Capture-based targeted sequencing using a T-cell control in myeloid malignancies and idiopathic cytopenias.

We report on a study of next-generation sequencing in 257 patients undergoing investigations for cytopenias. We sequenced bone marrow aspirates using a target enrichment panel comprising 82 genes and used T cells from paired blood as a control. One hundred and sixty patients had idiopathic cytopenias, 81 had myeloid malignancies and 16 had lymphoid malignancies or other diagnoses. Forty-seven of the 160 patients with idiopathic cytopenias had evidence of somatic pathogenic variants consistent with clonal cytopenias. Only 39 genes of the 82 tested were mutated in the 241 patients with either idiopathic cytopenias or myeloid neoplasms. We confirm that T cells can be used as a control to distinguish between germline and somatic variants. The use of paired analysis with a T-cell control significantly reduced the time molecular scientists spent reporting compared to unpaired analysis. We identified somatic variants of uncertain significance (VUS) in a higher proportion (24%) of patients with myeloid malignancies or clonal cytopenias compared to less than 2% of patients with non-clonal cytopenias. This suggests that somatic VUS are indicators of a clonal process. Lastly, we show that blood depleted of lymphocytes can be used in place of bone marrow as a source of material for sequencing.

Outcomes of Patients Treated With RCHOP With a PET-Adapted Approach for Consolidative Radiotherapy: A Retrospective Single-Center Study at the Royal Marsden Hospital.

BACKGROUND: Treatment with CHOP-based chemotherapy with consolidative radiotherapy (CRT) for primary mediastinal B cell lymphoma (PMBCL) has been the standard approach in the pre-rituximab era. Overtreatment with CRT for patients who may have already been cured by primary immunochemotherapy in the rituximab era is a significant concern due to the long-term toxicity associated with radiotherapy. Positron emission tomography (PET) may help to identify patients who may not benefit from further CRT. METHODS: We conducted a retrospective review of patients treated at the Royal Marsden Hospital between 2003 and 2020 for PMBCL to assess CRT use and survival outcomes. RESULTS: Forty-three patients were identified, with 95% of the patients receiving R-CHOP. CRT was given in 5 patients. Five-year event-free survival was 79% (95% confidence interval: 64%-89%) and 5-year overall survival was 88% (95% confidence interval: 73%-95%). Seven of 9 patients with DS4 did not receive CRT and instead monitored with serial PET scans. None of these 7 patients relapsed in the mediastinum. CONCLUSION: CRT may be omitted in patients with a negative end of treatment PET scans; however, careful observation may also obviate the need for CRT in PET positive patients.

In patients hospitalized with COVID-19, adding azithromycin to usual care did not reduce 28-d mortality.

SOURCE CITATION: RECOVERY Collaborative Group. Azithromycin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial. Lancet. 2021;397:605-12. 33545096.

Genomic landscape of platinum resistant and sensitive testicular cancers.

While most testicular germ cell tumours (TGCTs) exhibit exquisite sensitivity to platinum chemotherapy, ~10% are platinum resistant. To gain insight into the underlying mechanisms, we undertake whole exome sequencing and copy number analysis in 40 tumours from 26 cases with platinum-resistant TGCT, and combine this with published genomic data on an additional 624 TGCTs. We integrate analyses for driver mutations, mutational burden, global, arm-level and focal copy number (CN) events, and SNV and CN signatures. Albeit preliminary and observational in nature, these analyses provide support for a possible mechanistic link between early driver mutations in RAS and KIT and the widespread copy number events by which TGCT is characterised.

Biosecurity risks posed by a large sea-going passenger vessel: challenges of terrestrial arthropod species detection and eradication.

Large sea-going passenger vessels can pose a high biosecurity risk. The risk posed by marine species is well documented, but rarely the risk posed by terrestrial arthropods. We conducted the longest running, most extensive monitoring program of terrestrial arthropods undertaken on board a passenger vessel. Surveillance was conducted over a 19-month period on a large passenger (cruise) vessel that originated in the Baltic Sea (Estonia). The vessel was used as an accommodation facility to house workers at Barrow Island (Australia) for 15 months, during which 73,061 terrestrial arthropods (222 species - four non-indigenous (NIS) to Australia) were collected and identified on board. Detection of Tribolium destructor Uytt., a high-risk NIS to Australia, triggered an eradication effort on the vessel. This effort totalled more than 13,700 human hours and included strict biosecurity protocols to ensure that this and other non-indigenous species (NIS) were not spread from the vessel to Barrow Island or mainland Australia. Our data demonstrate that despite the difficulties of biosecurity on large vessels, stringent protocols can stop NIS spreading from vessels, even where vessel-wide eradication is not possible. We highlight the difficulties associated with detecting and eradicating NIS on large vessels and provide the first detailed list of species that inhabit a vessel of this kind.

Development and validation of PozQoL: a scale to assess quality of life of PLHIV.

BACKGROUND: Advances in medical treatment for HIV are driving major changes in HIV policy and practice, including the encouragement of intake and adherence to HIV antiretroviral treatment (ART) by people living with HIV (PLHIV) for both personal and public health benefits. However, there is increasing recognition that achieving these goals will require a concurrent focus on the broader psychological and social wellbeing of PLHIV. Increasingly calls are being been made to incorporate a stronger focus on quality of life (QoL) of PLHIV into HIV prevention policy. In order to achieve this goal, HIV community, support and healthcare services need a valid, short and practical way to evaluate QoL of PLHIV accessing their programs. Current QoL measures are either long, complex, restricted in their use, or expensive. To address these shortcomings, the PozQoL study aimed to develop, test and validate a short and freely available scale assessing QoL among PLHIV. METHODS: Drawing on a literature review, the prioritisation of domains and development of the initial pool of items was conducted in consultation with PLHIV community organisations in Australia. The items covered health concerns, psychological, social, and functional wellbeing. Testing involved a baseline and a follow-up survey of 465 adult Australians living with HIV. Participants were recruited through social media and various community organizations nationwide. The survey included the pilot PozQoL scale and other validated measures of health and wellbeing. RESULTS: Guided by an Exploratory Factor Analysis and conceptual considerations, a 13-item scale was developed. The PozQoL scale demonstrated high levels of fit in a Confirmatory Factor Analysis, very good internal consistency, test-retest reliability, and concurrent validity with other measures that approximated different aspects of QoL. CONCLUSION: The PozQoL scale has been tested in a diverse sample of adult PLHIV living in Australia, demonstrating very good reliability and validity. The insights from PLHIV and other stakeholders supported the balancing of statistical rigour and conceptual accuracy. The scale is now ready to be implemented and field-tested across a range of community, support and healthcare programs for PLHIV. This will make a significant contribution to the evaluation and enhancement of programs for PLHIV.

Zero-tolerance biosecurity protects high-conservation-value island nature reserve.

Barrow Island, north-west coast of Australia, is one of the world's significant conservation areas, harboring marsupials that have become extinct or threatened on mainland Australia as well as a rich diversity of plants and animals, some endemic. Access to construct a Liquefied Natural Gas (LNG) plant, Australia's largest infrastructure development, on the island was conditional on no non-indigenous species (NIS) becoming established. We developed a comprehensive biosecurity system to protect the island's biodiversity. From 2009 to 2015 more than 0.5 million passengers and 12.2 million tonnes of freight were transported to the island under the biosecurity system, requiring 1.5 million hrs of inspections. No establishments of NIS were detected. We made four observations that will assist development of biosecurity systems. Firstly, the frequency of detections of organisms corresponded best to a mixture log-normal distribution including the high number of zero inspections and extreme values involving rare incursions. Secondly, comprehensive knowledge of the island's biota allowed estimation of false positive detections (62% native species). Thirdly, detections at the border did not predict incursions on the island. Fourthly, the workforce detected more than half post-border incursions (59%). Similar approaches can and should be implemented for all areas of significant conservation value.

Symptom-to-Balloon Time is a Strong Predictor of Adverse Events Following Primary Percutaneous Coronary Intervention: Results From the Australian Capital Territory PCI Registry.

BACKGROUND: Notwithstanding improvements in door-to-balloon time, adverse event rates after primary PCI have remained steady. We analysed the effect of symptom-to-balloon (STB) time, a reflection of total ischaemic time, on major adverse cardiovascular events (MACE) and explored predictors of prolonged STB time. METHODS: The study population included 1002 consecutive patients (22.4% women) with a mean age of 62.3±13.2 years, who underwent primary PCI during 2008-2014. Groups were compared for STB ≤ and >240min. Primary endpoint was one-year MACE, a composite of death, reinfarction, stent thrombosis or target vessel revascularisation. RESULTS: Symptom-to-balloon time was available in 893 patients of which 588 (65.8%) had STB ≤240min and 305 (34.2%) had STB >240min. The incidence of one-year MACE increased significantly in a stepwise manner with increasing STB time (p for trend=0.003). Symptom-to-balloon time was an independent predictor of one-year MACE along with age >70 years, final TIMI flow <3, three vessel disease, cardiogenic shock and out-of-hospital cardiac arrest. We also performed a multivariate analysis to determine predictors of delayed treatment. Predictors of STB time >240min were age >70 years, female gender, diabetes, absence of prehospital catheter laboratory activation and presentation to a non-PCI centre. CONCLUSION: Incidence of MACE was strongly correlated with STB time and STB time was an independent predictor of MACE. We have identified specific subgroups with prolonged STB times (age >70, female gender, diabetes, absence of prehospital activation and presentation to a non-PCI centre). This information should inform future studies and strategies to minimise delays in these subgroups for improved outcomes.

T cell-rich lymphoid infiltrates with large B cells: a review of key entities and diagnostic approach.

Accurate diagnostic interpretation of a lymphoid population composed predominantly of small T cells, together with smaller numbers of large B cells, with or without a nodular architecture, is a common problem faced by the histopathologist. The differential diagnosis of this histological pattern is wide, ranging from reactive conditions such as drug reactions and viral infections, through borderline entities such as immunodeficiency-related lymphoproliferative disorders to lymphomas. The latter includes entities where the large B cells are primarily neoplastic (classical and nodular lymphocyte-predominant Hodgkin lymphomas and T cell/histiocyte-rich large B cell lymphoma) as well as T cell lymphomas such as angioimmunoblastic T cell lymphoma where the large B cells represent an epiphenomenon and may or may not be neoplastic. Several rare variants of these conditions, and the fact that treatment can significantly modify appearances, add to the diagnostic difficulty of these pathological entities. Unlike monomorphic lymphoid infiltrates, the histological pattern of T cell-rich proliferation with large B cells requires close evaluation of the inter-relationship between B cells and T cells, follicular dendritic cells and sometimes other inflammatory cells. Epstein-Barr virus plays a key role in several of these scenarios, and interpreting not only its presence but also its distribution within cellular subgroups is essential to accurate diagnosis and the avoidance of some important diagnostic pitfalls. An understanding of normal immunoarchitecture and lymphoid maturational pathways is also fundamental to resolving these cases, as is a knowledge of their common patterns of spread, which facilitates correlation with clinical and radiological findings.

Development of a targeted sequencing approach to identify prognostic, predictive and diagnostic markers in paediatric solid tumours.

The implementation of personalised medicine in childhood cancers has been limited by a lack of clinically validated multi-target sequencing approaches specific for paediatric solid tumours. In order to support innovative clinical trials in high-risk patients with unmet need, we have developed a clinically relevant targeted sequencing panel spanning 311 kb and comprising 78 genes involved in childhood cancers. A total of 132 samples were used for the validation of the panel, including Horizon Discovery cell blends (n=4), cell lines (n=15), formalin-fixed paraffin embedded (FFPE, n=83) and fresh frozen tissue (FF, n=30) patient samples. Cell blends containing known single nucleotide variants (SNVs, n=528) and small insertion-deletions (indels n=108) were used to define panel sensitivities of ≥98% for SNVs and ≥83% for indels [95% CI] and panel specificity of ≥98% [95% CI] for SNVs. FFPE samples performed comparably to FF samples (n=15 paired). Of 95 well-characterised genetic abnormalities in 33 clinical specimens and 13 cell lines (including SNVs, indels, amplifications, rearrangements and chromosome losses), 94 (98.9%) were detected by our approach. We have validated a robust and practical methodology to guide clinical management of children with solid tumours based on their molecular profiles. Our work demonstrates the value of targeted gene sequencing in the development of precision medicine strategies in paediatric oncology.

Rare disruptive mutations in ciliary function genes contribute to testicular cancer susceptibility.

Testicular germ cell tumour (TGCT) is the most common cancer in young men. Here we sought to identify risk factors for TGCT by performing whole-exome sequencing on 328 TGCT cases from 153 families, 634 sporadic TGCT cases and 1,644 controls. We search for genes that are recurrently affected by rare variants (minor allele frequency <0.01) with potentially damaging effects and evidence of segregation in families. A total of 8.7% of TGCT families carry rare disruptive mutations in the cilia-microtubule genes (CMG) as compared with 0.5% of controls (P=2.1 × 10-8). The most significantly mutated CMG is DNAAF1 with biallelic inactivation and loss of DNAAF1 expression shown in tumours from carriers. DNAAF1 mutation as a cause of TGCT is supported by a dnaaf1hu255h(+/-) zebrafish model, which has a 94% risk of TGCT. Our data implicate cilia-microtubule inactivation as a cause of TGCT and provide evidence for CMGs as cancer susceptibility genes.

Single-center Series of Bone Marrow Biopsy-Defined Large Granular Lymphocyte Leukemia: High Rates of Sustained Response to Oral Methotrexate.

INTRODUCTION: Large granular lymphocyte (LGL) leukemia is a rare chronic lymphoproliferative disorder, with few large series reported to date. Series using stringent diagnostic criteria incorporating bone marrow biopsy (BMB), immunophenotyping, and T-cell receptor rearrangements are even scarcer. PATIENTS AND METHODS: The present study was a single-center series of 39 patients with LGL leukemia diagnosed using immunohistochemical analysis of BMB samples and flow cytometric and molecular data. RESULTS: With a median follow-up of 3.2 years (range, 1.0-15.1 years), 15 patients (38%) never required treatment. Of the remaining 24 patients requiring treatment, 13 were initially treated with prednisolone, for an overall response rate (ORR) of 84.6% and a median duration of response (DOR) of 13.5 months (range, 5.7-70.3 months). Of the 24 patients, 9 received oral low-dose weekly methotrexate as first-line therapy, with 8 (89%) achieving a hematologic response and a median DOR of 132.7 months (range, 6.7-180.5 months). Another 5 patients received methotrexate after prednisolone failure; all 5 responded, with a median DOR of 14 months (range, 4-96 months). Only 2 patients developed progression during methotrexate therapy, and 4 patients experienced responses lasting ≥ 5 years. CONCLUSION: Single-agent oral methotrexate appears to be highly efficacious, resulting in long response durations and minimal toxicity.