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Hiatt SM, Lawlor JM, Handley LH, Latner DR, Bonnstetter ZT, Finnila CR, Thompson ML, Boston LB, Williams M, Nunez IR, Jenkins J, Kelley WV, Bebin EM, Lopez MA, Hurst ACE, Korf BR, Schmutz J, Grimwood J, Cooper GM. Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.22.24304633. [PMID: 38585854 PMCID: PMC10996728 DOI: 10.1101/2024.03.22.24304633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Variant detection from long-read genome sequencing (lrGS) has proven to be considerably more accurate and comprehensive than variant detection from short-read genome sequencing (srGS). However, the rate at which lrGS can increase molecular diagnostic yield for rare disease is not yet precisely characterized. We performed lrGS using Pacific Biosciences "HiFi" technology on 96 short-read-negative probands with rare disease that were suspected to be genetic. We generated hg38-aligned variants and de novo phased genome assemblies, and subsequently annotated, filtered, and curated variants using clinical standards. New disease-relevant or potentially relevant genetic findings were identified in 16/96 (16.7%) probands, eight of which (8/96, 8.33%) harbored pathogenic or likely pathogenic variants. Newly identified variants were visible in both srGS and lrGS in nine probands (~9.4%) and resulted from changes to interpretation mostly from recent gene-disease association discoveries. Seven cases included variants that were only interpretable in lrGS, including copy-number variants, an inversion, a mobile element insertion, two low-complexity repeat expansions, and a 1 bp deletion. While evidence for each of these variants is, in retrospect, visible in srGS, they were either: not called within srGS data, were represented by calls with incorrect sizes or structures, or failed quality-control and filtration. Thus, while reanalysis of older data clearly increases diagnostic yield, we find that lrGS allows for substantial additional yield (7/96, 7.3%) beyond srGS. We anticipate that as lrGS analysis improves, and as lrGS datasets grow allowing for better variant frequency annotation, the additional lrGS-only rare disease yield will grow over time.
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Affiliation(s)
- Susan M. Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - Lori H. Handley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Donald R. Latner
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | | | | | - Lori Beth Boston
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Melissa Williams
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - E. Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
| | - Michael A. Lopez
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
| | - Anna C. E. Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
| | - Bruce R. Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
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Gustafson JA, Gibson SB, Damaraju N, Zalusky MPG, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson Z, Storz SHR, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves C, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal CR, Zakarian C, Goodwin S, Jensen TD, Robb E, McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, Miller DE. Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.05.24303792. [PMID: 38496498 PMCID: PMC10942501 DOI: 10.1101/2024.03.05.24303792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Less than half of individuals with a suspected Mendelian condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control datasets for variant filtering and prioritization has made tertiary analysis of LRS data challenging. To address this, the 1000 Genomes Project ONT Sequencing Consortium aims to generate LRS data from at least 800 of the 1000 Genomes Project samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal patterns of human variation. Here, we present data from analysis of the first 100 samples, representing all 5 superpopulations and 19 subpopulations. These samples, sequenced to an average depth of coverage of 37x and sequence read N50 of 54 kbp, have high concordance with previous studies for identifying single nucleotide and indel variants outside of homopolymer regions. Using multiple structural variant (SV) callers, we identify an average of 24,543 high-confidence SVs per genome, including shared and private SVs likely to disrupt gene function as well as pathogenic expansions within disease-associated repeats that were not detected using short reads. Evaluation of methylation signatures revealed expected patterns at known imprinted loci, samples with skewed X-inactivation patterns, and novel differentially methylated regions. All raw sequencing data, processed data, and summary statistics are publicly available, providing a valuable resource for the clinical genetics community to discover pathogenic SVs.
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Affiliation(s)
- Jonas A. Gustafson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Sophia B. Gibson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nikhita Damaraju
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Miranda PG Zalusky
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lei Yang
- Pacific Northwest Research Institute, Seattle, WA, USA
| | | | | | - Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Nathan D. Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Human Technopole, Milan, Italy
| | - Qiuhui Li
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Angela L. Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Joy Goffena
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Zachery Anderson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sophie HR Storz
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sydney A. Ward
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Maisha Sinha
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Claudia Gonzaga-Jauregui
- International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México
| | - Wayne E. Clarke
- New York Genome Center, New York, NY, USA
- Outlier Informatics Inc., Saskatoon, SK, Canada
| | | | | | | | | | | | - Mahler Revsine
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Cate R. Paschal
- Department of Laboratories, Seattle Children’s Hospital, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Christina Zakarian
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Esther Robb
- Department of Computer Science, Stanford University, Stanford, CA, 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
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Justin M. Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mikhail Kolmogorov
- Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Richard N. McLaughlin
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - Harriet Dashnow
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Matt Loose
- Deep Seq, School of Life Sciences, University of Nottingham, Nottingham, England
| | - Miten Jain
- Department of Bioengineering, Department of Physics, Khoury College of Computer Sciences, Northeastern University, Boston, MA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Danny E. Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
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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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Gadgil RY, Rider SD, Shrestha R, Alhawach V, Hitch DC, Leffak M. Microsatellite break-induced replication generates highly mutagenized extrachromosomal circular DNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575055. [PMID: 38260482 PMCID: PMC10802558 DOI: 10.1101/2024.01.12.575055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Extrachromosomal circular DNAs (eccDNAs) are produced from all regions of the eucaryotic genome. In tumors, highly transcribed eccDNAs have been implicated in oncogenesis, neoantigen production and resistance to chemotherapy. Here we show that unstable microsatellites capable of forming hairpin, triplex, quadruplex and AT-rich structures generate eccDNAs when integrated at a common ectopic site in human cells. These non-B DNA prone microsatellites form eccDNAs by replication-dependent mechanisms. The microsatellite-based eccDNAs are highly mutagenized and display template switches to sister chromatids and to nonallelic chromosomal sites. High frequency mutagenesis occurs within the eccDNA microsatellites and extends bidirectionally for several kilobases into flanking DNA and nonallelic DNA. Mutations include mismatches, short duplications, longer nontemplated insertions and large deletions. Template switching leads to recurrent deletions and recombination domains within the eccDNAs. Template switching events are microhomology-mediated, but do not occur at all potential sites of complementarity. Each microsatellite exhibits a distinct pattern of recombination, microhomology choice and base substitution signature. Depletion of Rad51, the COPS2 signalosome subunit or POLη alter the eccDNA mutagenic profiles. We propose an asynchronous capture model based on break-induced replication from microsatellite-induced DNA breaks for the generation and circularization of mutagenized eccDNAs and genomic homologous recombination deficiency (HRD) scars.
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Nasalingkhan C, Sirinonthanawech N, Noree C. Robust assembly of the aldehyde dehydrogenase Ald4p in Saccharomyces cerevisiae. Biol Open 2023; 12:bio060070. [PMID: 37767855 PMCID: PMC10602002 DOI: 10.1242/bio.060070] [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: 07/10/2023] [Accepted: 09/26/2023] [Indexed: 09/29/2023] Open
Abstract
As part of our studies of yeast aldehyde dehydrogenase (Ald4p) assembly, we identified a population of transformants (SWORD strain) that show more robust filament formation of GFP-tagged Ald4p (Ald4p-GFP) than that of a wild type ALD4::GFP strain. Sequencing of the ALD4 gene in the SWORD strain showed that the increased assembly was not due to changes to the ALD4 coding sequence, suggesting that a second mutation site was altering Ald4p assembly. Using short-read whole-genome sequencing, we identified spontaneous mutations in FLO9. Introduction of the SWORD allele of FLO9 into a wild-type ALD4::GFP yeast strain revealed that the changes to FLO9 were a contributor to the increased length of Ald4p-GFP filaments we observe in the SWORD strain and that this effect was not due to an increase in Ald4p protein levels. However, the expression of the FLO9 (SWORD) allele in wild-type yeast did not fully recapitulate the length control defect we observed in SWORD strains, arguing that there are additional genes contributing to the filament length phenotype. For our future work, this FLO9 from SWORD will be tested whether it could show global effect, promoting the assembly of some other filament-forming enzymes.
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Affiliation(s)
- Channarong Nasalingkhan
- Institute of Molecular Biosciences, Mahidol University, 25/25 Phuttamonthon 4 Road, Salaya, Phuttamonthon, Nakhon Pathom 73170Thailand
| | - Naraporn Sirinonthanawech
- Institute of Molecular Biosciences, Mahidol University, 25/25 Phuttamonthon 4 Road, Salaya, Phuttamonthon, Nakhon Pathom 73170Thailand
| | - Chalongrat Noree
- Institute of Molecular Biosciences, Mahidol University, 25/25 Phuttamonthon 4 Road, Salaya, Phuttamonthon, Nakhon Pathom 73170Thailand
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Mastrorosa FK, Miller DE, Eichler EE. Applications of long-read sequencing to Mendelian genetics. Genome Med 2023; 15:42. [PMID: 37316925 DOI: 10.1186/s13073-023-01194-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/18/2023] [Indexed: 06/16/2023] Open
Abstract
Advances in clinical genetic testing, including the introduction of exome sequencing, have uncovered the molecular etiology for many rare and previously unsolved genetic disorders, yet more than half of individuals with a suspected genetic disorder remain unsolved after complete clinical evaluation. A precise genetic diagnosis may guide clinical treatment plans, allow families to make informed care decisions, and permit individuals to participate in N-of-1 trials; thus, there is high interest in developing new tools and techniques to increase the solve rate. Long-read sequencing (LRS) is a promising technology for both increasing the solve rate and decreasing the amount of time required to make a precise genetic diagnosis. Here, we summarize current LRS technologies, give examples of how they have been used to evaluate complex genetic variation and identify missing variants, and discuss future clinical applications of LRS. As costs continue to decrease, LRS will find additional utility in the clinical space fundamentally changing how pathological variants are discovered and eventually acting as a single-data source that can be interrogated multiple times for clinical service.
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Affiliation(s)
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
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7
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Lecoquierre F, Quenez O, Fourneaux S, Coutant S, Vezain M, Rolain M, Drouot N, Boland A, Olaso R, Meyer V, Deleuze JF, Dabbagh D, Gilles I, Gayet C, Saugier-Veber P, Goldenberg A, Guerrot AM, Nicolas G. High diagnostic potential of short and long read genome sequencing with transcriptome analysis in exome-negative developmental disorders. Hum Genet 2023; 142:773-783. [PMID: 37076692 DOI: 10.1007/s00439-023-02553-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/05/2023] [Indexed: 04/21/2023]
Abstract
Exome sequencing (ES) has become the method of choice for diagnosing rare diseases, while the availability of short-read genome sequencing (SR-GS) in a medical setting is increasing. In addition, new sequencing technologies, such as long-read genome sequencing (LR-GS) and transcriptome sequencing, are being increasingly used. However, the contribution of these techniques compared to widely used ES is not well established, particularly in regards to the analysis of non-coding regions. In a pilot study of five probands affected by an undiagnosed neurodevelopmental disorder, we performed trio-based short-read GS and long-read GS as well as case-only peripheral blood transcriptome sequencing. We identified three new genetic diagnoses, none of which affected the coding regions. More specifically, LR-GS identified a balanced inversion in NSD1, highlighting a rare mechanism of Sotos syndrome. SR-GS identified a homozygous deep intronic variant of KLHL7 resulting in a neoexon inclusion, and a de novo mosaic intronic 22-bp deletion in KMT2D, leading to the diagnosis of Perching and Kabuki syndromes, respectively. All three variants had a significant effect on the transcriptome, which showed decreased gene expression, mono-allelic expression and splicing defects, respectively, further validating the effect of these variants. Overall, in undiagnosed patients, the combination of short and long read GS allowed the detection of cryptic variations not or barely detectable by ES, making it a highly sensitive method at the cost of more complex bioinformatics approaches. Transcriptome sequencing is a valuable complement for the functional validation of variations, particularly in the non-coding genome.
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Affiliation(s)
- François Lecoquierre
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France.
| | - Olivier Quenez
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Steeve Fourneaux
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Sophie Coutant
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Myriam Vezain
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Marion Rolain
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Nathalie Drouot
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Vincent Meyer
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Dana Dabbagh
- Department of Pediatrics, Elbeuf Hospital, Elbeuf, France
| | | | - Claire Gayet
- Department of Pediatrics, CHU Rouen, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Alice Goldenberg
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Anne-Marie Guerrot
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Gaël Nicolas
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France.
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8
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Payne ZL, Penny GM, Turner TN, Dutcher SK. A gap-free genome assembly of Chlamydomonas reinhardtii and detection of translocations induced by CRISPR-mediated mutagenesis. PLANT COMMUNICATIONS 2023; 4:100493. [PMID: 36397679 PMCID: PMC10030371 DOI: 10.1016/j.xplc.2022.100493] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/26/2022] [Accepted: 11/15/2022] [Indexed: 05/04/2023]
Abstract
Genomic assemblies of the unicellular green alga Chlamydomonas reinhardtii have provided important resources for researchers. However, assembly errors, large gaps, and unplaced scaffolds as well as strain-specific variants currently impede many types of analysis. By combining PacBio HiFi and Oxford Nanopore long-read technologies, we generated a de novo genome assembly for strain CC-5816, derived from crosses of strains CC-125 and CC-124. Multiple methods of evaluating genome completeness and base-pair error rate suggest that the final telomere-to-telomere assembly is highly accurate. The CC-5816 assembly enabled previously difficult analyses that include characterization of the 17 centromeres, rDNA arrays on three chromosomes, and 56 insertions of organellar DNA into the nuclear genome. Using Nanopore sequencing, we identified sites of cytosine (CpG) methylation, which are enriched at centromeres. We analyzed CRISPR-Cas9 insertional mutants in the PF23 gene. Two of the three alleles produced progeny that displayed patterns of meiotic inviability that suggested the presence of a chromosomal aberration. Mapping Nanopore reads from pf23-2 and pf23-3 onto the CC-5816 genome showed that these two strains each carry a translocation that was initiated at the PF23 gene locus on chromosome 11 and joined with chromosomes 5 or 3, respectively. The translocations were verified by demonstrating linkage between loci on the two translocated chromosomes in meiotic progeny. The three pf23 alleles display the expected short-cilia phenotype, and immunoblotting showed that pf23-2 lacks the PF23 protein. Our CC-5816 genome assembly will undoubtedly provide an important tool for the Chlamydomonas research community.
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Affiliation(s)
- Zachary L Payne
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Gervette M Penny
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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9
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Conlin LK, Aref-Eshghi E, McEldrew DA, Luo M, Rajagopalan R. Long-read sequencing for molecular diagnostics in constitutional genetic disorders. Hum Mutat 2022; 43:1531-1544. [PMID: 36086952 PMCID: PMC9561063 DOI: 10.1002/humu.24465] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/11/2022]
Abstract
Long-read sequencing (LRS) has been around for more than a decade, but widespread adoption of the technology has been slow due to the perceived high error rates and high sequencing cost. This is changing due to the recent advancements to produce highly accurate sequences and the reducing costs. LRS promises significant improvement over short read sequencing in four major areas: (1) better detection of structural variation (2) better resolution of highly repetitive or nonunique regions (3) accurate long-range haplotype phasing and (4) the detection of base modifications natively from the sequencing data. Several successful applications of LRS have demonstrated its ability to resolve molecular diagnoses where short-read sequencing fails to identify a cause. However, the argument for increased diagnostic yield from LRS remains to be validated. Larger cohort studies may be required to establish the realistic boundaries of LRS's clinical utility and analytical validity, as well as the development of standards for clinical applications. We discuss the limitations of the current standard of care, and contrast with the applications and advantages of two major LRS platforms, PacBio and Oxford Nanopore, for molecular diagnostics of constitutional disorders, and present a critical argument about the potential of LRS in diagnostic settings.
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Affiliation(s)
- Laura K. Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Erfan Aref-Eshghi
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Deborah A. McEldrew
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Minjie Luo
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ramakrishnan Rajagopalan
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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10
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Eigenhuis KN, Somsen HB, van den Berg DLC. Transcription Pause and Escape in Neurodevelopmental Disorders. Front Neurosci 2022; 16:846272. [PMID: 35615272 PMCID: PMC9125161 DOI: 10.3389/fnins.2022.846272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription pause-release is an important, highly regulated step in the control of gene expression. Modulated by various factors, it enables signal integration and fine-tuning of transcriptional responses. Mutations in regulators of pause-release have been identified in a range of neurodevelopmental disorders that have several common features affecting multiple organ systems. This review summarizes current knowledge on this novel subclass of disorders, including an overview of clinical features, mechanistic details, and insight into the relevant neurodevelopmental processes.
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11
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Danis D, Jacobsen JOB, Balachandran P, Zhu Q, Yilmaz F, Reese J, Haimel M, Lyon GJ, Helbig I, Mungall CJ, Beck CR, Lee C, Smedley D, Robinson PN. SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing. Genome Med 2022; 14:44. [PMID: 35484572 PMCID: PMC9047340 DOI: 10.1186/s13073-022-01046-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 04/12/2022] [Indexed: 01/18/2023] Open
Abstract
Structural variants (SVs) are implicated in the etiology of Mendelian diseases but have been systematically underascertained owing to sequencing technology limitations. Long-read sequencing enables comprehensive detection of SVs, but approaches for prioritization of candidate SVs are needed. Structural variant Annotation and analysis (SvAnna) assesses all classes of SVs and their intersection with transcripts and regulatory sequences, relating predicted effects on gene function with clinical phenotype data. SvAnna places 87% of deleterious SVs in the top ten ranks. The interpretable prioritizations offered by SvAnna will facilitate the widespread adoption of long-read sequencing in diagnostic genomics. SvAnna is available at https://github.com/TheJacksonLaboratory/SvAnn a .
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Affiliation(s)
- Daniel Danis
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Julius O. B. Jacobsen
- grid.4868.20000 0001 2171 1133William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ UK
| | - Parithi Balachandran
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Qihui Zhu
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Feyza Yilmaz
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Justin Reese
- grid.184769.50000 0001 2231 4551Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Matthias Haimel
- grid.511293.d0000 0004 6104 8403Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria ,grid.416346.2St. Anna Children’s Cancer Research Institute, Vienna, Austria ,grid.418729.10000 0004 0392 6802CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria ,grid.486422.e0000000405446183Present address: Global Computational Biology and Digital Sciences, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Gholson J. Lyon
- grid.420001.70000 0000 9813 9625Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, USA ,grid.212340.60000000122985718Biology PhD Program, The Graduate Center, The City University of New York, New York, USA
| | - Ingo Helbig
- grid.239552.a0000 0001 0680 8770Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.239552.a0000 0001 0680 8770The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.239552.a0000 0001 0680 8770Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Neurology, University of Pennsylvania, Philadelphia, PA USA
| | - Christopher J. Mungall
- grid.184769.50000 0001 2231 4551Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Christine R. Beck
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA ,grid.208078.50000000419370394Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06032 USA ,grid.63054.340000 0001 0860 4915Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269 USA
| | - Charles Lee
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Damian Smedley
- grid.4868.20000 0001 2171 1133William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ UK
| | - Peter N. Robinson
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA ,grid.208078.50000000419370394Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06032 USA
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12
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Bukowska-Olech E, Sowińska-Seidler A, Larysz D, Gawliński P, Koczyk G, Popiel D, Gurba-Bryśkiewicz L, Materna-Kiryluk A, Adamek Z, Szczepankiewicz A, Dominiak P, Glista F, Matuszewska K, Jamsheer A. Results from Genetic Studies in Patients Affected with Craniosynostosis: Clinical and Molecular Aspects. Front Mol Biosci 2022; 9:865494. [PMID: 35591945 PMCID: PMC9112228 DOI: 10.3389/fmolb.2022.865494] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/21/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Craniosynostosis (CS) represents a highly heterogeneous genetic condition whose genetic background has not been yet revealed. The abnormality occurs either in isolated form or syndromic, as an element of hundreds of different inborn syndromes. Consequently, CS may often represent a challenging diagnostic issue. Methods: We investigated a three-tiered approach (karyotyping, Sanger sequencing, followed by custom gene panel/chromosomal microarray analysis, and exome sequencing), coupled with prioritization of variants based on dysmorphological assessment and description in terms of human phenotype ontology. In addition, we have also performed a statistical analysis of the obtained clinical data using the nonparametric test χ2. Results: We achieved a 43% diagnostic success rate and have demonstrated the complexity of mutations’ type harbored by the patients, which were either chromosomal aberrations, copy number variations, or point mutations. The majority of pathogenic variants were found in the well-known CS genes, however, variants found in genes associated with chromatinopathies or RASopathies are of particular interest. Conclusion: We have critically summarized and then optimised a cost-effective diagnostic algorithm, which may be helpful in a daily diagnostic routine and future clinical research of various CS types. Moreover, we have pinpointed the possible underestimated co-occurrence of CS and intellectual disability, suggesting it may be overlooked when intellectual disability constitutes a primary clinical complaint. On the other hand, in any case of already detected syndromic CS and intellectual disability, the possible occurrence of clinical features suggestive for chromatinopathies or RASopathies should also be considered.
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Affiliation(s)
- Ewelina Bukowska-Olech
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- *Correspondence: Ewelina Bukowska-Olech, ; Aleksander Jamsheer,
| | - Anna Sowińska-Seidler
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Dawid Larysz
- Department of Head and Neck Surgery for Children and Adolescents, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
- Prof. St. Popowski Regional Specialized Children's Hospital, Olsztyn, Poland
| | - Paweł Gawliński
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Grzegorz Koczyk
- Centers for Medical Genetics GENESIS, Poznan, Poland
- Biometry and Bioinformatics Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | | | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- Centers for Medical Genetics GENESIS, Poznan, Poland
| | | | - Aleksandra Szczepankiewicz
- Molecular and Cell Biology Unit, Department of Paediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Filip Glista
- Poznan University of Medical Sciences, Poznan, Poland
| | - Karolina Matuszewska
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- Centers for Medical Genetics GENESIS, Poznan, Poland
| | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- Centers for Medical Genetics GENESIS, Poznan, Poland
- *Correspondence: Ewelina Bukowska-Olech, ; Aleksander Jamsheer,
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13
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Acosta-Uribe J, Aguillón D, Cochran JN, Giraldo M, Madrigal L, Killingsworth BW, Singhal R, Labib S, Alzate D, Velilla L, Moreno S, García GP, Saldarriaga A, Piedrahita F, Hincapié L, López HE, Perumal N, Morelo L, Vallejo D, Solano JM, Reiman EM, Surace EI, Itzcovich T, Allegri R, Sánchez-Valle R, Villegas-Lanau A, White CL, Matallana D, Myers RM, Browning SR, Lopera F, Kosik KS. A neurodegenerative disease landscape of rare mutations in Colombia due to founder effects. Genome Med 2022; 14:27. [PMID: 35260199 PMCID: PMC8902761 DOI: 10.1186/s13073-022-01035-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 02/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Colombian population, as well as those in other Latin American regions, arose from a recent tri-continental admixture among Native Americans, Spanish invaders, and enslaved Africans, all of whom passed through a population bottleneck due to widespread infectious diseases that left small isolated local settlements. As a result, the current population reflects multiple founder effects derived from diverse ancestries. METHODS We characterized the role of admixture and founder effects on the origination of the mutational landscape that led to neurodegenerative disorders under these historical circumstances. Genomes from 900 Colombian individuals with Alzheimer's disease (AD) [n = 376], frontotemporal lobar degeneration-motor neuron disease continuum (FTLD-MND) [n = 197], early-onset dementia not otherwise specified (EOD) [n = 73], and healthy participants [n = 254] were analyzed. We examined their global and local ancestry proportions and screened this cohort for deleterious variants in disease-causing and risk-conferring genes. RESULTS We identified 21 pathogenic variants in AD-FTLD related genes, and PSEN1 harbored the majority (11 pathogenic variants). Variants were identified from all three continental ancestries. TREM2 heterozygous and homozygous variants were the most common among AD risk genes (102 carriers), a point of interest because the disease risk conferred by these variants differed according to ancestry. Several gene variants that have a known association with MND in European populations had FTLD phenotypes on a Native American haplotype. Consistent with founder effects, identity by descent among carriers of the same variant was frequent. CONCLUSIONS Colombian demography with multiple mini-bottlenecks probably enhanced the detection of founder events and left a proportionally higher frequency of rare variants derived from the ancestral populations. These findings demonstrate the role of genomically defined ancestry in phenotypic disease expression, a phenotypic range of different rare mutations in the same gene, and further emphasize the importance of inclusiveness in genetic studies.
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Affiliation(s)
- Juliana Acosta-Uribe
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA.,Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - David Aguillón
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | | | - Margarita Giraldo
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia.,Instituto Neurológico de Colombia (INDEC), Medellín, Colombia
| | - Lucía Madrigal
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Bradley W Killingsworth
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Rijul Singhal
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Sarah Labib
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Diana Alzate
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Lina Velilla
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Sonia Moreno
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Gloria P García
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Amanda Saldarriaga
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Francisco Piedrahita
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Liliana Hincapié
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Hugo E López
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Nithesh Perumal
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Leonilde Morelo
- Department of Internal Medicine, School of Medicine, Universidad del Sinú, Montería, Colombia
| | - Dionis Vallejo
- Department of Neurology, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Juan Marcos Solano
- Department of Neurology, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | | | - Ezequiel I Surace
- Laboratorio de Enfermedades Neurodegenerativas (Fleni-CONICET), Buenos Aires, Argentina
| | - Tatiana Itzcovich
- Laboratorio de Enfermedades Neurodegenerativas (Fleni-CONICET), Buenos Aires, Argentina
| | - Ricardo Allegri
- Centro de Memoria y Envejecimiento (Fleni-CONICET), Buenos Aires, Argentina
| | - Raquel Sánchez-Valle
- Alzheimer's Disease and Other Cognitive Disorders Unit, Hospital Clínic de Barcelona, IDIBAPS and University of Barcelona, Barcelona, Spain
| | - Andrés Villegas-Lanau
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Charles L White
- Neuropathology Section, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Diana Matallana
- Instituto de Envejecimiento, Department of Psychiatry, School of Medicine, Pontifical Xaverian University, Bogotá, Colombia.,Department of Mental Health, Hospital Universitario Santa Fe de Bogotá, Bogotá, Colombia
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Francisco Lopera
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia.
| | - Kenneth S Kosik
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA.
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14
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Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology. Genes (Basel) 2022; 13:genes13020333. [PMID: 35205378 PMCID: PMC8871714 DOI: 10.3390/genes13020333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
During the last decade, genetic testing has emerged as an important etiological diagnostic tool for Mendelian diseases, including pediatric neurological conditions. A genetic diagnosis has a considerable impact on disease management and treatment; however, many cases remain undiagnosed after applying standard diagnostic sequencing techniques. This review discusses various methods to improve the molecular diagnostic rates in these genomic cold cases. We discuss extended analysis methods to consider, non-Mendelian inheritance models, mosaicism, dual/multiple diagnoses, periodic re-analysis, artificial intelligence tools, and deep phenotyping, in addition to integrating various omics methods to improve variant prioritization. Last, novel genomic technologies, including long-read sequencing, artificial long-read sequencing, and optical genome mapping are discussed. In conclusion, a more comprehensive molecular analysis and a timely re-analysis of unsolved cases are imperative to improve diagnostic rates. In addition, our current understanding of the human genome is still limited due to restrictions in technologies. Novel technologies are now available that improve upon some of these limitations and can capture all human genomic variation more accurately. Last, we recommend a more routine implementation of high molecular weight DNA extraction methods that is coherent with the ability to use and/or optimally benefit from these novel genomic methods.
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15
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Miller DE, Sulovari A, Wang T, Loucks H, Hoekzema K, Munson KM, Lewis AP, Fuerte EPA, Paschal CR, Walsh T, Thies J, Bennett JT, Glass I, Dipple KM, Patterson K, Bonkowski ES, Nelson Z, Squire A, Sikes M, Beckman E, Bennett RL, Earl D, Lee W, Allikmets R, Perlman SJ, Chow P, Hing AV, Wenger TL, Adam MP, Sun A, Lam C, Chang I, Zou X, Austin SL, Huggins E, Safi A, Iyengar AK, Reddy TE, Majoros WH, Allen AS, Crawford GE, Kishnani PS, King MC, Cherry T, Chong JX, Bamshad MJ, Nickerson DA, Mefford HC, Doherty D, Eichler EE. Targeted long-read sequencing identifies missing disease-causing variation. Am J Hum Genet 2021; 108:1436-1449. [PMID: 34216551 PMCID: PMC8387463 DOI: 10.1016/j.ajhg.2021.06.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/07/2021] [Indexed: 12/28/2022] Open
Abstract
Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.
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Affiliation(s)
- Danny E Miller
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA.
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Hailey Loucks
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Edith P Almanza Fuerte
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Catherine R Paschal
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Tom Walsh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jenny Thies
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - James T Bennett
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Laboratories, Seattle Children's Hospital, Seattle, WA 98105, USA; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Ian Glass
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Katrina M Dipple
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Karynne Patterson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Emily S Bonkowski
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Zoe Nelson
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Audrey Squire
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Megan Sikes
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Erika Beckman
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Robin L Bennett
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Dawn Earl
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Winston Lee
- Department of Genetics and Development, Columbia University, New York, NY 10032, USA; Department of Ophthalmology, Columbia University, New York, NY 10032, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Seth J Perlman
- Department of Neurology, Seattle Children's Hospital, University of Washington, Seattle, WA 98105, USA
| | - Penny Chow
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98195, USA
| | - Anne V Hing
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tara L Wenger
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Margaret P Adam
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Angela Sun
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Christina Lam
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Irene Chang
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Xue Zou
- Program in Computational Biology & Bioinformatics, Duke University, Durham, NC 27710, USA
| | - Stephanie L Austin
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Erin Huggins
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Alexias Safi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Apoorva K Iyengar
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University; Durham, NC 27708, USA
| | - Timothy E Reddy
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - William H Majoros
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - Gregory E Crawford
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Priya S Kishnani
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Mary-Claire King
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tim Cherry
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Dan Doherty
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Developmental Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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16
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Mangin A, de Pontual L, Tsai YC, Monteil L, Nizon M, Boisseau P, Mercier S, Ziegle J, Harting J, Heiner C, Gourdon G, Tomé S. Robust Detection of Somatic Mosaicism and Repeat Interruptions by Long-Read Targeted Sequencing in Myotonic Dystrophy Type 1. Int J Mol Sci 2021; 22:2616. [PMID: 33807660 PMCID: PMC7962047 DOI: 10.3390/ijms22052616] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 02/07/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is the most complex and variable trinucleotide repeat disorder caused by an unstable CTG repeat expansion, reaching up to 4000 CTG in the most severe cases. The genetic and clinical variability of DM1 depend on the sex and age of the transmitting parent, but also on the CTG repeat number, presence of repeat interruptions and/or on the degree of somatic instability. Currently, it is difficult to simultaneously and accurately determine these contributing factors in DM1 patients due to the limitations of gold standard methods used in molecular diagnostics and research laboratories. Our study showed the efficiency of the latest PacBio long-read sequencing technology to sequence large CTG trinucleotides, detect multiple and single repeat interruptions and estimate the levels of somatic mosaicism in DM1 patients carrying complex CTG repeat expansions inaccessible to most methods. Using this innovative approach, we revealed the existence of de novo CCG interruptions associated with CTG stabilization/contraction across generations in a new DM1 family. We also demonstrated that our method is suitable to sequence the DM1 locus and measure somatic mosaicism in DM1 families carrying more than 1000 pure CTG repeats. Better characterization of expanded alleles in DM1 patients can significantly improve prognosis and genetic counseling, not only in DM1 but also for other tandem DNA repeat disorders.
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Affiliation(s)
- Antoine Mangin
- Centre de Recherche en Myologie, Inserm, Institut de Myologie, Sorbonne Université, F-75013 Paris, France; (A.M.); (L.d.P.); (G.G.)
- Dementia Research Institute, Cardiff University, Cardiff CF10 3AT, UK
| | - Laure de Pontual
- Centre de Recherche en Myologie, Inserm, Institut de Myologie, Sorbonne Université, F-75013 Paris, France; (A.M.); (L.d.P.); (G.G.)
| | - Yu-Chih Tsai
- Pacific Biosciences, Menlo Park, CA 94025, USA; (Y.-C.T.); (J.Z.); (J.H.); (C.H.)
| | - Laetitia Monteil
- Genetics Department of the Hospital of Toulouse, F-31059 Toulouse, France;
| | - Mathilde Nizon
- CHU de Nantes, Service de Génétique Médicale, Laboratoire de Génétique Moléculaire, F-44000 Nantes, France; (M.N.); (P.B.)
| | - Pierre Boisseau
- CHU de Nantes, Service de Génétique Médicale, Laboratoire de Génétique Moléculaire, F-44000 Nantes, France; (M.N.); (P.B.)
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, Centre de Référence des Maladies Neuromusculaires AOC, F-44000 Nantes, France;
| | - Janet Ziegle
- Pacific Biosciences, Menlo Park, CA 94025, USA; (Y.-C.T.); (J.Z.); (J.H.); (C.H.)
| | - John Harting
- Pacific Biosciences, Menlo Park, CA 94025, USA; (Y.-C.T.); (J.Z.); (J.H.); (C.H.)
| | - Cheryl Heiner
- Pacific Biosciences, Menlo Park, CA 94025, USA; (Y.-C.T.); (J.Z.); (J.H.); (C.H.)
| | - Geneviève Gourdon
- Centre de Recherche en Myologie, Inserm, Institut de Myologie, Sorbonne Université, F-75013 Paris, France; (A.M.); (L.d.P.); (G.G.)
| | - Stéphanie Tomé
- Centre de Recherche en Myologie, Inserm, Institut de Myologie, Sorbonne Université, F-75013 Paris, France; (A.M.); (L.d.P.); (G.G.)
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