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

HemaSphere, Journal Year: 2023, Volume and Issue: 7(8), P. e925 - e925

Published: July 17, 2023

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 variants (SVs), single-nucleotide (SNVs), and small insertions-deletions, new subtype-defining therapeutic targets may be detected. We analyzed somatic alterations in 60 patients diagnosed with BCP-ALL subtypes, ETV6::RUNX1 + classical hyperdiploid (HD), using conventional cytogenetics, single nucleotide polymorphism (SNP) array, whole exome (WES), novel optical genome mapping (OGM) technique. Ninety-five percent SVs detected by cytogenetics SNP-array were verified OGM. OGM an additional 677 identified methods, including (subclonal) IKZF1 deletions. Based on OGM, harbored 2.7 times more than HD BCP-ALL, mainly focal Besides known development genes ( ETV6 , PAX5 BTG1, CDKN2A ), we 19 recurrently altered regions (in n ≥ 3) 9p21.3 FOCAD/HACD4 8p11.21 IKBKB 1p34.3 ZMYM1 4q24 MANBA 8p23.1 MSRA 10p14 SFMBT2 as well ETV6::RUNX1+ subtype-specific (12p13.1 GPRC5A 12q24.21 MED13L 18q11.2 MIB1 20q11.22 NCOA6 )). 3 fusion SFMBT2::DGKD, PDS5B::STAG2, TDRD5::LPCAT2 for which sequence expression validated long-read transcriptome sequencing, respectively. WES double hits SNVs BTG1 STAG2 TBL1XR1 NSD2 ) same patient demonstrating power combined approach define genomic BCP-ALL.

Language: Английский

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Clinical Cytogenetics: Current Practices and Beyond

The Journal of Applied Laboratory Medicine, Journal Year: 2024, Volume and Issue: 9(1), P. 61 - 75

Published: Jan. 1, 2024

Abstract Background Throughout history, the field of cytogenetics has witnessed significant changes due to constant evolution technologies used assess chromosome number and structure. Similar single nucleotide variant detection from Sanger sequencing next-generation sequencing, identification alterations progressed banding fluorescence in situ hybridization (FISH) chromosomal microarrays. More recently, emerging such as optical genome mapping have made noteworthy contributions clinical laboratory testing cytogenetics. Content In this review, we journey through some most pivotal discoveries that shaped development testing. We also explore current test offerings, their uses limitations, future directions technology advancements. Summary Cytogenetics methods, including targeted assessments like FISH, continue hold crucial roles cytogenetic These methods offer a rapid turnaround time, especially for conditions with known etiology involving recognized aberrations. Additionally, laboratories flexibility now employ higher-throughput methodologies enhance resolution cases greater complexity.

Language: Английский

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Exome Sequencing and Optical Genome Mapping in Molecularly Unsolved Cases of Duchenne Muscular Dystrophy: Identification of a Causative X-Chromosomal Inversion Disrupting the DMD Gene

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(19), P. 14716 - 14716

Published: Sept. 28, 2023

Duchenne muscular dystrophy (DMD) is a severe progressive muscle disease that mainly affects boys due to X-linked recessive inheritance. In most affected individuals, MLPA or sequencing-based techniques detect deletions, duplications, point mutations in the dystrophin-encoding DMD gene. However, small subset of patients clinically diagnosed with DMD, molecular cause not identified these routine methods. Evaluation 60 our center revealed three cases without known genetic cause. DNA samples were analyzed using whole-exome sequencing (WES) and, if unconclusive, optical genome mapping (OGM). WES led diagnosis two cases: one patient was found carry splice mutation gene had been during previous Sanger sequencing. second patient, we detected variants fukutin (FKTN) presumed be disease-causing. third unremarkable, but OGM an inversion disrupting (~1.28 Mb) subsequently confirmed long-read These results highlight importance reanalyzing unsolved and demonstrate useful method for identifying large structural unremarkable exome

Language: Английский

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Novel NUP98::ASH1L Gene Fusion in Acute Myeloid Leukemia Detected by Optical Genome Mapping

Cancers, Journal Year: 2023, Volume and Issue: 15(11), P. 2942 - 2942

Published: May 27, 2023

Optical genome mapping (OGM) recently has demonstrated the potential to improve genetic diagnostics in acute myeloid leukemia (AML). In this study, OGM was utilized as a tool for detection of genome-wide structural variants and disease monitoring. A previously unrecognized NUP98::ASH1L fusion detected an adult patient with secondary AML. identified NUP98 Absent, Small, or Homeotic-Like Histone Lysine Methyltransferase (ASH1L) result complex rearrangement between chromosomes 1 11. pipeline measurement rare (Rare Variant Pipeline, Bionano Genomics, San Diego, CA, USA) used detection. As other fusions are relevant classification, demonstrates necessity methods such cytogenetic Furthermore, showed discordant variant allele frequencies at different time points over course treatment pressure, indicating clonal evolution. These results support be valuable primary AML well longitudinal testing monitoring deepening our understanding genetically heterogenous diseases.

Language: Английский

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OMKar: optical map based automated karyotyping of genomes to identify constitutional abnormalities

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 14, 2025

The whole genome karyotype refers to the sequence of large chromosomal segments that make up an individual's genotype. analysis, which includes descriptions aneuploidies and other rearrangements is crucial for understanding genetic risk factors, diagnosis, treatment decisions, counseling linked constitutional disorders. current karyotyping standard based on microscopic examination chromosomes, a complex process requires high expertise offers Mb scale resolution. Optical Genome Mapping (OGM) technology can identify DNA lesions in cost-effective manner. In this paper, we developed OMKar, method uses OGM data create virtual karyotype. OMKar processes Structural (SV) Copy Number (CN) Variants as inputs encodes them into compact breakpoint graph. It recomputes copy numbers using Integer Linear Programming maintain CN balance then identifies constrained Eulerian paths representing entire donor chromosomes. tests 38 simulations disorders, reconstructed with 88% precision 95% recall SV concordance Jaccard score concordance. We applied 50 prenatal, 41 postnatal, 63 parental samples from ten different sites. correct 144 out 154 samples, covering 25 aneuploidies, 32 balanced translocations, 72 82 unbalanced variations. Detected disorders included Cri-du-chat, Wolf-Hirschhorn, Prader-Willi deletions, Down, Turner syndromes. Importantly, it identified plausible mechanism five cases disorder were not detected by technologies. Together, these results demonstrate robustness OGM-based karyotyping. publicly available at https://github.com/siavashre/OMKar .

Language: Английский

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Clinical Utility of Optical Genome Mapping as an Additional Tool in a Standard Cytogenetic Workup in Hematological Malignancies

Cancers, Journal Year: 2025, Volume and Issue: 17(9), P. 1436 - 1436

Published: April 25, 2025

Background and Objective: The primary objective of this study is to evaluate the added value optical genome mapping (OGM) when integrated into standard cytogenetic workup (SCGW) for hematological malignancies. Methods: cohort comprised 519 cases with different types OGM SCGW (including G-banded karyotyping fluorescence in situ hybridization) were performed on blood and/or bone marrow. analytical sensitivity OGM, defined as detection all additional cytogenomic aberrations, its clinical utility, referring aberrations diagnostic, prognostic, or therapeutic significance, assessed. Results: led increased utility 58% 15% cases, respectively. varied across malignancies, highest T-lymphoblast leukemia (52%), followed by mixed phenotype acute (43%), B-lymphoblastic (37%), other B-cell lymphomas (22%), mature T-cell leukemia/lymphoma (20%), chronic lymphocytic (14%), myeloid (13%), multiple myeloma mantle cell lymphoma (8%), myelodysplastic/myeloproliferative neoplasms (6%), myelodysplastic syndrome (5%), myeloproliferative (0%). Conclusion: Compared SCGW, detects approximately cases. provides at varying rates Given these differences, strategic triaging can help maximize focusing diseases where it offers most significant benefit.

Language: Английский

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Integration of Optical Genome Mapping in the Cytogenomic and Molecular Work‐Up of Hematological Malignancies: Expert Recommendations From the International Consortium for Optical Genome Mapping

American Journal of Hematology, Journal Year: 2025, Volume and Issue: unknown

Published: April 30, 2025

ABSTRACT The latest updates to the classification of hematolymphoid malignancies using World Health Organization (WHO, 5th ed.) and ICC (International Consensus Classification) criteria highlight critical need for comprehensive precise cytogenomic data diagnosis, prognostication, treatment. This presents significant challenges clinical laboratories, requiring a complex workflow multiple assays detect different types structural chromosomal variants (copy number changes, fusions, inversions) across entire genome. Optical genome mapping (OGM) is an advanced tool genome‐wide detection alterations at gene/exon level. Studies demonstrate that OGM facilitates identification novel biomarkers, improves risk stratification, expands therapeutic targets personalized treatment strategies. easy implement highly accurate in detecting (SVs) various diagnostic entities. Consequently, many centers are integrating into cytogenetic hematological malignancies. However, systemic adoption has remained limited due lack expert recommendations on indications, testing algorithms, result interpretation. To address this, experts from International Consortium relevant multidisciplinary fields developed integration as standard‐of‐care assay settings. These standardize use ensure high‐quality data, guide trial design development, provide basis models.

Language: Английский

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Analytic Validation of Optical Genome Mapping in Hematological Malignancies

Biomedicines, Journal Year: 2023, Volume and Issue: 11(12), P. 3263 - 3263

Published: Dec. 9, 2023

Structural variations (SVs) play a key role in the pathogenicity of hematological malignancies. Standard-of-care (SOC) methods such as karyotyping and fluorescence situ hybridization (FISH), which have been employed globally for past three decades, significant limitations terms resolution number recurrent aberrations that can be simultaneously assessed, respectively. Next-generation sequencing (NGS)-based technologies are now widely used to detect clinically sequence variants but limited their ability accurately SVs. Optical genome mapping (OGM) is an emerging technology enabling genome-wide detection all classes SVs at significantly higher than FISH. OGM requires neither cultured cells nor amplification DNA, addressing culture biases. This study reports clinical validation laboratory-developed test (LDT) according stringent regulatory (CAP/CLIA) guidelines SV different In total, 60 cases with malignancies (of various subtypes), 18 controls, 2 cancer cell lines were this study. Ultra-high-molecular-weight DNA was extracted from samples, fluorescently labeled, run on Bionano Saphyr system. A total 215 datasets, Inc.luding replicates, generated, analyzed successfully. Sample data then using either disease-specific or pan-cancer-specific BED files prioritize calls known diagnostically prognostically relevant. Sensitivity, specificity, reproducibility 100%, 96%, Following validation, 14 10 controls outside laboratories showing 96.4%. found more relevant compared SOC testing due its resolution. The results demonstrate superiority over traditional accurate diagnosis

Language: Английский

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The Evolution of Treatment Policies and Outcomes for Patients Aged 60 and Older with Acute Myeloid Leukemia: A Population-Based Analysis over Two Decades

Cancers, Journal Year: 2024, Volume and Issue: 16(23), P. 3907 - 3907

Published: Nov. 21, 2024

Acute myeloid leukemia (AML) is a malignancy of the bone marrow with median age at diagnosis 70 years. AML difficult to treat, especially in older patients, among whom outcomes have historically been poor. Over last two decades, greater understanding molecular mechanisms pathology has led development new drugs and multiple updates treatment guidelines.

Language: Английский

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Clinical Utility of Optical Genome Mapping and 523-Gene Next Generation Sequencing Panel for Comprehensive Evaluation of Myeloid Cancers

Cancers, Journal Year: 2023, Volume and Issue: 15(12), P. 3214 - 3214

Published: June 16, 2023

The standard-of-care (SOC) for genomic testing of myeloid cancers primarily relies on karyotyping/fluorescent in situ hybridization (FISH) (cytogenetic analysis) and targeted gene panels (usually ≤54 genes) that harbor hotspot pathogenic variants (molecular genetic analysis). Despite this combinatorial approach, ~50% cancer genomes remain cytogenetically normal, the limited sequencing variant profiles obtained from are unable to resolve molecular etiology many tumors. In study, we evaluated performance clinical utility use optical genome mapping (OGM) a 523-gene next-generation (NGS) panel comprehensive profiling 30 tumors compared it SOC cytogenetic methods (karyotyping FISH) 54-gene NGS panel. OGM had an analytical concordance 100% with karyotyping, FISH, panel, respectively. Importantly, IPSS-R risk group changed very good/good poor 22% MDS (2/9) cases based (karyotyping, vs. panel), while additionally identifying six compound heterozygous events potential relevance (6/30, 20%). This cost-effective approach using demonstrated increased yield actionable targets can potentially result improved outcomes.

Language: Английский

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