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Yasmin T, Sadia A, Nadeem L, Basra MAR, Rice ML, Raza MH. Whole Genome Analysis in Consanguineous Families Reveals New Loci for Speech Sound Disorder (SSD). Genes (Basel) 2024; 15:1069. [PMID: 39202429 PMCID: PMC11354014 DOI: 10.3390/genes15081069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/09/2024] [Accepted: 08/09/2024] [Indexed: 09/03/2024] Open
Abstract
Speech is the most common means of communication in humans. Any defect in accurate speech production ability results in the development of speech sound disorder (SSD), a condition that can significantly impair an individual's academic performance, social interactions, and relationships with peers and adults. This study investigated the genetic basis of SSD in three Pakistani families. We performed family-based genome-wide parametric linkage analysis and homozygosity mapping in three consanguineous families with SSD from the Punjab province of Pakistan. The Test for Assessment of Articulation and Phonology in Urdu (TAAPU) was used to analyze the speech articulation data and determine the Percentage Correct Consonants (PCC) score. The PCC score defined the affected and unaffected individuals in each family. Parametric linkage analysis revealed a linkage to chromosome 5 (5q21.3-5q23.1) with a significant logarithm of the odds (LOD) score of 3.13 in a Pakistani family with specific language impairment-97 (PKSLI-97) under an autosomal recessive mode of inheritance. The other two families showed a suggestive linkage at 6p22.1, 14q12, and 16q12.1 under the recessive mode of inheritance. Interestingly, homozygosity mapping showed a loss of heterozygosity in the linkage region at 5q15-5q23.1, shared among seven affected (mostly in the younger generation) and one unaffected individual of PKSLI-97. Our analysis identified the 6p22 locus previously implicated in dyslexia, childhood apraxia of speech (CAS), and language impairment, confirming the role of KIAA0319 and DCDC2 in this locus. These findings provide statistical evidence for the genomic regions associated with articulation disorder and offer future opportunities to further the role of genes in speech production.
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Affiliation(s)
- Tahira Yasmin
- Centre for Clinical and Nutritional Chemistry, School of Chemistry, University of the Punjab, Lahore 54590, Pakistan; (T.Y.); (A.S.); (L.N.); (M.A.R.B.)
| | - Aatika Sadia
- Centre for Clinical and Nutritional Chemistry, School of Chemistry, University of the Punjab, Lahore 54590, Pakistan; (T.Y.); (A.S.); (L.N.); (M.A.R.B.)
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, Norrköping Campus, 60221 Norrköping, Sweden
| | - Laraib Nadeem
- Centre for Clinical and Nutritional Chemistry, School of Chemistry, University of the Punjab, Lahore 54590, Pakistan; (T.Y.); (A.S.); (L.N.); (M.A.R.B.)
| | - Muhammad Asim Raza Basra
- Centre for Clinical and Nutritional Chemistry, School of Chemistry, University of the Punjab, Lahore 54590, Pakistan; (T.Y.); (A.S.); (L.N.); (M.A.R.B.)
| | - Mabel L. Rice
- Speech-Language-Hearing Sciences & Disorders, University of Kansas, Lawrence, KS 66045, USA;
| | - Muhammad Hashim Raza
- Speech-Language-Hearing Sciences & Disorders, University of Kansas, Lawrence, KS 66045, USA;
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Naseri A, Zhi D, Zhang S. Discovery of runs-of-homozygosity diplotype clusters and their associations with diseases in UK Biobank. eLife 2024; 13:e81698. [PMID: 38905121 PMCID: PMC11249732 DOI: 10.7554/elife.81698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 06/20/2024] [Indexed: 06/23/2024] Open
Abstract
Runs-of-homozygosity (ROH) segments, contiguous homozygous regions in a genome were traditionally linked to families and inbred populations. However, a growing literature suggests that ROHs are ubiquitous in outbred populations. Still, most existing genetic studies of ROH in populations are limited to aggregated ROH content across the genome, which does not offer the resolution for mapping causal loci. This limitation is mainly due to a lack of methods for the efficient identification of shared ROH diplotypes. Here, we present a new method, ROH-DICE (runs-of-homozygous diplotype cluster enumerator), to find large ROH diplotype clusters, sufficiently long ROHs shared by a sufficient number of individuals, in large cohorts. ROH-DICE identified over 1 million ROH diplotypes that span over 100 single nucleotide polymorphisms (SNPs) and are shared by more than 100 UK Biobank participants. Moreover, we found significant associations of clustered ROH diplotypes across the genome with various self-reported diseases, with the strongest associations found between the extended human leukocyte antigen (HLA) region and autoimmune disorders. We found an association between a diplotype covering the homeostatic iron regulator (HFE) gene and hemochromatosis, even though the well-known causal SNP was not directly genotyped or imputed. Using a genome-wide scan, we identified a putative association between carriers of an ROH diplotype in chromosome 4 and an increase in mortality among COVID-19 patients (p-value = 1.82 × 10-11). In summary, our ROH-DICE method, by calling out large ROH diplotypes in a large outbred population, enables further population genetics into the demographic history of large populations. More importantly, our method enables a new genome-wide mapping approach for finding disease-causing loci with multi-marker recessive effects at a population scale.
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Affiliation(s)
- Ardalan Naseri
- Department of Computer Science, University of Central FloridaOrlandoUnited States
| | - Degui Zhi
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at HoustonHoustonUnited States
| | - Shaojie Zhang
- Department of Computer Science, University of Central FloridaOrlandoUnited States
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3
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Yasmin T, Andres EM, Ashraf K, Basra MAR, Raza MH. Genome-wide analysis of runs of homozygosity in Pakistani controls with no history of speech or language-related developmental phenotypes. Ann Hum Biol 2023; 50:100-107. [PMID: 36786444 PMCID: PMC10284496 DOI: 10.1080/03014460.2023.2180087] [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: 08/03/2022] [Accepted: 01/27/2023] [Indexed: 02/15/2023]
Abstract
BACKGROUND Runs of homozygosity (ROHs) analysis of controls provide a convenient resource to minimize the association of false positive results of disease-associated ROHs and genetic variants for simple and complex disorders in individuals from the same population. Evidence for the value of ROHs to speech or language-related traits is restricted due to the absence of population-matched behaviourally defined controls and limited family-based studies. AIM This study aims to identify common ROHs in the Pakistani population, focussing on the total length and frequency of ROHs of variable sizes, shared ROHs, and their genomic distribution. SUBJECTS AND METHODS We performed homozygosity analysis (in PLINK) of 86 individuals (39 males, 47 females) with no history of speech or language-related phenotypes (controls) who had been genotyped with the Illumina Infinium QC Array-24. RESULTS ROHs of 1-<4 megabases (Mb) were frequent in unrelated individuals. We observed ROHs over 20 Mb among six individuals. Over 30 percent of the identified ROHs were shared among several individuals, indicating consanguinity's effect on the Pakistani population. CONCLUSION Our findings serve as a foundation for family-based genetic studies of consanguineous families with speech or language-related disorders to ultimately narrow the homozygosity regions of interest to identify pathogenic variants.
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Affiliation(s)
- Tahira Yasmin
- Centre for Clinical and Nutritional Chemistry, School of Chemistry, University of The Punjab, Lahore, Pakistan
| | - Erin M. Andres
- Thompson Center for Autism & Neurodevelopment, University of Missouri, Columbia, MO, USA
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, 66045, USA
| | - Komal Ashraf
- Centre for Clinical and Nutritional Chemistry, School of Chemistry, University of The Punjab, Lahore, Pakistan
| | - Muhammad Asim Raza Basra
- Centre for Clinical and Nutritional Chemistry, School of Chemistry, University of The Punjab, Lahore, Pakistan
| | - Muhammad Hashim Raza
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, 66045, USA
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4
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Gavriilidi I, De Meester G, Van Damme R, Baeckens S. How to behave when marooned: the behavioural component of the island syndrome remains underexplored. Biol Lett 2022; 18:20220030. [PMID: 35440235 PMCID: PMC9039784 DOI: 10.1098/rsbl.2022.0030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/25/2022] [Indexed: 12/16/2022] Open
Abstract
Animals on islands typically depart from their mainland relatives in assorted aspects of their biology. Because they seem to occur in concert, and to some extent evolve convergently in disparate taxa, these changes are referred to as the 'island syndrome'. While morphological, physiological and life-history components of the island syndrome have received considerable attention, much less is known about how insularity affects behaviour. In this paper, we argue why changes in personality traits and cognitive abilities can be expected to form part of the island syndrome. We provide an overview of studies that have compared personality traits and cognitive abilities between island and mainland populations, or among islands. Overall, the pickings are remarkably slim. There is evidence that animals on islands tend to be bolder than on the mainland, but effects on other personality traits go either way. The evidence for effects of insularity on cognitive abilities or style is highly circumstantial and very mixed. Finally, we consider the ecological drivers that may induce such changes, and the mechanisms through which they might occur. We conclude that our knowledge of the behavioural and cognitive responses to island environments remains limited, and we encourage behavioural biologists to make more use of these 'natural laboratories for evolution'.
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Affiliation(s)
- Ioanna Gavriilidi
- Functional Morphology Lab, Department of Biology, University of Antwerp, Wilrijk, Belgium
- Section of Zoology and Marine Biology, Department of Biology, National and Kapodistrian University of Athens, Greece
| | - Gilles De Meester
- Functional Morphology Lab, Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Raoul Van Damme
- Functional Morphology Lab, Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Simon Baeckens
- Functional Morphology Lab, Department of Biology, University of Antwerp, Wilrijk, Belgium
- Evolution and Optics of Nanostructures Lab, Department of Biology, Ghent University, Ghent, Belgium
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Peng Q, Ehlers CL. Long tracks of homozygosity predict the severity of alcohol use disorders in an American Indian population. Mol Psychiatry 2021; 26:2200-2211. [PMID: 33398086 PMCID: PMC8254832 DOI: 10.1038/s41380-020-00989-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 11/30/2020] [Accepted: 12/07/2020] [Indexed: 11/20/2022]
Abstract
Runs of homozygosity (ROH) arise when an individual inherits two copies of the same haplotype segment. While ROH are ubiquitous across human populations, Native populations-with shared parental ancestry arising from isolation and endogamy-can carry a substantial enrichment for ROH. We have been investigating genetic and environmental risk factors for alcohol use disorders (AUD) in a group of American Indians (AI) who have higher rates of AUD than the general U. S. population. Here we explore whether ROH might be associated with incidence and severity of AUD in this admixed AI population (n = 742) that live on geographically contiguous reservations, using low-coverage whole genome sequences. We have found that the genomic regions in the ROH that were identified in this population had significantly elevated American Indian heritage compared with the rest of the genome. Increased ROH abundance and ROH burden are likely risk factors for AUD severity in this AI population, especially in those diagnosed with severe and moderate AUD. The association between ROH and AUD was mostly driven by ROH of moderate lengths between 1 and 2 Mb. An ROH island on chromosome 1p32.3 and a rare ROH pool on chromosome 3p12.3 were found to be significantly associated with AUD severity. They contain genes involved in lipid metabolism, oxidative stress and inflammatory responses; and OSBPL9 was found to reside on the consensus part of the ROH island. These data demonstrate that ROH are associated with risk for AUD severity in this AI population.
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Affiliation(s)
- Qian Peng
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Cindy L Ehlers
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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6
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Naseri A, Zhi D, Zhang S. Discovery of runs-of-homozygosity diplotype clusters and their associations with diseases in UK Biobank. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.10.26.20220004. [PMID: 33140058 PMCID: PMC7605569 DOI: 10.1101/2020.10.26.20220004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Runs of homozygosity (ROH) segments, contiguous homozygous regions in a genome were traditionally linked to families and inbred populations. However, a growing literature suggests that ROHs are ubiquitous in outbred populations. Still, most existing genetic studies of ROH in populations are limited to aggregated ROH content across the genome, which does not offer the resolution for mapping causal loci. This limitation is mainly due to a lack of methods for efficient identification of shared ROH diplotypes. Here, we present a new method, ROH-DICE, to find large ROH diplotype clusters, sufficiently long ROHs shared by a sufficient number of individuals, in large cohorts. ROH-DICE identified over 1 million ROH diplotypes that span over 100 SNPs and shared by more than 100 UK Biobank participants. Moreover, we found significant associations of clustered ROH diplotypes across the genome with various self-reported diseases, with the strongest associations found between the extended HLA region and autoimmune disorders. We found an association between a diplotype covering the HFE gene and haemochromatosis, even though the well-known causal SNP was not directly genotyped nor imputed. Using genome-wide scan, we identified a putative association between carriers of an ROH diplotype in chromosome 4 and an increase of mortality among COVID-19 patients. In summary, our ROH-DICE method, by calling out large ROH diplotypes in a large outbred population, enables further population genetics into the demographic history of large populations. More importantly, our method enables a new genome-wide mapping approach for finding disease-causing loci with multi-marker recessive effects at population scale.
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Affiliation(s)
- Ardalan Naseri
- Department of Computer Science, University of Central Florida, Orlando, Florida 32816, USA
| | - Degui Zhi
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, Florida 32816, USA
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7
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Szpiech ZA, Mak ACY, White MJ, Hu D, Eng C, Burchard EG, Hernandez RD. Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity. Am J Hum Genet 2019; 105:747-762. [PMID: 31543216 PMCID: PMC6817522 DOI: 10.1016/j.ajhg.2019.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022] Open
Abstract
Runs of homozygosity (ROH) are important genomic features that manifest when an individual inherits two haplotypes that are identical by descent. Their length distributions are informative about population history, and their genomic locations are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. We have previously shown that ROH, and especially long ROH that are likely the result of recent parental relatedness, are enriched for homozygous deleterious coding variation in a worldwide sample of outbred individuals. However, the distribution of ROH in admixed populations and their relationship to deleterious homozygous genotypes is understudied. Here we analyze whole-genome sequencing data from 1,441 unrelated individuals from self-identified African American, Puerto Rican, and Mexican American populations. These populations are three-way admixed between European, African, and Native American ancestries and provide an opportunity to study the distribution of deleterious alleles partitioned by local ancestry and ROH. We re-capitulate previous findings that long ROH are enriched for deleterious variation genome-wide. We then partition by local ancestry and show that deleterious homozygotes arise at a higher rate when ROH overlap African ancestry segments than when they overlap European or Native American ancestry segments of the genome. These results suggest that, while ROH on any haplotype background are associated with an inflation of deleterious homozygous variation, African haplotype backgrounds may play a particularly important role in the genetic architecture of complex diseases for admixed individuals, highlighting the need for further study of these populations.
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Affiliation(s)
- Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Department of Biological Sciences, Auburn University, Auburn, AL 36842, USA.
| | - Angel C Y Mak
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Marquitta J White
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada; Genome Quebec Innovation Center, McGill University, Montreal, QC H3A 0G1, Canada.
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8
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Iourov IY, Vorsanova SG, Zelenova MA, Vasin KS, Kurinnaia OS, Korostelev SA, Yurov YB. [Epigenomic variations manifesting as a loss of heterozygosity affecting imprinted genes represent a molecular mechanism of autism spectrum disorders and intellectual disability in children]. Zh Nevrol Psikhiatr Im S S Korsakova 2019; 119:91-97. [PMID: 31317896 DOI: 10.17116/jnevro201911905191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AIM Long continuous stretches of homozygosity (LCSH) are regularly detected in studies using molecular karyotyping (SNP array). Despite this type of variation being able to provide meaningful data on the parents' kinship, uniparental disomy and chromosome rearrangements, LCSH are rarely considered as a possible epigenetic cause of neurodevelopmental disorders. Despite their direct relationship to imprinting, LCSH in imprinted loci have not been considered in terms of pathogenicity. The present work is aimed at studying LCSH in chromosomal regions containing imprinted genes previously associated with disease in children with idiopathic intellectual disability, autism, congenital malformations and/or epilepsy. MATERIAL AND METHODS Five hundred and four patients with autism spectrum disorders and intellectual disability were examined. RESULTS LCSH affecting imprinted loci associated with various diseases were identified in 40 (7.9%) individuals. Chromosomal region 7q21.3 was affected in twenty three cases, 15q11.2 in twelve, 11p15.5 in five, 7q32.2 in four. Four patients had 2 LCSH affecting imprinted loci. Besides one LCSH in 7q31.33q32.3 (~4 Mbp) region, all LCSH were 1-1.6 Mbp. Clinically, these cases resembled the corresponding imprinting diseases (e.g. Silver-Russell, Beckwith-Wiedemann, Prader-Willi, Angelman syndromes). Parental kinship was identified in 8 cases (1.59%), which were not affected by LCSH at imprinted loci. CONCLUSION The present study shows that LCSH affecting chromosomal regions 7q21.3, 7q32.2, 11p15.5 and 15p11.2 occur in about 7.9% of children with intellectual disability, autism, congenital malformations and/or epilepsy. Consequently, this type of epigenetic mutations is obviously common in a group of children with neurodevelopmental disorders. LCSH less than 2.5-10 Mbp are usually ignored in molecular karyotyping (SNP array) studies and, therefore, an important epigenetic cause of intellectual disability, autism or epilepsy with high probability remains without attention.
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Affiliation(s)
- I Y Iourov
- Mental Health Research Center, Moscow, Russia; Veltishchev Research Clinical Institute of Pediatric of Pirogov Russian National Research Medical University, Moscow, Russia; Russian Medical Academy for Postgraduate Continuing Education, Moscow, Russia
| | - S G Vorsanova
- Mental Health Research Center, Moscow, Russia; Veltishchev Research Clinical Institute of Pediatric of Pirogov Russian National Research Medical University, Moscow, Russia
| | - M A Zelenova
- Mental Health Research Center, Moscow, Russia; Veltishchev Research Clinical Institute of Pediatric of Pirogov Russian National Research Medical University, Moscow, Russia
| | - K S Vasin
- Mental Health Research Center, Moscow, Russia; Veltishchev Research Clinical Institute of Pediatric of Pirogov Russian National Research Medical University, Moscow, Russia
| | - O S Kurinnaia
- Mental Health Research Center, Moscow, Russia; Veltishchev Research Clinical Institute of Pediatric of Pirogov Russian National Research Medical University, Moscow, Russia
| | - S A Korostelev
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Yu B Yurov
- Mental Health Research Center, Moscow, Russia; Veltishchev Research Clinical Institute of Pediatric of Pirogov Russian National Research Medical University, Moscow, Russia
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Kornilov SA, Tan M, Aljughaiman A, Naumova OY, Grigorenko EL. Genome-Wide Homozygosity Mapping Reveals Genes Associated With Cognitive Ability in Children From Saudi Arabia. Front Genet 2019; 10:888. [PMID: 31620175 PMCID: PMC6759945 DOI: 10.3389/fgene.2019.00888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 08/22/2019] [Indexed: 11/28/2022] Open
Abstract
Recent studies of the genetic foundations of cognitive ability rely on large samples (in extreme, hundreds of thousands) of individuals from relatively outbred populations of mostly European ancestry. Hypothesizing that the genetic foundation of cognitive ability depends on the broader population-specific genetic context, we performed a genome-wide association study and homozygosity mapping of cognitive ability estimates obtained through latent variable modeling in a sample of 354 children from a consanguineous population of Saudi Arabia. Approximately half of the sample demonstrated significantly elevated homozygosity levels indicative of inbreeding, and among those with elevated levels, homozygosity was negatively associated with cognitive ability. Further homozygosity mapping identified a specific run, inclusive of the GRIA4 gene, that survived corrections for multiple testing for association with cognitive ability. The results suggest that in a consanguineous population, a notable proportion of the variance in cognitive ability in the normal range in children might be regulated by population-specific mechanisms such as patterns of elevated homozygosity. This observation has implications for the field's understanding of the etiological bases of intelligence and its variability around the world.
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Affiliation(s)
- Sergey A. Kornilov
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX, United States
- Department of Psychology, University of Houston, Houston, TX, USA
| | - Mei Tan
- Department of Psychology, University of Houston, Houston, TX, USA
| | | | - Oxana Yu Naumova
- Department of Psychology, University of Houston, Houston, TX, USA
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Elena L. Grigorenko
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX, United States
- Department of Psychology, University of Houston, Houston, TX, USA
- Child Study Center, Yale University, New Haven, CT, USA
- Moscow State University for Psychology and Education, Moscow, Russia
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Wanchai V, Jin J, Bircan E, Eng C, Orloff M. Genome-wide tracts of homozygosity and exome analyses reveal repetitive elements with Barrets esophagus/esophageal adenocarcinoma risk. BMC Bioinformatics 2019; 20:98. [PMID: 30871476 PMCID: PMC6419328 DOI: 10.1186/s12859-019-2622-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Barrett's esophagus (BE) is most commonly seen as the condition in which the normal squamous epithelium lining of the esophagus is replaced by goblet cells. Many studies show that BE is a predisposing factor for the development of esophageal adenocarcinoma (EAC), a particularly lethal cancer. The use of single nucleotide polymorphisms (SNPs) to map BE/EAC genes has previously provided insufficient genetic information to fully characterize the heterogeneous nature of the disease. We therefore hypothesize that rigorous interrogation of other types of genomic changes, e.g. tracts of homozygosity (TOH), repetitive elements, and insertion/deletions, may provide a comprehensive understanding of the development of BE/EAC. RESULTS First, we used a case-control framework to identify TOHs by using SNPs and tested for association with BE/EAC. Second, we used a case only approach on a validation series of eight samples subjected to exome sequencing to identify repeat elements and insertion/deletions. Third, insertion/deletions and repeat elements identified in the exomes were then mapped onto genes in the significant TOH regions. Overall, 24 TOH regions were significantly differentially represented among cases, as compared to controls (adjusted-P = 0.002-0.039). Interestingly, four BE/EAC-associated genes within the TOH regions consistently showed insertions and deletions that overlapped across eight exomes. Predictive functional analysis identified NOTCH, WNT, and G-protein inflammation pathways that affect BE and EAC. CONCLUSIONS The integration of common TOHs (cTOHs) with repetitive elements, insertions, and deletions within exomes can help functionally prioritize factors contributing to low to moderate penetrance predisposition to BE/EAC.
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Affiliation(s)
- Visanu Wanchai
- Arkansas Center for Genomic Epidemiology & Medicine and The Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Jing Jin
- The Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Emine Bircan
- The Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Charis Eng
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44195 USA
| | - Mohammed Orloff
- The Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
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Chaves TF, Oliveira LF, Ocampos M, Barbato IT, de Luca GR, Barbato Filho JH, de Camargo Pinto LL, Bernardi P, Maris AF. Long contiguous stretches of homozygosity detected by chromosomal microarrays (CMA) in patients with neurodevelopmental disorders in the South of Brazil. BMC Med Genomics 2019; 12:50. [PMID: 30866944 PMCID: PMC6417136 DOI: 10.1186/s12920-019-0496-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/28/2019] [Indexed: 01/14/2023] Open
Abstract
Background Currently, chromosomal microarrays (CMA) are recommended as first-tier test in the investigation of developmental disorders to examine copy number variations. The modern platforms also include probes for single nucleotide polymorphisms (SNPs) that detect homozygous regions in the genome, such as long contiguous stretches of homozygosity (LCSH) also named runs of homozygosity (ROH). LCHS are chromosomal segments resulting from complete or segmental chromosomal homozygosity, which may be indicative of uniparental disomy (UPD), consanguinity, as well as replicative DNA repair events, however also are common findings in normal populations. Knowing common LCSH of a population, which probably represent ancestral haplotypes of low-recombination regions in the genome, facilitates the interpretation of LCSH found in patients, allowing to prioritize those with possible clinical significance. However, population records of ancestral haplotype derived LCSH by SNP arrays are still scarce, particularly for countries such as Brazil where even for the clinic, microarrays that include SNPs are difficult to request due to their high cost. Methods In this study, we evaluate the frequencies and implications of LCSH detected by Affymetrix CytoScan® HD or 750 K platforms in 430 patients with neurodevelopmental disorders in southern Brazil. LCSH were analyzed in the context of pathogenic significance and also explored to identify ancestral haplotype derived LCSH. The criteria for considering a region as LCSH was homozygosis ≥3 Mbp on an autosome. Results In 95% of the patients, at least one LCSH was detected, a total of 1478 LCSH in 407 patients. In 2.6%, the findings were suggestive of UPD. For about 8.5% LCSH suggest offspring from first to fifth grade, more likely to have a clinical impact. Considering recurrent LCSH found at a frequency of 5% or more, we outline 11 regions as potentially representing ancestral haplotypes in our population. The region most involved with homozygosity was 16p11.2p11.1 (49%), followed by 1q21.2q21.3 (21%), 11p11.2p11.12 (19%), 3p21.31p21.2 (16%), 15q15 1q33p32.3 (12%), 2q11.1q12.1 (9%), 1p33p32.3 (6%), 20q11.21q11.23 (6%), 10q22.1q23.31 (5%), 6p22.2p22 (5%), and 7q11.22q11.23 (5%). Conclusions In this work, we show the importance and usefulness of interpreting LCSH in the results of CMA wich incorporate SNPs.
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Affiliation(s)
- Tiago Fernando Chaves
- Biologist, PhD Student in Cell Biology and Development, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
| | - Luan Freitas Oliveira
- Biomedic, PhD Student in Cell Biology and Development, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Maristela Ocampos
- Biologist, PhD in Biotechnology and Molecular Biology, Laboratory Neurogene, Florianópolis, SC, Brazil
| | - Ingrid Tremel Barbato
- Biologist and MSc in Chemical Engineering, Laboratory Neurogene, Florianópolis, SC, Brazil
| | - Gisele Rozone de Luca
- Medical Neuropediatrist, Children's Hospital Joana de Gusmão, Florianópolis, SC, Brazil
| | | | | | - Pricila Bernardi
- Medical Geneticist, University Hospital Professor Polydoro Ernani de São Thiago, Florianópolis, SC, Brazil
| | - Angelica Francesca Maris
- Biologist, PhD in Molecular Biology and Genetics, University Professor in the Department of Cell Biology, Embryology and Genetics, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
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Ceballos FC, Joshi PK, Clark DW, Ramsay M, Wilson JF. Runs of homozygosity: windows into population history and trait architecture. Nat Rev Genet 2018; 19:220-234. [PMID: 29335644 DOI: 10.1038/nrg.2017.109] [Citation(s) in RCA: 382] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Long runs of homozygosity (ROH) arise when identical haplotypes are inherited from each parent and thus a long tract of genotypes is homozygous. Cousin marriage or inbreeding gives rise to such autozygosity; however, genome-wide data reveal that ROH are universally common in human genomes even among outbred individuals. The number and length of ROH reflect individual demographic history, while the homozygosity burden can be used to investigate the genetic architecture of complex disease. We discuss how to identify ROH in genome-wide microarray and sequence data, their distribution in human populations and their application to the understanding of inbreeding depression and disease risk.
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Affiliation(s)
- Francisco C Ceballos
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, Johannesburg, South Africa.,Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - David W Clark
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Braamfontein 2000, Johannesburg, South Africa
| | - James F Wilson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK.,Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
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13
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Giacopuzzi E, Gennarelli M, Minelli A, Gardella R, Valsecchi P, Traversa M, Bonvicini C, Vita A, Sacchetti E, Magri C. Exome sequencing in schizophrenic patients with high levels of homozygosity identifies novel and extremely rare mutations in the GABA/glutamatergic pathways. PLoS One 2017; 12:e0182778. [PMID: 28787007 PMCID: PMC5546675 DOI: 10.1371/journal.pone.0182778] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 07/24/2017] [Indexed: 11/18/2022] Open
Abstract
Inbreeding is a known risk factor for recessive Mendelian diseases and previous studies have suggested that it could also play a role in complex disorders, such as psychiatric diseases. Recent inbreeding results in the presence of long runs of homozygosity (ROHs) along the genome, which are also defined as autozygosity regions. Genetic variants in these regions have two alleles that are identical by descent, thus increasing the odds of bearing rare recessive deleterious mutations due to a homozygous state. A recent study showed a suggestive enrichment of long ROHs in schizophrenic patients, suggesting that recent inbreeding could play a role in the disease. To better understand the impact of autozygosity on schizophrenia risk, we selected, from a cohort of 180 Italian patients, seven subjects with extremely high numbers of large ROHs that were likely due to recent inbreeding and characterized the mutational landscape within their ROHs using Whole Exome Sequencing and, gene set enrichment analysis. We identified a significant overlap (17%; empirical p-value = 0.0171) between genes inside ROHs affected by low frequency functional homozygous variants (107 genes) and the group of most promising candidate genes mutated in schizophrenia. Moreover, in four patients, we identified novel and extremely rare damaging mutations in the genes involved in neurodevelopment (MEGF8) and in GABA/glutamatergic synaptic transmission (GAD1, FMN1, ANO2). These results provide insights into the contribution of rare recessive mutations and inbreeding as risk factors for schizophrenia. ROHs that are likely due to recent inbreeding harbor a combination of predisposing low-frequency variants and extremely rare variants that have a high impact on pivotal biological pathways implicated in the disease. In addition, this study confirms that focusing on patients with high levels of homozygosity could be a useful prioritization strategy for discovering new high-impact mutations in genetically complex disorders.
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Affiliation(s)
- Edoardo Giacopuzzi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Massimo Gennarelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Genetic Unit, IRCCS Centro S. Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Alessandra Minelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Rita Gardella
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Paolo Valsecchi
- Department of Clinical and Experimental Sciences, Neuroscience Section, University of Brescia, Brescia, Italy
- Department of Mental Health, Spedali Civili Hospital, Brescia, Italy
| | - Michele Traversa
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Cristian Bonvicini
- Genetic Unit, IRCCS Centro S. Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Antonio Vita
- Department of Clinical and Experimental Sciences, Neuroscience Section, University of Brescia, Brescia, Italy
- Department of Mental Health, Spedali Civili Hospital, Brescia, Italy
| | - Emilio Sacchetti
- Department of Clinical and Experimental Sciences, Neuroscience Section, University of Brescia, Brescia, Italy
- Department of Mental Health, Spedali Civili Hospital, Brescia, Italy
| | - Chiara Magri
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- * E-mail:
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14
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Metzger J, Nolte A, Uhde AK, Hewicker-Trautwein M, Distl O. Whole genome sequencing identifies missense mutation in MTBP in Shar-Pei affected with Autoinflammatory Disease (SPAID). BMC Genomics 2017; 18:348. [PMID: 28472921 PMCID: PMC5418765 DOI: 10.1186/s12864-017-3737-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 04/27/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Autoinflammatory diseases in dogs are characterized by complex disease processes with varying clinical signs. In Shar-Pei, signs of inflammation including fever and arthritis are known to be related with a breed-specific predisposition for Shar-Pei Autoinflammatory Disease (SPAID). RESULTS Clinical and histopathological examinations of two severely SPAID-affected Shar-Pei revealed signs of inflammation including fever, arthritis, and perivascular and diffuse dermatitis in both dogs. A multifocal accumulation of amyloid in different organs was found in one SPAID-affected case. Whole genome sequencing resulted in 37 variants, which were homozygous mutant private mutations in SPAID-affected Shar-Pei. Nine SNVs with predicted damaging effects and three INDELs were further investigated in 102 Shar-Pei affected with SPAID, 62 unaffected Shar-Pei and 162 controls from 11 different dog breeds. The results showed the missense variant MTBP:g.19383758G > A in MTBP to be highly associated with SPAID in Shar-Pei. In the region of this gene a large ROH (runs of homozygosity) region could be detected exclusively in the two investigated SPAID-affected Shar-Pei compared to control dog breeds. No further SPAID-associated variant with predicted high or moderate effects could be found in genes identified in ROH regions. This MTBP variant was predicted to affect the MDN2-binding protein domain and consequently promote proinflammatory reactions. In the investigated group of Shar-Pei older than six years all dogs with the mutant genotype A/A were SPAID-affected whereas SPAID-unaffected dogs harbored the homozygous wildtype (G/G). Shar-Pei with a heterozygous genotype (G/A) were shown to have a 2.13-fold higher risk for disease development, which gave evidence for an incomplete dominant mode of inheritance. CONCLUSIONS The results of this study give strong evidence for a variant in MTBP related with proinflammatory processes via MTBP-MDM2 pathway. Thus, these results enable a reliable detection of SPAID in Shar-Pei dogs.
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Affiliation(s)
- Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17p, 30559 Hannover, Germany
| | - Anna Nolte
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559 Hannover, Germany
| | - Ann-Kathrin Uhde
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559 Hannover, Germany
| | - Marion Hewicker-Trautwein
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559 Hannover, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17p, 30559 Hannover, Germany
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15
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Kumpulainen M, Anderson H, Svevar T, Kangasvuo I, Donner J, Pohjoismäki J. Founder representation and effective population size in old versus young breeds-genetic diversity of Finnish and Nordic Spitz. J Anim Breed Genet 2017; 134:422-433. [DOI: 10.1111/jbg.12262] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 01/27/2017] [Indexed: 11/30/2022]
Affiliation(s)
- M. Kumpulainen
- Finnish Spitz Club / Suomen pystykorvajärjestö; Äänekoski Finland
| | - H. Anderson
- Genoscoper Laboratories Oy; Helsinki Finland
| | - T. Svevar
- Finnish Spitz Club / Suomen pystykorvajärjestö; Malax Finland
| | - I. Kangasvuo
- Finnish Spitz Club / Suomen pystykorvajärjestö; Inari Finland
| | - J. Donner
- Genoscoper Laboratories Oy; Helsinki Finland
| | - J. Pohjoismäki
- Department of Environmental and Biological Sciences; University of Eastern Finland; Joensuu Finland
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16
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Heterozygosity Ratio, a Robust Global Genomic Measure of Autozygosity and Its Association with Height and Disease Risk. Genetics 2016; 204:893-904. [PMID: 27585849 DOI: 10.1534/genetics.116.189936] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/17/2016] [Indexed: 02/06/2023] Open
Abstract
Greater genetic variability in an individual is protective against recessive disease. However, existing quantifications of autozygosity, such as runs of homozygosity (ROH), have proved highly sensitive to genotyping density and have yielded inconclusive results about the relationship of diversity and disease risk. Using genotyping data from three data sets with >43,000 subjects, we demonstrated that an alternative approach to quantifying genetic variability, the heterozygosity ratio, is a robust measure of diversity and is positively associated with the nondisease trait height and several disease phenotypes in subjects of European ancestry. The heterozygosity ratio is the number of heterozygous sites in an individual divided by the number of nonreference homozygous sites and is strongly affected by the degree of genetic admixture of the population and varies across human populations. Unlike quantifications of ROH, the heterozygosity ratio is not sensitive to the density of genotyping performed. Our results establish the heterozygosity ratio as a powerful new statistic for exploring the patterns and phenotypic effects of different levels of genetic variation in populations.
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17
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Iourov IY, Vorsanova SG, Korostelev SA, Zelenova MA, Yurov YB. Long contiguous stretches of homozygosity spanning shortly the imprinted loci are associated with intellectual disability, autism and/or epilepsy. Mol Cytogenet 2015; 8:77. [PMID: 26478745 PMCID: PMC4608298 DOI: 10.1186/s13039-015-0182-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/27/2015] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Long contiguous stretches of homozygosity (LCSH) (regions/runs of homozygosity) are repeatedly detected by single-nucleotide polymorphism (SNP) chromosomal microarrays. Providing important clues regarding parental relatedness (consanguinity), uniparental disomy, chromosomal recombination or rearrangements, LCSH are rarely considered as a possible epigenetic cause of neurodevelopmental disorders. Additionally, despite being relevant to imprinting, LCSH at imprinted loci have not been truly addressed in terms of pathogenicity. In this study, we examined LCSH in children with unexplained intellectual disability, autism, congenital malformations and/or epilepsy focusing on chromosomal regions which harbor imprinted disease genes. RESULTS Out of 267 cases, 14 (5.2 %) were found to have LCSH at imprinted loci associated with a clinical outcome. There were 5 cases of LCSH at 15p11.2, 4 cases of LCSH at 7q31.2, 3 cases of LCSH at 11p15.5, and 2 cases of LCSH at 7q21.3. Apart from a case of LCSH at 7q31.33q32.3 (~4 Mb in size), all causative LCSH were 1-1.5 Mb in size. Clinically, these cases were characterized by a weak resemblance to corresponding imprinting diseases (i.e., Silver-Russell, Beckwith-Wiedemann, and Prader-Willi/Angelman syndromes), exhibiting distinctive intellectual disability, autistic behavior, developmental delay, seizures and/or facial dysmorphisms. Parental consanguinity was detected in 8 cases (3 %), and these cases did not exhibit LCSH at imprinted loci. CONCLUSIONS This study demonstrates that shorter LCSH at chromosomes 7q21.3, 7q31.2, 11p15.5, and 15p11.2 occur with a frequency of about 5 % in the children with intellectual disability, autism, congenital malformations and/or epilepsy. Consequently, this type of epigenetic mutations appears to be the most common one among children with neurodevelopmental diseases. Finally, since LCSH less than 2.5-10 Mb in size are generally ignored in diagnostic SNP microarray studies, one can conclude that an important epigenetic cause of intellectual disability, autism or epilepsy is actually overlooked.
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Affiliation(s)
- Ivan Y Iourov
- Mental Health Research Center, 117152 Moscow, Russia ; Separated Structural Unit "Clinical Research Institute of Pediatrics", Russian National Research Medical University named after N.I. Pirogov, Ministry of Health of Russian Federation, 125412 Moscow, Russia ; Department of Medical Genetics, Russian Medical Academy of Postgraduate Education, 123995 Moscow, Russia
| | - Svetlana G Vorsanova
- Mental Health Research Center, 117152 Moscow, Russia ; Separated Structural Unit "Clinical Research Institute of Pediatrics", Russian National Research Medical University named after N.I. Pirogov, Ministry of Health of Russian Federation, 125412 Moscow, Russia
| | | | - Maria A Zelenova
- Mental Health Research Center, 117152 Moscow, Russia ; Separated Structural Unit "Clinical Research Institute of Pediatrics", Russian National Research Medical University named after N.I. Pirogov, Ministry of Health of Russian Federation, 125412 Moscow, Russia
| | - Yuri B Yurov
- Mental Health Research Center, 117152 Moscow, Russia ; Separated Structural Unit "Clinical Research Institute of Pediatrics", Russian National Research Medical University named after N.I. Pirogov, Ministry of Health of Russian Federation, 125412 Moscow, Russia
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18
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Gamsiz ED, Sciarra LN, Maguire AM, Pescosolido MF, van Dyck LI, Morrow EM. Discovery of Rare Mutations in Autism: Elucidating Neurodevelopmental Mechanisms. Neurotherapeutics 2015; 12:553-71. [PMID: 26105128 PMCID: PMC4489950 DOI: 10.1007/s13311-015-0363-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Autism spectrum disorder (ASD) is a group of highly genetic neurodevelopmental disorders characterized by language, social, cognitive, and behavioral abnormalities. ASD is a complex disorder with a heterogeneous etiology. The genetic architecture of autism is such that a variety of different rare mutations have been discovered, including rare monogenic conditions that involve autistic symptoms. Also, de novo copy number variants and single nucleotide variants contribute to disease susceptibility. Finally, autosomal recessive loci are contributing to our understanding of inherited factors. We will review the progress that the field has made in the discovery of these rare genetic variants in autism. We argue that mutation discovery of this sort offers an important opportunity to identify neurodevelopmental mechanisms in disease. The hope is that these mechanisms will show some degree of convergence that may be amenable to treatment intervention.
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Affiliation(s)
- Ece D. Gamsiz
- />Department of Molecular Biology, Cell Biology and Biochemistry (MCB), and Institute for Brain Science, Brown University, Providence, RI USA
- />Developmental Disorders Genetics Research Program, Emma Pendleton Bradley Hospital and Department of Psychiatry and Human Behavior, Brown University Medical School, Providence, RI USA
| | - Laura N. Sciarra
- />Department of Molecular Biology, Cell Biology and Biochemistry (MCB), and Institute for Brain Science, Brown University, Providence, RI USA
- />Neuroscience Graduate Program (NSGP), Brown University, Providence, RI USA
| | - Abbie M. Maguire
- />Department of Molecular Biology, Cell Biology and Biochemistry (MCB), and Institute for Brain Science, Brown University, Providence, RI USA
- />Molecular Biology, Cell Biology and Biochemistry (MCB) Graduate Training Program, Brown University, Providence, RI USA
| | - Matthew F. Pescosolido
- />Department of Molecular Biology, Cell Biology and Biochemistry (MCB), and Institute for Brain Science, Brown University, Providence, RI USA
- />Neuroscience Graduate Program (NSGP), Brown University, Providence, RI USA
| | - Laura I. van Dyck
- />Department of Molecular Biology, Cell Biology and Biochemistry (MCB), and Institute for Brain Science, Brown University, Providence, RI USA
| | - Eric M. Morrow
- />Department of Molecular Biology, Cell Biology and Biochemistry (MCB), and Institute for Brain Science, Brown University, Providence, RI USA
- />Developmental Disorders Genetics Research Program, Emma Pendleton Bradley Hospital and Department of Psychiatry and Human Behavior, Brown University Medical School, Providence, RI USA
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Belcaro C, Dipresa S, Morini G, Pecile V, Skabar A, Fabretto A. CTNND2 deletion and intellectual disability. Gene 2015; 565:146-9. [PMID: 25839933 DOI: 10.1016/j.gene.2015.03.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/20/2015] [Accepted: 03/24/2015] [Indexed: 01/30/2023]
Abstract
Neurodevelopmental disorders are a group of diseases characterized by either structural or functional alterations. The clinical spectrum can vary from isolated intellectual disability to more complex syndromes. Molecular karyotyping can explain 14%-18% of cases due to the presence of large pathogenic CNVs. Moreover, small CNVs involving single genes might result in a monogenic disease. In this article we report two cases of intragenic CTNND2 deletion, detected by molecular karyotyping, in patients with isolated intellectual disability.
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Affiliation(s)
- Chiara Belcaro
- Department of Medical Sciences, University of Trieste, Italy.
| | - Savina Dipresa
- Department of Medical Sciences, University of Trieste, Italy
| | - Giovanna Morini
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Vanna Pecile
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Aldo Skabar
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Antonella Fabretto
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
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