We report a child with an antenatally detected brain tumor that progressed over three years’ time despite surgery, chemo- and proton therapy. Retrospective whole-genome and transcriptome sequencing with methylation analysis of primary tumor tissue led to the molecular diagnosis infant-type hemispheric glioma, and identified a novel SNRNP70::ALK fusion, providing a therapeutic target for compassionate-use precision treatment with the ALK tyrosine kinase inhibitor lorlatinib. Functional studies confirmed the fusion protein to be expressed and active in the patient’s tumor. After two years of therapy, the child has sustained partial tumor regression on MRI and no new neurological symptoms. We conclude that comprehensive multi-omics analyses are required for correct molecular diagnosis in childhood CNS tumors and can radically impact patient outcome by identifying molecular targets for precision treatment.

Molecular tumor boards are supported by clinical decision support system (CDSS) tools for the interpretation of complex molecular data towards personalized treatments. Current CDSS tools are genomics-focused and characterized by tight couplings between data ingestion, guideline-based reasoning logic and curated knowledgebases. Next-generation CDSS solutions should integrate multimodal data and learn from outcomes in an interoperable ecosystem, leveraging explainable, trustworthy output from AI models through rigorous clinical validation processes.

Chronic lymphocytic leukemia (CLL) is a paradigmatic malignancy driven by intraclonal diversity and dynamic evolutionary processes. High-resolution genomic profiling has demonstrated that CLL progression rarely follows a linear trajectory; rather, it is characterized by a complex and evolving (sub)clonal architecture shaped by intrinsic biological features and extrinsic factors, including therapeutic pressure. Recurrent genetic alterations affect key signaling pathways and cellular processes, including B-cell receptor and NF-κB signaling, DNA damage response, RNA processing, and apoptosis. Many of these lesions arise as subclonal events and subsequently expand, thereby influencing disease progression, therapeutic resistance, and transformation. Over the past decade, the treatment paradigm in CLL has shifted from chemoimmunotherapy to targeted agents, resulting in substantial clinical benefit. Nevertheless, the emergence of therapeutic resistance remains a major challenge. In this review, we summarize current knowledge of clonal evolution and resistance mechanisms in CLL. Resistance to chemoimmunotherapy is frequently driven by genetic lesions, such as TP53 aberrations, and by expansion of resistant microclones. In contrast, targeted therapies select for distinct resistance mechanisms, such as BTK and PLCG2 mutations in patients treated with BTK inhibitors, as well as activation of alternative survival pathways. We further discuss emerging technologies, including single-cell sequencing and integrative multi-omics approaches. Finally, we highlight the need for future studies addressing resistance in evolving clinical contexts, such as combination targeted therapies, bispecific antibodies, and CAR T-cell therapy. Taken together, a deeper understanding of clonal evolution is central to the development of personalized therapeutic strategies and to improving long-term outcomes for patients with CLL.

Chronic lymphocytic leukemia (CLL) comprises immunogenetically defined stereotyped subsets of patients with distinct B-cell receptor immunoglobulin (BcR IG) features and clinical trajectories, yet the molecular pathways underlying subset-specific differences remain incompletely characterized. To resolve disease-relevant heterogeneity obscured in bulk analyses, we performed integrated single-cell transcriptomic and immunogenetic profiling of 48,557 malignant and bystander immune cells from 13 treatment-naïve primary patient samples representing poor-prognostic subsets #1 and #2 and the indolent subset #4. Despite inter-patient variability, leukemic cells exhibited pronounced subset-specific transcriptional features, with enrichment of hypoxia-related genes in subset #1, oxidative phosphorylation (OXPHOS), MYC/E2F targets, and mTORC1 signaling in subset #2, and negative enrichment of hypoxia, apoptosis, and reactive oxygen species-related pathways in subset #4. Notably, compared with indolent subset #4, aggressive subsets #1 and #2 harbored increased proportions of metabolically active and recently emigrated/proliferative leukemic cells, characterized by a CXCR4dim CD5bright transcriptional phenotype and concerted enrichment of MYC target genes, mTORC1 signaling, oxidative phosphorylation, and BcR signaling. Immunogenetic analyses revealed dominant malignant clones with evidence of intraclonal immunogenetic diversification in 11/13 cases. T cells were dominated by effector-memory phenotypes exhibiting progressive differentiation toward terminal cytotoxic states, accompanied by exhaustion-associated programs, and expanded T-cell clones largely restricted to terminal states. Ligand–receptor analysis further indicated co-stimulatory and inhibitory signaling between leukemic and immune cells. Together, this study provides an integrated view of the transcriptional and immunogenetic landscape of three major stereotyped CLL subsets, linking BcR IG configuration with proliferative capacity and microenvironmental crosstalk, thereby shaping clonal behavior.

The integration of BTK and BCL2 inhibitors into the treatment of patients with chronic lymphocytic leukemia (CLL) represents a paradigm shift and has led to significant improvements in clinical outcomes, including prolonged survival and enhanced quality of life. However, despite the efficacy of these agents, resistance to targeted therapy remains a major challenge, ultimately resulting in treatment failure and disease progression for a significant proportion of patients. Related to this, diagnostic testing for genetic variants associated with resistance, such as mutations in BTK, PLCG2 and BCL2, may become an increasingly common part of clinical routine practice. Addressing the need for placing the current knowledge in context, here we summarize the evidence from clinical studies and examine the underlying biology of both genetic and non-genetic resistance. Furthermore, we outline methodological approaches for the detection of gene alterations associated with targeted therapy resistance, discuss how to interpret these findings and highlight interpretation challenges. Finally, we offer insights into the clinical relevance of identifying genetic resistance to inform personalized treatment strategies and improve patient outcomes.

Despite the well-established adverse impact of del(11q) in chronic lymphocytic leukemia (CLL), the prognostic significance of somatic ATM mutations remains uncertain. We evaluated the effects of ATM aberrations (del(11q) and/or ATM mutations) on time-to-first-treatment (TTFT) in 3631 untreated patients with CLL, in the context of IGHV gene mutational status and mutations in nine CLL-related genes. ATM mutations were present in 246 cases (6.8%), frequently co-occurring with del(11q) (112/246 cases, 45.5%). ATM-mutated patients displayed a different spectrum of genetic abnormalities when comparing IGHV-mutated (M-CLL) and unmutated (U-CLL) cases: M-CLL was enriched for SF3B1 and NFKBIE mutations, whereas U-CLL showed mutual exclusivity with trisomy 12 and TP53 mutations. Isolated ATM mutations were rare, affecting 1.2% of Binet A patients and <1% of M-CLL cases. While univariable analysis revealed shorter TTFT for Binet A patients with any ATM aberration compared to ATM-wildtype, multivariable analysis identified only del(11q), trisomy 12, SF3B1, and EGR2 mutations as independent prognosticators of shorter TTFT among Binet A patients and within M-CLL and U-CLL subgroups. These findings highlight del(11q), and not ATM mutations, as a key biomarker of increased risk of early progression and need for therapy, particularly in otherwise indolent M-CLL, providing insights into risk-stratification and therapeutic decision-making.

PURPOSE:The MyPal study (ClinicalTrials.gov identifier: NCT04370457) is a randomized controlled clinical trial assessing an eHealth intervention on the quality of life (QoL) of patients with chronic lymphocytic leukemia (CLL) and myelodysplastic syndromes (MDS). METHODS:Patients who were receiving or had previously received treatment for CLL or MDS were randomly assigned (1:1) to access the MyPal digital health platform versus standard of care. The MyPal platform included a smartphone application used to report QoL status and symptoms via standardized questionnaires or spontaneous reporting. The primary end point was QoL at 12 months, assessed by the European Organisation for Research and Treatment of Cancer (EORTC) QLQ-C30 General Questionnaire and the EuroQol EQ-5D-3L. Secondary end points included physical and emotional functioning, measured by the Integrated Palliative Care Outcome Scale (IPOS) scale, satisfaction with care, measured by the EORTC PATSAT-C33, and overall survival (OS). Additionally, the Edmonton Symptom Assessment System (ESAS), Brief Pain Inventory (BPI), and Emotion Thermometers (ET) QoL questionnaires were assessed only in the intervention group. RESULTS:A total of 171 patients (97 and 74 in the control and intervention arms, respectively) who answered multiple questionnaires were analyzed. The intervention group reported a significant decrease in pain (β2 = -0.48 [-0.77 to -0.19], P < .001) compared with the control group (β1 = 0.3 [0.09 to 0.5], P = .01). Communication and pain measured by IPOS reduced equally in both groups (β2 = 0 [-0.03 to 0.02], P = .82; β2 = -0.01 [-0.02 to 0], P = .1, respectively). Family involvement significantly increased over time only for the intervention group. The other items of EORTC QLQ-C30, EuroQol EQ-5D-3L, IPOS, and PATSAT-C33 remained unchanged in both groups. The intervention group displayed a significant improvement in all ESAS, BPI, and ET scales. OS was similar in both groups. CONCLUSION:The MyPal intervention improved several QoL aspects and led to a statistically significant decrease in pain compared with the control group.

In chronic lymphocytic leukemia, the reliability of next-generation sequencing (NGS) to detect TP53 variants ≤10% allelic frequency (low-VAF) is debated. We tested the ability to detect 23 such variants in 41 different laboratories using their NGS method of choice. The sensitivity was 85.6%, 94.5%, and 94.8% at 1%, 2%, and 3% VAF cut-off, respectively. While only one false positive (FP) result was reported at >2% VAF, it was more challenging to distinguish true variants <2% VAF from background noise (37 FPs reported by 9 laboratories). The impact of low-VAF variants on time-to-second-treatment (TTST) and overall survival (OS) was investigated in a series of 1092 patients. Among patients not treated with targeted agents, patients with low-VAF TP53 variants had shorter TTST and OS versus wt-TP53 patients, and the relative risk of second-line treatment or death increased continuously with increasing VAF. Targeted therapy in ≥2 line diminished the difference in OS between patients with low-VAF TP53 variants and wt-TP53 patients, while patients with high-VAF TP53 variants had inferior OS compared to wild type-TP53 cases. Altogether, NGS-based approaches are technically capable of detecting low-VAF variants. No strict threshold can be suggested from a technical standpoint, laboratories reporting TP53 mutations should participate in a standardized validation set-up. Finally, whereas low-VAF variants affected outcomes in patients receiving chemoimmunotherapy, their impact on those treated with novel therapies remains undetermined. Our results pave the way for the harmonized and accurate TP53 assessment, which is indispensable for elucidating the role of TP53 mutations in targeted treatment.

Recurrent mutations in the third base of U1 spliceosomal RNA responsible for marked splicing and expression abnormalities have been described in chronic lymphocytic leukemia (CLL) and some solid tumors. However, the clinical significance of these mutations in large and independent CLL cohorts as well as their presence in other B-cell neoplasms is unknown. Here we characterized U1 mutations in 1670 CLL and 363 mature B-cell lymphomas. We confirmed that the g.3A>C U1 mutation is found in 3.5% of CLL, which conferred rapid disease progression independently of the main biological and clinical prognostic markers of the disease. Additionally, a recurrent g.9C>T mutation was found in 1.5% of CLL causing downstream splicing alterations and associated with adverse prognosis. We also identified a g.4C>T mutation in 10% of diffuse large B-cell lymphomas of the germinal center subtype and a g.7A>G mutation in 30% of EBV-negative Burkitt lymphomas, both of which altered the splicing pattern of multiple genes. This study reveals novel, recurrent, and tumor-specific U1 mutations in mature B-cell neoplasms with biological and prognostic implications, thus establishing U1 as a novel pan-B-cell malignancy driver gene.

SF3B1 mutations are recurrent in chronic lymphocytic leukemia (CLL), particularly enriched in clinically aggressive stereotyped subset #2. To investigate their impact, we conducted RNA-sequencing of 18 SF3B1MUT and 17 SF3B1WT subset #2 cases and identified 80 significant alternative splicing events (ASEs). Notable ASEs concerned exon inclusion in the non-canonical BAF (ncBAF) chromatin remodeling complex subunit, BRD9, and splice variants in eight additional ncBAF complex interactors. Long-read RNA-sequencing confirmed the presence of splice variants, and extended analysis of 139 CLL cases corroborated their association with SF3B1 mutations. Overexpression of SF3B1K700E induced exon inclusion in BRD9, resulting in a novel splice isoform with an alternative C-terminus. Protein interactome analysis of the BRD9 splice isoform revealed augmented ncBAF complex interaction, while exhibiting decreased binding of auxiliary proteins, including SPEN, BRCA2, and CHD9. Additionally, integrative multi-omics analysis identified a ncBAF complex-bound gene quartet on chromosome 1 with higher expression levels and more accessible chromatin in SF3B1MUT CLL. Finally, Cancer Dependency Map analysis and BRD9 inhibition displayed BRD9 dependency and sensitivity in cell lines and primary CLL cells. In conclusion, spliceosome dysregulation caused by SF3B1 mutations leads to multiple ASEs and an altered ncBAF complex interactome, highlighting a novel pathobiological mechanism in SF3B1MUT CLL.

Gene panel sequencing has become a common diagnostic tool for detecting somatically acquired mutations in myeloid neoplasms. However, many panels have restricted content, provide insufficient sensitivity levels, or lack clinically validated workflows. We here describe the development and validation of the Genomic Medicine Sweden myeloid gene panel (GMS-MGP), a capture-based 191 gene panel including mandatory genes in contemporary guidelines as well as emerging candidates. The GMS-MGP displayed uniform coverage across all targets, including recognized difficult GC-rich areas. The validation of 117 previously described somatic variants showed a 100% concordance with a limit-of-detection of a 0.5% variant allele frequency (VAF), achieved by utilizing error correction and filtering against a panel-of-normals. A national interlaboratory comparison investigating 56 somatic variants demonstrated highly concordant results in both detection rate and reported VAFs. In addition, prospective analysis of 323 patients analyzed with the GMS-MGP as part of standard-of-care identified clinically significant genes as well as recurrent mutations in less well-studied genes. In conclusion, the GMS-MGP workflow supports sensitive detection of all clinically relevant genes, facilitates novel findings, and is, based on the capture-based design, easy to update once new guidelines become available. The GMS-MGP provides an important step toward nationally harmonized precision diagnostics of myeloid malignancies.

Abstract BACKGROUND Whole genome sequencing (WGS) is the most informative singular molecular assay in cancer diagnosis. Recent evidence demonstrates that WGS can add diagnostic information and change the management of childhood cancer, and thus is being increasingly employed in clinical settings globally. However, it remains unknown whether WGS can accurately recapitulate existing multi-assay standard-of-care (SOC) genomic testing used in pediatric cancer diagnostics. In this study we evaluate the concordance between WGS and SOC findings from an unselected cohort of children across 8 centres from two healthcare systems (England and Sweden) that offer routine WGS. METHODS We compared WGS and SOC genomic test reports for children under 18 years presenting with new or relapsed cancer between January 2021 and November 2023 across 2 English centres; Cambridge University Hospital and Great Ormond Street Hospital, and 6 Swedish centres; Gothenburg, Karolinska, Linköping, Lund, Umeå and Uppsala. Only WGS findings reported to clinicians were evaluated, without re-analysis of genomes. Tests were described as ‘concordant’ where WGS and SOC were in complete concordance (positive or negative) for all SOC-detected variants. Discordance described occasions where SOC detected findings not identified by WGS. ‘Additional findings’ described cases where WGS provided disease-relevant findings above SOC testing. Only disease-relevant variants were considered in the analysis. RESULTS A cohort of 1032 patients with 1841 SOC molecular tests was included – 436 with haematological malignancies and 596 with solid tumor malignancies (528 from England, and 504 from Sweden). WGS recapitulated 99.3% of SOC tests performed, across all types of genomic alteration (1829/1841). Of the 12 instances of discordance, 3 related to poor WGS sample purity, 5 were gene fusions, 1 low variant allele frequency (0.02) internal tandem duplication, 2 single nucleotide variants and 1 copy-number aberration. WGS provided additional disease relevant findings in 19.7% of cases (203/1032). DISCUSSION Deployment of available SOC genomic testing for cancer diagnostics is highly variable across nations, individual centres and disease entities, and is usually dictated by test availability, cost and likely clinical yield, in a non-agnostic manner. For the first time we demonstrate, across two national systems, that WGS faithfully recapitulates the vast majority of SOC findings irrespective of mutation class, cancer type and variant calling algorithm. Sample quality and intra-tumoral heterogeneity likely account for the few discrepancies observed. Barriers to implementation of routine WGS as the only molecular diagnostic assay for pediatric cancer are cost, analytical expertise, and turnaround time (TAT). Our group is systematically studying the health economic benefits of WGS as a single assay to replace all SOC testing. Finally, an ongoing collaborative project aimed at reducing TAT to under 48 hours using novel technology has demonstrated feasibility in a small number of patients to date. Citation Format: Jonathan Kennedy, Sarah M. Leiter, Angus Hodder, Sheng-Yuan Kan, Jack Bartram, Giuseppe Barone, Michael Gattens, Matthew J. Murray, Sam Behjati, Patrick Tarpey, Matthew Cullen, Antony Ceraulo, Karin Langenberg, Jan Molenaar, Sandra Wessman, Frida Abel, Gustaf Ljungman, Geraldine Giraud, Hakon Anderson Blomstrand, Zdenek Rohan, Anna Staffas, Christina Orsmark-Pietras, Tatjana Pandzic, Irina Golovleva, Linda Fogelstrand, Jonas Abrahamsson, Ulrika Norèn-Nyström, Josefine Palle, Thoas Fioretos, Lucia Cavelier Franco, Gisela Barbany, Nadège Corradini, Gudrun Schleirmacher, Richard Rosenquist, David Gisselsson, Aditi Vedi. Whole genome sequencing can reproduce all standard-of-care diagnostics for childhood cancer: Results from two national systems [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pediatric Cancer Research; 2024 Sep 5-8; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl):Abstract nr B011.

Patients with chronic lymphocytic leukemia (CLL) exhibit diverse clinical outcomes. An expanding array of genetic tests is now employed to facilitate the identification of patients with high-risk disease and inform treatment decisions. These tests encompass molecular cytogenetic analysis, focusing on recurrent chromosomal alterations, particularly del(17p). Additionally, sequencing is utilized to identify TP53 mutations and to determine the somatic hypermutation status of the immunoglobulin heavy variable gene. Concurrently, a swift advancement of targeted treatment has led to the implementation of novel strategies for patients with CLL, including kinase and BCL2 inhibitors. This review explores both current and emerging diagnostic tests aimed at identifying high-risk patients who should benefit from targeted therapies. We outline existing treatment paradigms, emphasizing the importance of matching the right treatment to the right patient beyond genetic stratification, considering the crucial balance between safety and efficacy. We also take into consideration the practical and logistical issues when choosing a management strategy for each individual patient. Furthermore, we delve into the mechanisms underlying therapy resistance and stress the relevance of monitoring measurable residual disease to guide treatment decisions. Finally, we underscore the necessity of aggregating real-world data, adopting a global perspective, and ensuring patient engagement. Taken together, we argue that precision medicine is not the mere application of precision diagnostics and accessibility of precision therapies in CLL but encompasses various aspects of the patient journey (e.g., lifestyle exposures and comorbidities) and their preferences toward achieving true personalized medicine for patients with CLL.

In chronic lymphocytic leukemia (CLL), analysis of TP53 aberrations (deletion and/or mutation) is a crucial part of treatment decision-making algorithms. Technological and treatment advances have resulted in the need for an update of the last recommendations for TP53 analysis in CLL, published by ERIC, the European Research Initiative on CLL, in 2018. Based on the current knowledge of the relevance of low-burden TP53-mutated clones, a specific variant allele frequency (VAF) cut-off for reporting TP53 mutations is no longer recommended, but instead, the need for thorough method validation by the reporting laboratory is emphasized. The result of TP53 analyses should always be interpreted within the context of available laboratory and clinical information, treatment indication, and therapeutic options. Methodological aspects of introducing next-generation sequencing (NGS) in routine practice are discussed with a focus on reliable detection of low-burden clones. Furthermore, potential interpretation challenges are presented, and a simplified algorithm for the classification of TP53 variants in CLL is provided, representing a consensus based on previously published guidelines. Finally, the reporting requirements are highlighted, including a template for clinical reports of TP53 aberrations. These recommendations are intended to assist diagnosticians in the correct assessment of TP53 mutation status, but also physicians in the appropriate understanding of the lab reports, thus decreasing the risk of misinterpretation and incorrect management of patients in routine practice whilst also leading to improved stratification of patients with CLL in clinical trials.

Introduction Due to disease- and treatment-related immune defects, patients with chronic lymphocytic leukemia (CLL) have an increased risk of severe disease and death from COVID-19, as well as impaired responses to SARS-CoV-2 vaccination. Thus, we performed a retrospective nationwide analysis on the risk of severe disease and death in individuals with CLL compared to matched controls without CLL in Sweden during the first 3 years of the COVID-19 pandemic in Sweden, using multiple national and population-based registers. The impact of vaccination status and specific CLL directed therapies on outcome, during different phases of the pandemic was also studied. Methods We conducted a nationwide cohort study considering all SARS-CoV-2 infection episodes (>90 days between positive PCR tests) from individuals born 1930-2003, residing in Sweden from 1 February 2020 to 31 March 2023. Data from multiple nationwide registers with high coverage (including, but not limited to, the Total Population Register, the National Cause of Death Register, the National Vaccination Register and the INCA CLL register) were used. An infection episode was classified as exposed to CLL when a CLL diagnosis was registered any time before and up until 90 days after the positive PCR test. Each exposed episode was matched to an unexposed episode using a combination of exact and propensity score-based matching without replacement. Exact matching included age category, sex, born in Sweden, residential region, infection episode number, calendar month of positive PCR test, and SARS-CoV-2 variant. Propensity score matching included calendar week, age, and more detailed information on region of birth and residential region. Primary outcome was 90-day all-cause mortality, and secondary outcomes were 90-day COVID-19 mortality, COVID-19 hospital admission and ICU admission. Standardized mean difference (SMD) was used to assess balance before and after matching. Risk ratios (RRs) adjusted for matching factors as well as income quartile, education level, COVID-19 vaccination status, and comorbidities (based on prescription drug use) were calculated using modified Poisson regression with confidence intervals (CIs) derived from a sandwich variance estimator. Results From a population of 8,275,839 individuals (6,653 with CLL, 8,269,186 without CLL), 2,088,163 first infection episodes (1,289 CLL, 2,086,874 no CLL) and 140,041 subsequent infection episodes (83 CLL, 139,958 no CLL) were identified. From these, 1,369 episodes from individuals with CLL were matched to the same number of controls. The matching removed substantial differences observed in age, sex, region of birth, and SARS-CoV-2 variant. After matching, SMD values >0.1 were only observed for education level, immunosuppressive drug use, and COVID-19 vaccination status. The 90-day all-cause mortality was 15% (n=199) in individuals with CLL and 8% (n=113) in controls, of which 63% (n=126) and 47% (n=53) had a COVID-19 diagnosis as main cause of death. The adjusted RR (95% CI) was 1.71 (1.38-2.11) for CLL compared with controls. The 90-day all-cause mortality rate in CLL was 25% (64/258) for Wild-type, 12% (23/194) for Alpha/Delta, and 12% (112/916) for Omicron. The adjusted RRs (95% CIs) for Wild-type, Alpha/Delta, and Omicron were 1.79 (1.26-2.54), 2.17 (1.08-4.33), and 1.59 (1.19-2.12). The adjusted RR (95% CI) was 1.64 (1.21-2.24) for unvaccinated, 1.57 (1.17-2.10) for >2 doses, 1.59 (1.16-2.18) for >3 doses, and 1.97 (1.21-3.20) for >4 doses. The adjusted RR (95% CI) was 2.41 (1.79-3.24) when restricting analyses to 90-day COVID-19 mortality. Risks were also significantly increased for COVID-19 hospital admission and ICU admission. When including all 2,228,204 episodes, the adjusted RR (95% CI) was 1.68 (1.48-1.90), similar to the matched cohort analysis. Conclusions SARS-CoV-2 infected individuals with CLL had a 2.4 times higher 90-day all-cause mortality, COVID-19 hospital and ICU admission compared with matched controls. This increased risk remained throughout different SARS-CoV-2 variant periods, reinforcing the importance of sustained efforts to protect this frail patient population from infection also during the endemic phase of COVID-19. However, the consistent RR of death compared to controls through different vaccination statuses indicates a benefit in protection from death in individuals with CLL similar to that seen in controls.

Defining minimal standards for data collection is key to creating interoperative, searchable genomic and clinical databases. We highlight here the 1+Million Genomes Minimal Dataset for Cancer, encompassing 140 items in 8 domains to foster the collection of cancer data, inform transnational cooperation and advance precision cancer medicine.

AIMS AND BACKGROUND:Whole-genome sequencing (WGS) is increasingly applied in clinical practice and expected to replace standard-of-care (SoC) genetic diagnostics in hematological malignancies. This study aims to assess and compare the fully burdened cost ('micro-costing') per patient for Swedish laboratories using WGS and SoC, respectively, in pediatric and adult patients with acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). METHODS:The resource use and cost details associated with SoC, e.g. chromosome banding analysis, fluorescent in situ hybridization, and targeted sequencing analysis, were collected via activity-based costing methods from four diagnostic laboratories. For WGS, corresponding data was collected from two of the centers. A simulation-based scenario model was developed for analyzing the WGS cost based on different annual sample throughput to evaluate economy of scale. RESULTS:The average SoC total cost per patient was €2,465 for pediatric AML and €2,201 for pediatric ALL, while in adults, the corresponding cost was €2,458 for AML and €1,207 for ALL. The average WGS cost (90x tumor/30x normal; sequenced on the Illumina NovaSeq 6000 platform) was estimated to €3,472 based on an annual throughput of 2,500 analyses, however, with an annual volume of 7,500 analyses the average cost would decrease by 23% to €2,671. CONCLUSION:In summary, WGS is currently more costly than SoC, however the cost can be reduced by utilizing laboratories with higher throughput and by the expected decline in cost of reagents. Our data provides guidance to decision-makers for the resource allocation needed when implementing WGS in diagnostics of hematological malignancies.