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Grochowski CM, Bengtsson JD, Du H, Gandhi M, Lun MY, Mehaffey MG, Park K, Höps W, Benito E, Hasenfeld P, Korbel JO, Mahmoud M, Paulin LF, Jhangiani SN, Hwang JP, Bhamidipati SV, Muzny DM, Fatih JM, Gibbs RA, Pendleton M, Harrington E, Juul S, Lindstrand A, Sedlazeck FJ, Pehlivan D, Lupski JR, Carvalho CMB. Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci. CELL GENOMICS 2024; 4:100590. [PMID: 38908378 DOI: 10.1016/j.xgen.2024.100590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/27/2023] [Accepted: 05/31/2024] [Indexed: 06/24/2024]
Abstract
The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a complex genomic rearrangement (CGR). Although it has been identified as an important pathogenic DNA mutation signature in genomic disorders and cancer genomes, its architecture remains unresolved. Here, we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the DNA of 24 patients identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted structural variant (SV) haplotypes. Using a combination of short-read genome sequencing (GS), long-read GS, optical genome mapping, and single-cell DNA template strand sequencing (strand-seq), the haplotype structure was resolved in 18 samples. The point of template switching in 4 samples was shown to be a segment of ∼2.2-5.5 kb of 100% nucleotide similarity within inverted repeat pairs. These data provide experimental evidence that inverted low-copy repeats act as recombinant substrates. This type of CGR can result in multiple conformers generating diverse SV haplotypes in susceptible dosage-sensitive loci.
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Affiliation(s)
| | | | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mira Gandhi
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Ming Yin Lun
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | | | - KyungHee Park
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Wolfram Höps
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Eva Benito
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Patrick Hasenfeld
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Medhat Mahmoud
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Luis F Paulin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - James Paul Hwang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sravya V Bhamidipati
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - Sissel Juul
- Oxford Nanopore Technologies, New York, NY 10013, USA
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden; Department of Clinical Genetics and Genomics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Fritz J Sedlazeck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Rice University, Houston TX 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
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2
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Kopčilová J, Ptáčková H, Kramářová T, Fajkusová L, Réblová K, Zeman J, Honzík T, Zdražilová L, Zámečník J, Balážová P, Viestová K, Kolníková M, Hansíková H, Zídková J. Large TRAPPC11 gene deletions as a cause of muscular dystrophy and their estimated genesis. J Med Genet 2024:jmg-2024-110016. [PMID: 38955476 DOI: 10.1136/jmg-2024-110016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
BACKGROUND Transport protein particle (TRAPP) is a multiprotein complex that functions in localising proteins to the Golgi compartment. The TRAPPC11 subunit has been implicated in diseases affecting muscle, brain, eye and to some extent liver. We present three patients who are compound heterozygotes for a missense variant and a structural variant in the TRAPPC11 gene. TRAPPC11 structural variants have not yet been described in association with a disease. In order to reveal the estimated genesis of identified structural variants, we performed sequencing of individual breakpoint junctions and analysed the extent of homology and the presence of repetitive elements in and around the breakpoints. METHODS Biochemical methods including isoelectric focusing on serum transferrin and apolipoprotein C-III, as well as mitochondrial respiratory chain complex activity measurements, were used. Muscle biopsy samples underwent histochemical analysis. Next-generation sequencing was employed for identifying sequence variants associated with neuromuscular disorders, and Sanger sequencing was used to confirm findings. RESULTS We suppose that non-homologous end joining is a possible mechanism of deletion origin in two patients and non-allelic homologous recombination in one patient. Analyses of mitochondrial function performed in patients' skeletal muscles revealed an imbalance of mitochondrial metabolism, which worsens with age and disease progression. CONCLUSION Our results contribute to further knowledge in the field of neuromuscular diseases and mutational mechanisms. This knowledge is important for understanding the molecular nature of human diseases and allows us to improve strategies for identifying disease-causing mutations.
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Affiliation(s)
- Johana Kopčilová
- Centre of Molecular Biology and Genetics, Brno University Hospital, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Hana Ptáčková
- Department of Pediatrics and Inherited Metabolic Disorders, Charles University, First Faculty of Medicine, and General University Hospital in Prague, Prague, Czech Republic
| | - Tereza Kramářová
- Centre of Molecular Biology and Genetics, Brno University Hospital, Brno, Czech Republic
| | - Lenka Fajkusová
- Centre of Molecular Biology and Genetics, Brno University Hospital, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kamila Réblová
- Centre of Molecular Biology and Genetics, Brno University Hospital, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jiří Zeman
- Department of Pediatrics and Inherited Metabolic Disorders, Charles University, First Faculty of Medicine, and General University Hospital in Prague, Prague, Czech Republic
| | - Tomáš Honzík
- Department of Pediatrics and Inherited Metabolic Disorders, Charles University, First Faculty of Medicine, and General University Hospital in Prague, Prague, Czech Republic
| | - Lucie Zdražilová
- Department of Pediatrics and Inherited Metabolic Disorders, Charles University, First Faculty of Medicine, and General University Hospital in Prague, Prague, Czech Republic
| | - Josef Zámečník
- Department of Pathology and Molecular Medicine, Charles University, Second Faculty of Medicine, and Faculty Hospital Motol, Prague, Czech Republic
| | - Patrícia Balážová
- Department of Pediatric Neurology, Medical Faculty of Comenius University and Children Faculty Hospital, Bratislava, Slovakia
| | - Karin Viestová
- Department of Pediatric Neurology, Medical Faculty of Comenius University and Children Faculty Hospital, Bratislava, Slovakia
| | - Miriam Kolníková
- Department of Pediatric Neurology, Medical Faculty of Comenius University and Children Faculty Hospital, Bratislava, Slovakia
| | - Hana Hansíková
- Department of Pediatrics and Inherited Metabolic Disorders, Charles University, First Faculty of Medicine, and General University Hospital in Prague, Prague, Czech Republic
| | - Jana Zídková
- Centre of Molecular Biology and Genetics, Brno University Hospital, Brno, Czech Republic
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3
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Massier M, Doco-Fenzy M, Egloff M, Le Guillou X, Le Guyader G, Redon S, Benech C, Le Millier K, Uguen K, Ropars J, Sacaze E, Audebert-Bellanger S, Apetrei A, Molin A, Gruchy N, Vincent-Devulder A, Spodenkiewicz M, Jacquin C, Loron G, Thibaud M, Delplancq G, Brisset S, Lesieur-Sebellin M, Malan V, Romana S, Rio M, Marlin S, Amiel J, Marquet V, Dauriat B, Moradkhani K, Mercier S, Isidor B, Arpin S, Pujalte M, Jedraszak G, Pebrel-Richard C, Salaun G, Laffargue F, Boudjarane J, Missirian C, Chelloug N, Toutain A, Chiesa J, Keren B, Mignot C, Gouy E, Jaillard S, Landais E, Poirsier C. 3q29 duplications: A cohort of 46 patients and a literature review. Am J Med Genet A 2024; 194:e63531. [PMID: 38421086 DOI: 10.1002/ajmg.a.63531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 03/02/2024]
Abstract
Duplications of the 3q29 cytoband are rare chromosomal copy number variations (CNVs) (overlapping or recurrent ~1.6 Mb 3q29 duplications). They have been associated with highly variable neurodevelopmental disorders (NDDs) with various associated features or reported as a susceptibility factor to the development of learning disabilities and neuropsychiatric disorders. The smallest region of overlap and the phenotype of 3q29 duplications remain uncertain. We here report a French cohort of 31 families with a 3q29 duplication identified by chromosomal microarray analysis (CMA), including 14 recurrent 1.6 Mb duplications, eight overlapping duplications (>1 Mb), and nine small duplications (<1 Mb). Additional genetic findings that may be involved in the phenotype were identified in 11 patients. Focusing on apparently isolated 3q29 duplications, patients present mainly mild NDD as suggested by a high rate of learning disabilities in contrast to a low proportion of patients with intellectual disabilities. Although some are de novo, most of the 3q29 duplications are inherited from a parent with a similar mild phenotype. Besides, the study of small 3q29 duplications does not provide evidence for any critical region. Our data suggest that the overlapping and recurrent 3q29 duplications seem to lead to mild NDD and that a severe or syndromic clinical presentation should warrant further genetic analyses.
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Affiliation(s)
- Marie Massier
- Department of Genetics, Reims University Hospital, Reims, France
| | - Martine Doco-Fenzy
- Department of Genetics, Reims University Hospital, Reims, France
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Matthieu Egloff
- Department of Genetics, Poitiers University Hospital, Poitiers, France
- University of Poitiers, INSERM, LNEC, Department of Genetics, Poitiers University Hospital, Poitiers, France
| | - Xavier Le Guillou
- Department of Genetics, Poitiers University Hospital, Poitiers, France
- University of Poitiers, CNRS, LMA, Department of Genetics, Poitiers University Hospital, Poitiers, France
| | | | - Sylvia Redon
- Department of Genetics, Brest University Hospital, Brest, France
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Caroline Benech
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | | | - Kevin Uguen
- Department of Genetics, Brest University Hospital, Brest, France
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Juliette Ropars
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
| | - Elise Sacaze
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
| | - Séverine Audebert-Bellanger
- Department of Genetics, Brest University Hospital, Brest, France
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
| | - Andreea Apetrei
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | - Arnaud Molin
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | - Nicolas Gruchy
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | - Aline Vincent-Devulder
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | | | - Clémence Jacquin
- Department of Genetics, Reims University Hospital, Reims, France
| | - Gauthier Loron
- Department of Neonatal Medicine and Pediatric Intensive Care, University of Reims Champagne-Ardenne, CReSTIC, Reims University Hospital, Reims, France
| | - Marie Thibaud
- Department of Pediatrics, American Memorial Hospital, Reims, France
| | | | - Sophie Brisset
- Constitutional Genetics Unit, Versailles Hospital, Le Chesnay, France
| | - Marion Lesieur-Sebellin
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Valérie Malan
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Serge Romana
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Marlène Rio
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Sandrine Marlin
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Jeanne Amiel
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Valentine Marquet
- Department of Cytogenetics, Clinical Genetics and Reproductive Biology, Limoges University Hospital, Limoges, France
| | - Benjamin Dauriat
- Department of Cytogenetics, Clinical Genetics and Reproductive Biology, Limoges University Hospital, Limoges, France
| | | | - Sandra Mercier
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Bertrand Isidor
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Stéphanie Arpin
- Department of Genetics, Tours University Hospital, UMR 1253, iBrain, University of Tours, Inserm, Tours, France
| | | | - Guillaume Jedraszak
- Constitutional Genetic Laboratory, University Hospital of Amiens & UR4666 HEMATIM, University of Picardie Jules Verne, Amiens, France
| | - Céline Pebrel-Richard
- Cytogenetic Medical Department; UIC Cytogenetics of Rare Diseases and Reproduction (GRUIC ADERGEN), Rare Diseases Reference Center (CRMR): Developmental Anomalies and Malformative Syndromes in the Auvergne Region, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Gaëlle Salaun
- Cytogenetic Medical Department; UIC Cytogenetics of Rare Diseases and Reproduction (GRUIC ADERGEN), Rare Diseases Reference Center (CRMR): Developmental Anomalies and Malformative Syndromes in the Auvergne Region, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Fanny Laffargue
- Department of Medical Genetics, UIC ADDIR (GRIUC ADERGEN), Constitutive Reference Center CLAD South-East: Developmental anomalies and malformative syndromes, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - John Boudjarane
- Medical Genetics Department, Timone Enfants University Hospital, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Chantal Missirian
- Medical Genetics Department, Timone Enfants University Hospital, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Nora Chelloug
- Department of Medical Genetics, Toulouse University Hospital, Toulouse, France
| | - Annick Toutain
- Department of Genetics, Tours University Hospital, UMR 1253, iBrain, University of Tours, Inserm, Tours, France
| | - Jean Chiesa
- Department of Genetics, Nimes, University Hospital, Nimes University Hospital, Nimes, France
| | - Boris Keren
- Department of Genetics, APHP Sorbonne University, Paris, France
| | - Cyril Mignot
- Department of Genetics, APHP Sorbonne University, Paris, France
| | - Evan Gouy
- Department of Genetics, Hospices Civils de Lyon, Lyon, France
| | - Sylvie Jaillard
- Department of Cytogenetics and Cell Biology, Rennes university hospital, Rennes, France
| | - Emilie Landais
- Department of Genetics, Reims University Hospital, Reims, France
| | - Céline Poirsier
- Department of Genetics, Reims University Hospital, Reims, France
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4
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Eissa MMA, Alotibi RS, Alqahtani AS, Aldriwesh MG, Alismail H, Asiri NY, Alabdulkareem YM. Breaking new ground: Exploring de novo chromosomal rearrangements in 1p36 microdeletion. Int J Health Sci (Qassim) 2024; 18:70-77. [PMID: 38974650 PMCID: PMC11226937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024] Open
Abstract
Chromosomal structural variations (SVs) are linked to a wide range of phenotypes and arise due to disruptions during DNA replication, which can affect gene function within the SV regions. This case report details a patient diagnosed with neurodevelopmental delay. Detailed investigation through array comparative genomic hybridization revealed two pathogenic SVs on chromosome 1, which align with a 1p36 microdeletion, and a microduplication at 2p35.3, the latter being classified as a variant of unknown significance. The patient's clinical presentation is consistent with the 1p36 deletion syndrome, characterized by specific developmental delays and physical anomalies. Further genetic analysis suggests that these terminal rearrangements might stem from an unbalanced translocation between the short arms of chromosomes 1 and 2. This case underscores the complexity of interpreting multiple concurrent SVs and their cumulative effect on phenotype. Ongoing research into such chromosomal abnormalities will enhance our understanding of their clinical manifestations and guide more targeted therapeutic strategies.
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Affiliation(s)
- Mariam M. Al Eissa
- Department of Medicne, Medical School, AlFaisal University, Riyadh, Saudi Arabia
- Public Health Authority, Public Health Lab, Molecular Genetics Laboratory, Riyadh, Saudi Arabia
| | - Raniah S. Alotibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Amerh S. Alqahtani
- Department of Medical Genetics, King Saud Medical City, Riyadh, Saudi Arabia
| | - Marwh G. Aldriwesh
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Hanan Alismail
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Nouf Y. Asiri
- Department of Anesthesia, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Yara M. Alabdulkareem
- Department of Basic Sciences, College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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5
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Mazzonetto PC, Villela D, Krepischi ACV, Pierry PM, Bonaldi A, Almeida LGD, Paula MG, Bürger MC, de Oliveira AG, Fonseca GGG, Giugliani R, Riegel-Giugliani M, Bertola D, Yamamoto GL, Passos-Bueno MR, Campos GDS, Machado ACD, Mazzeu JF, Perrone E, Zechi-Ceide RM, Kokitsu-Nakata NM, Vieira TP, Steiner CE, Gil-da-Silva-Lopes VL, Vieira DKR, Boy R, de Pina-Neto JM, Scapulatempo-Neto C, Milanezi F, Rosenberg C. Low-pass whole genome sequencing as a cost-effective alternative to chromosomal microarray analysis for low- and middle-income countries. Am J Med Genet A 2024:e63802. [PMID: 38924610 DOI: 10.1002/ajmg.a.63802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Low-pass whole genome sequencing (LP-WGS) has been applied as alternative method to detect copy number variants (CNVs) in the clinical setting. Compared with chromosomal microarray analysis (CMA), the sequencing-based approach provides a similar resolution of CNV detection at a lower cost. In this study, we assessed the efficiency and reliability of LP-WGS as a more affordable alternative to CMA. A total of 1363 patients with unexplained neurodevelopmental delay/intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies were enrolled. Those patients were referred from 15 nonprofit organizations and university centers located in different states in Brazil. The analysis of LP-WGS at 1x coverage (>50kb) revealed a positive testing result in 22% of the cases (304/1363), in which 219 and 85 correspond to pathogenic/likely pathogenic (P/LP) CNVs and variants of uncertain significance (VUS), respectively. The 16% (219/1363) diagnostic yield observed in our cohort is comparable to the 15%-20% reported for CMA in the literature. The use of commercial software, as demonstrated in this study, simplifies the implementation of the test in clinical settings. Particularly for countries like Brazil, where the cost of CMA presents a substantial barrier to most of the population, LP-WGS emerges as a cost-effective alternative for investigating copy number changes in cytogenetics.
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Affiliation(s)
- Patricia C Mazzonetto
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
| | | | - Ana C V Krepischi
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | | | | | | | | | | | | | - Roberto Giugliani
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Casa dos Raros - House of Rares, Centro de Atenção Integral e Treinamento em Doenças Raras, Porto Alegre, Brazil
- INAGEMP, Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
| | - Mariluce Riegel-Giugliani
- Casa dos Raros - House of Rares, Centro de Atenção Integral e Treinamento em Doenças Raras, Porto Alegre, Brazil
- INAGEMP, Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
| | - Débora Bertola
- Instituto da Criança, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Guilherme Lopes Yamamoto
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Instituto da Criança, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Gabriele da Silva Campos
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana Claudia Dantas Machado
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Juliana F Mazzeu
- Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
| | - Eduardo Perrone
- Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Roseli M Zechi-Ceide
- Department of Clinical Genetics and Molecular Biology, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, São Paulo, Brazil
| | - Nancy M Kokitsu-Nakata
- Department of Clinical Genetics and Molecular Biology, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, São Paulo, Brazil
| | - Társis Paiva Vieira
- Department of Translational Medicine - Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Carlos Eduardo Steiner
- Department of Translational Medicine - Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Vera Lúcia Gil-da-Silva-Lopes
- Department of Translational Medicine - Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Daniela Koeller Rodrigues Vieira
- Municipal Secretary of Health of Angra dos Reis, Rio de Janeiro, Brazil
- National Institute of Women, Children and Adolescents Health Fernandes Figueira/Oswaldo Cruz Foundation (IFF/FIOCRUZ), Rio de Janeiro, Brazil
| | - Raquel Boy
- State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | - Carla Rosenberg
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
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6
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Kojak N, Kuno J, Fittipaldi KE, Khan A, Wenger D, Glasser M, Donnianni RA, Tang Y, Zhang J, Huling K, Ally R, Mujica AO, Turner T, Magardino G, Huang PY, Kerk SY, Droguett G, Prissette M, Rojas J, Gomez T, Gagliardi A, Hunt C, Rabinowitz JS, Gong G, Poueymirou W, Chiao E, Zambrowicz B, Siao CJ, Kajimura D. Somatic and intergenerational G4C2 hexanucleotide repeat instability in a human C9orf72 knock-in mouse model. Nucleic Acids Res 2024; 52:5732-5755. [PMID: 38597682 PMCID: PMC11162798 DOI: 10.1093/nar/gkae250] [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: 06/12/2023] [Revised: 03/19/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
Expansion of a G4C2 repeat in the C9orf72 gene is associated with familial Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD). To investigate the underlying mechanisms of repeat instability, which occurs both somatically and intergenerationally, we created a novel mouse model of familial ALS/FTD that harbors 96 copies of G4C2 repeats at a humanized C9orf72 locus. In mouse embryonic stem cells, we observed two modes of repeat expansion. First, we noted minor increases in repeat length per expansion event, which was dependent on a mismatch repair pathway protein Msh2. Second, we found major increases in repeat length per event when a DNA double- or single-strand break (DSB/SSB) was artificially introduced proximal to the repeats, and which was dependent on the homology-directed repair (HDR) pathway. In mice, the first mode primarily drove somatic repeat expansion. Major changes in repeat length, including expansion, were observed when SSB was introduced in one-cell embryos, or intergenerationally without DSB/SSB introduction if G4C2 repeats exceeded 400 copies, although spontaneous HDR-mediated expansion has yet to be identified. These findings provide a novel strategy to model repeat expansion in a non-human genome and offer insights into the mechanism behind C9orf72 G4C2 repeat instability.
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Affiliation(s)
- Nada Kojak
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Junko Kuno
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | - David Wenger
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | - Yajun Tang
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Jade Zhang
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Katie Huling
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Roxanne Ally
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | - Pei Yi Huang
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Sze Yen Kerk
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | - Jose Rojas
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | | | - Guochun Gong
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | - Eric Chiao
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
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7
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Rothschild D, Susanto TT, Sui X, Spence JP, Rangan R, Genuth NR, Sinnott-Armstrong N, Wang X, Pritchard JK, Barna M. Diversity of ribosomes at the level of rRNA variation associated with human health and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.30.526360. [PMID: 36778251 PMCID: PMC9915487 DOI: 10.1101/2023.01.30.526360] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Ribosomal DNA and RNA (rDNA and rRNA) sequences are usually discarded from sequencing analyses. But with hundreds of copies of rDNA genes it is unknown whether they possess sequence variations that form different types of ribosomes that affect human physiology and disease. Here, we developed an algorithm for variant-calling between paralog genes (termed RGA) and compared rDNA variations found in short- and long-read sequencing data from the 1,000 Genomes Project (1KGP) and Genome In A Bottle (GIAB). We additionally developed a novel protocol for long-read sequencing full-length rRNA (RIBO-RT) from actively translating ribosomes. Our analyses identified hundreds of rDNA variants, most of which, surprisingly, are short insertion-deletions (indels) and dozens of highly abundant rRNA variants that are incorporated into translationally active ribosomes. To visualize variant ribosomes at the single cell level, we developed an in-situ rRNA sequencing method (SWITCH-seq) which revealed that variants are co-expressed within individual cells. Strikingly, by analyzing rDNA, we found that variants assemble into distinct ribosome subtypes. We discovered that these subtypes acquire different rRNA structures by successfully employing dimethyl sulfate (DMS) probing of full length rRNA. With this atlas we investigated rRNA variation changes across human tissues and cancer types. This revealed tissue-specific rRNA subtype expression in endoderm/ectoderm-derived tissues. In cancer, low abundant rRNA variants can become highly expressed, which suggests the presence of cancer-specific ribosomes. Together, this study identifies and comprehensively characterizes the diversity of ribosomes at the level of rRNA variants which is dominated by indel variants, their chromosomal location and unique structure as well as the association of ribosome variation with tissue-specific biology and cancer.
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8
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Jourdy Y, Chatron N, Frétigny M, Zawadzki C, Lienhart A, Stieltjes N, Rohrlich PS, Thauvin-Robinet C, Volot F, Hamida YF, Hariti G, Leuci A, Dargaud Y, Sanlaville D, Vinciguerra C. Whole F8 gene sequencing identified pathogenic structural variants in the remaining unsolved patients with severe hemophilia A. J Thromb Haemost 2024; 22:1616-1626. [PMID: 38484912 DOI: 10.1016/j.jtha.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/19/2024] [Accepted: 03/04/2024] [Indexed: 04/01/2024]
Abstract
BACKGROUND No F8 genetic abnormality is detected in approximately 1% to 2% of patients with severe hemophilia A (HA) using conventional genetic approaches. In these patients, deep intronic variation or F8 disrupting genomic rearrangement could be causal. OBJECTIVES The study aimed to identify the causal variation in families with a history of severe HA for whom genetic investigations failed. METHODS We performed whole F8 gene sequencing in 8 propositi. Genomic rearrangements were confirmed by Sanger sequencing of breakpoint junctions and/or quantitative polymerase chain reaction. RESULTS A structural variant disrupting F8 was found in each propositus, so that all the 815 families with a history of severe HA registered in our laboratory received a conclusive genetic diagnosis. These structural variants consisted of 3 balanced inversions, 3 large insertions of gained regions, and 1 retrotransposition of a mobile element. The 3 inversions were 105 Mb, 1.97 Mb, and 0.362 Mb in size. Among the insertions of gained regions, one corresponded to the insertion of a 34 kb gained region from chromosome 6q27 in F8 intron 6, another was the insertion of a 447 kb duplicated region from chromosome 9p22.1 in F8 intron 14, and the last one was the insertion of an Xq28 349 kb gained in F8 intron 5. CONCLUSION All the genetically unsolved cases of severe HA in this cohort were due to structural variants disrupting F8. This study highlights the effectiveness of whole F8 sequencing to improve the molecular diagnosis of HA when the conventional approach fails.
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Affiliation(s)
- Yohann Jourdy
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France; Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France.
| | - Nicolas Chatron
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France; Université Claude Bernard Lyon 1 - CNRS UMR 5261 -INSERM U1315, Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Lyon, France
| | - Mathilde Frétigny
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France
| | - Christophe Zawadzki
- Pôle de Biologie Pathologie Génétique, Institut d'Hématologie - Transfusion, CHU Lille, Lille, France
| | - Anne Lienhart
- Hospices Civils de Lyon, Lyon Hemophilia Center and Clinical Haemostasis Unit, Bron, France
| | | | | | - Christel Thauvin-Robinet
- Centre de Génétique, Centre de Référence, Déficiences Intellectuelles de Causes Rares, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | | | | | - Ghania Hariti
- Laboratoire de recherche en hémostase, Université d'Alger 1, Alger, Algérie
| | - Alexandre Leuci
- Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France
| | - Yesim Dargaud
- Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France; Hospices Civils de Lyon, Lyon Hemophilia Center and Clinical Haemostasis Unit, Bron, France
| | - Damien Sanlaville
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France; Université Claude Bernard Lyon 1 - CNRS UMR 5261 -INSERM U1315, Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Lyon, France
| | - Christine Vinciguerra
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France; Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France
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9
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Chen Q, Wu B, Li C, Ding L, Huang S, Wang J, Zhao J. Deciphering male influence in gynogenetic Pengze crucian carp ( Carassius auratus var. pengsenensis): insights from Nanopore sequencing of structural variations. Front Genet 2024; 15:1392110. [PMID: 38784042 PMCID: PMC11111978 DOI: 10.3389/fgene.2024.1392110] [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: 02/27/2024] [Accepted: 04/11/2024] [Indexed: 05/25/2024] Open
Abstract
In this study, we investigate gynogenetic reproduction in Pengze Crucian Carp (Carassius auratus var. pengsenensis) using third-generation Nanopore sequencing to uncover structural variations (SVs) in offspring. Our objective was to understand the role of male genetic material in gynogenesis by examining the genomes of both parents and their offspring. We discovered a notable number of male-specific structural variations (MSSVs): 1,195 to 1,709 MSSVs in homologous offspring, accounting for approximately 0.52%-0.60% of their detected SVs, and 236 to 350 MSSVs in heterologous offspring, making up about 0.10%-0.13%. These results highlight the significant influence of male genetic material on the genetic composition of offspring, particularly in homologous pairs, challenging the traditional view of asexual reproduction. The gene annotation of MSSVs revealed their presence in critical gene regions, indicating potential functional impacts. Specifically, we found 5 MSSVs in the exonic regions of protein-coding genes in homologous offspring, suggesting possible direct effects on protein structure and function. Validation of an MSSV in the exonic region of the polyunsaturated fatty acid 5-lipoxygenase gene confirmed male genetic material transmission in some offspring. This study underscores the importance of further research on the genetic diversity and gynogenesis mechanisms, providing valuable insights for reproductive biology, aquaculture, and fostering innovation in biological research and aquaculture practices.
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Affiliation(s)
- Qianhui Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Biyu Wu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Chao Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Liyun Ding
- Jiangxi Fisheries Research Institute, Nanchang, China
| | - Shiting Huang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Junjie Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jun Zhao
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
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10
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Muñoz-Oreja M, Sandoval A, Bruland O, Perez-Rodriguez D, Fernandez-Pelayo U, de Arbina AL, Villar-Fernandez M, Hernández-Eguiazu H, Hernández I, Park Y, Goicoechea L, Pascual-Frías N, Garcia-Ruiz C, Fernandez-Checa J, Martí-Carrera I, Gil-Bea FJ, Hasan MT, Gegg ME, Bredrup C, Knappskog PM, Gereñu-Lopetegui G, Varhaug KN, Bindoff LA, Spinazzola A, Yoon WH, Holt IJ. Elevated cholesterol in ATAD3 mutants is a compensatory mechanism that leads to membrane cholesterol aggregation. Brain 2024; 147:1899-1913. [PMID: 38242545 PMCID: PMC11068212 DOI: 10.1093/brain/awae018] [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: 07/20/2023] [Revised: 10/29/2023] [Accepted: 12/16/2023] [Indexed: 01/21/2024] Open
Abstract
Aberrant cholesterol metabolism causes neurological disease and neurodegeneration, and mitochondria have been linked to perturbed cholesterol homeostasis via the study of pathological mutations in the ATAD3 gene cluster. However, whether the cholesterol changes were compensatory or contributory to the disorder was unclear, and the effects on cell membranes and the wider cell were also unknown. Using patient-derived cells, we show that cholesterol perturbation is a conserved feature of pathological ATAD3 variants that is accompanied by an expanded lysosome population containing membrane whorls characteristic of lysosomal storage diseases. Lysosomes are also more numerous in Drosophila neural progenitor cells expressing mutant Atad3, which exhibit abundant membrane-bound cholesterol aggregates, many of which co-localize with lysosomes. By subjecting the Drosophila Atad3 mutant to nutrient restriction and cholesterol supplementation, we show that the mutant displays heightened cholesterol dependence. Collectively, these findings suggest that elevated cholesterol enhances tolerance to pathological ATAD3 variants; however, this comes at the cost of inducing cholesterol aggregation in membranes, which lysosomal clearance only partly mitigates.
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Affiliation(s)
- Mikel Muñoz-Oreja
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastian, Spain
- University of the Basque Country—Bizkaia Campus, 48940 Bilbao, Spain
- CIBERNED (Center for Networked Biomedical Research on Neurodegenerative Diseases, Ministry of Economy and Competitiveness, Institute Carlos III), 28031 Madrid, Spain
| | - Abigail Sandoval
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Ove Bruland
- Department of Medical Genetics, Haukeland University Hospital, Bergen 5021, Norway
| | - Diego Perez-Rodriguez
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK
| | - Uxoa Fernandez-Pelayo
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastian, Spain
| | - Amaia Lopez de Arbina
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastian, Spain
| | - Marina Villar-Fernandez
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastian, Spain
| | | | - Ixiar Hernández
- University of the Basque Country—Bizkaia Campus, 48940 Bilbao, Spain
| | - Yohan Park
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Leire Goicoechea
- Department of Cell Death and Proliferation, Institute of Biomedical Research of Barcelona (IIBB), CSIC, 08036 Barcelona, Spain
- Liver Unit, Hospital Clinic i Provincial de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBEREHD), 08036 Barcelona, Spain
| | - Nerea Pascual-Frías
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastian, Spain
- Center for Cooperative Research in Biomaterials (CIC BiomaGUNE), Basque Research and Technology Alliance (BRTA), 20014 San Sebastian, Spain
| | - Carmen Garcia-Ruiz
- Department of Cell Death and Proliferation, Institute of Biomedical Research of Barcelona (IIBB), CSIC, 08036 Barcelona, Spain
- Liver Unit, Hospital Clinic i Provincial de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBEREHD), 08036 Barcelona, Spain
| | - Jose Fernandez-Checa
- Department of Cell Death and Proliferation, Institute of Biomedical Research of Barcelona (IIBB), CSIC, 08036 Barcelona, Spain
- Liver Unit, Hospital Clinic i Provincial de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBEREHD), 08036 Barcelona, Spain
- Research Center for ALPD, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Itxaso Martí-Carrera
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastian, Spain
- University of the Basque Country—Bizkaia Campus, 48940 Bilbao, Spain
- CIBERNED (Center for Networked Biomedical Research on Neurodegenerative Diseases, Ministry of Economy and Competitiveness, Institute Carlos III), 28031 Madrid, Spain
- Pediatric Neurology, Hospital Universitario Donostia, 20014 San Sebastián, Spain
| | | | - Mazahir T Hasan
- Laboratory of Brain Circuits Therapeutics, Achucarro Basque Center for Neuroscience, Barrio Sarriena, s/n, E-48940 Leioa, Spain
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Matthew E Gegg
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK
| | - Cecilie Bredrup
- Department of Ophthalmology, Haukeland University Hospital, Bergen 5021, Norway
- Department of Clinical Medicine (K1), University of Bergen, Bergen 5020, Norway
| | | | - Gorka Gereñu-Lopetegui
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastian, Spain
- University of the Basque Country—Bizkaia Campus, 48940 Bilbao, Spain
- CIBERNED (Center for Networked Biomedical Research on Neurodegenerative Diseases, Ministry of Economy and Competitiveness, Institute Carlos III), 28031 Madrid, Spain
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Kristin N Varhaug
- Department of Clinical Medicine (K1), University of Bergen, Bergen 5020, Norway
- Department of Neurology, Haukeland University Hospital, Bergen 5021, Norway
| | - Laurence A Bindoff
- Department of Ophthalmology, Haukeland University Hospital, Bergen 5021, Norway
- Department of Clinical Medicine (K1), University of Bergen, Bergen 5020, Norway
- Department of Neurology, Haukeland University Hospital, Bergen 5021, Norway
| | - Antonella Spinazzola
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK
| | - Wan Hee Yoon
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Ian J Holt
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastian, Spain
- University of the Basque Country—Bizkaia Campus, 48940 Bilbao, Spain
- CIBERNED (Center for Networked Biomedical Research on Neurodegenerative Diseases, Ministry of Economy and Competitiveness, Institute Carlos III), 28031 Madrid, Spain
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
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11
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Malamon JS, Farrell JJ, Xia LC, Dombroski BA, Das RG, Way J, Kuzma AB, Valladares O, Leung YY, Scanlon AJ, Lopez IAB, Brehony J, Worley KC, Zhang NR, Wang LS, Farrer LA, Schellenberg GD, Lee WP, Vardarajan BN. A comparative study of structural variant calling in WGS from Alzheimer's disease families. Life Sci Alliance 2024; 7:e202302181. [PMID: 38418088 PMCID: PMC10902710 DOI: 10.26508/lsa.202302181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/01/2024] Open
Abstract
Detecting structural variants (SVs) in whole-genome sequencing poses significant challenges. We present a protocol for variant calling, merging, genotyping, sensitivity analysis, and laboratory validation for generating a high-quality SV call set in whole-genome sequencing from the Alzheimer's Disease Sequencing Project comprising 578 individuals from 111 families. Employing two complementary pipelines, Scalpel and Parliament, for SV/indel calling, we assessed sensitivity through sample replicates (N = 9) with in silico variant spike-ins. We developed a novel metric, D-score, to evaluate caller specificity for deletions. The accuracy of deletions was evaluated by Sanger sequencing. We generated a high-quality call set of 152,301 deletions of diverse sizes. Sanger sequencing validated 114 of 146 detected deletions (78.1%). Scalpel excelled in accuracy for deletions ≤100 bp, whereas Parliament was optimal for deletions >900 bp. Overall, 83.0% and 72.5% of calls by Scalpel and Parliament were validated, respectively, including all 11 deletions called by both Parliament and Scalpel between 101 and 900 bp. Our flexible protocol successfully generated a high-quality deletion call set and a truth set of Sanger sequencing-validated deletions with precise breakpoints spanning 1-17,000 bp.
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Affiliation(s)
- John S Malamon
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - John J Farrell
- Biomedical Genetics Section, Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA, USA
| | - Li Charlie Xia
- https://ror.org/03mtd9a03 Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Beth A Dombroski
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rueben G Das
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jessica Way
- Broad Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amanda B Kuzma
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Otto Valladares
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yuk Yee Leung
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Allison J Scanlon
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Irving Antonio Barrera Lopez
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jack Brehony
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kim C Worley
- https://ror.org/02pttbw34 Human Genome Sequencing Center, and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Nancy R Zhang
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Lindsay A Farrer
- Biomedical Genetics Section, Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA, USA
- Departments of Neurology and Ophthalmology, Boston University School of Medicine, Boston University, Boston, MA, USA
- Departments of Epidemiology and Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Badri N Vardarajan
- https://ror.org/01esghr10 Gertrude H. Sergievsky Center and Taub Institute of Aging Brain, Department of Neurology, Columbia University Medical Center, New York, NY, USA
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12
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Elron E, Maya I, Shefer-Averbuch N, Kahana S, Matar R, Klein K, Agmon-Fishman I, Gurevitch M, Basel-Salmon L, Levy M. The Diagnostic Yield of Chromosomal Microarray Analysis in Third-Trimester Fetal Abnormalities. Am J Perinatol 2024. [PMID: 38688298 DOI: 10.1055/s-0044-1786514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
OBJECTIVE This study aimed to determine the diagnostic yield of chromosomal microarray analysis (CMA) performed in cases of fetal abnormalities detected during the third trimester of pregnancy. STUDY DESIGN A retrospective review of medical records was conducted for women who underwent amniocentesis at or beyond 28 weeks of gestation between January 2017 and February 2023. CMA results of pregnancies with abnormal sonographic findings not detected before 28 weeks were included. RESULTS A total of 482 fetuses met the inclusion criteria. The average maternal age was 31.3 years, and the average gestational age at amniocentesis was 32.3 weeks. The overall diagnostic yield of CMA was 6.2% (30 clinically significant copy number variations [CNVs]). The yield was 16.4% in cases with two or more fetal malformations, while cases with a single anomaly revealed a diagnostic yield of 7.3%. Cases presenting isolated polyhydramnios or isolated fetal growth restriction had a lower yield of 9.3 and 5.4%, respectively. Of the 30 clinically significant cases, 19 (or 63.4%) exhibited recurrent CNVs. The remaining 11 cases (or 36.6%) presented unique CNVs. The theoretical yield of Noninvasive Prenatal Testing (NIPT) in our cohort is 2% for aneuploidy, which implies that it could potentially miss up to 70% of the significant findings that could be identified by CMA. In 80% of the fetuses (or 24 out of 30) with clinically significant CNVs, the structural abnormalities detected on fetal ultrasound examinations corresponded with the CMA results. CONCLUSION The 6.2% detection rate of significant CNVs in late-onset fetal anomalies confirms the value of CMA in third-trimester amniocentesis. The findings underscore the necessity of CMA for detecting CNVs potentially overlooked by NIPT and emphasize the importance of thorough genetic counseling. KEY POINTS · CMA yields 6.2% for third-trimester anomalies.. · NIPT may miss 70% of CMA findings.. · Ultrasound matched 80% of CMA results..
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Affiliation(s)
- Eyal Elron
- Department of Neonatology, Schneider Children's Medical Center, Petah Tikva, Israel
- Pediatric Genetics Unit, Schneider Children's Medical Center, Petah Tikva, Israel
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Idit Maya
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noa Shefer-Averbuch
- Pediatric Genetics Unit, Schneider Children's Medical Center, Petah Tikva, Israel
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Jesse Z. and Sara Lea Shafer Institute for Endocrinology and Diabetes, Schneider Children's Medical Center of Israel, The Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Sarit Kahana
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
| | - Reut Matar
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
| | - Kochav Klein
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
| | - Ifat Agmon-Fishman
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
| | - Merav Gurevitch
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
| | - Lina Basel-Salmon
- Pediatric Genetics Unit, Schneider Children's Medical Center, Petah Tikva, Israel
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Michal Levy
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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13
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Bilgrav Saether K, Eisfeldt J, Bengtsson J, Lun MY, Grochowski CM, Mahmoud M, Chao HT, Rosenfeld JA, Liu P, Schuy J, Ameur A, Hwang JP, Sedlazeck FJ, Bi W, Marom R, Nordgren A, Carvalho CMB, Lindstrand A. Mind the gap: the relevance of the genome reference to resolve rare and pathogenic inversions. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.22.24305780. [PMID: 38712270 PMCID: PMC11071548 DOI: 10.1101/2024.04.22.24305780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Both long-read genome sequencing (lrGS) and the recently published Telomere to Telomere (T2T) reference genome provide increased coverage and resolution across repetitive regions promising heightened structural variant detection and improved mapping. Inversions (INV), intrachromosomal segments which are rotated 180° and inserted back into the same chromosome, are a class of structural variants particularly challenging to detect due to their copy-number neutral state and association with repetitive regions. Inversions represent about 1/20 of all balanced structural chromosome aberrations and can lead to disease by gene disruption or altering regulatory regions of dosage sensitive genes in cis . Here we remapped the genome data from six individuals carrying unsolved cytogenetically detected inversions. An INV6 and INV10 were resolved using GRCh38 and T2T-CHM13. Finally, an INV9 required optical genome mapping, de novo assembly of lrGS data and T2T-CHM13. This inversion disrupted intron 25 of EHMT1, confirming a diagnosis of Kleefstra syndrome 1 (MIM#610253). These three inversions, only mappable in specific references, prompted us to investigate the presence and population frequencies of differential reference regions (DRRs) between T2T-CHM13, GRCh37, GRCh38, the chimpanzee and bonobo, and hundreds of megabases of DRRs were identified. Our results emphasize the significance of the chosen reference genome and the added benefits of lrGS and optical genome mapping in solving rearrangements in challenging regions of the genome. This is particularly important for inversions and may impact clinical diagnostics.
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14
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Redaelli S, Grati FR, Tritto V, Giannuzzi G, Recalcati MP, Sala E, Villa N, Crosti F, Roversi G, Malvestiti F, Zanatta V, Repetti E, Rodeschini O, Valtorta C, Catusi I, Romitti L, Martinoli E, Conconi D, Dalprà L, Lavitrano M, Riva P, Bentivegna A. Olfactory receptor genes and chromosome 11 structural aberrations: Players or spectators? HGG ADVANCES 2024; 5:100261. [PMID: 38160254 PMCID: PMC10820794 DOI: 10.1016/j.xhgg.2023.100261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024] Open
Abstract
The largest multi-gene family in metazoans is the family of olfactory receptor (OR) genes. Human ORs are organized in clusters over most chromosomes and seem to include >0.1% the human genome. Because 369 out of 856 OR genes are mapped on chromosome 11 (HSA11), we sought to determine whether they mediate structural rearrangements involving this chromosome. To this aim, we analyzed 220 specimens collected during diagnostic procedures involving structural rearrangements of chromosome 11. A total of 222 chromosomal abnormalities were included, consisting of inversions, deletions, translocations, duplications, and one insertion, detected by conventional chromosome analysis and/or fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (array-CGH). We verified by bioinformatics and statistical approaches the occurrence of breakpoints in cytobands with or without OR genes. We found that OR genes are not involved in chromosome 11 reciprocal translocations, suggesting that different DNA motifs and mechanisms based on homology or non-homology recombination can cause chromosome 11 structural alterations. We also considered the proximity between the chromosomal territories of chromosome 11 and its partner chromosomes involved in the translocations by using the deposited Hi-C data concerning the possible occurrence of chromosome interactions. Interestingly, most of the breakpoints are located in regions highly involved in chromosome interactions. Further studies should be carried out to confirm the potential role of chromosome territories' proximity in promoting genome structural variation, so fundamental in our understanding of the molecular basis of medical genetics and evolutionary genetics.
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Affiliation(s)
- Serena Redaelli
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Francesca Romana Grati
- R&D, Cytogenetics, Molecular Genetics and Medical Genetics Unit, Toma Advanced Biomedical Assays S.p.A. (ImpactLab), 21052 Busto Arsizio, Italy
| | - Viviana Tritto
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20122 Milan, Italy
| | | | - Maria Paola Recalcati
- IRCCS Istituto Auxologico Italiano, Medical Cytogenetics Laboratory, 20095 Cusano Milanino, Italy
| | - Elena Sala
- UC Medical Genetics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Nicoletta Villa
- UC Medical Genetics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Francesca Crosti
- UC Medical Genetics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Gaia Roversi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; UC Medical Genetics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Francesca Malvestiti
- R&D, Cytogenetics, Molecular Genetics and Medical Genetics Unit, Toma Advanced Biomedical Assays S.p.A. (ImpactLab), 21052 Busto Arsizio, Italy
| | - Valentina Zanatta
- R&D, Cytogenetics, Molecular Genetics and Medical Genetics Unit, Toma Advanced Biomedical Assays S.p.A. (ImpactLab), 21052 Busto Arsizio, Italy
| | - Elena Repetti
- R&D, Cytogenetics, Molecular Genetics and Medical Genetics Unit, Toma Advanced Biomedical Assays S.p.A. (ImpactLab), 21052 Busto Arsizio, Italy
| | - Ornella Rodeschini
- IRCCS Istituto Auxologico Italiano, Medical Cytogenetics Laboratory, 20095 Cusano Milanino, Italy
| | - Chiara Valtorta
- IRCCS Istituto Auxologico Italiano, Medical Cytogenetics Laboratory, 20095 Cusano Milanino, Italy
| | - Ilaria Catusi
- IRCCS Istituto Auxologico Italiano, Medical Cytogenetics Laboratory, 20095 Cusano Milanino, Italy
| | - Lorenza Romitti
- Pathology and Cytogenetics Laboratory, Clinical Pathology Department, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20162 Milan, Italy
| | - Emanuela Martinoli
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20122 Milan, Italy
| | - Donatella Conconi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Leda Dalprà
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; UC Medical Genetics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Marialuisa Lavitrano
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Paola Riva
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20122 Milan, Italy
| | - Angela Bentivegna
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy.
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15
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Chen Z, Finnell RH, Lei Y, Wang H. Progress and clinical prospect of genomic structural variants investigation. Sci Bull (Beijing) 2024; 69:705-708. [PMID: 38310047 DOI: 10.1016/j.scib.2024.01.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2024]
Affiliation(s)
- Zhongzhong Chen
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China; Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Richard H Finnell
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston 77030, USA; Departments of Molecular and Human Genetics and Medicine, Baylor College of Medicine, One Baylor Plaza, Houston 77030, USA
| | - Yunping Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston 77030, USA.
| | - Hongyan Wang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Metabolic Remodelling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200438, China; Children's Hospital of Fudan University, Shanghai 201102, China.
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16
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Keskus A, Bryant A, Ahmad T, Yoo B, Aganezov S, Goretsky A, Donmez A, Lansdon LA, Rodriguez I, Park J, Liu Y, Cui X, Gardner J, McNulty B, Sacco S, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Cook DE, Chang PC, Kolesnikov A, Carroll A, Molloy EK, Pushel I, Guest E, Pastinen T, Shafin K, Miga KH, Malikic S, Day CP, Robine N, Sahinalp C, Dean M, Farooqi MS, Paten B, Kolmogorov M. Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.22.24304756. [PMID: 38585974 PMCID: PMC10996739 DOI: 10.1101/2024.03.22.24304756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read sequencing offers the advantage of better mappability and long-range phasing, which results in substantial improvements in germline SV detection. However, current long-read SV detection methods do not generalize well to the analysis of somatic SVs in tumor genomes with complex rearrangements, heterogeneity, and aneuploidy. Here, we present Severus: a method for the accurate detection of different types of somatic SVs using a phased breakpoint graph approach. To benchmark various short- and long-read SV detection methods, we sequenced five tumor/normal cell line pairs with Illumina, Nanopore, and PacBio sequencing platforms; on this benchmark Severus showed the highest F1 scores (harmonic mean of the precision and recall) as compared to long-read and short-read methods. We then applied Severus to three clinical cases of pediatric cancer, demonstrating concordance with known genetic findings as well as revealing clinically relevant cryptic rearrangements missed by standard genomic panels.
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Affiliation(s)
- Ayse Keskus
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Tanveer Ahmad
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Byunggil Yoo
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | | | - Anton Goretsky
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Ataberk Donmez
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Lisa A. Lansdon
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Isabel Rodriguez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Jimin Park
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Yuelin Liu
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Xiwen Cui
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | | | - Samuel Sacco
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Jyoti Shetty
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yongmei Zhao
- Sequencing Facility Bioinformatics Group, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bao Tran
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | | | | | | | | | | | - Erin K. Molloy
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Irina Pushel
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Erin Guest
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Tomi Pastinen
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Kishwar Shafin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Salem Malikic
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Chi-Ping Day
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Cenk Sahinalp
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Midhat S. Farooqi
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | | | - Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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17
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Malekkou A, Tomazou M, Mavrikiou G, Dionysiou M, Georgiou T, Papaevripidou I, Alexandrou A, Sismani C, Drousiotou A, Grafakou O, Petrou PP. A novel large intragenic DPYD deletion causing dihydropyrimidine dehydrogenase deficiency: a case report. BMC Med Genomics 2024; 17:78. [PMID: 38528593 PMCID: PMC10962175 DOI: 10.1186/s12920-024-01846-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Dihydropyrimidine dehydrogenase (DPD), is the initial and rate-limiting enzyme in the catabolic pathway of pyrimidines. Deleterious variants in the DPYD gene cause DPD deficiency, a rare autosomal recessive disorder. The clinical spectrum of affected individuals is wide ranging from asymptomatic to severely affected patients presenting with intellectual disability, motor retardation, developmental delay and seizures. DPD is also important as the main enzyme in the catabolism of 5-fluorouracil (5-FU) which is extensively used as a chemotherapeutic agent. Even in the absence of clinical symptoms, individuals with either complete or partial DPD deficiency face a high risk of severe and even fatal fluoropyrimidine-associated toxicity. The identification of causative genetic variants in DPYD is therefore gaining increasing attention due to their potential use as predictive markers of fluoropyrimidine toxicity. METHODS A male infant patient displaying biochemical features of DPD deficiency was investigated by clinical exome sequencing. Bioinformatics tools were used for data analysis and results were confirmed by MLPA and Sanger sequencing. RESULTS A novel intragenic deletion of 71.2 kb in the DPYD gene was identified in homozygosity. The deletion, DPYD(NM_000110.4):c.850 + 23455_1128 + 8811del, eliminates exons 9 and 10 and may have resulted from a non-homologous end-joining event, as suggested by in silico analysis. CONCLUSIONS The study expands the spectrum of DPYD variants associated with DPD deficiency. Furthermore, it raises the concern that patients at risk for fluoropyrimidine toxicity due to DPYD deletions could be missed during pre-treatment genetic testing for the currently recommended single nucleotide polymorphisms.
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Affiliation(s)
- Anna Malekkou
- Biochemical Genetics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683, Nicosia, Cyprus
| | - Marios Tomazou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683, Nicosia, Cyprus
| | - Gavriella Mavrikiou
- Biochemical Genetics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683, Nicosia, Cyprus
| | - Maria Dionysiou
- Biochemical Genetics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683, Nicosia, Cyprus
| | - Theodoros Georgiou
- Biochemical Genetics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683, Nicosia, Cyprus
| | - Ioannis Papaevripidou
- Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683, Nicosia, Cyprus
| | - Angelos Alexandrou
- Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683, Nicosia, Cyprus
| | - Carolina Sismani
- Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683, Nicosia, Cyprus
| | - Anthi Drousiotou
- Biochemical Genetics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683, Nicosia, Cyprus
| | - Olga Grafakou
- Department of Pediatrics, Inborn Errors of Metabolism Clinic, Archbishop Makarios III Hospital, Korytsas 6, 2012, Nicosia, Cyprus
| | - Petros P Petrou
- Biochemical Genetics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683, Nicosia, Cyprus.
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18
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Lesack KJ, Wasmuth JD. The impact of FASTQ and alignment read order on structural variant calling from long-read sequencing data. PeerJ 2024; 12:e17101. [PMID: 38500526 PMCID: PMC10946394 DOI: 10.7717/peerj.17101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 02/21/2024] [Indexed: 03/20/2024] Open
Abstract
Background Structural variant (SV) calling from DNA sequencing data has been challenging due to several factors, including the ambiguity of short-read alignments, multiple complex SVs in the same genomic region, and the lack of "truth" datasets for benchmarking. Additionally, caller choice, parameter settings, and alignment method are known to affect SV calling. However, the impact of FASTQ read order on SV calling has not been explored for long-read data. Results Here, we used PacBio DNA sequencing data from 15 Caenorhabditis elegans strains and four Arabidopsis thaliana ecotypes to evaluate the sensitivity of different SV callers on FASTQ read order. Comparisons of variant call format files generated from the original and permutated FASTQ files demonstrated that the order of input data affected the SVs predicted by each caller. In particular, pbsv was highly sensitive to the order of the input data, especially at the highest depths where over 70% of the SV calls generated from pairs of differently ordered FASTQ files were in disagreement. These demonstrate that read order sensitivity is a complex, multifactorial process, as the differences observed both within and between species varied considerably according to the specific combination of aligner, SV caller, and sequencing depth. In addition to the SV callers being sensitive to the input data order, the SAMtools alignment sorting algorithm was identified as a source of variability following read order randomization. Conclusion The results of this study highlight the sensitivity of SV calling on the order of reads encoded in FASTQ files, which has not been recognized in long-read approaches. These findings have implications for the replication of SV studies and the development of consistent SV calling protocols. Our study suggests that researchers should pay attention to the input order sensitivity of read alignment sorting methods when analyzing long-read sequencing data for SV calling, as mitigating a source of variability could facilitate future replication work. These results also raise important questions surrounding the relationship between SV caller read order sensitivity and tool performance. Therefore, tool developers should also consider input order sensitivity as a potential source of variability during the development and benchmarking of new and improved methods for SV calling.
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Affiliation(s)
- Kyle J. Lesack
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, Alberta, Canada
| | - James D. Wasmuth
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, Alberta, Canada
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19
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Di Tommaso E, Giunta S. Dynamic interplay between human alpha-satellite DNA structure and centromere functions. Semin Cell Dev Biol 2024; 156:130-140. [PMID: 37926668 DOI: 10.1016/j.semcdb.2023.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023]
Abstract
Maintenance of genome stability relies on functional centromeres for correct chromosome segregation and faithful inheritance of the genetic information. The human centromere is the primary constriction within mitotic chromosomes made up of repetitive alpha-satellite DNA hierarchically organized in megabase-long arrays of near-identical higher order repeats (HORs). Centromeres are epigenetically specified by the presence of the centromere-specific histone H3 variant, CENP-A, which enables the assembly of the kinetochore for microtubule attachment. Notably, centromeric DNA is faithfully inherited as intact haplotypes from the parents to the offspring without intervening recombination, yet, outside of meiosis, centromeres are akin to common fragile sites (CFSs), manifesting crossing-overs and ongoing sequence instability. Consequences of DNA changes within the centromere are just starting to emerge, with unclear effects on intra- and inter-generational inheritance driven by centromere's essential role in kinetochore assembly. Here, we review evidence of meiotic selection operating to mitigate centromere drive, as well as recent reports on centromere damage, recombination and repair during the mitotic cell division. We propose an antagonistic pleiotropy interpretation to reconcile centromere DNA instability as both driver of aneuploidy that underlies degenerative diseases, while also potentially necessary for the maintenance of homogenized HORs for centromere function. We attempt to provide a framework for this conceptual leap taking into consideration the structural interface of centromere-kinetochore interaction and present case scenarios for its malfunctioning. Finally, we offer an integrated working model to connect DNA instability, chromatin, and structural changes with functional consequences on chromosome integrity.
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Affiliation(s)
- Elena Di Tommaso
- Laboratory of Genome Evolution, Department of Biology & Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Simona Giunta
- Laboratory of Genome Evolution, Department of Biology & Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy.
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20
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Helal AA, Saad BT, Saad MT, Mosaad GS, Aboshanab KM. Benchmarking long-read aligners and SV callers for structural variation detection in Oxford nanopore sequencing data. Sci Rep 2024; 14:6160. [PMID: 38486064 PMCID: PMC10940726 DOI: 10.1038/s41598-024-56604-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/08/2024] [Indexed: 03/18/2024] Open
Abstract
Structural variants (SVs) are one of the significant types of DNA mutations and are typically defined as larger-than-50-bp genomic alterations that include insertions, deletions, duplications, inversions, and translocations. These modifications can profoundly impact the phenotypic characteristics and contribute to disorders like cancer, response to treatment, and infections. Four long-read aligners and five SV callers have been evaluated using three Oxford Nanopore NGS human genome datasets in terms of precision, recall, and F1-score statistical metrics, depth of coverage, and speed of analysis. The best SV caller regarding recall, precision, and F1-score when matched with different aligners at different coverage levels tend to vary depending on the dataset and the specific SV types being analyzed. However, based on our findings, Sniffles and CuteSV tend to perform well across different aligners and coverage levels, followed by SVIM, PBSV, and SVDSS in the last place. The CuteSV caller has the highest average F1-score (82.51%) and recall (78.50%), and Sniffles has the highest average precision value (94.33%). Minimap2 as an aligner and Sniffles as an SV caller act as a strong base for the pipeline of SV calling because of their high speed and reasonable accomplishment. PBSV has a lower average F1-score, precision, and recall and may generate more false positives and overlook some actual SVs. Our results are valuable in the comprehensive evaluation of popular SV callers and aligners as they provide insight into the performance of several long-read aligners and SV callers and serve as a reference for researchers in selecting the most suitable tools for SV detection.
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Affiliation(s)
- Asmaa A Helal
- Department of Bioinformatics, HITS Solutions Co., Cairo, 11765, Egypt
| | - Bishoy T Saad
- Department of Bioinformatics, HITS Solutions Co., Cairo, 11765, Egypt.
| | - Mina T Saad
- Department of Bioinformatics, HITS Solutions Co., Cairo, 11765, Egypt
| | - Gamal S Mosaad
- Department of Bioinformatics, HITS Solutions Co., Cairo, 11765, Egypt
| | - Khaled M Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., Abassi, Cairo, 11566, Egypt.
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21
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Yu Y, Wang X, Fox J, Li Q, Yu Y, Hastings PJ, Chen K, Ira G. RPA and Rad27 limit templated and inverted insertions at DNA breaks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583931. [PMID: 38496432 PMCID: PMC10942419 DOI: 10.1101/2024.03.07.583931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Formation of templated insertions at DNA double-strand breaks (DSBs) is very common in cancer cells. The mechanisms and enzymes regulating these events are largely unknown. Here, we investigated templated insertions in yeast at DSBs using amplicon sequencing across a repaired locus. We document very short (most ∼5-34 bp), templated inverted duplications at DSBs. They are generated through a foldback mechanism that utilizes microhomologies adjacent to the DSB. Enzymatic requirements suggest a hybrid mechanism wherein one end requires Polδ-mediated synthesis while the other end is captured by nonhomologous end joining (NHEJ). This process is exacerbated in mutants with low levels or mutated RPA ( rtt105 Δ; rfa1 -t33) or extensive resection mutant ( sgs1 Δ exo1 Δ). Templated insertions from various distant genomic locations also increase in these mutants as well as in rad27 Δ and originate from fragile regions of the genome. Among complex insertions, common events are insertions of two sequences, originating from the same locus and with inverted orientation. We propose that these inversions are also formed by microhomology-mediated template switching. Taken together, we propose that a shortage of RPA typical in cancer cells is one possible factor stimulating the formation of templated insertions.
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22
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Olivucci G, Iovino E, Innella G, Turchetti D, Pippucci T, Magini P. Long read sequencing on its way to the routine diagnostics of genetic diseases. Front Genet 2024; 15:1374860. [PMID: 38510277 PMCID: PMC10951082 DOI: 10.3389/fgene.2024.1374860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
The clinical application of technological progress in the identification of DNA alterations has always led to improvements of diagnostic yields in genetic medicine. At chromosome side, from cytogenetic techniques evaluating number and gross structural defects to genomic microarrays detecting cryptic copy number variants, and at molecular level, from Sanger method studying the nucleotide sequence of single genes to the high-throughput next-generation sequencing (NGS) technologies, resolution and sensitivity progressively increased expanding considerably the range of detectable DNA anomalies and alongside of Mendelian disorders with known genetic causes. However, particular genomic regions (i.e., repetitive and GC-rich sequences) are inefficiently analyzed by standard genetic tests, still relying on laborious, time-consuming and low-sensitive approaches (i.e., southern-blot for repeat expansion or long-PCR for genes with highly homologous pseudogenes), accounting for at least part of the patients with undiagnosed genetic disorders. Third generation sequencing, generating long reads with improved mappability, is more suitable for the detection of structural alterations and defects in hardly accessible genomic regions. Although recently implemented and not yet clinically available, long read sequencing (LRS) technologies have already shown their potential in genetic medicine research that might greatly impact on diagnostic yield and reporting times, through their translation to clinical settings. The main investigated LRS application concerns the identification of structural variants and repeat expansions, probably because techniques for their detection have not evolved as rapidly as those dedicated to single nucleotide variants (SNV) identification: gold standard analyses are karyotyping and microarrays for balanced and unbalanced chromosome rearrangements, respectively, and southern blot and repeat-primed PCR for the amplification and sizing of expanded alleles, impaired by limited resolution and sensitivity that have not been significantly improved by the advent of NGS. Nevertheless, more recently, with the increased accuracy provided by the latest product releases, LRS has been tested also for SNV detection, especially in genes with highly homologous pseudogenes and for haplotype reconstruction to assess the parental origin of alleles with de novo pathogenic variants. We provide a review of relevant recent scientific papers exploring LRS potential in the diagnosis of genetic diseases and its potential future applications in routine genetic testing.
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Affiliation(s)
- Giulia Olivucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Surgical and Oncological Sciences, University of Palermo, Palermo, Italy
| | - Emanuela Iovino
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanni Innella
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Daniela Turchetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Tommaso Pippucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Pamela Magini
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
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23
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Rondón JJ, Pisarenco VA, Ramón Pardos-Blas J, Sánchez-Gracia A, Zardoya R, Rozas J. Comparative genomic analysis of chemosensory-related gene families in gastropods. Mol Phylogenet Evol 2024; 192:107986. [PMID: 38142794 DOI: 10.1016/j.ympev.2023.107986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/24/2023] [Accepted: 12/07/2023] [Indexed: 12/26/2023]
Abstract
Chemoreception is critical for the survival and reproduction of animals. Except for a reduced group of insects and chelicerates, the molecular identity of chemosensory proteins is poorly understood in invertebrates. Gastropoda is the extant mollusk class with the greatest species richness, including marine, freshwater, and terrestrial lineages, and likely, highly diverse chemoreception systems. Here, we performed a comprehensive comparative genome analysis taking advantage of the chromosome-level information of two Gastropoda species, one of which belongs to a lineage that underwent a whole genome duplication event. We identified thousands of previously uncharacterized chemosensory-related genes, the majority of them encoding G protein-coupled receptors (GPCR), mostly organized into clusters distributed across all chromosomes. We also detected gene families encoding degenerin epithelial sodium channels (DEG-ENaC), ionotropic receptors (IR), sensory neuron membrane proteins (SNMP), Niemann-Pick type C2 (NPC2) proteins, and lipocalins, although with a lower number of members. Our phylogenetic analysis of the GPCR gene family across protostomes revealed: (i) remarkable gene family expansions in Gastropoda; (ii) clades including members from all protostomes; and (iii) species-specific clades with a substantial number of receptors. For the first time, we provide new and valuable knowledge into the evolution of the chemosensory gene families in invertebrates other than arthropods.
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Affiliation(s)
- Johnma José Rondón
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Buenos Aires, Argentina; Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA-CONICET) Buenos Aires, Argentina
| | - Vadim A Pisarenco
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - José Ramón Pardos-Blas
- Departamento de Biodiversidad y Biologı́a Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biologı́a Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain.
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain.
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24
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Mazzonetto PC, Villela D, da Costa SS, Krepischi ACV, Milanezi F, Migliavacca MP, Pierry PM, Bonaldi A, Almeida LGD, De Souza CA, Kroll JE, Paula MG, Guarischi-Sousa R, Scapulatempo-Neto C, Rosenberg C. Low-pass whole genome sequencing is a reliable and cost-effective approach for copy number variant analysis in the clinical setting. Ann Hum Genet 2024; 88:113-125. [PMID: 37807935 DOI: 10.1111/ahg.12532] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/10/2023]
Abstract
INTRODUCTION Next generation sequencing technology has greatly reduced the cost and time required for sequencing a genome. An approach that is rapidly being adopted as an alternative method for CNV analysis is the low-pass whole genome sequencing (LP-WGS). Here, we evaluated the performance of LP-WGS to detect copy number variants (CNVs) in clinical cytogenetics. MATERIALS AND METHODS DNA samples with known CNVs detected by chromosomal microarray analyses (CMA) were selected for comparison and used as positive controls; our panel included 44 DNA samples (12 prenatal and 32 postnatal), comprising a total of 55 chromosome imbalances. The selected cases were chosen to provide a wide range of clinically relevant CNVs, the vast majority being associated with intellectual disability or recognizable syndromes. The chromosome imbalances ranged in size from 75 kb to 90.3 Mb, including aneuploidies and two cases of mosaicism. RESULTS All CNVs were successfully detected by LP-WGS, showing a high level of consistency and robust performance of the sequencing method. Notably, the size of chromosome imbalances detected by CMA and LP-WGS were compatible between the two different platforms, which indicates that the resolution and sensitivity of the LP-WGS approach are at least similar to those provided by CMA. DISCUSSION Our data show the potential use of LP-WGS to detect CNVs in clinical diagnosis and confirm the method as an alternative for chromosome imbalances detection. The diagnostic effectiveness and feasibility of LP-WGS, in this technical validation study, were evidenced by a clinically representative dataset of CNVs that allowed a systematic assessment of the detection power and the accuracy of the sequencing approach. Further, since the software used in this study is commercially available, the method can easily be tested and implemented in a routine diagnostic setting.
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Affiliation(s)
- Patricia C Mazzonetto
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
| | | | - Silvia Souza da Costa
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Ana C V Krepischi
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | | | | | | | | | | | | | | | | | | | | | - Carla Rosenberg
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
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25
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Orteu A, Kucka M, Gordon IJ, Ng’iru I, van der Heijden ESM, Talavera G, Warren IA, Collins S, ffrench-Constant RH, Martins DJ, Chan YF, Jiggins CD, Martin SH. Transposable Element Insertions Are Associated with Batesian Mimicry in the Pantropical Butterfly Hypolimnas misippus. Mol Biol Evol 2024; 41:msae041. [PMID: 38401262 PMCID: PMC10924252 DOI: 10.1093/molbev/msae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/26/2024] Open
Abstract
Hypolimnas misippus is a Batesian mimic of the toxic African Queen butterfly (Danaus chrysippus). Female H. misippus butterflies use two major wing patterning loci (M and A) to imitate three color morphs of D. chrysippus found in different regions of Africa. In this study, we examine the evolution of the M locus and identify it as an example of adaptive atavism. This phenomenon involves a morphological reversion to an ancestral character that results in an adaptive phenotype. We show that H. misippus has re-evolved an ancestral wing pattern present in other Hypolimnas species, repurposing it for Batesian mimicry of a D. chrysippus morph. Using haplotagging, a linked-read sequencing technology, and our new analytical tool, Wrath, we discover two large transposable element insertions located at the M locus and establish that these insertions are present in the dominant allele responsible for producing mimetic phenotype. By conducting a comparative analysis involving additional Hypolimnas species, we demonstrate that the dominant allele is derived. This suggests that, in the derived allele, the transposable elements disrupt a cis-regulatory element, leading to the reversion to an ancestral phenotype that is then utilized for Batesian mimicry of a distinct model, a different morph of D. chrysippus. Our findings present a compelling instance of convergent evolution and adaptive atavism, in which the same pattern element has independently evolved multiple times in Hypolimnas butterflies, repeatedly playing a role in Batesian mimicry of diverse model species.
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Affiliation(s)
- Anna Orteu
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Marek Kucka
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Ian J Gordon
- Centre of Excellence in Biodiversity, University of Rwanda, Huye, Rwanda
| | - Ivy Ng’iru
- Mpala Research Centre, Nanyuki 10400, Laikipia, Kenya
- School of Biosciences, Cardiff University, Cardiff CF 10 3AX, UK
- UK Centre for Ecology and Hydrology, Wallingford OX10 8BB, UK
| | - Eva S M van der Heijden
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, Barcelona, Catalonia, Spain
| | - Ian A Warren
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Steve Collins
- African Butterfly Research Institute, Nairobi, Kenya
| | | | - Dino J Martins
- Turkana Basin Institute, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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26
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Pinto LM, Pailas A, Bondarchenko M, Sharma AB, Neumann K, Rizzo AJ, Jeanty C, Nicot N, Racca C, Graham MK, Naughton C, Liu Y, Chen CL, Meakin PJ, Gilbert N, Britton S, Meeker AK, Heaphy CM, Larminat F, Van Dyck E. DAXX promotes centromeric stability independently of ATRX by preventing the accumulation of R-loop-induced DNA double-stranded breaks. Nucleic Acids Res 2024; 52:1136-1155. [PMID: 38038252 PMCID: PMC10853780 DOI: 10.1093/nar/gkad1141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
Maintaining chromatin integrity at the repetitive non-coding DNA sequences underlying centromeres is crucial to prevent replicative stress, DNA breaks and genomic instability. The concerted action of transcriptional repressors, chromatin remodelling complexes and epigenetic factors controls transcription and chromatin structure in these regions. The histone chaperone complex ATRX/DAXX is involved in the establishment and maintenance of centromeric chromatin through the deposition of the histone variant H3.3. ATRX and DAXX have also evolved mutually-independent functions in transcription and chromatin dynamics. Here, using paediatric glioma and pancreatic neuroendocrine tumor cell lines, we identify a novel ATRX-independent function for DAXX in promoting genome stability by preventing transcription-associated R-loop accumulation and DNA double-strand break formation at centromeres. This function of DAXX required its interaction with histone H3.3 but was independent of H3.3 deposition and did not reflect a role in the repression of centromeric transcription. DAXX depletion mobilized BRCA1 at centromeres, in line with BRCA1 role in counteracting centromeric R-loop accumulation. Our results provide novel insights into the mechanisms protecting the human genome from chromosomal instability, as well as potential perspectives in the treatment of cancers with DAXX alterations.
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Affiliation(s)
- Lia M Pinto
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
- Faculty of Science, Technology and Communication, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
- Discovery & Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Alexandros Pailas
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
- Faculty of Science, Technology and Communication, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Max Bondarchenko
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
- Faculty of Science, Technology and Communication, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Abhishek Bharadwaj Sharma
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
| | - Katrin Neumann
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
| | - Anthony J Rizzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Céline Jeanty
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
| | - Nathalie Nicot
- Translational Medicine Operations Hub, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
| | - Carine Racca
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), 31077 Toulouse Cedex 4, France
| | - Mindy K Graham
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Catherine Naughton
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 1QY, UK
| | - Yaqun Liu
- Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université, 75248 Paris Cedex 05, France
| | - Chun-Long Chen
- Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université, 75248 Paris Cedex 05, France
| | - Paul J Meakin
- Discovery & Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Nick Gilbert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 1QY, UK
| | - Sébastien Britton
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), 31077 Toulouse Cedex 4, France
| | - Alan K Meeker
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Christopher M Heaphy
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Florence Larminat
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), 31077 Toulouse Cedex 4, France
| | - Eric Van Dyck
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
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27
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Audano PA, Beck CR. Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement. Genome Res 2024; 34:7-19. [PMID: 38176712 PMCID: PMC10904011 DOI: 10.1101/gr.278203.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/02/2024] [Indexed: 01/06/2024]
Abstract
High-quality genome assemblies and sophisticated algorithms have increased sensitivity for a wide range of variant types, and breakpoint accuracy for structural variants (SVs, ≥50 bp) has improved to near base pair precision. Despite these advances, many SV breakpoint locations are subject to systematic bias affecting variant representation. To understand why SV breakpoints are inconsistent across samples, we reanalyzed 64 phased haplotypes constructed from long-read assemblies released by the Human Genome Structural Variation Consortium (HGSVC). We identify 882 SV insertions and 180 SV deletions with variable breakpoints not anchored in tandem repeats (TRs) or segmental duplications (SDs). SVs called from aligned sequencing reads increase breakpoint disagreements by 2×-16×. Sequence accuracy had a minimal impact on breakpoints, but we observe a strong effect of ancestry. We confirm that SNP and indel polymorphisms are enriched at shifted breakpoints and are also absent from variant callsets. Breakpoint homology increases the likelihood of imprecise SV calls and the distance they are shifted, and tandem duplications are the most heavily affected SVs. Because graph genome methods normalize SV calls across samples, we investigated graphs generated by two different methods and find the resulting breakpoints are subject to other technical biases affecting breakpoint accuracy. The breakpoint inconsistencies we characterize affect ∼5% of the SVs called in a human genome and can impact variant interpretation and annotation. These limitations underscore a need for algorithm development to improve SV databases, mitigate the impact of ancestry on breakpoints, and increase the value of callsets for investigating breakpoint features.
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Affiliation(s)
- Peter A Audano
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Christine R Beck
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA;
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
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28
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Ganesh VS, Riquin K, Chatron N, Lamar KM, Aziz MC, Monin P, O’Leary M, Goodrich JK, Garimella KV, England E, Yoon E, Weisburd B, Aguet F, Bacino CA, Murdock DR, Dai H, Rosenfeld JA, Emrick LT, Ketkar S, Sarusi Y, Sanlaville D, Kayani S, Broadbent B, Isidor B, Pengam A, Cogné B, MacArthur DG, Ulitsky I, Carvill GL, O’Donnell-Luria A. Novel syndromic neurodevelopmental disorder caused by de novo deletion of CHASERR, a long noncoding RNA. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.31.24301497. [PMID: 38496558 PMCID: PMC10942497 DOI: 10.1101/2024.01.31.24301497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Genes encoding long non-coding RNAs (lncRNAs) comprise a large fraction of the human genome, yet haploinsufficiency of a lncRNA has not been shown to cause a Mendelian disease. CHASERR is a highly conserved human lncRNA adjacent to CHD2-a coding gene in which de novo loss-of-function variants cause developmental and epileptic encephalopathy. Here we report three unrelated individuals each harboring an ultra-rare heterozygous de novo deletion in the CHASERR locus. We report similarities in severe developmental delay, facial dysmorphisms, and cerebral dysmyelination in these individuals, distinguishing them from the phenotypic spectrum of CHD2 haploinsufficiency. We demonstrate reduced CHASERR mRNA expression and corresponding increased CHD2 mRNA and protein in whole blood and patient-derived cell lines-specifically increased expression of the CHD2 allele in cis with the CHASERR deletion, as predicted from a prior mouse model of Chaserr haploinsufficiency. We show for the first time that de novo structural variants facilitated by Alu-mediated non-allelic homologous recombination led to deletion of a non-coding element (the lncRNA CHASERR) to cause a rare syndromic neurodevelopmental disorder. We also demonstrate that CHD2 has bidirectional dosage sensitivity in human disease. This work highlights the need to carefully evaluate other lncRNAs, particularly those upstream of genes associated with Mendelian disorders.
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Affiliation(s)
- Vijay S. Ganesh
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kevin Riquin
- Nantes Université, CHU de Nantes, CNRS, INSERM, L’institut du Thorax, Nantes, France
| | - Nicolas Chatron
- Institut Neuromyogène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Equipe Métabolisme énergétique et développement neuronal, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
- Service de génétique, Hospices Civils de Lyon, Lyon, France
| | - Kay-Marie Lamar
- Departments of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Miriam C. Aziz
- Departments of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Pauline Monin
- Service de génétique, Hospices Civils de Lyon, Lyon, France
| | - Melanie O’Leary
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia K. Goodrich
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kiran V. Garimella
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eleina England
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Esther Yoon
- Departments of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Ben Weisburd
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Francois Aguet
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David R. Murdock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lisa T. Emrick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shamika Ketkar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Yael Sarusi
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Damien Sanlaville
- Institut Neuromyogène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Equipe Métabolisme énergétique et développement neuronal, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
- Service de génétique, Hospices Civils de Lyon, Lyon, France
| | - Saima Kayani
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Bertrand Isidor
- Nantes Université, CHU de Nantes, CNRS, INSERM, L’institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique médicale, F-44000 Nantes, France
| | - Alisée Pengam
- Nantes Université, CHU de Nantes, Service de Génétique médicale, F-44000 Nantes, France
| | - Benjamin Cogné
- Nantes Université, CHU de Nantes, CNRS, INSERM, L’institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique médicale, F-44000 Nantes, France
| | - Daniel G. MacArthur
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, Australia
- Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Igor Ulitsky
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Gemma L. Carvill
- Departments of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Anne O’Donnell-Luria
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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29
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Abondio P, Bruno F, Passarino G, Montesanto A, Luiselli D. Pangenomics: A new era in the field of neurodegenerative diseases. Ageing Res Rev 2024; 94:102180. [PMID: 38163518 DOI: 10.1016/j.arr.2023.102180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/14/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
A pangenome is composed of all the genetic variability of a group of individuals, and its application to the study of neurodegenerative diseases may provide valuable insights into the underlying aspects of genetic heterogenetiy for these complex ailments, including gene expression, epigenetics, and translation mechanisms. Furthermore, a reference pangenome allows for the identification of previously undetected structural commonalities and differences among individuals, which may help in the diagnosis of a disease, support the prediction of what will happen over time (prognosis) and aid in developing novel treatments in the perspective of personalized medicine. Therefore, in the present review, the application of the pangenome concept to the study of neurodegenerative diseases will be discussed and analyzed for its potential to enable an improvement in diagnosis and prognosis for these illnesses, leading to the development of tailored treatments for individual patients from the knowledge of the genomic composition of a whole population.
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Affiliation(s)
- Paolo Abondio
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy.
| | - Francesco Bruno
- Academy of Cognitive Behavioral Sciences of Calabria (ASCoC), Lamezia Terme, Italy; Regional Neurogenetic Centre (CRN), Department of Primary Care, Azienda Sanitaria Provinciale Di Catanzaro, Viale A. Perugini, 88046 Lamezia Terme, CZ, Italy; Association for Neurogenetic Research (ARN), Lamezia Terme, CZ, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende 87036, Italy
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende 87036, Italy
| | - Donata Luiselli
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy
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Tian L, Chen CJ, Song YN, Xu K, Li NE, Zhang XH, Xie Y, Jin ZB, Li Y. Comprehensive genetic analysis reveals the mutational landscape of ABCA4-associated retinal dystrophy in a Chinese cohort. Gene 2024; 891:147832. [PMID: 37774808 DOI: 10.1016/j.gene.2023.147832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 10/01/2023]
Abstract
PURPOSE To depict the variant profiles of the ABCA4 gene in a large Chinese cohort of patients with ABCA4-associated retinal dystrophy (ABCA4-RD). METHODS We recruited 290 unrelated Chinese patients with ABCA4-RD and did ABCA4 mutational screening by a combination of Sanger sequencing, targeted exome sequencing, entire ABCA4 locus sequencing, and whole genome sequencing (WGS). The pathogenicity of variants was assessed using in silico tools or in vitro splicing assays following the American College of Medical Genetics and Genomics guidelines. RESULTS Two hundred sixty-eight distinct pathogenic variants were identified, and 57 were novel. In 580 alleles, 22 noncoding region variants outside canonical splice sites and 4 structural variations were found in 44 alleles accounting for 7.6% of all alleles. Bioinformatics analysis showed the complex mechanism of aberrant splicing productsnatural splice site disruption, branch point destruction, and cryptic splice site activation. Correspondingly, minigene assays validated the various abnormal splicing products, including exon skipping, exon elongation, partial exon deletion, and pseudoexon insertion. WGS identified the first inversion variation in ABCA4. CONCLUSIONS This study systematically depicted the variant profiles of ABCA4 and revealed the missing alleles of patients with ABCA4-RD in a large Chinese cohort. Our findings demonstrated the complexity of molecular diagnosis of Mendelian diseases and the efficiency of WGS for detecting structural variants.
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Affiliation(s)
- Lu Tian
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China; Department of Ophthalmology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Chun-Jie Chen
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Yu-Ning Song
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Ke Xu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Ni-En Li
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Xiao-Hui Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Yue Xie
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Yang Li
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China.
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31
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Auwerx C, Jõeloo M, Sadler MC, Tesio N, Ojavee S, Clark CJ, Mägi R, Reymond A, Kutalik Z. Rare copy-number variants as modulators of common disease susceptibility. Genome Med 2024; 16:5. [PMID: 38185688 PMCID: PMC10773105 DOI: 10.1186/s13073-023-01265-5] [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: 07/17/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND Copy-number variations (CNVs) have been associated with rare and debilitating genomic disorders (GDs) but their impact on health later in life in the general population remains poorly described. METHODS Assessing four modes of CNV action, we performed genome-wide association scans (GWASs) between the copy-number of CNV-proxy probes and 60 curated ICD-10 based clinical diagnoses in 331,522 unrelated white British UK Biobank (UKBB) participants with replication in the Estonian Biobank. RESULTS We identified 73 signals involving 40 diseases, all of which indicating that CNVs increased disease risk and caused earlier onset. We estimated that 16% of these associations are indirect, acting by increasing body mass index (BMI). Signals mapped to 45 unique, non-overlapping regions, nine of which being linked to known GDs. Number and identity of genes affected by CNVs modulated their pathogenicity, with many associations being supported by colocalization with both common and rare single-nucleotide variant association signals. Dissection of association signals provided insights into the epidemiology of known gene-disease pairs (e.g., deletions in BRCA1 and LDLR increased risk for ovarian cancer and ischemic heart disease, respectively), clarified dosage mechanisms of action (e.g., both increased and decreased dosage of 17q12 impacted renal health), and identified putative causal genes (e.g., ABCC6 for kidney stones). Characterization of the pleiotropic pathological consequences of recurrent CNVs at 15q13, 16p13.11, 16p12.2, and 22q11.2 in adulthood indicated variable expressivity of these regions and the involvement of multiple genes. Finally, we show that while the total burden of rare CNVs-and especially deletions-strongly associated with disease risk, it only accounted for ~ 0.02% of the UKBB disease burden. These associations are mainly driven by CNVs at known GD CNV regions, whose pleiotropic effect on common diseases was broader than anticipated by our CNV-GWAS. CONCLUSIONS Our results shed light on the prominent role of rare CNVs in determining common disease susceptibility within the general population and provide actionable insights for anticipating later-onset comorbidities in carriers of recurrent CNVs.
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Affiliation(s)
- Chiara Auwerx
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland.
| | - Maarja Jõeloo
- Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Marie C Sadler
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland
| | - Nicolò Tesio
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
| | - Sven Ojavee
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Charlie J Clark
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland.
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Behera S, Catreux S, Rossi M, Truong S, Huang Z, Ruehle M, Visvanath A, Parnaby G, Roddey C, Onuchic V, Cameron DL, English A, Mehtalia S, Han J, Mehio R, Sedlazeck FJ. Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573821. [PMID: 38260545 PMCID: PMC10802302 DOI: 10.1101/2024.01.02.573821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Research and medical genomics require comprehensive and scalable solutions to drive the discovery of novel disease targets, evolutionary drivers, and genetic markers with clinical significance. This necessitates a framework to identify all types of variants independent of their size (e.g., SNV/SV) or location (e.g., repeats). Here we present DRAGEN that utilizes novel methods based on multigenomes, hardware acceleration, and machine learning based variant detection to provide novel insights into individual genomes with ~30min computation time (from raw reads to variant detection). DRAGEN outperforms all other state-of-the-art methods in speed and accuracy across all variant types (SNV, indel, STR, SV, CNV) and further incorporates specialized methods to obtain key insights in medically relevant genes (e.g., HLA, SMN, GBA). We showcase DRAGEN across 3,202 genomes and demonstrate its scalability, accuracy, and innovations to further advance the integration of comprehensive genomics for research and medical applications.
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Affiliation(s)
- Sairam Behera
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | | | | | | | | | | | | | | | - Adam English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, TX, USA
- Department of Computer Science, Rice University, TX, USA
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33
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Smolka M, Paulin LF, Grochowski CM, Horner DW, Mahmoud M, Behera S, Kalef-Ezra E, Gandhi M, Hong K, Pehlivan D, Scholz SW, Carvalho CMB, Proukakis C, Sedlazeck FJ. Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol 2024:10.1038/s41587-023-02024-y. [PMID: 38168980 PMCID: PMC11217151 DOI: 10.1038/s41587-023-02024-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/11/2023] [Indexed: 01/05/2024]
Abstract
Calling structural variations (SVs) is technically challenging, but using long reads remains the most accurate way to identify complex genomic alterations. Here we present Sniffles2, which improves over current methods by implementing a repeat aware clustering coupled with a fast consensus sequence and coverage-adaptive filtering. Sniffles2 is 11.8 times faster and 29% more accurate than state-of-the-art SV callers across different coverages (5-50×), sequencing technologies (ONT and HiFi) and SV types. Furthermore, Sniffles2 solves the problem of family-level to population-level SV calling to produce fully genotyped VCF files. Across 11 probands, we accurately identified causative SVs around MECP2, including highly complex alleles with three overlapping SVs. Sniffles2 also enables the detection of mosaic SVs in bulk long-read data. As a result, we identified multiple mosaic SVs in brain tissue from a patient with multiple system atrophy. The identified SV showed a remarkable diversity within the cingulate cortex, impacting both genes involved in neuron function and repetitive elements.
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Affiliation(s)
- Moritz Smolka
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
| | - Luis F Paulin
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
| | | | - Dominic W Horner
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Queen Square Institute of Neurology, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sairam Behera
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
| | - Ester Kalef-Ezra
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Queen Square Institute of Neurology, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Mira Gandhi
- Pacific Northwest Research Institute (PNRI), Seattle, WA, USA
| | - Karl Hong
- Bionano Genomics, San Diego, CA, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Pacific Northwest Research Institute (PNRI), Seattle, WA, USA
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Queen Square Institute of Neurology, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
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Cao S, Sawettalake N, Shen L. Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce. Gigascience 2024; 13:giae043. [PMID: 38991853 PMCID: PMC11238431 DOI: 10.1093/gigascience/giae043] [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: 02/26/2024] [Revised: 04/24/2024] [Accepted: 06/22/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Lettuce, an important member of the Asteraceae family, is a globally cultivated cash vegetable crop. With a highly complex genome (∼2.5 Gb; 2n = 18) rich in repeat sequences, current lettuce reference genomes exhibit thousands of gaps, impeding a comprehensive understanding of the lettuce genome. FINDINGS Here, we present a near-complete gapless reference genome for cutting lettuce with high transformability, using long-read PacBio HiFi and Nanopore sequencing data. In comparison to stem lettuce genome, we identify 127,681 structural variations (SVs, present in 0.41 Gb of sequence), reflecting the divergence of leafy and stem lettuce. Interestingly, these SVs are related to transposons and DNA methylation states. Furthermore, we identify 4,612 whole-genome triplication genes exhibiting high expression levels associated with low DNA methylation levels and high N6-methyladenosine RNA modifications. DNA methylation changes are also associated with activation of genes involved in callus formation. CONCLUSIONS Our gapless lettuce genome assembly, an unprecedented achievement in the Asteraceae family, establishes a solid foundation for functional genomics, epigenomics, and crop breeding and sheds new light on understanding the complexity of gene regulation associated with the dynamics of DNA and RNA epigenetics in genome evolution.
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Affiliation(s)
- Shuai Cao
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Nunchanoke Sawettalake
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Lisha Shen
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
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35
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Gaitán N, Duitama J. A graph clustering algorithm for detection and genotyping of structural variants from long reads. Gigascience 2024; 13:giad112. [PMID: 38206589 PMCID: PMC10783151 DOI: 10.1093/gigascience/giad112] [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: 03/29/2023] [Revised: 08/02/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Structural variants (SVs) are genomic polymorphisms defined by their length (>50 bp). The usual types of SVs are deletions, insertions, translocations, inversions, and copy number variants. SV detection and genotyping is fundamental given the role of SVs in phenomena such as phenotypic variation and evolutionary events. Thus, methods to identify SVs using long-read sequencing data have been recently developed. FINDINGS We present an accurate and efficient algorithm to predict germline SVs from long-read sequencing data. The algorithm starts collecting evidence (signatures) of SVs from read alignments. Then, signatures are clustered based on a Euclidean graph with coordinates calculated from lengths and genomic positions. Clustering is performed by the DBSCAN algorithm, which provides the advantage of delimiting clusters with high resolution. Clusters are transformed into SVs and a Bayesian model allows to precisely genotype SVs based on their supporting evidence. This algorithm is integrated into the single sample variants detector of the Next Generation Sequencing Experience Platform, which facilitates the integration with other functionalities for genomics analysis. We performed multiple benchmark experiments, including simulation and real data, representing different genome profiles, sequencing technologies (PacBio HiFi, ONT), and read depths. CONCLUSION The results show that our approach outperformed state-of-the-art tools on germline SV calling and genotyping, especially at low depths, and in error-prone repetitive regions. We believe this work significantly contributes to the development of bioinformatic strategies to maximize the use of long-read sequencing technologies.
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Affiliation(s)
- Nicolás Gaitán
- Systems and Computing Engineering Department, Universidad de Los Andes, Bogotá 111711, Colombia
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de Los Andes, Bogotá 111711, Colombia
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36
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Xiao Y, Cheng D, Luo K, Li M, Tan Y, Lin G, Hu L. Evaluation of genetic risk of apparently balanced chromosomal rearrangement carriers by breakpoint characterization. J Assist Reprod Genet 2024; 41:147-159. [PMID: 37993578 PMCID: PMC10789712 DOI: 10.1007/s10815-023-02986-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/31/2023] [Indexed: 11/24/2023] Open
Abstract
PURPOSE To report genetic characteristics and associated risk of chromosomal breaks due to chromosomal rearrangements in large samples. METHODS MicroSeq, a technique that combines chromosome microdissection and next-generation sequencing, was used to identify chromosomal breakpoints. Long-range PCR and Sanger sequencing were used to precisely characterize 100 breakpoints in 50 ABCR carriers. RESULTS In addition to the recurrent regions of balanced rearrangement breaks in 8q24.13, 11q11.23, and 22q11.21 that had been documented, we have discovered a 10-Mb region of 12q24.13-q24.3 that could potentially be a sparse region of balanced rearrangement breaks. We found that 898 breakpoints caused gene disruption and a total of 188 breakpoints interrupted genes recorded in OMIM. The percentage of breakpoints that disrupted autosomal dominant genes recorded in OMIM was 25.53% (48/188). Fifty-four of the precisely characterized breakpoints had 1-8-bp microhomologous sequences. CONCLUSION Our findings provide a reference for the evaluation of the pathogenicity of mutations in related genes that cause protein truncation in clinical practice. According to the characteristics of breakpoints, non-homologous end joining and microhomology-mediated break-induced replication may be the main mechanism for ABCRs formation.
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Affiliation(s)
- Yanqin Xiao
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - Dehua Cheng
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410023, Hunan, China
| | - Keli Luo
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410023, Hunan, China
| | - Mengge Li
- National Engineering and Research Center of Human Stem Cells, Changsha, 410023, Hunan, China
- Hunan Guangxiu Hospital, Changsha, 410023, Hunan, China
| | - Yueqiu Tan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410023, Hunan, China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410023, Hunan, China
- National Engineering and Research Center of Human Stem Cells, Changsha, 410023, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, 410008, Hunan, China
| | - Liang Hu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China.
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410023, Hunan, China.
- National Engineering and Research Center of Human Stem Cells, Changsha, 410023, Hunan, China.
- Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, 410008, Hunan, China.
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Poot M. Methods of Detection and Mechanisms of Origin of Complex Structural Genome Variations. Methods Mol Biol 2024; 2825:39-65. [PMID: 38913302 DOI: 10.1007/978-1-0716-3946-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Based on classical karyotyping, structural genome variations (SVs) have generally been considered to be either "simple" (with one or two breakpoints) or "complex" (with more than two breakpoints). Studying the breakpoints of SVs at nucleotide resolution revealed additional, subtle structural variations, such that even "simple" SVs turned out to be "complex." Genome-wide sequencing methods, such as fosmid and paired-end mapping, short-read and long-read whole genome sequencing, and single-molecule optical mapping, also indicated that the number of SVs per individual was considerably larger than expected from karyotyping and high-resolution chromosomal array-based studies. Interestingly, SVs were detected in studies of cohorts of individuals without clinical phenotypes. The common denominator of all SVs appears to be a failure to accurately repair DNA double-strand breaks (DSBs) or to halt cell cycle progression if DSBs persist. This review discusses the various DSB response mechanisms during the mitotic cell cycle and during meiosis and their regulation. Emphasis is given to the molecular mechanisms involved in the formation of translocations, deletions, duplications, and inversions during or shortly after meiosis I. Recently, CRISPR-Cas9 studies have provided unexpected insights into the formation of translocations and chromothripsis by both breakage-fusion-bridge and micronucleus-dependent mechanisms.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Wuerzburg, Wuerzburg, Germany
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38
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Mendez-Dorantes C, Burns KH. LINE-1 retrotransposition and its deregulation in cancers: implications for therapeutic opportunities. Genes Dev 2023; 37:948-967. [PMID: 38092519 PMCID: PMC10760644 DOI: 10.1101/gad.351051.123] [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] [Indexed: 12/28/2023]
Abstract
Long interspersed element 1 (LINE-1) is the only protein-coding transposon that is active in humans. LINE-1 propagates in the genome using RNA intermediates via retrotransposition. This activity has resulted in LINE-1 sequences occupying approximately one-fifth of our genome. Although most copies of LINE-1 are immobile, ∼100 copies are retrotransposition-competent. Retrotransposition is normally limited via epigenetic silencing, DNA repair, and other host defense mechanisms. In contrast, LINE-1 overexpression and retrotransposition are hallmarks of cancers. Here, we review mechanisms of LINE-1 regulation and how LINE-1 may promote genetic heterogeneity in tumors. Finally, we discuss therapeutic strategies to exploit LINE-1 biology in cancers.
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Affiliation(s)
- Carlos Mendez-Dorantes
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kathleen H Burns
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
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39
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Hinch R, Donnelly P, Hinch AG. Meiotic DNA breaks drive multifaceted mutagenesis in the human germ line. Science 2023; 382:eadh2531. [PMID: 38033082 PMCID: PMC7615360 DOI: 10.1126/science.adh2531] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/29/2023] [Indexed: 12/02/2023]
Abstract
Meiotic recombination commences with hundreds of programmed DNA breaks; however, the degree to which they are accurately repaired remains poorly understood. We report that meiotic break repair is eightfold more mutagenic for single-base substitutions than was previously understood, leading to de novo mutation in one in four sperm and one in 12 eggs. Its impact on indels and structural variants is even higher, with 100- to 1300-fold increases in rates per break. We uncovered new mutational signatures and footprints relative to break sites, which implicate unexpected biochemical processes and error-prone DNA repair mechanisms, including translesion synthesis and end joining in meiotic break repair. We provide evidence that these mechanisms drive mutagenesis in human germ lines and lead to disruption of hundreds of genes genome wide.
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Affiliation(s)
- Robert Hinch
- Big Data Institute, University of Oxford; Oxford, UK
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford; Oxford, UK
- Genomics plc; Oxford, UK
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40
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Choo ZN, Behr JM, Deshpande A, Hadi K, Yao X, Tian H, Takai K, Zakusilo G, Rosiene J, Da Cruz Paula A, Weigelt B, Setton J, Riaz N, Powell SN, Busam K, Shoushtari AN, Ariyan C, Reis-Filho J, de Lange T, Imieliński M. Most large structural variants in cancer genomes can be detected without long reads. Nat Genet 2023; 55:2139-2148. [PMID: 37945902 PMCID: PMC10703688 DOI: 10.1038/s41588-023-01540-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/19/2023] [Indexed: 11/12/2023]
Abstract
Short-read sequencing is the workhorse of cancer genomics yet is thought to miss many structural variants (SVs), particularly large chromosomal alterations. To characterize missing SVs in short-read whole genomes, we analyzed 'loose ends'-local violations of mass balance between adjacent DNA segments. In the landscape of loose ends across 1,330 high-purity cancer whole genomes, most large (>10-kb) clonal SVs were fully resolved by short reads in the 87% of the human genome where copy number could be reliably measured. Some loose ends represent neotelomeres, which we propose as a hallmark of the alternative lengthening of telomeres phenotype. These pan-cancer findings were confirmed by long-molecule profiles of 38 breast cancer and melanoma cases. Our results indicate that aberrant homologous recombination is unlikely to drive the majority of large cancer SVs. Furthermore, analysis of mass balance in short-read whole genome data provides a surprisingly complete picture of cancer chromosomal structure.
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Affiliation(s)
- Zi-Ning Choo
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Tri-institutional MD PhD Program, Weill Cornell Medicine, New York, NY, USA
- Physiology and Biophysics PhD Program, Weill Cornell Medicine, New York, NY, USA
| | - Julie M Behr
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Tri-institutional PhD Program in Computational Biology and Medicine, New York, NY, USA
| | - Aditya Deshpande
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Tri-institutional PhD Program in Computational Biology and Medicine, New York, NY, USA
| | - Kevin Hadi
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Physiology and Biophysics PhD Program, Weill Cornell Medicine, New York, NY, USA
| | - Xiaotong Yao
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Tri-institutional PhD Program in Computational Biology and Medicine, New York, NY, USA
| | - Huasong Tian
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Kaori Takai
- Laboratory of Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - George Zakusilo
- Laboratory of Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Joel Rosiene
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Britta Weigelt
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeremy Setton
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simon N Powell
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Klaus Busam
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | - Titia de Lange
- Laboratory of Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Marcin Imieliński
- New York Genome Center, New York, NY, USA.
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA.
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.
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41
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Cascante SD, Besser A, Lee HL, Wang F, McCaffrey C, Grifo JA. Blinded rebiopsy and analysis of noneuploid embryos with 2 distinct preimplantation genetic testing platforms for aneuploidy. Fertil Steril 2023; 120:1161-1169. [PMID: 37574001 DOI: 10.1016/j.fertnstert.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/26/2023] [Accepted: 08/03/2023] [Indexed: 08/15/2023]
Abstract
OBJECTIVE To determine how often a noneuploid result from a single trophectoderm (TE) biopsy tested with the next-generation sequencing (NGS)-based preimplantation genetic testing for aneuploidy (PGT-A) is concordant with rebiopsies tested with a single-nucleotide polymorphism (SNP) array-based PGT-A platform. DESIGN Blinded prospective cohort study. SETTING University-affiliated fertility center. PATIENT(S) One hundred blastocysts were chosen from donated samples; on TE biopsy with NGS-based PGT-A, 40 had at least one whole chromosome full copy number aneuploidy alone, 20 had a single whole chromosome intermediate copy number ("whole chromosome mosaic"), 20 had a single full segmental aneuploidy (segA), and 20 had a single segmental intermediate copy number ("segmental mosaic"). INTERVENTIONS Four rebiopsies were collected from each embryo: 3 TE biopsies and the remaining embryo. Each rebiopsy was randomized, blinded, and assessed with an SNP array-based PGT-A platform that combines copy number and allele ratio analyses, without mosaicism reporting. MAIN OUTCOME MEASURE(S) Concordance between the NGS result and rebiopsy results and within each embryo's blinded rebiopsy results. RESULT(S) Next-generation sequencing-diagnosed whole chromosome aneuploidy (WCA) was reconfirmed in 95% (95% confidence interval [CI], 83%-99%) of embryos; 2 embryos with NGS-diagnosed WCA were called euploid on all conclusive rebiopsies. Among embryos with NGS-diagnosed whole chromosome mosaicism, 35% (95% CI, 15%-59%) were called euploid and 15% (95% CI, 3%-38%) were called whole chromosome aneuploid on all conclusive rebiopsies. A total of 30% (95% CI, 12%-54%) of embryos with NGS-diagnosed segA and 65% (95% CI, 41%-85%) of embryos with NGS-diagnosed segmental mosaicism were called euploid on all conclusive rebiopsies. In total, 13% (95% CI, 6%-25%) of embryos with NGS-diagnosed full copy number aneuploidy and 50% (95% CI, 34%-66%) of embryos with NGS-diagnosed mosaicism had uniformly euploid SNP results. Conversely, all embryos with at least one noneuploid SNP result (n = 72) either had SNP-diagnosed aneuploidy on another rebiopsy from the same embryo or NGS-diagnosed aneuploidy/mosaicism involving the same chromosome. CONCLUSION(S) Next-generation sequencing-diagnosed WCA is highly concordant with rebiopsies tested with an SNP array-based PGT-A; however, whole chromosome mosaicism, segA, and segmental mosaicism are less concordant, reinforcing that embryos with these results may have reproductive potential and be suitable for transfer.
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Affiliation(s)
- Sarah Druckenmiller Cascante
- Department of Obstetrics & Gynaecology, New York University Langone Prelude Fertility Center, New York, New York.
| | - Andria Besser
- Department of Obstetrics & Gynaecology, New York University Langone Prelude Fertility Center, New York, New York
| | - Hsiao-Ling Lee
- Department of Obstetrics & Gynaecology, New York University Langone Prelude Fertility Center, New York, New York
| | - Fang Wang
- Department of Obstetrics & Gynaecology, New York University Langone Prelude Fertility Center, New York, New York
| | - Caroline McCaffrey
- Department of Obstetrics & Gynaecology, New York University Langone Prelude Fertility Center, New York, New York
| | - James A Grifo
- Department of Obstetrics & Gynaecology, New York University Langone Prelude Fertility Center, New York, New York
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Oehler J, Morrow CA, Whitby MC. Gene duplication and deletion caused by over-replication at a fork barrier. Nat Commun 2023; 14:7730. [PMID: 38007544 PMCID: PMC10676400 DOI: 10.1038/s41467-023-43494-7] [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: 07/17/2023] [Accepted: 11/10/2023] [Indexed: 11/27/2023] Open
Abstract
Replication fork stalling can provoke fork reversal to form a four-way DNA junction. This remodelling of the replication fork can facilitate repair, aid bypass of DNA lesions, and enable replication restart, but may also pose a risk of over-replication during fork convergence. We show that replication fork stalling at a site-specific barrier in fission yeast can induce gene duplication-deletion rearrangements that are independent of replication restart-associated template switching and Rad51-dependent multi-invasion. Instead, they resemble targeted gene replacements (TGRs), requiring the DNA annealing activity of Rad52, the 3'-flap nuclease Rad16-Swi10, and mismatch repair protein Msh2. We propose that excess DNA, generated during the merging of a canonical fork with a reversed fork, can be liberated by a nuclease and integrated at an ectopic site via a TGR-like mechanism. This highlights how over-replication at replication termination sites can threaten genome stability in eukaryotes.
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Affiliation(s)
- Judith Oehler
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Carl A Morrow
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Matthew C Whitby
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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Klussmeier A, Putke K, Klasberg S, Kohler M, Sauter J, Schefzyk D, Schöfl G, Massalski C, Schäfer G, Schmidt AH, Roers A, Lange V. High population frequencies of MICA copy number variations originate from independent recombination events. Front Immunol 2023; 14:1297589. [PMID: 38035108 PMCID: PMC10684724 DOI: 10.3389/fimmu.2023.1297589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
MICA is a stress-induced ligand of the NKG2D receptor that stimulates NK and T cell responses and was identified as a key determinant of anti-tumor immunity. The MICA gene is located inside the MHC complex and is in strong linkage disequilibrium with HLA-B. While an HLA-B*48-linked MICA deletion-haplotype was previously described in Asian populations, little is known about other MICA copy number variations. Here, we report the genotyping of more than two million individuals revealing high frequencies of MICA duplications (1%) and MICA deletions (0.4%). Their prevalence differs between ethnic groups and can rise to 2.8% (Croatia) and 9.2% (Mexico), respectively. Targeted sequencing of more than 70 samples indicates that these copy number variations originate from independent nonallelic homologous recombination events between segmental duplications upstream of MICA and MICB. Overall, our data warrant further investigation of disease associations and consideration of MICA copy number data in oncological study protocols.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Axel Roers
- Institute for Immunology, Medical Faculty Carl Gustav Carus, University of Technology (TU) Dresden, Dresden, Germany
- Institute for Immunology, University Hospital Heidelberg, Heidelberg, Germany
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Bush ZD, Naftaly AFS, Dinwiddie D, Albers C, Hillers KJ, Libuda DE. Comprehensive detection of structural variation and transposable element differences between wild type laboratory lineages of C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523974. [PMID: 37961628 PMCID: PMC10634987 DOI: 10.1101/2023.01.13.523974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Genomic structural variations (SVs) and transposable elements (TEs) can be significant contributors to genome evolution, altered gene expression, and risk of genetic diseases. Recent advancements in long-read sequencing have greatly improved the quality of de novo genome assemblies and enhanced the detection of sequence variants at the scale of hundreds or thousands of bases. Comparisons between two diverged wild isolates of Caenorhabditis elegans, the Bristol and Hawaiian strains, have been widely utilized in the analysis of small genetic variations. Genetic drift, including SVs and rearrangements of repeated sequences such as TEs, can occur over time from long-term maintenance of wild type isolates within the laboratory. To comprehensively detect both large and small structural variations as well as TEs due to genetic drift, we generated de novo genome assemblies and annotations for each strain from our lab collection using both long- and short-read sequencing and compared our assemblies and annotations with that of other lab wild type strains. Within our lab assemblies, we annotate over 3.1Mb of sequence divergence between the Bristol and Hawaiian isolates: 337,584 SNPs, 94,503 small insertion-deletions (<50bp), and 4,334 structural variations (>50bp). Further, we define the location and movement of specific DNA TEs between N2 Bristol and CB4856 Hawaiian wild type isolates. Specifically, we find the N2 Bristol genome has 20.6% more TEs from the Tc1/mariner family than the CB4856 Hawaiian genome. Moreover, we identified Zator elements as the most abundant and mobile TE family in the genome. Using specific TE sequences with unique SNPs, we also identify 38 TEs that moved intrachromosomally and 9 TEs that moved interchromosomally between the N2 Bristol and CB4856 Hawaiian genomes. By comparing the de novo genome assembly of our lab collection Bristol isolate to the VC2010 Bristol assembly, we also reveal that lab lineages display over 2 Mb of total variation: 1,162 SNPs, 1,528 indels, and 897 SVs with 95% of the variation due to SVs. Overall, our work demonstrates the unique contribution of SVs and TEs to variation and genetic drift between wild type laboratory strains assumed to be isogenic despite growing evidence of genetic drift and phenotypic variation.
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Affiliation(s)
- Zachary D. Bush
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
| | - Alice F. S. Naftaly
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
| | - Devin Dinwiddie
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
| | - Cora Albers
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
| | - Kenneth J. Hillers
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California, USA
| | - Diana E. Libuda
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
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45
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Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Mol Ecol 2023. [PMID: 37843465 DOI: 10.1111/mec.17160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023]
Abstract
Inversions are thought to play a key role in adaptation and speciation, suppressing recombination between diverging populations. Genes influencing adaptive traits cluster in inversions, and changes in inversion frequencies are associated with environmental differences. However, in many organisms, it is unclear if inversions are geographically and taxonomically widespread. The intertidal snail, Littorina saxatilis, is one such example. Strong associations between putative polymorphic inversions and phenotypic differences have been demonstrated between two ecotypes of L. saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion polymorphism currently exists across the species range. Using whole genome data from 107 snails, most inversion polymorphisms were found to be widespread across the species range. The frequencies of some inversion arrangements were significantly different among ecotypes, suggesting a parallel adaptive role. Many inversions were also polymorphic in the sister species, L. arcana, hinting at an ancient origin.
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Affiliation(s)
- James Reeve
- Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Roger K Butlin
- Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Eva L Koch
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Sean Stankowski
- Institute of Science and Technology - Austria, Klosterneuburg, Austria
| | - Rui Faria
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
- Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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46
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Scieszka D, Bolt AM, McCormick MA, Brigman JL, Campen MJ. Aging, longevity, and the role of environmental stressors: a focus on wildfire smoke and air quality. FRONTIERS IN TOXICOLOGY 2023; 5:1267667. [PMID: 37900096 PMCID: PMC10600394 DOI: 10.3389/ftox.2023.1267667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Aging is a complex biological process involving multiple interacting mechanisms and is being increasingly linked to environmental exposures such as wildfire smoke. In this review, we detail the hallmarks of aging, emphasizing the role of telomere attrition, cellular senescence, epigenetic alterations, proteostasis, genomic instability, and mitochondrial dysfunction, while also exploring integrative hallmarks - altered intercellular communication and stem cell exhaustion. Within each hallmark of aging, our review explores how environmental disasters like wildfires, and their resultant inhaled toxicants, interact with these aging mechanisms. The intersection between aging and environmental exposures, especially high-concentration insults from wildfires, remains under-studied. Preliminary evidence, from our group and others, suggests that inhaled wildfire smoke can accelerate markers of neurological aging and reduce learning capabilities. This is likely mediated by the augmentation of circulatory factors that compromise vascular and blood-brain barrier integrity, induce chronic neuroinflammation, and promote age-associated proteinopathy-related outcomes. Moreover, wildfire smoke may induce a reduced metabolic, senescent cellular phenotype. Future interventions could potentially leverage combined anti-inflammatory and NAD + boosting compounds to counter these effects. This review underscores the critical need to study the intricate interplay between environmental factors and the biological mechanisms of aging to pave the way for effective interventions.
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Affiliation(s)
- David Scieszka
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM, United States
| | - Alicia M. Bolt
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM, United States
| | - Mark A. McCormick
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, United States
| | - Jonathan L. Brigman
- Department of Neurosciences, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, United States
| | - Matthew J. Campen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM, United States
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47
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Krannich T, Sarrias MH, Ben Aribi H, Shokrof M, Iacoangeli A, Al-Chalabi A, Sedlazeck FJ, Busby B, Al Khleifat A. VariantSurvival: a tool to identify genotype-treatment response. FRONTIERS IN BIOINFORMATICS 2023; 3:1277923. [PMID: 37885757 PMCID: PMC10598652 DOI: 10.3389/fbinf.2023.1277923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023] Open
Abstract
Motivation: For a number of neurological diseases, such as Alzheimer's disease, amyotrophic lateral sclerosis, and many others, certain genes are known to be involved in the disease mechanism. A common question is whether a structural variant in any such gene may be related to drug response in clinical trials and how this relationship can contribute to the lifecycle of drug development. Results: To this end, we introduce VariantSurvival, a tool that identifies changes in survival relative to structural variants within target genes. VariantSurvival matches annotated structural variants with genes that are clinically relevant to neurological diseases. A Cox regression model determines the change in survival between the placebo and clinical trial groups with respect to the number of structural variants in the drug target genes. We demonstrate the functionality of our approach with the exemplary case of the SETX gene. VariantSurvival has a user-friendly and lightweight graphical user interface built on the shiny web application package.
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Affiliation(s)
- Thomas Krannich
- Genome Competence Center (MF1), Robert Koch Institute, Berlin, Germany
| | - Marina Herrera Sarrias
- Computational Mathematics Division, Department of Mathematics, Stockholm University, Stockholm, Sweden
| | - Hiba Ben Aribi
- Faculty of Science of Tunis, University El Manar, Tunis, Tunisia
| | - Moustafa Shokrof
- Department of Computer Science, University of California, Davis, CA, United States
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Ben Busby
- DNAnexus, Mountain View, CA, United States
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
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48
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Grochowski CM, Bengtsson JD, Du H, Gandhi M, Lun MY, Mehaffey MG, Park K, Höps W, Benito-Garagorri E, Hasenfeld P, Korbel JO, Mahmoud M, Paulin LF, Jhangiani SN, Muzny DM, Fatih JM, Gibbs RA, Pendleton M, Harrington E, Juul S, Lindstrand A, Sedlazeck FJ, Pehlivan D, Lupski JR, Carvalho CMB. Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560172. [PMID: 37873367 PMCID: PMC10592851 DOI: 10.1101/2023.10.02.560172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a type of complex genomic rearrangement (CGR) hypothesized to result from replicative repair of DNA due to replication fork collapse. It is often mediated by a pair of inverted low-copy repeats (LCR) followed by iterative template switches resulting in at least two breakpoint junctions in cis . Although it has been identified as an important mutation signature of pathogenicity for genomic disorders and cancer genomes, its architecture remains unresolved and is predicted to display at least four structural variation (SV) haplotypes. Results Here we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the genomic DNA of 24 patients with neurodevelopmental disorders identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted SV haplotypes. Using a combination of short-read genome sequencing (GS), long- read GS, optical genome mapping and StrandSeq the haplotype structure was resolved in 18 samples. This approach refined the point of template switching between inverted LCRs in 4 samples revealing a DNA segment of ∼2.2-5.5 kb of 100% nucleotide similarity. A prediction model was developed to infer the LCR used to mediate the non-allelic homology repair. Conclusions These data provide experimental evidence supporting the hypothesis that inverted LCRs act as a recombinant substrate in replication-based repair mechanisms. Such inverted repeats are particularly relevant for formation of copy-number associated inversions, including the DUP-TRP/INV-DUP structures. Moreover, this type of CGR can result in multiple conformers which contributes to generate diverse SV haplotypes in susceptible loci .
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49
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Allou L, Mundlos S. Disruption of regulatory domains and novel transcripts as disease-causing mechanisms. Bioessays 2023; 45:e2300010. [PMID: 37381881 DOI: 10.1002/bies.202300010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 06/30/2023]
Abstract
Deletions, duplications, insertions, inversions, and translocations, collectively called structural variations (SVs), affect more base pairs of the genome than any other sequence variant. The recent technological advancements in genome sequencing have enabled the discovery of tens of thousands of SVs per human genome. These SVs primarily affect non-coding DNA sequences, but the difficulties in interpreting their impact limit our understanding of human disease etiology. The functional annotation of non-coding DNA sequences and methodologies to characterize their three-dimensional (3D) organization in the nucleus have greatly expanded our understanding of the basic mechanisms underlying gene regulation, thereby improving the interpretation of SVs for their pathogenic impact. Here, we discuss the various mechanisms by which SVs can result in altered gene regulation and how these mechanisms can result in rare genetic disorders. Beyond changing gene expression, SVs can produce novel gene-intergenic fusion transcripts at the SV breakpoints.
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Affiliation(s)
- Lila Allou
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Mundlos
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
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50
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Loehlin DW, McClain GL, Xu M, Kedia R, Root E. Demonstration of in vivo engineered tandem duplications of varying sizes using CRISPR and recombinases in Drosophila melanogaster. G3 (BETHESDA, MD.) 2023; 13:jkad155. [PMID: 37462278 PMCID: PMC10542505 DOI: 10.1093/g3journal/jkad155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/08/2023] [Accepted: 06/09/2023] [Indexed: 07/28/2023]
Abstract
Tandem gene duplicates are important parts of eukaryotic genome structure, yet the phenotypic effects of new tandem duplications are not well-understood, in part owing to a lack of techniques to build and modify them. We introduce a method, Recombinase-Mediated Tandem Duplication, to engineer specific tandem duplications in vivo using CRISPR and recombinases. We describe construction of four different tandem duplications of the Alcohol Dehydrogenase (Adh) gene in Drosophila melanogaster, with duplicated block sizes ranging from 4.2 to 20.7 kb. Flies with the Adh duplications show elevated ADH enzyme activity over unduplicated single copies. This approach to engineering duplications is combinatoric, opening the door to systematic study of the relationship between the structure of tandem duplications and their effects on expression.
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Affiliation(s)
- David W Loehlin
- Biology Department, Williams College, Williamstown, MA 01267, USA
| | | | - Manting Xu
- Biology Department, Williams College, Williamstown, MA 01267, USA
| | - Ria Kedia
- Biology Department, Williams College, Williamstown, MA 01267, USA
| | - Elise Root
- Biology Department, Williams College, Williamstown, MA 01267, USA
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