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An Z, Jiang A, Chen J. Toward understanding the role of genomic repeat elements in neurodegenerative diseases. Neural Regen Res 2025; 20:646-659. [PMID: 38886931 DOI: 10.4103/nrr.nrr-d-23-01568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 03/02/2024] [Indexed: 06/20/2024] Open
Abstract
Neurodegenerative diseases cause great medical and economic burdens for both patients and society; however, the complex molecular mechanisms thereof are not yet well understood. With the development of high-coverage sequencing technology, researchers have started to notice that genomic repeat regions, previously neglected in search of disease culprits, are active contributors to multiple neurodegenerative diseases. In this review, we describe the association between repeat element variants and multiple degenerative diseases through genome-wide association studies and targeted sequencing. We discuss the identification of disease-relevant repeat element variants, further powered by the advancement of long-read sequencing technologies and their related tools, and summarize recent findings in the molecular mechanisms of repeat element variants in brain degeneration, such as those causing transcriptional silencing or RNA-mediated gain of toxic function. Furthermore, we describe how in silico predictions using innovative computational models, such as deep learning language models, could enhance and accelerate our understanding of the functional impact of repeat element variants. Finally, we discuss future directions to advance current findings for a better understanding of neurodegenerative diseases and the clinical applications of genomic repeat elements.
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Affiliation(s)
- Zhengyu An
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Aidi Jiang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Jingqi Chen
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Shanghai, China
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2
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Tanudisastro HA, Deveson IW, Dashnow H, MacArthur DG. Sequencing and characterizing short tandem repeats in the human genome. Nat Rev Genet 2024; 25:460-475. [PMID: 38366034 DOI: 10.1038/s41576-024-00692-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
Short tandem repeats (STRs) are highly polymorphic sequences throughout the human genome that are composed of repeated copies of a 1-6-bp motif. Over 1 million variable STR loci are known, some of which regulate gene expression and influence complex traits, such as height. Moreover, variants in at least 60 STR loci cause genetic disorders, including Huntington disease and fragile X syndrome. Accurately identifying and genotyping STR variants is challenging, in particular mapping short reads to repetitive regions and inferring expanded repeat lengths. Recent advances in sequencing technology and computational tools for STR genotyping from sequencing data promise to help overcome this challenge and solve genetically unresolved cases and the 'missing heritability' of polygenic traits. Here, we compare STR genotyping methods, analytical tools and their applications to understand the effect of STR variation on health and disease. We identify emergent opportunities to refine genotyping and quality-control approaches as well as to integrate STRs into variant-calling workflows and large cohort analyses.
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Affiliation(s)
- Hope A Tanudisastro
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Ira W Deveson
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Harriet Dashnow
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.
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3
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Alizadeh S, Khamse S, Vafadar S, Bernhart SH, Afshar H, Vahedi M, Rezaei O, Delbari A, Ohadi M. The human SMAD9 (GCC) repeat links to natural selection and late-onset neurocognitive disorders. Neurol Sci 2024:10.1007/s10072-024-07637-y. [PMID: 38877206 DOI: 10.1007/s10072-024-07637-y] [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: 09/20/2023] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
INTRODUCTION Whereas (GCC)-repeats are overrepresented in genic regions, and mutation hotspots, they are largely unexplored with regard to their link with natural selection. Across numerous primate species and tissues, SMAD9 (SMAD Family Member 9) reaches highest level of expression in the human brain. This gene contains a (GCC)-repeat in the interval between + 1 and + 60 of the transcription start site, which is in the high-ranking (GCC)-repeats with respect to length. METHODS Here we sequenced this (GCC)-repeat in 396 Iranian individuals, consisting of late-onset neurocognitive disorder (NCD) (N = 181) and controls (N = 215). RESULTS We detected two predominantly abundant alleles of 7 and 9 repeats, forming 96.2% of the allele pool. The (GCC)7/(GCC)9 ratio was in the reverse order in the NCD group versus controls (p = 0.005), resulting from excess of (GCC)7 in the NCD group (p = 0.003) and (GCC)9 in the controls (p = 0.01). Five genotypes, predominantly consisting of (GCC)7 and lacking (GCC)9 were detected in the NCD group only (p = 0.008). The patients harboring those genotypes received the diagnoses of Alzheimer's disease (AD) and vascular dementia (VD). Five genotypes consisting of (GCC)9 and lacking (GCC)7 were detected in the control group only (p = 0.002). The group-specific genotypes formed approximately 4% of the genotype pool in the human samples studied. CONCLUSION We propose natural selection and a novel locus for late-onset AD and VD at the SMAD9 (GCC)-repeat in humans.
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Affiliation(s)
- Samira Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran
| | - Safoura Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran
| | - Sara Vafadar
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran
| | - Stephan H Bernhart
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107, Leipzig, Germany
| | - Hossein Afshar
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran
| | - Mohsen Vahedi
- Department of Biostatistics and Epidemiology, Paediatric Neurorehabilitation Research Centre, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Omid Rezaei
- Department of Psychiatry, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Ahmad Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran.
| | - Mina Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran.
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Olson DR, Wheeler TJ. ULTRA-Effective Labeling of Repetitive Genomic Sequence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597269. [PMID: 38895435 PMCID: PMC11185745 DOI: 10.1101/2024.06.03.597269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
In the age of long read sequencing, genomics researchers now have access to accurate repetitive DNA sequence (including satellites) that, due to the limitations of short read sequencing, could previously be observed only as unmappable fragments. Tools that annotate repetitive sequence are now more important than ever, so that we can better understand newly uncovered repetitive sequences, and also so that we can mitigate errors in bioinformatic software caused by those repetitive sequences. To that end, we introduce the 1.0 release of our tool for identifying and annotating locally-repetitive sequence, ULTRA (ULTRA Locates Tandemly Repetitive Areas). ULTRA is fast enough to use as part of an efficient annotation pipeline, produces state-of-the-art reliable coverage of repetitive regions containing many mutations, and provides interpretable statistics and labels for repetitive regions. It released under an open license, and available for download at https://github.com/TravisWheelerLab/ULTRA.
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Affiliation(s)
- Daniel R. Olson
- Department of Computer Science, University of Montana, Missoula, MT, USA
| | - Travis J. Wheeler
- Department of Computer Science, University of Montana, Missoula, MT, USA
- R. Ken Coit College of Pharmacy, University of Arizona, Tucson, AZ, USA
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5
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Hiatt L, Weisburd B, Dolzhenko E, VanNoy GE, Kurtas EN, Rehm HL, Quinlan A, Dashnow H. STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.21.24307682. [PMID: 38826469 PMCID: PMC11142282 DOI: 10.1101/2024.05.21.24307682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Approximately 3% of the human genome consists of repetitive elements called tandem repeats (TRs), which include short tandem repeats (STRs) of 1-6bp motifs and variable number tandem repeats (VNTRs) of 7+bp motifs. TR variants contribute to several dozen mono- and polygenic diseases but remain understudied and "enigmatic," particularly relative to single nucleotide variants. It remains comparatively challenging to interpret the clinical significance of TR variants. Although existing resources provide portions of necessary data for interpretation at disease-associated loci, it is currently difficult or impossible to efficiently invoke the additional details critical to proper interpretation, such as motif pathogenicity, disease penetrance, and age of onset distributions. It is also often unclear how to apply population information to analyses. We present STRchive (S-T-archive, http://strchive.org/ ), a dynamic resource consolidating information on TR disease loci in humans from research literature, up-to-date clinical resources, and large-scale genomic databases, with the goal of streamlining TR variant interpretation at disease-associated loci. We apply STRchive -including pathogenic thresholds, motif classification, and clinical phenotypes-to a gnomAD cohort of ∼18.5k individuals genotyped at 60 disease-associated loci. Through detailed literature curation, we demonstrate that the majority of TR diseases affect children despite being thought of as adult diseases. Additionally, we show that pathogenic genotypes can be found within gnomAD which do not necessarily overlap with known disease prevalence, and leverage STRchive to interpret locus-specific findings therein. We apply a diagnostic blueprint empowered by STRchive to relevant clinical vignettes, highlighting possible pitfalls in TR variant interpretation. As a living resource, STRchive is maintained by experts, takes community contributions, and will evolve as understanding of TR diseases progresses.
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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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Tajeddin N, Arabfard M, Alizadeh S, Salesi M, Khamse S, Delbari A, Ohadi M. Novel islands of GGC and GCC repeats coincide with human evolution. Gene 2024; 902:148194. [PMID: 38262548 DOI: 10.1016/j.gene.2024.148194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/29/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND Because of high mutation rate, overrepresentation in genic regions, and link with various neurological, neurodegenerative, and movement disorders, GGC and GCC short tandem repeats (STRs) are prone to natural selection. Among a number of lacking data, the 3-repeats of these STRs remain widely unexplored. RESULTS In a genome-wide search in human, here we mapped GGC and GCC STRs of ≥3-repeats, and found novel islands of up to 45 of those STRs, populating spans of 1 to 2 kb of genomic DNA. RGPD4 and NOC4L harbored the densest (GGC)3 (probability 3.09061E-71) and (GCC)3 (probability 1.72376E-61) islands, respectively, and were human-specific. We also found prime instances of directional incremented density of STRs at specific loci in human versus other species, including the FOXK2 and SKI GGC islands. The genes containing those islands significantly diverged in expression in human versus other species, and the proteins encoded by those genes interact closely in a physical interaction network, consequence of which may be human-specific characteristics such as higher order brain functions. CONCLUSION We report novel islands of GGC and GCC STRs of evolutionary relevance to human. The density, and in some instances, periodicity of these islands support them as a novel genomic entity, which need to be further explored in evolutionary, mechanistic, and functional platforms.
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Affiliation(s)
- N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Salesi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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8
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Uppili B, Faruq M. STRIDE-DB: a comprehensive database for exploration of instability and phenotypic relevance of short tandem repeats in the human genome. Database (Oxford) 2024; 2024:baae020. [PMID: 38602506 PMCID: PMC11008502 DOI: 10.1093/database/baae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/10/2023] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
Short Tandem Repeats (STRs) are genetic markers made up of repeating DNA sequences. The variations of the STRs are widely studied in forensic analysis, population studies and genetic testing for a variety of neuromuscular disorders. Understanding polymorphic STR variation and its cause is crucial for deciphering genetic information and finding links to various disorders. In this paper, we present STRIDE-DB, a novel and unique platform to explore STR Instability and its Phenotypic Relevance, and a comprehensive database of STRs in the human genome. We utilized RepeatMasker to identify all the STRs in the human genome (hg19) and combined it with frequency data from the 1000 Genomes Project. STRIDE-DB, a user-friendly resource, plays a pivotal role in investigating the relationship between STR variation, instability and phenotype. By harnessing data from genome-wide association studies (GWAS), ClinVar database, Alu loci, Haploblocks in genome and Conservation of the STRs, it serves as an important tool for researchers exploring the variability of STRs in the human genome and its direct impact on phenotypes. STRIDE-DB has its broad applicability and significance in various research domains like forensic sciences and other repeat expansion disorders. Database URL: https://stridedb.igib.res.in.
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Affiliation(s)
- Bharathram Uppili
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007, India
- CSIR-HRDC Campus, Academy for Scientific and Innovative Research, Ghaziabad 201002, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007, India
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Khamse S, Alizadeh S, Khorshid HRK, Delbari A, Tajeddin N, Ohadi M. A Hypermutable Region in the DISP2 Gene Links to Natural Selection and Late-Onset Neurocognitive Disorders in Humans. Mol Neurobiol 2024:10.1007/s12035-024-04155-y. [PMID: 38565786 DOI: 10.1007/s12035-024-04155-y] [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: 05/28/2023] [Accepted: 03/25/2024] [Indexed: 04/04/2024]
Abstract
(CCG) short tandem repeats (STRs) are predominantly enriched in genic regions, mutation hotspots for C to T truncating substitutions, and involved in various neurological and neurodevelopmental disorders. However, intact blocks of this class of STRs are widely overlooked with respect to their link with natural selection. The human neuron-specific gene, DISP2 (dispatched RND transporter family member 2), contains a (CCG) repeat in its 5' untranslated region. Here, we sequenced this STR in a sample of 448 Iranian individuals, consisting of late-onset neurocognitive disorder (NCD) (N = 203) and controls (N = 245). We found that the region spanning the (CCG) repeat was highly mutated, resulting in several flanking (CCG) residues. However, an 8-repeat of the (CCG) repeat was predominantly abundant (frequency = 0.92) across the two groups. While the overall distribution of genotypes was not different between the two groups (p > 0.05), we detected four genotypes in the NCD group only (2% of the NCD genotypes, Mid-p = 0.02), consisting of extreme short alleles, 5- and 6-repeats, that were not detected in the control group. The patients harboring those genotypes received the diagnoses of probable Alzheimer's disease and vascular dementia. We also found six genotypes in the control group only (2.5% of the control genotypes, Mid-p = 0.01) that consisted of the 8-repeat and extreme long alleles, 9- and 10-repeats, of which the 10-repeat was not detected in the NCD group. The (CCG) repeat specifically expanded in primates. In conclusion, we report an indication of natural selection at a novel hypermutable region in the human genome and divergent alleles and genotypes in late-onset NhCDs and controls. These findings reinforce the hypothesis that a collection of rare alleles and genotypes in a number of genes may unambiguously contribute to the cognition impairment component of late-onset NCDs.
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Affiliation(s)
- S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H R Khorram Khorshid
- Personalized Medicine and Genometabolomics Research Center, Hope Generation Foundation, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
| | - N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Department of Biology, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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Ma D, Lin Y, Zhang R, Wang S, Hu W, Ye M, Gao H, Wang L, Song Y, Guo H. Effect of uniparental disomy in parentage testing. Leg Med (Tokyo) 2024; 67:102381. [PMID: 38154315 DOI: 10.1016/j.legalmed.2023.102381] [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: 04/22/2023] [Revised: 11/21/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
Uniparental disomy (UPD) is a rare type of chromosomal aberration that may hinder the analysis of kinship during forensic identification. Here, we investigated these genetic findings to avoid false exclusions during parentage testing. Thirty-nine fluorescently labeled, autosomal short tandem repeats (STR) were amplified in three cases, to detect parent-child relationships. Twenty-three fluorescently labeled Y-chromosome STRs were also employed. These were subjected to capillary electrophoresis. The parentage index was calculated by the bipartite or tripartite model. Single nucleotide polymorphism (SNP) microarrays were performed to further investigate the genetic mechanisms. The conclusions supported the biological mother-child relationship in three cases. However, in all cases, the alleged father and child had three autosomal STR markers, constrained to a single chromosome, which did not conform to Mendelian inheritance rules. The genotyping of 23 Y-chromosome STRs did not reveal any violations of Mendelian law. The combination of STR profiling and SNP microarrays suggested that two children had maternal UPD of chromosome 7, whilst one had UPD of chromosome 2. After excluding the three incompatible loci, the conclusions supported the biological father-child relationship in all cases. The same results were obtained when parentage testing of trios was used. Uniparental disomy may complicate the judgment of kinship in parentage testing. The possibility of UPD should be considered when incompatible STR loci are found on the same chromosome. Genetic evidence obtained through additional molecular techniques can provide better interpretation of kinship in the presence of UPD and avoid false exclusions of biological relationships.
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Affiliation(s)
- Di Ma
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - YuMei Lin
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - RuanZhang Zhang
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Shayan Wang
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Wenlong Hu
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Mei Ye
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Hui Gao
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Lijuan Wang
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Yaqin Song
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Hui Guo
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China.
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11
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Arabfard M, Tajeddin N, Alizadeh S, Salesi M, Bayat H, Khorram Khorshid HR, Khamse S, Delbari A, Ohadi M. Dyads of GGC and GCC form hotspot colonies that coincide with the evolution of human and other great apes. BMC Genom Data 2024; 25:21. [PMID: 38383300 PMCID: PMC10880355 DOI: 10.1186/s12863-024-01207-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/11/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND GGC and GCC short tandem repeats (STRs) are of various evolutionary, biological, and pathological implications. However, the fundamental two-repeats (dyads) of these STRs are widely unexplored. RESULTS On a genome-wide scale, we mapped (GGC)2 and (GCC)2 dyads in human, and found monumental colonies (distance between each dyad < 500 bp) of extraordinary density, and in some instances periodicity. The largest (GCC)2 and (GGC)2 colonies were intergenic, homogeneous, and human-specific, consisting of 219 (GCC)2 on chromosome 2 (probability < 1.545E-219) and 70 (GGC)2 on chromosome 9 (probability = 1.809E-148). We also found that several colonies were shared in other great apes, and directionally increased in density and complexity in human, such as a colony of 99 (GCC)2 on chromosome 20, that specifically expanded in great apes, and reached maximum complexity in human (probability 1.545E-220). Numerous other colonies of evolutionary relevance in human were detected in other largely overlooked regions of the genome, such as chromosome Y and pseudogenes. Several of the genes containing or nearest to those colonies were divergently expressed in human. CONCLUSION In conclusion, (GCC)2 and (GGC)2 form unprecedented genomic colonies that coincide with the evolution of human and other great apes. The extent of the genomic rearrangements leading to those colonies support overlooked recombination hotspots, shared across great apes. The identified colonies deserve to be studied in mechanistic, evolutionary, and functional platforms.
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Affiliation(s)
- M Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Department of Biology, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Salesi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
- Research Center for Prevention of Oral and Dental Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - H Bayat
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H R Khorram Khorshid
- Personalized Medicine and Genometabolomics Research Center, Hope Generation Foundation, Tehran, Iran
| | - S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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12
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Fazal S, Danzi MC, Xu I, Kobren SN, Sunyaev S, Reuter C, Marwaha S, Wheeler M, Dolzhenko E, Lucas F, Wuchty S, Tekin M, Züchner S, Aguiar-Pulido V. RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci. Genome Biol 2024; 25:39. [PMID: 38297326 PMCID: PMC10832122 DOI: 10.1186/s13059-024-03171-4] [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: 04/03/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
Expansions of tandem repeats (TRs) cause approximately 60 monogenic diseases. We expect that the discovery of additional pathogenic repeat expansions will narrow the diagnostic gap in many diseases. A growing number of TR expansions are being identified, and interpreting them is a challenge. We present RExPRT (Repeat EXpansion Pathogenicity pRediction Tool), a machine learning tool for distinguishing pathogenic from benign TR expansions. Our results demonstrate that an ensemble approach classifies TRs with an average precision of 93% and recall of 83%. RExPRT's high precision will be valuable in large-scale discovery studies, which require prioritization of candidate loci for follow-up studies.
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Affiliation(s)
- Sarah Fazal
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building (BRB), Miami, FL, 33136, USA
| | - Matt C Danzi
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building (BRB), Miami, FL, 33136, USA
| | - Isaac Xu
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building (BRB), Miami, FL, 33136, USA
| | | | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02155, USA
| | - Chloe Reuter
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Shruti Marwaha
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Francesca Lucas
- Department of Computer Science, Delft University of Technology, Delft, The Netherlands
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, Miami, FL, USA
- Deptartment of Biology, University of Miami, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mustafa Tekin
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building (BRB), Miami, FL, 33136, USA
| | - Stephan Züchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building (BRB), Miami, FL, 33136, USA.
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13
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Alizadeh S, Khamse S, Tajeddin N, Khorram Khorshid HR, Delbari A, Ohadi M. A GCC repeat in RAB26 undergoes natural selection in human and harbors divergent genotypes in late-onset Alzheimer's disease. Gene 2024; 893:147968. [PMID: 37931854 DOI: 10.1016/j.gene.2023.147968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]
Abstract
Although mainly located in genic regions and being mutation hotspots, intact blocks of CG-rich trinucleotide short tandem repeats (STRs) are largely overlooked with respect to their link with natural selection. The human RAB26 (member RAS oncogene family) directs synaptic and secretory vesicles into preautophagosomal structures, inhibition of which specifically disrupts axonal transport of degradative organelles and leads to an axonal dystrophy, resembling Alzheimer's disease (AD). Human RAB26 contains a GCC repeat in the top 1st percent in respect of length. Here we sequenced this STR in 441 Iranian individuals, consisting of late-onset neurocognitive disorder (NCD) (N = 216) and controls (N = 225). In both groups, the 12-repeat allele and the 12/12 genotype were predominantly abundant. We found excess of homozygosity for non-12 alleles in the NCD group (Mid-P exact = 0.027). Furthermore, divergent genotypes were detected that were specific to the NCD group (2.8% of genotypes) (Mid-P exact = 0.006) or controls (3.1% of genotypes) (Mid-P exact = 0.004). The patients harboring divergent genotypes received the diagnosis of AD. Based on the predominant abundance of the 12-repeat and 12/12 genotype in both groups, excess of non-12 homozygosity in the NCD group, and divergent genotypes across the NCD and control groups, we propose natural selection at this locus and link with late-onset AD. Our findings strengthen the hypothesis that a collection of rare genotypes unambiguously contribute to the pathogenesis of late-onset NCDs, such as AD.
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Affiliation(s)
- S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H R Khorram Khorshid
- Personalized Medicine and Genometabolomics Research Center, Hope Generation Foundation, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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14
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Lu J, Toro C, Adams DR, Moreno CAM, Lee WP, Leung YY, Harms MB, Vardarajan B, Heinzen EL. LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants. BMC Genomics 2024; 25:115. [PMID: 38279154 PMCID: PMC10811831 DOI: 10.1186/s12864-023-09935-9] [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: 05/18/2023] [Accepted: 12/21/2023] [Indexed: 01/28/2024] Open
Abstract
BACKGROUND Short tandem repeats (STRs) are widely distributed across the human genome and are associated with numerous neurological disorders. However, the extent that STRs contribute to disease is likely under-estimated because of the challenges calling these variants in short read next generation sequencing data. Several computational tools have been developed for STR variant calling, but none fully address all of the complexities associated with this variant class. RESULTS Here we introduce LUSTR which is designed to address some of the challenges associated with STR variant calling by enabling more flexibility in defining STR loci, allowing for customizable modules to tailor analyses, and expanding the capability to call somatic and multiallelic STR variants. LUSTR is a user-friendly and easily customizable tool for targeted or unbiased genome-wide STR variant screening that can use either predefined or novel genome builds. Using both simulated and real data sets, we demonstrated that LUSTR accurately infers germline and somatic STR expansions in individuals with and without diseases. CONCLUSIONS LUSTR offers a powerful and user-friendly approach that allows for the identification of STR variants and can facilitate more comprehensive studies evaluating the role of pathogenic STR variants across human diseases.
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Affiliation(s)
- Jinfeng Lu
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- The Taub Institute for Research On Alzheimer's Disease and the Aging Brain, Gertrude H. Sergievsky Center, Department of Neurology, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, NY, 10032, USA.
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, 20892, USA
| | - David R Adams
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Wan-Ping Lee
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory MedicinePerelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yuk Yee Leung
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory MedicinePerelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mathew B Harms
- Department of Neurology, Division of Neuromuscular Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Badri Vardarajan
- The Taub Institute for Research On Alzheimer's Disease and the Aging Brain, Gertrude H. Sergievsky Center, Department of Neurology, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, NY, 10032, USA
| | - Erin L Heinzen
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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15
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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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16
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Chaisson MJP, Sulovari A, Valdmanis PN, Miller DE, Eichler EE. Advances in the discovery and analyses of human tandem repeats. Emerg Top Life Sci 2023; 7:361-381. [PMID: 37905568 PMCID: PMC10806765 DOI: 10.1042/etls20230074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023]
Abstract
Long-read sequencing platforms provide unparalleled access to the structure and composition of all classes of tandemly repeated DNA from STRs to satellite arrays. This review summarizes our current understanding of their organization within the human genome, their importance with respect to disease, as well as the advances and challenges in understanding their genetic diversity and functional effects. Novel computational methods are being developed to visualize and associate these complex patterns of human variation with disease, expression, and epigenetic differences. We predict accurate characterization of this repeat-rich form of human variation will become increasingly relevant to both basic and clinical human genetics.
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Affiliation(s)
- Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, U.S.A
- The Genomic and Epigenomic Regulation Program, USC Norris Cancer Center, University of Southern California, Los Angeles, CA 90089, U.S.A
| | - Arvis Sulovari
- Computational Biology, Cajal Neuroscience Inc, Seattle, WA 98102, U.S.A
| | - Paul N Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
| | - Danny E Miller
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, U.S.A
- Department of Pediatrics, University of Washington, Seattle, WA 98195, U.S.A
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, U.S.A
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17
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Read JL, Davies KC, Thompson GC, Delatycki MB, Lockhart PJ. Challenges facing repeat expansion identification, characterisation, and the pathway to discovery. Emerg Top Life Sci 2023; 7:339-348. [PMID: 37888797 PMCID: PMC10754332 DOI: 10.1042/etls20230019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/06/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023]
Abstract
Tandem repeat DNA sequences constitute a significant proportion of the human genome. While previously considered to be functionally inert, these sequences are now broadly accepted as important contributors to genetic diversity. However, the polymorphic nature of these sequences can lead to expansion beyond a gene-specific threshold, causing disease. More than 50 pathogenic repeat expansions have been identified to date, many of which have been discovered in the last decade as a result of advances in sequencing technologies and associated bioinformatic tools. Commonly utilised diagnostic platforms including Sanger sequencing, capillary array electrophoresis, and Southern blot are generally low throughput and are often unable to accurately determine repeat size, composition, and epigenetic signature, which are important when characterising repeat expansions. The rapid advances in bioinformatic tools designed specifically to interrogate short-read sequencing and the development of long-read single molecule sequencing is enabling a new generation of high throughput testing for repeat expansion disorders. In this review, we discuss some of the challenges surrounding the identification and characterisation of disease-causing repeat expansions and the technological advances that are poised to translate the promise of genomic medicine to individuals and families affected by these disorders.
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Affiliation(s)
- Justin L Read
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Kayli C Davies
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Genevieve C Thompson
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Parkville, Victoria, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
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18
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Margoliash J, Fuchs S, Li Y, Zhang X, Massarat A, Goren A, Gymrek M. Polymorphic short tandem repeats make widespread contributions to blood and serum traits. CELL GENOMICS 2023; 3:100458. [PMID: 38116119 PMCID: PMC10726533 DOI: 10.1016/j.xgen.2023.100458] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/09/2023] [Accepted: 11/07/2023] [Indexed: 12/21/2023]
Abstract
Short tandem repeats (STRs) are genomic regions consisting of repeated sequences of 1-6 bp in succession. Single-nucleotide polymorphism (SNP)-based genome-wide association studies (GWASs) do not fully capture STR effects. To study these effects, we imputed 445,720 STRs into genotype arrays from 408,153 White British UK Biobank participants and tested for association with 44 blood phenotypes. Using two fine-mapping methods, we identify 119 candidate causal STR-trait associations and estimate that STRs account for 5.2%-7.6% of causal variants identifiable from GWASs for these traits. These are among the strongest associations for multiple phenotypes, including a coding CTG repeat associated with apolipoprotein B levels, a promoter CGG repeat with platelet traits, and an intronic poly(A) repeat with mean platelet volume. Our study suggests that STRs make widespread contributions to complex traits, provides stringently selected candidate causal STRs, and demonstrates the need to consider a more complete view of genetic variation in GWASs.
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Affiliation(s)
- Jonathan Margoliash
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shai Fuchs
- Pediatric Endocrine and Diabetes Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Yang Li
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xuan Zhang
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Arya Massarat
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alon Goren
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Melissa Gymrek
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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19
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Yu SY, Xi YL, Xu FQ, Zhang J, Liu YS. Application of long read sequencing in rare diseases: The longer, the better? Eur J Med Genet 2023; 66:104871. [PMID: 38832911 DOI: 10.1016/j.ejmg.2023.104871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 06/06/2024]
Abstract
Rare diseases encompass a diverse group of genetic disorders that affect a small proportion of the population. Identifying the underlying genetic causes of these conditions presents significant challenges due to their genetic heterogeneity and complexity. Conventional short-read sequencing (SRS) techniques have been widely used in diagnosing and investigating of rare diseases, with limitations due to the nature of short-read lengths. In recent years, long read sequencing (LRS) technologies have emerged as a valuable tool in overcoming these limitations. This minireview provides a concise overview of the applications of LRS in rare disease research and diagnosis, including the identification of disease-causing tandem repeat expansions, structural variations, and comprehensive analysis of pathogenic variants with LRS.
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Affiliation(s)
- Si-Yan Yu
- Department of Pediatric Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China; The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yu-Lin Xi
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Fu-Qiang Xu
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jian Zhang
- Department of Medical Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China.
| | - Yan-Shan Liu
- Department of Pediatric Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China; Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
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20
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Meng X, Wang M, Luo M, Sun L, Yan Q, Liu Y. Systematic evaluation of multiple NGS platforms for structural variants detection. J Biol Chem 2023; 299:105436. [PMID: 37944616 PMCID: PMC10724692 DOI: 10.1016/j.jbc.2023.105436] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Structural variations (SV) are critical genome changes affecting human diseases. Although many hybridization-based methods exist, evaluating SVs through next-generation sequencing (NGS) data is still necessary for broader research exploration. Here, we comprehensively compared the performance of 16 SV callers and multiple NGS platforms using NA12878 whole genome sequencing (WGS) datasets. The results indicated that several SV callers performed well relatively, such as Manta, GRIDSS, LUMPY, TARDIS, FermiKit, and Wham. Meanwhile, all NGS platforms have a similar performance using a single software. Additionally, we found that the source of undetected SVs was mostly from long reads datasets, therefore, the more appropriate strategy for accurate SV detection will be an integration of long and shorter reads in the future. At present, in the period of NGS as a mainstream method in bioinformatics, our study would provide helpful and comprehensive guidelines for specific categories of SV research.
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Affiliation(s)
- Xuan Meng
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Miao Wang
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China
| | - Mingjie Luo
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China
| | - Lei Sun
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China
| | - Qin Yan
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China
| | - Yongfeng Liu
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China.
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21
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Zambrano AK, Cadena-Ullauri S, Guevara-Ramírez P, Paz-Cruz E, Tamayo-Trujillo R, Ruiz-Pozo VA, Doménech N, Ibarra-Rodríguez AA, Gaviria A. The Autosomal Short Tandem Repeat Polymorphisms Are Potentially Associated with Cardiovascular Disease Predisposition in the Latin American Population: A Mini Review. BIOMED RESEARCH INTERNATIONAL 2023; 2023:6152905. [PMID: 38027043 PMCID: PMC10651335 DOI: 10.1155/2023/6152905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/02/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023]
Abstract
According to the World Health Organization, cardiovascular diseases (CVDs) are the leading cause of death worldwide across nearly all ethnic groups. Inherited cardiac conditions comprise a wide spectrum of diseases that affect the heart, including abnormal structural features and functional impairments. In Latin America, CVDs are the leading cause of death within the region. Factors such as population aging, unhealthy diet, obesity, smoking, and a sedentary lifestyle have increased the risk of CVD. The Latin American population is characterized by its diverse ethnic composition with varying percentages of each ancestral component (African, European, and Native American ancestry). Short tandem repeats (STRs) are DNA sequences with 2-6 base pair repetitions and constitute ~3% of the human genome. Importantly, significant allele frequency variations exist between different populations. While studies have described that STRs are in noncoding regions of the DNA, increasing evidence suggests that simple sequence repeat variations may be critical for proper gene activity and regulation. Furthermore, several STRs have been identified as potential disease predisposition markers. The present review is aimed at comparing and describing the frequencies of autosomal STR polymorphisms potentially associated with cardiovascular disease predisposition in Latin America compared with other populations.
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Affiliation(s)
- Ana Karina Zambrano
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Santiago Cadena-Ullauri
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Patricia Guevara-Ramírez
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Elius Paz-Cruz
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Rafael Tamayo-Trujillo
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Viviana A. Ruiz-Pozo
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Nieves Doménech
- Instituto de Investigación Biomédica de A Coruña (INIBIC)-CIBERCV, Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidad da Coruña (UDC), La Coruña, Spain
| | | | - Aníbal Gaviria
- Laboratorio de Genética Molecular, Centros Médicos Especializados Cruz Roja Ecuatoriana, Quito, Ecuador
- Hemocentro Nacional, Cruz Roja Ecuatoriana, Quito, Ecuador
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22
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Baide‐Mairena H, Coget A, Leboucq N, Procaccio V, Blanluet M, Meyer P, Malinge M, François‐Heude M, Moreno M, Geneviève D, Marelli C, Roubertie A. Infantile-onset parkinsonism, dyskinesia, and developmental delay: do not forget polyglutamine defects! Ann Clin Transl Neurol 2023; 10:1937-1943. [PMID: 37491839 PMCID: PMC10578886 DOI: 10.1002/acn3.51858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/04/2023] [Accepted: 07/13/2023] [Indexed: 07/27/2023] Open
Abstract
We present the phenotype of an infant with the largest ATN1 CAG expansion reported to date (98 repeats). He presented at 4 months with developmental delay, poor eye contact, acquired microcephaly, failure to thrive. He progressively developed dystonia-parkinsonism with paroxysmal oromandibular and limbs dyskinesia and fatal outcome at 17 months. Cerebral MRI disclosed globus pallidus T2-WI hyperintensities and brain atrophy. Molecular analysis was performed post-mortem following the diagnosis of dentatorubral-pallidoluysian atrophy (DRPLA) in his symptomatic father. Polyglutamine expansion defects should be considered when neurodegenerative genetic disease is suspected even in infancy and parkinsonism can be a presentation of infantile-onset DRPLA.
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Affiliation(s)
- Heidy Baide‐Mairena
- Département de NeuropédiatrieHôpital Gui de ChauliacMontpellierFrance
- Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Arthur Coget
- Service de NeuroradiologieHôpital Gui de ChauliacMontpellierFrance
| | - Nicolas Leboucq
- Service de NeuroradiologieHôpital Gui de ChauliacMontpellierFrance
| | - Vincent Procaccio
- MitoLab, UMR CNRS 6015 – INSERM U1083, MitoVasc Institute, Angers University HospitalAngersFrance
| | - Maud Blanluet
- MitoLab, UMR CNRS 6015 – INSERM U1083, MitoVasc Institute, Angers University HospitalAngersFrance
| | - Pierre Meyer
- Département de NeuropédiatrieHôpital Gui de ChauliacMontpellierFrance
- Phymedexp, Montpellier University, Inserm, CNRSMontpellierFrance
| | - Marie‐Claire Malinge
- MitoLab, UMR CNRS 6015 – INSERM U1083, MitoVasc Institute, Angers University HospitalAngersFrance
| | | | - Mathis Moreno
- Département de NeuropédiatrieHôpital Gui de ChauliacMontpellierFrance
| | - David Geneviève
- Montpellier University, Inserm U1183MontpellierFrance
- Reference Center for Malformative Syndrome, Genetic Department, Montpellier HospitalMontpellierFrance
| | - Cecilia Marelli
- Expert Centre for Neurogenetic Diseases and Adult Mitochondrial and Metabolic Diseases, Department of NeurologyMontpellier University HospitalMontpellierFrance
- MMDNUniversity of Montpellier, EPHE, INSERMMontpellierFrance
| | - Agathe Roubertie
- Département de NeuropédiatrieHôpital Gui de ChauliacMontpellierFrance
- Institut des Neurosciences de Montpellier, INSERM U 1298MontpellierFrance
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23
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Wang X, Huang M, Budowle B, Ge J. TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads. Front Genet 2023; 14:1227176. [PMID: 37533432 PMCID: PMC10390829 DOI: 10.3389/fgene.2023.1227176] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/13/2023] [Indexed: 08/04/2023] Open
Abstract
Calling tandem repeat (TR) variants from DNA sequences is of both theoretical and practical significance. Some bioinformatics tools have been developed for detecting or genotyping TRs. However, little study has been done to genotyping TR alleles from long-read sequencing data, and the accuracy of genotyping TR alleles from next-generation sequencing data still needs to be improved. Herein, a novel algorithm is described to retrieve TR regions from sequence alignment, and a software program TRcaller has been developed and integrated into a web portal to call TR alleles from both short- and long-read sequences, both whole genome and targeted sequences generated from multiple sequencing platforms. All TR alleles are genotyped as haplotypes and the robust alleles will be reported, even multiple alleles in a DNA mixture. TRcaller could provide substantially higher accuracy (>99% in 289 human individuals) in detecting TR alleles with magnitudes faster (e.g., ∼2 s for 300x human sequence data) than the mainstream software tools. The web portal preselected 119 TR loci from forensics, genealogy, and disease related TR loci. TRcaller is validated to be scalable in various applications, such as DNA forensics and disease diagnosis, which can be expanded into other fields like breeding programs. Availability: TRcaller is available at https://www.trcaller.com/SignIn.aspx.
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Affiliation(s)
- Xuewen Wang
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Meng Huang
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
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24
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Simon CM. A Bayesian Treatment of the German Tank Problem. THE MATHEMATICAL INTELLIGENCER 2023; 46:117-127. [PMID: 38841650 PMCID: PMC11147940 DOI: 10.1007/s00283-023-10274-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 04/05/2023] [Indexed: 06/07/2024]
Affiliation(s)
- Cory M. Simon
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, OR USA
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25
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Olson ND, Wagner J, Dwarshuis N, Miga KH, Sedlazeck FJ, Salit M, Zook JM. Variant calling and benchmarking in an era of complete human genome sequences. Nat Rev Genet 2023:10.1038/s41576-023-00590-0. [PMID: 37059810 DOI: 10.1038/s41576-023-00590-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2023] [Indexed: 04/16/2023]
Abstract
Genetic variant calling from DNA sequencing has enabled understanding of germline variation in hundreds of thousands of humans. Sequencing technologies and variant-calling methods have advanced rapidly, routinely providing reliable variant calls in most of the human genome. We describe how advances in long reads, deep learning, de novo assembly and pangenomes have expanded access to variant calls in increasingly challenging, repetitive genomic regions, including medically relevant regions, and how new benchmark sets and benchmarking methods illuminate their strengths and limitations. Finally, we explore the possible future of more complete characterization of human genome variation in light of the recent completion of a telomere-to-telomere human genome reference assembly and human pangenomes, and we consider the innovations needed to benchmark their newly accessible repetitive regions and complex variants.
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Affiliation(s)
- Nathan D Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Justin Wagner
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nathan Dwarshuis
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Fritz J Sedlazeck
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, TX, USA
| | | | - Justin M Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
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26
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Ikemoto K, Fujimoto H, Fujimoto A. Localized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes. Hum Genomics 2023; 17:21. [PMID: 36895025 PMCID: PMC9996862 DOI: 10.1186/s40246-023-00467-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/01/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Long-read sequencing technologies have the potential to overcome the limitations of short reads and provide a comprehensive picture of the human genome. However, the characterization of repetitive sequences by reconstructing genomic structures at high resolution solely from long reads remains difficult. Here, we developed a localized assembly method (LoMA) that constructs highly accurate consensus sequences (CSs) from long reads. METHODS We developed LoMA by combining minimap2, MAFFT, and our algorithm, which classifies diploid haplotypes based on structural variants and CSs. Using this tool, we analyzed two human samples (NA18943 and NA19240) sequenced with the Oxford Nanopore sequencer. We defined target regions in each genome based on mapping patterns and then constructed a high-quality catalog of the human insertion solely from the long-read data. RESULTS The assessment of LoMA showed a high accuracy of CSs (error rate < 0.3%) compared with raw data (error rate > 8%) and superiority to a previous study. The genome-wide analysis of NA18943 and NA19240 identified 5516 and 6542 insertions (≥ 100 bp), respectively. Most insertions (~ 80%) were derived from tandem repeats and transposable elements. We also detected processed pseudogenes, insertions in transposable elements, and long insertions (> 10 kbp). Finally, our analysis suggested that short tandem duplications are associated with gene expression and transposons. CONCLUSIONS Our analysis showed that LoMA constructs high-quality sequences from long reads with substantial errors. This study revealed the true structures of the insertions with high accuracy and inferred the mechanisms for the insertions, thus contributing to future human genome studies. LoMA is available at our GitHub page: https://github.com/kolikem/loma .
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Affiliation(s)
- Ko Ikemoto
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo, Japan
| | - Hinano Fujimoto
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo, Japan
| | - Akihiro Fujimoto
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo, Japan.
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27
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Hamanaka K, Yamauchi D, Koshimizu E, Watase K, Mogushi K, Ishikawa K, Mizusawa H, Tsuchida N, Uchiyama Y, Fujita A, Misawa K, Mizuguchi T, Miyatake S, Matsumoto N. Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans. Genome Res 2023; 33:435-447. [PMID: 37307504 PMCID: PMC10078293 DOI: 10.1101/gr.277335.122] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 02/22/2023] [Indexed: 03/29/2023]
Abstract
Tandem repeats (TRs) are one of the largest sources of polymorphism, and their length is associated with gene regulation. Although previous studies reported several tandem repeats regulating gene splicing in cis (spl-TRs), no large-scale study has been conducted. In this study, we established a genome-wide catalog of 9537 spl-TRs with a total of 58,290 significant TR-splicing associations across 49 tissues (false discovery rate 5%) by using Genotype-Tissue expression (GTex) Project data. Regression models explaining splicing variation by using spl-TRs and other flanking variants suggest that at least some of the spl-TRs directly modulate splicing. In our catalog, two spl-TRs are known loci for repeat expansion diseases, spinocerebellar ataxia 6 (SCA6) and 12 (SCA12). Splicing alterations by these spl-TRs were compatible with those observed in SCA6 and SCA12. Thus, our comprehensive spl-TR catalog may help elucidate the pathomechanism of genetic diseases.
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Affiliation(s)
- Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | | | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Kei Watase
- Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kaoru Mogushi
- Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Kinya Ishikawa
- The Center for Personalized Medicine for Healthy Aging, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Hidehiro Mizusawa
- Department of Neurology, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8551, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan;
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28
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Points to consider in the detection of germline structural variants using next-generation sequencing: A statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100316. [PMID: 36507974 DOI: 10.1016/j.gim.2022.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
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29
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Martin-Trujillo A, Garg P, Patel N, Jadhav B, Sharp AJ. Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation. Genome Res 2023; 33:184-196. [PMID: 36577521 PMCID: PMC10069470 DOI: 10.1101/gr.277057.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022]
Abstract
Short tandem repeats (STRs) contribute significantly to genetic diversity in humans, including disease-causing variation. Although the effect of STR variation on gene expression has been extensively assessed, their impact on epigenetics has been poorly studied and limited to specific genomic regions. Here, we investigated the hypothesis that some STRs act as independent regulators of local DNA methylation in the human genome and modify risk of common human traits. To address these questions, we first analyzed two independent data sets comprising PCR-free whole-genome sequencing (WGS) and genome-wide DNA methylation levels derived from whole-blood samples in 245 (discovery cohort) and 484 individuals (replication cohort). Using genotypes for 131,635 polymorphic STRs derived from WGS using HipSTR, we identified 11,870 STRs that associated with DNA methylation levels (mSTRs) of 11,774 CpGs (Bonferroni P < 0.001) in our discovery cohort, with 90% successfully replicating in our second cohort. Subsequently, through fine-mapping using CAVIAR we defined 585 of these mSTRs as the likely causal variants underlying the observed associations (fm-mSTRs) and linked a fraction of these to previously reported genome-wide association study signals, providing insights into the mechanisms underlying complex human traits. Furthermore, by integrating gene expression data, we observed that 12.5% of the tested fm-mSTRs also modulate expression levels of nearby genes, reinforcing their regulatory potential. Overall, our findings expand the catalog of functional sequence variants that affect genome regulation, highlighting the importance of incorporating STRs in future genetic association analysis and epigenetics data for the interpretation of trait-associated variants.
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Affiliation(s)
- Alejandro Martin-Trujillo
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, New York 10029, USA
| | - Paras Garg
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, New York 10029, USA
| | - Nihir Patel
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, New York 10029, USA
| | - Bharati Jadhav
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, New York 10029, USA
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, New York 10029, USA
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30
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Fan C, Chen K, Wang Y, Ball EV, Stenson PD, Mort M, Bacolla A, Kehrer-Sawatzki H, Tainer JA, Cooper DN, Zhao H. Profiling human pathogenic repeat expansion regions by synergistic and multi-level impacts on molecular connections. Hum Genet 2023; 142:245-274. [PMID: 36344696 PMCID: PMC10290229 DOI: 10.1007/s00439-022-02500-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
Abstract
Whilst DNA repeat expansions cause numerous heritable human disorders, their origins and underlying pathological mechanisms are often unclear. We collated a dataset comprising 224 human repeat expansions encompassing 203 different genes, and performed a systematic analysis with respect to key topological features at the DNA, RNA and protein levels. Comparison with controls without known pathogenicity and genomic regions lacking repeats, allowed the construction of the first tool to discriminate repeat regions harboring pathogenic repeat expansions (DPREx). At the DNA level, pathogenic repeat expansions exhibited stronger signals for DNA regulatory factors (e.g. H3K4me3, transcription factor-binding sites) in exons, promoters, 5'UTRs and 5'genes but were not significantly different from controls in introns, 3'UTRs and 3'genes. Additionally, pathogenic repeat expansions were also found to be enriched in non-B DNA structures. At the RNA level, pathogenic repeat expansions were characterized by lower free energy for forming RNA secondary structure and were closer to splice sites in introns, exons, promoters and 5'genes than controls. At the protein level, pathogenic repeat expansions exhibited a preference to form coil rather than other types of secondary structure, and tended to encode surface-located protein domains. Guided by these features, DPREx ( http://biomed.nscc-gz.cn/zhaolab/geneprediction/# ) achieved an Area Under the Curve (AUC) value of 0.88 in a test on an independent dataset. Pathogenic repeat expansions are thus located such that they exert a synergistic influence on the gene expression pathway involving inter-molecular connections at the DNA, RNA and protein levels.
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Affiliation(s)
- Cong Fan
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang West Road, Guangzhou, 500001, People's Republic of China
| | - Ken Chen
- School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, 500001, China
| | - Yukai Wang
- School of Life Science, Sun Yat-Sen University, Guangzhou, 500001, China
| | - Edward V Ball
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA
| | | | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang West Road, Guangzhou, 500001, People's Republic of China.
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31
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Lang J, Xu Z, Wang Y, Sun J, Yang Z. NanoSTR: A method for detection of target short tandem repeats based on nanopore sequencing data. Front Mol Biosci 2023; 10:1093519. [PMID: 36743210 PMCID: PMC9889824 DOI: 10.3389/fmolb.2023.1093519] [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: 11/09/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023] Open
Abstract
Short tandem repeats (STRs) are widely present in the human genome. Studies have confirmed that STRs are associated with more than 30 diseases, and they have also been used in forensic identification and paternity testing. However, there are few methods for STR detection based on nanopore sequencing due to the challenges posed by the sequencing principles and the data characteristics of nanopore sequencing. We developed NanoSTR for detection of target STR loci based on the length-number-rank (LNR) information of reads. NanoSTR can be used for STR detection and genotyping based on long-read data from nanopore sequencing with improved accuracy and efficiency compared with other existing methods, such as Tandem-Genotypes and TRiCoLOR. NanoSTR showed 100% concordance with the expected genotypes using error-free simulated data, and also achieved >85% concordance using the standard samples (containing autosomal and Y-chromosomal loci) with MinION sequencing platform, respectively. NanoSTR showed high performance for detection of target STR markers. Although NanoSTR needs further optimization and development, it is useful as an analytical method for the detection of STR loci by nanopore sequencing. This method adds to the toolbox for nanopore-based STR analysis and expands the applications of nanopore sequencing in scientific research and clinical scenarios. The main code and the data are available at https://github.com/langjidong/NanoSTR.
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32
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Bustos BI, Billingsley K, Blauwendraat C, Gibbs JR, Gan-Or Z, Krainc D, Singleton AB, Lubbe SJ. Genome-wide contribution of common short-tandem repeats to Parkinson's disease genetic risk. Brain 2023; 146:65-74. [PMID: 36347471 DOI: 10.1093/brain/awac301] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/01/2022] [Accepted: 08/06/2022] [Indexed: 11/11/2022] Open
Abstract
Parkinson's disease is a complex neurodegenerative disorder with a strong genetic component, for which most known disease-associated variants are single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels). DNA repetitive elements account for >50% of the human genome; however, little is known of their contribution to Parkinson's disease aetiology. While select short tandem repeats (STRs) within candidate genes have been studied in Parkinson's disease, their genome-wide contribution remains unknown. Here we present the first genome-wide association study of STRs in Parkinson's disease. Through a meta-analysis of 16 imputed genome-wide association study cohorts from the International Parkinson's Disease Genomic Consortium (IPDGC), totalling 39 087 individuals (16 642 cases and 22 445 controls of European ancestry), we identified 34 genome-wide significant STR loci (P < 5.34 × 10-6), with the strongest signal located in KANSL1 [chr17:44 205 351:[T]11, P = 3 × 10-39, odds ratio = 1.31 (95% confidence interval = 1.26-1.36)]. Conditional-joint analyses suggested that four significant STRs mapping nearby NDUFAF2, TRIML2, MIRNA-129-1 and NCOR1 were independent from known risk SNPs. Including STRs in heritability estimates increased the variance explained by SNPs alone. Gene expression analysis of STRs (eSTRs) in RNA sequencing data from 13 brain regions identified significant associations of STRs influencing the expression of multiple genes, including known Parkinson's disease genes. Further functional annotation of candidate STRs revealed that significant eSTRs within NUDFAF2 and ZSWIM7 overlap with regulatory features and are associated with change in the expression levels of nearby genes. Here, we show that STRs at known and novel candidate loci contribute to Parkinson's disease risk and have functional effects in disease-relevant tissues and pathways, supporting previously reported disease-associated genes and giving further evidence for their functional prioritization. These data represent a valuable resource for researchers currently dissecting Parkinson's disease risk loci.
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Affiliation(s)
- Bernabe I Bustos
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kimberley Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cornelis Blauwendraat
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - J Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ziv Gan-Or
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada.,Department of Human Genetics, McGill University, Montréal, QC, Canada.,Department of Neurology and neurosurgery, McGill University, Montréal, QC, Canada
| | - Dimitri Krainc
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven J Lubbe
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
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33
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Vijayaraghavan P, Batalov S, Ding Y, Sanford E, Kingsmore SF, Dimmock D, Hobbs C, Bainbridge M. The Genomic landscape of short tandem repeats across multiple ancestries. PLoS One 2023; 18:e0279430. [PMID: 36701310 PMCID: PMC9879404 DOI: 10.1371/journal.pone.0279430] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/07/2022] [Indexed: 01/27/2023] Open
Abstract
Short Tandem Repeats (STRs) have been found to play a role in a myriad of complex traits and genetic diseases. We examined the variability in the lengths of over 850,000 STR loci in 996 children with suspected genetic disorders and 1,178 parents across six separate ancestral groups: Africans, Europeans, East Asians, Admixed Americans, Non-admixed Americans, and Pacific Islanders. For each STR locus we compared allele length between and within each ancestry group. In relation to Europeans, admixed Americans had the most similar STR lengths with only 623 positions either significantly expanded or contracted, while the divergence was highest in Africans, with 4,933 chromosomal positions contracted or expanded. We also examined probands to identify STR expansions at known pathogenic loci. The genes TCF4, AR, and DMPK showed significant expansions with lengths 250% greater than their various average allele lengths in 49, 162, and 11 individuals respectively. All 49 individuals containing an expansion in TCF4 and six individuals containing an expansion in DMPK presented with allele lengths longer than the known pathogenic length for these genes. Next, we identified individuals with significant expansions in highly conserved loci across all ancestries. Eighty loci in conserved regions met criteria for divergence. Two of these individuals were found to have exonic STR expansions: one in ZBTB4 and the other in SLC9A7, which is associated with X-linked mental retardation. Finally, we used parent-child trios to detect and analyze de novo mutations. In total, we observed 3,219 de novo expansions, where proband allele lengths are greater than twice the longest parental allele length. This work helps lay the foundation for understanding STR lengths genome-wide across ancestries and may help identify new disease genes and novel mechanisms of pathogenicity in known disease genes.
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Affiliation(s)
| | - Sergey Batalov
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States of America
| | - Yan Ding
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States of America
| | - Erica Sanford
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States of America
- Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Stephen F. Kingsmore
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States of America
| | - David Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States of America
| | - Charlotte Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States of America
| | - Matthew Bainbridge
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States of America
- * E-mail:
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34
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Recurrent repeat expansions in human cancer genomes. Nature 2023; 613:96-102. [PMID: 36517591 DOI: 10.1038/s41586-022-05515-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/02/2022] [Indexed: 12/16/2022]
Abstract
Expansion of a single repetitive DNA sequence, termed a tandem repeat (TR), is known to cause more than 50 diseases1,2. However, repeat expansions are often not explored beyond neurological and neurodegenerative disorders. In some cancers, mutations accumulate in short tracts of TRs, a phenomenon termed microsatellite instability; however, larger repeat expansions have not been systematically analysed in cancer3-8. Here we identified TR expansions in 2,622 cancer genomes spanning 29 cancer types. In seven cancer types, we found 160 recurrent repeat expansions (rREs), most of which (155/160) were subtype specific. We found that rREs were non-uniformly distributed in the genome with enrichment near candidate cis-regulatory elements, suggesting a potential role in gene regulation. One rRE, a GAAA-repeat expansion, located near a regulatory element in the first intron of UGT2B7 was detected in 34% of renal cell carcinoma samples and was validated by long-read DNA sequencing. Moreover, in preliminary experiments, treating cells that harbour this rRE with a GAAA-targeting molecule led to a dose-dependent decrease in cell proliferation. Overall, our results suggest that rREs may be an important but unexplored source of genetic variation in human cancer, and we provide a comprehensive catalogue for further study.
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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: 20] [Impact Index Per Article: 10.0] [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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Frontanilla TS, Valle-Silva G, Ayala J, Mendes-Junior CT. Open-Access Worldwide Population STR Database Constructed Using High-Coverage Massively Parallel Sequencing Data Obtained from the 1000 Genomes Project. Genes (Basel) 2022; 13:genes13122205. [PMID: 36553472 PMCID: PMC9778533 DOI: 10.3390/genes13122205] [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: 10/15/2022] [Revised: 11/13/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Achieving accurate STR genotyping by using next-generation sequencing data has been challenging. To provide the forensic genetics community with a reliable open-access STR database, we conducted a comprehensive genotyping analysis of a set of STRs of broad forensic interest obtained from 1000 Genome populations. We analyzed 22 STR markers using files of the high-coverage dataset of Phase 3 of the 1000 Genomes Project. We used HipSTR to call genotypes from 2504 samples obtained from 26 populations. We were not able to detect the D21S11 marker. The Hardy-Weinberg equilibrium analysis coupled with a comprehensive analysis of allele frequencies revealed that HipSTR was not able to identify longer alleles, which resulted in heterozygote deficiency. Nevertheless, AMOVA, a clustering analysis that uses STRUCTURE, and a Principal Coordinates Analysis showed a clear-cut separation between the four major ancestries sampled by the 1000 Genomes Consortium. Except for larger Penta D and Penta E alleles, and two very small Penta D alleles (2.2 and 3.2) usually observed in African populations, our analyses revealed that allele frequencies and genotypes offered as an open-access database are consistent and reliable.
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Affiliation(s)
- Tamara Soledad Frontanilla
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14049-900, SP, Brazil
| | - Guilherme Valle-Silva
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, SP, Brazil
| | - Jesus Ayala
- Facultad de Ingeniería Informática, Universidad de la Integración de las Americas, Asunción 00120-6, Paraguay
| | - Celso Teixeira Mendes-Junior
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, SP, Brazil
- Correspondence:
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Wang X, Budowle B, Ge J. USAT: a bioinformatic toolkit to facilitate interpretation and comparative visualization of tandem repeat sequences. BMC Bioinformatics 2022; 23:497. [PMID: 36402991 PMCID: PMC9675219 DOI: 10.1186/s12859-022-05021-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/29/2022] [Indexed: 11/21/2022] Open
Abstract
Background Tandem repeats (TR), highly variable genomic variants, are widely used in individual identification, disease diagnostics, and evolutionary studies. The recent advances in sequencing technologies and bioinformatic tools facilitate calling TR haplotypes genome widely. Both length-based and sequence-based TR alleles are used in different applications. However, sequence-based TR alleles could provide the highest precision in characterizing TR haplotypes. The need to identify the differences at the single nucleotide level between or among TR haplotypes with an easy-use bioinformatic tool is essential. Results In this study, we developed a Universal STR Allele Toolkit (USAT) for TR haplotype analysis, which takes TR haplotype output from existing tools to perform allele size conversion, sequence comparison of haplotypes, figure plotting, comparison for allele distribution, and interactive visualization. An exemplary application of USAT for analysis of the CODIS core STR loci for DNA forensics with benchmarking human individuals demonstrated the capabilities of USAT. USAT has user-friendly graphic interfaces and runs fast in major computing operating systems with parallel computing enabled. Conclusion USAT is a user-friendly bioinformatics software for interpretation, visualization, and comparisons of TRs. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-05021-1.
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Affiliation(s)
- Xuewen Wang
- grid.266869.50000 0001 1008 957XCenter for Human Identification, Health Science Center, University of North Texas, Fort Worth, TX USA
| | - Bruce Budowle
- grid.266869.50000 0001 1008 957XCenter for Human Identification, Health Science Center, University of North Texas, Fort Worth, TX USA ,grid.266871.c0000 0000 9765 6057Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX USA
| | - Jianye Ge
- grid.266869.50000 0001 1008 957XCenter for Human Identification, Health Science Center, University of North Texas, Fort Worth, TX USA ,grid.266871.c0000 0000 9765 6057Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX USA
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Morris AB, Bray R, Gebel HM, Cliff Sullivan H. A Primer on Chimerism Analysis: A Straightforward, Thorough Review. Lab Med 2022:6827470. [DOI: 10.1093/labmed/lmac132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Short tandem repeat (STR) analysis to assess chimerism is a critical aspect of routine care particularly in patients facing stem cell transplants but is also relevant in other clinical scenarios. STR analysis provides a means to assess donor and recipient cellular origins in a patient, and, as such, can inform engraftment, rejection, and relapse status in stem cell transplant recipients. In this review of STR testing, the most commonly used method to assess chimerism, its background, procedural details, and clinical utility are discussed.
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Affiliation(s)
- Anna B Morris
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine , Atlanta, GA , USA
| | - Robert Bray
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine , Atlanta, GA , USA
| | - Howard M Gebel
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine , Atlanta, GA , USA
| | - H Cliff Sullivan
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine , Atlanta, GA , USA
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Global abundance of short tandem repeats is non-random in rodents and primates. BMC Genom Data 2022; 23:77. [PMID: 36329409 PMCID: PMC9635179 DOI: 10.1186/s12863-022-01092-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background While of predominant abundance across vertebrate genomes and significant biological implications, the relevance of short tandem repeats (STRs) (also known as microsatellites) to speciation remains largely elusive and attributed to random coincidence for the most part. Here we collected data on the whole-genome abundance of mono-, di-, and trinucleotide STRs in nine species, encompassing rodents and primates, including rat, mouse, olive baboon, gelada, macaque, gorilla, chimpanzee, bonobo, and human. The collected data were used to analyze hierarchical clustering of the STR abundances in the selected species. Results We found massive differential STR abundances between the rodent and primate orders. In addition, while numerous STRs had random abundance across the nine selected species, the global abundance conformed to three consistent < clusters>, as follows: <rat, mouse>, <gelada, macaque, olive baboon>, and <gorilla, chimpanzee, bonobo, human>, which coincided with the phylogenetic distances of the selected species (p < 4E-05). Exceptionally, in the trinucleotide STR compartment, human was significantly distant from all other species. Conclusion Based on hierarchical clustering, we propose that the global abundance of STRs is non-random in rodents and primates, and probably had a determining impact on the speciation of the two orders. We also propose the STRs and STR lengths, which predominantly conformed to the phylogeny of the selected species, exemplified by (t)10, (ct)6, and (taa4). Phylogenetic and experimental platforms are warranted to further examine the observed patterns and the biological mechanisms associated with those STRs.
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A (GCC) repeat in SBF1 reveals a novel biological phenomenon in human and links to late onset neurocognitive disorder. Sci Rep 2022; 12:15480. [PMID: 36104480 PMCID: PMC9474449 DOI: 10.1038/s41598-022-19878-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 09/06/2022] [Indexed: 12/22/2022] Open
Abstract
The human SBF1 (SET binding factor 1) gene, alternatively known as MTMR5, is predominantly expressed in the brain, and its epigenetic dysregulation is linked to late-onset neurocognitive disorders (NCDs), such as Alzheimer’s disease. This gene contains a (GCC)-repeat at the interval between + 1 and + 60 of the transcription start site (SBF1-202 ENST00000380817.8). We sequenced the SBF1 (GCC)-repeat in a sample of 542 Iranian individuals, consisting of late-onset NCDs (N = 260) and controls (N = 282). While multiple alleles were detected at this locus, the 8 and 9 repeats were predominantly abundant, forming > 95% of the allele pool across the two groups. Among a number of anomalies, the allele distribution was significantly different in the NCD group versus controls (Fisher’s exact p = 0.006), primarily as a result of enrichment of the 8-repeat in the former. The genotype distribution departed from the Hardy–Weinberg principle in both groups (p < 0.001), and was significantly different between the two groups (Fisher’s exact p = 0.001). We detected significantly low frequency of the 8/9 genotype in both groups, higher frequency of this genotype in the NCD group, and reverse order of 8/8 versus 9/9 genotypes in the NCD group versus controls. Biased heterozygous/heterozygous ratios were also detected for the 6/8 versus 6/9 genotypes (in favor of 6/8) across the human samples studied (Fisher’s exact p = 0.0001). Bioinformatics studies revealed that the number of (GCC)-repeats may change the RNA secondary structure and interaction sites at least across human exon 1. This STR was specifically expanded beyond 2-repeats in primates. In conclusion, we report indication of a novel biological phenomenon, in which there is selection against certain heterozygous genotypes at a STR locus in human. We also report different allele and genotype distribution at this STR locus in late-onset NCD versus controls. In view of the location of this STR in the 5′ untranslated region, RNA/RNA or RNA/DNA heterodimer formation of the involved genotypes and alternative RNA processing and/or translation should be considered.
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Tarr I, Hesselson S, Iismaa SE, Rath E, Monger S, Troup M, Mishra K, Wong CM, Hsu PC, Junday K, Humphreys DT, Adlam D, Webb TR, Baranowska-Clarke AA, Hamby SE, Carss KJ, Samani NJ, Bax M, McGrath-Cadell L, Kovacic JC, Dunwoodie SL, Fatkin D, Muller DW, Graham RM, Giannoulatou E. Exploring the Genetic Architecture of Spontaneous Coronary Artery Dissection Using Whole-Genome Sequencing. Circ Genom Precis Med 2022; 15:e003527. [PMID: 35583931 PMCID: PMC9388555 DOI: 10.1161/circgen.121.003527] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background:
Spontaneous coronary artery dissection (SCAD) is a cause of acute coronary syndrome that predominantly affects women. Its pathophysiology remains unclear but connective tissue disorders (CTD) and other vasculopathies have been observed in many SCAD patients. A genetic component for SCAD is increasingly appreciated, although few genes have been robustly implicated. We sought to clarify the genetic cause of SCAD using targeted and genome-wide methods in a cohort of sporadic cases to identify both common and rare disease-associated variants.
Methods:
A cohort of 91 unrelated sporadic SCAD cases was investigated for rare, deleterious variants in genes associated with either SCAD or CTD, while new candidate genes were sought using rare variant collapsing analysis and identification of novel loss-of-function variants in genes intolerant to such variation. Finally, 2 SCAD polygenic risk scores were applied to assess the contribution of common variants.
Results:
We identified 10 cases with at least one rare, likely disease-causing variant in CTD-associated genes, although only one had a CTD phenotype. No genes were significantly associated with SCAD from genome-wide collapsing analysis, however, enrichment for TGF (transforming growth factor)-β signaling pathway genes was found with analysis of 24 genes harboring novel loss-of-function variants. Both polygenic risk scores demonstrated that sporadic SCAD cases have a significantly elevated genetic SCAD risk compared with controls.
Conclusions:
SCAD shares some genetic overlap with CTD, even in the absence of any major CTD phenotype. Consistent with a complex genetic architecture, SCAD patients also have a higher burden of common variants than controls.
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Affiliation(s)
- Ingrid Tarr
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
| | - Stephanie Hesselson
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
| | - Siiri E. Iismaa
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
- UNSW Sydney, Kensington, NSW, Australia (S.E.I., E.R., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
| | - Emma Rath
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
- UNSW Sydney, Kensington, NSW, Australia (S.E.I., E.R., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
| | - Steven Monger
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
| | - Michael Troup
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
| | - Ketan Mishra
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
| | - Claire M.Y. Wong
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
| | - Pei-Chen Hsu
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
| | - Keerat Junday
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
| | - David T. Humphreys
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
| | - David Adlam
- Department of Cardiovascular Sciences, NIHR Leicester Biomedical Research Centre, University of Leicester, United Kingdom (D.A., T.R.W., A.A.B.-C., S.E.H., N.J.S.)
| | - Tom R. Webb
- Department of Cardiovascular Sciences, NIHR Leicester Biomedical Research Centre, University of Leicester, United Kingdom (D.A., T.R.W., A.A.B.-C., S.E.H., N.J.S.)
| | - Anna A. Baranowska-Clarke
- UNSW Sydney, Kensington, NSW, Australia (S.E.I., E.R., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
| | - Stephen E. Hamby
- Department of Cardiovascular Sciences, NIHR Leicester Biomedical Research Centre, University of Leicester, United Kingdom (D.A., T.R.W., A.A.B.-C., S.E.H., N.J.S.)
| | - Keren J. Carss
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, United Kingdom (K.J.C.)
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, NIHR Leicester Biomedical Research Centre, University of Leicester, United Kingdom (D.A., T.R.W., A.A.B.-C., S.E.H., N.J.S.)
| | - Monique Bax
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
| | - Lucy McGrath-Cadell
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
- UNSW Sydney, Kensington, NSW, Australia (S.E.I., E.R., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
| | - Jason C. Kovacic
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
- UNSW Sydney, Kensington, NSW, Australia (S.E.I., E.R., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY (J.C.K.)
- Cardiology Department, St Vincent’s Hospital, Darlinghurst, NSW, Australia (J.C.K., D.F., D.W.M.M., R.M.G.)
| | - Sally L. Dunwoodie
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
- UNSW Sydney, Kensington, NSW, Australia (S.E.I., E.R., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
| | - Diane Fatkin
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
- UNSW Sydney, Kensington, NSW, Australia (S.E.I., E.R., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
- Cardiology Department, St Vincent’s Hospital, Darlinghurst, NSW, Australia (J.C.K., D.F., D.W.M.M., R.M.G.)
| | - David W.M. Muller
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
- UNSW Sydney, Kensington, NSW, Australia (S.E.I., E.R., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
- Cardiology Department, St Vincent’s Hospital, Darlinghurst, NSW, Australia (J.C.K., D.F., D.W.M.M., R.M.G.)
| | - Robert M. Graham
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
- UNSW Sydney, Kensington, NSW, Australia (S.E.I., E.R., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
- Cardiology Department, St Vincent’s Hospital, Darlinghurst, NSW, Australia (J.C.K., D.F., D.W.M.M., R.M.G.)
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia (I.T., S.H., S.E.I., E.R., S.M., M.T., K.M., C.M.Y.W., P.-C.H., K.J., D.T.H., M.B., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
- UNSW Sydney, Kensington, NSW, Australia (S.E.I., E.R., L.M.-C., J.C.K., S.L.D., D.F., D.W.M.M., R.M.G., E.G.)
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42
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Detection of repeat expansions in large next generation DNA and RNA sequencing data without alignment. Sci Rep 2022; 12:13124. [PMID: 35907931 PMCID: PMC9338934 DOI: 10.1038/s41598-022-17267-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/22/2022] [Indexed: 11/10/2022] Open
Abstract
Bioinformatic methods for detecting short tandem repeat expansions in short-read sequencing have identified new repeat expansions in humans, but require alignment information to identify repetitive motif enrichment at genomic locations. We present superSTR, an ultrafast method that does not require alignment. superSTR is used to process whole-genome and whole-exome sequencing data, and perform the first STR analysis of the UK Biobank, efficiently screening and identifying known and potential disease-associated STRs in the exomes of 49,953 biobank participants. We demonstrate the first bioinformatic screening of RNA sequencing data to detect repeat expansions in humans and mouse models of ataxia and dystrophy.
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43
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Chiu R, Rajan-Babu IS, Birol I, Friedman JM. Linked-read sequencing for detecting short tandem repeat expansions. Sci Rep 2022; 12:9352. [PMID: 35672336 PMCID: PMC9174224 DOI: 10.1038/s41598-022-13024-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/19/2022] [Indexed: 11/09/2022] Open
Abstract
Detection of short tandem repeat (STR) expansions with standard short-read sequencing is challenging due to the difficulty in mapping multicopy repeat sequences. In this study, we explored how the long-range sequence information of barcode linked-read sequencing (BLRS) can be leveraged to improve repeat-read detection. We also devised a novel algorithm using BLRS barcodes for distance estimation and evaluated its application for STR genotyping. Both approaches were designed for genotyping large expansions (> 1 kb) that cannot be sized accurately by existing methods. Using simulated and experimental data of genomes with STR expansions from multiple BLRS platforms, we validated the utility of barcode and phasing information in attaining better STR genotypes compared to standard short-read sequencing. Although the coverage bias of extremely GC-rich STRs is an important limitation of BLRS, BLRS is an effective strategy for genotyping many other STR loci.
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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.,Department of Medical and Molecular Genetics, King's College London, Strand, London, WC2R 2LS, UK
| | - 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.
| | - 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
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44
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Liu Z, Zhao G, Xiao Y, Zeng S, Yuan Y, Zhou X, Fang Z, He R, Li B, Zhao Y, Pan H, Wang Y, Yu G, Peng IF, Wang D, Meng Q, Xu Q, Sun Q, Yan X, Shen L, Jiang H, Xia K, Wang J, Guo J, Liang F, Li J, Tang B. Profiling the Genome-Wide Landscape of Short Tandem Repeats by Long-Read Sequencing. Front Genet 2022; 13:810595. [PMID: 35601492 PMCID: PMC9117641 DOI: 10.3389/fgene.2022.810595] [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: 11/07/2021] [Accepted: 03/30/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Short tandem repeats (STRs) are highly variable elements that play a pivotal role in multiple genetic diseases and the regulation of gene expression. Long-read sequencing (LRS) offers a potential solution to genome-wide STR analysis. However, characterizing STRs in human genomes using LRS on a large population scale has not been reported. Methods: We conducted the large LRS-based STR analysis in 193 unrelated samples of the Chinese population and performed genome-wide profiling of STR variation in the human genome. The repeat dynamic index (RDI) was introduced to evaluate the variability of STR. We sourced the expression data from the Genotype-Tissue Expression to explore the tissue specificity of highly variable STRs related genes across tissues. Enrichment analyses were also conducted to identify potential functional roles of the high variable STRs. Results: This study reports the large-scale analysis of human STR variation by LRS and offers a reference STR database based on the LRS dataset. We found that the disease-associated STRs (dSTRs) and STRs associated with the expression of nearby genes (eSTRs) were highly variable in the general population. Moreover, tissue-specific expression analysis showed that those highly variable STRs related genes presented the highest expression level in brain tissues, and enrichment pathways analysis found those STRs are involved in synaptic function-related pathways. Conclusion: Our study profiled the genome-wide landscape of STR using LRS and highlighted the highly variable STRs in the human genome, which provide a valuable resource for studying the role of STRs in human disease and complex traits.
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Affiliation(s)
- Zhenhua Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | | | - Sheng Zeng
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yanchun Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xun Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhenghuan Fang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Runcheng He
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yuwen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongxu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yige Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | | | | | | | - Qingtuan Meng
- Multi-Omics Research Center for Brain Disorders, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qiying Sun
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Xinxiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Kun Xia
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Junling Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Fan Liang
- GrandOmics Biosciences, Beijing, China
- *Correspondence: Beisha Tang, ; Jinchen Li, ; Fan Liang,
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- *Correspondence: Beisha Tang, ; Jinchen Li, ; Fan Liang,
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Multi-Omics Research Center for Brain Disorders, The First Affiliated Hospital of University of South China, Hengyang, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
- *Correspondence: Beisha Tang, ; Jinchen Li, ; Fan Liang,
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45
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Fang L, Liu Q, Monteys AM, Gonzalez-Alegre P, Davidson BL, Wang K. DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing. Genome Biol 2022; 23:108. [PMID: 35484600 PMCID: PMC9052667 DOI: 10.1186/s13059-022-02670-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/08/2022] [Indexed: 12/12/2022] Open
Abstract
Despite recent improvements in basecalling accuracy, nanopore sequencing still has higher error rates on short-tandem repeats (STRs). Instead of using basecalled reads, we developed DeepRepeat which converts ionic current signals into red-green-blue channels, thus transforming the repeat detection problem into an image recognition problem. DeepRepeat identifies and accurately quantifies telomeric repeats in the CHM13 cell line and achieves higher accuracy in quantifying repeats in long STRs than competing methods. We also evaluate DeepRepeat on genome-wide or candidate region datasets from seven different sources. In summary, DeepRepeat enables accurate quantification of long STRs and complements existing methods relying on basecalled reads.
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Affiliation(s)
- Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,School of Life Sciences, College of Science, University of Nevada, Las Vegas, 4505 S Maryland Pkwy, Las Vegas, NV, 89154, USA. .,Nevada Institute of Personalized Medicine, College of Science, University of Nevada, Las Vegas, 4505 S Maryland Pkwy, Las Vegas, NV, 89154, USA.
| | - Alex Mas Monteys
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Pedro Gonzalez-Alegre
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Beverly L Davidson
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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46
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Díaz-Rojas AR, Angeles-Estrada L, Pérez Vielma NM, Sánchez-Monroy V. Short tandem repeat (STR) instability in the oral mucosa of patients submitted to fixed orthodontic therapy: a limitation of STR profile quality for human identification. Forensic Sci Med Pathol 2022; 18:57-63. [PMID: 35098422 DOI: 10.1007/s12024-021-00451-4] [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] [Accepted: 12/15/2021] [Indexed: 11/26/2022]
Abstract
The purpose of this study was to evaluate changes in short tandem repeat (STR) profile quality before and after fixed orthodontic therapy. Samples of oral epithelial cells were obtained from 28 volunteers who had an indication for orthodontic treatment. The samples were collected before and three months after starting orthodontic treatment with fixed appliances. DNA extraction and integrity were evaluated by electrophoresis, and STR profiles were obtained by polymerase chain reaction amplification and STR typing via capillary electrophoresis. DNA electrophoresis showed a higher proportion (7/28, 25%) of DNA degradation in the samples collected after fixed orthodontic treatment compared to those obtained before starting orthodontic therapy (3/28, 11%), however, changes in DNA were not significant (p=0.289). In concordance all STR profiles showed complete genotyping; however, imbalances in the size of heterozygotes and in the signal were detected in 25% of STR profiles after orthodontic therapy. Moreover, STR instability was demonstrated by an increase in stutter bands detected in 60% of the DNA profiles after treatment and a spurious allele of the D195433 marker was found in one sample after treatment. The STR profiles of samples obtained from the oral cavity with orthodontic appliances should be interpreted with caution. STR instability increases the incidence of artifacts that could compromise the quality of the results of tests performed in forensic DNA laboratories.
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Affiliation(s)
- Arturo Rafael Díaz-Rojas
- Unidad de Especialidades Odontológicas, Secretaría de la Defensa Nacional, Estado de México, Mexico City, México
| | - Lucía Angeles-Estrada
- Unidad de Especialidades Odontológicas, Secretaría de la Defensa Nacional, Estado de México, Mexico City, México
- Facultad de Ciencias de la Salud, Universidad Anáhuac, Estado de México, Naucalpan de Juárez, México
| | - Nadia Mabel Pérez Vielma
- Sección de Estudios de Posgrado e Investigación, Centro Interdisciplinario de Ciencias de la Salud Unidad Santo Tómas, Instituto Politécnico Nacional, Ciudad de México, México
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47
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Gall-Duncan T, Sato N, Yuen RKC, Pearson CE. Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences. Genome Res 2022; 32:1-27. [PMID: 34965938 PMCID: PMC8744678 DOI: 10.1101/gr.269530.120] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/29/2021] [Indexed: 11/25/2022]
Abstract
Expansions of gene-specific DNA tandem repeats (TRs), first described in 1991 as a disease-causing mutation in humans, are now known to cause >60 phenotypes, not just disease, and not only in humans. TRs are a common form of genetic variation with biological consequences, observed, so far, in humans, dogs, plants, oysters, and yeast. Repeat diseases show atypical clinical features, genetic anticipation, and multiple and partially penetrant phenotypes among family members. Discovery of disease-causing repeat expansion loci accelerated through technological advances in DNA sequencing and computational analyses. Between 2019 and 2021, 17 new disease-causing TR expansions were reported, totaling 63 TR loci (>69 diseases), with a likelihood of more discoveries, and in more organisms. Recent and historical lessons reveal that properly assessed clinical presentations, coupled with genetic and biological awareness, can guide discovery of disease-causing unstable TRs. We highlight critical but underrecognized aspects of TR mutations. Repeat motifs may not be present in current reference genomes but will be in forthcoming gapless long-read references. Repeat motif size can be a single nucleotide to kilobases/unit. At a given locus, repeat motif sequence purity can vary with consequence. Pathogenic repeats can be "insertions" within nonpathogenic TRs. Expansions, contractions, and somatic length variations of TRs can have clinical/biological consequences. TR instabilities occur in humans and other organisms. TRs can be epigenetically modified and/or chromosomal fragile sites. We discuss the expanding field of disease-associated TR instabilities, highlighting prospects, clinical and genetic clues, tools, and challenges for further discoveries of disease-causing TR instabilities and understanding their biological and pathological impacts-a vista that is about to expand.
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Affiliation(s)
- Terence Gall-Duncan
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Nozomu Sato
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
| | - Ryan K C Yuen
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Christopher E Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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48
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Rajabi F, Jabalameli N, Rezaei N. The Concept of Immunogenetics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:1-17. [DOI: 10.1007/978-3-030-92616-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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Elevated common variant genetic risk for tourette syndrome in a densely-affected pedigree. Mol Psychiatry 2021; 26:7522-7529. [PMID: 34526668 PMCID: PMC8881309 DOI: 10.1038/s41380-021-01277-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/29/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022]
Abstract
Tourette syndrome (TS) is a highly heritable neuropsychiatric disorder with complex patterns of genetic inheritance. Recent genetic findings in TS have highlighted both numerous common variants with small effects and a few rare variants with moderate or large effects. Here we searched for genetic causes of TS in a large, densely-affected British pedigree using a systematic genomic approach. This pedigree spans six generations and includes 122 members, 85 of whom were individually interviewed, and 53 of whom were diagnosed as "cases" (consisting of 28 with definite or probable TS, 20 with chronic multiple tics [CMT], and five with obsessive-compulsive behaviors [OCB]). A total of 66 DNA samples were available (25 TS, 15 CMT, 4 OCB cases, and 22 unaffecteds) and all were genotyped using a dense single nucleotide polymorphism (SNP) array to identify shared segments, copy number variants (CNVs), and to calculate genetic risk scores. Eight cases were also whole genome sequenced to test whether any rare variants were shared identical by descent. While we did not identify any notable CNVs, single nucleotide variants, indels or repeat expansions of near-Mendelian effect, the most distinctive feature of this family proved to be an unusually high load of common risk alleles for TS. We found that cases within this family carried a higher load of TS common variant risk similar to that previously found in unrelated TS cases. Thus far, the strongest evidence from genetic data for contribution to TS risk in this family comes from multiple common risk variants rather than one or a few variants of strong effect.
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50
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Schröder C, Horsthemke B, Depienne C. GC-rich repeat expansions: associated disorders and mechanisms. MED GENET-BERLIN 2021; 33:325-335. [PMID: 38835438 PMCID: PMC11006399 DOI: 10.1515/medgen-2021-2099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 11/12/2021] [Indexed: 06/06/2024]
Abstract
Noncoding repeat expansions are a well-known cause of genetic disorders mainly affecting the central nervous system. Missed by most standard technologies used in routine diagnosis, pathogenic noncoding repeat expansions have to be searched for using specific techniques such as repeat-primed PCR or specific bioinformatics tools applied to genome data, such as ExpansionHunter. In this review, we focus on GC-rich repeat expansions, which represent at least one third of all noncoding repeat expansions described so far. GC-rich expansions are mainly located in regulatory regions (promoter, 5' untranslated region, first intron) of genes and can lead to either a toxic gain-of-function mediated by RNA toxicity and/or repeat-associated non-AUG (RAN) translation, or a loss-of-function of the associated gene, depending on their size and their methylation status. We herein review the clinical and molecular characteristics of disorders associated with these difficult-to-detect expansions.
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Affiliation(s)
- Christopher Schröder
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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