European recommendations and quality assurance for cytogenomic analysis of haematological neoplasms

Rack, KA; Berg, Eva van den; Haferlach, Claudia; Beverloo, H. Berna; Costa, Dolors; Espinet, Blanca; Foot, Nicola; Jeffries, Sally; Martin, Kristy-Jane; O’Connor, Sheila J.M.; Schoumans, Jacqueline; Talley, Polly; Telford, Nick; Stioui, Sabine; Zemanová, Zuzana; Hastings, Ros

doi:10.1038/s41375-019-0378-z

Cited by 116 publications

(132 citation statements)

References 82 publications

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“…In our cohort, the number of pathogenic or likely pathogenic variants was two orders of magnitude smaller than the number of coding variants passing quality control (50 vs 1146). This drop highlights the importance of including expert geneticists familiar with hematological malignancies and NGS technology within the multidisciplinary genomic tumor board, as it has been suggested before [13] [83].…”

Section: Common Sequencing Errors Detected In the Ngs Panelsmentioning

confidence: 96%

“…A total of 32 patient bone marrow (BM) samples were accrued: 17 with AML, 7 with MPN, 6 with MDS, and 2 with CMML. BM was the tissue of choice for analysis following European recommendations [13] Samples and data from patients included in the study were provided by the Biobank of the University of Navarra (UN) and were processed following standard operating procedures approved by the CEI (Comité de Ética de la Investigación) of UN. Patient's data were fully anonymized, and all patients provided informed written consent to have data from their medical records such as age, gender and diagnosis to be used for research purposes.…”

Section: Patient Samplesmentioning

confidence: 99%

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Assessment of the clinical utility of four NGS panels in myeloid malignancies. Suggestions for NGS panel choice or design

et al. 2020

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The diagnosis of myeloid neoplasms (MN) has significantly evolved through the last few decades. Next Generation Sequencing (NGS) is gradually becoming an essential tool to help clinicians with disease management. To this end, most specialized genetic laboratories have implemented NGS panels targeting a number of different genes relevant to MN. The aim of the present study is to evaluate the performance of four different targeted NGS gene panels based on their technical features and clinical utility. A total of 32 patient bone marrow samples were accrued and sequenced with 3 commercially available panels and 1 custom panel. Variants were classified by two geneticists based on their clinical relevance in MN. There was a difference in panel's depth of coverage. We found 11 discordant clinically relevant variants between panels, with a trend to miss long insertions. Our data show that there is a high risk of finding different mutations depending on the panel of choice, due both to the panel design and the data analysis method. Of note, CEBPA, CALR and FLT3 genes, remains challenging the use of NGS for diagnosis of MN in compliance with current guidelines. Therefore, conventional molecular testing might need to be kept in place for the correct diagnosis of MN for now. OPEN ACCESS Citation: Aguilera-Diaz A, Vazquez I, Ariceta B, Mañú A, Blasco-Iturri Z, Palomino-Echeverría S, et al. (2020) Assessment of the clinical utility of four NGS panels in myeloid malignancies. Suggestions for NGS panel choice or design. PLoS ONE 15(1): e0227986. https://doi.org/10.

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Section: Common Sequencing Errors Detected In the Ngs Panelsmentioning

confidence: 96%

Section: Patient Samplesmentioning

confidence: 99%

Assessment of the clinical utility of four NGS panels in myeloid malignancies. Suggestions for NGS panel choice or design

et al. 2020

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“…Multiplexing samples from different diseases and using small‐scale sequencing systems can help reduce TAT. In real world scenario of diagnosis of MDS and CMML, these TAT should be consistent with other cytogenetic tests (karyotype and fluorescence in situ hybridisation), and should not exceed, for most cases, 15 working days (Rack et al , ). Urgent referrals should be prioritized and, for these cases, results should try to be reported within 10 days.…”

Section: Sequencing Workflow and Quality Criteriamentioning

confidence: 99%

Spanish Guidelines for the use of targeted deep sequencing in myelodysplastic syndromes and chronic myelomonocytic leukaemia

et al. 2019

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Summary The landscape of medical sequencing has rapidly changed with the evolution of next generation sequencing (NGS). These technologies have contributed to the molecular characterization of the myelodysplastic syndromes (MDS) and chronic myelomonocytic leukaemia (CMML), through the identification of recurrent gene mutations, which are present in >80% of patients. These mutations contribute to a better classification and risk stratification of the patients. Currently, clinical laboratories include NGS genomic analyses in their routine clinical practice, in an effort to personalize the diagnosis, prognosis and treatment of MDS and CMML. NGS technologies have reduced the cost of large‐scale sequencing, but there are additional challenges involving the clinical validation of these technologies, as continuous advances are constantly being made. In this context, it is of major importance to standardize the generation, analysis, clinical interpretation and reporting of NGS data. To that end, the Spanish MDS Group (GESMD) has expanded the present set of guidelines, aiming to establish common quality standards for the adequate implementation of NGS and clinical interpretation of the results, hoping that this effort will ultimately contribute to the benefit of patients with myeloid malignancies.

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“…Different clinical testing guidelines define when to use which test in different political and geographical regions. 4; 5 In our laboratory we use a combination of karyotyping and FISH for CML and lymphoma; karyotyping, FISH and CNV-microarray for AML and ALL; karyotyping and CNV-microarray for MDS and MPN; CNV-microarray for CLL; and FISH and CNV-microarray on CD138 enriched plasma cells for MM. Also of note, FISH represents multiple distinct tests, targeting different loci, that also vary for different clinical indications.…”

Section: Introductionmentioning

confidence: 99%

Next generation cytogenetics: comprehensive assessment of 48 leukemia genomes by genome imaging

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et al. 2020

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Somatic structural variants are important for cancer development and progression. In a diagnostic set-up, especially for hematological malignancies, the comprehensive analysis of all cytogenetic aberrations in a given sample still requires a combination of techniques, such as karyotyping, fluorescence in situ hybridization and CNV-microarrays. We hypothesize that the combination of these classical approaches could be replaced by high-resolution genome imaging.Bone marrow aspirates or blood samples derived from 48 patients with leukemia, who received a clinical diagnoses of different types of hematological malignancies, were processed for genome imaging with the Bionano Genomics Saphyr system. In all cases cytogenetic abnormalities had previously been identified using standard of care workflows. Based on these diagnostic results, the samples were divided into two categories: simple cases (<5 aberrations, n=37) and complex cases (≥5 aberrations or an unspecified marker chromosome, n=11). By imaging the labelled ultra-long gDNA molecules (average N50 >250kb), we generated on average ∼280-fold mapped genome coverage per sample. Chromosomal aberrations were called by Bionano Genomics Rare variant pipeline (RVP) specialized for the detections of somatic variants.Per sample, on average a total of 1,454 high confidence SVs were called, and on average 44 (range: 14-130) of those were rare i.e. not present in the population control database. Importantly, for the simple cases, all clinically reported aberrations with variant allele frequencies higher than 10% were detected by genome imaging. This held true for deletions, insertions, inversions, aneuploidies and translocations. The results for the complex cases were also largely concordant between the standard of care workflow and optical mapping, and in several cases, optical mapping revealed higher complexity than previously known. SV and CNV calls detected by optical mapping were more complete than any other previous single test and likely delivered the most accurate and complete underlying genomic architecture. Even complex chromothripsis structures were resolved. Finally, optical mapping also identified multiple novel events, including balanced translocations that lead to potential novel fusion-genes, opening the potential to discover new prognostic and diagnostic biomarkers.The full concordance with diagnostic standard assays for simple cases and the overall great concordance with (previously likely incompletely understood) complex cases demonstrates the potential to replace classical cytogenetic tests with genome imaging. In addition, this holds the potential to rapidly map new fusion genes and identify novel SVs and CNVs as novel potential leukemia drivers.

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European recommendations and quality assurance for cytogenomic analysis of haematological neoplasms

Cited by 116 publications

References 82 publications

Assessment of the clinical utility of four NGS panels in myeloid malignancies. Suggestions for NGS panel choice or design

Assessment of the clinical utility of four NGS panels in myeloid malignancies. Suggestions for NGS panel choice or design

Spanish Guidelines for the use of targeted deep sequencing in myelodysplastic syndromes and chronic myelomonocytic leukaemia

Next generation cytogenetics: comprehensive assessment of 48 leukemia genomes by genome imaging

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