Optical Genome Mapping for Cytogenetic Diagnostics in AML

Nilius‐Eliliwi, Verena; Gerding, Wanda M.; Schroers, Roland; Nguyen, Huu Phuc; Vangala, Deepak B.

doi:10.3390/cancers15061684

Cited by 17 publications

(19 citation statements)

References 36 publications

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“…Around 20% of leukemic blasts are required for SNP‐array in a diagnostic setting for large CN alterations 34 , 35 . Our study and others 14 , 36 , 37 showed that OGM performance on samples with blast amounts of about 20%–30% could also detect alterations observed by conventional diagnostic methods. Hence, OGM could be an attractive option for routine diagnostic workup of hematological malignancies, as it has a fast turnaround time of ≈5 days from sample acquisition to data analysis.…”

Section: Discussionsupporting

confidence: 63%

Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood ETV6::RUNX1+ and High Hyperdiploid Acute Lymphoblastic Leukemia

et al. 2023

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The mutational landscape of B-cell precursor acute lymphoblastic leukemia (BCP-ALL), the most common pediatric cancer, is not fully described partially because commonly applied short-read next generation sequencing has a limited ability to identify structural variations. By combining comprehensive analysis of structural variants (SVs), single-nucleotide variants (SNVs), and small insertions-deletions, new subtype-defining and therapeutic targets may be detected. We analyzed the landscape of somatic alterations in 60 pediatric patients diagnosed with the most common BCP-ALL subtypes, ETV6::RUNX1+ and classical hyperdiploid (HD), using conventional cytogenetics, single nucleotide polymorphism (SNP) array, whole exome sequencing (WES), and the novel optical genome mapping (OGM) technique. Ninety-five percent of SVs detected by cytogenetics and SNP-array were verified by OGM. OGM detected an additional 677 SVs not identified using the conventional methods, including (subclonal) IKZF1 deletions. Based on OGM, ETV6::RUNX1+ BCP-ALL harbored 2.7 times more SVs than HD BCP-ALL, mainly focal deletions. Besides SVs in known leukemia development genes (ETV6, PAX5, BTG1, CDKN2A), we identified 19 novel recurrently altered regions (in n ≥ 3) including 9p21.3 (FOCAD/HACD4), 8p11.21 (IKBKB), 1p34.3 (ZMYM1), 4q24 (MANBA), 8p23.1 (MSRA), and 10p14 (SFMBT2), as well as ETV6::RUNX1+ subtype-specific SVs (12p13.1 (GPRC5A), 12q24.21 (MED13L), 18q11.2 (MIB1), 20q11.22 (NCOA6)). We detected 3 novel fusion genes (SFMBT2::DGKD, PDS5B::STAG2, and TDRD5::LPCAT2), for which the sequence and expression were validated by long-read and whole transcriptome sequencing, respectively. OGM and WES identified double hits of SVs and SNVs (ETV6, BTG1, STAG2, MANBA, TBL1XR1, NSD2) in the same patient demonstrating the power of the combined approach to define the landscape of genomic alterations in BCP-ALL.

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Section: Discussionsupporting

confidence: 63%

Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood ETV6::RUNX1+ and High Hyperdiploid Acute Lymphoblastic Leukemia

et al. 2023

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“…Ease of validation and implementation as well as genome-wide resolution and sensitivity in variant calling (≥5 kbp at low allele fraction from a heterogeneous DNA sample) are central considerations related to use of OGM in routine testing. To date, OGM has been successfully validated as a laboratory developed test in many laboratories worldwide, under a diverse set of regulatory bodies (Yang et al 2022, Rack et al 2022, Sahajpal et al 2022, Nilius-Eliliwi et al 2023). However, for achieving full benefits from this new technology, in addition to wet-lab processing and raw data analysis, variant review, interpretation, and reporting have to be streamlined and tailored to the needs of clinical laboratories.…”

Section: Introductionmentioning

confidence: 99%

“…To date, OGM has been successfully validated as a laboratory developed test in many laboratories worldwide, under a diverse set of regulatory bodies (Yang et al 2022, Rack et al 2022, Sahajpal et al 2022, Nilius-Eliliwi et al 2023. However, for achieving full benefits from this new technology, in addition to wet-lab processing and raw data analysis, variant review, in terpretation and reporting have to be streamlined and tailored to the needs of clinical laboratories.…”

Section: Introductionmentioning

confidence: 99%

Optical Genome Mapping improves detection and streamlines analysis of structural variants in myeloid neoplasms

Raca,

Sahoo,

Anwar Iqbal

et al. 2024

Preprint

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Accurate diagnosis and risk stratification of hematological malignancies require disease-specific laboratory testing procedures involving the use of hematopathology, flow cytometry, molecular, and cytogenetic testing. While individual laboratories develop unique workflows to accommodate volume, clinical needs, and staffing, cytogenetic laboratories generally require a multitude of targeted and genome-wide tests that detect clinically relevant aberrations in hematologic malignancies. Specifically, the frequent use of multiple FISH panels coupled with concurrent chromosome analysis, can be both labor, and resource intensive. Optical Genome Mapping (OGM) is a comprehensive cytogenetic solution for detecting structural variants with high resolution and increased accuracy for hematological malignancy subtypes at the DNA level without need of any cell culture regimens. A new software tool for analysis of OGM data called VIA (Variant Intelligence Applications), provides an integrative analysis, interpretation, and reporting solution for OGM and other datatypes. In this study, we performed retrospective review of 56 datasets, representing 10 unique myeloid cases to assess multi-user (technologist and laboratory director) analyses and classification. Interpretation and reporting of OGM results were 100% concordant between reviewers for four cases with negative results by standard of care (SOC) testing. For the other six cases, five pathognomonic gene fusions identified by SOC assays were unanimously reported as Tier 1A classification was unanimous for five sentinel gene fusion rearrangements identified by SOC. OGM also found additional structural variants of clinical relevance in five of the six cases that were not found by SOC methods. Leveraging automatic pre-classification of variants and a custom decision tree, the VIA software enabled complete analysis with a mean technologist review time (variant analysis and initial tier determination) of 30.7 minutes. The analysis, interpretation, and reporting workflow described in this pilot study provides a framework for standardized and streamlined reporting of clinically significant variant in myeloid malignancies using VIA.

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“…Unlike karyotyping, the analysis is based on the preparation of native high-molecular-weight DNA derived from the sample and is not influenced by the cell line cultivation and preparation method [ 10 ]. Thus, optical genome mapping not only enables the detection of most major structural rearrangements that can also be detected by karyotyping but also of minor variants that could be missed by other technologies on a genome-wide approach [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

Optical Genome Mapping Reveals Genomic Alterations upon Gene Editing in hiPSCs: Implications for Neural Tissue Differentiation and Brain Organoid Research

Gallego Villarejo,

Gerding,

Bachmann

et al. 2024

Cells

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Genome editing, notably CRISPR (cluster regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9), has revolutionized genetic engineering allowing for precise targeted modifications. This technique’s combination with human induced pluripotent stem cells (hiPSCs) is a particularly valuable tool in cerebral organoid (CO) research. In this study, CRISPR/Cas9-generated fluorescently labeled hiPSCs exhibited no significant morphological or growth rate differences compared with unedited controls. However, genomic aberrations during gene editing necessitate efficient genome integrity assessment methods. Optical genome mapping, a high-resolution genome-wide technique, revealed genomic alterations, including chromosomal copy number gain and losses affecting numerous genes. Despite these genomic alterations, hiPSCs retain their pluripotency and capacity to generate COs without major phenotypic changes but one edited cell line showed potential neuroectodermal differentiation impairment. Thus, this study highlights optical genome mapping in assessing genome integrity in CRISPR/Cas9-edited hiPSCs emphasizing the need for comprehensive integration of genomic and morphological analysis to ensure the robustness of hiPSC-based models in cerebral organoid research.

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Optical Genome Mapping for Cytogenetic Diagnostics in AML

Cited by 17 publications

References 36 publications

Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood ETV6::RUNX1+ and High Hyperdiploid Acute Lymphoblastic Leukemia

Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood ETV6::RUNX1+ and High Hyperdiploid Acute Lymphoblastic Leukemia

Optical Genome Mapping improves detection and streamlines analysis of structural variants in myeloid neoplasms

Optical Genome Mapping Reveals Genomic Alterations upon Gene Editing in hiPSCs: Implications for Neural Tissue Differentiation and Brain Organoid Research

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