scholarly journals Genome-wide patterns of de novo tandem repeat mutations and their contribution to autism spectrum disorders

2020 ◽  
Author(s):  
Ileena Mitra ◽  
Bonnie Huang ◽  
Nima Mousavi ◽  
Nichole Ma ◽  
Michael Lamkin ◽  
...  
Keyword(s):  
Copy Number ◽  
Tandem Repeats ◽  
De Novo ◽  
Fetal Brain ◽  
Autism Spectrum ◽  
Repetitive Behaviors ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Copy Number Changes

Autism Spectrum Disorder (ASD) is an early onset developmental disorder characterized by deficits in communication and social interaction and restrictive or repetitive behaviors1,2. Family studies demonstrate that ASD has a significant genetic basis3 with contributions both from inherited and de novo variants. While the majority of variance in liability to ASD is estimated to arise from common genetic variation4, it has been estimated that de novo mutations may contribute to 30% of all simplex cases, in which only a single child is affected per family5. Tandem repeats (TRs), consisting of approximately 1-20bp motifs repeated in tandem, comprise one of the largest sources of de novo mutations in humans6. Yet, largely due to technical challenges they present, de novo TR mutations have not yet been characterized on a genome-wide scale, and their contribution to ASD remains unexplored. Here, we develop novel bioinformatics tools for identifying and prioritizing de novo TR mutations from whole genome sequencing (WGS) data and use these to perform a genome-wide characterization of de novo TR mutations in ASD-affected probands and unaffected siblings. Compared to recent work on TRs in ASD7, we explicitly infer mutation events and their precise changes in repeat copy number, and primarily focus on more prevalent stepwise copy number changes rather than large or complex expansions. Our results demonstrate a significant genome-wide excess of TR mutations in ASD probands. TR mutations in probands tend to be larger, enriched in fetal brain regulatory regions, and predicted to be more evolutionarily deleterious compared to mutations observed in unaffected siblings. Overall, our results highlight the importance of considering repeat variants in future studies of de novo mutations.

scholarly journals Paternally inherited noncoding structural variants contribute to autism

2017 ◽  
Author(s):  
William M. Brandler ◽  
Danny Antaki ◽  
Madhusudan Gujral ◽  
Morgan L. Kleiber ◽  
Michelle S. Maile ◽  
...  
Keyword(s):  
De Novo ◽  
Fetal Brain ◽  
Wide Distribution ◽  
Autism Spectrum ◽  
Structural Variants ◽  
De Novo Mutations ◽  
Whole Genome Analysis ◽  
Protein Coding ◽  
Genome Wide ◽  
Exome Aggregation Consortium

AbstractThe genetic architecture of autism spectrum disorder (ASD) is known to consist of contributions from gene-disrupting de novo mutations and common variants of modest effect. We hypothesize that the unexplained heritability of ASD also includes rare inherited variants with intermediate effects. We investigated the genome-wide distribution and functional impact of structural variants (SVs) through whole genome analysis (≥30X coverage) of 3,169 subjects from 829 families affected by ASD. Genes that are intolerant to inactivating variants in the exome aggregation consortium (ExAC) were depleted for SVs in parents, specifically within fetal-brain promoters, UTRs and exons. Rare paternally-inherited SVs that disrupt promoters or UTRs were over-transmitted to probands (P = 0.0013) and not to their typically-developing siblings. Recurrent functional noncoding deletions implicate the gene LEO1 in ASD. Protein-coding SVs were also associated with ASD (P = 0.0025). Our results establish that rare inherited SVs predispose children to ASD, with differing contributions from each parent.

scholarly journals Genome Wide Variant Analysis of Simplex Autism Families with an Integrative Clinical-Bioinformatics Pipeline

2015 ◽  
Author(s):  
Laura T Jiménez-Barrón ◽  
Jason A O'Rawe ◽  
Yiyang Wu ◽  
Margaret Yoon ◽  
Han Fang ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
De Novo ◽  
Autism Spectrum ◽  
Repetitive Behaviors ◽  
Whole Genome ◽  
Sequencing Data ◽  
Bioinformatics Pipeline ◽  
Bioinformatics Tools ◽  
Genome Wide

Autism spectrum disorders (ASD) are a group of developmental disabilities that affect social interaction, communication and are characterized by repetitive behaviors. There is now a large body of evidence that suggests a complex role of genetics in ASD, in which many different loci are involved. Although many current population scale genomic studies have been demonstrably fruitful, these studies generally focus on analyzing a limited part of the genome or use a limited set of bioinformatics tools. These limitations preclude the analysis of genome-wide perturbations that may contribute to the development and severity of ASD-related phenotypes. To overcome these limitations, we have developed and utilized an integrative clinical and bioinformatics pipeline for generating a more complete and reliable set of genomic variants for downstream analyses. Our study focuses on the analysis of three simplex autism families consisting of one affected child, unaffected parents, and one unaffected sibling. All members were clinically evaluated and widely phenotyped. Genotyping arrays and whole genome sequencing were performed on each member, and the resulting sequencing data were analyzed using a variety of available bioinformatics tools. We searched for rare variants of putative functional impact that were found to be segregating according to de-novo, autosomal recessive, x-linked, mitochondrial and compound heterozygote transmission models. The resulting candidate variants included three small heterozygous CNVs, a rare heterozygous de novo nonsense mutation in MYBBP1A located within exon 1, and a novel de novo missense variant in LAMB3. Our work demonstrates how more comprehensive analyses that include rich clinical data and whole genome sequencing data can generate reliable results for use in downstream investigations. We are moving to implement our framework for the analysis and study of larger cohorts of families, where statistical rigor can accompany genetic findings.

scholarly journals Epilepsy subtype-specific copy number burden observed in a genome-wide study of 17 458 subjects

Brain ◽  
2020 ◽  
Vol 143 (7) ◽  
pp. 2106-2118 ◽  
Author(s):  
Lisa-Marie Niestroj ◽  
Eduardo Perez-Palma ◽  
Daniel P Howrigan ◽  
Yadi Zhou ◽  
Feixiong Cheng ◽  
...  
Keyword(s):  
Copy Number ◽  
Focal Epilepsy ◽  
Copy Number Variants ◽  
Epileptic Encephalopathy ◽  
Human Interactome ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Generalized Epilepsy ◽  
First Time

Abstract Cytogenic testing is routinely applied in most neurological centres for severe paediatric epilepsies. However, which characteristics of copy number variants (CNVs) confer most epilepsy risk and which epilepsy subtypes carry the most CNV burden, have not been explored on a genome-wide scale. Here, we present the largest CNV investigation in epilepsy to date with 10 712 European epilepsy cases and 6746 ancestry-matched controls. Patients with genetic generalized epilepsy, lesional focal epilepsy, non-acquired focal epilepsy, and developmental and epileptic encephalopathy were included. All samples were processed with the same technology and analysis pipeline. All investigated epilepsy types, including lesional focal epilepsy patients, showed an increase in CNV burden in at least one tested category compared to controls. However, we observed striking differences in CNV burden across epilepsy types and investigated CNV categories. Genetic generalized epilepsy patients have the highest CNV burden in all categories tested, followed by developmental and epileptic encephalopathy patients. Both epilepsy types also show association for deletions covering genes intolerant for truncating variants. Genome-wide CNV breakpoint association showed not only significant loci for genetic generalized and developmental and epileptic encephalopathy patients but also for lesional focal epilepsy patients. With a 34-fold risk for developing genetic generalized epilepsy, we show for the first time that the established epilepsy-associated 15q13.3 deletion represents the strongest risk CNV for genetic generalized epilepsy across the whole genome. Using the human interactome, we examined the largest connected component of the genes overlapped by CNVs in the four epilepsy types. We observed that genetic generalized epilepsy and non-acquired focal epilepsy formed disease modules. In summary, we show that in all common epilepsy types, 1.5–3% of patients carry epilepsy-associated CNVs. The characteristics of risk CNVs vary tremendously across and within epilepsy types. Thus, we advocate genome-wide genomic testing to identify all disease-associated types of CNVs.

scholarly journals Nexus Between Genome-Wide Copy Number Variations and Autism Spectrum Disorder in Northeast Han Chinese Population

2021 ◽  
Author(s):  
Shuang Qiu ◽  
Xianling Cong ◽  
Yan Li ◽  
Jikang Shi ◽  
Yingjia Qiu ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Copy Number ◽  
Chinese Population ◽  
Autism Spectrum ◽  
Han Chinese ◽  
Spectrum Disorder ◽  
Comparative Genomic ◽  
Han Chinese Population ◽  
Genome Wide ◽  
A Genome

Abstract Background: Autism spectrum disorder (ASD) is a common neurodevelopmental condition, with an increasing prevalence worldwide. Copy number variation (CNV), as one of genetic factors, is involved in ASD etiology. However, there exist substantial differences in terms of location and frequency of some CNVs in the general Asian population. Whole-genome studies of CNVs in Northeast Han Chinese samples are still lacking, necessitating our ongoing work to investigate the characteristics of CNVs in a Northeast Han Chinese population with clinically diagnosed ASD.Methods: We performed a genome-wide CNVs screening in Northeast Han Chinese individuals with ASD using array-based comparative genomic hybridization.Results: We found 22 kinds of CNVs (six deletions and 16 duplications) were potential pathogenic. These CNVs were distributed in chromosome 1p36.33, 1p36.31, 1q42.13, 2p23.1-p22.3, 5p15.33, 5p15.33-p15.2, 7p22.3, 7p22.3-p22.2, 7q22.1-q22.2, 10q23.2-q23.31, 10q26.2-q26.3, 11p15.5, 11q25, 12p12.1-p11.23, 14q11.2, 15q13.3, 16p13.3, 16q21, 22q13.31-q13.33, and Xq12-q13.1. Additionally, we found 20 potential pathogenic genes of ASD in our population, including eight protein coding genes (six duplications [DRD4, HRAS, OPHN1, SHANK3, SLC6A3, and TSC2] and two deletions [CHRNA7 and PTEN]) and 12 microRNAs genes (ten duplications [MIR202, MIR210, MIR3178, MIR339, MIR4516, MIR4717, MIR483, MIR675, MIR6821, and MIR940] and two deletions [MIR107 and MIR558]).Limitations: The sample size in our study may confer limited statistical power to discover significant findings. De novo or inherited of the CNVs were not be classified because of the lack of data from parents.Conclusions: We identified CNVs and genes implicated in ASD risks, conferring perception to further reveal ASD etiology.

scholarly journals Genome-wide profiling of heritable and de novo STR variations

2016 ◽  
Author(s):  
Thomas Willems ◽  
Dina Zielinski ◽  
Assaf Gordon ◽  
Melissa Gymrek ◽  
Yaniv Erlich
Keyword(s):  
Tandem Repeats ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Genetic Diseases ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
High Throughput Sequencing Data ◽  
Genome Wide ◽  
A Genome ◽  
Short Tandem

AbstractShort tandem repeats (STRs) are highly variable elements that play a pivotal role in multiple genetic diseases, population genetics applications, and forensic casework. However, STRs have proven problematic to genotype from high-throughput sequencing data. Here, we describe HipSTR, a novel haplotype-based method for robustly genotyping, haplotyping, and phasing STRs from whole genome sequencing data and report a genome-wide analysis and validation of de novo STR mutations.

scholarly journals Copy number evolution in simple and complex tandem repeats across the C57BL/6 and C57BL/10 inbred mouse lines

2021 ◽  
Author(s):  
Jullien M Flynn ◽  
Emily J Brown ◽  
Andrew G Clark
Keyword(s):  
Copy Number ◽  
Copy Number Change ◽  
Tandem Repeats ◽  
Inbred Mouse ◽  
Rate Of Change ◽  
Rates Of Change ◽  
Centromeric Repeat ◽  
Genome Wide ◽  
Copy Number Changes ◽  
Simple Repeats

Abstract Simple sequence tandem repeats are among the most rapidly evolving compartments of the genome. Some repeat expansions are associated with mammalian disease or meiotic segregation distortion, yet the rates of copy number change across generations are not well known. Here, we use 14 distinct sub-lineages of the C57BL/6 and C57BL/10 inbred mouse strains, which have been evolving independently over about 300 generations, to estimate the rates of copy number changes in genome-wide tandem repeats. Rates of change varied across repeats and across lines. Notably, CAG, whose expansions in coding regions are associated with many neurological and genetic disorders, was highly stable in copy number, likely indicating stabilizing selection. Rates of change were positively correlated with copy number, but the direction and magnitude of changes varied across lines. Some mouse lines experienced consistent losses or gains across most simple repeats, but this did not correlate with copy number changes in complex repeats. Rates of copy number change were similar between simple repeats and the more abundant complex repeats after normalization by copy number. Finally, the Y-specific centromeric repeat had a 4-fold higher rate of change than the homologous centromeric repeat on other chromosomes. Structural differences in satellite complexity, or restriction to the Y chromosome and elevated mutation rates of the male germline, may explain the higher rate of change. Overall, our work underscores the mutational fluidity of long tandem arrays of repeats, and the correlations and constraints between genome-wide tandem repeats which suggest that turnover is not a completely neutral process.

scholarly journals Association of Copy Number Variations in Autism Spectrum Disorders: A Systematic Review

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Elif Funda Sener
Keyword(s):  
Autism Spectrum Disorders ◽  
Complex Traits ◽  
Copy Number ◽  
De Novo ◽  
Genome Structure ◽  
Autism Spectrum ◽  
Copy Number Variations ◽  
Repetitive Behaviors ◽  
Wide Range ◽  
Spectrum Disorders

Autism spectrum disorders (ASDs) are characterized by language impairments, social deficits, and repetitive behaviors. The onset of symptoms occurs by the age of 3 and shows a lifelong persistence. Genetics plays a major role in the etiology of ASD. Except genetics, several potential risk factors (environmental factors and epigenetics) may contribute to ASD. Copy number variations (CNVs) are the most widespread structural variations in the human genome. These variations can alter the genome structure either by deletion or by duplication. CNVs can be de novo or inherited. Chromosomal rearrangements have been detected in 5–10% of the patients with ASD and recently copy number changes ranging from a few kilobases (kb) to several megabases (Mb) in size have been reported. Recent data have also revealed that submicroscopic CNVs can have a role in ASD, and de novo CNVs seem to be a more common risk factor in sporadic compared with inherited forms of ASD. CNVs are being implicated as a contributor to the pathophysiology of complex neurodevelopmental disorders and they can affect a wide range of human phenotypes including mental retardation (MR), autism, neuropsychiatric disorders, and susceptibility to other complex traits such as HIV, Crohn’s disease, and psoriasis. This review emphasizes the major CNVs reported to date in ASD.

scholarly journals Copy number evolution in simple and complex tandem repeats across the C57BL/6 and C57BL/10 inbred mouse lines

2021 ◽  
Author(s):  
Jullien M. Flynn ◽  
Emily J. Brown ◽  
Andrew G. Clark
Keyword(s):  
Copy Number ◽  
Copy Number Change ◽  
Tandem Repeats ◽  
Inbred Mouse ◽  
Rate Of Change ◽  
Rates Of Change ◽  
Centromeric Repeat ◽  
Genome Wide ◽  
Copy Number Changes ◽  
Simple Repeats

AbstractSimple sequence tandem repeats are among the most rapidly evolving compartments of the genome. Some repeat expansions are associated with mammalian disease or meiotic segregation distortion, yet the rates of copy number change across generations are not well known. Here, we use 14 distinct sub-lineages of the C57BL/6 and C57BL/10 inbred mouse strains, which have been evolving independently over about 300 generations, to estimate the rates of copy number changes in genome-wide tandem repeats. Rates of change varied across simple repeats and across lines. Notably, CAG, whose expansions in coding regions are associated with many neurological and other genetic disorders, was highly stable in copy number, likely indicating purifying selection. Rates of change were generally positively correlated with copy number, but the direction and magnitude of changes varied across lines. Some mouse lines experienced consistent losses or gains across most genome-wide simple repeats, but this did not correlate with copy number changes in complex repeats. Rates of copy number change were similar between simple repeats and the much more abundant complex repeats once they were normalized by copy number. Finally, the Y-specific centromeric repeat had a 4-fold higher rate of change than the homologous centromeric repeat on other chromosomes. Structural differences in satellite complexity, or restriction to the Y chromosome and the elevated mutation rate of the male germline, may explain the higher rate of change. Overall, our work underscores the mutational fluidity of long tandem arrays of repeats, and the correlations and constraints between genome-wide tandem repeats which suggest that turnover is not a completely neutral process.

scholarly journals Widespread RNA editing dysregulation in Autism Spectrum Disorders

2018 ◽  
Author(s):  
Stephen Tran ◽  
Hyun-Ik Jun ◽  
Jae Hoon Bahn ◽  
Adel Azghadi ◽  
Gokul Ramaswami ◽  
...  
Keyword(s):  
Rna Editing ◽  
Rna Binding ◽  
Fragile X ◽  
Brain Regions ◽  
Autism Spectrum ◽  
Neurodevelopmental Disease ◽  
Molecular Abnormalities ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale

AbstractAutism spectrum disorder (ASD) is a genetically complex, clinically heterogeneous neurodevelopmental disease. Recently, our understanding of the molecular abnormalities in ASD has been expanded through transcriptomic analyses of postmortem brains. However, a crucial molecular pathway involved in synaptic development, RNA editing, has not yet been studied on a genome-wide scale. Here, we profiled the global patterns of adenosine-to-inosine (A-to-I) editing in a large cohort of post-mortem ASD brains. Strikingly, we observed a global bias of hypo-editing in ASD brains, common to different brain regions and involving many genes with known neurobiological functions. Through genome-wide protein-RNA binding analyses and detailed molecular assays, we show that the Fragile X proteins, FMRP and FXR1P, interact with ADAR proteins and modulate A-to-I editing. Furthermore, we observed convergent patterns of RNA editing alterations in ASD and Fragile X syndrome, thus establishing RNA editing as a molecular link underlying these two highly related diseases. Our findings support a role for RNA editing dysregulation in ASD and highlight novel mechanisms for RNA editing regulation.

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