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Chaves TF, Ocampos M, Barbato IT, de Camargo Pinto LL, de Luca GR, Barbato Filho JH, Bernardi P, Costa Netto Muniz Y, Francesca Maris A. A cohort study of neurodevelopmental disorders and/or congenital anomalies using high resolution chromosomal microarrays in southern Brazil highlighting the significance of ASD. Sci Rep 2024; 14:3762. [PMID: 38355898 PMCID: PMC10867078 DOI: 10.1038/s41598-024-54385-2] [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: 11/10/2023] [Accepted: 02/12/2024] [Indexed: 02/16/2024] Open
Abstract
Chromosomal microarray (CMA) is the reference in evaluation of copy number variations (CNVs) in individuals with neurodevelopmental disorders (NDDs), such as intellectual disability (ID) and/or autism spectrum disorder (ASD), which affect around 3-4% of the world's population. Modern platforms for CMA, also include probes for single nucleotide polymorphisms (SNPs) that detect homozygous regions in the genome, such as long contiguous stretches of homozygosity (LCSH). These regions result from complete or segmental chromosomal homozygosis and may be indicative of uniparental disomy (UPD), inbreeding, population characteristics, as well as replicative DNA repair events. In this retrospective study, we analyzed CMA reading files requested by geneticists and neurologists for diagnostic purposes along with available clinical data. Our objectives were interpreting CNVs and assess the frequencies and implications of LCSH detected by Affymetrix CytoScan HD (41%) or 750K (59%) platforms in 1012 patients from the south of Brazil. The patients were mainly children with NDDs and/or congenital anomalies (CAs). A total of 206 CNVs, comprising 132 deletions and 74 duplications, interpreted as pathogenic, were found in 17% of the patients in the cohort and across all chromosomes. Additionally, 12% presented rare variants of uncertain clinical significance, including LPCNVs, as the only clinically relevant CNV. Within the realm of NDDs, ASD carries a particular importance, owing to its escalating prevalence and its growing repercussions for individuals, families, and communities. ASD was one clinical phenotype, if not the main reason for referral to testing, for about one-third of the cohort, and these patients were further analyzed as a sub-cohort. Considering only the patients with ASD, the diagnostic rate was 10%, within the range reported in the literature (8-21%). It was higher (16%) when associated with dysmorphic features and lower (7%) for "isolated" ASD (without ID and without dysmorphic features). In 953 CMAs of the whole cohort, LCSH (≥ 3 Mbp) were analyzed not only for their potential pathogenic significance but were also explored to identify common LCSH in the South Brazilians population. CMA revealed at least one LCSH in 91% of the patients. For about 11.5% of patients, the LCSH suggested consanguinity from the first to the fifth degree, with a greater probability of clinical impact, and in 2.8%, they revealed a putative UPD. LCSH found at a frequency of 5% or more were considered common LCSH in the general population, allowing us to delineate 10 regions as potentially representing ancestral haplotypes of neglectable clinical significance. The main referrals for CMA were developmental delay (56%), ID (33%), ASD (33%) and syndromic features (56%). Some phenotypes in this population may be predictive of a higher probability of indicating a carrier of a pathogenic CNV. Here, we present the largest report of CMA data in a cohort with NDDs and/or CAs from the South of Brazil. We characterize the rare CNVs found along with the main phenotypes presented by each patient and show the importance and usefulness of LCSH interpretation in CMA results that incorporate SNPs, as well as we illustrate the value of CMA to investigate CNV in ASD.
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Affiliation(s)
- Tiago Fernando Chaves
- Laboratório de Polimorfismos Genéticos (LAPOGE), Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
- Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
| | - Maristela Ocampos
- Laboratory Neurogene (former), Florianopolis, SC, Brazil
- Mercolab Diagnóstica (actual), Florianopolis, SC, Brazil
| | | | | | | | | | - Priscila Bernardi
- University Hospital Professor Polydoro Ernani de São Thiago, Florianópolis, SC, Brazil
| | - Yara Costa Netto Muniz
- Laboratório de Polimorfismos Genéticos (LAPOGE), Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Angelica Francesca Maris
- Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
- Children's Hospital Joana de Gusmão, Florianópolis, SC, Brazil.
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Roy B, Amemasor E, Hussain S, Castro K. UBE3A: The Role in Autism Spectrum Disorders (ASDs) and a Potential Candidate for Biomarker Studies and Designing Therapeutic Strategies. Diseases 2023; 12:7. [PMID: 38248358 PMCID: PMC10814747 DOI: 10.3390/diseases12010007] [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: 11/13/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024] Open
Abstract
Published reports from the CDC's Autism and Development Disabilities Monitoring Networks have shown that an average of 1 in every 44 (2.3%) 8-year-old children were estimated to have ASD in 2018. Many of the ASDs exhibiting varying degrees of autism-like phenotypes have chromosomal anomalies in the Chr15q11-q13 region. Numerous potential candidate genes linked with ASD reside in this chromosomal segment. However, several clinical, in vivo, and in vitro studies selected one gene more frequently than others randomly and unbiasedly. This gene codes for UBE3A or Ubiquitin protein ligase E3A [also known as E6AP ubiquitin-protein ligase (E6AP)], an enzyme involved in the cellular degradation of proteins. This gene has been listed as one of the several genes with a high potential of causing ASD in the Autism Database. The gain of function mutations, triplication, or duplication in the UBE3A gene is also associated with ASDs like Angelman Syndrome (AS) and Dup15q Syndrome. The genetic imprinting of UBE3A in the brain and a preference for neuronal maternal-specific expression are the key features of various ASDs. Since the UBE3A gene is involved in two main important diseases associated with autism-like symptoms, there has been widespread research going on in understanding the link between this gene and autism. Additionally, since no universal methodology or mechanism exists for identifying UBE3A-mediated ASD, it continues to be challenging for neurobiologists, neuroscientists, and clinicians to design therapies or diagnostic tools. In this review, we focus on the structure and functional aspects of the UBE3A protein, discuss the primary relevance of the 15q11-q13 region in the cause of ASDs, and highlight the link between UBE3A and ASD. We try to broaden the knowledge of our readers by elaborating on the possible mechanisms underlying UBE3A-mediated ASDs, emphasizing the usage of UBE3A as a prospective biomarker in the preclinical diagnosis of ASDs and discuss the positive outcomes, advanced developments, and the hurdles in the field of therapeutic strategies against UBE3A-mediated ASDs. This review is novel as it lays a very detailed and comprehensive platform for one of the most important genes associated with diseases showing autistic-like symptoms. Additionally, this review also attempts to lay optimistic feedback on the possible steps for the diagnosis, prevention, and therapy of these UBE3A-mediated ASDs in the upcoming years.
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Affiliation(s)
- Bidisha Roy
- Life Science Centre, Department of Biological Sciences, Rutgers University-Newark, Newark, NJ 07102, USA; (E.A.); (S.H.); (K.C.)
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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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Iourov IY, Gerasimov AP, Zelenova MA, Ivanova NE, Kurinnaia OS, Zabrodskaya YM, Demidova IA, Barantsevich ER, Vasin KS, Kolotii AD, Ushanov VV, Sitovskaya DA, Lobzhanidze TBA, Iuditskaia ME, Iakushev NS, Zhumatov MM, Vorsanova SG, Samochernyh KA. Cytogenomic epileptology. Mol Cytogenet 2023; 16:1. [PMID: 36600272 PMCID: PMC9814426 DOI: 10.1186/s13039-022-00634-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Molecular cytogenetic and cytogenomic studies have made a contribution to genetics of epilepsy. However, current genomic research of this devastative condition is generally focused on the molecular genetic aspects (i.e. gene hunting, detecting mutations in known epilepsy-associated genes, searching monogenic causes of epilepsy). Nonetheless, chromosomal abnormalities and copy number variants (CNVs) represent an important part of genetic defects causing epilepsy. Moreover, somatic chromosomal mosaicism and genome/chromosome instability seem to be a possible mechanism for a wide spectrum of epileptic conditions. This idea becomes even more attracting taking into account the potential of molecular neurocytogenetic (neurocytogenomic) studies of the epileptic brain. Unfortunately, analyses of chromosome numbers and structure in the affected brain or epileptogenic brain foci are rarely performed. Therefore, one may conclude that cytogenomic area of genomic epileptology is poorly researched. Accordingly, molecular cytogenetic and cytogenomic studies of the clinical cohorts and molecular neurocytogenetic analyses of the epileptic brain appear to be required. Here, we have performed a theoretical analysis to define the targets of the aforementioned studies and to highlight future directions for molecular cytogenetic and cytogenomic research of epileptic disorders in the widest sense. To succeed, we have formed a consortium, which is planned to perform at least a part of suggested research. Taking into account the nature of the communication, "cytogenomic epileptology" has been introduced to cover the research efforts in this field of medical genomics and epileptology. Additionally, initial results of studying cytogenomic variations in the Russian neurodevelopmental cohort are reviewed with special attention to epilepsy. In total, we have concluded that (i) epilepsy-associated cytogenomic variations require more profound research; (ii) ontological analyses of epilepsy genes affected by chromosomal rearrangements and/or CNVs with unraveling pathways implicating epilepsy-associated genes are beneficial for epileptology; (iii) molecular neurocytogenetic (neurocytogenomic) analysis of postoperative samples are warranted in patients suffering from epileptic disorders.
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Affiliation(s)
- Ivan Y. Iourov
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia ,grid.445984.00000 0001 2224 0652Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia
| | - Alexandr P. Gerasimov
- grid.452417.1Research Laboratory of Pediatric Neurosurgery, Polenov Neurosurgical Institute, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Maria A. Zelenova
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Natalya E. Ivanova
- grid.452417.1Scientific Department of Polenov Neurosurgical Institute, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Oksana S. Kurinnaia
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Yulia M. Zabrodskaya
- grid.452417.1Research Laboratory of Pathomorphology of the Nervous System, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Irina A. Demidova
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Evgeny R. Barantsevich
- grid.412460.5Postgraduate Neurology and Manual Medicine Department, Pavlov First Saint-Petersburg State Medical University, Saint Petersburg, Russia
| | - Kirill S. Vasin
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Alexey D. Kolotii
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Vseslav V. Ushanov
- grid.452417.1Department of Neurosurgery, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Darya A. Sitovskaya
- grid.452417.1Research Laboratory of Pathomorphology of the Nervous System, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Timur B.-A. Lobzhanidze
- grid.445931.e0000 0004 0471 4078Saint Petersburg State Pediatric Medical University, Saint Petersburg, Russia
| | - Maria E. Iuditskaia
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Nikita S. Iakushev
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Muslim M. Zhumatov
- grid.445931.e0000 0004 0471 4078Saint Petersburg State Pediatric Medical University, Saint Petersburg, Russia
| | - Svetlana G. Vorsanova
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Konstantin A. Samochernyh
- grid.452417.1Polenov Neurosurgical Institute, Almazov National Medical Research Centre, Saint Petersburg, Russia
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Mishra A, Prabha PK, Singla R, Kaur G, Sharma AR, Joshi R, Suroy B, Medhi B. Epigenetic Interface of Autism Spectrum Disorders (ASDs): Implications of Chromosome 15q11-q13 Segment. ACS Chem Neurosci 2022; 13:1684-1696. [PMID: 35635007 DOI: 10.1021/acschemneuro.2c00060] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Autism spectrum disorders (ASDs) are multifactorial in nature and include both genetic and environmental factors. The increasing evidence advocates an important role of epigenetics in ASD etiology. One of the most common forms of epigenetic changes observed in the case of neurodevelopmental disorders is imprinting which is tightly regulated by developmental and tissue-specific mechanisms. Interestingly, many of these disorders that demonstrate autism-like phenotypes at varying degrees have found involvement of chromosome 15q11-q13 segment. Numerous studies demonstrate occurrence of ASD in the presence of chromosomal abnormalities located mainly in Chr15q11-q13 region. Several plausible candidate genes associated with ASD are in this chromosomal segment, including gamma aminobutyric acid A (GABAA) receptor genes GABRB3, GABRA5 and GABRG3, UBE3A, ATP 10A, MKRN3, ZNF, MAGEL2, Necdin (NDN), and SNRPN. The main objective of this review is to highlight the contribution of epigenetic modulations in chromosome 15q11-q13 segment toward the genetic etiology and pathophysiology of ASD. The present review reports the abnormalities in epigenetic regulation on genes and genomic regions located on chromosome 15 in relation to either syndromic (15q11-q13 maternal duplication) or nonsyndromic forms of ASD. Furthermore, studies reviewed in this article demonstrate conditions in which epigenetic dysregulation has been found to be a pathological factor for ASD development, thereby supporting a role for epigenetics in the multifactorial etiologies of ASD. Also, on the basis of the evidence found so far, we strongly emphasize the need to develop future therapeutic strategies as well as screening procedures for ASD that target mechanisms involving genes located on the chromosomal 15q11-q13 segment.
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Affiliation(s)
- Abhishek Mishra
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Praisy K Prabha
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Rubal Singla
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Gurjeet Kaur
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Amit Raj Sharma
- Dept. of Neurology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Rupa Joshi
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Benjamin Suroy
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Bikash Medhi
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
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Vorsanova SG, Demidova IA, Kolotii AD, Kurinnaia OS, Kravets VS, Soloviev IV, Yurov YB, Iourov IY. Klinefelter syndrome mosaicism in boys with neurodevelopmental disorders: a cohort study and an extension of the hypothesis. Mol Cytogenet 2022; 15:8. [PMID: 35248137 PMCID: PMC8897849 DOI: 10.1186/s13039-022-00588-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/21/2022] [Indexed: 01/14/2023] Open
Abstract
Abstract
Background
Klinefelter syndrome is a common chromosomal (aneuploidy) disorder associated with an extra X chromosome in males. Regardless of numerous studies dedicated to somatic gonosomal mosaicism, Klinefelter syndrome mosaicism (KSM) has not been systematically addressed in clinical cohorts. Here, we report on the evaluation of KSM in a large cohort of boys with neurodevelopmental disorders. Furthermore, these data have been used for an extension of the hypothesis, which we have recently proposed in a report on Turner’s syndrome mosaicism in girls with neurodevelopmental disorders.
Results
Klinefelter syndrome-associated karyotypes were revealed in 49 (1.1%) of 4535 boys. Twenty one boys (0.5%) were non-mosaic 47,XXY individuals. KSM was found in 28 cases (0.6%) and manifested as mosaic aneuploidy (50,XXXXXY; 49,XXXXY; 48,XXXY; 48,XXYY; 47,XXY; and 45,X were detected in addition to 47,XXY/46,XY) and mosaic supernumerary marker chromosomes derived from chromosome X (ring chromosomes X and rearranged chromosomes X). It is noteworthy that KSM was concomitant with Rett-syndrome-like phenotypes caused by MECP2 mutations in 5 boys (0.1%).
Conclusion
Our study provides data on the occurrence of KSM in neurodevelopmental disorders among males. Accordingly, it is proposed that KSM may be a possible element of pathogenic cascades in psychiatric and neurodegenerative diseases. These observations allowed us to extend the hypothesis proposed in our previous report on the contribution of somatic gonosomal mosaicism (Turner’s syndrome mosaicism) to the etiology of neurodevelopmental disorders. Thus, it seems to be important to monitor KSM (a possible risk factor or a biomarker for adult-onset multifactorial brain diseases) and analysis of neuromarkers for aging in individuals with Klinefelter syndrome. Cases of two or more supernumerary chromosomes X were all associated with KSM. Finally, Rett syndrome-like phenotypes associated with KSM appear to be more common in males with neurodevelopmental disorders than previously recognized.
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Pellikaan K, van Woerden GM, Kleinendorst L, Rosenberg AGW, Horsthemke B, Grosser C, van Zutven LJCM, van Rossum EFC, van der Lely AJ, Resnick JL, Brüggenwirth HT, van Haelst MM, de Graaff LCG. The Diagnostic Journey of a Patient with Prader-Willi-Like Syndrome and a Unique Homozygous SNURF-SNRPN Variant; Bio-Molecular Analysis and Review of the Literature. Genes (Basel) 2021; 12:genes12060875. [PMID: 34200226 PMCID: PMC8227738 DOI: 10.3390/genes12060875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
Prader–Willi syndrome (PWS) is a rare genetic condition characterized by hypotonia, intellectual disability, and hypothalamic dysfunction, causing pituitary hormone deficiencies and hyperphagia, ultimately leading to obesity. PWS is most often caused by the loss of expression of a cluster of genes on chromosome 15q11.2-13. Patients with Prader–Willi-like syndrome (PWLS) display features of the PWS phenotype without a classical PWS genetic defect. We describe a 46-year-old patient with PWLS, including hypotonia, intellectual disability, hyperphagia, and pituitary hormone deficiencies. Routine genetic tests for PWS were normal, but a homozygous missense variant NM_003097.3(SNRPN):c.193C>T, p.(Arg65Trp) was identified. Single nucleotide polymorphism array showed several large regions of homozygosity, caused by high-grade consanguinity between the parents. Our functional analysis, the ‘Pipeline for Rapid in silico, in vivo, in vitro Screening of Mutations’ (PRiSM) screen, showed that overexpression of SNRPN-p.Arg65Trp had a dominant negative effect, strongly suggesting pathogenicity. However, it could not be confirmed that the variant was responsible for the phenotype of the patient. In conclusion, we present a unique homozygous missense variant in SNURF-SNRPN in a patient with PWLS. We describe the diagnostic trajectory of this patient and the possible contributors to her phenotype in light of the current literature on the genotype–phenotype relationship in PWS.
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Affiliation(s)
- Karlijn Pellikaan
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (K.P.); (A.G.W.R.); (E.F.C.v.R.); (A.J.v.d.L.)
- Dutch Centre of Reference for Prader-Willi Syndrome, 3015 GD Rotterdam, The Netherlands
| | - Geeske M. van Woerden
- Department of Neuroscience, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands;
- The ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands; (L.J.C.M.v.Z.); (H.T.B.)
| | - Lotte Kleinendorst
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, 1081 HV Amsterdam, The Netherlands; (L.K.); (M.M.v.H.)
| | - Anna G. W. Rosenberg
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (K.P.); (A.G.W.R.); (E.F.C.v.R.); (A.J.v.d.L.)
- Dutch Centre of Reference for Prader-Willi Syndrome, 3015 GD Rotterdam, The Netherlands
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (B.H.); (C.G.)
| | - Christian Grosser
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (B.H.); (C.G.)
- Praxis für Humangenetik Tübingen, 72076 Tuebingen, Germany
| | - Laura J. C. M. van Zutven
- Department of Clinical Genetics, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands; (L.J.C.M.v.Z.); (H.T.B.)
| | - Elisabeth F. C. van Rossum
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (K.P.); (A.G.W.R.); (E.F.C.v.R.); (A.J.v.d.L.)
- Obesity Center CGG, Erasmus MC, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands
| | - Aart J. van der Lely
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (K.P.); (A.G.W.R.); (E.F.C.v.R.); (A.J.v.d.L.)
| | - James L. Resnick
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA;
| | - Hennie T. Brüggenwirth
- Department of Clinical Genetics, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands; (L.J.C.M.v.Z.); (H.T.B.)
| | - Mieke M. van Haelst
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, 1081 HV Amsterdam, The Netherlands; (L.K.); (M.M.v.H.)
| | - Laura C. G. de Graaff
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (K.P.); (A.G.W.R.); (E.F.C.v.R.); (A.J.v.d.L.)
- Dutch Centre of Reference for Prader-Willi Syndrome, 3015 GD Rotterdam, The Netherlands
- The ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands
- Academic Centre for Growth Disorders, Erasmus MC Rotterdam, 3015 GD Rotterdam, The Netherlands
- Correspondence: ; Tel.: +31-618843010
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Jiang H, Ping Z, Wang J, Liu X, Jin Y, Li S, Zhou C, Huang P, Jin Y, Ai L, Chen J. A Beckwith-Wiedemann syndrome case with de novo 24 Mb duplication of chromosome 11p15.5p14.3. Mol Cytogenet 2021; 14:14. [PMID: 33658067 PMCID: PMC7931524 DOI: 10.1186/s13039-021-00532-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 01/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular genetic testing for the 11p15-associated imprinting disorder Beckwith-Wiedemann syndrome (BWS) is challenging because of the molecular heterogeneity and complexity of the affected imprinted regions. An integrated molecular approach to analyze the epigenetic-genetic alterations is required for accurate diagnosis of BWS. CASE PRESENTATION We reported a Chinese case with BWS detected by SNP array analysis and methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA). The genetic analysis showed a de novo duplication of 24 Mb at 11p15.5p14.3 is much longer than ever reported. MS-MLPA showed copy number changes with a peak height ratio value of 1.5 (three copies) at 11p15. The duplication of paternal origin with increase of methylation index of 0.68 at H19 and decreased methylation index of 0.37 at KCNQ1OT1. CONCLUSION Combined chromosome microarray analysis and methylation profiling provided reliable diagnosis for this paternally derived duplication of BWS. The phenotype associated with 11p15 duplications depends on the size, genetic content, parental inheritance and imprinting status. Identification of these rare duplications is crucial for genetic counselling.
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Affiliation(s)
- Huling Jiang
- Department of Prenatal Diagnosis Center, Maternity and Child Health Care Affiliated Hospital, Jiaxing University, Jiaxing, 314000, China
| | - Zepeng Ping
- Department of Prenatal Diagnosis Center, Maternity and Child Health Care Affiliated Hospital, Jiaxing University, Jiaxing, 314000, China
| | - Jianguo Wang
- Department of Prenatal Diagnosis Center, Maternity and Child Health Care Affiliated Hospital, Jiaxing University, Jiaxing, 314000, China
| | - Xiaodan Liu
- Department of Prenatal Diagnosis Center, Maternity and Child Health Care Affiliated Hospital, Jiaxing University, Jiaxing, 314000, China
| | - Yuxia Jin
- Department of Prenatal Diagnosis Center, Maternity and Child Health Care Affiliated Hospital, Jiaxing University, Jiaxing, 314000, China
| | - Suping Li
- Department of Prenatal Diagnosis Center, Maternity and Child Health Care Affiliated Hospital, Jiaxing University, Jiaxing, 314000, China
| | - Chiyan Zhou
- Department of Prenatal Diagnosis Center, Maternity and Child Health Care Affiliated Hospital, Jiaxing University, Jiaxing, 314000, China
| | - Pinghua Huang
- Department of Prenatal Diagnosis Center, Maternity and Child Health Care Affiliated Hospital, Jiaxing University, Jiaxing, 314000, China
| | - Yi Jin
- Department of Prenatal Diagnosis Center, Maternity and Child Health Care Affiliated Hospital, Jiaxing University, Jiaxing, 314000, China
| | - Ling Ai
- Department of Prenatal Diagnosis Center, Maternity and Child Health Care Affiliated Hospital, Jiaxing University, Jiaxing, 314000, China
| | - Jie Chen
- Department of Prenatal Diagnosis Center, Maternity and Child Health Care Affiliated Hospital, Jiaxing University, Jiaxing, 314000, China. .,Department of Pediatric Surgery, Xinhua Hospital Affiliated To Shanghai Jiao Tong University School Of Medicine, Shanghai, 200092, China.
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10
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Neklyudova AK, Portnova GV, Rebreikina AB, Voinova VY, Vorsanova SG, Iourov IY, Sysoeva OV. 40-Hz Auditory Steady-State Response (ASSR) as a Biomarker of Genetic Defects in the SHANK3 Gene: A Case Report of 15-Year-Old Girl with a Rare Partial SHANK3 Duplication. Int J Mol Sci 2021; 22:ijms22041898. [PMID: 33673024 PMCID: PMC7917917 DOI: 10.3390/ijms22041898] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/26/2021] [Accepted: 02/09/2021] [Indexed: 12/02/2022] Open
Abstract
SHANK3 encodes a scaffold protein involved in postsynaptic receptor density in glutamatergic synapses, including those in the parvalbumin (PV)+ inhibitory neurons—the key players in the generation of sensory gamma oscillations, such as 40-Hz auditory steady-state response (ASSR). However, 40-Hz ASSR was not studied in relation to SHANK3 functioning. Here, we present a 15-year-old girl (SH01) with previously unreported duplication of the first seven exons of the SHANK3 gene (22q13.33). SH01’s electroencephalogram (EEG) during 40-Hz click trains of 500 ms duration binaurally presented with inter-trial intervals of 500–800 ms were compared with those from typically developing children (n = 32). SH01 was diagnosed with mild mental retardation and learning disabilities (F70.88), dysgraphia, dyslexia, and smaller vocabulary than typically developing (TD) peers. Her clinical phenotype resembled the phenotype of previously described patients with 22q13.33 microduplications (≈30 reported so far). SH01 had mild autistic symptoms but below the threshold for ASD diagnosis and microcephaly. No seizures or MRI abnormalities were reported. While SH01 had relatively preserved auditory event-related potential (ERP) with slightly attenuated P1, her 40-Hz ASSR was totally absent significantly deviating from TD’s ASSR. The absence of 40-Hz ASSR in patients with microduplication, which affected the SHANK3 gene, indicates deficient temporal resolution of the auditory system, which might underlie language problems and represent a neurophysiological biomarker of SHANK3 abnormalities.
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Affiliation(s)
- Anastasia K. Neklyudova
- Laboratory of Human Higher Nervous Activity, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Science, 117485 Moscow, Russia; (A.K.N.); (G.V.P.); (A.B.R.)
| | - Galina V. Portnova
- Laboratory of Human Higher Nervous Activity, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Science, 117485 Moscow, Russia; (A.K.N.); (G.V.P.); (A.B.R.)
| | - Anna B. Rebreikina
- Laboratory of Human Higher Nervous Activity, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Science, 117485 Moscow, Russia; (A.K.N.); (G.V.P.); (A.B.R.)
| | - Victoria Yu Voinova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov, Russian National Research Medical University, Ministry of Health of Russian Federation, 125412 Moscow, Russia; (V.Y.V.); (S.G.V.); (I.Y.I.)
- Mental Health Research Center, 117152 Moscow, Russia
| | - Svetlana G. Vorsanova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov, Russian National Research Medical University, Ministry of Health of Russian Federation, 125412 Moscow, Russia; (V.Y.V.); (S.G.V.); (I.Y.I.)
- Mental Health Research Center, 117152 Moscow, Russia
| | - Ivan Y. Iourov
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov, Russian National Research Medical University, Ministry of Health of Russian Federation, 125412 Moscow, Russia; (V.Y.V.); (S.G.V.); (I.Y.I.)
- Mental Health Research Center, 117152 Moscow, Russia
| | - Olga V. Sysoeva
- Laboratory of Human Higher Nervous Activity, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Science, 117485 Moscow, Russia; (A.K.N.); (G.V.P.); (A.B.R.)
- Correspondence:
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11
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The Cytogenomic "Theory of Everything": Chromohelkosis May Underlie Chromosomal Instability and Mosaicism in Disease and Aging. Int J Mol Sci 2020; 21:ijms21218328. [PMID: 33171981 PMCID: PMC7664247 DOI: 10.3390/ijms21218328] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 01/28/2023] Open
Abstract
Mechanisms for somatic chromosomal mosaicism (SCM) and chromosomal instability (CIN) are not completely understood. During molecular karyotyping and bioinformatic analyses of children with neurodevelopmental disorders and congenital malformations (n = 612), we observed colocalization of regular chromosomal imbalances or copy number variations (CNV) with mosaic ones (n = 47 or 7.7%). Analyzing molecular karyotyping data and pathways affected by CNV burdens, we proposed a mechanism for SCM/CIN, which had been designated as “chromohelkosis” (from the Greek words chromosome ulceration/open wound). Briefly, structural chromosomal imbalances are likely to cause local instability (“wreckage”) at the breakpoints, which results either in partial/whole chromosome loss (e.g., aneuploidy) or elongation of duplicated regions. Accordingly, a function for classical/alpha satellite DNA (protection from the wreckage towards the centromere) has been hypothesized. Since SCM and CIN are ubiquitously involved in development, homeostasis and disease (e.g., prenatal development, cancer, brain diseases, aging), we have metaphorically (ironically) designate the system explaining chromohelkosis contribution to SCM/CIN as the cytogenomic “theory of everything”, similar to the homonymous theory in physics inasmuch as it might explain numerous phenomena in chromosome biology. Recognizing possible empirical and theoretical weaknesses of this “theory”, we nevertheless believe that studies of chromohelkosis-like processes are required to understand structural variability and flexibility of the genome.
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12
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Ozyilmaz B, Kirbiyik O, Ozdemir TR, Kaya OO, Kutbay YB, Erdogan KM, Guvenc MS, Koc A. The Efficiency of SNP-Based Microarrays in the Detection of Copy-Neutral Events at 15q11.2 and 11p15.5 Loci. J Pediatr Genet 2019; 9:9-18. [PMID: 31976138 DOI: 10.1055/s-0039-1698420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/30/2019] [Indexed: 12/24/2022]
Abstract
Prader-Willi, Angelman, Beckwith-Wiedemann, and Russell-Silver are imprinting syndromes. In this study, we aimed to compare the efficiency of single nucleotide polymorphism (SNP) microarray analysis with methylation-specific Multiplex ligation-dependent probe amplification (MS-MLPA) in the detection of uniparental disomy in these syndromes. The patient samples with regions of loss of heterozygosity (LOH), covering 15q11.2 and 11p15.5 critical loci, were analyzed with MS-MLPA to demonstrate the efficiency of SNP microarray in the detection of uniparental disomy (UPD). In a total of seven patients, LOH covering 15q11.2 and 11p15.5 critical loci was detected. Two (28.6%) of these seven patients showed aberrant methylation (suggesting UPD) in MS-MLPA. SNP microarray is a useful tool in the detection of LOH; however, it should be used with caution, since false-positive or false-negative LOH results can be obtained. Although methylation analysis is recommended as the first tier test in the diagnosis of most of the imprinting disorders, combining methylation analysis with SNP microarray can enhance our evaluation process.
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Affiliation(s)
- Berk Ozyilmaz
- Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
| | - Ozgur Kirbiyik
- Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
| | - Taha R Ozdemir
- Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
| | - Ozge Ozer Kaya
- Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
| | - Yasar B Kutbay
- Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
| | - Kadri M Erdogan
- Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
| | - Merve Saka Guvenc
- Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
| | - Altug Koc
- Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
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13
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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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14
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Fedorenko OY, Golimbet VE, Ivanova SА, Levchenko А, Gainetdinov RR, Semke AV, Simutkin GG, Gareeva АE, Glotov АS, Gryaznova A, Iourov IY, Krupitsky EM, Lebedev IN, Mazo GE, Kaleda VG, Abramova LI, Oleichik IV, Nasykhova YA, Nasyrova RF, Nikolishin AE, Kasyanov ED, Rukavishnikov GV, Timerbulatov IF, Brodyansky VM, Vorsanova SG, Yurov YB, Zhilyaeva TV, Sergeeva AV, Blokhina EA, Zvartau EE, Blagonravova AS, Aftanas LI, Bokhan NА, Kekelidze ZI, Klimenko TV, Anokhina IP, Khusnutdinova EK, Klyushnik TP, Neznanov NG, Stepanov VA, Schulze TG, Kibitov АО. Opening up new horizons for psychiatric genetics in the Russian Federation: moving toward a national consortium. Mol Psychiatry 2019; 24:1099-1111. [PMID: 30664668 PMCID: PMC6756082 DOI: 10.1038/s41380-019-0354-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 12/27/2018] [Accepted: 12/31/2018] [Indexed: 12/18/2022]
Abstract
We provide an overview of the recent achievements in psychiatric genetics research in the Russian Federation and present genotype-phenotype, population, epigenetic, cytogenetic, functional, ENIGMA, and pharmacogenetic studies, with an emphasis on genome-wide association studies. The genetic backgrounds of mental illnesses in the polyethnic and multicultural population of the Russian Federation are still understudied. Furthermore, genetic, genomic, and pharmacogenetic data from the Russian Federation are not adequately represented in the international scientific literature, are currently not available for meta-analyses and have never been compared with data from other populations. Most of these problems cannot be solved by individual centers working in isolation but warrant a truly collaborative effort that brings together all the major psychiatric genetic research centers in the Russian Federation in a national consortium. For this reason, we have established the Russian National Consortium for Psychiatric Genetics (RNCPG) with the aim to strengthen the power and rigor of psychiatric genetics research in the Russian Federation and enhance the international compatibility of this research.The consortium is set up as an open organization that will facilitate collaborations on complex biomedical research projects in human mental health in the Russian Federation and abroad. These projects will include genotyping, sequencing, transcriptome and epigenome analysis, metabolomics, and a wide array of other state-of-the-art analyses. Here, we discuss the challenges we face and the approaches we will take to unlock the huge potential that the Russian Federation holds for the worldwide psychiatric genetics community.
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Affiliation(s)
- Olga Yu Fedorenko
- Mental Health Research Institute, Tomsk National Research Medical Center of Russian Academy of Sciences, Tomsk, Russian Federation.
- National Research Tomsk Polytechnic University, Tomsk, Russian Federation.
| | | | - Svetlana А Ivanova
- Mental Health Research Institute, Tomsk National Research Medical Center of Russian Academy of Sciences, Tomsk, Russian Federation
- National Research Tomsk Polytechnic University, Tomsk, Russian Federation
| | - Аnastasia Levchenko
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russian Federation
| | - Raul R Gainetdinov
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russian Federation
| | - Arkady V Semke
- Mental Health Research Institute, Tomsk National Research Medical Center of Russian Academy of Sciences, Tomsk, Russian Federation
| | - German G Simutkin
- Mental Health Research Institute, Tomsk National Research Medical Center of Russian Academy of Sciences, Tomsk, Russian Federation
| | - Аnna E Gareeva
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, Russian Federation
- Federal State Educational Institution of Highest Education Bashkir State Medical University of Public Health Ministry of Russian Federation, Ufa, Russian Federation
| | - Аndrey S Glotov
- Laboratory of Biobanking and Genomic Medicine of Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russian Federation
| | - Anna Gryaznova
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU, Munich, Germany
| | - Ivan Y Iourov
- Mental Health Research Center, Moscow, Russian Federation
| | - Evgeny M Krupitsky
- V.M. Bekhterev National Medical Research Center for Psychiatry and Neurology, Saint Petersburg, Russian Federation
| | - Igor N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of Russian Academy of Sciences, Tomsk, Russian Federation
| | - Galina E Mazo
- V.M. Bekhterev National Medical Research Center for Psychiatry and Neurology, Saint Petersburg, Russian Federation
| | | | | | | | - Yulia A Nasykhova
- Laboratory of Biobanking and Genomic Medicine of Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russian Federation
| | - Regina F Nasyrova
- V.M. Bekhterev National Medical Research Center for Psychiatry and Neurology, Saint Petersburg, Russian Federation
| | - Anton E Nikolishin
- Serbsky National Medical Research Center on Psychiatry and Addictions, Moscow, Russian Federation
| | - Evgeny D Kasyanov
- V.M. Bekhterev National Medical Research Center for Psychiatry and Neurology, Saint Petersburg, Russian Federation
| | - Grigory V Rukavishnikov
- V.M. Bekhterev National Medical Research Center for Psychiatry and Neurology, Saint Petersburg, Russian Federation
| | - Ilgiz F Timerbulatov
- Federal State Educational Institution of Highest Education Bashkir State Medical University of Public Health Ministry of Russian Federation, Ufa, Russian Federation
| | - Vadim M Brodyansky
- Serbsky National Medical Research Center on Psychiatry and Addictions, Moscow, Russian Federation
| | - Svetlana G Vorsanova
- Veltischev Research and Clinical Institute for Pediatrics, the Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Yury B Yurov
- Mental Health Research Center, Moscow, Russian Federation
| | - Tatyana V Zhilyaeva
- Privolzhskiy Research Medical University, Nizhny Novgorod, Russian Federation
| | | | - Elena A Blokhina
- First Saint Petersburg Pavlov State Medical University, Saint Petersburg, Russian Federation
| | - Edwin E Zvartau
- First Saint Petersburg Pavlov State Medical University, Saint Petersburg, Russian Federation
| | - Anna S Blagonravova
- Privolzhskiy Research Medical University, Nizhny Novgorod, Russian Federation
| | - Lyubomir I Aftanas
- Federal State Scientific Budgetary Institution "Scientific Research Institute of Physiology and Basic Medicine,", Novosibirsk, Russian Federation
| | - Nikolay А Bokhan
- Mental Health Research Institute, Tomsk National Research Medical Center of Russian Academy of Sciences, Tomsk, Russian Federation
- National Research Tomsk State University, Tomsk, Russian Federation
| | - Zurab I Kekelidze
- Serbsky National Medical Research Center on Psychiatry and Addictions, Moscow, Russian Federation
| | - Tatyana V Klimenko
- Serbsky National Medical Research Center on Psychiatry and Addictions, Moscow, Russian Federation
| | - Irina P Anokhina
- Serbsky National Medical Research Center on Psychiatry and Addictions, Moscow, Russian Federation
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, Russian Federation
- Federal State Educational Institution of Highest Education Bashkir State Medical University of Public Health Ministry of Russian Federation, Ufa, Russian Federation
| | | | - Nikolay G Neznanov
- V.M. Bekhterev National Medical Research Center for Psychiatry and Neurology, Saint Petersburg, Russian Federation
| | - Vadim A Stepanov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of Russian Academy of Sciences, Tomsk, Russian Federation
- National Research Tomsk State University, Tomsk, Russian Federation
| | - Thomas G Schulze
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU, Munich, Germany
| | - Аleksandr О Kibitov
- Serbsky National Medical Research Center on Psychiatry and Addictions, Moscow, Russian Federation
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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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17
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Iourov IY, Zelenova MA, Vorsanova SG, Voinova VV, Yurov YB. 4q21.2q21.3 Duplication: Molecular and Neuropsychological Aspects. Curr Genomics 2018; 19:173-178. [PMID: 29606904 PMCID: PMC5850505 DOI: 10.2174/1389202918666170717161426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 11/20/2016] [Accepted: 01/20/2017] [Indexed: 12/15/2022] Open
Abstract
During the last decades, a large amount of newly described microduplications and microdeletions associated with intellectual disability (ID) and related neuropsychiatric diseases have been discovered. However, due to natural limitations, a significant part of them has not been the focus of multidisciplinary approaches. Here, we address previously undescribed chromosome 4q21.2q21.3 microduplication for gene prioritization, evaluation of cognitive abilities and estimation of genomic mechanisms for brain dysfunction by molecular cytogenetic (cytogenomic) and gene expression (meta-) analyses as well as for neuropsychological assessment. We showed that duplication at 4q21.2q21.3 is associated with moderate ID, cognitive deficits, developmental delay, language impairment, memory and attention problems, facial dysmorphisms, congenital heart defect and dentinogenesis imperfecta. Gene-expression meta-analysis prioritized the following genes: ENOPH1, AFF1, DSPP, SPARCL1, and SPP1. Furthermore, genotype/phenotype correlations allowed the attribution of each gene gain to each phenotypic feature. Neuropsychological testing showed visual-perceptual and fine motor skill deficits, reduced attention span, deficits of the nominative function and problems in processing both visual and aural information. Finally, emerging approaches including molecular cytogenetic, bioinformatic (genome/epigenome meta-analysis) and neuropsychological methods are concluded to be required for comprehensive neurological, genetic and neuropsychological descriptions of new genomic rearrangements/diseases associated with ID.
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Affiliation(s)
- Ivan Y Iourov
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Department of Medical Genetics, Russian Medical Academy of Postgraduate Education, Ministry of Health, Moscow, Russian Federation
| | - Maria A Zelenova
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Svetlana G Vorsanova
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Victoria V Voinova
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Yuri B Yurov
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Moscow State University of Psychology and Education, Moscow, Russian Federation
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18
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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: 361] [Impact Index Per Article: 60.2] [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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19
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Serologic Markers of Autism Spectrum Disorder. J Mol Neurosci 2017; 62:420-429. [PMID: 28730336 DOI: 10.1007/s12031-017-0950-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/12/2017] [Indexed: 12/27/2022]
Abstract
According to WHO data, about 67 million people worldwide are affected by autism, and this number grows by 14% annually. Among the possible causes of autism are genetic modifications, organic lesions of the central nervous system, metabolic disorders, influence of viral and bacterial infections, chemical influence to the mother's body during pregnancy, etc. The conducted research shows that research papers published until today do not name any potential protein markers that meet the requirements of the basic parameters for evaluating the efficiency of disease diagnostics, in particular high sensitivity, specificity, and accuracy. Conducting proteomic research on a big scale in order to detect serologic markers of protein nature associated with development of autism spectrum disorders seems to be highly relevant.
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20
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Aypar U, Hoppman NL, Thorland EC, Dawson DB. Patients with mosaic methylation patterns of the Prader-Willi/Angelman Syndrome critical region exhibit AS-like phenotypes with some PWS features. Mol Cytogenet 2016; 9:26. [PMID: 27006693 PMCID: PMC4802915 DOI: 10.1186/s13039-016-0233-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/09/2016] [Indexed: 01/29/2023] Open
Abstract
Background Loss of expression of imprinted genes in the 15q11.2-q13 region is known to cause either Prader-Willi syndrome (PWS) or Angelman syndrome (AS), depending on the parent of origin. In some patients (1 % in PWS and 2–4 % in AS), the disease is due to aberrant imprinting or gene silencing, or both. Results We report here a 4-year-old boy on whom a chromosomal microarray (CMA) was performed due to mild hand tremors, mild developmental delays, and clumsiness. CMA revealed absence of heterozygosity (AOH) spanning the entire chromosome 15, suggesting uniparental isodisomy 15. The patient had no definitive phenotypic features of PWS or AS. Methylation-sensitive multiplex ligation-dependent probe amplification (MS-MLPA) was performed to determine the parent of origin of the uniparental disomy (UPD) by examining methylation status at maternally imprinted sites. Interestingly, our patient had a mosaic methylation pattern. We identified nine additional previously tested patients with a similar mosaic methylation pattern. CMA was performed on these individuals retrospectively to test whether patients with mosaic methylation are more likely to have UPD of chromosome 15. Of the nine patients, only one had regions of AOH on chromosome 15; however, this patient had numerous regions of AOH on multiple chromosomes suggestive of consanguinity. Conclusion The patients with mosaic methylation had milder or atypical features of AS, and the majority also had some features characteristic of PWS. We suggest that quantitative methylation analysis be performed for cases of atypical PWS or AS. It is also important to follow up with methylation testing when whole-chromosome isodisomy is detected.
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Affiliation(s)
- Umut Aypar
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 USA
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 USA
| | - Erik C Thorland
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 USA
| | - D Brian Dawson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 USA
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