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Danecek P, Gardner EJ, Fitzgerald TW, Gallone G, Kaplanis J, Eberhardt RY, Wright CF, Firth HV, Hurles ME. Detection and characterization of copy-number variants from exome sequencing in the DDD study. GENETICS IN MEDICINE OPEN 2024; 2:101818. [PMID: 39669630 PMCID: PMC11613862 DOI: 10.1016/j.gimo.2024.101818] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 12/14/2024]
Abstract
Purpose Structural variants such as multiexon deletions and duplications are an important cause of disease but are often overlooked in standard exome/genome sequencing analysis. We aimed to evaluate the detection of copy-number variants (CNVs) from exome sequencing (ES) in comparison with genome-wide low-resolution and exon-resolution chromosomal microarrays (CMAs) and to characterize the properties of de novo CNVs in a large clinical cohort. Methods We performed CNV detection using ES of 9859 parent-offspring trios in the Deciphering Developmental Disorders (DDD) study and compared them with CNVs detected from exon-resolution array comparative genomic hybridization in 5197 probands from the DDD study. Results Integrating calls from multiple ES-based CNV algorithms using random forest machine learning generated a higher quality data set than using individual algorithms. Both ES- and array comparative genomic hybridization-based approaches had the same sensitivity of 89% and detected the same number of unique pathogenic CNVs not called by the other approach. Of DDD probands prescreened with low-resolution CMAs, 2.6% had a pathogenic CNV detected by higher-resolution assays. De novo CNVs were strongly enriched in known DD-associated genes and exhibited no bias in parental age or sex. Conclusion ES-based CNV calling has higher sensitivity than low-resolution CMAs currently in clinical use and comparable sensitivity to exon-resolution CMA. With sufficient investment in bioinformatic analysis, exome-based CNV detection could replace low-resolution CMA for detecting pathogenic CNVs.
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Affiliation(s)
- Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Eugene J. Gardner
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | | | - Giuseppe Gallone
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Joanna Kaplanis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Ruth Y. Eberhardt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Caroline F. Wright
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Helen V. Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Matthew E. Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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Takada S, Silva S, Zamorano I, Pérez A, Iwabuchi C, Miyake N. Human phenotype caused by biallelic KDM4B frameshift variant. Clin Genet 2024; 105:72-76. [PMID: 37526414 DOI: 10.1111/cge.14409] [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: 06/05/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023]
Abstract
KDM4B (MIM*609765, NM_015015.3, formerly JMJD2B) encodes a histone demethylase and regulates gene expression via demethylation, mainly of H3K9 tri-methylation. Heterozygous KDM4B loss-of-function variants cause autosomal dominant intellectual developmental disorder 65 (MIM#619320), which is characterized by global developmental delay, intellectual disability, language and gross motor delays, structural brain anomalies, characteristic facial features, and clinodactyly. Although the majority of reported patients have de novo pathogenic variants, some patients inherit pathogenic variants from affected parents. To our knowledge, only 23 patients with heterozygous KDM4B variants have been reported to date, and there are no reports of patients with biallelic KDM4B pathogenic variants. Herein, we report a female patient with a biallelic KDM4B frameshift variant (NM_015015.3: c.1384_1394delinsGGG, p.(Leu462Glyfs*43)) located at exon 12 of 23 protein-coding exons, which is thought to be subject to nonsense-mediated mRNA decay and no protein production. She presented developmental and language delays and a hypotonic and characteristic face. The patient's phenotype was more obvious than that of her mother, who is heterozygous for the same variant. Although declining birth rate (embryonic lethality in male mice) in homozygous knockout mice has been demonstrated, our report suggests that homozygous KDM4B frameshift variants can be viable in humans at least female.
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Affiliation(s)
- Sanami Takada
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Sebastián Silva
- Child Neurology Service, Hospital de Puerto Montt, Puerto Montt, Chile
- Escuela de Medicina, Universidad San Sebastián, Puerto Montt, Chile
| | - Ivonne Zamorano
- Adult Neurology Service, Hospital de Puerto Montt, Puerto Montt, Chile
| | - Andrea Pérez
- Radiology Service, Hospital de Puerto Montt, Puerto Montt, Chile
| | - Chisato Iwabuchi
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Noriko Miyake
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
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Jung B, Ahn K, Justice C, Norman L, Price J, Sudre G, Shaw P. Rare copy number variants in males and females with childhood attention-deficit/hyperactivity disorder. Mol Psychiatry 2023; 28:1240-1247. [PMID: 36517639 PMCID: PMC10010944 DOI: 10.1038/s41380-022-01906-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/18/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022]
Abstract
While childhood attention-deficit/hyperactivity disorder (ADHD) is more prevalent in males than females, genetic contributors to this effect have not been established. Here, we explore sex differences in the contribution of common and/or rare genetic variants to ADHD. Participants were from the Adolescent Brain and Cognitive Development study (N = 1253 youth meeting DSM-5 criteria for ADHD [mean age = 11.46 years [SD = 0.87]; 31% female] and 5577 unaffected individuals [mean age = 11.42 years [SD = 0.89]; 50% female], overall 66% White, non-Hispanic (WNH), 19% Black/African American, and 15% other races. Logistic regression tested for interactions between sex (defined genotypically) and both rare copy number variants (CNV) and polygenic (common variant) risk in association with ADHD. There was a significant interaction between sex and the presence of a CNV deletion larger than 200 kb, both in the entire cohort (β = -0.74, CI = [-1.27 to -0.20], FDR-corrected p = 0.048) and, at nominal significance levels in the WNH ancestry subcohort (β = -0.86, CI = [-1.51 to -0.20], p = 0.010). Additionally, the number of deleted genes interacted with sex in association with ADHD (whole cohort. β = -0.13, CI = [-0.23 to -0.029], FDR-corrected p = 0.048; WNH. β = -0.17, CI = [-0.29 to -0.050], FDR-corrected p = 0.044) as did the total length of CNV deletions (whole cohort. β = -0.12, CI = [-0.19 to -0.044], FDR-corrected p = 0.028; WNH. β = -0.17, CI = [-0.28 to -0.061], FDR-corrected p = 0.034). This sex effect was driven by increased odds of childhood ADHD for females but not males in the presence of CNV deletions. No similar sex effect was found for CNV duplications or polygenic risk scores. The association between CNV deletions and ADHD was partially mediated by measures of cognitive flexibility. In summary, CNV deletions were associated with increased odds for childhood ADHD in females, but not males.
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Affiliation(s)
- Benjamin Jung
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kwangmi Ahn
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Cristina Justice
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Luke Norman
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jolie Price
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Gustavo Sudre
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Philip Shaw
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
- Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892, USA.
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4
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Chen B, Zhan Y, Kessi M, Chen S, Xiong J, Deng X, Yang L, Peng J, Yin F, He F. Urine Organic Acids as Metabolic Indicators for Global Developmental Delay/Intellectual Disability in Chinese Children. Front Mol Biosci 2022; 8:792319. [PMID: 35036412 PMCID: PMC8757376 DOI: 10.3389/fmolb.2021.792319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/03/2021] [Indexed: 12/15/2022] Open
Abstract
Objective: The purpose of this study was to search for differential metabolites in urine organic acids, and to characterize metabolic features that can be used to identify metabolites for exploration of global developmental delay (GDD)/intellectual disability (ID) etiology and pathogenesis. Methods: We screened positive test results that could explain GDD/ID from 1,253 cases, and the major differential metabolites in 132 urine organic acids from the 1,230 cases with negative results (863 GDD cases, 367 ID cases), and 100 typically developing children (TD). Non-supervisory principal component analysis and orthogonal partial least squares discriminant analysis were used to develop models to distinguish GDD/ID from TD children, and to detect major differential metabolites. Results: We get 23 positive results that could identify the cause of GDD/ID from 1253 cases diagnosed with GDD/ID. Among 1,230 negative results, we get the differential metabolites of the GDD group and the ID group had the same trend compared with the TD group. Twenty four differential metabolites were obtained from the GDD group, and 25 from the ID group (VIP > 1.0, p < 0.01). These differential metabolites were mainly related to the following pathways: the synthesis and degradation of ketone bodies, citrate cycle, alanine, aspartate and glutamate metabolism, pyrimidine metabolism, butanoate metabolism, pyruvate metabolism, fatty acid biosynthesis, valine, leucine and isoleucine degradation. Conclusion: The use of metabolomics research methods to detect urine organic acids of children with GDD/ID can discover differential metabolites, which might be valuable for future research on the etiology, pathogenesis, prognosis and possible interventions of GDD/ID. The significantly altered differential metabolites indicators could therefore be potential diagnostic biomarkers for GDD/ID.
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Affiliation(s)
- Baiyu Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Yalan Zhan
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Miriam Kessi
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Shimeng Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Juan Xiong
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Xiaolu Deng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Lifen Yang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fang He
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
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Li S, Chen LL, Wang XH, Zhu HJ, Li XL, Feng X, Guo L, Ou XH, Ma JY. Chromosomal variants accumulate in genomes of the spontaneous aborted fetuses revealed by chromosomal microarray analysis. PLoS One 2021; 16:e0259518. [PMID: 34727132 PMCID: PMC8562782 DOI: 10.1371/journal.pone.0259518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/20/2021] [Indexed: 01/18/2023] Open
Abstract
Spontaneous abortion is an impeding factor for the success rates of human assistant reproductive technology (ART). Causes of spontaneous abortion include not only the pregnant mothers’ health conditions and lifestyle habits, but also the fetal development potential. Evidences had shown that fetal chromosome aneuploidy is associated with fetal spontaneous abortion, however, it is still not definite that whether other genome variants, like copy number variations (CNVs) or loss of heterozygosity (LOHs) is associated with the spontaneous abortion. To assess the relationship between the fetal genome variants and abortion during ART, a chromosomal microarray data including chromosomal information of 184 spontaneous aborted fetuses, 147 adult female patients and 78 adult male patients during ART were collected. We firstly analyzed the relationship of fetal aneuploidy with maternal ages and then compared the numbers and lengths of CNVs (< 4Mbp) and LOHs among adults and aborted fetuses. In addition to the already known association between chromosomal aneuploidy and maternal ages, from the chromosomal microarray data we found that the numbers and the accumulated lengths of short CNVs and LOHs in the aborted fetuses were significantly larger or longer than those in adults. Our findings indicated that the increased numbers and accumulated lengths of CNVs or LOHs might be associated with the spontaneous abortion during ART.
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Affiliation(s)
- Sen Li
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, China
- Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Lei-Ling Chen
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, China
- Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Xing-Hua Wang
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Hai-Jing Zhu
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, China
- Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Xiao-Long Li
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, China
- Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Xie Feng
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, China
- Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Lei Guo
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, China
- Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Xiang-Hong Ou
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, China
- Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
- Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Jun-Yu Ma
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, China
- Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
- * E-mail:
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6
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Qiao L, Xu L, Yu L, Wynn J, Hernan R, Zhou X, Farkouh-Karoleski C, Krishnan US, Khlevner J, De A, Zygmunt A, Crombleholme T, Lim FY, Needelman H, Cusick RA, Mychaliska GB, Warner BW, Wagner AJ, Danko ME, Chung D, Potoka D, Kosiński P, McCulley DJ, Elfiky M, Azarow K, Fialkowski E, Schindel D, Soffer SZ, Lyon JB, Zalieckas JM, Vardarajan BN, Aspelund G, Duron VP, High FA, Sun X, Donahoe PK, Shen Y, Chung WK. Rare and de novo variants in 827 congenital diaphragmatic hernia probands implicate LONP1 as candidate risk gene. Am J Hum Genet 2021; 108:1964-1980. [PMID: 34547244 PMCID: PMC8546037 DOI: 10.1016/j.ajhg.2021.08.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/25/2021] [Indexed: 12/21/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly that is often accompanied by other anomalies. Although the role of genetics in the pathogenesis of CDH has been established, only a small number of disease-associated genes have been identified. To further investigate the genetics of CDH, we analyzed de novo coding variants in 827 proband-parent trios and confirmed an overall significant enrichment of damaging de novo variants, especially in constrained genes. We identified LONP1 (lon peptidase 1, mitochondrial) and ALYREF (Aly/REF export factor) as candidate CDH-associated genes on the basis of de novo variants at a false discovery rate below 0.05. We also performed ultra-rare variant association analyses in 748 affected individuals and 11,220 ancestry-matched population control individuals and identified LONP1 as a risk gene contributing to CDH through both de novo and ultra-rare inherited largely heterozygous variants clustered in the core of the domains and segregating with CDH in affected familial individuals. Approximately 3% of our CDH cohort who are heterozygous with ultra-rare predicted damaging variants in LONP1 have a range of clinical phenotypes, including other anomalies in some individuals and higher mortality and requirement for extracorporeal membrane oxygenation. Mice with lung epithelium-specific deletion of Lonp1 die immediately after birth, most likely because of the observed severe reduction of lung growth, a known contributor to the high mortality in humans. Our findings of both de novo and inherited rare variants in the same gene may have implications in the design and analysis for other genetic studies of congenital anomalies.
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Affiliation(s)
- Lu Qiao
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Le Xu
- Department of Pediatrics, University of California, San Diego Medical School, San Diego, CA 92093, USA
| | - Lan Yu
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rebecca Hernan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xueya Zhou
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Usha S Krishnan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julie Khlevner
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Aliva De
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Annette Zygmunt
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Foong-Yen Lim
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Howard Needelman
- University of Nebraska Medical Center College of Medicine, Omaha, NE 68114, USA
| | - Robert A Cusick
- University of Nebraska Medical Center College of Medicine, Omaha, NE 68114, USA
| | | | - Brad W Warner
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amy J Wagner
- Children's Hospital of Wisconsin, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melissa E Danko
- Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN 37232, USA
| | - Dai Chung
- Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN 37232, USA
| | | | | | - David J McCulley
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 52726, USA
| | | | - Kenneth Azarow
- Oregon Health & Science University, Portland, OR 97239, USA
| | | | | | | | - Jane B Lyon
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Jill M Zalieckas
- Department of Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Badri N Vardarajan
- Department of Neurology, Taub Institute for Research on Alzheimer Disease and the Aging Brain and the Gertrude H. Sergievsky Center, Columbia University, New York, NY 10032, USA
| | - Gudrun Aspelund
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vincent P Duron
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Frances A High
- Department of Surgery, Boston Children's Hospital, Boston, MA 02115, USA; Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xin Sun
- Department of Pediatrics, University of California, San Diego Medical School, San Diego, CA 92093, USA
| | - Patricia K Donahoe
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA; JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA.
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7
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Lange M, Begolli R, Giakountis A. Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine. Noncoding RNA 2021; 7:47. [PMID: 34449663 PMCID: PMC8395730 DOI: 10.3390/ncrna7030047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/26/2021] [Accepted: 08/01/2021] [Indexed: 12/11/2022] Open
Abstract
The cancer genome is characterized by extensive variability, in the form of Single Nucleotide Polymorphisms (SNPs) or structural variations such as Copy Number Alterations (CNAs) across wider genomic areas. At the molecular level, most SNPs and/or CNAs reside in non-coding sequences, ultimately affecting the regulation of oncogenes and/or tumor-suppressors in a cancer-specific manner. Notably, inherited non-coding variants can predispose for cancer decades prior to disease onset. Furthermore, accumulation of additional non-coding driver mutations during progression of the disease, gives rise to genomic instability, acting as the driving force of neoplastic development and malignant evolution. Therefore, detection and characterization of such mutations can improve risk assessment for healthy carriers and expand the diagnostic and therapeutic toolbox for the patient. This review focuses on functional variants that reside in transcribed or not transcribed non-coding regions of the cancer genome and presents a collection of appropriate state-of-the-art methodologies to study them.
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Affiliation(s)
- Marios Lange
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
| | - Rodiola Begolli
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
| | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
- Institute for Fundamental Biomedical Research, B.S.R.C “Alexander Fleming”, 34 Fleming Str., 16672 Vari, Greece
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8
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Wang J, Wang Y, Wang L, Chen WY, Sheng M. The diagnostic yield of intellectual disability: combined whole genome low-coverage sequencing and medical exome sequencing. BMC Med Genomics 2020; 13:70. [PMID: 32429945 PMCID: PMC7236547 DOI: 10.1186/s12920-020-0726-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/29/2020] [Indexed: 02/06/2023] Open
Abstract
Background Intellectual disability (ID) is a heterogeneous neurodevelopmental disorder with a complex genetic underpinning in its etiology. Chromosome microarray (CMA) is recommended as the first-tier diagnostic test for ID due to high detection rate of copy number variation (CNV). Methods To identify an appropriate clinical detection scheme for ID in Han Chinese patients, whole genome low-coverage sequencing was performed as the first-tier diagnostic test, and medical exome sequencing (MES) as the second-tier diagnostic test for patients with negative results of CNVs. Results A total of 19 pathogenic CNVs in 16/95(16.84%) ID patients and 10 pathogenic single-nucleotide variations (SNVs), including 6 novel mutations in 8/95(8.42%) ID patients were identified on whom no pathogenic CNVs were discovered. The detection rate of CNVs in ID with multiple congenital anomalies (MCA) subgroup was significantly higher than ID with autism spectrum disorders and other IDs subgroups. And the single-nucleotide variations showed a higher occurrence rate in the other IDs subgroup. Conclusions There were differences in the diagnostic yields of different variation types among the three ID subgroups. Our findings provided a new perspective on appropriate clinical detection scheme in different ID subgroups based on statistically significant differences among the three ID subgroups. The application of whole genome low-coverage sequencing as the first-tier diagnostic test for ID with MCA subgroup and MES as the first-tier diagnostic test for other ID subgroup was considered as an efficient clinical detection scheme.
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Affiliation(s)
- Jun Wang
- Department of Neurology, Affiliated Children's Hospital of Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Yan Wang
- Department of Neurology, Affiliated Children's Hospital of Capital Institute of Pediatrics, Beijing, 100020, China
| | - Liwen Wang
- Department of Neurology, Affiliated Children's Hospital of Capital Institute of Pediatrics, Beijing, 100020, China
| | - Wang Yang Chen
- Kaiumph Medical Diagnostics Co,Ltd, Beijing, 100102, China
| | - Min Sheng
- Kaiumph Medical Diagnostics Co,Ltd, Beijing, 100102, China
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9
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Lantieri F, Gimelli S, Viaggi C, Stathaki E, Malacarne M, Santamaria G, Grossi A, Mosconi M, Sloan-Béna F, Prato AP, Coviello D, Ceccherini I. Copy number variations in candidate genomic regions confirm genetic heterogeneity and parental bias in Hirschsprung disease. Orphanet J Rare Dis 2019; 14:270. [PMID: 31767031 PMCID: PMC6878652 DOI: 10.1186/s13023-019-1205-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 09/13/2019] [Indexed: 11/26/2022] Open
Abstract
Background Hirschsprung Disease (HSCR) is a congenital defect of the intestinal innervations characterized by complex inheritance. Many susceptibility genes including RET, the major HSCR gene, and several linked regions and associated loci have been shown to contribute to disease pathogenesis. Nonetheless, a proportion of patients still remains unexplained. Copy Number Variations (CNVs) have already been involved in HSCR, and for this reason we performed Comparative Genomic Hybridization (CGH), using a custom array with high density probes. Results A total of 20 HSCR candidate regions/genes was tested in 55 sporadic patients and four patients with already known chromosomal aberrations. Among 83 calls, 12 variants were experimentally validated, three of which involving the HSCR crucial genes SEMA3A/3D, NRG1, and PHOX2B. Conversely RET involvement in HSCR does not seem to rely on the presence of CNVs while, interestingly, several gains and losses did co-occur with another RET defect, thus confirming that more than one predisposing event is necessary for HSCR to develop. New loci were also shown to be involved, such as ALDH1A2, already found to play a major role in the enteric nervous system. Finally, all the inherited CNVs were of maternal origin. Conclusions Our results confirm a wide genetic heterogeneity in HSCR occurrence and support a role of candidate genes in expression regulation and cell signaling, thus contributing to depict further the molecular complexity of the genomic regions involved in the Enteric Nervous System development. The observed maternal transmission bias for HSCR associated CNVs supports the hypothesis that in females these variants might be more tolerated, requiring additional alterations to develop HSCR disease.
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Affiliation(s)
- Francesca Lantieri
- Dipartimento di Scienze della Salute, sezione di Biostatistica, Universita' degli Studi di Genova, 16132, Genoa, Italy
| | - Stefania Gimelli
- Department of Medical Genetic and Laboratories, University Hospitals of Geneva, Geneva, Switzerland
| | - Chiara Viaggi
- S.C. Laboratorio Genetica Umana, Ospedali Galliera, Genoa, Italy
| | - Elissavet Stathaki
- Department of Medical Genetic and Laboratories, University Hospitals of Geneva, Geneva, Switzerland
| | - Michela Malacarne
- S.C. Laboratorio Genetica Umana, Ospedali Galliera, Genoa, Italy.,Present address: U.O.C. Laboratorio di Genetica Umana, IRCCS Istituto Giannina Gaslini, Genoa, 16148, Italy
| | - Giuseppe Santamaria
- U.O.C. Genetica Medica, IRCCS, Istituto Giannina Gaslini, 16148, Genoa, Italy
| | - Alice Grossi
- U.O.C. Genetica Medica, IRCCS, Istituto Giannina Gaslini, 16148, Genoa, Italy
| | - Manuela Mosconi
- UOC Chirurgia Pediatrica, Istituto Giannina Gaslini, 16148, Genoa, Italy
| | - Frédérique Sloan-Béna
- Department of Medical Genetic and Laboratories, University Hospitals of Geneva, Geneva, Switzerland
| | - Alessio Pini Prato
- UOC Chirurgia Pediatrica, Istituto Giannina Gaslini, 16148, Genoa, Italy.,Present address: Children Hospital, AON SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Domenico Coviello
- S.C. Laboratorio Genetica Umana, Ospedali Galliera, Genoa, Italy.,Present address: U.O.C. Laboratorio di Genetica Umana, IRCCS Istituto Giannina Gaslini, Genoa, 16148, Italy
| | - Isabella Ceccherini
- U.O.C. Genetica Medica, IRCCS, Istituto Giannina Gaslini, 16148, Genoa, Italy.
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10
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Cheng SSW, Chan KYK, Leung KKP, Au PKC, Tam WK, Li SKM, Luk HM, Kan ASY, Chung BHY, Lo IFM, Tang MHY. Experience of chromosomal microarray applied in prenatal and postnatal settings in Hong Kong. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:196-207. [PMID: 30903683 DOI: 10.1002/ajmg.c.31697] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 12/14/2022]
Abstract
Chromosomal microarray (CMA) is recommended as a first tier investigation for patients with developmental delay (DD), intellectual disability (ID), autistic spectrum disorder (ASD), and multiple congenital anomalies (MCA). It is widely used in the prenatal and postnatal settings for detection of chromosomal aberrations. This is a retrospective review of all array comparative genomic hybridization (aCGH/ array CGH) findings ascertained in two major prenatal and postnatal genetic diagnostic centers in Hong Kong from June 2012 to December 2017. Medical records were reviewed for cases with pathogenic and variants of uncertain clinical significance (VUS). Classification of copy number variants (CNVs) was based on current knowledge and experience by August 2018. The aims of this review are to study the diagnostic yield of array CGH application in prenatal and postnatal settings in Hong Kong and to describe the spectrum of abnormalities found. Prenatal indications included abnormal ultrasound findings, positive Down syndrome screening, abnormal noninvasive prenatal test results, advanced maternal age and family history of chromosomal or genetic abnormalities. Postnatal indications included unexplained DD, ID, ASD, and MCA. A total of 1,261 prenatal subjects and 3,096 postnatal patients were reviewed. The prenatal diagnostic yield of pathogenic CNV and VUS (excluding those detectable by karyotype) was 3.5%. The postnatal diagnostic yield of pathogenic CNV was 15.2%. The detection rates for well-defined microdeletion and microduplication syndromes were 4.6% in prenatal and 6.1% (1 in 16 index patients) in postnatal cases, respectively. Chromosomes 15, 16, and 22 accounted for over 21 and 25% of pathogenic CNVs detected in prenatal and postnatal cohorts, respectively. This review provides the first large scale overview of genomic imbalance of mostly Chinese patients in prenatal and postnatal settings.
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Affiliation(s)
| | - Kelvin Y K Chan
- Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Hong Kong
| | | | - Patrick K C Au
- Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Hong Kong
| | - Wai-Keung Tam
- Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Hong Kong
| | - Samuel K M Li
- Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Hong Kong
| | - Ho-Ming Luk
- Department of Health, Clinical Genetic Service, Hong Kong
| | - Anita S Y Kan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Hong Kong
| | - Brian H Y Chung
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, HKSAR.,Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, HKSAR
| | - Ivan F M Lo
- Department of Health, Clinical Genetic Service, Hong Kong
| | - Mary H Y Tang
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, HKSAR
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11
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Qi H, Yu L, Zhou X, Wynn J, Zhao H, Guo Y, Zhu N, Kitaygorodsky A, Hernan R, Aspelund G, Lim FY, Crombleholme T, Cusick R, Azarow K, Danko ME, Chung D, Warner BW, Mychaliska GB, Potoka D, Wagner AJ, ElFiky M, Wilson JM, Nickerson D, Bamshad M, High FA, Longoni M, Donahoe PK, Chung WK, Shen Y. De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders. PLoS Genet 2018; 14:e1007822. [PMID: 30532227 PMCID: PMC6301721 DOI: 10.1371/journal.pgen.1007822] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 12/20/2018] [Accepted: 11/08/2018] [Indexed: 12/24/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a severe birth defect that is often accompanied by other congenital anomalies. Previous exome sequencing studies for CDH have supported a role of de novo damaging variants but did not identify any recurrently mutated genes. To investigate further the genetics of CDH, we analyzed de novo coding variants in 362 proband-parent trios including 271 new trios reported in this study. We identified four unrelated individuals with damaging de novo variants in MYRF (P = 5.3x10(-8)), including one likely gene-disrupting (LGD) and three deleterious missense (D-mis) variants. Eight additional individuals with de novo LGD or missense variants were identified from our other genetic studies or from the literature. Common phenotypes of MYRF de novo variant carriers include CDH, congenital heart disease and genitourinary abnormalities, suggesting that it represents a novel syndrome. MYRF is a membrane associated transcriptional factor highly expressed in developing diaphragm and is depleted of LGD variants in the general population. All de novo missense variants aggregated in two functional protein domains. Analyzing the transcriptome of patient-derived diaphragm fibroblast cells suggest that disease associated variants abolish the transcription factor activity. Furthermore, we showed that the remaining genes with damaging variants in CDH significantly overlap with genes implicated in other developmental disorders. Gene expression patterns and patient phenotypes support pleiotropic effects of damaging variants in these genes on CDH and other developmental disorders. Finally, functional enrichment analysis implicates the disruption of regulation of gene expression, kinase activities, intra-cellular signaling, and cytoskeleton organization as pathogenic mechanisms in CDH.
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Affiliation(s)
- Hongjian Qi
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Applied Mathematics and Applied Physics, Columbia University, New York, New York, United States of America
| | - Lan Yu
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Xueya Zhou
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Julia Wynn
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Haoquan Zhao
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, United States of America
| | - Yicheng Guo
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
| | - Na Zhu
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Alexander Kitaygorodsky
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, United States of America
| | - Rebecca Hernan
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Gudrun Aspelund
- Department of Surgery, Columbia University Medical Center, New York, New York, United States of America
| | - Foong-Yen Lim
- Cincinnati Children's Hospital, Cincinnati, Ohio, United States of America
| | | | - Robert Cusick
- Children's Hospital & Medical Center of Omaha, University of Nebraska College of Medicine, Omaha, Nebraska, United States of America
| | - Kenneth Azarow
- Department of Surgery, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Melissa E Danko
- Monroe Carell Jr. Children's Hospital, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Dai Chung
- Monroe Carell Jr. Children's Hospital, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Brad W Warner
- Washington University, St. Louis Children's Hospital, St. Louis, Missouri, United States of America
| | - George B Mychaliska
- University of Michigan, CS Mott Children's Hospital, Ann Arbor, Michigan, United States of America
| | - Douglas Potoka
- Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Amy J Wagner
- Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Mahmoud ElFiky
- Department of Pediatric Surgery, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Jay M Wilson
- Department of Surgery, Boston Children's Hospital, Boston, Massachusetts, United States of America
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Debbie Nickerson
- University of Washington, Seattle, Washington, United States of America
| | - Michael Bamshad
- University of Washington, Seattle, Washington, United States of America
| | - Frances A High
- Department of Surgery, Boston Children's Hospital, Boston, Massachusetts, United States of America
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Mauro Longoni
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Patricia K Donahoe
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Wendy K Chung
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
- Department of Medicine, Columbia University, New York, New York, United States of America
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, United States of America
- JP Sulzberger Columbia Genome Center, Columbia University Medical Center, New York, New York, United States of America
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12
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Brandler WM, Antaki D, Gujral M, Kleiber ML, Whitney J, Maile MS, Hong O, Chapman TR, Tan S, Tandon P, Pang T, Tang SC, Vaux KK, Yang Y, Harrington E, Juul S, Turner DJ, Thiruvahindrapuram B, Kaur G, Wang Z, Kingsmore SF, Gleeson JG, Bisson D, Kakaradov B, Telenti A, Venter JC, Corominas R, Toma C, Cormand B, Rueda I, Guijarro S, Messer KS, Nievergelt CM, Arranz MJ, Courchesne E, Pierce K, Muotri AR, Iakoucheva LM, Hervas A, Scherer SW, Corsello C, Sebat J. Paternally inherited cis-regulatory structural variants are associated with autism. Science 2018; 360:327-331. [PMID: 29674594 DOI: 10.1126/science.aan2261] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 08/07/2017] [Accepted: 02/27/2018] [Indexed: 12/15/2022]
Abstract
The genetic basis of autism spectrum disorder (ASD) is known to consist of contributions from de novo mutations in variant-intolerant genes. We hypothesize that rare inherited structural variants in cis-regulatory elements (CRE-SVs) of these genes also contribute to ASD. We investigated this by assessing the evidence for natural selection and transmission distortion of CRE-SVs in whole genomes of 9274 subjects from 2600 families affected by ASD. In a discovery cohort of 829 families, structural variants were depleted within promoters and untranslated regions, and paternally inherited CRE-SVs were preferentially transmitted to affected offspring and not to their unaffected siblings. The association of paternal CRE-SVs was replicated in an independent sample of 1771 families. Our results suggest that rare inherited noncoding variants predispose children to ASD, with differing contributions from each parent.
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Affiliation(s)
- William M Brandler
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.,Human Longevity, Inc., San Diego, CA 92121, USA
| | - Danny Antaki
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.,Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Madhusudan Gujral
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Morgan L Kleiber
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Joe Whitney
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Michelle S Maile
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Oanh Hong
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Timothy R Chapman
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Shirley Tan
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Prateek Tandon
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Timothy Pang
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Rady Children's Hospital, San Diego, CA 92123, USA
| | - Shih C Tang
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Rady Children's Hospital, San Diego, CA 92123, USA
| | - Keith K Vaux
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Yan Yang
- Oxford Nanopore Technologies, Inc., NY 10013, USA
| | | | - Sissel Juul
- Oxford Nanopore Technologies, Inc., NY 10013, USA
| | | | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Gaganjot Kaur
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Zhuozhi Wang
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA 92123, USA
| | - Joseph G Gleeson
- Howard Hughes Medical Institute, Rady Children's Institute of Genomic Medicine, Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
| | | | | | | | - J Craig Venter
- Human Longevity, Inc., San Diego, CA 92121, USA.,J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Roser Corominas
- Genetics Unit, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Claudio Toma
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Catalonia, Spain.,Neuroscience Research Australia, Sydney, Australia.,School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Bru Cormand
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain.,Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Catalonia, Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Catalonia, Spain.,Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues, Catalonia, Spain
| | - Isabel Rueda
- Department of Psychiatry, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Silvina Guijarro
- Child and Adolescent Mental Health Unit, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
| | - Karen S Messer
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA 92093, USA
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Maria J Arranz
- Research Laboratory Unit, Fundacio Docencia I Recerca Mutua Terrassa, Barcelona, Spain
| | - Eric Courchesne
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA 92093, USA
| | - Karen Pierce
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA 92093, USA
| | - Alysson R Muotri
- Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Lilia M Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Amaia Hervas
- Child and Adolescent Mental Health Unit, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
| | - Stephen W Scherer
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,McLaughlin Centre, University of Toronto, Toronto, Canada
| | - Christina Corsello
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Rady Children's Hospital, San Diego, CA 92123, USA
| | - Jonathan Sebat
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA. .,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
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13
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Xu M, Ji Y, Zhang T, Jiang X, Fan Y, Geng J, Li F. Clinical Application of Chromosome Microarray Analysis in Han Chinese Children with Neurodevelopmental Disorders. Neurosci Bull 2018; 34:981-991. [PMID: 29948840 DOI: 10.1007/s12264-018-0238-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/05/2018] [Indexed: 02/04/2023] Open
Abstract
Chromosome microarray analysis (CMA) is a cost-effective molecular cytogenetic technique that has been used as a first-line diagnostic test in neurodevelopmental disorders in the USA since 2011. The impact of CMA results on clinical practice in China is not yet well studied, so we aimed to better evaluate this phenomenon. We analyzed the CMA results from 434 patients in our clinic, and characterized their molecular diagnoses, clinical features, and follow-up clinical actions based on these results. The overall diagnostic yield for our patients was 13.6% (59 out of 434). This gave a detection rate of 14.7% for developmental delay/intellectual disability (DD/ID, 38/259) and 12% for autism spectrum disorders (ASDs, 21/175). Thirty-three recurrent (n ≥ 2) variants were found, distributed at six chromosomal loci involving known chromosome syndromes (such as DiGeorge, Williams Beuren, and Angelman/Prader-Willi syndromes). The spectrum of positive copy number variants in our study was comparable to that reported in Caucasian populations, but with specific characteristics. Parental origin tests indicated an effect involving a significant maternal transmission bias to sons. The majority of patients with positive results (94.9%) had benefits, allowing earlier diagnosis (36/59), prioritized full clinical management (28/59), medication changes (7/59), a changed prognosis (30/59), and prenatal genetic counseling (15/59). Our results provide information on de novo mutations in Chinese children with DD/ID and/or ASDs. Our data showed that microarray testing provides immediate clinical utility for patients. It is expected that the personalized medical care of children with developmental disabilities will lead to improved outcomes in long-term developmental potential. We advocate using the diagnostic yield of clinically actionable results to evaluate CMA as it provides information of both clinical validity and clinical utility.
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Affiliation(s)
- Mingyu Xu
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Yiting Ji
- Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Ting Zhang
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Xiaodong Jiang
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.,Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430016, China
| | - Yun Fan
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Juan Geng
- Hangzhou Joingenome Diagnostics, Hangzhou, 311188, China.
| | - Fei Li
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China. .,Shanghai Institute of Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
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14
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Pal LR, Kundu K, Yin Y, Moult J. CAGI4 SickKids clinical genomes challenge: A pipeline for identifying pathogenic variants. Hum Mutat 2017; 38:1169-1181. [PMID: 28512736 PMCID: PMC5577808 DOI: 10.1002/humu.23257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 12/21/2022]
Abstract
Compared with earlier more restricted sequencing technologies, identification of rare disease variants using whole-genome sequence has the possibility of finding all causative variants, but issues of data quality and an overwhelming level of background variants complicate the analysis. The CAGI4 SickKids clinical genome challenge provided an opportunity to assess the landscape of variants found in a difficult set of 25 unsolved rare disease cases. To address the challenge, we developed a three-stage pipeline, first carefully analyzing data quality, then classifying high-quality gene-specific variants into seven categories, and finally examining each candidate variant for compatibility with the often complex phenotypes of these patients for final prioritization. Variants consistent with the phenotypes were found in 24 out of the 25 cases, and in a number of these, there are prioritized variants in multiple genes. Data quality analysis suggests that some of the selected variants are likely incorrect calls, complicating interpretation. The data providers followed up on three suggested variants with Sanger sequencing, and in one case, a prioritized variant was confirmed as likely causative by the referring physician, providing a diagnosis in a previously intractable case.
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Affiliation(s)
- Lipika R. Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850
| | - Kunal Kundu
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Yizhou Yin
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
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Skryabin NA, Vasilyev SA, Lebedev IN. Epigenetic silencing of genomic structural variations. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417100106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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