1
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Li M, Wang L, Li A, Wang B, Yang X, Zhang Y, Chen C, Sun F, Zhu Z, Ye L. Integrated analyses reveal unexpected complex inversion and recombination in RH genes. Blood Adv 2024; 8:3154-3165. [PMID: 38551808 PMCID: PMC11222952 DOI: 10.1182/bloodadvances.2023012147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/28/2024] [Indexed: 06/15/2024] Open
Abstract
ABSTRACT Phenotype D-- is associated with severe hemolytic transfusion reactions and hemolytic disease of the fetus and newborn. It is typically caused by defective RHCE genes. In this study, we identified a D-- phenotype proband and verified Rh phenotypes of other 6 family members. However, inconsistent results between the phenotypic analysis and Sanger sequencing revealed intact RHCE exons with no mutations in the D-- proband, but the protein was not expressed. Subsequent whole-genome sequencing by Oxford Nanopore Technologies of the proband revealed an inversion with ambiguous breakpoints in intron 2 and intron 7 and copy number variation loss in the RHCE gene region. Given that the RHCE gene is highly homologous to the RHD gene, we conducted a comprehensive analysis using Pacific Biosciences long-read target sequencing, Bionano optical genome mapping, and targeted next-generation sequencing. Our findings revealed that the proband had 2 novel recombinant RHCE haplotypes, RHCE∗Ce(1-2)-D(3-10) and RHCE∗Ce(1-2)-D(3-10)-Ce(10-8)-Ce(3-10), with clear-cut breakpoints identified. Furthermore, the RH haplotypes of the family members were identified and verified. In summary, we made, to our knowledge, a novel discovery of hereditary large inversion and recombination events occurring between the RHD and RHCE genes, leading to a lack of RhCE expression. This highlights the advantages of using integrated genetic analyses and also provides new insights into RH genotyping.
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Affiliation(s)
- Minghao Li
- Immunohematology Laboratory, Shanghai Institute of Blood Transfusion, Shanghai Blood Centre, Shanghai, China
| | - Liping Wang
- Blood Transfusion Department, Weifang People’s Hospital, Shandong, China
| | - Aijing Li
- Immunohematology Laboratory, Shanghai Institute of Blood Transfusion, Shanghai Blood Centre, Shanghai, China
| | - Bo Wang
- Xi’an Haorui Genomics Technology Company Limited, Chang’an District, Xi’an, Shaanxi, China
| | - Xiaohong Yang
- Xi’an Haorui Genomics Technology Company Limited, Chang’an District, Xi’an, Shaanxi, China
| | - Yue Zhang
- Xi’an Haorui Genomics Technology Company Limited, Chang’an District, Xi’an, Shaanxi, China
| | - Chaoqiong Chen
- Xi’an Haorui Genomics Technology Company Limited, Chang’an District, Xi’an, Shaanxi, China
| | - Futing Sun
- Blood Transfusion Department, Weifang People’s Hospital, Shandong, China
| | - Ziyan Zhu
- Immunohematology Laboratory, Shanghai Institute of Blood Transfusion, Shanghai Blood Centre, Shanghai, China
| | - Luyi Ye
- Immunohematology Laboratory, Shanghai Institute of Blood Transfusion, Shanghai Blood Centre, Shanghai, China
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2
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Kumar KR, Cowley MJ, Davis RL. Next-Generation Sequencing and Emerging Technologies. Semin Thromb Hemost 2024. [PMID: 38692283 DOI: 10.1055/s-0044-1786397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Genetic sequencing technologies are evolving at a rapid pace with major implications for research and clinical practice. In this review, the authors provide an updated overview of next-generation sequencing (NGS) and emerging methodologies. NGS has tremendously improved sequencing output while being more time and cost-efficient in comparison to Sanger sequencing. The authors describe short-read sequencing approaches, such as sequencing by synthesis, ion semiconductor sequencing, and nanoball sequencing. Third-generation long-read sequencing now promises to overcome many of the limitations of short-read sequencing, such as the ability to reliably resolve repeat sequences and large genomic rearrangements. By combining complementary methods with massively parallel DNA sequencing, a greater insight into the biological context of disease mechanisms is now possible. Emerging methodologies, such as advances in nanopore technology, in situ nucleic acid sequencing, and microscopy-based sequencing, will continue the rapid evolution of this area. These new technologies hold many potential applications for hematological disorders, with the promise of precision and personalized medical care in the future.
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Affiliation(s)
- Kishore R Kumar
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Molecular Medicine Laboratory, Concord Hospital, Sydney, Australia
| | - Mark J Cowley
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Computational Biology Group, Children's Cancer Institute, University of New South Wales, Randwick, New South Wales, Australia
| | - Ryan L Davis
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, New South Wales, Australia
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3
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Xu H, Gao H, Wang C, Cheng X, Li Z, Lei C, Huang X, Li W, Yue Z, Tian S, Zhao X, Xue T, Xing T, Li J, Wang Y, Duan Y, Wang T, Zhang R. Optical Genome Mapping Reveals Novel Structural Variants in Lymphoblastic Lymphoma. J Pediatr Hematol Oncol 2024; 46:e71-e82. [PMID: 38018972 DOI: 10.1097/mph.0000000000002787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 10/15/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Accurate histologic and molecular genetic diagnosis is critical for the pathogenesis study of pediatric patients with lymphoblastic lymphoma (LBL). Optical genome mapping (OGM) as all-in-one process allows the detection of most major genomic risk markers, which addresses some of the limitations associated with conventional cytogenomic testing, such as low resolution and throughput, difficulty in ascertaining genomic localization, and orientation of segments in duplication, inversions, and insertions. Here, for the first time, we examined the cytogenetics of 5 children with LBL using OGM. METHODS OGM was used to analyze 5 samples of pediatric LBL patients treated according to the modified NHL-BFM95 backbone regimen. Whole-exon Sequencing (WES) was used to confirm the existence of structural variants (SVs) identified by OGM with potentially clinical significance on MGI Tech (DNBSEQ-T7) platform. According to the fusion exon sequences revealed by WES, the HBS1L :: AHI1 fusion mRNA in case 4 was amplified by cDNA-based PCR. RESULTS In total, OGM identified 251 rare variants (67 insertions, 129 deletions, 3 inversion, 25 duplications, 15 intrachromosomal translocations, and 12 interchromosomal translocations) and 229 copy number variants calls (203 gains and 26 losses). Besides all of the reproducible and pathologically significant genomic SVs detected by conventional cytogenetic techniques, OGM identified more SVs with definite or potential pathologic significance that were not detected by traditional methods, including 2 new fusion genes, HBS1L :: AHI1 and GRIK1::NSDHL , which were confirmed by WES and/or Reverse Transcription-Polymerase Chain Reaction. CONCLUSIONS Our results demonstrate the feasibility of OGM to detect genomic aberrations, which may play an important role in the occurrence and development of lymphomagenesis as an important driving factor.
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Affiliation(s)
- Hanli Xu
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University
| | - Huixia Gao
- Hematology Center, Beijing Children's Hospital, Capital Medical University; National Center for Children's Health
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children, Ministry of Education
- National Key Discipline of Pediatrics, Capital Medical University
| | - Chanjuan Wang
- Hematology Center, Beijing Children's Hospital, Capital Medical University; National Center for Children's Health
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children, Ministry of Education
- National Key Discipline of Pediatrics, Capital Medical University
| | - Xiyu Cheng
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University
| | - Zhigang Li
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University
- National Center for Children's Health
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children, Ministry of Education
- National Key Discipline of Pediatrics, Capital Medical University, Beijing
| | - Cui Lei
- Hematology Center, Beijing Children's Hospital, Capital Medical University; National Center for Children's Health
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children, Ministry of Education
- National Key Discipline of Pediatrics, Capital Medical University
| | - XiaoTong Huang
- Hematology Center, Beijing Children's Hospital, Capital Medical University; National Center for Children's Health
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children, Ministry of Education
- National Key Discipline of Pediatrics, Capital Medical University
| | - Weijing Li
- Hematology Center, Beijing Children's Hospital, Capital Medical University; National Center for Children's Health
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children, Ministry of Education
- National Key Discipline of Pediatrics, Capital Medical University
| | - Zhixia Yue
- Hematology Center, Beijing Children's Hospital, Capital Medical University; National Center for Children's Health
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children, Ministry of Education
- National Key Discipline of Pediatrics, Capital Medical University
| | - Shuo Tian
- Hematology Center, Beijing Children's Hospital, Capital Medical University; National Center for Children's Health
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children, Ministry of Education
- National Key Discipline of Pediatrics, Capital Medical University
| | - Xiaoxi Zhao
- Hematology Center, Beijing Children's Hospital, Capital Medical University; National Center for Children's Health
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children, Ministry of Education
- National Key Discipline of Pediatrics, Capital Medical University
| | - Tianlin Xue
- Hematology Center, Beijing Children's Hospital, Capital Medical University; National Center for Children's Health
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children, Ministry of Education
- National Key Discipline of Pediatrics, Capital Medical University
| | - Tianyu Xing
- Hematology Center, Beijing Children's Hospital, Capital Medical University; National Center for Children's Health
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children, Ministry of Education
- National Key Discipline of Pediatrics, Capital Medical University
| | - Jun Li
- Hematology Center, Beijing Children's Hospital, Capital Medical University; National Center for Children's Health
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children, Ministry of Education
- National Key Discipline of Pediatrics, Capital Medical University
| | - Ying Wang
- Hematology Center, Beijing Children's Hospital, Capital Medical University; National Center for Children's Health
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children, Ministry of Education
- National Key Discipline of Pediatrics, Capital Medical University
| | - Yanlong Duan
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children, Ministry of Education
- National Key Discipline of Pediatrics, Capital Medical University
- National Center for Children's Health
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, China
| | - Tianyou Wang
- Hematology Center, Beijing Children's Hospital, Capital Medical University; National Center for Children's Health
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children, Ministry of Education
- National Key Discipline of Pediatrics, Capital Medical University
| | - Ruidong Zhang
- Hematology Center, Beijing Children's Hospital, Capital Medical University; National Center for Children's Health
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children, Ministry of Education
- National Key Discipline of Pediatrics, Capital Medical University
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4
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Li L, Hong C, Xu J, Chung CYL, Leung AKY, Boncan DAT, Cheng L, Lo KW, Lai PBS, Wong J, Zhou J, Cheng ASL, Chan TF, Yue F, Yip KY. Accurate identification of structural variations from cancer samples. Brief Bioinform 2023; 25:bbad520. [PMID: 38233091 PMCID: PMC10794023 DOI: 10.1093/bib/bbad520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024] Open
Abstract
Structural variations (SVs) are commonly found in cancer genomes. They can cause gene amplification, deletion and fusion, among other functional consequences. With an average read length of hundreds of kilobases, nano-channel-based optical DNA mapping is powerful in detecting large SVs. However, existing SV calling methods are not tailored for cancer samples, which have special properties such as mixed cell types and sub-clones. Here we propose the Cancer Optical Mapping for detecting Structural Variations (COMSV) method that is specifically designed for cancer samples. It shows high sensitivity and specificity in benchmark comparisons. Applying to cancer cell lines and patient samples, COMSV identifies hundreds of novel SVs per sample.
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Affiliation(s)
- Le Li
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Chenyang Hong
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Jie Xu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60208, USA
| | - Claire Yik-Lok Chung
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Alden King-Yung Leung
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Delbert Almerick T Boncan
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Lixin Cheng
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kwok-Wai Lo
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Paul B S Lai
- Department of Surgery, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - John Wong
- Department of Surgery, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Jingying Zhou
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Alfred Sze-Lok Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Ting-Fung Chan
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60208, USA
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA
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5
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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: 30] [Impact Index Per Article: 30.0] [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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6
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Iqbal MA, Broeckel U, Levy B, Skinner S, Sahajpal NS, Rodriguez V, Stence A, Awayda K, Scharer G, Skinner C, Stevenson R, Bossler A, Nagy PL, Kolhe R. Multisite Assessment of Optical Genome Mapping for Analysis of Structural Variants in Constitutional Postnatal Cases. J Mol Diagn 2023; 25:175-188. [PMID: 36828597 PMCID: PMC10851778 DOI: 10.1016/j.jmoldx.2022.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/13/2022] [Accepted: 12/06/2022] [Indexed: 02/24/2023] Open
Abstract
This study compares optical genome mapping (OGM) performed at multiple sites with current standard-of-care (SOC) methods used in clinical cytogenetics. This study included 50 negative controls and 359 samples from individuals (patients) with suspected genetic conditions referred for cytogenetic testing. OGM was performed using the Saphyr system and Bionano Access software version 1.7. Structural variants, including copy number variants, aneuploidy, and regions of homozygosity, were detected and classified according to American College of Medical Genetics and Genomics guidelines. Repeated expansions in FMR1 and contractions in facioscapulohumeral dystrophy 1 were also analyzed. OGM results were compared with SOC for technical concordance, clinical classification concordance, intrasite and intersite reproducibility, and ability to provide additional, clinically relevant information. Across five testing sites, 98.8% (404/409) of samples yielded successful OGM data for analysis and interpretation. Overall, technical concordance for OGM to detect previously reported SOC results was 99.5% (399/401). The blinded analysis and variant classification agreement between SOC and OGM was 97.6% (364/373). Replicate analysis of 130 structural variations was 100% concordant. On the basis of this demonstration of the analytic validity and clinical utility of OGM by this multisite assessment, the authors recommend this technology as an alternative to existing SOC tests for rapid detection and diagnosis in postnatal constitutional disorders.
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Affiliation(s)
- M Anwar Iqbal
- DNA Microarray CGH Laboratory, Department of Pathology, University of Rochester Medical Center, Rochester, New York
| | - Ulrich Broeckel
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Brynn Levy
- Columbia University Medical Center, New York, New York
| | | | - Nikhil S Sahajpal
- Greenwood Genetic Center, Greenwood, South Carolina; Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | | | - Aaron Stence
- Department of Pathology, Carver College of Medicine, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Kamel Awayda
- DNA Microarray CGH Laboratory, Department of Pathology, University of Rochester Medical Center, Rochester, New York
| | - Gunter Scharer
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | | | | | | | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia.
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7
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Zhang S, Pei Z, Lei C, Zhu S, Deng K, Zhou J, Yang J, Lu D, Sun X, Xu C, Xu C. Detection of cryptic balanced chromosomal rearrangements using high-resolution optical genome mapping. J Med Genet 2023; 60:274-284. [PMID: 35710108 DOI: 10.1136/jmedgenet-2022-108553] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/28/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Chromosomal rearrangements have profound consequences in diverse human genetic diseases. Currently, the detection of balanced chromosomal rearrangements (BCRs) mainly relies on routine cytogenetic G-banded karyotyping. However, cryptic BCRs are hard to detect by karyotyping, and the risk of miscarriage or delivering abnormal offspring with congenital malformations in carrier couples is significantly increased. In the present study, we aimed to investigate the potential of single-molecule optical genome mapping (OGM) in unravelling cryptic chromosomal rearrangements. METHODS Eleven couples with normal karyotypes that had abortions/affected offspring with unbalanced rearrangements were enrolled. Ultra-high-molecular-weight DNA was isolated from peripheral blood cells and processed via OGM. The genome assembly was performed followed by variant calling and annotation. Meanwhile, multiple detection strategies, including FISH, long-range-PCR amplicon-based next-generation sequencing and Sanger sequencing were implemented to confirm the results obtained from OGM. RESULTS High-resolution OGM successfully detected cryptic reciprocal translocation in all recruited couples, which was consistent with the results of FISH and sequencing. All high-confidence cryptic chromosomal translocations detected by OGM were confirmed by sequencing analysis of rearrangement breakpoints. Moreover, OGM revealed additional complex rearrangement events such as inverted aberrations, further refining potential genetic interpretation. CONCLUSION To the best of our knowledge, this is the first study wherein OGM facilitate the rapid and robust detection of cryptic chromosomal reciprocal translocations in clinical practice. With the excellent performance, our findings suggest that OGM is well qualified as an accurate, comprehensive and first-line method for detecting cryptic BCRs in routine clinical testing.
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Affiliation(s)
- Shuo Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Zhenle Pei
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Caixia Lei
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Saijuan Zhu
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Ke Deng
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jing Zhou
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jingmin Yang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China.,NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning, Science and Technology Research Institute, Chongqing, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China.,NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning, Science and Technology Research Institute, Chongqing, China
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chenming Xu
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Congjian Xu
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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8
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Yang Y, Hao W. Identification of a familial complex chromosomal rearrangement by optical genome mapping. Mol Cytogenet 2022; 15:41. [PMID: 36127686 PMCID: PMC9490972 DOI: 10.1186/s13039-022-00619-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Complex chromosomal rearrangements (CCRs) are rare chromosomal structural variations, containing a variety of rearrangements such as translocation, inversion and/or insertion. With the development of cytogenetic and molecular genetic techniques, some chromosomal rearrangements that were initially considered to be simple reciprocal translocations in the past might eventually involve more complex chromosomal rearrangements. CASE PRESENTATION In this case, a pregnant woman, who had a spontaneous abortion last year, had abnormal prenatal test results again in the second pregnancy. Applying a combination of genetic methods including karyotype analysis, chromosomal microarray analysis, fluorescence in situ hybridization and optical genome mapping confirmed that the pregnant woman was a carrier of a CCR involving three chromosomes and four breakpoints, and the CCR was paternal-origin. Her first and second pregnancy abnormalities were caused by chromosomal microdeletions and microduplications due to the malsegregations of the derivative chromosomes. CONCLUSIONS We presented a rare familial CCR involving three chromosomes and four breakpoints. This study provided precise and detailed information for the subsequent reproductive decision-making and genetic counselling of the patient.
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Affiliation(s)
- Yang Yang
- Prenatal Diagnosis Center, Hangzhou Maternity and Child Care Hospital, #369 Kunpeng Road, Shangcheng District, Hangzhou, 310008, Zhejiang, China
| | - Wang Hao
- Prenatal Diagnosis Center, Hangzhou Maternity and Child Care Hospital, #369 Kunpeng Road, Shangcheng District, Hangzhou, 310008, Zhejiang, China. .,Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
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9
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Labarge B, Hennessy M, Zhang L, Goldrich D, Chartrand S, Purnell C, Wright S, Goldenberg D, Broach JR. Human Papillomavirus Integration Strictly Correlates with Global Genome Instability in Head and Neck Cancer. Mol Cancer Res 2022; 20:1420-1428. [PMID: 35657601 PMCID: PMC9437566 DOI: 10.1158/1541-7786.mcr-21-0831] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 04/29/2022] [Accepted: 05/31/2022] [Indexed: 01/07/2023]
Abstract
Human papillomavirus (HPV)-positive head and neck cancers, predominantly oropharyngeal squamous cell carcinoma (OPSCC), exhibit epidemiologic, clinical, and molecular characteristics distinct from those OPSCCs lacking HPV. We applied a combination of whole-genome sequencing and optical genome mapping to interrogate the genome structure of HPV-positive OPSCCs. We found that the virus had integrated in the host genome in two thirds of the tumors examined but resided solely extrachromosomally in the other third. Integration of the virus occurred at essentially random sites within the genome. Focal amplification of the virus and the genomic sequences surrounding it often occurred subsequent to integration, with the number of tandem repeats in the chromosome accounting for the increased copy number of the genome sequences flanking the site of integration. In all cases, viral integration correlated with pervasive genome-wide somatic alterations at sites distinct from that of viral integration and comprised multiple insertions, deletions, translocations, inversions, and point mutations. Few or no somatic mutations were present in tumors with only episomal HPV. Our data could be interpreted by positing that episomal HPV is captured in the host genome following an episode of global genome instability during tumor development. Viral integration correlated with higher grade tumors, which may be explained by the associated extensive mutation of the genome and suggests that HPV integration status may inform prognosis. IMPLICATIONS Our results indicate that HPV integration in head and neck cancer correlates with extensive pangenomic structural variation, which may have prognostic implications.
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Affiliation(s)
- Brandon Labarge
- Department of Otolaryngology, Penn State College of Medicine, Hershey, Pennsylvania.,Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania
| | - Max Hennessy
- Department of Otolaryngology, Penn State College of Medicine, Hershey, Pennsylvania.,Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania
| | - Lijun Zhang
- Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania
| | - David Goldrich
- Department of Otolaryngology, Penn State College of Medicine, Hershey, Pennsylvania.,Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania
| | - Scott Chartrand
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Carson Purnell
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Sage Wright
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania
| | - David Goldenberg
- Department of Otolaryngology, Penn State College of Medicine, Hershey, Pennsylvania
| | - James R. Broach
- Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania.,Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania.,Corresponding Author: James R. Broach, Department of Biochemistry, Penn State College of Medicine, Hershey, PA 17033. Phone: 717-531-8586; E-mail:
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10
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Morita Y, Kishino Y, Fukuda K, Tohyama S. Scalable manufacturing of clinical-grade differentiated cardiomyocytes derived from human-induced pluripotent stem cells for regenerative therapy. Cell Prolif 2022; 55:e13248. [PMID: 35534945 PMCID: PMC9357358 DOI: 10.1111/cpr.13248] [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: 11/04/2021] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 12/17/2022] Open
Abstract
Basic research on human pluripotent stem cell (hPSC)‐derived cardiomyocytes (CMs) for cardiac regenerative therapy is one of the most active and complex fields to achieve this alternative to heart transplantation and requires the integration of medicine, science, and engineering. Mortality in patients with heart failure remains high worldwide. Although heart transplantation is the sole strategy for treating severe heart failure, the number of donors is limited. Therefore, hPSC‐derived CM (hPSC‐CM) transplantation is expected to replace heart transplantation. To achieve this goal, for basic research, various issues should be considered, including how to induce hPSC proliferation efficiently for cardiac differentiation, induce hPSC‐CMs, eliminate residual undifferentiated hPSCs and non‐CMs, and assess for the presence of residual undifferentiated hPSCs in vitro and in vivo. In this review, we discuss the current stage of resolving these issues and future directions for realizing hPSC‐based cardiac regenerative therapy.
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Affiliation(s)
- Yuika Morita
- Department of Cardiology, Keio University School of Medicine, Tokyo, Japan
| | - Yoshikazu Kishino
- Department of Cardiology, Keio University School of Medicine, Tokyo, Japan
| | - Keiichi Fukuda
- Department of Cardiology, Keio University School of Medicine, Tokyo, Japan
| | - Shugo Tohyama
- Department of Cardiology, Keio University School of Medicine, Tokyo, Japan
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11
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Lipoprotein(a) beyond the kringle IV repeat polymorphism: The complexity of genetic variation in the LPA gene. Atherosclerosis 2022; 349:17-35. [PMID: 35606073 PMCID: PMC7613587 DOI: 10.1016/j.atherosclerosis.2022.04.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 02/23/2022] [Accepted: 04/01/2022] [Indexed: 12/24/2022]
Abstract
High lipoprotein(a) [Lp(a)] concentrations are one of the most important genetically determined risk factors for cardiovascular disease. Lp(a) concentrations are an enigmatic trait largely controlled by one single gene (LPA) that contains a complex interplay of several genetic elements with many surprising effects discussed in this review. A hypervariable coding copy number variation (the kringle IV type-2 repeat, KIV-2) generates >40 apolipoprotein(a) protein isoforms and determines the median Lp(a) concentrations. Carriers of small isoforms with up to 22 kringle IV domains have median Lp(a) concentrations up to 5 times higher than those with large isoforms (>22 kringle IV domains). The effect of the apo(a) isoforms are, however, modified by many functional single nucleotide polymorphisms (SNPs) distributed over the complete range of allele frequencies (<0.1% to >20%) with very pronounced effects on Lp(a) concentrations. A complex interaction is present between the apo (a) isoforms and LPA SNPs, with isoforms partially masking the effect of functional SNPs and, vice versa, SNPs lowering the Lp(a) concentrations of affected isoforms. This picture is further complicated by SNP-SNP interactions, a poorly understood role of other polymorphisms such as short tandem repeats and linkage structures that are poorly captured by common R2 values. A further layer of complexity derives from recent findings that several functional SNPs are located in the KIV-2 repeat and are thus not accessible to conventional sequencing and genotyping technologies. A critical impact of the ancestry on correlation structures and baseline Lp(a) values becomes increasingly evident. This review provides a comprehensive overview on the complex genetic architecture of the Lp(a) concentrations in plasma, a field that has made tremendous progress with the introduction of new technologies. Understanding the genetics of Lp(a) might be a key to many mysteries of Lp(a) and booster new ideas on the metabolism of Lp(a) and possible interventional targets.
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12
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Zhong C, Liu M, Pan X, Zhu H. Tumorigenicity Risk of iPSCs in vivo: Nip it in the Bud. PRECISION CLINICAL MEDICINE 2022; 5:pbac004. [PMID: 35692443 PMCID: PMC9026204 DOI: 10.1093/pcmedi/pbac004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/18/2022] [Accepted: 01/23/2022] [Indexed: 11/17/2022] Open
Abstract
In 2006, Takahashi and Yamanaka first created induced pluripotent stem cells from mouse fibroblasts via the retroviral introduction of genes encoding the transcription factors Oct3/4, Sox2, Klf44, and c-Myc. Since then, the future clinical application of somatic cell reprogramming technology has become an attractive research topic in the field of regenerative medicine. Of note, considerable interest has been placed in circumventing ethical issues linked to embryonic stem cell research. However, tumorigenicity, immunogenicity, and heterogeneity may hamper attempts to deploy this technology therapeutically. This review highlights the progress aimed at reducing induced pluripotent stem cells tumorigenicity risk and how to assess the safety of induced pluripotent stem cells cell therapy products.
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Affiliation(s)
- Chaoliang Zhong
- Department of Cell Biology, Naval Medical University, Shanghai, China
| | - Miao Liu
- Department of Cell Biology, Naval Medical University, Shanghai, China
| | - Xinghua Pan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, Guangdong, China
- Shenzhen Bay Laboratory, Shenzhen 518032, Guangdong, China
| | - Haiying Zhu
- Department of Cell Biology, Naval Medical University, Shanghai, China
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13
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Evaluation of copy number variants for genetic hearing loss: a review of current approaches and recent findings. Hum Genet 2021; 141:387-400. [PMID: 34811589 DOI: 10.1007/s00439-021-02365-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/02/2021] [Indexed: 01/22/2023]
Abstract
Structural variation includes a change in copy number, orientation, or location of a part of the genome. Copy number variants (CNVs) are a common cause of genetic hearing loss, comprising nearly 20% of diagnosed cases. While large deletions involving the gene STRC are the most common pathogenic CNVs, a significant proportion of known hearing loss genes also contain pathogenic CNVs. In this review, we provide an overview of currently used methods for detection of CNVs in genes known to cause hearing loss including molecular techniques such as multiplex ligation probe amplification (MLPA) and digital droplet polymerase chain reaction (ddPCR), array-CGH and single-nucleotide polymorphism (SNP) arrays, as well as techniques for detection of CNVs using next-generation sequencing data analysis including targeted gene panel, exome, and genome sequencing data. In addition, in this review, we compile published data on pathogenic hearing loss CNVs to provide an up-to-date overview. We show that CNVs have been identified in 29 different non-syndromic hearing loss genes. An understanding of the contribution of CNVs to genetic hearing loss is critical to the current diagnosis of hearing loss and is crucial for future gene therapies. Thus, evaluation for CNVs is required in any modern pipeline for genetic diagnosis of hearing loss.
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14
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Délot EC, Vilain E. Towards improved genetic diagnosis of human differences of sex development. Nat Rev Genet 2021; 22:588-602. [PMID: 34083777 PMCID: PMC10598994 DOI: 10.1038/s41576-021-00365-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 02/05/2023]
Abstract
Despite being collectively among the most frequent congenital developmental conditions worldwide, differences of sex development (DSD) lack recognition and research funding. As a result, what constitutes optimal management remains uncertain. Identification of the individual conditions under the DSD umbrella is challenging and molecular genetic diagnosis is frequently not achieved, which has psychosocial and health-related repercussions for patients and their families. New genomic approaches have the potential to resolve this impasse through better detection of protein-coding variants and ascertainment of under-recognized aetiology, such as mosaic, structural, non-coding or epigenetic variants. Ultimately, it is hoped that better outcomes data, improved understanding of the molecular causes and greater public awareness will bring an end to the stigma often associated with DSD.
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Affiliation(s)
- Emmanuèle C Délot
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA.
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15
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Neveling K, Mantere T, Vermeulen S, Oorsprong M, van Beek R, Kater-Baats E, Pauper M, van der Zande G, Smeets D, Weghuis DO, Stevens-Kroef MJPL, Hoischen A. Next-generation cytogenetics: Comprehensive assessment of 52 hematological malignancy genomes by optical genome mapping. Am J Hum Genet 2021; 108:1423-1435. [PMID: 34237281 DOI: 10.1016/j.ajhg.2021.06.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 06/01/2021] [Indexed: 02/06/2023] Open
Abstract
Somatic structural variants (SVs) are important drivers of cancer development and progression. In a diagnostic set-up, especially for hematological malignancies, the comprehensive analysis of all SVs in a given sample still requires a combination of cytogenetic techniques, including karyotyping, FISH, and CNV microarrays. We hypothesize that the combination of these classical approaches could be replaced by optical genome mapping (OGM). Samples from 52 individuals with a clinical diagnosis of a hematological malignancy, divided into simple (<5 aberrations, n = 36) and complex (≥5 aberrations, n = 16) cases, were processed for OGM, reaching on average: 283-fold genome coverage. OGM called a total of 918 high-confidence SVs per sample, of which, on average, 13 were rare and >100 kb. In addition, on average, 73 CNVs were called per sample, of which six were >5 Mb. For the 36 simple cases, all clinically reported aberrations were detected, including deletions, insertions, inversions, aneuploidies, and translocations. For the 16 complex cases, results were largely concordant between standard-of-care and OGM, but OGM often revealed higher complexity than previously recognized. Detailed technical comparison with standard-of-care tests showed high analytical validity of OGM, resulting in a sensitivity of 100% and a positive predictive value of >80%. Importantly, OGM resulted in a more complete assessment than any previous single test and most likely reported the most accurate underlying genomic architecture (e.g., for complex translocations, chromoanagenesis, and marker chromosomes). In conclusion, the excellent concordance of OGM with diagnostic standard assays demonstrates its potential to replace classical cytogenetic tests as well as to rapidly map novel leukemia drivers.
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Affiliation(s)
- Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Radboud Institute of Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tuomo Mantere
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Susan Vermeulen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Michiel Oorsprong
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Ronald van Beek
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Ellen Kater-Baats
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Marc Pauper
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Guillaume van der Zande
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Dominique Smeets
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Daniel Olde Weghuis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | | | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6532 GA Nijmegen, the Netherlands.
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16
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Cope H, Barseghyan H, Bhattacharya S, Fu Y, Hoppman N, Marcou C, Walley N, Rehder C, Deak K, Alkelai A, Vilain E, Shashi V. Detection of a mosaic CDKL5 deletion and inversion by optical genome mapping ends an exhaustive diagnostic odyssey. Mol Genet Genomic Med 2021; 9:e1665. [PMID: 33955715 PMCID: PMC8372083 DOI: 10.1002/mgg3.1665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Currently available structural variant (SV) detection methods do not span the complete spectrum of disease-causing SVs. Optical genome mapping (OGM), an emerging technology with the potential to resolve diagnostic dilemmas, was performed to investigate clinically-relevant SVs in a 4-year-old male with an epileptic encephalopathy of undiagnosed molecular origin. METHODS OGM was utilized to image long, megabase-size DNA molecules, fluorescently labeled at specific sequence motifs throughout the genome with high sensitivity for detection of SVs greater than 500 bp in size. OGM results were confirmed in a CLIA-certified laboratory via mate-pair sequencing. RESULTS OGM identified a mosaic, de novo 90 kb deletion and inversion on the X chromosome disrupting the CDKL5 gene. Detection of the mosaic deletion, which had been previously undetected by chromosomal microarray, an infantile epilepsy panel including exon-level microarray for CDKL5, exome sequencing as well as genome sequencing, resulted in a diagnosis of X-linked dominant early infantile epileptic encephalopathy-2. CONCLUSION OGM affords an effective technology for the detection of SVs, especially those that are mosaic, since these remain difficult to detect with current NGS technologies and with conventional chromosomal microarrays. Further research in undiagnosed populations with OGM is warranted.
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Affiliation(s)
- Heidi Cope
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Hayk Barseghyan
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
- Department of genomics and Precision MedicineSchool of Medicine and Health SciencesGeorge Washington UniversityWashingtonDCUSA
- Bionano Genomics IncSan DiegoCAUSA
| | | | - Yulong Fu
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
| | - Nicole Hoppman
- Division of Laboratory Genetics and GenomicsDepartment of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Cherisse Marcou
- Division of Laboratory Genetics and GenomicsDepartment of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Nicole Walley
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Catherine Rehder
- Department of PathologyDuke University Medical CenterDurhamNCUSA
| | - Kristen Deak
- Department of PathologyDuke University Medical CenterDurhamNCUSA
| | - Anna Alkelai
- Institute for Genomic MedicineColumbia University Medical CenterNew YorkNYUSA
| | - Eric Vilain
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
- Department of genomics and Precision MedicineSchool of Medicine and Health SciencesGeorge Washington UniversityWashingtonDCUSA
| | - Vandana Shashi
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
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17
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Mosley TJ, Johnston HR, Cutler DJ, Zwick ME, Mulle JG. Sex-specific recombination patterns predict parent of origin for recurrent genomic disorders. BMC Med Genomics 2021; 14:154. [PMID: 34107974 PMCID: PMC8190997 DOI: 10.1186/s12920-021-00999-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 06/02/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Structural rearrangements of the genome, which generally occur during meiosis and result in large-scale (> 1 kb) copy number variants (CNV; deletions or duplications ≥ 1 kb), underlie genomic disorders. Recurrent pathogenic CNVs harbor similar breakpoints in multiple unrelated individuals and are primarily formed via non-allelic homologous recombination (NAHR). Several pathogenic NAHR-mediated recurrent CNV loci demonstrate biases for parental origin of de novo CNVs. However, the mechanism underlying these biases is not well understood. METHODS We performed a systematic, comprehensive literature search to curate parent of origin data for multiple pathogenic CNV loci. Using a regression framework, we assessed the relationship between parental CNV origin and the male to female recombination rate ratio. RESULTS We demonstrate significant association between sex-specific differences in meiotic recombination and parental origin biases at these loci (p = 1.07 × 10-14). CONCLUSIONS Our results suggest that parental origin of CNVs is largely influenced by sex-specific recombination rates and highlight the need to consider these differences when investigating mechanisms that cause structural variation.
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Affiliation(s)
- Trenell J Mosley
- Graduate Program in Genetics and Molecular Biology, Laney Graduate School, Emory University, 201 Dowman Drive, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
| | - H Richard Johnston
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
- Emory Integrated Computational Core, Emory University, 101 Woodruff Circle, Atlanta, GA, 30322, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Drive, Atlanta, GA, 30322, USA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA.
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA.
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18
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Boti MA, Adamopoulos PG, Tsiakanikas P, Scorilas A. Nanopore Sequencing Unveils Diverse Transcript Variants of the Epithelial Cell-Specific Transcription Factor Elf-3 in Human Malignancies. Genes (Basel) 2021; 12:genes12060839. [PMID: 34072506 PMCID: PMC8227732 DOI: 10.3390/genes12060839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023] Open
Abstract
The human E74-like ETS transcription factor 3 (Elf-3) is an epithelium-specific member of the ETS family, all members of which are characterized by a highly conserved DNA-binding domain. Elf-3 plays a crucial role in epithelial cell differentiation by participating in morphogenesis and terminal differentiation of the murine small intestinal epithelium, and also acts as an indispensable regulator of mesenchymal to epithelial transition, underlying its significant involvement in development and in pathological states, such as cancer. Although previous research works have deciphered the functional role of Elf-3 in normal physiology as well as in tumorigenesis, the present study highlights for the first time the wide spectrum of ELF3 mRNAs that are transcribed, providing an in-depth analysis of splicing events and exon/intron boundaries in a broad panel of human cell lines. The implementation of a versatile targeted nanopore sequencing approach led to the identification of 25 novel ELF3 mRNA transcript variants (ELF3 v.3–v.27) with new alternative splicing events, as well as two novel exons. Although the current study provides a qualitative transcriptional profile regarding ELF3, further studies must be conducted, so the biological function of all novel alternative transcript variants as well as the putative protein isoforms are elucidated.
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19
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Lestringant V, Duployez N, Penther D, Luquet I, Derrieux C, Lutun A, Preudhomme C, West M, Ouled-Haddou H, Devoldere C, Marolleau JP, Garçon L, Jedraszak G, Ferret Y. Optical genome mapping, a promising alternative to gold standard cytogenetic approaches in a series of acute lymphoblastic leukemias. Genes Chromosomes Cancer 2021; 60:657-667. [PMID: 33982372 DOI: 10.1002/gcc.22971] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 12/12/2022] Open
Abstract
Acute lymphoblastic leukemias (ALL) are characterized by a large number of cytogenetic abnormalities of clinical interest that require the use of several complementary techniques. Optical genome mapping (OGM) is based on analysis of ultra-high molecular weight DNA molecules that provides a high-resolution genome-wide analysis highlighting copy number and structural anomalies, including balanced translocations. We compared OGM to standard techniques (karyotyping, fluorescent in situ hybridization, single nucleotide polymorphism-array and reverse transcription multiplex ligation-dependent probe amplification) in 10 selected B or T-ALL. Eighty abnormalities were found using standard techniques of which 72 (90%) were correctly detected using OGM. Eight discrepancies were identified, while 12 additional anomalies were found by OGM. Among the discrepancies, four were detected in raw data but not retained because of filtering issues. However, four were truly missed, either because of a low variant allele frequency or because of a low coverage of some regions. Of the additional anomalies revealed by OGM, seven were confirmed by another technique, some of which are recurrent in ALL such as LMO2-TRA and MYC-TRB fusions. Despite false positive anomalies due to background noise and a case of inter-sample contamination secondarily identified, the OGM technology was relatively simple to use with little practice. Thus, OGM represents a promising alternative to cytogenetic techniques currently performed for ALL characterization. It enables a time and cost effective analysis allowing identification of complex cytogenetic events, including those currently inaccessible to standard techniques.
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Affiliation(s)
| | - Nicolas Duployez
- Univ. Lille, CNRS, Inserm, CHU Lille, Département d'Hématologie, UMR9020 - UMR-S 1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
| | - Dominique Penther
- Department of Oncology Genetics, Henri Becquerel Center, Rouen, France
| | | | - Coralie Derrieux
- Laboratoire d'hématologie, Centre de Biologie - Pathologie- génétique, Lille, France
| | - Anne Lutun
- Service d'Hématologie, Oncologie, Immunologie et Rhumatologie Pédiatriques, CHU Amiens Picardie, France
| | - Claude Preudhomme
- Univ. Lille, CNRS, Inserm, CHU Lille, Département d'Hématologie, UMR9020 - UMR-S 1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
| | - Michaela West
- Genotyping, Sequencing and optical mapping Platform (Gentyane), Clermont-Ferrand, France
| | | | - Catherine Devoldere
- Service d'Hématologie, Oncologie, Immunologie et Rhumatologie Pédiatriques, CHU Amiens Picardie, France
| | - Jean-Pierre Marolleau
- EA4666 HEMATIM, UPJV, Amiens, France.,Service d'Hématologie Clinique, CHU Amiens Picardie, France
| | - Loïc Garçon
- Service d'Hématologie Biologique, CHU Amiens Picardie, France.,EA4666 HEMATIM, UPJV, Amiens, France.,Laboratoire de Génétique Constitutionnelle, CHU Amiens Picardie, France
| | - Guillaume Jedraszak
- EA4666 HEMATIM, UPJV, Amiens, France.,Laboratoire de Génétique Constitutionnelle, CHU Amiens Picardie, France
| | - Yann Ferret
- Service d'Hématologie Biologique, CHU Amiens Picardie, France
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20
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Zhu Y, Gujar AD, Wong CH, Tjong H, Ngan CY, Gong L, Chen YA, Kim H, Liu J, Li M, Mil-Homens A, Maurya R, Kuhlberg C, Sun F, Yi E, deCarvalho AC, Ruan Y, Verhaak RGW, Wei CL. Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. Cancer Cell 2021; 39:694-707.e7. [PMID: 33836152 PMCID: PMC8119378 DOI: 10.1016/j.ccell.2021.03.006] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/05/2020] [Accepted: 03/12/2021] [Indexed: 12/13/2022]
Abstract
Extrachromosomal, circular DNA (ecDNA) is emerging as a prevalent yet less characterized oncogenic alteration in cancer genomes. We leverage ChIA-PET and ChIA-Drop chromatin interaction assays to characterize genome-wide ecDNA-mediated chromatin contacts that impact transcriptional programs in cancers. ecDNAs in glioblastoma patient-derived neurosphere and prostate cancer cell cultures are marked by widespread intra-ecDNA and genome-wide chromosomal interactions. ecDNA-chromatin contact foci are characterized by broad and high-level H3K27ac signals converging predominantly on chromosomal genes of increased expression levels. Prostate cancer cells harboring synthetic ecDNA circles composed of characterized enhancers result in the genome-wide activation of chromosomal gene transcription. Deciphering the chromosomal targets of ecDNAs at single-molecule resolution reveals an association with actively expressed oncogenes spatially clustered within ecDNA-directed interaction networks. Our results suggest that ecDNA can function as mobile transcriptional enhancers to promote tumor progression and manifest a potential synthetic aneuploidy mechanism of transcription control in cancer.
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Affiliation(s)
- Yanfen Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Amit D Gujar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Chee-Hong Wong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Harianto Tjong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Liang Gong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Yi-An Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Jihe Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Meihong Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Adam Mil-Homens
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Rahul Maurya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Chris Kuhlberg
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Fanyue Sun
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Eunhee Yi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Ana C deCarvalho
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
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21
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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: 10] [Impact Index Per Article: 3.3] [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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22
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Uppuluri L, Varapula D, Young E, Riethman H, Xiao M. Single-molecule telomere length characterization by optical mapping in nano-channel array: Perspective and review on telomere length measurement. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2021; 82:103562. [PMID: 33310082 PMCID: PMC8500550 DOI: 10.1016/j.etap.2020.103562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/02/2020] [Accepted: 12/08/2020] [Indexed: 05/11/2023]
Abstract
In humans, the telomere consists of tandem 5'TTAGGG3' DNA repeats on both ends of all 46 chromosomes. Telomere shortening has been linked to aging and age-related diseases. Similarly, telomere length changes have been associated with chemical exposure, molecular-level DNA damage, and tumor development. Telomere elongation has been associated to tumor development, caused due to chemical exposure and molecular-level DNA damage. The methods used to study these effects mostly rely on average telomere length as a biomarker. The mechanisms regulating subtelomere-specific and haplotype-specific telomere lengths in humans remain understudied and poorly understood, primarily because of technical limitations in obtaining these data for all chromosomes. Recent studies have shown that it is the short telomeres that are crucial in preserving chromosome stability. The identity and frequency of specific critically short telomeres potentially is a useful biomarker for studying aging, age-related diseases, and cancer. Here, we will briefly review the role of telomere length, its measurement, and our recent single-molecule telomere length measurement assay. With this assay, one can measure individual telomere lengths as well as identify their physically linked subtelomeric DNA. This assay can also positively detect telomere loss, characterize novel subtelomeric variants, haplotypes, and previously uncharacterized recombined subtelomeres. We will also discuss its applications in aging cells and cancer cells, highlighting the utility of the single molecule telomere length assay.
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Affiliation(s)
- Lahari Uppuluri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Dharma Varapula
- 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
| | - Harold Riethman
- Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA, USA.
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA; Institute of Molecular Medicine and Infectious Disease, School of Medicine, Drexel University, Philadelphia, PA, USA.
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23
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Abid HZ, Young E, McCaffrey J, Raseley K, Varapula D, Wang HY, Piazza D, Mell J, Xiao M. Customized optical mapping by CRISPR-Cas9 mediated DNA labeling with multiple sgRNAs. Nucleic Acids Res 2021; 49:e8. [PMID: 33231685 PMCID: PMC7826249 DOI: 10.1093/nar/gkaa1088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/16/2020] [Accepted: 10/27/2020] [Indexed: 01/01/2023] Open
Abstract
Whole-genome mapping technologies have been developed as a complementary tool to provide scaffolds for genome assembly and structural variation analysis (1,2). We recently introduced a novel DNA labeling strategy based on a CRISPR-Cas9 genome editing system, which can target any 20bp sequences. The labeling strategy is specifically useful in targeting repetitive sequences, and sequences not accessible to other labeling methods. In this report, we present customized mapping strategies that extend the applications of CRISPR-Cas9 DNA labeling. We first design a CRISPR-Cas9 labeling strategy to interrogate and differentiate the single allele differences in NGG protospacer adjacent motifs (PAM sequence). Combined with sequence motif labeling, we can pinpoint the single-base differences in highly conserved sequences. In the second strategy, we design mapping patterns across a genome by selecting sets of specific single-guide RNAs (sgRNAs) for labeling multiple loci of a genomic region or a whole genome. By developing and optimizing a single tube synthesis of multiple sgRNAs, we demonstrate the utility of CRISPR-Cas9 mapping with 162 sgRNAs targeting the 2Mb Haemophilus influenzae chromosome. These CRISPR-Cas9 mapping approaches could be particularly useful for applications in defining long-distance haplotypes and pinpointing the breakpoints in large structural variants in complex genomes and microbial mixtures.
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MESH Headings
- Alleles
- Base Sequence
- Benzoxazoles/analysis
- CRISPR-Cas Systems
- Chromosome Mapping/methods
- Chromosomes, Bacterial/genetics
- Computer Simulation
- Conserved Sequence/genetics
- DNA-Directed RNA Polymerases
- Drug Resistance, Bacterial/genetics
- Fluorescent Dyes/analysis
- Gene Editing/methods
- Genome, Bacterial
- Genome, Human
- Haemophilus influenzae/drug effects
- Haemophilus influenzae/genetics
- Haplotypes/genetics
- Humans
- Lab-On-A-Chip Devices
- Nalidixic Acid/pharmacology
- Novobiocin/pharmacology
- Nucleotide Motifs/genetics
- Polymorphism, Single Nucleotide
- Quinolinium Compounds/analysis
- RNA, Guide, CRISPR-Cas Systems/chemical synthesis
- RNA, Guide, CRISPR-Cas Systems/genetics
- Repetitive Sequences, Nucleic Acid/genetics
- Sequence Alignment
- Staining and Labeling/methods
- Viral Proteins
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Affiliation(s)
- Heba Z Abid
- 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
| | - Jennifer McCaffrey
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Kaitlin Raseley
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Dharma Varapula
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Hung-Yi Wang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Danielle Piazza
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA
| | - Joshua Mell
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, 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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24
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Linked-Read Whole Genome Sequencing Solves a Double DMD Gene Rearrangement. Genes (Basel) 2021; 12:genes12020133. [PMID: 33494189 PMCID: PMC7909759 DOI: 10.3390/genes12020133] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 01/25/2023] Open
Abstract
Next generation sequencing (NGS) has changed our approach to diagnosis of genetic disorders. Nowadays, the most comprehensive application of NGS is whole genome sequencing (WGS) that is able to detect virtually all DNA variations. However, even after accurate WGS, many genetic conditions remain unsolved. This may be due to the current NGS protocols, based on DNA fragmentation and short reads. To overcome these limitations, we applied a linked-read sequencing technology that combines single-molecule barcoding with short-read WGS. We were able to assemble haplotypes and distinguish between alleles along the genome. As an exemplary case, we studied the case of a female carrier of X-linked muscular dystrophy with an unsolved genetic status. A deletion of exons 16–29 in DMD gene was responsible for the disease in her family, but she showed a normal dosage of these exons by Multiplex Ligation-dependent Probe Amplification (MLPA) and array CGH. This situation is usually considered compatible with a “non-carrier” status. Unexpectedly, the girl also showed an increased dosage of flanking exons 1–15 and 30–34. Using linked-read WGS, we were able to distinguish between the two X chromosomes. In the first allele, we found the 16–29 deletion, while the second allele showed a 1–34 duplication: in both cases, linked-read WGS correctly mapped the borders at single-nucleotide resolution. This duplication in trans apparently restored the normal dosage of exons 16–29 seen by quantitative assays. This had a dramatic impact in genetic counselling, by converting a non-carrier into a double carrier status prediction. We conclude that linked-read WGS should be considered as a valuable option to improve our understanding of unsolved genetic conditions.
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25
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Bhattacharya S, Barseghyan H, Délot EC, Vilain E. nanotatoR: a tool for enhanced annotation of genomic structural variants. BMC Genomics 2021; 22:10. [PMID: 33407088 PMCID: PMC7789800 DOI: 10.1186/s12864-020-07182-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/22/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Whole genome sequencing is effective at identification of small variants, but because it is based on short reads, assessment of structural variants (SVs) is limited. The advent of Optical Genome Mapping (OGM), which utilizes long fluorescently labeled DNA molecules for de novo genome assembly and SV calling, has allowed for increased sensitivity and specificity in SV detection. However, compared to small variant annotation tools, OGM-based SV annotation software has seen little development, and currently available SV annotation tools do not provide sufficient information for determination of variant pathogenicity. RESULTS We developed an R-based package, nanotatoR, which provides comprehensive annotation as a tool for SV classification. nanotatoR uses both external (DGV; DECIPHER; Bionano Genomics BNDB) and internal (user-defined) databases to estimate SV frequency. Human genome reference GRCh37/38-based BED files are used to annotate SVs with overlapping, upstream, and downstream genes. Overlap percentages and distances for nearest genes are calculated and can be used for filtration. A primary gene list is extracted from public databases based on the patient's phenotype and used to filter genes overlapping SVs, providing the analyst with an easy way to prioritize variants. If available, expression of overlapping or nearby genes of interest is extracted (e.g. from an RNA-Seq dataset, allowing the user to assess the effects of SVs on the transcriptome). Most quality-control filtration parameters are customizable by the user. The output is given in an Excel file format, subdivided into multiple sheets based on SV type and inheritance pattern (INDELs, inversions, translocations, de novo, etc.). nanotatoR passed all quality and run time criteria of Bioconductor, where it was accepted in the April 2019 release. We evaluated nanotatoR's annotation capabilities using publicly available reference datasets: the singleton sample NA12878, mapped with two types of enzyme labeling, and the NA24143 trio. nanotatoR was also able to accurately filter the known pathogenic variants in a cohort of patients with Duchenne Muscular Dystrophy for which we had previously demonstrated the diagnostic ability of OGM. CONCLUSIONS The extensive annotation enables users to rapidly identify potential pathogenic SVs, a critical step toward use of OGM in the clinical setting.
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Affiliation(s)
- Surajit Bhattacharya
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, 20010, USA
| | - Hayk Barseghyan
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, 20010, USA.,Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, 20052, USA.,Bionano Genomics Inc, San Diego, CA, 92121, USA
| | - Emmanuèle C Délot
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, 20010, USA.,Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, 20052, USA
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, 20010, USA. .,Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, 20052, USA.
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26
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Schwartz C, Lenderts B, Feigenbutz L, Barone P, Llaca V, Fengler K, Svitashev S. CRISPR-Cas9-mediated 75.5-Mb inversion in maize. NATURE PLANTS 2020; 6:1427-1431. [PMID: 33299151 DOI: 10.1038/s41477-020-00817-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/04/2020] [Indexed: 05/11/2023]
Abstract
CRISPR-Cas is a powerful double-strand-break technology with wide-ranging applications from gene discovery to commercial product development. Thus far, this tool has been almost exclusively used for gene knockouts and deletions, with a few examples of gene edits and targeted gene insertions. Here, we demonstrate the application of CRISPR-Cas9 technology to mediate targeted 75.5-Mb pericentric inversion in chromosome 2 in one of the elite maize inbred lines from Corteva Agriscience. This inversion unlocks a large chromosomal region containing substantial genetic variance for recombination, thus providing opportunities for the development of new maize varieties with improved phenotypes.
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27
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Identification of a likely pathogenic structural variation in the LAMA1 gene by Bionano optical mapping. NPJ Genom Med 2020; 5:31. [PMID: 33083009 PMCID: PMC7538933 DOI: 10.1038/s41525-020-0138-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/03/2020] [Indexed: 01/10/2023] Open
Abstract
Recent advances in Bionano optical mapping (BOM) provide a great insight into the determination of structural variants (SVs), but its utility in identification of clinical likely pathogenic variants needs to be further demonstrated and proved. In a family with two consecutive pregnancies affected with ventriculomegaly, a splicing likely pathogenic variant at the LAMA1 locus (NM_005559: c. 4663 + 1 G > C) inherited from the father was identified in the proband by whole-exome sequencing, and no other pathogenic variant associated with the clinical phenotypes was detected. SV analysis by BOM revealed an ~48 kb duplication at the LAMA1 locus in the maternal sample. Real-time quantitative PCR and Sanger sequencing further confirmed the duplication as c.859-153_4806 + 910dup. Based on these variants, we hypothesize that the fetuses have Poretti-Boltshauser syndrome (PBS) presenting with ventriculomegaly. With the ability to determine single nucleotide variants and SVs, the strategy adopted here might be useful to detect cases missed by current routine screening methods. In addition, our study may broaden the phenotypic spectrum of fetuses with PBS.
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28
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Yuan Y, Chung CYL, Chan TF. Advances in optical mapping for genomic research. Comput Struct Biotechnol J 2020; 18:2051-2062. [PMID: 32802277 PMCID: PMC7419273 DOI: 10.1016/j.csbj.2020.07.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/08/2020] [Accepted: 07/24/2020] [Indexed: 12/28/2022] Open
Abstract
Recent advances in optical mapping have allowed the construction of improved genome assemblies with greater contiguity. Optical mapping also enables genome comparison and identification of large-scale structural variations. Association of these large-scale genomic features with biological functions is an important goal in plant and animal breeding and in medical research. Optical mapping has also been used in microbiology and still plays an important role in strain typing and epidemiological studies. Here, we review the development of optical mapping in recent decades to illustrate its importance in genomic research. We detail its applications and algorithms to show its specific advantages. Finally, we discuss the challenges required to facilitate the optimization of optical mapping and improve its future development and application.
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Key Words
- 3D, three-dimensional
- DBG, de Bruijn graph
- DLS, direct label and strain
- DNA, deoxyribonucleic acid
- Genome assembly
- Hi-C, high-throughput chromosome conformation capture
- Mb, million base pair
- Next generation sequencing
- OLC, overlap-layout-consensus
- Optical mapping
- PCR, polymerase chain reaction
- PacBio, Pacific Biosciences
- SRS, short-read sequencing
- SV, structural variation
- Structural variation
- bp, base pair
- kb, kilobase pair
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Affiliation(s)
- Yuxuan Yuan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
- AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Claire Yik-Lok Chung
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
- AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong SAR, China
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29
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Abid HZ, McCaffrey J, Raseley K, Young E, Lassahn K, Varapula D, Riethman H, Xiao M. Single-molecule analysis of subtelomeres and telomeres in Alternative Lengthening of Telomeres (ALT) cells. BMC Genomics 2020; 21:485. [PMID: 32669102 PMCID: PMC7364475 DOI: 10.1186/s12864-020-06901-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/08/2020] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Telomeric DNA is typically comprised of G-rich tandem repeat motifs and maintained by telomerase (Greider CW, Blackburn EH; Cell 51:887-898; 1987). In eukaryotes lacking telomerase, a variety of DNA repair and DNA recombination based pathways for telomere maintenance have evolved in organisms normally dependent upon telomerase for telomere elongation (Webb CJ, Wu Y, Zakian VA; Cold Spring Harb Perspect Biol 5:a012666; 2013); collectively called Alternative Lengthening of Telomeres (ALT) pathways. By measuring (TTAGGG) n tract lengths from the same large DNA molecules that were optically mapped, we simultaneously analyzed telomere length dynamics and subtelomere-linked structural changes at a large number of specific subtelomeric loci in the ALT-positive cell lines U2OS, SK-MEL-2 and Saos-2. RESULTS Our results revealed loci-specific ALT telomere features. For example, while each subtelomere included examples of single molecules with terminal (TTAGGG) n tracts as well as examples of recombinant telomeric single molecules, the ratio of these molecules was subtelomere-specific, ranging from 33:1 (19p) to 1:25 (19q) in U2OS. The Saos-2 cell line shows a similar percentage of recombinant telomeres. The frequency of recombinant subtelomeres of SK-MEL-2 (11%) is about half that of U2OS and Saos-2 (24 and 19% respectively). Terminal (TTAGGG) n tract lengths and heterogeneity levels, the frequencies of telomere signal-free ends, and the frequency and size of retained internal telomere-like sequences (ITSs) at recombinant telomere fusion junctions all varied according to the specific subtelomere involved in a particular cell line. Very large linear extrachromosomal telomere repeat (ECTR) DNA molecules were found in all three cell lines; these are in principle capable of templating synthesis of new long telomere tracts via break-induced repair (BIR) long-tract DNA synthesis mechanisms and contributing to the very long telomere tract length and heterogeneity characteristic of ALT cells. Many of longest telomere tracts (both end-telomeres and linear ECTRs) displayed punctate CRISPR/Cas9-dependent (TTAGGG) n labeling patterns indicative of interspersion of stretches of non-canonical telomere repeats. CONCLUSION Identifying individual subtelomeres and characterizing linked telomere (TTAGGG) n tract lengths and structural changes using our new single-molecule methodologies reveals the structural consequences of telomere damage, repair and recombination mechanisms in human ALT cells in unprecedented molecular detail and significant differences in different ALT-positive cell lines.
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Affiliation(s)
- Heba Z Abid
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Jennifer McCaffrey
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Kaitlin Raseley
- 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
| | - Katy Lassahn
- School of Medical Diagnostic and Transnational Sciences, Old Dominion University, Norfolk, VA, USA
| | - Dharma Varapula
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Harold Riethman
- School of Medical Diagnostic and Transnational Sciences, Old Dominion University, Norfolk, VA, USA.
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA. .,Institute of Molecular Medicine and Infectious Disease, School of Medicine, Drexel University, Philadelphia, PA, USA.
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30
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Bruel A, Vitobello A, Tran Mau‐Them F, Nambot S, Sorlin A, Denommé‐Pichon A, Delanne J, Moutton S, Callier P, Duffourd Y, Philippe C, Faivre L, Thauvin‐Robinet C. Next‐generation
sequencing approaches and challenges in the diagnosis of developmental anomalies and intellectual disability. Clin Genet 2020; 98:433-444. [DOI: 10.1111/cge.13764] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Ange‐Line Bruel
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Déficiences Intellectuelles de causes rares, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Antonio Vitobello
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Frédéric Tran Mau‐Them
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Sophie Nambot
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Arthur Sorlin
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Maladies dermatologiques en mosaïque Service de dermatologie, CHU Dijon Bourgogne Dijon France
| | - Anne‐Sophie Denommé‐Pichon
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Julian Delanne
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Sébastien Moutton
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Patrick Callier
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Yannis Duffourd
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Christophe Philippe
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Laurence Faivre
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Christel Thauvin‐Robinet
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Déficiences Intellectuelles de causes rares, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
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Abstract
Identifying structural variation (SV) is essential for genome interpretation but has been historically difficult due to limitations inherent to available genome technologies. Detection methods that use ensemble algorithms and emerging sequencing technologies have enabled the discovery of thousands of SVs, uncovering information about their ubiquity, relationship to disease and possible effects on biological mechanisms. Given the variability in SV type and size, along with unique detection biases of emerging genomic platforms, multiplatform discovery is necessary to resolve the full spectrum of variation. Here, we review modern approaches for investigating SVs and proffer that, moving forwards, studies integrating biological information with detection will be necessary to comprehensively understand the impact of SV in the human genome.
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Affiliation(s)
- Steve S Ho
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan E Mills
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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32
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Wand NO, Smith DA, Wilkinson AA, Rushton AE, Busby SJW, Styles IB, Neely RK. DNA barcodes for rapid, whole genome, single-molecule analyses. Nucleic Acids Res 2020; 47:e68. [PMID: 30918971 PMCID: PMC6614835 DOI: 10.1093/nar/gkz212] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/13/2019] [Accepted: 03/18/2019] [Indexed: 01/01/2023] Open
Abstract
We report an approach for visualizing DNA sequence and using these ‘DNA barcodes’ to search complex mixtures of genomic material for DNA molecules of interest. We demonstrate three applications of this methodology; identifying specific molecules of interest from a dataset containing gigabasepairs of genome; identification of a bacterium from such a dataset and, finally, by locating infecting virus molecules in a background of human genomic material. As a result of the dense fluorescent labelling of the DNA, individual barcodes of the order 40 kb pairs in length can be reliably identified. This means DNA can be prepared for imaging using standard handling and purification techniques. The recorded dataset provides stable physical and electronic records of the total genomic content of a sample that can be readily searched for a molecule or region of interest.
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Affiliation(s)
- Nathaniel O Wand
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.,Physical Sciences of Imaging in the Biomedical Sciences Centre for Doctoral Training, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Darren A Smith
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Andrew A Wilkinson
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Ashleigh E Rushton
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Stephen J W Busby
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Iain B Styles
- School of Computer Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Robert K Neely
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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33
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Dai Y, Li P, Wang Z, Liang F, Yang F, Fang L, Huang Y, Huang S, Zhou J, Wang D, Cui L, Wang K. Single-molecule optical mapping enables quantitative measurement of D4Z4 repeats in facioscapulohumeral muscular dystrophy (FSHD). J Med Genet 2020; 57:109-120. [PMID: 31506324 PMCID: PMC7029236 DOI: 10.1136/jmedgenet-2019-106078] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/06/2019] [Accepted: 08/09/2019] [Indexed: 12/28/2022]
Abstract
PURPOSE Facioscapulohumeral muscular dystrophy (FSHD) is a common adult muscular dystrophy. Over 95% of FSHD cases are associated with contraction of the D4Z4 tandem repeat (~3.3 kb per unit) at 4q35 with a specific genomic configuration (haplotype) called 4qA. Molecular diagnosis of FSHD typically requires pulsed-field gel electrophoresis with Southern blotting. We aim to develop novel genomic and computational methods for characterising D4Z4 repeat numbers in FSHD. METHODS We leveraged a single-molecule optical mapping platform that maps locations of restriction enzyme sites on high molecular weight (>150 kb) DNA molecules. We developed bioinformatics methods to address several challenges, including the differentiation of 4qA with 4qB alleles, the differentiation of 4q35 and 10q26 segmental duplications, the quantification of repeat numbers with different enzymes that may or may not have recognition sites within D4Z4 repeats. We evaluated the method on 25 human subjects (13 patients, 3 individual control subjects, 9 control subjects from 3 families) labelled by the Nb.BssSI and/or Nt.BspQI enzymes. RESULTS We demonstrated that the method gave a direct quantitative measurement of repeat numbers on D4Z4 repeats with 4qA allelic configuration and the levels of postzygotic mosaicism. Our method had high concordance with Southern blots from several cohorts on two platforms (Bionano Saphyr and Bionano Irys), but with improved quantification of repeat numbers. CONCLUSION While the study is limited by small sample size, our results demonstrated that single-molecule optical mapping is a viable approach for more refined analysis on genotype-phenotype relationships in FSHD, especially when postzygotic mosaicism is present.
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Affiliation(s)
- Yi Dai
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Pidong Li
- GrandOmics Biosciences, Beijing, China
| | - Zhiqiang Wang
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Center of Neuroscience, Fujian Medical University, Fuzhou, China
| | - Fan Liang
- GrandOmics Biosciences, Beijing, China
| | - Fan Yang
- GrandOmics Biosciences, Beijing, China
| | - Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Yu Huang
- Department of Medical Genetics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Shangzhi Huang
- Department of Medical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | | | | | - Liying Cui
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China, Beijing, China
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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34
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Young E, Abid HZ, Kwok PY, Riethman H, Xiao M. Comprehensive Analysis of Human Subtelomeres by Whole Genome Mapping. PLoS Genet 2020; 16:e1008347. [PMID: 31986135 PMCID: PMC7004388 DOI: 10.1371/journal.pgen.1008347] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 02/06/2020] [Accepted: 10/15/2019] [Indexed: 12/03/2022] Open
Abstract
Detailed comprehensive knowledge of the structures of individual long-range telomere-terminal haplotypes are needed to understand their impact on telomere function, and to delineate the population structure and evolution of subtelomere regions. However, the abundance of large evolutionarily recent segmental duplications and high levels of large structural variations have complicated both the mapping and sequence characterization of human subtelomere regions. Here, we use high throughput optical mapping of large single DNA molecules in nanochannel arrays for 154 human genomes from 26 populations to present a comprehensive look at human subtelomere structure and variation. The results catalog many novel long-range subtelomere haplotypes and determine the frequencies and contexts of specific subtelomeric duplicons on each chromosome arm, helping to clarify the currently ambiguous nature of many specific subtelomere structures as represented in the current reference sequence (HG38). The organization and content of some duplicons in subtelomeres appear to show both chromosome arm and population-specific trends. Based upon these trends we estimate a timeline for the spread of these duplication blocks.
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Affiliation(s)
- Eleanor Young
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Heba Z. Abid
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA, United States of America
- Department of Dermatology, University of California–San Francisco, San Francisco, CA, United States of America
- Institute for Human Genetics, University of California–San Francisco, San Francisco, CA, United States of America
| | - Harold Riethman
- Medical Diagnostic & Translational Sciences, Old Dominium University, Norfolk, VA, United States of America
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
- Institute of Molecular Medicine and Infectious Disease in the School of Medicine, Drexel University, Philadelphia, PA, United States of America
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35
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Heft IE, Mostovoy Y, Levy-Sakin M, Ma W, Stevens AJ, Pastor S, McCaffrey J, Boffelli D, Martin DI, Xiao M, Kennedy MA, Kwok PY, Sikela JM. The Driver of Extreme Human-Specific Olduvai Repeat Expansion Remains Highly Active in the Human Genome. Genetics 2020; 214:179-191. [PMID: 31754017 PMCID: PMC6944415 DOI: 10.1534/genetics.119.302782] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/05/2019] [Indexed: 11/18/2022] Open
Abstract
Sequences encoding Olduvai protein domains (formerly DUF1220) show the greatest human lineage-specific increase in copy number of any coding region in the genome and have been associated, in a dosage-dependent manner, with brain size, cognitive aptitude, autism, and schizophrenia. Tandem intragenic duplications of a three-domain block, termed the Olduvai triplet, in four NBPF genes in the chromosomal 1q21.1-0.2 region, are primarily responsible for the striking human-specific copy number increase. Interestingly, most of the Olduvai triplets are adjacent to, and transcriptionally coregulated with, three human-specific NOTCH2NL genes that have been shown to promote cortical neurogenesis. Until now, the underlying genomic events that drove the Olduvai hyperamplification in humans have remained unexplained. Here, we show that the presence or absence of an alternative first exon of the Olduvai triplet perfectly discriminates between amplified (58/58) and unamplified (0/12) triplets. We provide sequence and breakpoint analyses that suggest the alternative exon was produced by an nonallelic homologous recombination-based mechanism involving the duplicative transposition of an existing Olduvai exon found in the CON3 domain, which typically occurs at the C-terminal end of NBPF genes. We also provide suggestive in vitro evidence that the alternative exon may promote instability through a putative G-quadraplex (pG4)-based mechanism. Lastly, we use single-molecule optical mapping to characterize the intragenic structural variation observed in NBPF genes in 154 unrelated individuals and 52 related individuals from 16 families and show that the presence of pG4-containing Olduvai triplets is strongly correlated with high levels of Olduvai copy number variation. These results suggest that the same driver of genomic instability that allowed the evolutionarily recent, rapid, and extreme human-specific Olduvai expansion remains highly active in the human genome.
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Affiliation(s)
- Ilea E Heft
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Yulia Mostovoy
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Michal Levy-Sakin
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Walfred Ma
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Aaron J Stevens
- Department of Pathology, University of Otago, Christchurch, New Zealand 8140
| | - Steven Pastor
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania 19104
| | - Jennifer McCaffrey
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania 19104
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, Oakland, California 94609
| | - David I Martin
- Children's Hospital Oakland Research Institute, Oakland, California 94609
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania 19104
| | - Martin A Kennedy
- Department of Pathology, University of Otago, Christchurch, New Zealand 8140
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California, San Francisco, California
- Department of Dermatology, University of California, San Francisco, California
- Institute for Human Genetics, University of California, San Francisco, California
| | - James M Sikela
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado 80045
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36
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Müller V, Dvirnas A, Andersson J, Singh V, Kk S, Johansson P, Ebenstein Y, Ambjörnsson T, Westerlund F. Enzyme-free optical DNA mapping of the human genome using competitive binding. Nucleic Acids Res 2019; 47:e89. [PMID: 31165870 PMCID: PMC6735870 DOI: 10.1093/nar/gkz489] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/03/2019] [Accepted: 05/22/2019] [Indexed: 01/24/2023] Open
Abstract
Optical DNA mapping (ODM) allows visualization of long-range sequence information along single DNA molecules. The data can for example be used for detecting long range structural variations, for aiding DNA sequence assembly of complex genomes and for mapping epigenetic marks and DNA damage across the genome. ODM traditionally utilizes sequence specific marks based on nicking enzymes, combined with a DNA stain, YOYO-1, for detection of the DNA contour. Here we use a competitive binding approach, based on YOYO-1 and netropsin, which highlights the contour of the DNA molecules, while simultaneously creating a continuous sequence specific pattern, based on the AT/GC variation along the detected molecule. We demonstrate and validate competitive-binding-based ODM using bacterial artificial chromosomes (BACs) derived from the human genome and then turn to DNA extracted from white blood cells. We generalize our findings with in-silico simulations that show that we can map a vast majority of the human genome. Finally, we demonstrate the possibility of combining competitive binding with enzymatic labeling by mapping DNA damage sites induced by the cytotoxic drug etoposide to the human genome. Overall, we demonstrate that competitive-binding-based ODM has the potential to be used both as a standalone assay for studies of the human genome, as well as in combination with enzymatic approaches, some of which are already commercialized.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Albertas Dvirnas
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - John Andersson
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Vandana Singh
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Sriram Kk
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Pegah Johansson
- Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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37
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Dai Z, Li T, Li J, Han Z, Pan Y, Tang S, Diao X, Luo M. High-throughput long paired-end sequencing of a Fosmid library by PacBio. PLANT METHODS 2019; 15:142. [PMID: 31788019 PMCID: PMC6878638 DOI: 10.1186/s13007-019-0525-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Large insert paired-end sequencing technologies are important tools for assembling genomes, delineating associated breakpoints and detecting structural rearrangements. To facilitate the comprehensive detection of inter- and intra-chromosomal structural rearrangements or variants (SVs) and complex genome assembly with long repeats and segmental duplications, we developed a new method based on single-molecule real-time synthesis sequencing technology for generating long paired-end sequences of large insert DNA libraries. RESULTS A Fosmid vector, pHZAUFOS3, was developed with the following new features: (1) two 18-bp non-palindromic I-SceI sites flank the cloning site, and another two sites are present in the skeleton of the vector, allowing long DNA inserts (and the long paired-ends in this paper) to be recovered as single fragments and the vector (~ 8 kb) to be fragmented into 2-3 kb fragments by I-SceI digestion and therefore was effectively removed from the long paired-ends (5-10 kb); (2) the chloramphenicol (Cm) resistance gene and replicon (oriV), necessary for colony growth, are located near the two sides of the cloning site, helping to increase the proportion of the paired-end fragments to single-end fragments in the paired-end libraries. Paired-end libraries were constructed by ligating the size-selected, mechanically sheared pooled Fosmid DNA fragments to the Ampicillin (Amp) resistance gene fragment and screening the colonies with Cm and Amp. We tested this method on yeast and Setaria italica Yugu1. Fosmid-size paired-ends with an average length longer than 2 kb for each end were generated. The N50 scaffold lengths of the de novo assemblies of the yeast and S. italica Yugu1 genomes were significantly improved. Five large and five small structural rearrangements or assembly errors spanning tens of bp to tens of kb were identified in S. italica Yugu1 including deletions, inversions, duplications and translocations. CONCLUSIONS We developed a new method for long paired-end sequencing of large insert libraries, which can efficiently improve the quality of de novo genome assembly and identify large and small structural rearrangements or assembly errors.
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Affiliation(s)
- Zhaozhao Dai
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Tong Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jiadong Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zhifei Han
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yonglong Pan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10081 China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10081 China
| | - Meizhong Luo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
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38
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Giani AM, Gallo GR, Gianfranceschi L, Formenti G. Long walk to genomics: History and current approaches to genome sequencing and assembly. Comput Struct Biotechnol J 2019; 18:9-19. [PMID: 31890139 PMCID: PMC6926122 DOI: 10.1016/j.csbj.2019.11.002] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/03/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
Genomes represent the starting point of genetic studies. Since the discovery of DNA structure, scientists have devoted great efforts to determine their sequence in an exact way. In this review we provide a comprehensive historical background of the improvements in DNA sequencing technologies that have accompanied the major milestones in genome sequencing and assembly, ranging from early sequencing methods to Next-Generation Sequencing platforms. We then focus on the advantages and challenges of the current technologies and approaches, collectively known as Third Generation Sequencing. As these technical advancements have been accompanied by progress in analytical methods, we also review the bioinformatic tools currently employed in de novo genome assembly, as well as some applications of Third Generation Sequencing technologies and high-quality reference genomes.
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Key Words
- BAC, Bacterial Artificial Chromosome
- Bioinformatics
- Genome assembly
- HGP, Human Genome Project
- HMW, high molecular weight
- HapMap, haplotype map
- NGS, Next Generation Sequencing
- Next-generation
- OLC, Overlap-Layout-Consensus
- QV, Quality Value (QV)
- Reference
- SBS, Sequencing by Synthesis
- SMRT, Single Molecule Real-Time
- SNPs, Single Nucleotide Polymorphisms
- SRA, Short Read Archive
- SV, Structural Variant
- Sequencing
- TGS, Third Generation Sequencing
- Third-generation
- WGS, Whole Genome Sequencing
- ZMW, Zero-Mode Waveguide
- bp, base pair
- dNTPs, deoxynucleoside triphosphates
- ddNTP, 2,3-dideoxynucleoside triphosphate
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Affiliation(s)
- Alice Maria Giani
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
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Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, Corces MR, Granja JM, Chen X, Coruh C, Abnousi A, Houston J, Ye Z, Hu R, Yu M, Kim H, Law JA, Verhaak RGW, Hu M, Furnari FB, Chang HY, Ren B, Bafna V, Mischel PS. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature 2019; 575:699-703. [PMID: 31748743 PMCID: PMC7094777 DOI: 10.1038/s41586-019-1763-5] [Citation(s) in RCA: 284] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 09/26/2019] [Indexed: 01/01/2023]
Abstract
Oncogenes are commonly amplified on particles of extrachromosomal DNA (ecDNA) in cancer1,2, but our understanding of the structure of ecDNA and its effect on gene regulation is limited. Here, by integrating ultrastructural imaging, long-range optical mapping and computational analysis of whole-genome sequencing, we demonstrate the structure of circular ecDNA. Pan-cancer analyses reveal that oncogenes encoded on ecDNA are among the most highly expressed genes in the transcriptome of the tumours, linking increased copy number with high transcription levels. Quantitative assessment of the chromatin state reveals that although ecDNA is packaged into chromatin with intact domain structure, it lacks higher-order compaction that is typical of chromosomes and displays significantly enhanced chromatin accessibility. Furthermore, ecDNA is shown to have a significantly greater number of ultra-long-range interactions with active chromatin, which provides insight into how the structure of circular ecDNA affects oncogene function, and connects ecDNA biology with modern cancer genomics and epigenetics.
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Affiliation(s)
- Sihan Wu
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Kristen M Turner
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Boundless Bio, Inc., La Jolla, CA, USA
| | - Nam Nguyen
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
- Boundless Bio, Inc., La Jolla, CA, USA
| | - Ramya Raviram
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Marcella Erb
- UCSD Light Microscopy Core Facility, Department of Neurosciences, University of California at San Diego, La Jolla, CA, USA
| | - Jennifer Santini
- UCSD Light Microscopy Core Facility, Department of Neurosciences, University of California at San Diego, La Jolla, CA, USA
| | - Jens Luebeck
- Bioinformatics & Systems Biology Graduate Program, University of California at San Diego, La Jolla, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
| | - Yarui Diao
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Department of Cell Biology, Regeneration Next Initiative, Duke University School of Medicine, Durham, NC, USA
- Department of Orthopaedic Surgery, Regeneration Next Initiative, Duke University School of Medicine, Durham, NC, USA
| | - Bin Li
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Wenjing Zhang
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Nathan Jameson
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Xingqi Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ceyda Coruh
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Armen Abnousi
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Jack Houston
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Zhen Ye
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Miao Yu
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Frank B Furnari
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California at San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA.
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA.
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA.
- Department of Pathology, University of California at San Diego, La Jolla, CA, USA.
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40
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Abrosimova LA, Kisil OV, Romanova EA, Oretskaya TS, Kubareva EA. Nicking Endonucleases as Unique Tools for Biotechnology and Gene Engineering. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019050017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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41
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Chuang HM, Reifenberger JG, Bhandari AB, Dorfman KD. Extension distribution for DNA confined in a nanochannel near the Odijk regime. J Chem Phys 2019; 151:114903. [PMID: 31542006 DOI: 10.1063/1.5121305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
DNA confinement in a nanochannel typically is understood via mapping to the confinement of an equivalent neutral polymer by hard walls. This model has proven to be effective for confinement in relatively large channels where hairpin formation is frequent. An analysis of existing experimental data for Escherichia coli DNA extension in channels smaller than the persistence length, combined with an additional dataset for λ-DNA confined in a 34 nm wide channel, reveals a breakdown in this approach as the channel size approaches the Odijk regime of strong confinement. In particular, the predicted extension distribution obtained from the asymptotic solution to the weakly correlated telegraph model for a confined wormlike chain deviates significantly from the experimental distribution obtained for DNA confinement in the 34 nm channel, and the discrepancy cannot be resolved by treating the alignment fluctuations or the effective channel size as fitting parameters. We posit that the DNA-wall electrostatic interactions, which are sensible throughout a significant fraction of the channel cross section in the Odijk regime, are the source of the disagreement between theory and experiment. Dimensional analysis of the wormlike chain propagator in channel confinement reveals the importance of a dimensionless parameter, reflecting the magnitude of the DNA-wall electrostatic interactions relative to thermal energy, which has not been considered explicitly in the prevailing theories for DNA confinement in a nanochannel.
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Affiliation(s)
- Hui-Min Chuang
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Jeffrey G Reifenberger
- Bionano Genomics, Inc., 9640 Towne Centre Drive, Suite 100, San Diego, California 92121, USA
| | - Aditya Bikram Bhandari
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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Morrow BE, McDonald-McGinn DM, Emanuel BS, Vermeesch JR, Scambler PJ. Molecular genetics of 22q11.2 deletion syndrome. Am J Med Genet A 2019; 176:2070-2081. [PMID: 30380194 DOI: 10.1002/ajmg.a.40504] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/11/2018] [Accepted: 07/17/2018] [Indexed: 02/02/2023]
Abstract
The 22q11.2 deletion syndrome (22q11.2DS) is a congenital malformation and neuropsychiatric disorder caused by meiotic chromosome rearrangements. One of the goals of this review is to summarize the current state of basic research studies of 22q11.2DS. It highlights efforts to understand the mechanisms responsible for the 22q11.2 deletion that occurs in meiosis. This mechanism involves the four sets of low copy repeats (LCR22) that are dispersed in the 22q11.2 region and the deletion is mediated by nonallelic homologous recombination events. This review also highlights selected genes mapping to the 22q11.2 region that may contribute to the typical clinical findings associated with the disorder and explain that mutations in genes on the remaining allele can uncover rare recessive conditions. Another important aspect of 22q11.2DS is the existence of phenotypic heterogeneity. While some patients are mildly affected, others have severe medical, cognitive, and/or psychiatric challenges. Variability may be due in part to the presence of genetic modifiers. This review discusses current genome-wide efforts to identify such modifiers that could shed light on molecular pathways required for normal human development, cognition or behavior.
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Affiliation(s)
- Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Donna M McDonald-McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Beverly S Emanuel
- Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Joris R Vermeesch
- Center for Human Genetics, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Peter J Scambler
- Institute of Child Health, University College London, London, UK
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43
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Douglas GM, Langille MGI. Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes. Genome Biol Evol 2019; 11:2750-2766. [PMID: 31504488 PMCID: PMC6777429 DOI: 10.1093/gbe/evz184] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2019] [Indexed: 12/16/2022] Open
Abstract
High-throughput shotgun metagenomics sequencing has enabled the profiling of myriad natural communities. These data are commonly used to identify gene families and pathways that were potentially gained or lost in an environment and which may be involved in microbial adaptation. Despite the widespread interest in these events, there are no established best practices for identifying gene gain and loss in metagenomics data. Horizontal gene transfer (HGT) represents several mechanisms of gene gain that are especially of interest in clinical microbiology due to the rapid spread of antibiotic resistance genes in natural communities. Several additional mechanisms of gene gain and loss, including gene duplication, gene loss-of-function events, and de novo gene birth are also important to consider in the context of metagenomes but have been less studied. This review is largely focused on detecting HGT in prokaryotic metagenomes, but methods for detecting these other mechanisms are first discussed. For this article to be self-contained, we provide a general background on HGT and the different possible signatures of this process. Lastly, we discuss how improved assembly of genomes from metagenomes would be the most straight-forward approach for improving the inference of gene gain and loss events. Several recent technological advances could help improve metagenome assemblies: long-read sequencing, determining the physical proximity of contigs, optical mapping of short sequences along chromosomes, and single-cell metagenomics. The benefits and limitations of these advances are discussed and open questions in this area are highlighted.
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Affiliation(s)
- Gavin M Douglas
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Morgan G I Langille
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
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44
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León NY, Reyes AP, Harley VR. A clinical algorithm to diagnose differences of sex development. Lancet Diabetes Endocrinol 2019; 7:560-574. [PMID: 30803928 DOI: 10.1016/s2213-8587(18)30339-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 12/15/2022]
Abstract
The diagnosis and management of children born with ambiguous genitalia is challenging for clinicians. Such differences of sex development (DSDs) are congenital conditions in which chromosomal, gonadal, or anatomical sex is atypical. The aetiology of DSDs is very heterogenous and a precise diagnosis is essential for management of genetic, endocrine, surgical, reproductive, and psychosocial issues. In this Review, we outline a step-by-step approach, compiled in a diagnostic algorithm, for the clinical assessment and molecular diagnosis of a patient with ambiguity of the external genitalia on initial presentation. We appraise established and emerging technologies and their effect on diagnosis, and discuss current controversies.
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Affiliation(s)
- Nayla Y León
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Melbourne, VIC, Australia
| | - Alejandra P Reyes
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Melbourne, VIC, Australia; Genetics Department, Children's Hospital of Mexico Federico Gómez, Mexico City, Mexico
| | - Vincent R Harley
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Melbourne, VIC, Australia.
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45
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Pounraja VK, Jayakar G, Jensen M, Kelkar N, Girirajan S. A machine-learning approach for accurate detection of copy number variants from exome sequencing. Genome Res 2019; 29:1134-1143. [PMID: 31171634 PMCID: PMC6633262 DOI: 10.1101/gr.245928.118] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/04/2019] [Indexed: 11/25/2022]
Abstract
Copy number variants (CNVs) are a major cause of several genetic disorders, making their detection an essential component of genetic analysis pipelines. Current methods for detecting CNVs from exome-sequencing data are limited by high false-positive rates and low concordance because of inherent biases of individual algorithms. To overcome these issues, calls generated by two or more algorithms are often intersected using Venn diagram approaches to identify "high-confidence" CNVs. However, this approach is inadequate, because it misses potentially true calls that do not have consensus from multiple callers. Here, we present CN-Learn, a machine-learning framework that integrates calls from multiple CNV detection algorithms and learns to accurately identify true CNVs using caller-specific and genomic features from a small subset of validated CNVs. Using CNVs predicted by four exome-based CNV callers (CANOES, CODEX, XHMM, and CLAMMS) from 503 samples, we demonstrate that CN-Learn identifies true CNVs at higher precision (∼90%) and recall (∼85%) rates while maintaining robust performance even when trained with minimal data (∼30 samples). CN-Learn recovers twice as many CNVs compared to individual callers or Venn diagram-based approaches, with features such as exome capture probe count, caller concordance, and GC content providing the most discriminatory power. In fact, ∼58% of all true CNVs recovered by CN-Learn were either singletons or calls that lacked support from at least one caller. Our study underscores the limitations of current approaches for CNV identification and provides an effective method that yields high-quality CNVs for application in clinical diagnostics.
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Affiliation(s)
- Vijay Kumar Pounraja
- Bioinformatics and Genomics Graduate Program of the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Gopal Jayakar
- The Schreyer Honors College, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Matthew Jensen
- Bioinformatics and Genomics Graduate Program of the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Neil Kelkar
- The Schreyer Honors College, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Santhosh Girirajan
- Bioinformatics and Genomics Graduate Program of the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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46
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Slatko BE, Gardner AF, Ausubel FM. Overview of Next-Generation Sequencing Technologies. ACTA ACUST UNITED AC 2019; 122:e59. [PMID: 29851291 DOI: 10.1002/cpmb.59] [Citation(s) in RCA: 383] [Impact Index Per Article: 76.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High throughput DNA sequencing methodology (next generation sequencing; NGS) has rapidly evolved over the past 15 years and new methods are continually being commercialized. As the technology develops, so do increases in the number of corresponding applications for basic and applied science. The purpose of this review is to provide a compendium of NGS methodologies and associated applications. Each brief discussion is followed by web links to the manufacturer and/or web-based visualizations. Keyword searches, such as with Google, may also provide helpful internet links and information. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
| | | | - Frederick M Ausubel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
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47
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Genome maps across 26 human populations reveal population-specific patterns of structural variation. Nat Commun 2019; 10:1025. [PMID: 30833565 PMCID: PMC6399254 DOI: 10.1038/s41467-019-08992-7] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/12/2019] [Indexed: 01/10/2023] Open
Abstract
Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome. Large structural variants (SV) are understudied in human genetics research because of the difficulty to detect them in the routinely generated short-read sequencing data. Here, the authors generate optical genome maps of 154 individuals from 26 populations that allow comprehensive examination of large SVs.
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48
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Abstract
Affordable, high-throughput DNA sequencing has accelerated the pace of genome assembly over the past decade. Genome assemblies from high-throughput, short-read sequencing, however, are often not as contiguous as the first generation of genome assemblies. Whereas early genome assembly projects were often aided by clone maps or other mapping data, many current assembly projects forego these scaffolding data and only assemble genomes into smaller segments. Recently, new technologies have been invented that allow chromosome-scale assembly at a lower cost and faster speed than traditional methods. Here, we give an overview of the problem of chromosome-scale assembly and traditional methods for tackling this problem. We then review new technologies for chromosome-scale assembly and recent genome projects that used these technologies to create highly contiguous genome assemblies at low cost.
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Affiliation(s)
- Edward S. Rice
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA;,
| | - Richard E. Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA;,
- Dovetail Genomics, LLC, Santa Cruz, California 95060, USA
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49
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Bocklandt S, Hastie A, Cao H. Bionano Genome Mapping: High-Throughput, Ultra-Long Molecule Genome Analysis System for Precision Genome Assembly and Haploid-Resolved Structural Variation Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1129:97-118. [DOI: 10.1007/978-981-13-6037-4_7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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50
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Wee Y, Bhyan SB, Liu Y, Lu J, Li X, Zhao M. The bioinformatics tools for the genome assembly and analysis based on third-generation sequencing. Brief Funct Genomics 2018; 18:1-12. [DOI: 10.1093/bfgp/ely037] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/03/2018] [Accepted: 10/19/2018] [Indexed: 02/06/2023] Open
Affiliation(s)
- YongKiat Wee
- School of Science and Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland, Australia
| | - Salma Begum Bhyan
- School of Science and Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland, Australia
| | - Yining Liu
- The School of Public Health, Institute for Chemical Carcinogenesis,Guangzhou Medical University, Dongfengxi Road, Guangzhou, China
| | - Jiachun Lu
- The School of Public Health, Institute for Chemical Carcinogenesis,Guangzhou Medical University, Dongfengxi Road, Guangzhou, China
- The School of Public Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaoyan Li
- Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung & Blood Vessel Disease, Beijing, China
| | - Min Zhao
- School of Science and Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland, Australia
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