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Lee ST. Application of Optical Genome Mapping to the Genetic Diagnosis of Facioscapulohumeral Muscular Dystrophy 1. Ann Lab Med 2024; 44:383-384. [PMID: 38845487 PMCID: PMC11169772 DOI: 10.3343/alm.2024.0197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Affiliation(s)
- Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
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Zou YS, Klausner M, Ghabrial J, Stinnett V, Long P, Morsberger L, Murry JB, Beierl K, Gocke CD, Xian RR, Toomer KH, Ye JC, Orlowski RZ, Huff CA, Ali SA, Imus PH, Gocke CB, Tang G. A comprehensive approach to evaluate genetic abnormalities in multiple myeloma using optical genome mapping. Blood Cancer J 2024; 14:78. [PMID: 38702349 PMCID: PMC11068911 DOI: 10.1038/s41408-024-01059-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Affiliation(s)
- Ying S Zou
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Melanie Klausner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jen Ghabrial
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Victoria Stinnett
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Patty Long
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Laura Morsberger
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jaclyn B Murry
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Katie Beierl
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rena R Xian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kevin H Toomer
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jing Christine Ye
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Robert Z Orlowski
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Carol Ann Huff
- Department of Oncology, The Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Syed Abbas Ali
- Department of Oncology, The Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Philip H Imus
- Department of Oncology, The Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christian B Gocke
- Department of Oncology, The Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 6565 MD Anderson Blvd, Houston, TX, 77030, USA
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Finlay D, Murad R, Hong K, Lee J, Pang AWC, Lai CY, Clifford B, Burian C, Mason J, Hastie AR, Yin J, Vuori K. Detection of Genomic Structural Variations Associated with Drug Sensitivity and Resistance in Acute Leukemia. Cancers (Basel) 2024; 16:418. [PMID: 38254907 PMCID: PMC10814465 DOI: 10.3390/cancers16020418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Acute leukemia is a particularly problematic collection of hematological cancers, and, while somewhat rare, the survival rate of patients is typically abysmal without bone marrow transplantation. Furthermore, traditional chemotherapies used as standard-of-care for patients cause significant side effects. Understanding the evolution of leukemia to identify novel targets and, therefore, drug treatment regimens is a significant medical need. Genomic rearrangements and other structural variations (SVs) have long been known to be causative and pathogenic in multiple types of cancer, including leukemia. These SVs may be involved in cancer initiation, progression, clonal evolution, and drug resistance, and a better understanding of SVs from individual patients may help guide therapeutic options. Here, we show the utilization of optical genome mapping (OGM) to detect known and novel SVs in the samples of patients with leukemia. Importantly, this technology provides an unprecedented level of granularity and quantitation unavailable to other current techniques and allows for the unbiased detection of novel SVs, which may be relevant to disease pathogenesis and/or drug resistance. Coupled with the chemosensitivities of these samples to FDA-approved oncology drugs, we show how an impartial integrative analysis of these diverse datasets can be used to associate the detected genomic rearrangements with multiple drug sensitivity profiles. Indeed, an insertion in the gene MUSK is shown to be associated with increased sensitivity to the clinically relevant agent Idarubicin, while partial tandem duplication events in the KMT2A gene are related to the efficacy of another frontline treatment, Cytarabine.
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Affiliation(s)
- Darren Finlay
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (R.M.)
| | - Rabi Murad
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (R.M.)
| | - Karl Hong
- Bionano Genomics Inc., San Diego, CA 92121, USA
| | - Joyce Lee
- Bionano Genomics Inc., San Diego, CA 92121, USA
| | | | - Chi-Yu Lai
- Bionano Genomics Inc., San Diego, CA 92121, USA
| | | | | | - James Mason
- Scripps MD Anderson, La Jolla, CA 92037, USA
| | | | - Jun Yin
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (R.M.)
| | - Kristiina Vuori
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (R.M.)
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Pang AWC, Kosco K, Sahajpal NS, Sridhar A, Hauenstein J, Clifford B, Estabrook J, Chitsazan AD, Sahoo T, Iqbal A, Kolhe R, Raca G, Hastie AR, Chaubey A. Analytic Validation of Optical Genome Mapping in Hematological Malignancies. Biomedicines 2023; 11:3263. [PMID: 38137484 PMCID: PMC10741484 DOI: 10.3390/biomedicines11123263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/23/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Structural variations (SVs) play a key role in the pathogenicity of hematological malignancies. Standard-of-care (SOC) methods such as karyotyping and fluorescence in situ hybridization (FISH), which have been employed globally for the past three decades, have significant limitations in terms of resolution and the number of recurrent aberrations that can be simultaneously assessed, respectively. Next-generation sequencing (NGS)-based technologies are now widely used to detect clinically significant sequence variants but are limited in their ability to accurately detect SVs. Optical genome mapping (OGM) is an emerging technology enabling the genome-wide detection of all classes of SVs at a significantly higher resolution than karyotyping and FISH. OGM requires neither cultured cells nor amplification of DNA, addressing the limitations of culture and amplification biases. This study reports the clinical validation of OGM as a laboratory-developed test (LDT) according to stringent regulatory (CAP/CLIA) guidelines for genome-wide SV detection in different hematological malignancies. In total, 60 cases with hematological malignancies (of various subtypes), 18 controls, and 2 cancer cell lines were used for this study. Ultra-high-molecular-weight DNA was extracted from the samples, fluorescently labeled, and run on the Bionano Saphyr system. A total of 215 datasets, Inc.luding replicates, were generated, and analyzed successfully. Sample data were then analyzed using either disease-specific or pan-cancer-specific BED files to prioritize calls that are known to be diagnostically or prognostically relevant. Sensitivity, specificity, and reproducibility were 100%, 100%, and 96%, respectively. Following the validation, 14 cases and 10 controls were run and analyzed using OGM at three outside laboratories showing reproducibility of 96.4%. OGM found more clinically relevant SVs compared to SOC testing due to its ability to detect all classes of SVs at higher resolution. The results of this validation study demonstrate the superiority of OGM over traditional SOC methods for the detection of SVs for the accurate diagnosis of various hematological malignancies.
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Affiliation(s)
| | | | - Nikhil S. Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | | | | | | | | | | | | | - Anwar Iqbal
- DNA Microarray CGH Laboratory, Department of Pathology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, USA
| | - Alex R. Hastie
- Bionano, San Diego, CA 92121, USA; (A.W.C.P.)
- Bionano Laboratories, San Diego, CA 92121, USA
| | - Alka Chaubey
- Bionano, San Diego, CA 92121, USA; (A.W.C.P.)
- Bionano Laboratories, San Diego, CA 92121, USA
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