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Wong HS, Wadon M, Evans A, Kirov G, Modi N, O'Donovan MC, Thapar A. Contribution of de novo and inherited rare CNVs to very preterm birth. J Med Genet 2020; 57:552-557. [PMID: 32051258 DOI: 10.1136/jmedgenet-2019-106619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/23/2019] [Accepted: 01/12/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND The genomic contribution to adverse health sequelae in babies born very preterm (<32 weeks' gestation) is unknown. We conducted an investigation of rare CNVs in infants born very preterm as part of a study to determine the feasibility and acceptability of a larger, well-powered genome-wide investigation in the UK, with follow-up using linked National Health Service records and DNA storage for additional research. METHODS We studied 488 parent-offspring trios. We performed genotyping using Illumina Infinium OmniExpress Arrays. CNV calling and quality control (QC) were undertaken using published protocols. We examined de novo CNVs in infants and the rate of known pathogenic variants in infants, mothers and fathers and compared these with published comparator data. We defined rare pathogenic CNVs as those consistently reported to be associated with clinical phenotypes. RESULTS We identified 14 de novo CNVs, representing a mutation rate of 2.9%, compared with 2.1% reported in control populations. The median size of these CNV was much higher than in comparator data (717 kb vs 255 kb). The rate of pathogenic CNVs was 4.3% in infants, 2.7% in mothers and 2% in fathers, compared with 2.3% in UK Biobank participants. CONCLUSION Our findings suggest that the rate of de novo CNVs, especially rare pathogenic CNVs, could be elevated in those born very preterm. However, we will need to conduct a much larger study to corroborate this conclusion.
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Affiliation(s)
- Hilary S Wong
- Department of Paediatrics, Cambridge University, Cambridge, UK
| | - Megan Wadon
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Alexandra Evans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Neena Modi
- Section of Neonatal Medicine, Imperial College London, London, UK
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Anita Thapar
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
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2
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Ueoka I, Pham HTN, Matsumoto K, Yamaguchi M. Autism Spectrum Disorder-Related Syndromes: Modeling with Drosophila and Rodents. Int J Mol Sci 2019; 20:E4071. [PMID: 31438473 PMCID: PMC6747505 DOI: 10.3390/ijms20174071] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/17/2019] [Accepted: 08/18/2019] [Indexed: 12/11/2022] Open
Abstract
Whole exome analyses have identified a number of genes associated with autism spectrum disorder (ASD) and ASD-related syndromes. These genes encode key regulators of synaptogenesis, synaptic plasticity, cytoskeleton dynamics, protein synthesis and degradation, chromatin remodeling, transcription, and lipid homeostasis. Furthermore, in silico studies suggest complex regulatory networks among these genes. Drosophila is a useful genetic model system for studies of ASD and ASD-related syndromes to clarify the in vivo roles of ASD-associated genes and the complex gene regulatory networks operating in the pathogenesis of ASD and ASD-related syndromes. In this review, we discuss what we have learned from studies with vertebrate models, mostly mouse models. We then highlight studies with Drosophila models. We also discuss future developments in the related field.
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Affiliation(s)
- Ibuki Ueoka
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 603-8585, Japan
| | - Hang Thi Nguyet Pham
- Department of Pharmacology and Biochemistry, National Institute of Medicinal Materials, Hanoi 110100, Vietnam
| | - Kinzo Matsumoto
- Division of Medicinal Pharmacology, Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Masamitsu Yamaguchi
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 603-8585, Japan.
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3
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Griswold AJ, Van Booven D, Cuccaro ML, Haines JL, Gilbert JR, Pericak-Vance MA. Identification of rare noncoding sequence variants in gamma-aminobutyric acid A receptor, alpha 4 subunit in autism spectrum disorder. Neurogenetics 2018; 19:17-26. [PMID: 29151244 PMCID: PMC5792317 DOI: 10.1007/s10048-017-0529-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 11/08/2017] [Indexed: 12/13/2022]
Abstract
Alterations of the gamma-aminobutyric acid (GABA) signaling system has been strongly linked to the pathophysiology of autism spectrum disorder (ASD). Genetic associations of common variants in GABA receptor subunits, in particular GABRA4 on chromosome 4p12, with ASD have been replicated by several studies. Moreover, molecular investigations have identified altered transcriptional and translational levels of this gene and protein in brains of ASD individuals. Since the genotyped common variants are likely not the functional variants contributing to the molecular consequences or underlying ASD phenotype, this study aims to examine rare sequence variants in GABRA4, including those outside the protein coding regions of the gene. We comprehensively re-sequenced the entire protein coding and noncoding portions of the gene and putative regulatory sequences in 82 ASD individuals and 55 developmentally typical pediatric controls, all homozygous for the most significant previously associated ASD risk allele (G/G at rs1912960). We identified only a single common, coding variant, and no association of any single marker or set of variants with ASD. Functional annotation of noncoding variants identified several rare variants in putative regulatory sites. Finally, a rare variant unique to ASD cases, in an evolutionary conserved site of the 3'UTR, shows a trend toward decreasing gene expression. Hence, GABRA4 rare variants in noncoding DNA may be variants of modest physiological effects in ASD etiology.
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Affiliation(s)
- Anthony J Griswold
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA.
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA.
| | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
| | - John R Gilbert
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
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4
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Firouzabadi SG, Kariminejad R, Vameghi R, Darvish H, Ghaedi H, Banihashemi S, Firouzkouhi Moghaddam M, Jamali P, Mofidi Tehrani HF, Dehghani H, Narooie-Nejad M, Jamshidi J, Tafakhori A, Sadabadi S, Najmabadi H, Behjati F. Copy Number Variants in Patients with Autism and Additional Clinical Features: Report of VIPR2 Duplication and a Novel Microduplication Syndrome. Mol Neurobiol 2016; 54:7019-7027. [PMID: 27796743 DOI: 10.1007/s12035-016-0202-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/11/2016] [Indexed: 10/20/2022]
Abstract
Autism is a common neurodevelopmental disorder estimated to affect 1 in 68 children. Many studies have shown the role of copy number variants (CNVs) as a major contributor in the etiology of autism with the overall detection rate of about 10-15 % and over 20 % when syndromic forms of autism exist. In this study, we used array CGH to identify CNVs in 15 Iranian patients with autism. To elevate our diagnostic yield, we selected the sporadic patients who had additional clinical features including intellectual disability (ID), craniofacial anomaly, and seizure. Six out of 15 patients showed clinically relevant CNVs including pathogenic and likely pathogenic copy number gains or losses. We report a novel gene duplication syndrome (10q21.2q21.3 microduplication) and present a new evidence for VIPR2 duplication, as a candidate gene for autism. Furthermore, we describe the first manifesting carrier female with deletion of SLC6A8 and BCAP31 genes on Xq28. Our findings suggest that there might be a higher prevalence of clinically significant CNVs in patients with autism and additional clinical manifestations. The CNV analysis in such patients could lead to the discovery of novel syndromes as well as unraveling the etiology of autism.
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Affiliation(s)
| | | | - Roshanak Vameghi
- Pediatric Neurorehabilitation Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Darvish
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Ghaedi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Susan Banihashemi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mahboubeh Firouzkouhi Moghaddam
- Child and Adolescent Psychiatry Department, Zahedan University of Medical Sciences, Zahedan, Iran.,Research Center for Children and Adolescents Health, Zahedan University of Medical Sciences, Zahedan, Iran
| | | | | | - Hossein Dehghani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mehrnaz Narooie-Nejad
- Genetics of Non-communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Javad Jamshidi
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Abbas Tafakhori
- Department of Neurology, School of Medicine, Imam Khomeini Hospital and Iranian Center of Neurological Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeid Sadabadi
- Bahar Education and Rehabilitation Center for the handicapped, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran
| | - Farkhondeh Behjati
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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5
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Grice SJ, Liu JL, Webber C. Synergistic interactions between Drosophila orthologues of genes spanned by de novo human CNVs support multiple-hit models of autism. PLoS Genet 2015; 11:e1004998. [PMID: 25816101 PMCID: PMC4376901 DOI: 10.1371/journal.pgen.1004998] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 01/12/2015] [Indexed: 01/30/2023] Open
Abstract
Autism spectrum disorders (ASDs) are highly heritable and characterised by deficits in social interaction and communication, as well as restricted and repetitive behaviours. Although a number of highly penetrant ASD gene variants have been identified, there is growing evidence to support a causal role for combinatorial effects arising from the contributions of multiple loci. By examining synaptic and circadian neurological phenotypes resulting from the dosage variants of unique human:fly orthologues in Drosophila, we observe numerous synergistic interactions between pairs of informatically-identified candidate genes whose orthologues are jointly affected by large de novo copy number variants (CNVs). These CNVs were found in the genomes of individuals with autism, including a patient carrying a 22q11.2 deletion. We first demonstrate that dosage alterations of the unique Drosophila orthologues of candidate genes from de novo CNVs that harbour only a single candidate gene display neurological defects similar to those previously reported in Drosophila models of ASD-associated variants. We then considered pairwise dosage changes within the set of orthologues of candidate genes that were affected by the same single human de novo CNV. For three of four CNVs with complete orthologous relationships, we observed significant synergistic effects following the simultaneous dosage change of gene pairs drawn from a single CNV. The phenotypic variation observed at the Drosophila synapse that results from these interacting genetic variants supports a concordant phenotypic outcome across all interacting gene pairs following the direction of human gene copy number change. We observe both specificity and transitivity between interactors, both within and between CNV candidate gene sets, supporting shared and distinct genetic aetiologies. We then show that different interactions affect divergent synaptic processes, demonstrating distinct molecular aetiologies. Our study illustrates mechanisms through which synergistic effects resulting from large structural variation can contribute to human disease.
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Affiliation(s)
- Stuart J. Grice
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Ji-Long Liu
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Caleb Webber
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail:
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6
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Skafidas E, Testa R, Zantomio D, Chana G, Everall IP, Pantelis C. Predicting the diagnosis of autism spectrum disorder using gene pathway analysis. Mol Psychiatry 2014; 19:504-10. [PMID: 22965006 PMCID: PMC3966080 DOI: 10.1038/mp.2012.126] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 07/09/2012] [Indexed: 12/27/2022]
Abstract
Autism spectrum disorder (ASD) depends on a clinical interview with no biomarkers to aid diagnosis. The current investigation interrogated single-nucleotide polymorphisms (SNPs) of individuals with ASD from the Autism Genetic Resource Exchange (AGRE) database. SNPs were mapped to Kyoto Encyclopedia of Genes and Genomes (KEGG)-derived pathways to identify affected cellular processes and develop a diagnostic test. This test was then applied to two independent samples from the Simons Foundation Autism Research Initiative (SFARI) and Wellcome Trust 1958 normal birth cohort (WTBC) for validation. Using AGRE SNP data from a Central European (CEU) cohort, we created a genetic diagnostic classifier consisting of 237 SNPs in 146 genes that correctly predicted ASD diagnosis in 85.6% of CEU cases. This classifier also predicted 84.3% of cases in an ethnically related Tuscan cohort; however, prediction was less accurate (56.4%) in a genetically dissimilar Han Chinese cohort (HAN). Eight SNPs in three genes (KCNMB4, GNAO1, GRM5) had the largest effect in the classifier with some acting as vulnerability SNPs, whereas others were protective. Prediction accuracy diminished as the number of SNPs analyzed in the model was decreased. Our diagnostic classifier correctly predicted ASD diagnosis with an accuracy of 71.7% in CEU individuals from the SFARI (ASD) and WTBC (controls) validation data sets. In conclusion, we have developed an accurate diagnostic test for a genetically homogeneous group to aid in early detection of ASD. While SNPs differ across ethnic groups, our pathway approach identified cellular processes common to ASD across ethnicities. Our results have wide implications for detection, intervention and prevention of ASD.
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Affiliation(s)
- E Skafidas
- Centre for Neural Engineering, The University
of Melbourne, Parkville, VIC, Australia
| | - R Testa
- Melbourne Neuropsychiatry Centre, Department
of Psychiatry, The University of Melbourne & Melbourne Health,
Parkville, VIC, Australia,Department of Psychology, Monash
University, Clayton, VIC, Australia
| | - D Zantomio
- Department of Haematology, Austin
Health, Heidelberg, VIC, Australia
| | - G Chana
- Department of Psychiatry, The University of
Melbourne, Parkville, Victoria,
Australia
| | - I P Everall
- Department of Psychiatry, The University of
Melbourne, Parkville, Victoria,
Australia
| | - C Pantelis
- Melbourne Neuropsychiatry Centre, Department
of Psychiatry, The University of Melbourne & Melbourne Health,
Parkville, VIC, Australia,Department of Psychiatry, The University of
Melbourne, Parkville, Victoria,
Australia,National Neuroscience Facility (NNF), Level 3, 161
Barry Street, Carlton South, VIC
3053, Australia. E-mail:
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7
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Li X, Chen S, Xie W, Vogel I, Choy KW, Chen F, Christensen R, Zhang C, Ge H, Jiang H, Yu C, Huang F, Wang W, Jiang H, Zhang X. PSCC: sensitive and reliable population-scale copy number variation detection method based on low coverage sequencing. PLoS One 2014; 9:e85096. [PMID: 24465483 PMCID: PMC3897425 DOI: 10.1371/journal.pone.0085096] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 11/22/2013] [Indexed: 11/28/2022] Open
Abstract
Background Copy number variations (CNVs) represent an important type of genetic variation that deeply impact phenotypic polymorphisms and human diseases. The advent of high-throughput sequencing technologies provides an opportunity to revolutionize the discovery of CNVs and to explore their relationship with diseases. However, most of the existing methods depend on sequencing depth and show instability with low sequence coverage. In this study, using low coverage whole-genome sequencing (LCS) we have developed an effective population-scale CNV calling (PSCC) method. Methodology/Principal Findings In our novel method, two-step correction was used to remove biases caused by local GC content and complex genomic characteristics. We chose a binary segmentation method to locate CNV segments and designed combined statistics tests to ensure the stable performance of the false positive control. The simulation data showed that our PSCC method could achieve 99.7%/100% and 98.6%/100% sensitivity and specificity for over 300 kb CNV calling in the condition of LCS (∼2×) and ultra LCS (∼0.2×), respectively. Finally, we applied this novel method to analyze 34 clinical samples with an average of 2× LCS. In the final results, all the 31 pathogenic CNVs identified by aCGH were successfully detected. In addition, the performance comparison revealed that our method had significant advantages over existing methods using ultra LCS. Conclusions/Significance Our study showed that PSCC can sensitively and reliably detect CNVs using low coverage or even ultra-low coverage data through population-scale sequencing.
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Affiliation(s)
| | - Shengpei Chen
- BGI-Shenzhen, Shenzhen, China ; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | | | - Ida Vogel
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | | | - Rikke Christensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Haojun Jiang
- BGI-Shenzhen, Shenzhen, China ; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | | | - Fang Huang
- Guangzhou Children's Social Welfare Home, Guangzhou, China
| | - Wei Wang
- BGI-Shenzhen, Shenzhen, China ; Clinical laboratory of BGI Health, Shenzhen, China
| | | | - Xiuqing Zhang
- BGI-Shenzhen, Shenzhen, China ; The Guangdong Enterprise Key Laboratory of Human Disease Genomics, BGI-Shenzhen, Shenzhen, China
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8
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9
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Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data. BMC Bioinformatics 2012; 13:305. [PMID: 23157288 PMCID: PMC3563612 DOI: 10.1186/1471-2105-13-305] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 11/07/2012] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND DNA capture technologies combined with high-throughput sequencing now enable cost-effective, deep-coverage, targeted sequencing of complete exomes. This is well suited for SNP discovery and genotyping. However there has been little attention devoted to Copy Number Variation (CNV) detection from exome capture datasets despite the potentially high impact of CNVs in exonic regions on protein function. RESULTS As members of the 1000 Genomes Project analysis effort, we investigated 697 samples in which 931 genes were targeted and sampled with 454 or Illumina paired-end sequencing. We developed a rigorous Bayesian method to detect CNVs in the genes, based on read depth within target regions. Despite substantial variability in read coverage across samples and targeted exons, we were able to identify 107 heterozygous deletions in the dataset. The experimentally determined false discovery rate (FDR) of the cleanest dataset from the Wellcome Trust Sanger Institute is 12.5%. We were able to substantially improve the FDR in a subset of gene deletion candidates that were adjacent to another gene deletion call (17 calls). The estimated sensitivity of our call-set was 45%. CONCLUSIONS This study demonstrates that exonic sequencing datasets, collected both in population based and medical sequencing projects, will be a useful substrate for detecting genic CNV events, particularly deletions. Based on the number of events we found and the sensitivity of the methods in the present dataset, we estimate on average 16 genic heterozygous deletions per individual genome. Our power analysis informs ongoing and future projects about sequencing depth and uniformity of read coverage required for efficient detection.
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10
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Craniofacial dysmorphism and developmental disorders among children with chromosomal microdeletions and duplications of unknown significance. J Dev Behav Pediatr 2011; 32:600-4. [PMID: 21918468 DOI: 10.1097/dbp.0b013e31823299d6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Microarray comparative genomic hybridization is an extremely sensitive technology that increasingly identifies deletions and duplications of unknown significance. Our objective was to determine whether children with autism and other developmental delays who have genomic imbalances manifest more craniofacial dysmorphism and have lower cognitive scores than children from the same clinic population who have normal microarrays. METHOD A clinical geneticist, blinded to the history, reviewed photographs for craniofacial dysmorphism. Forty-five (24%) of 187 children who had a microarray had a deletion or duplication >200 kb. Thirty-six of those with abnormal microarrays (11 microdeletions and 25 duplications) had completed their evaluation, which included 3 deletions and 10 duplications of unknown significance. Subjects with and without microarray anomalies did not differ in age, sex, growth parameters, parental age or education level, insurance status, or cognitive scores. RESULTS Twenty-eight (78%) of the 36 children with microarray anomalies had craniofacial dysmorphism as compared with 45% of those with normal microarrays (p = .0005). Among the 13 children with microarray abnormalities of unknown significance, 10 (77%) were dysmorphic, similar to 18 (78%) of 23 who had a genomic imbalance known to affect development. Among the 10 children with dysmorphism and a microarray anomaly of unknown significance, 7 also had an IQ ≤70 and/or a diagnosis of autism. CONCLUSION Microdeletions and duplications not previously known to be associated with human disease were strongly associated with craniofacial dysmorphism, cognitive scores ≤70, and a diagnosis of autism in this clinic population, providing presumptive evidence that these genomic imbalances are clinically significant.
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11
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Vorsanova SG, Yurov YB, Soloviev IV, Iourov IY. Molecular cytogenetic diagnosis and somatic genome variations. Curr Genomics 2011; 11:440-6. [PMID: 21358989 PMCID: PMC3018725 DOI: 10.2174/138920210793176010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 05/26/2010] [Accepted: 06/01/2010] [Indexed: 12/22/2022] Open
Abstract
Human molecular cytogenetics integrates the knowledge on chromosome and genome organization at the molecular and cellular levels in health and disease. Molecular cytogenetic diagnosis is an integral part of current genomic medicine and is the standard of care in medical genetics and cytogenetics, reproductive medicine, pediatrics, neuropsychiatry and oncology. Regardless numerous advances in this field made throughout the last two decades, researchers and practitioners who apply molecular cytogenetic techniques may encounter several problems that are extremely difficult to solve. One of them is undoubtedly the occurrence of somatic genome and chromosome variations, leading to genomic and chromosomal mosaicism, which are related but not limited to technological and evaluative limitations as well as multiplicity of interpretations. More dramatically, current biomedical literature almost lacks descriptions, guidelines or solutions of these problems. The present article overviews all these problems and gathers those exclusive data acquired from studies of genome and chromosome instability that is relevant to identification and interpretations of this fairly common cause of somatic genomic variations and chromosomal mosaicism. Although the way to define pathogenic value of all the intercellular variations of the human genome is far from being completely understood, it is possible to propose recommendations on molecular cytogenetic diagnosis and management of somatic genome variations in clinical population.
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Affiliation(s)
- S G Vorsanova
- Institute of Pediatrics and Children Surgery, Rosmedtechnologii
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12
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Spectrum of large copy number variations in 26 diverse Indian populations: potential involvement in phenotypic diversity. Hum Genet 2011; 131:131-43. [PMID: 21744140 DOI: 10.1007/s00439-011-1050-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 06/19/2011] [Indexed: 10/18/2022]
Abstract
Copy number variations (CNVs) have provided a dynamic aspect to the apparently static human genome. We have analyzed CNVs larger than 100 kb in 477 healthy individuals from 26 diverse Indian populations of different linguistic, ethnic and geographic backgrounds. These CNVRs were identified using the Affymetrix 50K Xba 240 Array. We observed 1,425 and 1,337 CNVRs in the deletion and amplification sets, respectively, after pooling data from all the populations. More than 50% of the genes encompassed entirely in CNVs had both deletions and amplifications. There was wide variability across populations not only with respect to CNV extent (ranging from 0.04-1.14% of genome under deletion and 0.11-0.86% under amplification) but also in terms of functional enrichments of processes like keratinization, serine proteases and their inhibitors, cadherins, homeobox, olfactory receptors etc. These did not correlate with linguistic, ethnic, geographic backgrounds and size of populations. Certain processes were near exclusive to deletion (serine proteases, keratinization, olfactory receptors, GPCRs) or duplication (homeobox, serine protease inhibitors, embryonic limb morphogenesis) datasets. Populations having same enriched processes were observed to contain genes from different genomic loci. Comparison of polymorphic CNVRs (5% or more) with those cataloged in Database of Genomic Variants revealed that 78% (2473) of the genes in CNVRs in Indian populations are novel. Validation of CNVs using Sequenom MassARRAY revealed extensive heterogeneity in CNV boundaries. Exploration of CNV profiles in such diverse populations would provide a widely valuable resource for understanding diversity in phenotypes and disease.
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13
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Griswold AJ, Ma D, Sacharow SJ, Robinson JL, Jaworski JM, Wright HH, Abramson RK, Lybaek H, Øyen N, Cuccaro ML, Gilbert JR, Pericak-Vance MA. A de novo 1.5 Mb microdeletion on chromosome 14q23.2-23.3 in a patient with autism and spherocytosis. Autism Res 2011; 4:221-7. [PMID: 21360829 DOI: 10.1002/aur.186] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 01/06/2011] [Indexed: 11/09/2022]
Abstract
Autism is a neuro-developmental disorder characterized by deficits in social interaction and communication as well as restricted interests or repetitive behaviors. Cytogenetic studies have implicated large chromosomal aberrations in the etiology of approximately 5-7% of autism patients, and the recent advent of array-based techniques allows the exploration of submicroscopic copy number variations (CNVs). We genotyped a 14-year-old boy with autism, spherocytosis and other physical dysmorphia, his parents, and two non-autistic siblings with the Illumina Human 1M Beadchip as part of a study of the molecular genetics of autism and determined copy number variants using the PennCNV algorithm. We identified and validated a de novo 1.5 Mb microdeletion of 14q23.2-23.3 in our autistic patient. This region contains 15 genes, including spectrin beta (SPTB), encoding a cytoskeletal protein previously associated with spherocytosis, methylenetetrahydrofolate dehydrogenase 1 (MTHFD1), a folate metabolizing enzyme previously associated with bipoloar disorder and schizophrenia, pleckstrin homology domain-containing family G member 3 (PLEKHG3), a guanide nucleotide exchange enriched in the brain, and churchill domain containing protein 1 (CHURC1), homologs of which regulate neuronal development in model organisms. While a similar deletion has previously been reported in a family with spherocytosis, severe learning disabilities, and mild mental retardation, this is the first implication of chr14q23.2-23.3 in the etiology of autism and points to MTHFD1, PLEKHG3, and CHURC1 as potential candidate genes contributing to autism risk.
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Affiliation(s)
- Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida 33136, USA
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Copy number variation in the dosage-sensitive 16p11.2 interval accounts for only a small proportion of autism incidence: A systematic review and meta-analysis. Genet Med 2011; 13:377-84. [DOI: 10.1097/gim.0b013e3182076c0c] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Warden M, Pique-Regi R, Ortega A, Asgharzadeh S. Bioinformatics for copy number variation data. Methods Mol Biol 2011; 719:235-49. [PMID: 21370087 DOI: 10.1007/978-1-61779-027-0_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Copy number variation is known to be an important component of structural variation in the human genome. Greater than 1 kb in size, these gains and losses of genetic material are known to confer risk to many human diseases, both Mendelian and complex. Therefore, the technologies used to detect copy number variation have been quickly improving in both throughput and cost. From comparative genomic hybridization to synthetic high-density oligonucleotide arrays to next-generation sequencing methods, algorithms used to estimate copy number are plentiful. Here we describe a practical introduction to the copy number variation technology and available analysis methods, and demonstrate the analysis flow on an example case.
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Affiliation(s)
- Melissa Warden
- Department of Pediatrics and Pathology, Keck School of Medicine, Childrens Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
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Sponheim E. Er Aspergers syndrom blitt vanligere? TIDSSKRIFT FOR DEN NORSKE LEGEFORENING 2011; 131:561. [DOI: 10.4045/tidsskr.10.1381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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Current world literature. Curr Opin Pediatr 2010; 22:246-55. [PMID: 20299870 DOI: 10.1097/mop.0b013e32833846de] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Treadwell-Deering DE, Powell MP, Potocki L. Cognitive and behavioral characterization of the Potocki-Lupski syndrome (duplication 17p11.2). J Dev Behav Pediatr 2010; 31:137-43. [PMID: 20110824 DOI: 10.1097/dbp.0b013e3181cda67e] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE To describe the cognitive and behavioral phenotypic features of the Potocki-Lupski syndrome (duplication 17p11.2), a recently recognized syndrome with multiple congenital anomalies and developmental delays. METHOD Fifteen subjects were enrolled in an extensive multidisciplinary clinical protocol. Cognitive and behavior evaluations included a parent-report medical and psychological history form, intellectual assessment and assessments of adaptive behavior, executive functioning, and maladaptive behavior and emotions. Eight of the families completed an Autism Diagnostic Interview-Revised and Autism Diagnostic Observation Schedule-Generic. RESULTS The majority of patients (13 of 15) presented with intellectual disability. Moreover, the majority of patients also had moderate to severe behavioral difficulties, including atypicality, withdrawal, anxiety, and inattention. Many patients characterized also presented with autistic symptom pictures, some of whom (10 of 15) met diagnostic criteria for an autistic spectrum disorder, namely autistic disorder or pervasive developmental disorder not otherwise specified. CONCLUSION This work expands on the behavioral phenotype of duplication 17p11.2 (Potocki-Lupski syndrome). Further phenotypic analysis will aid in clinical diagnosis, counseling, and management of this newly characterized microduplication syndrome. The association between this syndrome and autistic spectrum disorder may contribute to further understanding the etiology of the pervasive developmental disorders.
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Affiliation(s)
- Diane E Treadwell-Deering
- Division of Child and Adolescent Psychiatry, The Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX 77030-2399, USA.
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