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Posar A, Visconti P, Magini P, Ambrosini E, Severi G, Seri M. Deletion of 4q13.2q21.1 chromosome and autism spectrum disorder. J Pediatr Neurosci 2022. [DOI: 10.4103/jpn.jpn_98_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Liu L, Feng X, Li H, Cheng Li S, Qian Q, Wang Y. Deep learning model reveals potential risk genes for ADHD, especially Ephrin receptor gene EPHA5. Brief Bioinform 2021; 22:bbab207. [PMID: 34109382 PMCID: PMC8575025 DOI: 10.1093/bib/bbab207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/30/2021] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
Attention deficit hyperactivity disorder (ADHD) is a common neurodevelopmental disorder. Although genome-wide association studies (GWAS) identify the risk ADHD-associated variants and genes with significant P-values, they may neglect the combined effect of multiple variants with insignificant P-values. Here, we proposed a convolutional neural network (CNN) to classify 1033 individuals diagnosed with ADHD from 950 healthy controls according to their genomic data. The model takes the single nucleotide polymorphism (SNP) loci of P-values $\le{1\times 10^{-3}}$, i.e. 764 loci, as inputs, and achieved an accuracy of 0.9018, AUC of 0.9570, sensitivity of 0.8980 and specificity of 0.9055. By incorporating the saliency analysis for the deep learning network, a total of 96 candidate genes were found, of which 14 genes have been reported in previous ADHD-related studies. Furthermore, joint Gene Ontology enrichment and expression Quantitative Trait Loci analysis identified a potential risk gene for ADHD, EPHA5 with a variant of rs4860671. Overall, our CNN deep learning model exhibited a high accuracy for ADHD classification and demonstrated that the deep learning model could capture variants' combining effect with insignificant P-value, while GWAS fails. To our best knowledge, our model is the first deep learning method for the classification of ADHD with SNPs data.
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Affiliation(s)
- Lu Liu
- Peking University Sixth Hospital/Institute of Mental Health, National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital) & the Key Laboratory of Mental Health, Ministry of Health (Peking University), 100191, Beijing, China
| | - Xikang Feng
- School of Software, Northwestern Polytechnical University, Xi’an, 710072, Shaanxi, China
| | - Haimei Li
- Peking University Sixth Hospital/Institute of Mental Health, National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital) & the Key Laboratory of Mental Health, Ministry of Health (Peking University), 100191, Beijing, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong, China
| | - Qiujin Qian
- Peking University Sixth Hospital/Institute of Mental Health, National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital) & the Key Laboratory of Mental Health, Ministry of Health (Peking University), 100191, Beijing, China
| | - Yufeng Wang
- Peking University Sixth Hospital/Institute of Mental Health, National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital) & the Key Laboratory of Mental Health, Ministry of Health (Peking University), 100191, Beijing, China
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Maldžienė Ž, Vaitėnienė EM, Aleksiūnienė B, Utkus A, Preikšaitienė E. A case report of familial 4q13.3 microdeletion in three individuals with syndromic intellectual disability. BMC Med Genomics 2020; 13:63. [PMID: 32299451 PMCID: PMC7160938 DOI: 10.1186/s12920-020-0711-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 04/08/2020] [Indexed: 01/23/2023] Open
Abstract
Background Interstitial 4q deletions are rare chromosomal alterations. Most of the previously reported deletions involving the 4q13.3 region are large chromosomal alterations with a common loss of band 4q21 resulting in marked growth restriction, severe intellectual disability, and absent or severely delayed speech. A microdeletion of 4q13.3 hasn’t been previously reported. We discuss the involvement of genes and the observed phenotype, comparing it with that of previously reported patients. Case presentation We report on a 4q13.3 microdeletion detected in three affected individuals of a Lithuanian family. The clinical features of two affected children and their affected mother are very similar and include short stature, congenital heart defect, skeletal anomalies, minor facial anomalies, delayed puberty, and intellectual disability. Whole genome SNP microarray analysis of one child revealed an interstitial 4q13.3 microdeletion, 1.56 Mb in size. FISH analysis confirmed the deletion in the proband and identified the same deletion in her affected sib and mother, while it was not detected in a healthy sib. Deletion includes ADAMTS3, ANKRD17, COX18, GC, and NPFFR2 protein-coding genes. Conclusions Our findings suggest that 4q13.3 microdeletion is a cause of a recognizable phenotype of three affected individuals. The detected microdeletion is the smallest interstitial deletion in 4q13. We highlight ADAMTS3, ANKRD17 and RNU4ATAC9P as candidate genes for intellectual disability, growth retardation and congenital heart defect.
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Affiliation(s)
- Živilė Maldžienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių st. 2, 08661, Vilnius, LT, Lithuania.
| | | | - Beata Aleksiūnienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių st. 2, 08661, Vilnius, LT, Lithuania
| | - Algirdas Utkus
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių st. 2, 08661, Vilnius, LT, Lithuania
| | - Eglė Preikšaitienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių st. 2, 08661, Vilnius, LT, Lithuania
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Wang F, Zhao B. UBA6 and Its Bispecific Pathways for Ubiquitin and FAT10. Int J Mol Sci 2019; 20:ijms20092250. [PMID: 31067743 PMCID: PMC6539292 DOI: 10.3390/ijms20092250] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 12/25/2022] Open
Abstract
Questions have been raised since the discovery of UBA6 and its significant coexistence with UBE1 in the ubiquitin–proteasome system (UPS). The facts that UBA6 has the dedicated E2 enzyme USE1 and the E1–E2 cascade can activate and transfer both ubiquitin and ubiquitin-like protein FAT10 have attracted a great deal of attention to the regulational mechanisms of the UBA6–USE1 cascade and to how FAT10 and ubiquitin differentiate with each other. This review recapitulates the latest advances in UBA6 and its bispecific UBA6–USE1 pathways for both ubiquitin and FAT10. The intricate networks of UBA6 and its interplays with ubiquitin and FAT10 are briefly reviewed, as are their individual and collective functions in diverse physiological conditions.
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Affiliation(s)
- Fengting Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Bo Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.
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Shimbo H, Oyoshi T, Kurosawa K. Contiguous gene deletion neighboring TWIST1 identified in a patient with Saethre-Chotzen syndrome associated with neurodevelopmental delay: Possible contribution of HDAC9. Congenit Anom (Kyoto) 2018; 58:33-35. [PMID: 28220539 DOI: 10.1111/cga.12216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 02/11/2017] [Accepted: 02/14/2017] [Indexed: 01/10/2023]
Abstract
Saethre-Chotzen syndrome (SCS) is an autosomal dominant craniosynostotic disorder characterized by coronal synostosis, facial asymmetry, ptosis, and limb abnormalities. Haploinsufficiency of TWIST1, a basic helix-loop-helix transcription factor is responsible for SCS. Here, we report a 15-month-old male patient with typical clinical features of SCS in addition to developmental delay, which is a rare complication in SCS. He showed a de novo 0.9-Mb microdeletion in 7p21, in which TWIST1, NPMIP13, FERD3L, TWISTNB, and HDAC9 were included. In comparison with previously reported patients, HDAC9 was suggested to contribute to developmental delay in SCS patients with 7p21 mirodeletions.
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Affiliation(s)
- Hiroko Shimbo
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Tatsuki Oyoshi
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
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Shimojima K, Narai S, Togawa M, Doumoto T, Sangu N, Vanakker OM, de Paepe A, Edwards M, Whitehall J, Brescianini S, Petit F, Andrieux J, Yamamoto T. 7p22.1 microdeletions involving ACTB associated with developmental delay, short stature, and microcephaly. Eur J Med Genet 2016; 59:502-6. [PMID: 27633570 DOI: 10.1016/j.ejmg.2016.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 04/23/2016] [Accepted: 09/11/2016] [Indexed: 10/21/2022]
Abstract
There are no published reports of patients harboring microdeletions involving the 7p22.1 region. Although 7p22.1 microdeletions are rare, some reports have shown microduplications encompassing this region. In this study, we report five patients with overlapping deletions of the 7p22.1 region. The patients exhibited clinical similarities including non-specific developmental delay, short stature, microcephaly, and other distinctive features. The shortest region of overlap within the 7p22.1 region includes five genes, FBXL18, ACTB, FSCN1, RNF216, and ZNF815P. Of these genes, only ACTB is known to be associated with an autosomal dominant trait. Dominant negative mutations in ACTB are responsible for Baraitser-Winter syndrome 1. We analyzed ACTB expression in immortalized lymphocytes derived from one of the patients and found that it was reduced to approximately half that observed in controls. This indicates that ACTB expression is linearly correlated with the gene copy number. We suggest that haploinsufficiency of ACTB may be responsible for the clinical features of patients with 7p22.1 microdeletions.
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Affiliation(s)
- Keiko Shimojima
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, Japan; Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
| | - Satoshi Narai
- Department of Pediatrics, Tottori Prefectural Central Hospital, Tottori, Japan
| | - Masami Togawa
- Department of Pediatrics, Tottori Prefectural Central Hospital, Tottori, Japan
| | - Tomotsune Doumoto
- Department of Pediatrics, Tottori Prefectural Central Hospital, Tottori, Japan
| | - Noriko Sangu
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan; Department of Oral and Maxillofacial Surgery, Tokyo Women's Medical University, Tokyo, Japan
| | | | - Anne de Paepe
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Matthew Edwards
- Department of Paediatrics, School of Medicine, University of Western Sydney, New South Wales, Australia
| | - John Whitehall
- Department of Paediatrics, School of Medicine, University of Western Sydney, New South Wales, Australia
| | - Sally Brescianini
- Centre for Genetic Education, University of Sydney, New South Wales, Australia
| | - Florence Petit
- CHU Lille, Hopital Jeanne de Flandre, Service de Genetique Clinique, F-59000 Lille, France
| | - Joris Andrieux
- CHU Lille, Hopital Jeanne de Flandre, Laboratoire de Genetique Medicale, F-59000 Lille, France
| | - Toshiyuki Yamamoto
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan.
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Molpeceres RG, Rodriguez EU, García HG, Pino Vázquez MA, Hernanz Sanz JL, Álvarez Guisasola FJ. A rare case of acrocephaly: Saethre-Chotzen syndrome or Crouzon? CASE REPORTS IN PERINATAL MEDICINE 2016. [DOI: 10.1515/crpm-2015-0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Acrocephaly is a common neonatal craniofacial malformation. Saethre-Chotzen syndrome (SCS) is one of the acrocephaly related syndromes less frequently described in the literature. A female newborn term was admitted to our Neonatal Unit to study craniofacial dysmorphia without family history of interest. Pregnancy, childbirth and the neonatal period were uneventful. She had exotropia, short anterior-posterior cranial diameter, flat occiput and wide normotensive anterior fontanelle (beginning at the nose root, continuing through the sagittal suture with the posterior fontanelle) without syndactyly. The scanner imaging confirmed an acrocephaly with fusion of bilateral coronal sutures. We initially suspected a cranyosinostosis due to a Crouzon syndrome or SCS. After differential diagnosis and genetic study the patient was diagnosed as having SCS due to a de novo TWIST1 gene mutation. The craniofacial dysmorphias were corrected early by neurosurgical with good results. This case shows a new example of the phenotypic and genotypic variability of these TWIST1 gene mutations.
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Barthelemy J, Hanenberg H, Leffak M. FANCJ is essential to maintain microsatellite structure genome-wide during replication stress. Nucleic Acids Res 2016; 44:6803-16. [PMID: 27179029 PMCID: PMC5001596 DOI: 10.1093/nar/gkw433] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 05/06/2016] [Indexed: 12/15/2022] Open
Abstract
Microsatellite DNAs that form non-B structures are implicated in replication fork stalling, DNA double strand breaks (DSBs) and human disease. Fanconi anemia (FA) is an inherited disorder in which mutations in at least nineteen genes are responsible for the phenotypes of genome instability and cancer predisposition. FA pathway proteins are active in the resolution of non-B DNA structures including interstrand crosslinks, G quadruplexes and DNA triplexes. In FANCJ helicase depleted cells, we show that hydroxyurea or aphidicolin treatment leads to loss of microsatellite polymerase chain reaction signals and to chromosome recombination at an ectopic hairpin forming CTG/CAG repeat in the HeLa genome. Moreover, diverse endogenous microsatellite signals were also lost upon replication stress after FANCJ depletion, and in FANCJ null patient cells. The phenotype of microsatellite signal instability is specific for FANCJ apart from the intact FA pathway, and is consistent with DSBs at microsatellites genome-wide in FANCJ depleted cells following replication stress.
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Affiliation(s)
- Joanna Barthelemy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - Helmut Hanenberg
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany Department of Otorhinolaryngology & Head/Neck Surgery, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Michael Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
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Quintela I, Barros F, Fernandez-Prieto M, Martinez-Regueiro R, Castro-Gago M, Carracedo A, Gomez-Lado C, Eiris J. Interstitial microdeletions including the chromosome band 4q13.2 and the UBA6 gene as possible causes of intellectual disability and behavior disorder. Am J Med Genet A 2015; 167A:3113-20. [PMID: 26284580 DOI: 10.1002/ajmg.a.37291] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 08/02/2015] [Indexed: 12/27/2022]
Abstract
The few proximal 4q chromosomal aberrations identified in patients with neurodevelopmental phenotypes that have been published to date are variable in type, size and breakpoints and, therefore, encompass different chromosome bands and genes, making the establishment of genotype-phenotype correlations a challenging task. Here, microarray-based copy number analysis allowed us the detection of two novel and partially overlapping deletions in two unrelated families. In Family 1, a 4q13.1-q13.2 deletion of 3.84 Mb was identified in a mother with mild intellectual disability and in her two children, both with mild intellectual disability and attention deficit hyperactivity disorder. In Family 2, a de novo 4q13.2-q13.3 deletion of 6.81 Mb was detected in a female patient, born to unaffected parents, with a diagnosis of mild intellectual disability, behavioral disorder and facial dysmorphism. The shortest region of overlap between these two aberrations is located at chromosome 4q13.2 and includes 17 genes amongst of which we suggest UBA6 (ubiquitin-like modifier-activating enzyme 6) as a strong candidate gene for these phenotypes.
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Affiliation(s)
- Ines Quintela
- Grupo de Medicina Xenomica - Universidade de Santiago de Compostela, Centro Nacional de Genotipado - Plataforma de Recursos Biomoleculares y Bioinformaticos - Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Santiago de Compostela, Spain
| | - Francisco Barros
- Grupo de Medicina Xenomica-USC, CIBERER, Fundacion Publica Galega de Medicina Xenomica - SERGAS, Santiago de Compostela, Spain
| | - Montse Fernandez-Prieto
- Grupo de Medicina Xenomica-USC, CIBERER, Fundacion Publica Galega de Medicina Xenomica - SERGAS, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Rocio Martinez-Regueiro
- Departamento de Psicologia Clinica y Psicobiologia - Universidade de Santiago de Compostela, Grupo de Medicina Xenomica-USC, Santiago de Compostela, Spain
| | - Manuel Castro-Gago
- Departamento de Pediatria, Hospital Clinico Universitario de Santiago de Compostela - Unidad de Neurologia Pediatrica, Santiago de Compostela, Spain
| | - Angel Carracedo
- Grupo de Medicina Xenomica - Universidade de Santiago de Compostela, Centro Nacional de Genotipado - Plataforma de Recursos Biomoleculares y Bioinformaticos - Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Santiago de Compostela, Spain.,Grupo de Medicina Xenomica-USC, CIBERER, Fundacion Publica Galega de Medicina Xenomica - SERGAS, Santiago de Compostela, Spain.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Carmen Gomez-Lado
- Departamento de Pediatria, Hospital Clinico Universitario de Santiago de Compostela - Unidad de Neurologia Pediatrica, Santiago de Compostela, Spain
| | - Jesus Eiris
- Departamento de Pediatria, Hospital Clinico Universitario de Santiago de Compostela - Unidad de Neurologia Pediatrica, Santiago de Compostela, Spain
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Kiser DP, Rivero O, Lesch KP. Annual research review: The (epi)genetics of neurodevelopmental disorders in the era of whole-genome sequencing--unveiling the dark matter. J Child Psychol Psychiatry 2015; 56:278-95. [PMID: 25677560 DOI: 10.1111/jcpp.12392] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/13/2015] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND SCOPE Neurodevelopmental disorders (NDDs) are defined by a wide variety of behavioural phenotypes, psychopathology and clinically informed categorical classifications. Diagnostic entities include intellectual disability (ID), the autism spectrum (ASD) and attention-deficit/hyperactivity disorder (ADHD). The aetiopathogenesis of these conditions and disorders involves an interaction between both genetic and environmental risk factors on the developmental trajectory. Despite their remarkable genetic heterogeneity and complexity of pathophysiological mechanisms, NDDs display an overlap in their phenotypic features, a considerable degree of comorbidity as well as sharing of genetic and environmental risk factors. This review aims to provide an overview of the genetics and epigenetic of NDDs. FINDINGS Recent evidence suggests a critical role of defined and tightly regulated neurodevelopmental programs running out of control in NDDs, most notably neuronal proliferation and migration, synapse formation and remodelling, as well as neural network configuration resulting in compromised systems connectivity and function. Moreover, the machinery of epigenetic programming, interacting with genetic liability, impacts many of those processes and pathways, thus modifying vulnerability of, and resilience to, NDDs. Consequently, the categorically defined entities of ID, ADHD and ASD are increasingly viewed as disorders on a multidimensional continuum of molecular and cellular deficiencies in neurodevelopment. As such, this range of NDDs displays a broad phenotypic diversity, which may be explained by a combination and interplay of underlying loss- and potential gain-of-function traits. CONCLUSION In this overview, we discuss a backbone continuum concept of NDDs by summarizing pertinent findings in genetics and epigenetics. We also provide an appraisal of the genetic overlap versus differences, with a focus on genome-wide screening approaches for (epi)genetic variation. Finally, we conclude with insights from evolutionary psychobiology suggesting positive selection for discrete NDD-associated traits.
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Affiliation(s)
- Dominik P Kiser
- Division of Molecular Psychiatry, Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University of Wuerzburg, Wuerzburg, Germany
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