1
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Kim JH, Koh IG, Lee H, Lee GH, Song DY, Kim SW, Kim Y, Han JH, Bong G, Lee J, Byun H, Son JH, Kim YR, Lee Y, Kim JJ, Park JW, Kim IB, Choi JK, Jang JH, Trost B, Lee J, Kim E, Yoo HJ, An JY. Short tandem repeat expansions in cortical layer-specific genes implicate in phenotypic severity and adaptability of autism spectrum disorder. Psychiatry Clin Neurosci 2024; 78:405-415. [PMID: 38751214 DOI: 10.1111/pcn.13676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/14/2024] [Accepted: 04/15/2024] [Indexed: 07/06/2024]
Abstract
AIM Short tandem repeats (STRs) are repetitive DNA sequences and highly mutable in various human disorders. While the involvement of STRs in various genetic disorders has been extensively studied, their role in autism spectrum disorder (ASD) remains largely unexplored. In this study, we aimed to investigate genetic association of STR expansions with ASD using whole genome sequencing (WGS) and identify risk loci associated with ASD phenotypes. METHODS We analyzed WGS data of 634 ASD families and performed genome-wide evaluation for 12,929 STR loci. We found rare STR expansions that exceeded normal repeat lengths in autism cases compared to unaffected controls. By integrating single cell RNA and ATAC sequencing datasets of human postmortem brains, we prioritized STR loci in genes specifically expressed in cortical development stages. A deep learning method was used to predict functionality of ASD-associated STR loci. RESULTS In ASD cases, rare STR expansions predominantly occurred in early cortical layer-specific genes involved in neurodevelopment, highlighting the cellular specificity of STR-associated genes in ASD risk. Leveraging deep learning prediction models, we demonstrated that these STR expansions disrupted the regulatory activity of enhancers and promoters, suggesting a potential mechanism through which they contribute to ASD pathogenesis. We found that individuals with ASD-associated STR expansions exhibited more severe ASD phenotypes and diminished adaptability compared to non-carriers. CONCLUSION Short tandem repeat expansions in cortical layer-specific genes are associated with ASD and could potentially be a risk genetic factor for ASD. Our study is the first to show evidence of STR expansion associated with ASD in an under-investigated population.
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Affiliation(s)
- Jae Hyun Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - In Gyeong Koh
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Hyeji Lee
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Gang-Hee Lee
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Da-Yea Song
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Soo-Whee Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Yujin Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Jae Hyun Han
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Psychiatry, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Republic of Korea
| | - Guiyoung Bong
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeewon Lee
- Department of Psychiatry, Soonchunhyang University College of Medicine, Asan, Republic of Korea
| | - Heejung Byun
- Department of Neuropsychiatry, Seoul Metropolitan Children's Hospital, Seoul, Republic of Korea
| | - Ji Hyun Son
- Department of Neuropsychiatry, Seoul Metropolitan Children's Hospital, Seoul, Republic of Korea
| | - Ye Rim Kim
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yoojeong Lee
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Justine Jaewon Kim
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jung Woo Park
- Center for Biomedical Computing, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, Republic of Korea
| | - Il Bin Kim
- Department of Psychiatry, Hanyang University Guri Hospital, Guri, Republic of Korea
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Brett Trost
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Junehawk Lee
- Center for Biomedical Computing, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, Republic of Korea
| | - Eunjoon Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Hee Jeong Yoo
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Republic of Korea
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2
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Chiu R, Rajan-Babu IS, Friedman JM, Birol I. A comprehensive tandem repeat catalog of the human genome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.19.24309173. [PMID: 38947075 PMCID: PMC11213036 DOI: 10.1101/2024.06.19.24309173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
With the increasing availability of long-read sequencing data, high-quality human genome assemblies, and software for fully characterizing tandem repeats, genome-wide genotyping of tandem repeat loci on a population scale becomes more feasible. Such efforts not only expand our knowledge of the tandem repeat landscape in the human genome but also enhance our ability to differentiate pathogenic tandem repeat mutations from benign polymorphisms. To this end, we analyzed 272 genomes assembled using datasets from three public initiatives that employed different long-read sequencing technologies. Here, we report a catalog of over 18 million tandem repeat loci, many of which were previously unannotated. Some of these loci are highly polymorphic, and many of them reside within coding sequences.
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Affiliation(s)
- Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Indhu-Shree Rajan-Babu
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
- BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
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3
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Yoon JG, Lee S, Cho J, Kim N, Kim S, Kim MJ, Kim SY, Moon J, Chae JH. Diagnostic uplift through the implementation of short tandem repeat analysis using exome sequencing. Eur J Hum Genet 2024; 32:584-587. [PMID: 38308084 PMCID: PMC11061289 DOI: 10.1038/s41431-024-01542-w] [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: 09/14/2023] [Revised: 11/22/2023] [Accepted: 01/10/2024] [Indexed: 02/04/2024] Open
Abstract
To date, approximately 50 short tandem repeat (STR) disorders have been identified; yet, clinical laboratories rarely conduct STR analysis on exomes. To assess its diagnostic value, we analyzed STRs in 6099 exomes from 2510 families with mostly suspected neurogenetic disorders. We employed ExpansionHunter and REViewer to detect pathogenic repeat expansions, confirming them using orthogonal methods. Genotype-phenotype correlations led to the diagnosis of thirteen individuals in seven previously undiagnosed families, identifying three autosomal dominant disorders: dentatorubral-pallidoluysian atrophy (n = 3), spinocerebellar ataxia type 7 (n = 2), and myotonic dystrophy type 1 (n = 2), resulting in a diagnostic gain of 0.28% (7/2510). Additionally, we found expanded ATXN1 alleles (≥39 repeats) with varying patterns of CAT interruptions in twelve individuals, accounting for approximately 0.19% in the Korean population. Our study underscores the importance of integrating STR analysis into exome sequencing pipeline, broadening the application of exome sequencing for STR assessments.
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Affiliation(s)
- Jihoon G Yoon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seungbok Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Jaeso Cho
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Narae Kim
- Department of Neurology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sheehyun Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Jangsup Moon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Department of Neurology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Jong-Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea.
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4
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Marín O. Parvalbumin interneuron deficits in schizophrenia. Eur Neuropsychopharmacol 2024; 82:44-52. [PMID: 38490084 DOI: 10.1016/j.euroneuro.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/16/2024] [Indexed: 03/17/2024]
Abstract
Parvalbumin-expressing (PV+) interneurons represent one of the most abundant subclasses of cortical interneurons. Owing to their specific electrophysiological and synaptic properties, PV+ interneurons are essential for gating and pacing the activity of excitatory neurons. In particular, PV+ interneurons are critically involved in generating and maintaining cortical rhythms in the gamma frequency, which are essential for complex cognitive functions. Deficits in PV+ interneurons have been frequently reported in postmortem studies of schizophrenia patients, and alterations in gamma oscillations are a prominent electrophysiological feature of the disease. Here, I summarise the main features of PV+ interneurons and review clinical and preclinical studies linking the developmental dysfunction of cortical PV+ interneurons with the pathophysiology of schizophrenia.
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Affiliation(s)
- Oscar Marín
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom; Medical Research Council Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, United Kingdom.
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5
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Fehlings DL, Zarrei M, Engchuan W, Sondheimer N, Thiruvahindrapuram B, MacDonald JR, Higginbotham EJ, Thapa R, Behlim T, Aimola S, Switzer L, Ng P, Wei J, Danthi PS, Pellecchia G, Lamoureux S, Ho K, Pereira SL, de Rijke J, Sung WWL, Mowjoodi A, Howe JL, Nalpathamkalam T, Manshaei R, Ghaffari S, Whitney J, Patel RV, Hamdan O, Shaath R, Trost B, Knights S, Samdup D, McCormick A, Hunt C, Kirton A, Kawamura A, Mesterman R, Gorter JW, Dlamini N, Merico D, Hilali M, Hirschfeld K, Grover K, Bautista NX, Han K, Marshall CR, Yuen RKC, Subbarao P, Azad MB, Turvey SE, Mandhane P, Moraes TJ, Simons E, Maxwell G, Shevell M, Costain G, Michaud JL, Hamdan FF, Gauthier J, Uguen K, Stavropoulos DJ, Wintle RF, Oskoui M, Scherer SW. Comprehensive whole-genome sequence analyses provide insights into the genomic architecture of cerebral palsy. Nat Genet 2024; 56:585-594. [PMID: 38553553 DOI: 10.1038/s41588-024-01686-x] [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: 12/23/2022] [Accepted: 02/13/2024] [Indexed: 04/17/2024]
Abstract
We performed whole-genome sequencing (WGS) in 327 children with cerebral palsy (CP) and their biological parents. We classified 37 of 327 (11.3%) children as having pathogenic/likely pathogenic (P/LP) variants and 58 of 327 (17.7%) as having variants of uncertain significance. Multiple classes of P/LP variants included single-nucleotide variants (SNVs)/indels (6.7%), copy number variations (3.4%) and mitochondrial mutations (1.5%). The COL4A1 gene had the most P/LP SNVs. We also analyzed two pediatric control cohorts (n = 203 trios and n = 89 sib-pair families) to provide a baseline for de novo mutation rates and genetic burden analyses, the latter of which demonstrated associations between de novo deleterious variants and genes related to the nervous system. An enrichment analysis revealed previously undescribed plausible candidate CP genes (SMOC1, KDM5B, BCL11A and CYP51A1). A multifactorial CP risk profile and substantial presence of P/LP variants combine to support WGS in the diagnostic work-up across all CP and related phenotypes.
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Affiliation(s)
- Darcy L Fehlings
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Neal Sondheimer
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Jeffrey R MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Edward J Higginbotham
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ritesh Thapa
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Tarannum Behlim
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Sabrina Aimola
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Lauren Switzer
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Pamela Ng
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - John Wei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Prakroothi S Danthi
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sylvia Lamoureux
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Karen Ho
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sergio L Pereira
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jill de Rijke
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wilson W L Sung
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alireza Mowjoodi
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jennifer L Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Roozbeh Manshaei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Siavash Ghaffari
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Joseph Whitney
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rohan V Patel
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Omar Hamdan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rulan Shaath
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shannon Knights
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Grandview Children's Centre, Oshawa, Ontario, Canada
| | - Dawa Samdup
- Department of Pediatrics, Queen's University, Kingston, Ontario, Canada
| | - Anna McCormick
- Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, Ontario, Canada
| | - Carolyn Hunt
- Grandview Children's Centre, Oshawa, Ontario, Canada
| | - Adam Kirton
- Department of Pediatrics, Department of Clinical Neuroscience, University of Calgary, Calgary, Alberta, Canada
| | - Anne Kawamura
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ronit Mesterman
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Jan Willem Gorter
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Nomazulu Dlamini
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Neurosciences and Mental Health Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Daniele Merico
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Deep Genomics Inc., Toronto, Ontario, Canada
- Vevo Therapeutics Inc., San Francisco, CA, USA
| | - Murto Hilali
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kyle Hirschfeld
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kritika Grover
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nelson X Bautista
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kara Han
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christian R Marshall
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ryan K C Yuen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Padmaja Subbarao
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Meghan B Azad
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Stuart E Turvey
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Piush Mandhane
- Faculty of Medicine & Dentistry, Pediatrics Department, University of Alberta, Edmonton, Alberta, Canada
| | - Theo J Moraes
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Program in Translation Medicine & Division of Respiratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elinor Simons
- Department of Pediatrics and Child Health, Section of Allergy and Clinical Immunology, University of Manitoba, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - George Maxwell
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - Michael Shevell
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Departments of Pediatrics and Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
| | - Gregory Costain
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jacques L Michaud
- Departments of Pediatrics and Neurosciences, Université de Montréal, Montréal, Québec, Canada
- CHU Sainte-Justine Azrieli Research Center, Montréal, Québec, Canada
| | - Fadi F Hamdan
- CHU Sainte-Justine Azrieli Research Center, Montréal, Québec, Canada
- Department of Pediatrics, Université de Montréal, Montréal, Québec, Canada
| | - Julie Gauthier
- CHU Sainte-Justine Azrieli Research Center, Montréal, Québec, Canada
- Department of Pediatrics, Université de Montréal, Montréal, Québec, Canada
| | - Kevin Uguen
- CHU Sainte-Justine Azrieli Research Center, Montréal, Québec, Canada
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Richard F Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maryam Oskoui
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Departments of Pediatrics and Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada.
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6
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Wu Z, Li T, Jiang Z, Zheng J, Gu Y, Liu Y, Liu Y, Xie Z. Human pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles. Nucleic Acids Res 2024; 52:2212-2230. [PMID: 38364871 PMCID: PMC10954445 DOI: 10.1093/nar/gkae086] [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: 05/30/2023] [Revised: 01/18/2024] [Accepted: 01/27/2024] [Indexed: 02/18/2024] Open
Abstract
Nonreference sequences (NRSs) are DNA sequences present in global populations but absent in the current human reference genome. However, the extent and functional significance of NRSs in the human genomes and populations remains unclear. Here, we de novo assembled 539 genomes from five genetically divergent human populations using long-read sequencing technology, resulting in the identification of 5.1 million NRSs. These were merged into 45284 unique NRSs, with 29.7% being novel discoveries. Among these NRSs, 38.7% were common across the five populations, and 35.6% were population specific. The use of a graph-based pangenome approach allowed for the detection of 565 transcript expression quantitative trait loci on NRSs, with 426 of these being novel findings. Moreover, 26 NRS candidates displayed evidence of adaptive selection within human populations. Genes situated in close proximity to or intersecting with these candidates may be associated with metabolism and type 2 diabetes. Genome-wide association studies revealed 14 NRSs to be significantly associated with eight phenotypes. Additionally, 154 NRSs were found to be in strong linkage disequilibrium with 258 phenotype-associated SNPs in the GWAS catalogue. Our work expands the understanding of human NRSs and provides novel insights into their functions, facilitating evolutionary and biomedical researches.
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Affiliation(s)
- Zhikun Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Tong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zehang Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jingjing Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yizhou Gu
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China
- University of Wisconsin-Madison, WI, USA
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yun Liu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China
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7
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Mitina A, Khan M, Lesurf R, Yin Y, Engchuan W, Hamdan O, Pellecchia G, Trost B, Backstrom I, Guo K, Pallotto LM, Lam Doong PH, Wang Z, Nalpathamkalam T, Thiruvahindrapuram B, Papaz T, Pearson CE, Ragoussis J, Subbarao P, Azad MB, Turvey SE, Mandhane P, Moraes TJ, Simons E, Scherer SW, Lougheed J, Mondal T, Smythe J, Altamirano-Diaz L, Oechslin E, Mital S, Yuen RKC. Genome-wide enhancer-associated tandem repeats are expanded in cardiomyopathy. EBioMedicine 2024; 101:105027. [PMID: 38418263 PMCID: PMC10944212 DOI: 10.1016/j.ebiom.2024.105027] [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: 09/29/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/01/2024] Open
Abstract
BACKGROUND Cardiomyopathy is a clinically and genetically heterogeneous heart condition that can lead to heart failure and sudden cardiac death in childhood. While it has a strong genetic basis, the genetic aetiology for over 50% of cardiomyopathy cases remains unknown. METHODS In this study, we analyse the characteristics of tandem repeats from genome sequence data of unrelated individuals diagnosed with cardiomyopathy from Canada and the United Kingdom (n = 1216) and compare them to those found in the general population. We perform burden analysis to identify genomic and epigenomic features that are impacted by rare tandem repeat expansions (TREs), and enrichment analysis to identify functional pathways that are involved in the TRE-associated genes in cardiomyopathy. We use Oxford Nanopore targeted long-read sequencing to validate repeat size and methylation status of one of the most recurrent TREs. We also compare the TRE-associated genes to those that are dysregulated in the heart tissues of individuals with cardiomyopathy. FINDINGS We demonstrate that tandem repeats that are rarely expanded in the general population are predominantly expanded in cardiomyopathy. We find that rare TREs are disproportionately present in constrained genes near transcriptional start sites, have high GC content, and frequently overlap active enhancer H3K27ac marks, where expansion-related DNA methylation may reduce gene expression. We demonstrate the gene silencing effect of expanded CGG tandem repeats in DIP2B through promoter hypermethylation. We show that the enhancer-associated loci are found in genes that are highly expressed in human cardiomyocytes and are differentially expressed in the left ventricle of the heart in individuals with cardiomyopathy. INTERPRETATION Our findings highlight the underrecognized contribution of rare tandem repeat expansions to the risk of cardiomyopathy and suggest that rare TREs contribute to ∼4% of cardiomyopathy risk. FUNDING Government of Ontario (RKCY), The Canadian Institutes of Health Research PJT 175329 (RKCY), The Azrieli Foundation (RKCY), SickKids Catalyst Scholar in Genetics (RKCY), The University of Toronto McLaughlin Centre (RKCY, SM), Ted Rogers Centre for Heart Research (SM), Data Sciences Institute at the University of Toronto (SM), The Canadian Institutes of Health Research PJT 175034 (SM), The Canadian Institutes of Health Research ENP 161429 under the frame of ERA PerMed (SM, RL), Heart and Stroke Foundation of Ontario & Robert M Freedom Chair in Cardiovascular Science (SM), Bitove Family Professorship of Adult Congenital Heart Disease (EO), Canada Foundation for Innovation (SWS, JR), Canada Research Chair (PS), Genome Canada (PS, JR), The Canadian Institutes of Health Research (PS).
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Affiliation(s)
- Aleksandra Mitina
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Mahreen Khan
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto; Toronto, Ontario, Canada
| | - Robert Lesurf
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Yue Yin
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Worrawat Engchuan
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Omar Hamdan
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Giovanna Pellecchia
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Brett Trost
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Ian Backstrom
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Keyi Guo
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Linda M Pallotto
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Phoenix Hoi Lam Doong
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Zhuozhi Wang
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Thomas Nalpathamkalam
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Bhooma Thiruvahindrapuram
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Tanya Papaz
- Ted Rogers Centre for Heart Research; Toronto, Ontario, Canada; Division of Cardiology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto; Toronto, Ontario, Canada
| | - Christopher E Pearson
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto; Toronto, Ontario, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Padmaja Subbarao
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Department of Physiology, University of Toronto, Toronto, Ontario, Canada; Program in Translation Medicine & Division of Respiratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Meghan B Azad
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Stuart E Turvey
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Piushkumar Mandhane
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Theo J Moraes
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Program in Translation Medicine & Division of Respiratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elinor Simons
- Department of Pediatrics and Child Health, Section of Allergy and Clinical Immunology, University of Manitoba, Winnipeg, Manitoba, Canada; Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada; Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
| | - Jane Lougheed
- Division of Cardiology, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Tapas Mondal
- Division of Cardiology, Department of Pediatrics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - John Smythe
- Division of Cardiology, Department of Pediatrics, Kingston General Hospital, Kingston, Ontario, Canada
| | - Luis Altamirano-Diaz
- Division of Cardiology, Department of Pediatrics, London Health Sciences Centre, London, Ontario, Canada
| | - Erwin Oechslin
- Division of Cardiology, Toronto Adult Congenital Heart Disease Program at Peter Munk Cardiac Centre, Department of Medicine, University Health Network, and University of Toronto, Toronto, Ontario, Canada
| | - Seema Mital
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; Ted Rogers Centre for Heart Research; Toronto, Ontario, Canada; Division of Cardiology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto; Toronto, Ontario, Canada.
| | - Ryan K C Yuen
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada.
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8
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Hannan AJ. Repeating themes of plastic genes and therapeutic schemes targeting the 'tandem repeatome'. Brain Commun 2024; 6:fcae047. [PMID: 38449715 PMCID: PMC10917440 DOI: 10.1093/braincomms/fcae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 01/24/2024] [Accepted: 02/17/2024] [Indexed: 03/08/2024] Open
Abstract
This scientific commentary refers to 'Modification of Huntington's disease by short tandem repeats' by Hong et al. (https://doi.org/10.1093/braincomms/fcae016) in Brain Communications.
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Affiliation(s)
- Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Australia
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Australia
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9
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Dolzhenko E, English A, Dashnow H, De Sena Brandine G, Mokveld T, Rowell WJ, Karniski C, Kronenberg Z, Danzi MC, Cheung WA, Bi C, Farrow E, Wenger A, Chua KP, Martínez-Cerdeño V, Bartley TD, Jin P, Nelson DL, Zuchner S, Pastinen T, Quinlan AR, Sedlazeck FJ, Eberle MA. Characterization and visualization of tandem repeats at genome scale. Nat Biotechnol 2024:10.1038/s41587-023-02057-3. [PMID: 38168995 DOI: 10.1038/s41587-023-02057-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/06/2023] [Indexed: 01/05/2024]
Abstract
Tandem repeat (TR) variation is associated with gene expression changes and numerous rare monogenic diseases. Although long-read sequencing provides accurate full-length sequences and methylation of TRs, there is still a need for computational methods to profile TRs across the genome. Here we introduce the Tandem Repeat Genotyping Tool (TRGT) and an accompanying TR database. TRGT determines the consensus sequences and methylation levels of specified TRs from PacBio HiFi sequencing data. It also reports reads that support each repeat allele. These reads can be subsequently visualized with a companion TR visualization tool. Assessing 937,122 TRs, TRGT showed a Mendelian concordance of 98.38%, allowing a single repeat unit difference. In six samples with known repeat expansions, TRGT detected all expansions while also identifying methylation signals and mosaicism and providing finer repeat length resolution than existing methods. Additionally, we released a database with allele sequences and methylation levels for 937,122 TRs across 100 genomes.
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Affiliation(s)
| | - Adam English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Harriet Dashnow
- Departments of Human Genetics and Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
| | | | - Tom Mokveld
- Pacific Biosciences of California, Menlo Park, CA, USA
| | | | | | | | - Matt C Danzi
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Chengpeng Bi
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Emily Farrow
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Aaron Wenger
- Pacific Biosciences of California, Menlo Park, CA, USA
| | - Khi Pin Chua
- Pacific Biosciences of California, Menlo Park, CA, USA
| | - Verónica Martínez-Cerdeño
- Institute for Pediatric Regenerative Medicine, Shriner's Hospital for Children and UC Davis School of Medicine, Sacramento, CA, USA
- Department of Pathology & Laboratory Medicine, UC Davis School of Medicine, Sacramento, CA, USA
- MIND Institute, UC Davis School of Medicine, Sacramento, CA, USA
| | - Trevor D Bartley
- Institute for Pediatric Regenerative Medicine, Shriner's Hospital for Children and UC Davis School of Medicine, Sacramento, CA, USA
- Department of Pathology & Laboratory Medicine, UC Davis School of Medicine, Sacramento, CA, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - David L Nelson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Aaron R Quinlan
- Departments of Human Genetics and Biomedical Informatics, University of Utah, Salt Lake City, UT, 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
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10
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Birnbaum R. Rediscovering tandem repeat variation in schizophrenia: challenges and opportunities. Transl Psychiatry 2023; 13:402. [PMID: 38123544 PMCID: PMC10733427 DOI: 10.1038/s41398-023-02689-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Tandem repeats (TRs) are prevalent throughout the genome, constituting at least 3% of the genome, and often highly polymorphic. The high mutation rate of TRs, which can be orders of magnitude higher than single-nucleotide polymorphisms and indels, indicates that they are likely to make significant contributions to phenotypic variation, yet their contribution to schizophrenia has been largely ignored by recent genome-wide association studies (GWAS). Tandem repeat expansions are already known causative factors for over 50 disorders, while common tandem repeat variation is increasingly being identified as significantly associated with complex disease and gene regulation. The current review summarizes key background concepts of tandem repeat variation as pertains to disease risk, elucidating their potential for schizophrenia association. An overview of next-generation sequencing-based methods that may be applied for TR genome-wide identification is provided, and some key methodological challenges in TR analyses are delineated.
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Affiliation(s)
- Rebecca Birnbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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11
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Panoyan MA, Wendt FR. The role of tandem repeat expansions in brain disorders. Emerg Top Life Sci 2023; 7:249-263. [PMID: 37401564 DOI: 10.1042/etls20230022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/05/2023] [Accepted: 06/19/2023] [Indexed: 07/05/2023]
Abstract
The human genome contains numerous genetic polymorphisms contributing to different health and disease outcomes. Tandem repeat (TR) loci are highly polymorphic yet under-investigated in large genomic studies, which has prompted research efforts to identify novel variations and gain a deeper understanding of their role in human biology and disease outcomes. We summarize the current understanding of TRs and their implications for human health and disease, including an overview of the challenges encountered when conducting TR analyses and potential solutions to overcome these challenges. By shedding light on these issues, this article aims to contribute to a better understanding of the impact of TRs on the development of new disease treatments.
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Affiliation(s)
- Mary Anne Panoyan
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada
| | - Frank R Wendt
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Forensic Science Program, University of Toronto, Mississauga, ON, Canada
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12
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Hannan AJ. Expanding horizons of tandem repeats in biology and medicine: Why 'genomic dark matter' matters. Emerg Top Life Sci 2023; 7:ETLS20230075. [PMID: 38088823 PMCID: PMC10754335 DOI: 10.1042/etls20230075] [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: 10/25/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023]
Abstract
Approximately half of the human genome includes repetitive sequences, and these DNA sequences (as well as their transcribed repetitive RNA and translated amino-acid repeat sequences) are known as the repeatome. Within this repeatome there are a couple of million tandem repeats, dispersed throughout the genome. These tandem repeats have been estimated to constitute ∼8% of the entire human genome. These tandem repeats can be located throughout exons, introns and intergenic regions, thus potentially affecting the structure and function of tandemly repetitive DNA, RNA and protein sequences. Over more than three decades, more than 60 monogenic human disorders have been found to be caused by tandem-repeat mutations. These monogenic tandem-repeat disorders include Huntington's disease, a variety of ataxias, amyotrophic lateral sclerosis and frontotemporal dementia, as well as many other neurodegenerative diseases. Furthermore, tandem-repeat disorders can include fragile X syndrome, related fragile X disorders, as well as other neurological and psychiatric disorders. However, these monogenic tandem-repeat disorders, which were discovered via their dominant or recessive modes of inheritance, may represent the 'tip of the iceberg' with respect to tandem-repeat contributions to human disorders. A previous proposal that tandem repeats may contribute to the 'missing heritability' of various common polygenic human disorders has recently been supported by a variety of new evidence. This includes genome-wide studies that associate tandem-repeat mutations with autism, schizophrenia, Parkinson's disease and various types of cancers. In this article, I will discuss how tandem-repeat mutations and polymorphisms could contribute to a wide range of common disorders, along with some of the many major challenges of tandem-repeat biology and medicine. Finally, I will discuss the potential of tandem repeats to be therapeutically targeted, so as to prevent and treat an expanding range of human disorders.
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Affiliation(s)
- Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Victoria 3010, Australia
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13
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Batista-Brito R, Majumdar A, Nuño A, Ward C, Barnes C, Nikouei K, Vinck M, Cardin JA. Developmental loss of ErbB4 in PV interneurons disrupts state-dependent cortical circuit dynamics. Mol Psychiatry 2023; 28:3133-3143. [PMID: 37069344 PMCID: PMC10618960 DOI: 10.1038/s41380-023-02066-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/28/2023] [Accepted: 04/03/2023] [Indexed: 04/19/2023]
Abstract
GABAergic inhibition plays an important role in the establishment and maintenance of cortical circuits during development. Neuregulin 1 (Nrg1) and its interneuron-specific receptor ErbB4 are key elements of a signaling pathway critical for the maturation and proper synaptic connectivity of interneurons. Using conditional deletions of the ERBB4 gene in mice, we tested the role of this signaling pathway at two developmental timepoints in parvalbumin-expressing (PV) interneurons, the largest subpopulation of cortical GABAergic cells. Loss of ErbB4 in PV interneurons during embryonic, but not late postnatal development leads to alterations in the activity of excitatory and inhibitory cortical neurons, along with severe disruption of cortical temporal organization. These impairments emerge by the end of the second postnatal week, prior to the complete maturation of the PV interneurons themselves. Early loss of ErbB4 in PV interneurons also results in profound dysregulation of excitatory pyramidal neuron dendritic architecture and a redistribution of spine density at the apical dendritic tuft. In association with these deficits, excitatory cortical neurons exhibit normal tuning for sensory inputs, but a loss of state-dependent modulation of the gain of sensory responses. Together these data support a key role for early developmental Nrg1/ErbB4 signaling in PV interneurons as a powerful mechanism underlying the maturation of both the inhibitory and excitatory components of cortical circuits.
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Affiliation(s)
- Renata Batista-Brito
- Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave, The Bronx, NY, 10461, USA.
- Department of Neuroscience, Yale University School of Medicine, 333 Cedar St., New Haven, CT, 06520, USA.
- Department of Psychiatry and Behavioral Sciences, Einstein College of Medicine, 1300 Morris Park Ave, The Bronx, NY, 10461, USA.
- Department of Genetics, Einstein College of Medicine, 1300 Morris Park Ave, The Bronx, NY, 10461, USA.
| | - Antara Majumdar
- Department of Neuroscience, Yale University School of Medicine, 333 Cedar St., New Haven, CT, 06520, USA
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Sherrington Road, Oxford, OX1 3PT, England
| | - Alejandro Nuño
- Department of Neuroscience, Yale University School of Medicine, 333 Cedar St., New Haven, CT, 06520, USA
| | - Claire Ward
- Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave, The Bronx, NY, 10461, USA
| | - Clayton Barnes
- Department of Neuroscience, Yale University School of Medicine, 333 Cedar St., New Haven, CT, 06520, USA
| | - Kasra Nikouei
- Department of Neuroscience, Yale University School of Medicine, 333 Cedar St., New Haven, CT, 06520, USA
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Martin Vinck
- Department of Neuroscience, Yale University School of Medicine, 333 Cedar St., New Haven, CT, 06520, USA
- Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, Deutschordenstraße 46, 60528, Frankfurt, Germany
| | - Jessica A Cardin
- Department of Neuroscience, Yale University School of Medicine, 333 Cedar St., New Haven, CT, 06520, USA.
- Kavli Institute of Neuroscience, Yale University, 333 Cedar St., New Haven, CT, 06520, USA.
- Wu Tsai Institute, Yale University, 100 College St., New Haven, CT, 06520, USA.
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14
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Weisburd B, Tiao G, Rehm HL. Insights from a genome-wide truth set of tandem repeat variation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539588. [PMID: 37214979 PMCID: PMC10197592 DOI: 10.1101/2023.05.05.539588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Tools for genotyping tandem repeats (TRs) from short read sequencing data have improved significantly over the past decade. Extensive comparisons of these tools to gold standard diagnostic methods like RP-PCR have confirmed their accuracy for tens to hundreds of well-studied loci. However, a scarcity of high-quality orthogonal truth data limited our ability to measure tool accuracy for the millions of other loci throughout the genome. To address this, we developed a TR truth set based on the Synthetic Diploid Benchmark (SynDip). By identifying the subset of insertions and deletions that represent TR expansions or contractions with motifs between 2 and 50 base pairs, we obtained accurate genotypes for 139,795 pure and 6,845 interrupted repeats in a single diploid sample. Our approach did not require running existing genotyping tools on short read or long read sequencing data and provided an alternative, more accurate view of tandem repeat variation. We applied this truth set to compare the strengths and weaknesses of widely-used tools for genotyping TRs, evaluated the completeness of existing genome-wide TR catalogs, and explored the properties of tandem repeat variation throughout the genome. We found that, without filtering, ExpansionHunter had higher accuracy than GangSTR and HipSTR over a wide range of motifs and allele sizes. Also, when errors in allele size occurred, ExpansionHunter tended to overestimate expansion sizes, while GangSTR tended to underestimate them. Additionally, we saw that widely-used TR catalogs miss between 16% and 41% of variant loci in the truth set. These results suggest that genome-wide analyses would benefit from genotyping a larger set of loci as well as further tool development that builds on the strengths of current algorithms. To that end, we developed a new catalog of 2.8 million loci that captures 95% of variant loci in the truth set, and created a modified version of ExpansionHunter that runs 2 to 3x faster than the original while producing the same output.
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Affiliation(s)
- Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Grace Tiao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
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15
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Nakamura T, Takata A. The molecular pathology of schizophrenia: an overview of existing knowledge and new directions for future research. Mol Psychiatry 2023; 28:1868-1889. [PMID: 36878965 PMCID: PMC10575785 DOI: 10.1038/s41380-023-02005-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 03/08/2023]
Abstract
Despite enormous efforts employing various approaches, the molecular pathology in the schizophrenia brain remains elusive. On the other hand, the knowledge of the association between the disease risk and changes in the DNA sequences, in other words, our understanding of the genetic pathology of schizophrenia, has dramatically improved over the past two decades. As the consequence, now we can explain more than 20% of the liability to schizophrenia by considering all analyzable common genetic variants including those with weak or no statistically significant association. Also, a large-scale exome sequencing study identified single genes whose rare mutations substantially increase the risk for schizophrenia, of which six genes (SETD1A, CUL1, XPO7, GRIA3, GRIN2A, and RB1CC1) showed odds ratios larger than ten. Based on these findings together with the preceding discovery of copy number variants (CNVs) with similarly large effect sizes, multiple disease models with high etiological validity have been generated and analyzed. Studies of the brains of these models, as well as transcriptomic and epigenomic analyses of patient postmortem tissues, have provided new insights into the molecular pathology of schizophrenia. In this review, we overview the current knowledge acquired from these studies, their limitations, and directions for future research that may redefine schizophrenia based on biological alterations in the responsible organ rather than operationalized criteria.
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Affiliation(s)
- Takumi Nakamura
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Atsushi Takata
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
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16
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Wright SE, Todd PK. Native functions of short tandem repeats. eLife 2023; 12:e84043. [PMID: 36940239 PMCID: PMC10027321 DOI: 10.7554/elife.84043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/08/2023] [Indexed: 03/21/2023] Open
Abstract
Over a third of the human genome is comprised of repetitive sequences, including more than a million short tandem repeats (STRs). While studies of the pathologic consequences of repeat expansions that cause syndromic human diseases are extensive, the potential native functions of STRs are often ignored. Here, we summarize a growing body of research into the normal biological functions for repetitive elements across the genome, with a particular focus on the roles of STRs in regulating gene expression. We propose reconceptualizing the pathogenic consequences of repeat expansions as aberrancies in normal gene regulation. From this altered viewpoint, we predict that future work will reveal broader roles for STRs in neuronal function and as risk alleles for more common human neurological diseases.
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Affiliation(s)
- Shannon E Wright
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- Neuroscience Graduate Program, University of Michigan–Ann ArborAnn ArborUnited States
- Department of Neuroscience, Picower InstituteCambridgeUnited States
| | - Peter K Todd
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- VA Ann Arbor Healthcare SystemAnn ArborUnited States
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Styk J, Pös Z, Pös O, Radvanszky J, Turnova EH, Buglyó G, Klimova D, Budis J, Repiska V, Nagy B, Szemes T. Microsatellite instability assessment is instrumental for Predictive, Preventive and Personalised Medicine: status quo and outlook. EPMA J 2023; 14:143-165. [PMID: 36866160 PMCID: PMC9971410 DOI: 10.1007/s13167-023-00312-w] [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: 08/31/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023]
Abstract
A form of genomic alteration called microsatellite instability (MSI) occurs in a class of tandem repeats (TRs) called microsatellites (MSs) or short tandem repeats (STRs) due to the failure of a post-replicative DNA mismatch repair (MMR) system. Traditionally, the strategies for determining MSI events have been low-throughput procedures that typically require assessment of tumours as well as healthy samples. On the other hand, recent large-scale pan-tumour studies have consistently highlighted the potential of massively parallel sequencing (MPS) on the MSI scale. As a result of recent innovations, minimally invasive methods show a high potential to be integrated into the clinical routine and delivery of adapted medical care to all patients. Along with advances in sequencing technologies and their ever-increasing cost-effectiveness, they may bring about a new era of Predictive, Preventive and Personalised Medicine (3PM). In this paper, we offered a comprehensive analysis of high-throughput strategies and computational tools for the calling and assessment of MSI events, including whole-genome, whole-exome and targeted sequencing approaches. We also discussed in detail the detection of MSI status by current MPS blood-based methods and we hypothesised how they may contribute to the shift from conventional medicine to predictive diagnosis, targeted prevention and personalised medical services. Increasing the efficacy of patient stratification based on MSI status is crucial for tailored decision-making. Contextually, this paper highlights drawbacks both at the technical level and those embedded deeper in cellular/molecular processes and future applications in routine clinical testing.
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Affiliation(s)
- Jakub Styk
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia ,Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia
| | - Zuzana Pös
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia ,Institute of Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Ondrej Pös
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia
| | - Jan Radvanszky
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Institute of Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia ,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia
| | - Evelina Hrckova Turnova
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Slovgen Ltd, 841 04 Bratislava, Slovakia
| | - Gergely Buglyó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Daniela Klimova
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
| | - Jaroslav Budis
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia ,Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Vanda Repiska
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia ,Medirex Group Academy, NPO, 949 05 Nitra, Slovakia
| | - Bálint Nagy
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Tomas Szemes
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia ,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia
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18
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Bassett AS. Clinical genetics of schizophrenia and related neuropsychiatric disorders. Psychiatry Res 2023; 319:114992. [PMID: 36463725 DOI: 10.1016/j.psychres.2022.114992] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 11/29/2022]
Abstract
Rare structural variants have turned out to be the long sought for genetic variants of (relatively) high effect size for schizophrenia. Delineating the 22q11.2 microdeletion as the first molecular subtype of schizophrenia was a milestone in schizophrenia research, foreshadowing a more general role for rare copy number variation (CNV) in schizophrenia. The 22q11.2 microdeletion has a high effect size - one in every four individuals born with this deletion develops schizophrenia - and a relatively high prevalence for a rare condition. Discovery of this human genetic high-risk model for schizophrenia has shown how genetics can change clinical management, and also provide new opportunities for animal and cellular models. Further new findings indicate a role for tandem repeat expansion, other less complex rare variants, and collective background effects of common variants in the genetics of schizophrenia. Thus, the genetic architecture of schizophrenia is taking shape, with further advances on the horizon.
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Affiliation(s)
- Anne S Bassett
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada; Clinical Genetics Research Program, and Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; The Dalglish Family 22q Clinic, Department of Psychiatry and Division of Cardiology, Department of Medicine, and Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.
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19
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Rare tandem repeat expansions associate with genes involved in synaptic and neuronal signaling functions in schizophrenia. Mol Psychiatry 2023; 28:475-482. [PMID: 36380236 PMCID: PMC9812781 DOI: 10.1038/s41380-022-01857-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 10/14/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022]
Abstract
Tandem repeat expansions (TREs) are associated with over 60 monogenic disorders and have recently been implicated in complex disorders such as cancer and autism spectrum disorder. The role of TREs in schizophrenia is now emerging. In this study, we have performed a genome-wide investigation of TREs in schizophrenia. Using genome sequence data from 1154 Swedish schizophrenia cases and 934 ancestry-matched population controls, we have detected genome-wide rare (<0.1% population frequency) TREs that have motifs with a length of 2-20 base pairs. We find that the proportion of individuals carrying rare TREs is significantly higher in the schizophrenia group. There is a significantly higher burden of rare TREs in schizophrenia cases than in controls in genic regions, particularly in postsynaptic genes, in genes overlapping brain expression quantitative trait loci, and in brain-expressed genes that are differentially expressed between schizophrenia cases and controls. We demonstrate that TRE-associated genes are more constrained and primarily impact synaptic and neuronal signaling functions. These results have been replicated in an independent Canadian sample that consisted of 252 schizophrenia cases of European ancestry and 222 ancestry-matched controls. Our results support the involvement of rare TREs in schizophrenia etiology.
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20
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Lim M, Carollo A, Neoh MJY, Esposito G. Mapping miRNA Research in Schizophrenia: A Scientometric Review. Int J Mol Sci 2022; 24:ijms24010436. [PMID: 36613876 PMCID: PMC9820708 DOI: 10.3390/ijms24010436] [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: 10/30/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Micro RNA (miRNA) research has great implications in uncovering the aetiology of neuropsychiatric conditions due to the role of miRNA in brain development and function. Schizophrenia, a complex yet devastating neuropsychiatric disorder, is one such condition that had been extensively studied in the realm of miRNA. Although a relatively new field of research, this area of study has progressed sufficiently to warrant dozens of reviews summarising findings from past to present. However, as a majority of reviews cannot encapsulate the full body of research, there is still a need to synthesise the diversity of publications made in this area in a systematic but easy-to-understand manner. Therefore, this study adopted bibliometrics and scientometrics, specifically document co-citation analysis (DCA), to review the literature on miRNAs in the context of schizophrenia over the course of history. From a literature search on Scopus, 992 papers were found and analysed with CiteSpace. DCA analysis generated a network of 13 major clusters with different thematic focuses within the subject area. Finally, these clusters are qualitatively discussed. miRNA research has branched into schizophrenia, among other medical and psychiatric conditions, due to previous findings in other forms of non-coding RNA. With the rise of big data, bioinformatics analyses are increasingly common in this field of research. The future of research is projected to rely more heavily on interdisciplinary collaboration. Additionally, it can be expected that there will be more translational studies focusing on the application of these findings to the development of effective treatments.
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Affiliation(s)
- Mengyu Lim
- Psychology Program, School of Social Sciences, Nanyang Technological University, Singapore 639818, Singapore
| | - Alessandro Carollo
- Department of Psychology and Cognitive Science, University of Trento, 38068 Rovereto, Italy
| | - Michelle Jin Yee Neoh
- Psychology Program, School of Social Sciences, Nanyang Technological University, Singapore 639818, Singapore
| | - Gianluca Esposito
- Department of Psychology and Cognitive Science, University of Trento, 38068 Rovereto, Italy
- Correspondence:
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21
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Dashnow H, Pedersen BS, Hiatt L, Brown J, Beecroft SJ, Ravenscroft G, LaCroix AJ, Lamont P, Roxburgh RH, Rodrigues MJ, Davis M, Mefford HC, Laing NG, Quinlan AR. STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci. Genome Biol 2022; 23:257. [PMID: 36517892 PMCID: PMC9753380 DOI: 10.1186/s13059-022-02826-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Expansions of short tandem repeats (STRs) cause many rare diseases. Expansion detection is challenging with short-read DNA sequencing data since supporting reads are often mapped incorrectly. Detection is particularly difficult for "novel" STRs, which include new motifs at known loci or STRs absent from the reference genome. We developed STRling to efficiently count k-mers to recover informative reads and call expansions at known and novel STR loci. STRling is sensitive to known STR disease loci, has a low false discovery rate, and resolves novel STR expansions to base-pair position accuracy. It is fast, scalable, open-source, and available at: github.com/quinlan-lab/STRling .
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Affiliation(s)
- Harriet Dashnow
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT USA
| | - Brent S. Pedersen
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT USA ,grid.7692.a0000000090126352Utrecht University Medical Center, Utrecht, The Netherlands
| | - Laurel Hiatt
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT USA
| | - Joe Brown
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT USA
| | - Sarah J. Beecroft
- Pawsey Supercomputing Research Centre, Kensington, WA Australia ,grid.1012.20000 0004 1936 7910Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Perth, WA Australia
| | - Gianina Ravenscroft
- grid.1012.20000 0004 1936 7910Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Perth, WA Australia
| | - Amy J. LaCroix
- grid.34477.330000000122986657Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
| | - Phillipa Lamont
- grid.416195.e0000 0004 0453 3875Neurogenetic Unit, Royal Perth Hospital, Perth, WA Australia
| | - Richard H. Roxburgh
- grid.414055.10000 0000 9027 2851Neurology, Auckland City Hospital, Auckland, New Zealand
| | - Miriam J. Rodrigues
- grid.414055.10000 0000 9027 2851Neurology, Auckland City Hospital, Auckland, New Zealand ,grid.9654.e0000 0004 0372 3343Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Mark Davis
- grid.413880.60000 0004 0453 2856Neurogenetics Unit, Department of Diagnostic Genomics, PathWest Laboratory Medicine, Western Australian Department of Health, Nedlands, Australia
| | - Heather C. Mefford
- grid.34477.330000000122986657Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
| | - Nigel G. Laing
- grid.1012.20000 0004 1936 7910Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Perth, WA Australia ,grid.413880.60000 0004 0453 2856Neurogenetics Unit, Department of Diagnostic Genomics, PathWest Laboratory Medicine, Western Australian Department of Health, Nedlands, Australia
| | - Aaron R. Quinlan
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT USA
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