for revision procedures, successful fusion of arthrodesis, and postoperative complications. Results: Of the 57 patients who underwent MCP joint arthrodesis of the thumb using the XMCP fusion device, a total of 43 (75%) completed the phone survey. The average age of patients was 67 years with an average clinical follow-up of 9 months (range 1-65 months). Patients who participated in the phone survey questionnaire had an average QuickDASH score of 24.7 ± 20.5. Average perceived NRS scores were 6.2 ± 3.5 and 1.2 ± 2.1 before and after surgery, respectively. Average perceived grip strength of patients was 3 ± 1.3 out of 5. When evaluating for concurrent procedures, there was no statistically significant difference in pre- or postoperative NRS scores. In total, 38 (88%) patients were satisfied with the procedure, and 39 (91%) patients would undergo the procedure again. Conclusion: Metacarpophalangeal joint arthrodesis of the thumb with the intramedullary fusion device is reproducible, allows for immediate use without immobilization, has a low number of complications, and provides improved function and pain relief. Level of Evidence: Therapeutic III.

Dual plating in the metastatic distal humerus: Benefits may outweigh the risks.

Background: Impending and complete pathologic fractures of the distal humerus are rare complications of metastatic cancer. Surgical treatment aims to quickly restore function and minimize pain. Plate and screw fixation (PSF) is a common method for addressing these lesions, but unlike in orthopaedic trauma, there are no clear guidelines for best management. While dual PSF theoretically provides better support and reduces the chance of reoperation due to tumor progression, single PSF is currently the more common choice. Materials and methods: Between March 2008 and September 2021, 35 consecutive patients who underwent PSF for distal humerus metastasis or multiple myeloma were retrospectively reviewed. The proportion of patients who developed various postoperative complications, including infection, nonunion, deep vein thrombosis, tumor progression, and radial nerve palsy, as well as those requiring reoperation, was calculated. Mann-Whitney U test, Pearson's chi-squared, and Fisher's exact test were used to investigate differences between the single and dual PSF groups with statistical significance defined as p ≤ 0.05. Results: There was no significant difference (p = 0.259) in revision rate, although 3 of 21 (14.3 %) single PSF patients required reoperation compared to 0 of 14 (0.0 %) dual PSF patients. The revisions were performed in one patient due to refracture and in two patients due to tumor progression. Although not statistically significant, a larger percentage of single PSF patients developed a postoperative complication compared to dual PSF patients [odds ratio 0.42 (95 % confidence interval 0.071 to 2.5); p = 0.431]. Single PSF did lead to shorter operative time compared to dual PSF [p < 0.001]. Conclusion: Dual PSF is non-inferior to single PSF and potentially results in fewer reoperations and postoperative complications in distal humerus pathologic lesions, although it leads to longer operative time. The current study is limited by small sample size due to the rarity of distal humerus metastatic lesions.

Sense of time is slower following exhaustive cycling exercise.

Subjective perception of time is altered during vigorous exercise. This could be due in part to the fatigue associated with physical activity at high intensities. The aim of this study was to determine the effect of fatigue, specifically, on subjective time perception. Twenty-six healthy, untrained subjects (17 men/9 women; age = 26.0 ± 4.3 years; V ˙ O 2 peak = 38.13 ± 5.62 mL/kg/min) completed a maximal aerobic exercise test on a cycle ergometer. Time perception was assessed before (PRE) and after (POST) the exercise test using a time production task wherein subjects started a stopwatch and stopped it once they believed a designated time period had passed. This time produced with the stopwatch was the estimate of the target time that was compared to the target time interval. Relative error of the timing task was significantly higher for POST (0.112 ± 0.260) than for PRE (0.028 ± 0.173), p = .032, η2 = .178. Subjects produced ~ 8.4% more time than the target intervals when fatigued, which is indicative of a slower sense of time perception. A shift in attentional focus from timing to the sensations associated with fatigue is a possible factor to explain this result. Future studies which investigate the effects of exercise on time perception should consider the impact of fatigue experienced during exercise.

Incidence and survival for childhood cancer by endorsed non-stage prognostic indicators in Australia.

BACKGROUND: An international expert panel recently recommended 15 'non-stage prognostic indicators' (NSPIs) across eight childhood cancers, classified as essential or additional, for collection in population-based cancer registries. We aimed to describe the incidence distribution and survival of each of these NSPIs. PROCEDURES: Cases were extracted from the Australian Childhood Cancer Registry. The study cohort (n = 4187) comprised all children aged under 15 years diagnosed with an eligible cancer between 2010 and 2018, with follow-up until 31 December 2020. NSPI data were collected directly from each patient's medical records. Differences in 5-year relative survival were assessed using multivariable flexible parametric models, adjusted for sex and age group at diagnosis. RESULTS: The availability of data varied, exceeding 85% for all essential NSPIs apart from histologic subtype for Wilms tumours (69%) and lineage for acute lymphoblastic leukaemia (78%). Information on additional NSPIs tended to be recorded less often, particularly cytogenetic subtype for non-alveolar rhabdomyosarcoma (28%) and astrocytoma (4%). Eight NSPIs exhibited a significant difference in survival, with the largest disparity occurring among children with astrocytoma according to tumour grade (5-year relative survival of 18% for grade IV disease compared with 99% for grade I disease; p < .001). CONCLUSIONS: Our findings demonstrate that most of the recommended NSPIs can be retrieved from medical records in Australia in recent years, allowing the capability of assessing survival within patient subgroups of clinical interest. Reporting of NSPI data has the capability to inform local and global understanding of population-level disparities in childhood cancer survival.

Characterization of Human Engraftment and Hemophagocytic Lymphohistiocytosis in NSG-SGM3 Neonate Mice Engrafted with Purified CD34+ Hematopoietic Stem Cells.

Immunodeficient mice bearing human immune systems, or "humanized" chimeric mice, are widely used in basic research, along with the preclinical stages of drug development. Nonobese diabetic-severe combined immunodeficiency (NOD-SCID) IL2Rγnull (NSG) mice expressing human stem cell factor, granulocyte-macrophage colony stimulating factor, and interleukin-3 (NSG-SGM3) support robust development of human myeloid cells and T cells but have reduced longevity due to the development of fatal hemophagocytic lymphohistiocytosis (HLH). Here, we describe an optimized protocol for development of human immune chimerism in NSG-SGM3 mice. We demonstrate that efficient human CD45+ reconstitution can be achieved and HLH delayed by engraftment of neonatal NSG-SGM3 with low numbers of human umbilical cord-derived CD34+ hematopoietic stem cells in the absence of preconditioning irradiation.

Establishment of a tissue-engineered colon cancer model for comparative analysis of cancer cell lines.

To overcome the limitations of in vitro two-dimensional (2D) cancer models in mimicking the complexities of the native tumor milieu, three-dimensional (3D) engineered cancer models using biomimetic materials have been introduced to more closely recapitulate the key attributes of the tumor microenvironment. Specifically, for colorectal cancer (CRC), a few studies have developed 3D engineered tumor models to investigate cell-cell interactions or efficacy of anti-cancer drugs. However, recapitulation of CRC cell line phenotypic differences within a 3D engineered matrix has not been systematically investigated. Here, we developed an in vitro 3D engineered CRC (3D-eCRC) tissue model using the natural-synthetic hybrid biomaterial PEG-fibrinogen and three CRC cell lines, HCT 116, HT-29, and SW480. To better recapitulate native tumor conditions, our 3D-eCRC model supported higher cell density encapsulation (20 × 106 cells/mL) and enabled longer term maintenance (29 days) as compared to previously reported in vitro CRC models. The 3D-eCRCs formed using each cell line demonstrated line-dependent differences in cellular and tissue properties, including cellular growth and morphology, cell subpopulations, cell size, cell granularity, migration patterns, tissue growth, gene expression, and tissue stiffness. Importantly, these differences were found to be most prominent from Day 22 to Day 29, thereby indicating the importance of long-term culture of engineered CRC tissues for recapitulation and investigation of mechanistic differences and drug response. Our 3D-eCRC tissue model showed high potential for supporting future in vitro comparative studies of disease progression, metastatic mechanisms, and anti-cancer drug candidate response in a CRC cell line-dependent manner.

Primary B cell lymphoma of the patella presenting as anterior knee pain: A case report.

Case: A 76-year-old female with a history of multiple falls on the patella presented with worsening knee pain, swelling, and reduced range of motion. Radiographs revealed tricompartmental osteoarthritis and subtle erosion of the posterior cortex of the patella that was missed by the referring orthopedist and radiologist. Her persistent pain prompted an MRI, revealing a mass later confirmed to be primary diffuse large B-cell lymphoma of the patella after biopsy and appropriate metastatic workup. Conclusion: Primary B-cell patellar lymphoma is a rarely described cause of knee pain requiring broad differential diagnosis and multidisciplinary workup in order to avoid erroneous treatment and ensure prompt oncologic treatment.

Biologic and clinical features of childhood gamma delta T-ALL: identification of STAG2/LMO2 γδ T-ALL as an extremely high risk leukemia in the very young.

PURPOSE: Gamma delta T-cell receptor-positive acute lymphoblastic leukemia (γδ T-ALL) is a high-risk but poorly characterized disease. METHODS: We studied clinical features of 200 pediatric γδ T-ALL, and compared the prognosis of 93 cases to 1,067 protocol-matched non-γδ T-ALL. Genomic features were defined by transcriptome and genome sequencing. Experimental modeling was used to examine the mechanistic impacts of genomic alterations. Therapeutic vulnerabilities were identified by high throughput drug screening of cell lines and xenografts. RESULTS: γδ T-ALL in children under three was extremely high-risk with 5-year event-free survival (33% v. 70% [age 3-<10] and 73% [age ≥10], P =9.5 x 10 -5 ) and 5-year overall survival (49% v. 78% [age 3-<10] and 81% [age ≥10], P =0.002), differences not observed in non-γδ T-ALL. γδ T-ALL in this age group was enriched for genomic alterations activating LMO2 activation and inactivating STAG2 inactivation ( STAG2/LMO2 ). Mechanistically, we show that inactivation of STAG2 profoundly perturbs chromatin organization by altering enhancer-promoter looping resulting in deregulation of gene expression associated with T-cell differentiation. Drug screening showed resistance to prednisolone, consistent with clinical slow treatment response, but identified a vulnerability in DNA repair pathways arising from STAG2 inactivation, which was efficaciously targeted by Poly(ADP-ribose) polymerase (PARP) inhibition, with synergism with HDAC inhibitors. Ex-vivo drug screening on PDX cells validated the efficacy of PARP inhibitors as well as other potential targets including nelarabine. CONCLUSION: γδ T-ALL in children under the age of three is extremely high-risk and enriched for STAG2/LMO2 ALL. STAG2 loss perturbs chromatin conformation and differentiation, and STAG2/LMO2 ALL is sensitive to PARP inhibition. These data provide a diagnostic and therapeutic framework for pediatric γδ T-ALL. SUPPORT: The authors are supported by the American and Lebanese Syrian Associated Charities of St Jude Children's Research Hospital, NCI grants R35 CA197695, P50 CA021765 (C.G.M.), the Henry Schueler 41&9 Foundation (C.G.M.), and a St. Baldrick's Foundation Robert J. Arceci Innovation Award (C.G.M.), Gabriella Miller Kids First X01HD100702 (D.T.T and C.G.M.) and R03CA256550 (D.T.T. and C.G.M.), F32 5F32CA254140 (L.M.), and a Garwood Postdoctoral Fellowship of the Hematological Malignancies Program of the St Jude Children's Research Hospital Comprehensive Cancer Center (S.K.). This project was supported by the National Cancer Institute of the National Institutes of Health under the following award numbers: U10CA180820, UG1CA189859, U24CA114766, U10CA180899, U10CA180866 and U24CA196173. DISCLAIMER: The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The funding agencies were not directly involved in the design of the study, gathering, analysis and interpretation of the data, writing of the manuscript, or decision to submit the manuscript for publication.

Reproducible Bioinformatics Analysis Workflows for Detecting IGH Gene Fusions in B-Cell Acute Lymphoblastic Leukaemia Patients.

B-cell acute lymphoblastic leukaemia (B-ALL) is characterised by diverse genomic alterations, the most frequent being gene fusions detected via transcriptomic analysis (mRNA-seq). Due to its hypervariable nature, gene fusions involving the Immunoglobulin Heavy Chain (IGH) locus can be difficult to detect with standard gene fusion calling algorithms and significant computational resources and analysis times are required. We aimed to optimize a gene fusion calling workflow to achieve best-case sensitivity for IGH gene fusion detection. Using Nextflow, we developed a simplified workflow containing the algorithms FusionCatcher, Arriba, and STAR-Fusion. We analysed samples from 35 patients harbouring IGH fusions (IGH::CRLF2 n = 17, IGH::DUX4 n = 15, IGH::EPOR n = 3) and assessed the detection rates for each caller, before optimizing the parameters to enhance sensitivity for IGH fusions. Initial results showed that FusionCatcher and Arriba outperformed STAR-Fusion (85-89% vs. 29% of IGH fusions reported). We found that extensive filtering in STAR-Fusion hindered IGH reporting. By adjusting specific filtering steps (e.g., read support, fusion fragments per million total reads), we achieved a 94% reporting rate for IGH fusions with STAR-Fusion. This analysis highlights the importance of filtering optimization for IGH gene fusion events, offering alternative workflows for difficult-to-detect high-risk B-ALL subtypes.

Paediatric B lymphoblastic leukaemia with hyperdiploidy and a false-positive KMT2A fluorescence in situ hybridization result.

The dramatic improvement in the event-free survival of paediatric B-lymphoblastic leukaemia (B-ALL) has led to risk-stratified treatment. Through a combination of clinical features, cytogenetic abnormalities and assessment of treatment response, patients are stratified to receive different intensities of therapy. The presence of high hyperdiploidy (>50 chromosomes) is considered a favourable genetic feature. Conversely, KMT2A fusion genes in B-ALL are associated with a poor prognosis, resulting in intensification of treatment. We present a seven-year-old female with B-ALL, a high hyperdiploid karyotype (56 chromosomes) and KMT2A rearrangement detected on FISH, but with no productive fusion identified. Single nucleotide polymorphism (SNP) array suggested the KMT2A rearrangement was due to chromosome 11 chromothripsis. Subsequent targeted RNA fusion panel and whole transcriptomic sequencing (mRNA-seq) did not detect an expressed KMT2A fusion. Differential expression analyses of the mRNA-seq data led to clustering of this case with other hyperdiploid cases, consistent with the hyperdiploid cytogenetic results. Given the additional intensity and potential toxicity of high-risk treatment, unusual findings by chromosome analysis, FISH and/or chromosomal microarray should prompt consideration of testing for a KMT2A fusion by another method to avoid misclassification.