A Study Protocol for Validation and Implementation of Whole-Genome and -Transcriptome Sequencing as a Comprehensive Precision Diagnostic Test in Acute Leukemias

Berglund, Eva; Barbany, Gisela; Orsmark-Pietras, Christina; Fogelstrand, Linda; Abrahamsson, Jonas; Golovleva, Irina; Hallböök, Heléne; Höglund, Martin; Lazarević, Vladimir; Levin, Lars‐Åke; Nordlund, Jessica; Norén‐Nyström, Ulrika; Palle, Josefine; Thangavelu, Tharshini; Palmqvist, Lars; Wirta, Valtteri; Cavelier, Lucia; Fioretos, Thoas; Rosenquist, Richard

doi:10.3389/fmed.2022.842507

Cited by 19 publications

(19 citation statements)

References 22 publications

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“…are being addressed [18,19]. Indeed, some national healthcare providers, such as the NHS Genomic Medicine Service and Genomic Medicine, Sweden, are offering WGS as a genetic test for haematological and other paediatric malignancies [20]. To date, WGS has been used to explore the genomic landscape of B-ALL subtyped by WTS [17].…”

Section: Introductionmentioning

confidence: 99%

Whole genome sequencing provides comprehensive genetic testing in childhood B-cell acute lymphoblastic leukaemia

et al. 2023

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Childhood B-cell acute lymphoblastic leukaemia (B-ALL) is characterised by recurrent genetic abnormalities that drive risk-directed treatment strategies. Using current techniques, accurate detection of such aberrations can be challenging, due to the rapidly expanding list of key genetic abnormalities. Whole genome sequencing (WGS) has the potential to improve genetic testing, but requires comprehensive validation. We performed WGS on 210 childhood B-ALL samples annotated with clinical and genetic data. We devised a molecular classification system to subtype these patients based on identification of key genetic changes in tumour-normal and tumour-only analyses. This approach detected 294 subtype-defining genetic abnormalities in 96% (202/210) patients. Novel genetic variants, including fusions involving genes in the MAP kinase pathway, were identified. WGS results were concordant with standard-of-care methods and whole transcriptome sequencing (WTS). We expanded the catalogue of genetic profiles that reliably classify PAX5alt and ETV6::RUNX1-like subtypes. Our novel bioinformatic pipeline improved detection of DUX4 rearrangements (DUX4-r): a good-risk B-ALL subtype with high survival rates. Overall, we have validated that WGS provides a standalone, reliable genetic test to detect all subtype-defining genetic abnormalities in B-ALL, accurately classifying patients for the risk-directed treatment stratification, while simultaneously performing as a research tool to identify novel disease biomarkers.

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Section: Introductionmentioning

confidence: 99%

Whole genome sequencing provides comprehensive genetic testing in childhood B-cell acute lymphoblastic leukaemia

et al. 2023

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“…18,19 Indeed, some national healthcare providers, such as the NHS Genomic Medicine Service and Genomic Medicine, Sweden, are offering WGS as a genetic test for haematological and other paediatric malignancies. 20 To date, WGS has been used to explore the genomic landscape of B-ALL subtyped by WTS. 17 A comparable DNA-based molecular schema for subtyping with comprehensive validation of WGS as a standalone diagnostic tool in B-ALL has not been performed.…”

Section: Introductionmentioning

confidence: 99%

Whole genome sequencing provides comprehensive genetic testing in childhood B-cell acute lymphoblastic leukaemia

Ryan

Peden

Kingsbury

et al. 2022

Preprint

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Childhood B-cell acute lymphoblastic leukaemia (B-ALL) is characterised by recurrent genetic abnormalities that drive risk-directed treatment strategies. Using current techniques, accurate detection of such aberrations is challenging, due to the rapidly expanding list of key genetic abnormalities. Whole genome sequencing (WGS) has the potential to revolutionise genetic testing, but requires comprehensive validation. We performed WGS on 210 childhood B-ALL samples annotated with clinical and genetic data. We devised a molecular classification system to subtype these patients based on identification of key genetic changes in tumour-normal and tumour-only analyses. This approach detected 294 subtype-defining genetic abnormalities in 96% (202/210) patients. Novel genetic variants, including fusions involving genes in the MAP kinase pathway, were identified. There was excellent concordance with standard-of-care methods and whole transcriptome sequencing (WTS). We expanded the catalogue of genetic profiles that reliably classify PAX5alt and ETV6::RUNX1-like subtypes. Our novel bioinformatic pipeline improved detection of DUX4 rearrangements (DUX4-r). We defined the excellent survival rates of DUX4-r and ETV6::RUNX1-like subtypes. Overall, we comprehensively validated that WGS provides a standalone, reliable genetic test to detect all subtype-defining genetic abnormalities in B-ALL, accurately classifying patients for risk-directed treatment stratification, while simultaneously performing as an excellent research tool to identify novel disease biomarkers.

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“…Compared with the standard of care multi-testing, WGS/WTS performed equally well or better in identifying clinically relevant genetic aberrations in acute leukemia patients and changed the risk classification in a proportion of cases ( 15 , 41 ). Within Genomic Medicine Sweden, a national study evaluating WGS and WTS in acute leukemia diagnostics is ongoing, with the ultimate aim to replace the standard of care methods ( 42 , 43 ). With decreasing sequencing costs, these types of studies will hopefully provide the required impetus to gradually implement these powerful techniques in the diagnostic setting.…”

Section: Discussionmentioning

confidence: 99%

Patient-Specific Assays Based on Whole-Genome Sequencing Data to Measure Residual Disease in Children With Acute Lymphoblastic Leukemia: A Proof of Concept Study

et al. 2022

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Risk-adapted treatment in acute lymphoblastic leukemia (ALL) relies on genetic information and measurable residual disease (MRD) monitoring. In this proof of concept study, DNA from diagnostic bone marrow (BM) of six children with ALL, without stratifying genetics or central nervous system (CNS) involvement, underwent whole-genome sequencing (WGS) to identify structural variants (SVs) in the leukemic blasts. Unique sequences generated by SVs were targeted with patient-specific droplet digital PCR (ddPCR) assays. Genomic DNA (gDNA) from BM and cell-free DNA (cfDNA) from plasma and cerebrospinal fluid (CSF) were analyzed longitudinally. WGS with 30× coverage enabled target identification in all cases. Limit of quantifiability (LoQ) and limit of detection (LoD) for the ddPCR assays (n = 15) were up to 10−5 and 10−6, respectively. All targets were readily detectable in a multiplexed ddPCR with minimal DNA input (1 ng of gDNA) at a 10−1 dilution, and targets for half of the patients were also detectable at a 10−2 dilution. The level of MRD in BM at end of induction and end of consolidation block 1 was in a comparable range between ddPCR and clinical routine methods for samples with detectable residual disease, although our approach consistently detected higher MRD values for patients with B-cell precursor ALL. Additionally, several samples with undetectable MRD by flow cytometry were MRD-positive by ddPCR. In plasma, the level of leukemic targets decreased in cfDNA over time following the MRD level detected in BM. cfDNA was successfully extracted from all diagnostic CSF samples (n = 6), and leukemic targets were detected in half of these. The results suggest that our approach to design molecular assays, together with ddPCR quantification, is a technically feasible option for accurate MRD quantification and that cfDNA may contribute valuable information regarding MRD and low-grade CNS involvement.

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A Study Protocol for Validation and Implementation of Whole-Genome and -Transcriptome Sequencing as a Comprehensive Precision Diagnostic Test in Acute Leukemias

Cited by 19 publications

References 22 publications

Whole genome sequencing provides comprehensive genetic testing in childhood B-cell acute lymphoblastic leukaemia

Whole genome sequencing provides comprehensive genetic testing in childhood B-cell acute lymphoblastic leukaemia

Whole genome sequencing provides comprehensive genetic testing in childhood B-cell acute lymphoblastic leukaemia

Patient-Specific Assays Based on Whole-Genome Sequencing Data to Measure Residual Disease in Children With Acute Lymphoblastic Leukemia: A Proof of Concept Study

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