1
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Shelton WJ, Zandpazandi S, Nix JS, Gokden M, Bauer M, Ryan KR, Wardell CP, Vaske OM, Rodriguez A. Long-read sequencing for brain tumors. Front Oncol 2024; 14:1395985. [PMID: 38915364 PMCID: PMC11194609 DOI: 10.3389/fonc.2024.1395985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024] Open
Abstract
Brain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in the advanced molecular characterization of brain tumors for diagnosis, prognosis, and treatment. Since the implementation of molecular biomarkers by the WHO CNS in 2016, the genomics of brain tumors has been integrated into diagnostic criteria. Long-read sequencing, also known as third generation sequencing, is an emerging technique that allows for the sequencing of longer DNA segments leading to improved detection of structural variants and epigenetics. These capabilities are opening a way for better characterization of brain tumors. Here, we present a comprehensive summary of the state of the art of third-generation sequencing in the application for brain tumor diagnosis, prognosis, and treatment. We discuss the advantages and potential new implementations of long-read sequencing into clinical paradigms for neuro-oncology patients.
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Affiliation(s)
- William J. Shelton
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Sara Zandpazandi
- Department of Neurosurgery, Medical University of South Carolina, Charleston, SC, United States
| | - J Stephen Nix
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Murat Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Katie Rose Ryan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Christopher P. Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Olena Morozova Vaske
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Analiz Rodriguez
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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2
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Ishida Y, Murata T, Kakiuchi N, Ogawa S, Kabashima K. Emergence of multiple revertant keratinocyte clones in a patient with KID syndrome. J Eur Acad Dermatol Venereol 2024; 38:e285-e287. [PMID: 37907277 DOI: 10.1111/jdv.19595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/23/2023] [Indexed: 11/02/2023]
Affiliation(s)
- Y Ishida
- Department of Dermatology, Kyoto University, Kyoto, Japan
| | - T Murata
- Department of Dermatology, Hyogo Medical University, Hyogo, Japan
| | - N Kakiuchi
- The Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - S Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - K Kabashima
- Department of Dermatology, Kyoto University, Kyoto, Japan
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3
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Alsabbagh MM. Keratitis-ichthyosis-deafness syndrome: A comprehensive review of cutaneous and systemic manifestations. Pediatr Dermatol 2023; 40:19-27. [PMID: 36444857 DOI: 10.1111/pde.15201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/05/2022] [Indexed: 11/30/2022]
Abstract
Keratitis-ichthyosis-deafness syndrome is a rare genetic disease presenting with cutaneous, ocular, and otic defects. This comprehensive review provides insight into the clinical presentations, highlighting the cutaneous manifestations including histopathology and treatment options.
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Affiliation(s)
- Manahel Mahmood Alsabbagh
- Department of Molecular Medicine, Princess Al-Jawhara Center for Molecular Medicine and Inherited Disorders, Arabian Gulf University, Manama, Kingdom of Bahrain
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4
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Miller AR, Wijeratne S, McGrath SD, Schieffer KM, Miller KE, Lee K, Mathew M, LaHaye S, Fitch JR, Kelly BJ, White P, Mardis ER, Wilson RK, Cottrell CE, Magrini V. Pacific Biosciences Fusion and Long Isoform Pipeline for Cancer Transcriptome-Based Resolution of Isoform Complexity. J Mol Diagn 2022; 24:1292-1306. [PMID: 36191838 DOI: 10.1016/j.jmoldx.2022.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 08/05/2022] [Accepted: 09/13/2022] [Indexed: 01/13/2023] Open
Abstract
Genomic profiling using short-read sequencing has utility in detecting disease-associated variation in both DNA and RNA. However, given the frequent occurrence of structural variation in cancer, molecular profiling using long-read sequencing improves the resolution of such events. For example, the Pacific Biosciences long-read RNA-sequencing (Iso-Seq) transcriptome protocol provides full-length isoform characterization, discernment of allelic phasing, and isoform discovery, and identifies expressed fusion partners. The Pacific Biosciences Fusion and Long Isoform Pipeline (PB_FLIP) incorporates a suite of RNA-sequencing software analysis tools and scripts to identify expressed fusion partners and isoforms. In addition, sequencing of a commercial reference (Spike-In RNA Variants) with known isoform complexity was performed and demonstrated high recall of the Iso-Seq and PB_FLIP workflow to benchmark our protocol and analysis performance. This study describes the utility of Iso-Seq and PB_FLIP analysis in improving deconvolution of complex structural variants and isoform detection within an institutional pediatric and adolescent/young adult translational cancer research cohort. The exemplar case studies demonstrate that Iso-Seq and PB_FLIP discover novel expressed fusion partners, resolve complex intragenic alterations, and discriminate between allele-specific expression profiles.
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Affiliation(s)
- Anthony R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Saranga Wijeratne
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Sean D McGrath
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Katherine E Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Mariam Mathew
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - James R Fitch
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio; Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, Ohio
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio.
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio
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5
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Revertant Mosaicism in Genodermatoses: Natural Gene Therapy Right before Your Eyes. Biomedicines 2022; 10:biomedicines10092118. [PMID: 36140224 PMCID: PMC9495737 DOI: 10.3390/biomedicines10092118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022] Open
Abstract
Revertant mosaicism (RM) is the intriguing phenomenon in which nature itself has successfully done what medical science is so eagerly trying to achieve: correcting the effect of disease-causing germline variants and thereby reversing the disease phenotype back to normal. RM was molecularly confirmed for the first time in a genodermatosis in 1997, the genetic skin condition junctional epidermolysis bullosa (EB). At that time, RM was considered an extraordinary phenomenon. However, several important discoveries have changed this conception in the past few decades. First, RM has now been identified in all major subtypes of EB. Second, RM has also been identified in many other genodermatoses. Third, a theoretical mathematical exercise concluded that reverse mutations should be expected in all patients with a recessive subtype of EB or any other genodermatosis. This has shifted the paradigm from RM being an extraordinary phenomenon to it being something that every physician working in the field of genodermatoses should be looking for in every patient. It has also raised hope for new treatment options in patients with genodermatoses. In this review, we summarize the current knowledge on RM and discuss the perspectives of RM for the future treatment of patients with genodermatoses.
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6
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Third-Generation Cytogenetic Analysis: Diagnostic Application of Long-Read Sequencing. J Mol Diagn 2022; 24:711-718. [PMID: 35526834 DOI: 10.1016/j.jmoldx.2022.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/23/2022] [Accepted: 03/25/2022] [Indexed: 11/21/2022] Open
Abstract
Copy number variants (CNVs) play important roles in the pathogenesis of several genetic syndromes. Traditional and molecular karyotyping are considered the first-tier diagnostic tests to detect macroscopic and cryptic deletions/duplications. However, their time-consuming and laborious experimental protocols protract diagnostic times from 3 to 15 days. Nanopore sequencing has the ability to reduce time to results for the detection of CNVs with the same resolution of current state-of-the-art diagnostic tests. Nanopore sequencing was compared to molecular karyotyping for the detection of pathogenic CNVs of seven patients with previously diagnosed causative CNVs of different sizes and cellular fractions. Larger chromosomal anomalies included trisomy 21 and mosaic tetrasomy 12p. Among smaller CNVs, two genomic imbalances of 1.3 Mb, a small deletion of 170 kb, and two mosaic deletions (1.2 Mb and 408 kb) were tested. DNA was sequenced and data generated during runs were analyzed in online mode. All pathogenic CNVs were identified with detection time inversely proportional to size and cellular fraction. Aneuploidies were called after only 30 minutes of sequencing, whereas 30 hours were needed to call small CNVs. These results demonstrate the clinical utility of our approach that allows the molecular diagnosis of genomic disorders within a 30-minute to 30-hour time frame and its easy implementation as a routinary diagnostic tool.
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7
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Lambert LH, Shaikh N, Marx JL, Ramsey DJ. End-stage crystalline maculopathy with retinal atrophy in Sjögren-Larsson syndrome: a case report and review of the literature. THERAPEUTIC ADVANCES IN RARE DISEASE 2022; 3:26330040221122496. [PMID: 37180414 PMCID: PMC10032463 DOI: 10.1177/26330040221122496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/03/2022] [Indexed: 05/16/2023]
Abstract
Sjögren-Larsson syndrome (SLS) is a rare, autosomal recessive neurocutaneous disorder. It is caused by the inheritance of sequence variants in the ALDH3A2 gene, which codes for fatty aldehyde dehydrogenase (FALDH). Universal signs of the condition are congenital ichthyosis, spastic paresis of the lower and upper limbs, and reduced intellectual ability. In addition to this clinical triad, patients with SLS experience dry eyes and decreased visual acuity caused by a progressive retinal degeneration. Examination of the retina in patients with SLS often reveals glistening yellow crystal-like deposits surrounding the fovea. This crystalline retinopathy often develops in childhood and is considered pathognomonic for the disease. The metabolic disorder typically shortens lifespan to half that of the unaffected population. However, now that patients with SLS live longer, it becomes increasingly important to understand the natural course of the disease. Our case describes a 58-year-old woman with advanced SLS whose ophthalmic examination illustrates the end-stage of the retinal degeneration. Optical coherence tomography (OCT) and fluorescein angiography confirm the disease is restricted to the neural retina with dramatic thinning of the macula. This case is unique since it is among the most advanced both in terms of chronological age and severity of retinal disease. While the accumulation of fatty aldehydes, alcohols, and other precursor molecules is the probable cause of retinal toxicity, a more complete understanding of the course of retinal degeneration may aid in the development of future treatments. The aim of our presentation of this case is to increase awareness of the disease and to foster interest in therapeutic research which may benefit patients with this rare condition.
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Affiliation(s)
- Lester H. Lambert
- Department of Ophthalmology, Tufts University
School of Medicine, Boston, MA, USA
- Department of Surgery, Division of
Ophthalmology, Lahey Hospital & Medical Center, Burlington, MA,
USA
| | - Noreen Shaikh
- Department of Ophthalmology, Tufts University
School of Medicine, Boston, MA, USA
- Department of Ophthalmology, Beth Israel
Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jeffrey L. Marx
- Department of Ophthalmology, Tufts University
School of Medicine, Boston, MA, USA
- Department of Surgery, Division of
Ophthalmology, Lahey Hospital & Medical Center, Burlington, MA,
USA
| | - David J. Ramsey
- Department of Ophthalmology, Tufts University
School of Medicine, Boston, MA, USA
- Department of Surgery, Division of
Ophthalmology, Lahey Hospital & Medical Center, 41 Mall Road,
Burlington, MA, 01803, USA
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8
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Olafsson S, Anderson CA. Somatic mutations provide important and unique insights into the biology of complex diseases. Trends Genet 2021; 37:872-881. [PMID: 34226062 DOI: 10.1016/j.tig.2021.06.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
Somatic evolution of cells within the body is well known to lead to cancers. However, spread of somatic mutations within a tissue over time may also contribute to the pathogenesis of non-neoplastic diseases. Recent years have seen the publication of many studies aiming to characterize somatic evolution in healthy tissues. A logical next step is to extend such work to diseased conditions. As our understanding of the interplay between somatic mutations and non-neoplastic disease grows, opportunities for the joint study of germline and somatic variants will present themselves. Here, we present our thoughts on the utility of somatic mutations for understanding both the causes and consequences of common complex disease and the challenges that remain for the joint study of the soma and germline.
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Affiliation(s)
| | - Carl A Anderson
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK.
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9
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Scatena C, Murtas D, Tomei S. Cutaneous Melanoma Classification: The Importance of High-Throughput Genomic Technologies. Front Oncol 2021; 11:635488. [PMID: 34123788 PMCID: PMC8193952 DOI: 10.3389/fonc.2021.635488] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Cutaneous melanoma is an aggressive tumor responsible for 90% of mortality related to skin cancer. In the recent years, the discovery of driving mutations in melanoma has led to better treatment approaches. The last decade has seen a genomic revolution in the field of cancer. Such genomic revolution has led to the production of an unprecedented mole of data. High-throughput genomic technologies have facilitated the genomic, transcriptomic and epigenomic profiling of several cancers, including melanoma. Nevertheless, there are a number of newer genomic technologies that have not yet been employed in large studies. In this article we describe the current classification of cutaneous melanoma, we review the current knowledge of the main genetic alterations of cutaneous melanoma and their related impact on targeted therapies, and we describe the most recent high-throughput genomic technologies, highlighting their advantages and disadvantages. We hope that the current review will also help scientists to identify the most suitable technology to address melanoma-related relevant questions. The translation of this knowledge and all actual advancements into the clinical practice will be helpful in better defining the different molecular subsets of melanoma patients and provide new tools to address relevant questions on disease management. Genomic technologies might indeed allow to better predict the biological - and, subsequently, clinical - behavior for each subset of melanoma patients as well as to even identify all molecular changes in tumor cell populations during disease evolution toward a real achievement of a personalized medicine.
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Affiliation(s)
- Cristian Scatena
- Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Daniela Murtas
- Department of Biomedical Sciences, Section of Cytomorphology, University of Cagliari, Cagliari, Italy
| | - Sara Tomei
- Omics Core, Integrated Genomics Services, Research Department, Sidra Medicine, Doha, Qatar
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10
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Garg S. Computational methods for chromosome-scale haplotype reconstruction. Genome Biol 2021; 22:101. [PMID: 33845884 PMCID: PMC8040228 DOI: 10.1186/s13059-021-02328-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/25/2021] [Indexed: 12/13/2022] Open
Abstract
High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid genomes, and metagenomes provide important insights into genetic variation associated with disease and biodiversity. However, whole-genome short read sequencing does not yield haplotype information spanning whole chromosomes directly. Computational assembly of shorter haplotype fragments is required for haplotype reconstruction, which can be challenging owing to limited fragment lengths and high haplotype and repeat variability across genomes. Recent advancements in long-read and chromosome-scale sequencing technologies, alongside computational innovations, are improving the reconstruction of haplotypes at the level of whole chromosomes. Here, we review recent and discuss methodological progress and perspectives in these areas.
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Affiliation(s)
- Shilpa Garg
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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11
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Gusic M, Prokisch H. Genetic basis of mitochondrial diseases. FEBS Lett 2021; 595:1132-1158. [PMID: 33655490 DOI: 10.1002/1873-3468.14068] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/13/2022]
Abstract
Mitochondrial disorders are monogenic disorders characterized by a defect in oxidative phosphorylation and caused by pathogenic variants in one of over 340 different genes. The implementation of whole-exome sequencing has led to a revolution in their diagnosis, duplicated the number of associated disease genes, and significantly increased the diagnosed fraction. However, the genetic etiology of a substantial fraction of patients exhibiting mitochondrial disorders remains unknown, highlighting limitations in variant detection and interpretation, which calls for improved computational and DNA sequencing methods, as well as the addition of OMICS tools. More intriguingly, this also suggests that some pathogenic variants lie outside of the protein-coding genes and that the mechanisms beyond the Mendelian inheritance and the mtDNA are of relevance. This review covers the current status of the genetic basis of mitochondrial diseases, discusses current challenges and perspectives, and explores the contribution of factors beyond the protein-coding regions and monogenic inheritance in the expansion of the genetic spectrum of disease.
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Affiliation(s)
- Mirjana Gusic
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Germany
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Germany
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12
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Abstract
Mosaicism refers to the occurrence of two or more genomes in an individual derived from a single zygote. Germline mosaicism is a mutation that is limited to the gonads and can be transmitted to offspring. Somatic mosaicism is a postzygotic mutation that occurs in the soma, and it may occur at any developmental stage or in adult tissues. Mosaic variation may be classified in six ways: (a) germline or somatic origin, (b) class of DNA mutation (ranging in scale from single base pairs to multiple chromosomes), (c) developmental context, (d) body location(s), (e) functional consequence (including deleterious, neutral, or advantageous), and (f) additional sources of mosaicism, including mitochondrial heteroplasmy, exogenous DNA sources such as vectors, and epigenetic changes such as imprinting and X-chromosome inactivation. Technological advances, including single-cell and other next-generation sequencing, have facilitated improved sensitivity and specificity to detect mosaicism in a variety of biological contexts.
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Affiliation(s)
- Jeremy Thorpe
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA; , .,Program in Biochemistry, Cellular, and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287, USA;
| | - Ikeoluwa A Osei-Owusu
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA; , .,Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA;
| | | | - Rossella Tupler
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Department of Biomedical, Metabolic, and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy;
| | - Jonathan Pevsner
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA; , .,Program in Biochemistry, Cellular, and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287, USA; .,Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA; .,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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13
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Martínez-Glez V, Tenorio J, Nevado J, Gordo G, Rodríguez-Laguna L, Feito M, de Lucas R, Pérez-Jurado LA, Ruiz Pérez VL, Torrelo A, Spinner NB, Happle R, Biesecker LG, Lapunzina P. A six-attribute classification of genetic mosaicism. Genet Med 2020; 22:1743-1757. [PMID: 32661356 PMCID: PMC8581815 DOI: 10.1038/s41436-020-0877-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 01/23/2023] Open
Abstract
Mosaicism denotes an individual who has at least two populations of cells with distinct genotypes that are derived from a single fertilized egg. Genetic variation among the cell lines can involve whole chromosomes, structural or copy number variants, small or single nucleotide variants, or epigenetic variants. The mutational events that underlie mosaic variants occur during mitotic cell divisions after fertilization and zygote formation. The initiating mutational event can occur in any types of cell at any time in development, leading to enormous variation in the distribution and phenotypic effect of mosaicism. A number of classification proposals have been put forward to classify genetic mosaicism into categories based on the location, pattern, and mechanisms of the disease. We here propose a new classification of genetic mosaicism that considers the affected tissue, the pattern and distribution of the mosaicism, the pathogenicity of the variant, the direction of the change (benign to pathogenic vs. pathogenic to benign), and the postzygotic mutational mechanism. The accurate and comprehensive categorization and subtyping of mosaicisms is important and has potential clinical utility to define the natural history of these disorders, tailor follow-up frequency and interventions, estimate recurrence risks, and guide therapeutic decisions.
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Affiliation(s)
- Víctor Martínez-Glez
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. .,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.
| | - Jair Tenorio
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - Julián Nevado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - Gema Gordo
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Lara Rodríguez-Laguna
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Marta Feito
- Department of Pediatric Dermatology, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Raúl de Lucas
- Department of Pediatric Dermatology, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Luis A Pérez-Jurado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Genetics Unit, Universitat Pompeu Fabra and Hospital del Mar Research Institute (IMIM), Barcelona, Spain.,Women's and Children's Hospital, South Australia Medical and Health Research Institute (SAHMRI) and University of Adelaide, Adelaide, SA, Australia
| | - Víctor L Ruiz Pérez
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.,Instituto de Investigaciones Biomédicas de Madrid (CSIC-UAM), Madrid, Spain
| | - Antonio Torrelo
- Department of Pediatrics, Hospital Universitario Niño Jesús, Madrid, Spain
| | - Nancy B Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicines at The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rudolf Happle
- Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, USA
| | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. .,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.
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14
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Staps P, van Gaalen J, van Domburg P, Steijlen PM, Ferdinandusse S, den Heijer T, Seyger MMB, Theelen T, Willemsen MAAP. Sjögren-Larsson syndrome: The mild end of the phenotypic spectrum. JIMD Rep 2020; 53:61-70. [PMID: 32395410 PMCID: PMC7203653 DOI: 10.1002/jmd2.12099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/19/2020] [Accepted: 01/21/2020] [Indexed: 12/18/2022] Open
Abstract
Sjögren-Larsson syndrome (SLS) is a rare inborn error of lipid metabolism. The syndrome is caused by mutations in the ALDH3A2 gene, resulting in a deficiency of fatty aldehyde dehydrogenase. Most patients have a clearly recognizable severe phenotype, with congenital ichthyosis, intellectual disability, and spastic diplegia. In this study, we describe two patients with a remarkably mild phenotype. In both patients, males with actual ages of 45 and 61 years, the diagnosis was only established at an adult age. Their skin had been moderately affected from childhood onward, and both men remained ambulant with mild spasticity of their legs. Cognitive development, as reflected by school performance and professional career, had been unremarkable. Magnetic resonance spectroscopy of the first patient was lacking the characteristic lipid peak. We performed a literature search to identify additional SLS patients with a mild phenotype. We compared the clinical, radiologic, and molecular features of the mildly affected patients with the classical phenotype. We found 10 cases in the literature with a molecular proven diagnosis and a mild phenotype. Neither a genotype-phenotype correlation nor an alternative explanation for the strikingly mild phenotypes was found. New biochemical techniques to study the underlying metabolic defect in SLS, like lipidomics, may in the future help to unravel the reasons for the exceptionally mild phenotypes. In the meantime, it is important to recognize these mildly affected patients to provide them with appropriate care and genetic counseling, and to increase our insights in the true disease spectrum of SLS.
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Affiliation(s)
- Pippa Staps
- Department of Pediatric NeurologyRadboud University Medical Center, Amalia Children's Hospital, Donders Institute for Brain Cognition and BehaviourNijmegenThe Netherlands
| | - Judith van Gaalen
- Department of Neurology, Donders Institute for Brain Cognition and BehaviourRadboud University Medical CenterNijmegenThe Netherlands
| | | | - Peter M. Steijlen
- Department of Dermatology, The GROW School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology & MetabolismAmsterdam UMC, University of AmsterdamAmsterdamThe Netherlands
| | - Tom den Heijer
- Department of NeurologyFranciscus Gasthuis and VlietlandRotterdamThe Netherlands
| | - Marieke M. B. Seyger
- Department of DermatologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Thomas Theelen
- Department of Ophthalmology, Donders Institute for Brain Cognition and BehaviourRadboud University Medical CenterNijmegenThe Netherlands
| | - Michèl A. A. P. Willemsen
- Department of Pediatric NeurologyRadboud University Medical Center, Amalia Children's Hospital, Donders Institute for Brain Cognition and BehaviourNijmegenThe Netherlands
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15
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Abstract
Genomic sequencing technologies have revolutionized mutation detection of the genetic diseases in the past few years. In recent years, the third generation sequencing (TGS) has been gaining insight into more genetic diseases owing to the single molecular and real time sequencing technology. This paper reviews the genomic sequencing revolutionary history first and then focuses on the genetic diseases discovered through the TGS and the clinical effects of the TGS, which is followed by the discussion of the improvement in the bioinformatic analysis for the TGS and its limitations. In summary, the TGS has been enhancing the diagnostic accuracy of genetic diseases in molecular level as well as paving a new way for basic researches and therapies.
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Affiliation(s)
- Tiantian Xiao
- Clinic of Neonatology, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Neonatology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Wenhao Zhou
- Clinic of Neonatology, Children's Hospital of Fudan University, Shanghai 201102, China.,Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China.,Key Laboratory of Neonatal Diseases, Children's Hospital of Fudan University, Shanghai 201102, China
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16
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Nomura T. Recombination-induced revertant mosaicism in ichthyosis with confetti and loricrin keratoderma. J Dermatol Sci 2019; 97:94-100. [PMID: 31928837 DOI: 10.1016/j.jdermsci.2019.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 12/26/2019] [Accepted: 12/26/2019] [Indexed: 01/23/2023]
Abstract
Revertant mosaicism refers to a condition in which a pathogenic germline mutation is spontaneously corrected in somatic cells, resulting in the presence of two or more cell populations with different genotypes in an organism arising from a single fertilized egg. If the revertant cells are clonally expanded due to a survival advantage over the surrounding mutant cells, patients benefit from this self-healing phenomenon which leads to the development of milder-than-expected clinical phenotypes; in genetic skin diseases, patients with revertant mosaicism present with small islands of healthy skin. To date, revertant mosaicism has been reported in ∼50 genetic diseases involving the skin, blood, liver, muscle, and brain. In this review, I briefly summarize current knowledge on revertant mosaicism in two particular skin diseases, ichthyosis with confetti (IWC) and loricrin keratoderma (LK), both of which develop numerous revertant skin patches. Notably, homologous recombination (HR) is the only mechanism underlying the reversion of pathogenic mutations in IWC and LK, and this was identified following the analysis of ∼50 revertant epidermis samples. All the samples showed long-tract loss of heterozygosity (LOH) that originated at regions centromeric to pathogenic mutations and extended to the telomere of the mutation-harboring chromosomes. Elucidating the molecular mechanisms underlying revertant mosaicism in IWC and LK-especially how mutant proteins induce long-tract LOH-would potentially expand the possibility of manipulating HR to induce the reversion of disease-causing mutations and help devising novel therapies not only for IWC and LK but also for other intractable genetic diseases.
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Affiliation(s)
- Toshifumi Nomura
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan.
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17
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Ardui S, Ameur A, Vermeesch JR, Hestand MS. Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 2019; 46:2159-2168. [PMID: 29401301 PMCID: PMC5861413 DOI: 10.1093/nar/gky066] [Citation(s) in RCA: 393] [Impact Index Per Article: 78.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/23/2018] [Indexed: 12/30/2022] Open
Abstract
Short read massive parallel sequencing has emerged as a standard diagnostic tool in the medical setting. However, short read technologies have inherent limitations such as GC bias, difficulties mapping to repetitive elements, trouble discriminating paralogous sequences, and difficulties in phasing alleles. Long read single molecule sequencers resolve these obstacles. Moreover, they offer higher consensus accuracies and can detect epigenetic modifications from native DNA. The first commercially available long read single molecule platform was the RS system based on PacBio's single molecule real-time (SMRT) sequencing technology, which has since evolved into their RSII and Sequel systems. Here we capsulize how SMRT sequencing is revolutionizing constitutional, reproductive, cancer, microbial and viral genetic testing.
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Affiliation(s)
- Simon Ardui
- Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala 75108, Sweden.,School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | | | - Matthew S Hestand
- Department of Human Genetics, KU Leuven, Leuven 3000, Belgium.,Department of Clinical Genetics, VU University Medical Center, Amsterdam 1081 BT, The Netherlands
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18
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Twaroski K, Eide C, Riddle MJ, Xia L, Lees CJ, Chen W, Mathews W, Keene DR, McGrath JA, Tolar J. Revertant mosaic fibroblasts in recessive dystrophic epidermolysis bullosa. Br J Dermatol 2019; 181:1247-1253. [PMID: 30924923 DOI: 10.1111/bjd.17943] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2019] [Indexed: 01/10/2023]
Abstract
BACKGROUND Revertant mosaicism has been described previously in recessive dystrophic epidermolysis bullosa (RDEB), manifesting as regions of skin with normal mechanical and biological characteristics. Here we report the discovery of revertant dermal fibroblasts, unique in that all other documented cases of revertant mosaicism occur in epidermal keratinocytes. OBJECTIVES To determine the cause of revertant mosaicism found in a patient with RDEB from isolated epidermal keratinocytes and dermal fibroblasts in blister and mosaic skin regions. METHODS Skin biopsies were taken from blister and mosaic skin regions of a patient with RDEB. Allele identification was confirmed and the type VII collagen (C7) content and COL7A1 expression profile of isolated keratinocytes and fibroblasts was determined. RESULTS Keratinocytes isolated from the mosaic area had a slight increase in C7, although overall expression of COL7A1 was unchanged between blister and mosaic fibroblasts. Differential allele expression was identified in blister and mosaic fibroblasts using targeted RNA sequencing (TREx), where the allele harbouring a point mutation was preferentially expressed over that containing a frameshift mutation. A crossing over event was identified in mosaic fibroblasts that was not present in blister fibroblasts, yielding a functional COL7A1 allele in a subset of cells. CONCLUSIONS In documenting a novel case of revertant mosaicism in RDEB, we have identified dermal fibroblasts as having the capacity to correct blistering functionally. We have also pioneered the use of TREx in quantifying allele-specific expression. Using fibroblasts instead of keratinocytes for RDEB therapies offers advantages in the local and systemic therapy of RDEB. What's already known about this topic? Revertant mosaicism has been previously documented in patients with recessive dystrophic epidermolysis bullosa (RDEB), however, it has only been found in epidermal keratinocytes. What does this study add? We have demonstrated that COL7A1 gene reversion in dermal fibroblasts occurs and is able to form functional skin in a patient with RDEB. Additionally, we have pioneered a new application for targeted RNA sequencing in quantifying allele-specific expression in fibroblasts and keratinocytes. What is the translational message? This opens up possibilities for using fibroblasts as local and systemic therapy for patients with RDEB.
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Affiliation(s)
| | - C Eide
- Department of Pediatrics, Division of Blood and Marrow Transplantation, Medical School, University of Minnesota, Minneapolis, MN, U.S.A
| | - M J Riddle
- Department of Pediatrics, Division of Blood and Marrow Transplantation, Medical School, University of Minnesota, Minneapolis, MN, U.S.A
| | - L Xia
- Department of Pediatrics, Division of Blood and Marrow Transplantation, Medical School, University of Minnesota, Minneapolis, MN, U.S.A
| | - C J Lees
- Department of Pediatrics, Division of Blood and Marrow Transplantation, Medical School, University of Minnesota, Minneapolis, MN, U.S.A
| | | | - W Mathews
- Department of Pediatrics, Division of Blood and Marrow Transplantation, Medical School, University of Minnesota, Minneapolis, MN, U.S.A
| | - D R Keene
- Shriners Hospital for Children, Medical Genetics and Biochemistry & Molecular Biology, Oregon Health & Science University, Portland, OR, U.S.A
| | - J A McGrath
- St. John's Institute of Dermatology, King's College London, London, U.K
| | - J Tolar
- Stem Cell Institute and.,Department of Pediatrics, Division of Blood and Marrow Transplantation, Medical School, University of Minnesota, Minneapolis, MN, U.S.A
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19
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Mantere T, Kersten S, Hoischen A. Long-Read Sequencing Emerging in Medical Genetics. Front Genet 2019; 10:426. [PMID: 31134132 PMCID: PMC6514244 DOI: 10.3389/fgene.2019.00426] [Citation(s) in RCA: 226] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/18/2019] [Indexed: 12/12/2022] Open
Abstract
The wide implementation of next-generation sequencing (NGS) technologies has revolutionized the field of medical genetics. However, the short read lengths of currently used sequencing approaches pose a limitation for the identification of structural variants, sequencing repetitive regions, phasing of alleles and distinguishing highly homologous genomic regions. These limitations may significantly contribute to the diagnostic gap in patients with genetic disorders who have undergone standard NGS, like whole exome or even genome sequencing. Now, the emerging long-read sequencing (LRS) technologies may offer improvements in the characterization of genetic variation and regions that are difficult to assess with the prevailing NGS approaches. LRS has so far mainly been used to investigate genetic disorders with previously known or strongly suspected disease loci. While these targeted approaches already show the potential of LRS, it remains to be seen whether LRS technologies can soon enable true whole genome sequencing routinely. Ultimately, this could allow the de novo assembly of individual whole genomes used as a generic test for genetic disorders. In this article, we summarize the current LRS-based research on human genetic disorders and discuss the potential of these technologies to facilitate the next major advancements in medical genetics.
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Affiliation(s)
- Tuomo Mantere
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Simone Kersten
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Internal Medicine, Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Internal Medicine, Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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20
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Sayeb M, Riahi Z, Laroussi N, Bonnet C, Romdhane L, Mkaouar R, Zaouak A, Marrakchi J, Abdessalem G, Messaoud O, Bouchniba O, Ghilane N, Mokni M, Besbes G, Yacoub‐Youssef H, Petit C, Abdelhak S. A Tunisian family with a novel mutation in the gene
CYP
4F22
for lamellar ichthyosis and co‐occurrence of hearing loss in a child due to mutation in the
SLC
26A4
gene. Int J Dermatol 2019; 58:1439-1443. [DOI: 10.1111/ijd.14452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 03/06/2019] [Accepted: 03/11/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Marwa Sayeb
- Laboratory of Biomedical Genomics and Oncogenetics (LR11IPT05) University of Tunis El Manar Pasteur Institut of Tunis Tunis Tunisia
| | - Zied Riahi
- Laboratory of Biomedical Genomics and Oncogenetics (LR11IPT05) University of Tunis El Manar Pasteur Institut of Tunis Tunis Tunisia
- INSERM UMRS 1120 Vision Institut Paris France
- University of Paris VI UPMC Sorbonnes Paris France
| | - Nadia Laroussi
- Laboratory of Biomedical Genomics and Oncogenetics (LR11IPT05) University of Tunis El Manar Pasteur Institut of Tunis Tunis Tunisia
| | - Crystel Bonnet
- INSERM UMRS 1120 Vision Institut Paris France
- University of Paris VI UPMC Sorbonnes Paris France
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics (LR11IPT05) University of Tunis El Manar Pasteur Institut of Tunis Tunis Tunisia
- Department of Biology Faculty of Science of Bizerte Université Tunis Carthage ZarzounaTunisia
| | - Rahma Mkaouar
- Laboratory of Biomedical Genomics and Oncogenetics (LR11IPT05) University of Tunis El Manar Pasteur Institut of Tunis Tunis Tunisia
| | - Anissa Zaouak
- Department of Dermatology Habib Thameur Hospital TunisTunisia
| | | | - Ghaith Abdessalem
- Laboratory of Biomedical Genomics and Oncogenetics (LR11IPT05) University of Tunis El Manar Pasteur Institut of Tunis Tunis Tunisia
| | - Olfa Messaoud
- Laboratory of Biomedical Genomics and Oncogenetics (LR11IPT05) University of Tunis El Manar Pasteur Institut of Tunis Tunis Tunisia
| | - Oussema Bouchniba
- Departement of Biochemistry Habib Bourguiba Hospital MedenineTunisia
| | - Nacer Ghilane
- Departement of Biochemistry Habib Bourguiba Hospital MedenineTunisia
| | - Mourad Mokni
- Department of Dermatology CHU La Rabta Tunis Tunis Tunisia
| | - Ghazi Besbes
- Department of Otorhinolaryngology CHU La Rabta TunisTunisia
| | - Houda Yacoub‐Youssef
- Laboratory of Biomedical Genomics and Oncogenetics (LR11IPT05) University of Tunis El Manar Pasteur Institut of Tunis Tunis Tunisia
| | - Christine Petit
- INSERM UMRS 1120 Vision Institut Paris France
- University of Paris VI UPMC Sorbonnes Paris France
- Unité de Génétique et Physiologie de l'Audition Institut Pasteur Paris France
- Collège de France Paris France
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics (LR11IPT05) University of Tunis El Manar Pasteur Institut of Tunis Tunis Tunisia
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21
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Suzuki S, Nomura T, Miyauchi T, Takeda M, Fujita Y, Nishie W, Akiyama M, Ishida-Yamamoto A, Shimizu H. Somatic recombination underlies frequent revertant mosaicism in loricrin keratoderma. Life Sci Alliance 2019; 2:2/1/e201800284. [PMID: 30718378 PMCID: PMC6362306 DOI: 10.26508/lsa.201800284] [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: 12/18/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/01/2023] Open
Abstract
We demonstrate that revertant mosaicism frequently occurs in loricrin keratoderma and that somatic recombination is the major mechanism underlying this therapeutically important phenomenon. Revertant mosaicism is a phenomenon in which pathogenic mutations are rescued by somatic events, representing a form of natural gene therapy. Here, we report on the first evidence for revertant mosaicism in loricrin keratoderma (LK), an autosomal dominant form of ichthyosis caused by mutations in LOR on 1q21.3. We identified two unrelated LK families exhibiting dozens of previously unreported white spots, which increased in both number and size with age. Biopsies of these spots revealed that they had normal histology and that causal LOR mutations were lost. Notably, dense single nucleotide polymorphism mapping identified independent copy-neutral loss-of-heterozygosity events on chromosome 1q extending from regions centromeric to LOR to the telomere in all investigated spots, suggesting that somatic recombination represents a common reversion mechanism in LK. Furthermore, we demonstrated that reversion of LOR mutations confers a growth advantage to cells in vitro, but the clinically limited size of revertant spots suggests the existence of mechanisms constraining revertant clone expansion. Nevertheless, the identification of revertant mosaicism in LK might pave the way for revertant therapy for this intractable disease.
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Affiliation(s)
- Shotaro Suzuki
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Toshifumi Nomura
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Toshinari Miyauchi
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Masae Takeda
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Yasuyuki Fujita
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Wataru Nishie
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Masashi Akiyama
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Hiroshi Shimizu
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
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22
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Wilbe M, Gudmundsson S, Johansson J, Ameur A, Stattin EL, Annerén G, Malmgren H, Frykholm C, Bondeson ML. A novel approach using long-read sequencing and ddPCR to investigate gonadal mosaicism and estimate recurrence risk in two families with developmental disorders. Prenat Diagn 2017; 37:1146-1154. [PMID: 28921562 PMCID: PMC5725701 DOI: 10.1002/pd.5156] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/04/2017] [Accepted: 09/06/2017] [Indexed: 12/17/2022]
Abstract
Objective De novo mutations contribute significantly to severe early‐onset genetic disorders. Even if the mutation is apparently de novo, there is a recurrence risk due to parental germ line mosaicism, depending on in which gonadal generation the mutation occurred. Methods We demonstrate the power of using SMRT sequencing and ddPCR to determine parental origin and allele frequencies of de novo mutations in germ cells in two families whom had undergone assisted reproduction. Results In the first family, a TCOF1 variant c.3156C>T was identified in the proband with Treacher Collins syndrome. The variant affects splicing and was determined to be of paternal origin. It was present in <1% of the paternal germ cells, suggesting a very low recurrence risk. In the second family, the couple had undergone several unsuccessful pregnancies where a de novo mutation PTPN11 c.923A>C causing Noonan syndrome was identified. The variant was present in 40% of the paternal germ cells suggesting a high recurrence risk. Conclusions Our findings highlight a successful strategy to identify the parental origin of mutations and to investigate the recurrence risk in couples that have undergone assisted reproduction with an unknown donor or in couples with gonadal mosaicism that will undergo preimplantation genetic diagnosis. What's already known about this topic?
De novo mutations contribute significantly to severe early‐onset genetic disorders.
what does this study add?
A novel successful strategy to identify the parental origin of de novo mutations and to investigate the recurrence risk by SMRT sequencing and ddPCR.
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Affiliation(s)
- Maria Wilbe
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sanna Gudmundsson
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Josefin Johansson
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Eva-Lena Stattin
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Göran Annerén
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Helena Malmgren
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Carina Frykholm
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marie-Louise Bondeson
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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