1
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Ghabrial J, Stinnett V, Ribeiro E, Klausner M, Morsberger L, Long P, Middlezong W, Xian R, Gocke C, Lin MT, Rooper L, Baraban E, Argani P, Pallavajjala A, Murry JB, Gross JM, Zou YS. Diagnostic and Prognostic/Therapeutic Significance of Comprehensive Analysis of Bone and Soft Tissue Tumors Using Optical Genome Mapping and Next-generation Sequencing. Mod Pathol 2024:100684. [PMID: 39675429 DOI: 10.1016/j.modpat.2024.100684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 11/05/2024] [Accepted: 11/27/2024] [Indexed: 12/17/2024]
Abstract
Detecting somatic structural variants (SVs), copy number variants (CNVs), and mutations in bone and soft tissue tumors is essential for accurately diagnosing, treating, and prognosticating outcomes. Optical genome mapping (OGM) holds promise to yield useful data on SVs and CNVs but requires fresh or snap-frozen tissue. This study aimed to evaluate the clinical utility of data from OGM compared to current standard-of-care cytogenetic testing. We evaluated 60 consecutive specimens from bone and soft tissue tumors using OGM and karyotyping, FISH, gene fusion assays, and deep next-generation sequencing (NGS). OGM accurately identified diagnostic SVs/CNVs previously detected by karyotyping and FISH (specificity=100%). OGM identified diagnostic and pathogenic SVs/CNVs (∼23% of cases) undetected by karyotyping (cryptic/submicroscopic). OGM allowed detection and further characterization of complex structural rearrangements including chromoanagenesis (27% of cases) and complex 3-6-way translocations (15% of cases). In addition to identifying 321 SVs and CNVs among cases with chromoanagenesis events, OGM identified approximately 9 SVs and 12 CNVs per sample. A combination of OGM and deep NGS data identified diagnostic and pathogenic SVs, CNVs, and mutations in ∼98% of cases. Our cohort contained the most extensive collection of bone and soft tissue tumors profiled by OGM. OGM had excellent concordance with standard-of-care cytogenetic testing, detecting and assigning high-resolution genome-wide genomic abnormalities with higher sensitivity than routine testing. This is the first and largest study to provide insights into the clinical utility of combined OGM and deep sequencing for the pathologic diagnosis and potential prognostication of bone and soft tissue tumors in routine clinical practice.
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Affiliation(s)
- 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
| | - Efrain Ribeiro
- 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
| | - Laura Morsberger
- 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
| | | | - Rena Xian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ming-Tseh Lin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lisa Rooper
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ezra Baraban
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pedram Argani
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aparna Pallavajjala
- 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
| | - John M Gross
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Ying S Zou
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Dan A, Burtavel LM, Coman MC, Focsa IO, Duta-Ion S, Juganaru IR, Zaruha AG, Codreanu PC, Strugari IM, Hotinceanu IA, Bohiltea LC, Radoi VE. Genetic Blueprints in Lung Cancer: Foundations for Targeted Therapies. Cancers (Basel) 2024; 16:4048. [PMID: 39682234 DOI: 10.3390/cancers16234048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 11/17/2024] [Accepted: 11/30/2024] [Indexed: 12/18/2024] Open
Abstract
Lung cancer, a malignant neoplasm originating from the epithelial cells of the lung, is characterized by its aggressive growth and poor prognosis, making it a leading cause of cancer-related mortality globally [...].
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Affiliation(s)
- Andra Dan
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Livia-Malina Burtavel
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Madalin-Codrut Coman
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Ina-Ofelia Focsa
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Simona Duta-Ion
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Ioana-Ruxandra Juganaru
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Andra-Giorgiana Zaruha
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Patricia-Christina Codreanu
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Irina-Maria Strugari
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Iulian-Andrei Hotinceanu
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Laurentiu-Camil Bohiltea
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- "Alessandrescu-Rusescu" National Institute for Maternal and Child Health, 20382 Bucharest, Romania
| | - Viorica-Elena Radoi
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- "Alessandrescu-Rusescu" National Institute for Maternal and Child Health, 20382 Bucharest, Romania
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3
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Budurlean L, Tukaramrao DB, Zhang L, Dovat S, Broach J. Integrating Optical Genome Mapping and Whole Genome Sequencing in Somatic Structural Variant Detection. J Pers Med 2024; 14:291. [PMID: 38541033 PMCID: PMC10971281 DOI: 10.3390/jpm14030291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 04/10/2024] Open
Abstract
Structural variants drive tumorigenesis by disrupting normal gene function through insertions, inversions, translocations, and copy number changes, including deletions and duplications. Detecting structural variants is crucial for revealing their roles in tumor development, clinical outcomes, and personalized therapy. Presently, most studies rely on short-read data from next-generation sequencing that aligns back to a reference genome to determine if and, if so, where a structural variant occurs. However, structural variant discovery by short-read sequencing is challenging, primarily because of the difficulty in mapping regions of repetitive sequences. Optical genome mapping (OGM) is a recent technology used for imaging and assembling long DNA strands to detect structural variations. To capture the structural variant landscape more thoroughly in the human genome, we developed an integrated pipeline that combines Bionano OGM and Illumina whole-genome sequencing and applied it to samples from 29 pediatric B-ALL patients. The addition of OGM allowed us to identify 511 deletions, 506 insertions, 93 duplications/gains, and 145 translocations that were otherwise missed in the short-read data. Moreover, we identified several novel gene fusions, the expression of which was confirmed by RNA sequencing. Our results highlight the benefit of integrating OGM and short-read detection methods to obtain a comprehensive analysis of genetic variation that can aid in clinical diagnosis, provide new therapeutic targets, and improve personalized medicine in cancers driven by structural variation.
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Affiliation(s)
- Laura Budurlean
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | | | - Lijun Zhang
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sinisa Dovat
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
- Department of Pediatrics, Penn State Cancer Institute, Hershey, PA 17033, USA
| | - James Broach
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
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4
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Barford RG, Whittle E, Weir L, Fong FC, Goodman A, Hartley HE, Allinson LM, Tweddle DA. Use of Optical Genome Mapping to Detect Structural Variants in Neuroblastoma. Cancers (Basel) 2023; 15:5233. [PMID: 37958407 PMCID: PMC10647738 DOI: 10.3390/cancers15215233] [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: 09/25/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Neuroblastoma is the most common extracranial solid tumour in children, accounting for 15% of paediatric cancer deaths. Multiple genetic abnormalities have been identified as prognostically significant in neuroblastoma patients. Optical genome mapping (OGM) is a novel cytogenetic technique used to detect structural variants, which has not previously been tested in neuroblastoma. We used OGM to identify copy number and structural variants (SVs) in neuroblastoma which may have been missed by standard cytogenetic techniques. METHODS Five neuroblastoma cell lines (SH-SY5Y, NBLW, GI-ME-N, NB1691 and SK-N-BE2(C)) and two neuroblastoma tumours were analysed using OGM with the Bionano Saphyr® instrument. The results were analysed using Bionano Access software and compared to previous genetic analyses including G-band karyotyping, FISH (fluorescent in situ hybridisation), single-nucleotide polymorphism (SNP) array and RNA fusion panels for cell lines, and SNP arrays and whole genome sequencing (WGS) for tumours. RESULTS OGM detected copy number abnormalities found using previous methods and provided estimates for absolute copy numbers of amplified genes. OGM identified novel SVs, including fusion genes in two cell lines of potential clinical significance. CONCLUSIONS OGM can reliably detect clinically significant structural and copy number variations in a single test. OGM may prove to be more time- and cost-effective than current standard cytogenetic techniques for neuroblastoma.
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Affiliation(s)
- Ruby G. Barford
- Wolfson Childhood Cancer Research Centre, Translational & Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (R.G.B.); (F.C.F.); (H.E.H.); (L.M.A.)
| | - Emily Whittle
- Newcastle Genetics Laboratory, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne NE1 3BZ, UK; (E.W.); (L.W.); (A.G.)
| | - Laura Weir
- Newcastle Genetics Laboratory, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne NE1 3BZ, UK; (E.W.); (L.W.); (A.G.)
| | - Fang Chyi Fong
- Wolfson Childhood Cancer Research Centre, Translational & Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (R.G.B.); (F.C.F.); (H.E.H.); (L.M.A.)
| | - Angharad Goodman
- Newcastle Genetics Laboratory, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne NE1 3BZ, UK; (E.W.); (L.W.); (A.G.)
| | - Hannah E. Hartley
- Wolfson Childhood Cancer Research Centre, Translational & Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (R.G.B.); (F.C.F.); (H.E.H.); (L.M.A.)
| | - Lisa M. Allinson
- Wolfson Childhood Cancer Research Centre, Translational & Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (R.G.B.); (F.C.F.); (H.E.H.); (L.M.A.)
| | - Deborah A. Tweddle
- Wolfson Childhood Cancer Research Centre, Translational & Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (R.G.B.); (F.C.F.); (H.E.H.); (L.M.A.)
- Great North Children’s Hospital, Newcastle upon Tyne NE1 4LP, UK
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5
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Shi S, Huang P, Yan R, Li R. Identification of complex and cryptic chromosomal rearrangements by optical genome mapping. Mol Cytogenet 2023; 16:5. [PMID: 37101225 PMCID: PMC10134526 DOI: 10.1186/s13039-023-00636-2] [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: 12/11/2022] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Optical genome mapping (OGM) has developed into a highly promising method for detecting structural variants (SVs) in human genomes. Complex chromosomal rearrangements (CCRs) and cryptic translocations are rare events that are considered difficult to detect by routine cytogenetic methods. In this study, OGM was applied to delineate the precise chromosomal rearrangements in three cases with uncertain or unconfirmed CCRs detected by conventional karyotyping and one case with a cryptic translocation suggested by fetal chromosomal microarray analysis (CMA). RESULTS In the three cases with CCRs, OGM not only confirmed or revised the original karyotyping results but also refined the precise chromosomal structures. In the case with a suspected translocation not detected by karyotyping, OGM efficiently identified the cryptic translocation and defined the genomic breakpoints with relatively high accuracy. CONCLUSIONS Our study confirmed OGM as a robust alternative approach to karyotyping for the detection of chromosomal structural rearrangements, including CCRs and cryptic translocations.
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Affiliation(s)
- Shanshan Shi
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Jinan University, No. 613 Huangpu West Road, Guangzhou, 510630, People's Republic of China
| | - Peizhi Huang
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ruiling Yan
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Jinan University, No. 613 Huangpu West Road, Guangzhou, 510630, People's Republic of China.
| | - Ruiman Li
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Jinan University, No. 613 Huangpu West Road, Guangzhou, 510630, People's Republic of China.
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6
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Levy B, Baughn LB, Akkari Y, Chartrand S, LaBarge B, Claxton D, Lennon PA, Cujar C, Kolhe R, Kroeger K, Pitel B, Sahajpal N, Sathanoori M, Vlad G, Zhang L, Fang M, Kanagal-Shamanna R, Broach JR. Optical genome mapping in acute myeloid leukemia: a multicenter evaluation. Blood Adv 2023; 7:1297-1307. [PMID: 36417763 PMCID: PMC10119592 DOI: 10.1182/bloodadvances.2022007583] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/25/2022] Open
Abstract
Detection of hallmark genomic aberrations in acute myeloid leukemia (AML) is essential for diagnostic subtyping, prognosis, and patient management. However, cytogenetic/cytogenomic techniques used to identify those aberrations, such as karyotyping, fluorescence in situ hybridization (FISH), or chromosomal microarray analysis (CMA), are limited by the need for skilled personnel as well as significant time, cost, and labor. Optical genome mapping (OGM) provides a single, cost-effective assay with a significantly higher resolution than karyotyping and with a comprehensive genome-wide analysis comparable with CMA and the added unique ability to detect balanced structural variants (SVs). Here, we report in a real-world setting the performance of OGM in a cohort of 100 AML cases that were previously characterized by karyotype alone or karyotype and FISH or CMA. OGM identified all clinically relevant SVs and copy number variants (CNVs) reported by these standard cytogenetic methods when representative clones were present in >5% allelic fraction. Importantly, OGM identified clinically relevant information in 13% of cases that had been missed by the routine methods. Three cases reported with normal karyotypes were shown to have cryptic translocations involving gene fusions. In 4% of cases, OGM findings would have altered recommended clinical management, and in an additional 8% of cases, OGM would have rendered the cases potentially eligible for clinical trials. The results from this multi-institutional study indicate that OGM effectively recovers clinically relevant SVs and CNVs found by standard-of-care methods and reveals additional SVs that are not reported. Furthermore, OGM minimizes the need for labor-intensive multiple cytogenetic tests while concomitantly maximizing diagnostic detection through a standardized workflow.
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Affiliation(s)
- Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Linda B. Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Yassmine Akkari
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH
| | - Scott Chartrand
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA
| | - Brandon LaBarge
- Department of Otolaryngology, Penn State College of Medicine, Hershey, PA
| | - David Claxton
- Department of Hematology and Oncology, Department of Medicine, Penn State College of Medicine, Hershey, PA
| | | | - Claudia Cujar
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA
| | - Kate Kroeger
- Cytogenetics Laboratory, Seattle Cancer Care Alliance, Seattle, WA
| | - Beth Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Nikhil Sahajpal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA
| | | | - George Vlad
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Lijun Zhang
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA
| | - Min Fang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - James R. Broach
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA
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7
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Uppuluri L, Wang Y, Young E, Wong JS, Abid HZ, Xiao M. Multiplex structural variant detection by whole-genome mapping and nanopore sequencing. Sci Rep 2022; 12:6512. [PMID: 35444207 PMCID: PMC9021263 DOI: 10.1038/s41598-022-10483-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/08/2022] [Indexed: 11/26/2022] Open
Abstract
Identification of structural variants (SVs) breakpoints is important in studying mutations, mutagenic causes, and functional impacts. Next-generation sequencing and whole-genome optical mapping are extensively used in SV discovery and characterization. However, multiple platforms and computational approaches are needed for comprehensive analysis, making it resource-intensive and expensive. Here, we propose a strategy combining optical mapping and cas9-assisted targeted nanopore sequencing to analyze SVs. Optical mapping can economically and quickly detect SVs across a whole genome but does not provide sequence-level information or precisely resolve breakpoints. Furthermore, since only a subset of all SVs is known to affect biology, we attempted to type a subset of all SVs using targeted nanopore sequencing. Using our approach, we resolved the breakpoints of five deletions, five insertions, and an inversion, in a single experiment.
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Affiliation(s)
- Lahari Uppuluri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA.,Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, PA, USA
| | - Yilin Wang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eleanor Young
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Jessica S Wong
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Heba Z Abid
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA. .,Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA.
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8
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Uppuluri L, Jadhav T, Wang Y, Xiao M. Multicolor Whole-Genome Mapping in Nanochannels for Genetic Analysis. Anal Chem 2021; 93:9808-9816. [PMID: 34232611 PMCID: PMC9705121 DOI: 10.1021/acs.analchem.1c01373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Analysis of structural variations (SVs) is important to understand mutations underlying genetic disorders and pathogenic conditions. However, characterizing SVs using short-read, high-throughput sequencing technology is difficult. Although long-read sequencing technologies are being increasingly employed in characterizing SVs, their low throughput and high costs discourage widespread adoption. Sequence motif-based optical mapping in nanochannels is useful in whole-genome mapping and SV detection, but it is not possible to precisely locate the breakpoints or estimate the copy numbers. We present here a universal multicolor mapping strategy in nanochannels combining conventional sequence-motif labeling system with Cas9-mediated target-specific labeling of any 20-base sequences (20mers) to create custom labels and detect new features. The sequence motifs are labeled with green fluorophores and the 20mers are labeled with red fluorophores. Using this strategy, it is possible to not only detect the SVs but also utilize custom labels to interrogate the features not accessible to motif-labeling, locate breakpoints, and precisely estimate copy numbers of genomic repeats. We validated our approach by quantifying the D4Z4 copy numbers, a known biomarker for facioscapulohumeral muscular dystrophy (FSHD) and estimating the telomere length, a clinical biomarker for assessing disease risk factors in aging-related diseases and malignant cancers. We also demonstrate the application of our methodology in discovering transposable long non-interspersed Elements 1 (LINE-1) insertions across the whole genome.
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Affiliation(s)
- Lahari Uppuluri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Tanaya Jadhav
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Yilin Wang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
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9
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Jeffet J, Margalit S, Michaeli Y, Ebenstein Y. Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale. Essays Biochem 2021; 65:51-66. [PMID: 33739394 PMCID: PMC8056043 DOI: 10.1042/ebc20200021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information content. This includes large-scale genetic aberrations, as well as diverse epigenetic patterns that are crucial for regulating specific cell functions. These genetic and epigenetic patterns operate in concert in order to maintain specific cellular functions in health and disease. Single-molecule optical genome mapping is a high-throughput genome analysis method that is based on imaging long chromosomal fragments stretched in nanochannel arrays. The access to long DNA molecules coupled with fluorescent tagging of various genomic information presents a unique opportunity to study genetic and epigenetic patterns in the genome at a single-molecule level over large genomic distances. Optical mapping entwines synergistically chemical, physical, and computational advancements, to uncover invaluable biological insights, inaccessible by sequencing technologies. Here we describe the method's basic principles of operation, and review the various available mechanisms to fluorescently tag genomic information. We present some of the recent biological and clinical impact enabled by optical mapping and present recent approaches for increasing the method's resolution and accuracy. Finally, we discuss how multiple layers of genomic information may be mapped simultaneously on the same DNA molecule, thus paving the way for characterizing multiple genomic observables on individual DNA molecules.
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Affiliation(s)
- Jonathan Jeffet
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sapir Margalit
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Michaeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
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10
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Krause A, Roma L, Lorber T, Dietsche T, Perrina V, Müller DC, Lardinois D, Ruiz C, Savic Prince S, Piscuoglio S, Ng CKY, Bubendorf L. Genomic evolutionary trajectory of metastatic squamous cell carcinoma of the lung. Transl Lung Cancer Res 2021; 10:1792-1803. [PMID: 34012793 PMCID: PMC8107762 DOI: 10.21037/tlcr-21-48] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/05/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND The extent of inter- and intratumoral genomic heterogeneity and the clonal evolution of metastatic squamous cell carcinoma of the lung (LUSC) are poorly understood. Genomic studies of LUSC are challenged by their low tumor cell content. We sought to define the genomic landscape and evolutionary trajectories of metastatic LUSC combining nuclei-flow sorting and whole exome sequencing. METHODS Five patients with primary LUSC and six matched metastases were investigated. Tumor nuclei were sorted based on ploidy and expression of cytokeratin to enrich for tumor cells for whole exome sequencing. RESULTS Flow-sorting increased the mean tumor purity from 26% (range, 12-50%) to 73% (range, 42-93%). Overall, primary LUSCs and their matched metastases shared a median of 79% (range, 67-85%) of copy number aberrations (CNAs) and 74% (range, 65-94%) of non-synonymous mutations, including in tumor suppressor genes such as TP53. Furthermore, the ploidy of the tumors remained unchanged between primary and metastasis in 4/5 patients over time. We found differences in the mutational signatures of shared mutations compared to the private mutations in the primary or metastasis. CONCLUSIONS Our results demonstrate a close genomic relationship between primary LUSCs and their matched metastases, suggesting late dissemination of the metastases from the primary tumors during tumor evolution.
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Affiliation(s)
- Arthur Krause
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Luca Roma
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Thomas Lorber
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Tanja Dietsche
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Valeria Perrina
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - David C. Müller
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Christian Ruiz
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Spasenija Savic Prince
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Salvatore Piscuoglio
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine; University of Basel, Basel, Switzerland
| | - Charlotte K. Y. Ng
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Lukas Bubendorf
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
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11
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Goldrich DY, LaBarge B, Chartrand S, Zhang L, Sadowski HB, Zhang Y, Pham K, Way H, Lai CYJ, Pang AWC, Clifford B, Hastie AR, Oldakowski M, Goldenberg D, Broach JR. Identification of Somatic Structural Variants in Solid Tumors by Optical Genome Mapping. J Pers Med 2021; 11:142. [PMID: 33670576 PMCID: PMC7921992 DOI: 10.3390/jpm11020142] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 12/12/2022] Open
Abstract
Genomic structural variants comprise a significant fraction of somatic mutations driving cancer onset and progression. However, such variants are not readily revealed by standard next-generation sequencing. Optical genome mapping (OGM) surpasses short-read sequencing in detecting large (>500 bp) and complex structural variants (SVs) but requires isolation of ultra-high-molecular-weight DNA from the tissue of interest. We have successfully applied a protocol involving a paramagnetic nanobind disc to a wide range of solid tumors. Using as little as 6.5 mg of input tumor tissue, we show successful extraction of high-molecular-weight genomic DNA that provides a high genomic map rate and effective coverage by optical mapping. We demonstrate the system's utility in identifying somatic SVs affecting functional and cancer-related genes for each sample. Duplicate/triplicate analysis of select samples shows intra-sample reliability but also intra-sample heterogeneity. We also demonstrate that simply filtering SVs based on a GRCh38 human control database provides high positive and negative predictive values for true somatic variants. Our results indicate that the solid tissue DNA extraction protocol, OGM and SV analysis can be applied to a wide variety of solid tumors to capture SVs across the entire genome with functional importance in cancer prognosis and treatment.
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Affiliation(s)
- David Y. Goldrich
- Department of Otolaryngology—Head and Neck Surgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (D.Y.G.); (B.L.); (D.G.)
| | - Brandon LaBarge
- Department of Otolaryngology—Head and Neck Surgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (D.Y.G.); (B.L.); (D.G.)
| | - Scott Chartrand
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (S.C.); (L.Z.)
| | - Lijun Zhang
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (S.C.); (L.Z.)
| | - Henry B. Sadowski
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - Yang Zhang
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - Khoa Pham
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - Hannah Way
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - Chi-Yu Jill Lai
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - Andy Wing Chun Pang
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - Benjamin Clifford
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - Alex R. Hastie
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - Mark Oldakowski
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - David Goldenberg
- Department of Otolaryngology—Head and Neck Surgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (D.Y.G.); (B.L.); (D.G.)
| | - James R. Broach
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (S.C.); (L.Z.)
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