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Carlisle SG, Albasha H, Michelena HI, Sabate-Rotes A, Bianco L, De Backer J, Mosquera LM, Yetman AT, Bissell MM, Andreassi MG, Foffa I, Hui DS, Caffarelli A, Kim YY, Guo D, Citro R, De Marco M, Tretter JT, McBride KL, Milewicz DM, Body SC, Prakash SK. Rare genomic copy number variants implicate new candidate genes for bicuspid aortic valve. PLoS One 2024; 19:e0304514. [PMID: 39240962 DOI: 10.1371/journal.pone.0304514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/14/2024] [Indexed: 09/08/2024] Open
Abstract
Bicuspid aortic valve (BAV), the most common congenital heart defect, is a major cause of aortic valve disease requiring valve interventions and thoracic aortic aneurysms predisposing to acute aortic dissections. The spectrum of BAV ranges from early onset valve and aortic complications (EBAV) to sporadic late onset disease. Rare genomic copy number variants (CNVs) have previously been implicated in the development of BAV and thoracic aortic aneurysms. We determined the frequency and gene content of rare CNVs in EBAV probands (n = 272) using genome-wide SNP microarray analysis and three complementary CNV detection algorithms (cnvPartition, PennCNV, and QuantiSNP). Unselected control genotypes from the Database of Genotypes and Phenotypes were analyzed using identical methods. We filtered the data to select large genic CNVs that were detected by multiple algorithms. Findings were replicated in a BAV cohort with late onset sporadic disease (n = 5040). We identified 3 large and rare (< 1,1000 in controls) CNVs in EBAV probands. The burden of CNVs intersecting with genes known to cause BAV when mutated was increased in case-control analysis. CNVs intersecting with GATA4 and DSCAM were enriched in cases, recurrent in other datasets, and segregated with disease in families. In total, we identified potentially pathogenic CNVs in 9% of EBAV cases, implicating alterations of candidate genes at these loci in the pathogenesis of BAV.
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Affiliation(s)
- Steven G Carlisle
- University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Hasan Albasha
- University College Dublin School of Medicine, Dublin, Ireland
| | | | | | - Lisa Bianco
- Vall d'Hebron University Hospital, Barcelona, Spain
| | | | | | - Anji T Yetman
- University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | | | | | - Ilenia Foffa
- Consiglio Nazionale delle Richerche (CNR), Instituto di Fisiologia Clinica, Pisa, Italy
| | - Dawn S Hui
- University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Anthony Caffarelli
- Hoag Memorial Hospital Presbyterian, Newport Beach, California, United States of America
| | - Yuli Y Kim
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dongchuan Guo
- University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Rodolfo Citro
- University Hospital "San Giovanni di Dio e Ruggi d'Aragona," Salerno, Italy
| | - Margot De Marco
- Schola Medica Salernitana, University of Salerno, Baronissi, Italy
| | | | - Kim L McBride
- University of Calgary Cumming School of Medicine, Calgary, Alberta, Canada
| | - Dianna M Milewicz
- University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Simon C Body
- Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Siddharth K Prakash
- University of Texas Health Science Center at Houston, Houston, Texas, United States of America
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Elsayed LEO, AlHarbi NA, Alqarni AM, Eltayeb HHE, Mostafa NMM, Abdulrahim MM, Zaid HIB, Alanzi LM, Ababtain SA, Aldulaijan K, Aloyouni SY, Othman MAK, Alkheilewi MA, Binduraihem AM, Alrukban HA, Ahmed HY, AlRadini FA, Alahdal HM, Mushiba AM, Alzaher OA. Chromosome 16p11.2 microdeletion syndrome with microcephaly and Dandy-Walker malformation spectrum: expanding the known phenotype. Hum Genomics 2024; 18:95. [PMID: 39232803 PMCID: PMC11376027 DOI: 10.1186/s40246-024-00662-0] [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: 12/20/2023] [Accepted: 08/19/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND Chromosome 16p11.2 deletions and duplications were found to be the second most common copy number variation (CNV) reported in cases with clinical presentation suggestive of chromosomal syndromes. Chromosome 16p11.2 deletion syndrome shows remarkable phenotypic heterogeneity with a wide variability of presentation extending from normal development and cognition to severe phenotypes. The clinical spectrum ranges from neurocognitive and global developmental delay (GDD), intellectual disability, and language defects (dysarthria /apraxia) to neuropsychiatric and autism spectrum disorders. Other presentations include dysmorphic features, congenital malformations, insulin resistance, and a tendency for obesity. Our study aims to narrow the gap of knowledge in Saudi Arabia and the Middle Eastern and Northern African (MENA) region about genetic disorders, particularly CNV-associated disorders. Despite their rarity, genetic studies in the MENA region revealed high potential with remarkable genetic and phenotypic novelty. RESULTS We identified a heterozygous de novo recurrent proximal chromosome 16p11.2 microdeletion by microarray (arr[GRCh38]16p11.2(29555974_30166595)x1) [(arr[GRCh37]16p11.2(29567295_30177916)x1)] and confirmed by whole exome sequencing (arr[GRCh37]16p11.2(29635211_30199850)x1). We report a Saudi girl with severe motor and cognitive disability, myoclonic epilepsy, deafness, and visual impairment carrying the above-described deletion. Our study broadens the known phenotypic spectrum associated with recurrent proximal 16p11.2 microdeletion syndrome to include developmental dysplasia of the hip, optic atrophy, and a flat retina. Notably, the patient exhibited a rare combination of microcephaly, features consistent with the Dandy-Walker spectrum, and a thin corpus callosum (TCC), which are extremely infrequent presentations in patients with the 16p11.2 microdeletion. Additionally, the patient displayed areas of skin and hair hypopigmentation, attributed to a homozygous hypomorphic allele in the TYR gene. CONCLUSION This report expands on the clinical phenotype associated with proximal 16p11.2 microdeletion syndrome, highlighting the potential of genetic research in Saudi Arabia and the MENA region. It underscores the importance of similar future studies.
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Affiliation(s)
- Liena Elbaghir Omer Elsayed
- Department of Basic Sciences, College of Medicine, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Norah Ayed AlHarbi
- Department of Internal Medicine, College of Medicine, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia.
| | - Ashwaq Mohammed Alqarni
- Foundation Year of Health Colleges, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Huda Hussein Elwasila Eltayeb
- Department of Basic Sciences, College of Medicine, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Noura Mostafa Mohamed Mostafa
- Department of Basic Sciences, College of Medicine, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
- Medical Biochemistry Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Maha Mohammed Abdulrahim
- Research and Academic Accreditation, Academic Affairs, King Abdullah bin Abdulaziz University Hospital, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Hadeel Ibrahim Bin Zaid
- Out-Patient department, King Abdullah bin Abdulaziz University Hospital, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Latifah Mansour Alanzi
- Department of Pathology and Laboratory Medicine, King Abdullah Bin Abdulaziz University Hospital, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Sarah Abdullah Ababtain
- Genetics Section, Research Department, Health Sciences Research Center, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Khawlah Aldulaijan
- Genetics Section, Research Department, Health Sciences Research Center, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Sheka Yagub Aloyouni
- Genetics Section, Research Department, Health Sciences Research Center, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | | | | | - Adel Mohammed Binduraihem
- Genetics Section, Research Department, Health Sciences Research Center, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Hadeel Abdollah Alrukban
- Pediatric Department, Division of Genetic and Metabolic, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Hiba Yousif Ahmed
- Pediatrics department, King Abdullah bin Abdulaziz University Hospital, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Faten Abdullah AlRadini
- Family and Community Medicine Department, College of Medicine, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Hadil Mohammad Alahdal
- Department of Biology, College of Science, Princes Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Aziza Mufareh Mushiba
- Pediatrics department, King Abdullah bin Abdulaziz University Hospital, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Omaima Abdulazeem Alzaher
- Pediatric Department, College of Medicine, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
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Zhuang J, Zhang N, Fu W, Jiang Y, Chen Y, Chen C. Prenatal diagnosis of fetuses with 15q11.2 BP1-BP2 microdeletion in the Chinese population: a seven-year single-center retrospective study. Mol Cytogenet 2024; 17:20. [PMID: 39218907 PMCID: PMC11367773 DOI: 10.1186/s13039-024-00690-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 08/25/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND The 15q11.2 BP1-BP2 microdeletion syndrome is associated with developmental delays, language impairments, neurobehavioral disorders, and psychiatric complications. The aim of the present study was to provide prenatal and postnatal clinical data for 16 additional fetuses diagnosed with the 15q11.2 BP1-BP2 microdeletion syndrome in the Chinese population. METHODS A total of 5,789 pregnancy women that underwent amniocentesis were enrolled in the present study. Both karyotype analysis and chromosomal microarray analysis (CMA) were conducted on these subjects to detect chromosomal abnormalities and copy number variants (CNVs). Whole exome sequencing (WES) was performed to investigate sequence variants in subjects with clinical abnormalities after birth. RESULTS Sixteen fetuses with 15q11.2 BP1-BP2 microdeletion were identified in the present study, with a detection rate of 0.28% (16/5,789). The 15q11.2 BP1-BP2 microdeletion fragments ranged from 311.8 kb to 849.7 kb, encompassing the NIPA1, NIPA2, CYFIP1, and TUBGCP5 genes. The follow-up results regarding pregnancy outcomes showed that five cases opted for pregnancy termination, while the remaining cases continued with their pregnancies. Subsequent postnatal follow-up indicated that only one case with the 15q11.2 BP1-BP2 microdeletion displayed neurodevelopmental disorders, demonstrating an incomplete penetrance rate of 9.09% (1/11). CONCLUSION The majority of fetuses with the 15q11.2 microdeletion exhibit typical features during early childhood, indicating a low penetrance and mild impact. Nonetheless, pregnancies involving fetuses with the 15q11.2 microdeletion require thorough prenatal counseling. Additionally, enhanced supervision and extended postnatal monitoring are warranted for those who choose to proceed with their pregnancies.
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Affiliation(s)
- Jianlong Zhuang
- Prenatal diagnosis center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, China.
| | - Na Zhang
- Prenatal diagnosis center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, China
| | - Wanyu Fu
- Prenatal diagnosis center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, China
| | - Yuying Jiang
- Prenatal diagnosis center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, China
| | - Yu'e Chen
- Department of Ultrasound, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, China.
| | - Chunnuan Chen
- Department of Neurology, Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian Province, China.
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Zhou W, Wang C, Fu L, Shi W, Zhang A, Jia Z, Zhao X, Fu D, Zheng B. Copy number variants at 4q31.3 affecting the regulatory region of FBXW7 associated with neurodevelopmental delay. Clin Genet 2024; 106:354-359. [PMID: 38780184 DOI: 10.1111/cge.14548] [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: 01/11/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
Emerging research has demonstrated that genomic alterations disrupting topologically associated domains (TADs) and chromatin interactions underlie the pathogenic mechanisms of specific copy number variants (CNVs) in neurodevelopmental disorders. We report two patients with a de novo deletion and a duplication in chromosome 4q31, potentially causing FBX-related neurodevelopmental syndrome by affecting the regulatory region of FBXW7. High-throughput chromosome conformation capture (Hi-C) analysis using available capture data in neural progenitor cells revealed the rewiring of the TAD boundary close to FBXW7. Both patients exhibited facial dysmorphisms, cardiac and limb abnormalities, and neurodevelopmental delays, showing significant clinical overlap with previously reported FBXW7-related features. We also included an additional 10 patients with CNVs in the 4q31 region from the literature and the DECIPHER database for Hi-C analysis, which confirmed that disruption of the regulatory region of FBXW7 likely contributes to the developmental defects observed in these patients.
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Affiliation(s)
- Wei Zhou
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chunli Wang
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Luhan Fu
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Shi
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Aihua Zhang
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Zhanjun Jia
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoke Zhao
- Department of Rehabilitation Medicine, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Dalin Fu
- Department of Rehabilitation Medicine, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Bixia Zheng
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
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Rahaie Z, Rabiee HR, Alinejad-Rokny H. CNVDeep: deep association of copy number variants with neurocognitive disorders. BMC Bioinformatics 2024; 25:283. [PMID: 39210319 PMCID: PMC11360772 DOI: 10.1186/s12859-024-05874-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 07/17/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Copy number variants (CNVs) have become increasingly instrumental in understanding the etiology of all diseases and phenotypes, including Neurocognitive Disorders (NDs). Among the well-established regions associated with ND are small parts of chromosome 16 deletions (16p11.2) and chromosome 15 duplications (15q3). Various methods have been developed to identify associations between CNVs and diseases of interest. The majority of methods are based on statistical inference techniques. However, due to the multi-dimensional nature of the features of the CNVs, these methods are still immature. The other aspect is that regions discovered by different methods are large, while the causative regions may be much smaller. RESULTS In this study, we propose a regularized deep learning model to select causal regions for the target disease. With the help of the proximal [20] gradient descent algorithm, the model utilizes the group LASSO concept and embraces a deep learning model in a sparsity framework. We perform the CNV analysis for 74,811 individuals with three types of brain disorders, autism spectrum disorder (ASD), schizophrenia (SCZ), and developmental delay (DD), and also perform cumulative analysis to discover the regions that are common among the NDs. The brain expression of genes associated with diseases has increased by an average of 20 percent, and genes with homologs in mice that cause nervous system phenotypes have increased by 18 percent (on average). The DECIPHER data source also seeks other phenotypes connected to the detected regions alongside gene ontology analysis. The target diseases are correlated with some unexplored regions, such as deletions on 1q21.1 and 1q21.2 (for ASD), deletions on 20q12 (for SCZ), and duplications on 8p23.3 (for DD). Furthermore, our method is compared with other machine learning algorithms. CONCLUSIONS Our model effectively identifies regions associated with phenotypic traits using regularized deep learning. Rather than attempting to analyze the whole genome, CNVDeep allows us to focus only on the causative regions of disease.
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Affiliation(s)
- Zahra Rahaie
- BCB Group, DML, Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Hamid R Rabiee
- BCB Group, DML, Department of Computer Engineering, Sharif University of Technology, Tehran, Iran.
| | - Hamid Alinejad-Rokny
- UNSW Biomedical Machine Learning Lab (BML), School of Biomedical Engineering, UNSW Sydney, Sydney, Australia.
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Sugiyama Y, Okada S, Daigaku Y, Kusumoto E, Ito T. Strategic targeting of Cas9 nickase induces large segmental duplications. CELL GENOMICS 2024; 4:100610. [PMID: 39053455 DOI: 10.1016/j.xgen.2024.100610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 04/15/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024]
Abstract
Gene/segmental duplications play crucial roles in genome evolution and variation. Here, we introduce paired nicking-induced amplification (PNAmp) for their experimental induction. PNAmp strategically places two Cas9 nickases upstream and downstream of a replication origin on opposite strands. This configuration directs the sister replication forks initiated from the origin to break at the nicks, generating a pair of one-ended double-strand breaks. If homologous sequences flank the two break sites, then end resection converts them to single-stranded DNAs that readily anneal to drive duplication of the region bounded by the homologous sequences. PNAmp induces duplication of segments as large as ∼1 Mb with efficiencies exceeding 10% in the budding yeast Saccharomyces cerevisiae. Furthermore, appropriate splint DNAs allow PNAmp to duplicate/multiplicate even segments not bounded by homologous sequences. We also provide evidence for PNAmp in mammalian cells. Therefore, PNAmp provides a prototype method to induce structural variations by manipulating replication fork progression.
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Affiliation(s)
- Yuki Sugiyama
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Satoshi Okada
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Yasukazu Daigaku
- Cancer Genome Dynamics Project, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Emiko Kusumoto
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan.
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Pereira SSS, Pinto IP, Santos VCDP, Silva RC, Costa EOA, da Cruz AS, da Cruz AD, da Silva CC, Minasi LB. Analysis of parental origin of de novo pathogenic CNVs in patients with intellectual disability. Genet Mol Biol 2024; 47:e20230313. [PMID: 39136576 PMCID: PMC11320663 DOI: 10.1590/1678-4685-gmb-2023-0313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 06/25/2024] [Indexed: 08/16/2024] Open
Abstract
Chromosomal Microarray Analysis (CMA) has increased the comprehension of the mechanisms of copy number variation (CNV) formation, classification of these rearrangements, type of recurrence, and its origin, and has also been a powerful approach to identifying CNVs in individuals with intellectual disability. The aim of this study was to establish the parental origin of de novo pathogenic CNV in a cohort of patients with intellectual disability from the public health system of Goiás-Brazil. CMA was done in 76 trios and we identified 15 de novo pathogenic CNVs in 12 patients with intellectual disability. In a total of 15 de novo pathogenic CNV, 60% were derived from the maternal germline and 40% from the paternal germline. CNV flanked by low copy repeats (LCR) were identified in 46.7% and most of them were of maternal origin. No significant association was observed between paternal age and the mutation rate of de novo CNVs. The presence of high-identity LCRs increases the occurrence of CNV formation mediated by non-allelic homologous recombination and the majority of paternal CNVs are non-recurrent. The mechanism of formation of these CNV may have been by microhomology-mediated break-induced replication or non-homologous end joining.
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Affiliation(s)
- Samara Socorro Silva Pereira
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Programa de Pós-Graduação em Genética e Biologia Molecular, Goiânia, GO, Brazil
| | - Irene Plaza Pinto
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Victor Cortázio do Prado Santos
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Programa de Pós-Graduação em Genética e Biologia Molecular, Goiânia, GO, Brazil
| | - Rafael Carneiro Silva
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Emília Oliveira Alves Costa
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Alex Silva da Cruz
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Aparecido Divino da Cruz
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Secretaria Estadual de Saúde de Goiás, Centro Estadual de Reabilitação e Readaptação Dr. Henrique Santillo, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Programa de Pós-Graduação em Genética e Biologia Molecular, Goiânia, GO, Brazil
| | - Cláudio Carlos da Silva
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Secretaria Estadual de Saúde de Goiás, Centro Estadual de Reabilitação e Readaptação Dr. Henrique Santillo, Goiânia, GO, Brazil
| | - Lysa Bernardes Minasi
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
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Forsyth JK, Zhu J, Chavannes AS, Trevorrow ZH, Hyat M, Sievertsen SA, Ferreira-Ianone S, Conomos MP, Nuechterlein KH, Asarnow RF, Green MF, Karlsgodt KH, Perkins DO, Cannon TD, Addington JM, Cadenhead KS, Cornblatt BA, Keshavan MS, Mathalon DH, Stone WS, Tsuang MT, Walker EF, Woods SW, Narr KL, McEwen SC, Schleifer CH, Yee CM, Diehl CK, Guha A, Miller GA, Alexander-Bloch AF, Seidlitz J, Bethlehem RAI, Ophoff RA, Bearden CE. Fetal Gene Regulatory Gene Deletions are Associated with Poor Cognition and Altered Cortical Morphology in Schizophrenia and Community-Based Samples. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.02.24311302. [PMID: 39211869 PMCID: PMC11361264 DOI: 10.1101/2024.08.02.24311302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Schizophrenia spectrum disorders (SSDs) are characterized by substantial clinical and genetic heterogeneity. Multiple recurrent copy number variants (CNVs) increase risk for SSDs; however, how known risk CNVs and broader genome-wide CNVs influence clinical variability is unclear. The current study examined associations between borderline intellectual functioning or childhood-onset psychosis, known risk CNVs, and burden of deletions affecting genes in 18 previously validated neurodevelopmental gene-sets in 618 SSD individuals. CNV associations were assessed for replication in 235 SSD relatives and 583 controls, and 9,930 youth from the Adolescent Brain Cognitive Development (ABCD) Study. Known SSD- and neurodevelopmental disorder (NDD)-risk CNVs were associated with borderline intellectual functioning in SSD cases (odds ratios (OR) = 7.09 and 4.57, respectively); NDD-risk deletions were nominally associated with childhood-onset psychosis (OR = 4.34). Furthermore, deletion of genes involved in regulating gene expression during fetal brain development was associated with borderline intellectual functioning across SSD cases and non-cases (OR = 2.58), with partial replication in the ABCD cohort. Exploratory analyses of cortical morphology showed associations between fetal gene regulatory gene deletions and altered gray matter volume and cortical thickness across cohorts. Results highlight contributions of known risk CNVs to phenotypic variability in SSD and the utility of a neurodevelopmental framework for identifying mechanisms that influence phenotypic variability in SSDs, as well as the broader population, with implications for personalized medicine approaches to care.
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Porubsky D, Dashnow H, Sasani TA, Logsdon GA, Hallast P, Noyes MD, Kronenberg ZN, Mokveld T, Koundinya N, Nolan C, Steely CJ, Guarracino A, Dolzhenko E, Harvey WT, Rowell WJ, Grigorev K, Nicholas TJ, Oshima KK, Lin J, Ebert P, Watkins WS, Leung TY, Hanlon VCT, McGee S, Pedersen BS, Goldberg ME, Happ HC, Jeong H, Munson KM, Hoekzema K, Chan DD, Wang Y, Knuth J, Garcia GH, Fanslow C, Lambert C, Lee C, Smith JD, Levy S, Mason CE, Garrison E, Lansdorp PM, Neklason DW, Jorde LB, Quinlan AR, Eberle MA, Eichler EE. A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.606142. [PMID: 39149261 PMCID: PMC11326147 DOI: 10.1101/2024.08.05.606142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Using five complementary short- and long-read sequencing technologies, we phased and assembled >95% of each diploid human genome in a four-generation, 28-member family (CEPH 1463) allowing us to systematically assess de novo mutations (DNMs) and recombination. From this family, we estimate an average of 192 DNMs per generation, including 75.5 de novo single-nucleotide variants (SNVs), 7.4 non-tandem repeat indels, 79.6 de novo indels or structural variants (SVs) originating from tandem repeats, 7.7 centromeric de novo SVs and SNVs, and 12.4 de novo Y chromosome events per generation. STRs and VNTRs are the most mutable with 32 loci exhibiting recurrent mutation through the generations. We accurately assemble 288 centromeres and six Y chromosomes across the generations, documenting de novo SVs, and demonstrate that the DNM rate varies by an order of magnitude depending on repeat content, length, and sequence identity. We show a strong paternal bias (75-81%) for all forms of germline DNM, yet we estimate that 17% of de novo SNVs are postzygotic in origin with no paternal bias. We place all this variation in the context of a high-resolution recombination map (~3.5 kbp breakpoint resolution). We observe a strong maternal recombination bias (1.36 maternal:paternal ratio) with a consistent reduction in the number of crossovers with increasing paternal (r=0.85) and maternal (r=0.65) age. However, we observe no correlation between meiotic crossover locations and de novo SVs, arguing against non-allelic homologous recombination as a predominant mechanism. The use of multiple orthogonal technologies, near-telomere-to-telomere phased genome assemblies, and a multi-generation family to assess transmission has created the most comprehensive, publicly available "truth set" of all classes of genomic variants. The resource can be used to test and benchmark new algorithms and technologies to understand the most fundamental processes underlying human genetic variation.
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Affiliation(s)
- David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Harriet Dashnow
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Thomas A Sasani
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Present address: Department of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Pille Hallast
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Michelle D Noyes
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Nidhi Koundinya
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Cody J Steely
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Department of Internal Medicine, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Andrea Guarracino
- Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - William J Rowell
- Department of Internal Medicine, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Kirill Grigorev
- Blue Marble Space Institute of Science, Seattle, WA, USA
- Core Unit Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Thomas J Nicholas
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Keisuke K Oshima
- Present address: Department of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jiadong Lin
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Peter Ebert
- Core Unit Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - W Scott Watkins
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Tiffany Y Leung
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada
| | | | - Sean McGee
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Brent S Pedersen
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Michael E Goldberg
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Hannah C Happ
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Hyeonsoo Jeong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Present address: Altos Labs, San Diego, CA, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Daniel D Chan
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada
| | - Yanni Wang
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada
| | - Jordan Knuth
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Gage H Garcia
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Joshua D Smith
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Erik Garrison
- Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Deborah W Neklason
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | | | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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10
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Bohaczuk SC, Amador ZJ, Li C, Mallory BJ, Swanson EG, Ranchalis J, Vollger MR, Munson KM, Walsh T, Hamm MO, Mao Y, Lieber A, Stergachis AB. Resolving the chromatin impact of mosaic variants with targeted Fiber-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.602608. [PMID: 39026856 PMCID: PMC11257596 DOI: 10.1101/2024.07.09.602608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Accurately quantifying the functional consequences of non-coding mosaic variants requires the pairing of DNA sequence with both accessible and closed chromatin architectures along individual DNA molecules-a pairing that cannot be achieved using traditional fragmentation-based chromatin assays. We demonstrate that targeted single-molecule chromatin fiber sequencing (Fiber-seq) achieves this, permitting single-molecule, long-read genomic and epigenomic profiling across targeted >100 kilobase loci with ~10-fold enrichment over untargeted sequencing. Targeted Fiber-seq reveals that pathogenic expansions of the DMPK CTG repeat that underlie Myotonic Dystrophy 1 are characterized by somatic instability and disruption of multiple nearby regulatory elements, both of which are repeat length-dependent. Furthermore, we reveal that therapeutic adenine base editing of the segmentally duplicated γ-globin (HBG1/HBG2) promoters in primary human hematopoietic cells induced towards an erythroblast lineage increases the accessibility of the HBG1 promoter as well as neighboring regulatory elements. Overall, we find that these non-protein coding mosaic variants can have complex impacts on chromatin architectures, including extending beyond the regulatory element harboring the variant.
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Affiliation(s)
- Stephanie C. Bohaczuk
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Zachary J. Amador
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Chang Li
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Elliott G. Swanson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jane Ranchalis
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Mitchell R. Vollger
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Tom Walsh
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Morgan O. Hamm
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Yizi Mao
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Andre Lieber
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Andrew B. Stergachis
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
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11
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Zeng Y, Ding H, Wang X, Huang Y, Liu L, Du L, Lu J, Wu J, Zeng Y, Mai M, Zhu J, Yu L, He W, Guo F, Peng H, Yao C, Qi Y, Liu Y, Li F, Yang J, Hu R, Liang J, Wang J, Wang W, Zhang Y, Yin A. High positive predictive value of CNVs detected by clinical exome sequencing in suspected genetic diseases. J Transl Med 2024; 22:644. [PMID: 38982507 PMCID: PMC11234535 DOI: 10.1186/s12967-024-05468-1] [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: 04/07/2024] [Accepted: 07/03/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Genetic disorders often manifest as abnormal fetal or childhood development. Copy number variations (CNVs) represent a significant genetic mechanism underlying such disorders. Despite their importance, the effectiveness of clinical exome sequencing (CES) in detecting CNVs, particularly small ones, remains incompletely understood. We aimed to evaluate the detection of both large and small CNVs using CES in a substantial clinical cohort, including parent-offspring trios and proband only analysis. METHODS We conducted a retrospective analysis of CES data from 2428 families, collected from 2018 to 2021. Detected CNV were categorized as large or small, and various validation techniques including chromosome microarray (CMA), Multiplex ligation-dependent probe amplification assay (MLPA), and/or PCR-based methods, were employed for cross-validation. RESULTS Our CNV discovery pipeline identified 171 CNV events in 154 cases, resulting in an overall detection rate of 6.3%. Validation was performed on 113 CNVs from 103 cases to assess CES reliability. The overall concordance rate between CES and other validation methods was 88.49% (100/113). Specifically, CES demonstrated complete consistency in detecting large CNV. However, for small CNVs, consistency rates were 81.08% (30/37) for deletions and 73.91% (17/23) for duplications. CONCLUSION CES demonstrated high sensitivity and reliability in CNV detection. It emerges as an economical and dependable option for the clinical CNV detection in cases of developmental abnormalities, especially fetal structural abnormalities.
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Affiliation(s)
- Yimo Zeng
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Hongke Ding
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Xingwang Wang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Yanlin Huang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Ling Liu
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Li Du
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Jian Lu
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Jing Wu
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Yukun Zeng
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Mingqin Mai
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Juan Zhu
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Lihua Yu
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Wei He
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Fangfang Guo
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Haishan Peng
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Cuize Yao
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Yiming Qi
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Yuan Liu
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Fake Li
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Jiexia Yang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Rong Hu
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Jie Liang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Jicheng Wang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Wei Wang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Yan Zhang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China.
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China.
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China.
| | - Aihua Yin
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China.
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China.
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China.
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12
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Abedini SS, Akhavantabasi S, Liang Y, Heng JIT, Alizadehsani R, Dehzangi I, Bauer DC, Alinejad-Rokny H. A critical review of the impact of candidate copy number variants on autism spectrum disorder. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 794:108509. [PMID: 38977176 DOI: 10.1016/j.mrrev.2024.108509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/14/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder (NDD) influenced by genetic, epigenetic, and environmental factors. Recent advancements in genomic analysis have shed light on numerous genes associated with ASD, highlighting the significant role of both common and rare genetic mutations, as well as copy number variations (CNVs), single nucleotide polymorphisms (SNPs) and unique de novo variants. These genetic variations disrupt neurodevelopmental pathways, contributing to the disorder's complexity. Notably, CNVs are present in 10 %-20 % of individuals with autism, with 3 %-7 % detectable through cytogenetic methods. While the role of submicroscopic CNVs in ASD has been recently studied, their association with genomic loci and genes has not been thoroughly explored. In this review, we focus on 47 CNV regions linked to ASD, encompassing 1632 genes, including protein-coding genes and long non-coding RNAs (lncRNAs), of which 659 show significant brain expression. Using a list of ASD-associated genes from SFARI, we detect 17 regions harboring at least one known ASD-related protein-coding gene. Of the remaining 30 regions, we identify 24 regions containing at least one protein-coding gene with brain-enriched expression and a nervous system phenotype in mouse mutants, and one lncRNA with both brain-enriched expression and upregulation in iPSC to neuron differentiation. This review not only expands our understanding of the genetic diversity associated with ASD but also underscores the potential of lncRNAs in contributing to its etiology. Additionally, the discovered CNVs will be a valuable resource for future diagnostic, therapeutic, and research endeavors aimed at prioritizing genetic variations in ASD.
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Affiliation(s)
- Seyedeh Sedigheh Abedini
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia; School of Biotechnology & Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Shiva Akhavantabasi
- Department of Molecular Biology and Genetics, Yeni Yuzyil University, Istanbul, Turkey; Ghiaseddin Jamshid Kashani University, Andisheh University Town, Danesh Blvd, 3441356611, Abyek, Qazvin, Iran
| | - Yuheng Liang
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Julian Ik-Tsen Heng
- Curtin Health Innovation Research Institute, Curtin University, Bentley 6845, Australia
| | - Roohallah Alizadehsani
- Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Victoria, Australia
| | - Iman Dehzangi
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; Department of Computer Science, Rutgers University, Camden, NJ 08102, USA
| | - Denis C Bauer
- Transformational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, Australia; Applied BioSciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, Australia
| | - Hamid Alinejad-Rokny
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia; Tyree Institute of Health Engineering (IHealthE), UNSW Sydney, Sydney, NSW 2052, Australia.
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13
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Lodewijk GA, de Geus M, Guimarães RLFP, Jacobs FMJ. Emergence of the ZNF675 Gene During Primate Evolution-Influenced Human Neurodevelopment Through Changing HES1 Autoregulation. J Comp Neurol 2024; 532:e25648. [PMID: 38958676 DOI: 10.1002/cne.25648] [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: 12/31/2023] [Revised: 04/27/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024]
Abstract
In this study, we investigated recurrent copy number variations (CNVs) in the 19p12 locus, which are associated with neurodevelopmental disorders. The two genes in this locus, ZNF675 and ZNF681, arose via gene duplication in primates, and their presence in several pathological CNVs in the human population suggests that either or both of these genes are required for normal human brain development. ZNF675 and ZNF681 are members of the Krüppel-associated box zinc finger (KZNF) protein family, a class of transcriptional repressors important for epigenetic silencing of specific genomic regions. About 170 primate-specific KZNFs are present in the human genome. Although KZNFs are primarily associated with repressing retrotransposon-derived DNA, evidence is emerging that they can be co-opted for other gene regulatory processes. We show that genetic deletion of ZNF675 causes developmental defects in cortical organoids, and our data suggest that part of the observed neurodevelopmental phenotype is mediated by a gene regulatory role of ZNF675 on the promoter of the neurodevelopmental gene Hes family BHLH transcription factor 1 (HES1). We also find evidence for the recently evolved regulation of genes involved in neurological disorders, microcephalin 1 and sestrin 3. We show that ZNF675 interferes with HES1 auto-inhibition, a process essential for the maintenance of neural progenitors. As a striking example of how some KZNFs have integrated into preexisting gene expression networks, these findings suggest the emergence of ZNF675 has caused a change in the balance of HES1 autoregulation. The association of ZNF675 CNV with human developmental disorders and ZNF675-mediated regulation of neurodevelopmental genes suggests that it evolved into an important factor for human brain development.
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Affiliation(s)
- Gerrald A Lodewijk
- Swammerdam Institute for Life Sciences, Evolutionary Neurogenomics, University of Amsterdam, Amsterdam, The Netherlands
| | - Matthijs de Geus
- Swammerdam Institute for Life Sciences, Evolutionary Neurogenomics, University of Amsterdam, Amsterdam, The Netherlands
| | - Rita L F P Guimarães
- Swammerdam Institute for Life Sciences, Evolutionary Neurogenomics, University of Amsterdam, Amsterdam, The Netherlands
| | - Frank M J Jacobs
- Swammerdam Institute for Life Sciences, Evolutionary Neurogenomics, University of Amsterdam, Amsterdam, The Netherlands
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14
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Burghel GJ, Ellingford JM, Wright R, Bradford L, Miller J, Watt C, Edgerley J, Naeem F, Banka S. Systematic reanalysis of copy number losses of uncertain clinical significance. J Med Genet 2024; 61:621-625. [PMID: 38604752 DOI: 10.1136/jmg-2023-109559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 03/28/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND Reanalysis of exome/genome data improves diagnostic yield. However, the value of reanalysis of clinical array comparative genomic hybridisation (aCGH) data has never been investigated. Case-by-case reanalysis can be challenging in busy diagnostic laboratories. METHODS AND RESULTS We harmonised historical postnatal clinical aCGH results from ~16 000 patients tested via our diagnostic laboratory over ~7 years with current clinical guidance. This led to identification of 37 009 copy number losses (CNLs) including 33 857 benign, 2173 of uncertain significance and 979 pathogenic. We found benign CNLs to be significantly less likely to encompass haploinsufficient genes compared with the pathogenic or CNLs of uncertain significance in our database. Based on this observation, we developed a reanalysis pipeline using up-to-date disease association data and haploinsufficiency scores and shortlisted 207 CNLs of uncertain significance encompassing at least one autosomal dominant disease-gene associated with haploinsufficiency or loss-of-function mechanism. Clinical scientist reviews led to reclassification of 15 CNLs of uncertain significance as pathogenic or likely pathogenic. This was ~0.7% of the starting cohort of 2173 CNLs of uncertain significance and 7.2% of 207 shortlisted CNLs. The reclassified CNLs included first cases of CNV-mediated disease for some genes where all previously described cases involved only point variants. Interestingly, some CNLs could not be reclassified because the phenotypes of patients with CNLs seemed distinct from the known clinical features resulting from point variants, thus raising questions about accepted underlying disease mechanisms. CONCLUSIONS Reanalysis of clinical aCGH data increases diagnostic yield.
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Affiliation(s)
- George J Burghel
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Jamie M Ellingford
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Ronnie Wright
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Lauren Bradford
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Jake Miller
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Christopher Watt
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Jonathan Edgerley
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Farah Naeem
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
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15
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Wang Y, Ma J, Wang J, Zhang L, Xu L, Chen Y, Zhu B, Wang Z, Gao H, Li J, Gao X. Genome-Wide Detection of Copy Number Variations and Their Potential Association with Carcass and Meat Quality Traits in Pingliang Red Cattle. Int J Mol Sci 2024; 25:5626. [PMID: 38891814 PMCID: PMC11172001 DOI: 10.3390/ijms25115626] [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: 04/30/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Copy number variation (CNV) serves as a significant source of genetic diversity in mammals and exerts substantial effects on various complex traits. Pingliang red cattle, an outstanding indigenous resource in China, possess remarkable breeding value attributed to their tender meat and superior marbling quality. However, the genetic mechanisms influencing carcass and meat quality traits in Pingliang red cattle are not well understood. We generated a comprehensive genome-wide CNV map for Pingliang red cattle using the GGP Bovine 100K SNP chip. A total of 755 copy number variable regions (CNVRs) spanning 81.03 Mb were identified, accounting for approximately 3.24% of the bovine autosomal genome. Among these, we discovered 270 potentially breed-specific CNVRs in Pingliang red cattle, including 143 gains, 73 losses, and 54 mixed events. Functional annotation analysis revealed significant associations between these specific CNVRs and important traits such as carcass and meat quality, reproduction, exterior traits, growth traits, and health traits. Additionally, our network and transcriptome analysis highlighted CACNA2D1, CYLD, UBXN2B, TG, NADK, and ITGA9 as promising candidate genes associated with carcass weight and intramuscular fat deposition. The current study presents a genome-wide CNV map in Pingliang red cattle, highlighting breed-specific CNVRs, and transcriptome findings provide valuable insights into the underlying genetic characteristics of Pingliang red cattle. These results offer potential avenues for enhancing meat quality through a targeted breeding program.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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16
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Sefik E, Duan K, Li Y, Sholar B, Evans L, Pincus J, Ammar Z, Murphy MM, Klaiman C, Saulnier CA, Pulver SL, Goldman-Yassen AE, Guo Y, Walker EF, Li L, Mulle JG, Shultz S. Structural deviations of the posterior fossa and the cerebellum and their cognitive links in a neurodevelopmental deletion syndrome. Mol Psychiatry 2024:10.1038/s41380-024-02584-8. [PMID: 38744992 DOI: 10.1038/s41380-024-02584-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
High-impact genetic variants associated with neurodevelopmental disorders provide biologically-defined entry points for mechanistic investigation. The 3q29 deletion (3q29Del) is one such variant, conferring a 40-100-fold increased risk for schizophrenia, as well as high risk for autism and intellectual disability. However, the mechanisms leading to neurodevelopmental disability remain largely unknown. Here, we report the first in vivo quantitative neuroimaging study in individuals with 3q29Del (N = 24) and neurotypical controls (N = 1608) using structural MRI. Given prior radiology reports of posterior fossa abnormalities in 3q29Del, we focused our investigation on the cerebellum and its tissue-types and lobules. Additionally, we compared the prevalence of cystic/cyst-like malformations of the posterior fossa between 3q29Del and controls and examined the association between neuroanatomical findings and quantitative traits to probe gene-brain-behavior relationships. 3q29Del participants had smaller cerebellar cortex volumes than controls, before and after correction for intracranial volume (ICV). An anterior-posterior gradient emerged in finer grained lobule-based and voxel-wise analyses. 3q29Del participants also had larger cerebellar white matter volumes than controls following ICV-correction and displayed elevated rates of posterior fossa arachnoid cysts and mega cisterna magna findings independent of cerebellar volume. Cerebellar white matter and subregional gray matter volumes were associated with visual-perception and visual-motor integration skills as well as IQ, while cystic/cyst-like malformations yielded no behavioral link. In summary, we find that abnormal development of cerebellar structures may represent neuroimaging-based biomarkers of cognitive and sensorimotor function in 3q29Del, adding to the growing evidence identifying cerebellar pathology as an intersection point between syndromic and idiopathic forms of neurodevelopmental disabilities.
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Affiliation(s)
- Esra Sefik
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychology, Emory University, Atlanta, GA, USA
| | - Kuaikuai Duan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science, Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, USA
| | - Yiheng Li
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Brittney Sholar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Lindsey Evans
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Jordan Pincus
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Zeena Ammar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Melissa M Murphy
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Cheryl Klaiman
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Celine A Saulnier
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Neurodevelopmental Assessment & Consulting Services, Atlanta, GA, USA
| | - Stormi L Pulver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Adam E Goldman-Yassen
- Department of Radiology, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Ying Guo
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elaine F Walker
- Department of Psychology, Emory University, Atlanta, GA, USA
| | - Longchuan Li
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Jennifer G Mulle
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA.
| | - Sarah Shultz
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA.
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17
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Kingdom R, Beaumont RN, Wood AR, Weedon MN, Wright CF. Genetic modifiers of rare variants in monogenic developmental disorder loci. Nat Genet 2024; 56:861-868. [PMID: 38637616 PMCID: PMC11096126 DOI: 10.1038/s41588-024-01710-0] [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: 12/07/2022] [Accepted: 03/06/2024] [Indexed: 04/20/2024]
Abstract
Rare damaging variants in a large number of genes are known to cause monogenic developmental disorders (DDs) and have also been shown to cause milder subclinical phenotypes in population cohorts. Here, we show that carrying multiple (2-5) rare damaging variants across 599 dominant DD genes has an additive adverse effect on numerous cognitive and socioeconomic traits in UK Biobank, which can be partially counterbalanced by a higher educational attainment polygenic score (EA-PGS). Phenotypic deviators from expected EA-PGS could be partly explained by the enrichment or depletion of rare DD variants. Among carriers of rare DD variants, those with a DD-related clinical diagnosis had a substantially lower EA-PGS and more severe phenotype than those without a clinical diagnosis. Our results suggest that the overall burden of both rare and common variants can modify the expressivity of a phenotype, which may then influence whether an individual reaches the threshold for clinical disease.
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Affiliation(s)
- Rebecca Kingdom
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Robin N Beaumont
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Andrew R Wood
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Michael N Weedon
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Caroline F Wright
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK.
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18
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Schmilovich Z, Bourque VR, Douard E, Huguet G, Poulain C, Ross JP, Alipour P, Castonguay CÉ, Younis N, Jean-Louis M, Saci Z, Pausova Z, Paus T, Schuman G, Porteous D, Davies G, Redmond P, Harris SE, Deary IJ, Whalley H, Hayward C, Dion PA, Jacquemont S, Rouleau GA. Copy-number variants and polygenic risk for intelligence confer risk for autism spectrum disorder irrespective of their effects on cognitive ability. Front Psychiatry 2024; 15:1369767. [PMID: 38751416 PMCID: PMC11094536 DOI: 10.3389/fpsyt.2024.1369767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/05/2024] [Indexed: 05/18/2024] Open
Abstract
Introduction Rare copy number variants (CNVs) and polygenic risk for intelligence (PRS-IQ) both confer susceptibility for autism spectrum disorder (ASD) but have opposing effects on cognitive ability. The field has struggled to disentangle the effects of these two classes of genomic variants on cognitive ability from their effects on ASD susceptibility, in part because previous studies did not include controls with cognitive measures. We aim to investigate the impact of these genomic variants on ASD risk while adjusting for their known effects on cognitive ability. Methods In a cohort of 8,426 subjects with ASD and 169,804 controls with cognitive assessments, we found that rare coding CNVs and PRS-IQ increased ASD risk, even after adjusting for their effects on cognitive ability. Results Bottom decile PRS-IQ and CNVs both decreased cognitive ability but had opposing effects on ASD risk. Models combining both classes of variants showed that the effects of rare CNVs and PRS-IQ on ASD risk and cognitive ability were largely additive, further suggesting that susceptibility for ASD is conferred independently from its effects on cognitive ability. Despite imparting mostly additive effects on ASD risk, rare CNVs and PRS-IQ showed opposing effects on core and associated features and developmental history among subjects with ASD. Discussion Our findings suggest that cognitive ability itself may not be the factor driving the underlying liability for ASD conferred by these two classes of genomic variants. In other words, ASD risk and cognitive ability may be two distinct manifestations of CNVs and PRS-IQ. This study also highlights the challenge of understanding how genetic risk for ASD maps onto its dimensional traits.
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Affiliation(s)
- Zoe Schmilovich
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Vincent-Raphaël Bourque
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Elise Douard
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Guillaume Huguet
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Cécile Poulain
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jay P. Ross
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Paria Alipour
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Charles-Étienne Castonguay
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Nadine Younis
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Martineau Jean-Louis
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Zohra Saci
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Tomas Paus
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Departments of Psychiatry of Neuroscience, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Departments of Psychology and Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Gunter Schuman
- Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, London, United Kingdom
| | - David Porteous
- Lothian Birth Cohorts Group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, United Kingdom
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, The University of Edinburgh, Edinburgh, United Kingdom
| | - Gail Davies
- Lothian Birth Cohorts Group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Redmond
- Lothian Birth Cohorts Group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah E. Harris
- Lothian Birth Cohorts Group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Ian J. Deary
- Lothian Birth Cohorts Group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Heather Whalley
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, The University of Edinburgh, Edinburgh, United Kingdom
| | - Caroline Hayward
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, The University of Edinburgh, Edinburgh, United Kingdom
| | - Patrick A. Dion
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Sébastien Jacquemont
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Guy A. Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
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19
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Gillani R, Collins RL, Crowdis J, Garza A, Jones JK, Walker M, Sanchis-Juan A, Whelan C, Pierce-Hoffman E, Talkowski M, Brand H, Haigis K, LoPiccolo J, AlDubayan SH, Gusev A, Crompton BD, Janeway KA, Van Allen EM. Rare germline structural variants increase risk for pediatric solid tumors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.27.591484. [PMID: 38746320 PMCID: PMC11092455 DOI: 10.1101/2024.04.27.591484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Pediatric solid tumors are rare malignancies that represent a leading cause of death by disease among children in developed countries. The early age-of-onset of these tumors suggests that germline genetic factors are involved, yet conventional germline testing for short coding variants in established predisposition genes only identifies pathogenic events in 10-15% of patients. Here, we examined the role of germline structural variants (SVs)-an underexplored form of germline variation-in pediatric extracranial solid tumors using germline genome sequencing of 1,766 affected children, their 943 unaffected relatives, and 6,665 adult controls. We discovered a sex-biased association between very large (>1 megabase) germline chromosomal abnormalities and a four-fold increased risk of solid tumors in male children. The overall impact of germline SVs was greatest in neuroblastoma, where we revealed burdens of ultra-rare SVs that cause loss-of-function of highly expressed, mutationally intolerant, neurodevelopmental genes, as well as noncoding SVs predicted to disrupt three-dimensional chromatin domains in neural crest-derived tissues. Collectively, our results implicate rare germline SVs as a predisposing factor to pediatric solid tumors that may guide future studies and clinical practice.
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Affiliation(s)
- Riaz Gillani
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Ryan L. Collins
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Amanda Garza
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jill K. Jones
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Mark Walker
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alba Sanchis-Juan
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Chris Whelan
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emma Pierce-Hoffman
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Talkowski
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Harrison Brand
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin Haigis
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Jaclyn LoPiccolo
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Saud H. AlDubayan
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA
- College of Medicine, King Saudi bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Alexander Gusev
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Brian D. Crompton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Katie A. Janeway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Eliezer M. Van Allen
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
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20
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Ye F, Xu X, Wang Y, Chen L, Shan Q, Wang Q, Jin F. The yield of SNP microarray analysis for fetal ultrasound cardiac abnormalities. BMC Pregnancy Childbirth 2024; 24:244. [PMID: 38580914 PMCID: PMC10998306 DOI: 10.1186/s12884-024-06428-9] [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: 09/04/2023] [Accepted: 03/15/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND Chromosomal microarray analysis (CMA) has emerged as a critical instrument in prenatal diagnostic procedures, notably in assessing congenital heart diseases (CHD). Nonetheless, current research focuses solely on CHD, overlooking the necessity for thorough comparative investigations encompassing fetuses with varied structural abnormalities or those without apparent structural anomalies. OBJECTIVE This study sought to assess the relation of single nucleotide polymorphism-based chromosomal microarray analysis (SNP-based CMA) in identifying the underlying causes of fetal cardiac ultrasound abnormalities. METHODS A total of 2092 pregnant women who underwent prenatal diagnosis from 2017 to 2022 were included in the study and divided into four groups based on the presence of ultrasound structural abnormalities and the specific type of abnormality. The results of the SNP-Array test conducted on amniotic fluid samples from these groups were analyzed. RESULTS Findings from the study revealed that the non-isolated CHD group exhibited the highest incidence of aneuploidy, overall chromosomal abnormalities, and trisomy 18, demonstrating statistically significant differences from the other groups (p < 0.001). Regarding the distribution frequency of copy number variation (CNV) segment size, no statistically significant distinctions were observed between the isolated CHD group and the non-isolated CHD group (p > 0.05). The occurrence rates of 22q11.2 and 15q11.2 were also not statistically different between the isolated CHD group and the non-isolated congenital heart defect group (p > 0.05). CONCLUSION SNP-based CMA enhances the capacity to detect abnormal CNVs in CHD fetuses, offering valuable insights for diagnosing chromosomal etiology and facilitating genetic counseling. This research contributes to the broader understanding of the utility of SNP-based CMA in the context of fetal cardiac ultrasound abnormalities.
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Affiliation(s)
- Fenglei Ye
- Department of Reproductive Endocrinology, Key Laboratory of Reproductive Genetics of National Ministry of Education, Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310000, China
- Department of Obstetrics, Lishui Maternal and Child Health Hospital, Lishui, 323000, China
| | - Xiayuan Xu
- Department of Reproductive Endocrinology, Key Laboratory of Reproductive Genetics of National Ministry of Education, Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310000, China
- Department of Laboratory, Jinhua Maternal and Child Health Hospital, Jinhua, 321000, China
| | - Yi Wang
- Department of Obstetrics, Lishui Maternal and Child Health Hospital, Lishui, 323000, China
| | - Lifang Chen
- Department of Reproductive Endocrinology, Key Laboratory of Reproductive Genetics of National Ministry of Education, Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310000, China
- Department of Obstetrics, Lishui Maternal and Child Health Hospital, Lishui, 323000, China
| | - Qunda Shan
- Department of Reproductive Endocrinology, Key Laboratory of Reproductive Genetics of National Ministry of Education, Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310000, China
- Department of Prenatal Diagnosis Center, Lishui Maternal and Child Health Hospital, Lishui, 323000, China
| | - Qijing Wang
- Department of Reproductive Endocrinology, Key Laboratory of Reproductive Genetics of National Ministry of Education, Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310000, China.
- Department of Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China.
| | - Fan Jin
- Department of Reproductive Endocrinology, Key Laboratory of Reproductive Genetics of National Ministry of Education, Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310000, China.
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21
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Ung DC, Pietrancosta N, Badillo EB, Raux B, Tapken D, Zlatanovic A, Doridant A, Pode-Shakked B, Raas-Rothschild A, Elpeleg O, Abu-Libdeh B, Hamed N, Papon MA, Marouillat S, Thépault RA, Stevanin G, Elegheert J, Letellier M, Hollmann M, Lambolez B, Tricoire L, Toutain A, Hepp R, Laumonnier F. GRID1/GluD1 homozygous variants linked to intellectual disability and spastic paraplegia impair mGlu1/5 receptor signaling and excitatory synapses. Mol Psychiatry 2024; 29:1205-1215. [PMID: 38418578 PMCID: PMC11176079 DOI: 10.1038/s41380-024-02469-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 03/01/2024]
Abstract
The ionotropic glutamate delta receptor GluD1, encoded by the GRID1 gene, is involved in synapse formation, function, and plasticity. GluD1 does not bind glutamate, but instead cerebellin and D-serine, which allow the formation of trans-synaptic bridges, and trigger transmembrane signaling. Despite wide expression in the nervous system, pathogenic GRID1 variants have not been characterized in humans so far. We report homozygous missense GRID1 variants in five individuals from two unrelated consanguineous families presenting with intellectual disability and spastic paraplegia, without (p.Thr752Met) or with (p.Arg161His) diagnosis of glaucoma, a threefold phenotypic association whose genetic bases had not been elucidated previously. Molecular modeling and electrophysiological recordings indicated that Arg161His and Thr752Met mutations alter the hinge between GluD1 cerebellin and D-serine binding domains and the function of this latter domain, respectively. Expression, trafficking, physical interaction with metabotropic glutamate receptor mGlu1, and cerebellin binding of GluD1 mutants were not conspicuously altered. Conversely, upon expression in neurons of dissociated or organotypic slice cultures, we found that both GluD1 mutants hampered metabotropic glutamate receptor mGlu1/5 signaling via Ca2+ and the ERK pathway and impaired dendrite morphology and excitatory synapse density. These results show that the clinical phenotypes are distinct entities segregating in the families as an autosomal recessive trait, and caused by pathophysiological effects of GluD1 mutants involving metabotropic glutamate receptor signaling and neuronal connectivity. Our findings unravel the importance of GluD1 receptor signaling in sensory, cognitive and motor functions of the human nervous system.
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Affiliation(s)
- Dévina C Ung
- UMR 1253, iBrain, Université de Tours, Inserm, 37032, Tours, France
| | - Nicolas Pietrancosta
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine, 75005, Paris, France
- Laboratoire des biomolécules, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | | | - Brigitt Raux
- Univ. Bordeaux, CNRS, IINS, UMR 5297, F-33000, Bordeaux, France
| | - Daniel Tapken
- Department of Biochemistry I - Receptor Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, D-44780, Bochum, Germany
| | - Andjela Zlatanovic
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine, 75005, Paris, France
| | - Adrien Doridant
- Univ. Bordeaux, CNRS, IINS, UMR 5297, F-33000, Bordeaux, France
| | - Ben Pode-Shakked
- The Institute for Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, 5262000, Israel
- Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, 5262000, Israel
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Annick Raas-Rothschild
- The Institute for Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, 5262000, Israel
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Bassam Abu-Libdeh
- Department of Pediatrics, Makassed Hospital and Faculty of Medicine, Al-Quds University, East Jerusalem, Jerusalem, Palestine
| | - Nasrin Hamed
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 69978, Israel
- Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, 5262000, Israel
| | | | | | | | - Giovanni Stevanin
- Univ. Bordeaux, INCIA, UMR 5287 CNRS EPHE, F-33000, Bordeaux, France
| | | | | | - Michael Hollmann
- Department of Biochemistry I - Receptor Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, D-44780, Bochum, Germany
| | - Bertrand Lambolez
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine, 75005, Paris, France
| | - Ludovic Tricoire
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine, 75005, Paris, France
| | - Annick Toutain
- UMR 1253, iBrain, Université de Tours, Inserm, 37032, Tours, France.
- Unité fonctionnelle de Génétique Médicale, Centre Hospitalier Universitaire, 37044, Tours, France.
| | - Régine Hepp
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine, 75005, Paris, France.
| | - Frédéric Laumonnier
- UMR 1253, iBrain, Université de Tours, Inserm, 37032, Tours, France.
- Service de Génétique, Centre Hospitalier Universitaire, 37044, Tours, France.
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22
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Gustafson JA, Gibson SB, Damaraju N, Zalusky MPG, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson Z, Storz SHR, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves C, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal CR, Zakarian C, Goodwin S, Jensen TD, Robb E, McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, Miller DE. Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.05.24303792. [PMID: 38496498 PMCID: PMC10942501 DOI: 10.1101/2024.03.05.24303792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Less than half of individuals with a suspected Mendelian condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control datasets for variant filtering and prioritization has made tertiary analysis of LRS data challenging. To address this, the 1000 Genomes Project ONT Sequencing Consortium aims to generate LRS data from at least 800 of the 1000 Genomes Project samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal patterns of human variation. Here, we present data from analysis of the first 100 samples, representing all 5 superpopulations and 19 subpopulations. These samples, sequenced to an average depth of coverage of 37x and sequence read N50 of 54 kbp, have high concordance with previous studies for identifying single nucleotide and indel variants outside of homopolymer regions. Using multiple structural variant (SV) callers, we identify an average of 24,543 high-confidence SVs per genome, including shared and private SVs likely to disrupt gene function as well as pathogenic expansions within disease-associated repeats that were not detected using short reads. Evaluation of methylation signatures revealed expected patterns at known imprinted loci, samples with skewed X-inactivation patterns, and novel differentially methylated regions. All raw sequencing data, processed data, and summary statistics are publicly available, providing a valuable resource for the clinical genetics community to discover pathogenic SVs.
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Affiliation(s)
- Jonas A. Gustafson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Sophia B. Gibson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nikhita Damaraju
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Miranda PG Zalusky
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lei Yang
- Pacific Northwest Research Institute, Seattle, WA, USA
| | | | | | - Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Nathan D. Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Human Technopole, Milan, Italy
| | - Qiuhui Li
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Angela L. Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Joy Goffena
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Zachery Anderson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sophie HR Storz
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sydney A. Ward
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Maisha Sinha
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Claudia Gonzaga-Jauregui
- International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México
| | - Wayne E. Clarke
- New York Genome Center, New York, NY, USA
- Outlier Informatics Inc., Saskatoon, SK, Canada
| | | | | | | | | | | | - Mahler Revsine
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Cate R. Paschal
- Department of Laboratories, Seattle Children’s Hospital, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Christina Zakarian
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Esther Robb
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | | | | | | | - Fritz J. Sedlazeck
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Justin M. Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mikhail Kolmogorov
- Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Richard N. McLaughlin
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - Harriet Dashnow
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Matt Loose
- Deep Seq, School of Life Sciences, University of Nottingham, Nottingham, England
| | - Miten Jain
- Department of Bioengineering, Department of Physics, Khoury College of Computer Sciences, Northeastern University, Boston, MA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Danny E. Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
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23
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Cavalli A, Caraffi SG, Rizzi S, Trimarchi G, Napoli M, Frattini D, Spagnoli C, Garavelli L, Fusco C. Heterozygous truncating variant of TAOK1 in a boy with periventricular nodular heterotopia: a case report and literature review of TAOK1-related neurodevelopmental disorders. BMC Med Genomics 2024; 17:68. [PMID: 38443934 PMCID: PMC10916022 DOI: 10.1186/s12920-024-01840-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 02/28/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Thousand and one amino-acid kinase 1 (TAOK1) encodes the MAP3K protein kinase TAO1, which has recently been displayed to be essential for neuronal maturation and cortical differentiation during early brain development. Heterozygous variants in TAOK1 have been reported in children with neurodevelopmental disorders, with or without macrocephaly, hypotonia and mild dysmorphic traits. Literature reports lack evidence of neuronal migration disorders in TAOK1 patients, although studies in animal models suggest this possibility. CASE PRESENTATION We provide a clinical description of a child with a neurodevelopmental disorder due to a novel TAOK1 truncating variant, whose brain magnetic resonance imaging displays periventricular nodular heterotopia. CONCLUSIONS To our knowledge, this is the first report of a neuronal migration disorder in a patient with a TAOK1-related neurodevelopmental disorder, thus supporting the hypothesized pathogenic mechanisms of TAOK1 defects.
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Affiliation(s)
- Anna Cavalli
- Child Neurology and Psychiatry Unit, Dipartimento Materno-Infantile, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy.
| | - Stefano Giuseppe Caraffi
- Medical Genetics Unit, Dipartimento Materno-Infantile, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy
| | - Susanna Rizzi
- Child Neurology and Psychiatry Unit, Dipartimento Materno-Infantile, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy
| | - Gabriele Trimarchi
- Medical Genetics Unit, Dipartimento Materno-Infantile, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy
| | - Manuela Napoli
- Neuroradiology Unit, Arcispedale santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy
| | - Daniele Frattini
- Child Neurology and Psychiatry Unit, Dipartimento Materno-Infantile, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy
| | - Carlotta Spagnoli
- Child Neurology and Psychiatry Unit, Dipartimento Materno-Infantile, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy
| | - Livia Garavelli
- Medical Genetics Unit, Dipartimento Materno-Infantile, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy
| | - Carlo Fusco
- Child Neurology and Psychiatry Unit, Dipartimento Materno-Infantile, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy
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24
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Tolezano GC, Bastos GC, da Costa SS, Freire BL, Homma TK, Honjo RS, Yamamoto GL, Passos-Bueno MR, Koiffmann CP, Kim CA, Vianna-Morgante AM, de Lima Jorge AA, Bertola DR, Rosenberg C, Krepischi ACV. Burden of Rare Copy Number Variants in Microcephaly: A Brazilian Cohort of 185 Microcephalic Patients and Review of the Literature. J Autism Dev Disord 2024; 54:1181-1212. [PMID: 36502452 DOI: 10.1007/s10803-022-05853-z] [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] [Accepted: 11/26/2022] [Indexed: 12/14/2022]
Abstract
Microcephaly presents heterogeneous genetic etiology linked to several neurodevelopmental disorders (NDD). Copy number variants (CNVs) are a causal mechanism of microcephaly whose investigation is a crucial step for unraveling its molecular basis. Our purpose was to investigate the burden of rare CNVs in microcephalic individuals and to review genes and CNV syndromes associated with microcephaly. We performed chromosomal microarray analysis (CMA) in 185 Brazilian patients with microcephaly and evaluated microcephalic patients carrying < 200 kb CNVs documented in the DECIPHER database. Additionally, we reviewed known genes and CNV syndromes causally linked to microcephaly through the PubMed, OMIM, DECIPHER, and ClinGen databases. Rare clinically relevant CNVs were detected in 39 out of the 185 Brazilian patients investigated by CMA (21%). In 31 among the 60 DECIPHER patients carrying < 200 kb CNVs, at least one known microcephaly gene was observed. Overall, four gene sets implicated in microcephaly were disclosed: known microcephaly genes; genes with supporting evidence of association with microcephaly; known macrocephaly genes; and novel candidates, including OTUD7A, BBC3, CNTN6, and NAA15. In the review, we compiled 957 known microcephaly genes and 58 genomic CNV loci, comprising 13 duplications and 50 deletions, which have already been associated with clinical findings including microcephaly. We reviewed genes and CNV syndromes previously associated with microcephaly, reinforced the high CMA diagnostic yield for this condition, pinpointed novel candidate loci linked to microcephaly deserving further evaluation, and provided a useful resource for future research on the field of neurodevelopment.
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Affiliation(s)
- Giovanna Cantini Tolezano
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Giovanna Civitate Bastos
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Bruna Lucheze Freire
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Thais Kataoka Homma
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Rachel Sayuri Honjo
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Guilherme Lopes Yamamoto
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Maria Rita Passos-Bueno
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Celia Priszkulnik Koiffmann
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Chong Ae Kim
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Angela Maria Vianna-Morgante
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Alexander Augusto de Lima Jorge
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Débora Romeo Bertola
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
- Institute of Biosciences, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
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25
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Porubsky D, Eichler EE. A 25-year odyssey of genomic technology advances and structural variant discovery. Cell 2024; 187:1024-1037. [PMID: 38290514 DOI: 10.1016/j.cell.2024.01.002] [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: 10/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 02/01/2024]
Abstract
This perspective focuses on advances in genome technology over the last 25 years and their impact on germline variant discovery within the field of human genetics. The field has witnessed tremendous technological advances from microarrays to short-read sequencing and now long-read sequencing. Each technology has provided genome-wide access to different classes of human genetic variation. We are now on the verge of comprehensive variant detection of all forms of variation for the first time with a single assay. We predict that this transition will further transform our understanding of human health and biology and, more importantly, provide novel insights into the dynamic mutational processes shaping our genomes.
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Affiliation(s)
- David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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26
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Zhang Y, Liu W, Duan J. On the core segmentation algorithms of copy number variation detection tools. Brief Bioinform 2024; 25:bbae022. [PMID: 38340093 PMCID: PMC10858679 DOI: 10.1093/bib/bbae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/26/2023] [Indexed: 02/12/2024] Open
Abstract
Shotgun sequencing is a high-throughput method used to detect copy number variants (CNVs). Although there are numerous CNV detection tools based on shotgun sequencing, their quality varies significantly, leading to performance discrepancies. Therefore, we conducted a comprehensive analysis of next-generation sequencing-based CNV detection tools over the past decade. Our findings revealed that the majority of mainstream tools employ similar detection rationale: calculates the so-called read depth signal from aligned sequencing reads and then segments the signal by utilizing either circular binary segmentation (CBS) or hidden Markov model (HMM). Hence, we compared the performance of those two core segmentation algorithms in CNV detection, considering varying sequencing depths, segment lengths and complex types of CNVs. To ensure a fair comparison, we designed a parametrical model using mainstream statistical distributions, which allows for pre-excluding bias correction such as guanine-cytosine (GC) content during the preprocessing step. The results indicate the following key points: (1) Under ideal conditions, CBS demonstrates high precision, while HMM exhibits a high recall rate. (2) For practical conditions, HMM is advantageous at lower sequencing depths, while CBS is more competitive in detecting small variant segments compared to HMM. (3) In case involving complex CNVs resembling real sequencing, HMM demonstrates more robustness compared with CBS. (4) When facing large-scale sequencing data, HMM costs less time compared with the CBS, while their memory usage is approximately equal. This can provide an important guidance and reference for researchers to develop new tools for CNV detection.
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Affiliation(s)
- Yibo Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Wenyu Liu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Junbo Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
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27
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Auwerx C, Jõeloo M, Sadler MC, Tesio N, Ojavee S, Clark CJ, Mägi R, Reymond A, Kutalik Z. Rare copy-number variants as modulators of common disease susceptibility. Genome Med 2024; 16:5. [PMID: 38185688 PMCID: PMC10773105 DOI: 10.1186/s13073-023-01265-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND Copy-number variations (CNVs) have been associated with rare and debilitating genomic disorders (GDs) but their impact on health later in life in the general population remains poorly described. METHODS Assessing four modes of CNV action, we performed genome-wide association scans (GWASs) between the copy-number of CNV-proxy probes and 60 curated ICD-10 based clinical diagnoses in 331,522 unrelated white British UK Biobank (UKBB) participants with replication in the Estonian Biobank. RESULTS We identified 73 signals involving 40 diseases, all of which indicating that CNVs increased disease risk and caused earlier onset. We estimated that 16% of these associations are indirect, acting by increasing body mass index (BMI). Signals mapped to 45 unique, non-overlapping regions, nine of which being linked to known GDs. Number and identity of genes affected by CNVs modulated their pathogenicity, with many associations being supported by colocalization with both common and rare single-nucleotide variant association signals. Dissection of association signals provided insights into the epidemiology of known gene-disease pairs (e.g., deletions in BRCA1 and LDLR increased risk for ovarian cancer and ischemic heart disease, respectively), clarified dosage mechanisms of action (e.g., both increased and decreased dosage of 17q12 impacted renal health), and identified putative causal genes (e.g., ABCC6 for kidney stones). Characterization of the pleiotropic pathological consequences of recurrent CNVs at 15q13, 16p13.11, 16p12.2, and 22q11.2 in adulthood indicated variable expressivity of these regions and the involvement of multiple genes. Finally, we show that while the total burden of rare CNVs-and especially deletions-strongly associated with disease risk, it only accounted for ~ 0.02% of the UKBB disease burden. These associations are mainly driven by CNVs at known GD CNV regions, whose pleiotropic effect on common diseases was broader than anticipated by our CNV-GWAS. CONCLUSIONS Our results shed light on the prominent role of rare CNVs in determining common disease susceptibility within the general population and provide actionable insights for anticipating later-onset comorbidities in carriers of recurrent CNVs.
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Affiliation(s)
- Chiara Auwerx
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland.
| | - Maarja Jõeloo
- Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Marie C Sadler
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland
| | - Nicolò Tesio
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
| | - Sven Ojavee
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Charlie J Clark
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland.
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Liénard C, Pintart A, Bomont P. Neuronal Autophagy: Regulations and Implications in Health and Disease. Cells 2024; 13:103. [PMID: 38201307 PMCID: PMC10778363 DOI: 10.3390/cells13010103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/02/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Autophagy is a major degradative pathway that plays a key role in sustaining cell homeostasis, integrity, and physiological functions. Macroautophagy, which ensures the clearance of cytoplasmic components engulfed in a double-membrane autophagosome that fuses with lysosomes, is orchestrated by a complex cascade of events. Autophagy has a particularly strong impact on the nervous system, and mutations in core components cause numerous neurological diseases. We first review the regulation of autophagy, from autophagosome biogenesis to lysosomal degradation and associated neurodevelopmental/neurodegenerative disorders. We then describe how this process is specifically regulated in the axon and in the somatodendritic compartment and how it is altered in diseases. In particular, we present the neuronal specificities of autophagy, with the spatial control of autophagosome biogenesis, the close relationship of maturation with axonal transport, and the regulation by synaptic activity. Finally, we discuss the physiological functions of autophagy in the nervous system, during development and in adulthood.
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Affiliation(s)
- Caroline Liénard
- NeuroMyoGene Institute—PGNM, CNRS UMR 5261—INSERM U1315, University of Claude Bernard Lyon 1, 69008 Lyon, France; (C.L.); (A.P.)
- CHU Montpellier, University of Montpellier, 34295 Montpellier, France
| | - Alexandre Pintart
- NeuroMyoGene Institute—PGNM, CNRS UMR 5261—INSERM U1315, University of Claude Bernard Lyon 1, 69008 Lyon, France; (C.L.); (A.P.)
| | - Pascale Bomont
- NeuroMyoGene Institute—PGNM, CNRS UMR 5261—INSERM U1315, University of Claude Bernard Lyon 1, 69008 Lyon, France; (C.L.); (A.P.)
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Cai M, Lv A, Zhao W, Xu L, Lin N, Huang H. Intrauterine ultrasound phenotyping, molecular characteristics, and postnatal follow-up of fetuses with the 15q11.2 BP1-BP2 microdeletion syndrome: a single-center, retrospective clinical study. BMC Pregnancy Childbirth 2024; 24:23. [PMID: 38172840 PMCID: PMC10763152 DOI: 10.1186/s12884-023-06223-y] [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: 09/03/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
OBJECTIVES The 15q11.2 BP1-BP2 microdeletion is associated with neurodevelopmental diseases. However, most studies on this microdeletion have focused on adults and children. Thus, in this study, we summarized the molecular characteristics of fetuses with the 15q11.2 BP1-BP2 microdeletion and their postnatal follow-up to guide prenatal diagnosis. METHODS Ten thousand fetuses were retrospectively subjected to karyotype analysis and chromosome microarray analysis. RESULTS Chromosome microarray analysis revealed that 37 (0.4%) of the 10,000 fetuses had 15q11.2 BP1-BP2 microdeletions. The fragment size of the 15q11.2 BP1-BP2 region was approximately 312-855 kb and encompassed TUBGCP5, CYFIP1, NIPA2, and NIPA1 genes. Twenty-five of the 37 fetuses with this microdeletion showed phenotypic abnormalities. The most common ultrasonic structural abnormality was congenital heart disease, followed by renal dysplasia and Dandy-Walker malformation. The 15q11.2 BP1-BP2 microdeletion was inherited from the father and mother in 6 and 10 cases, respectively, and de novo inherited in 4 cases. In the postnatal follow-up, 16.1% of the children had postnatal abnormalities. CONCLUSION Fetuses with the 15q11.2 BP1-BP2 microdeletion showed high proportions of phenotypic abnormalities, but the specificity of penetrance was low. Thus, fetuses with this syndrome are potentially at a higher risk of postnatal growth/behavioral problems and require continuous monitoring of growth and development.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Aixiang Lv
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Wantong Zhao
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China.
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China.
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China.
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30
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Byeon S, Yadav S. Pleiotropic functions of TAO kinases and their dysregulation in neurological disorders. Sci Signal 2024; 17:eadg0876. [PMID: 38166033 DOI: 10.1126/scisignal.adg0876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/07/2023] [Indexed: 01/04/2024]
Abstract
Thousand and one amino acid kinases (TAOKs) are relatively understudied and functionally pleiotropic protein kinases that have emerged as important regulators of neurodevelopment. Through their conserved amino-terminal catalytic domain, TAOKs mediate phosphorylation at serine/threonine residues in their substrates, but it is their divergent regulatory carboxyl-terminal domains that confer both exquisite functional specification and cellular localization. In this Review, we discuss the physiological roles of TAOKs and the intricate signaling pathways, molecular interactions, and cellular behaviors they modulate-from cell stress responses, division, and motility to tissue homeostasis, immunity, and neurodevelopment. These insights are then integrated into an analysis of the known and potential impacts of disease-associated variants of TAOKs, with a focus on neurodevelopmental disorders, pain and addiction, and neurodegenerative diseases. Translating this foundation into clinical benefits for patients will require greater structural and functional differentiation of the TAOKs afforded by their individually specialized domains.
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Affiliation(s)
- Sujin Byeon
- Graduate Program in Neuroscience, University of Washington, Seattle, WA 98195, USA
| | - Smita Yadav
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
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31
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Chen S, Francioli LC, Goodrich JK, Collins RL, Kanai M, Wang Q, Alföldi J, Watts NA, Vittal C, Gauthier LD, Poterba T, Wilson MW, Tarasova Y, Phu W, Grant R, Yohannes MT, Koenig Z, Farjoun Y, Banks E, Donnelly S, Gabriel S, Gupta N, Ferriera S, Tolonen C, Novod S, Bergelson L, Roazen D, Ruano-Rubio V, Covarrubias M, Llanwarne C, Petrillo N, Wade G, Jeandet T, Munshi R, Tibbetts K, O'Donnell-Luria A, Solomonson M, Seed C, Martin AR, Talkowski ME, Rehm HL, Daly MJ, Tiao G, Neale BM, MacArthur DG, Karczewski KJ. A genomic mutational constraint map using variation in 76,156 human genomes. Nature 2024; 625:92-100. [PMID: 38057664 DOI: 10.1038/s41586-023-06045-0] [Citation(s) in RCA: 102] [Impact Index Per Article: 102.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/03/2023] [Indexed: 12/08/2023]
Abstract
The depletion of disruptive variation caused by purifying natural selection (constraint) has been widely used to investigate protein-coding genes underlying human disorders1-4, but attempts to assess constraint for non-protein-coding regions have proved more difficult. Here we aggregate, process and release a dataset of 76,156 human genomes from the Genome Aggregation Database (gnomAD)-the largest public open-access human genome allele frequency reference dataset-and use it to build a genomic constraint map for the whole genome (genomic non-coding constraint of haploinsufficient variation (Gnocchi)). We present a refined mutational model that incorporates local sequence context and regional genomic features to detect depletions of variation. As expected, the average constraint for protein-coding sequences is stronger than that for non-coding regions. Within the non-coding genome, constrained regions are enriched for known regulatory elements and variants that are implicated in complex human diseases and traits, facilitating the triangulation of biological annotation, disease association and natural selection to non-coding DNA analysis. More constrained regulatory elements tend to regulate more constrained protein-coding genes, which in turn suggests that non-coding constraint can aid the identification of constrained genes that are as yet unrecognized by current gene constraint metrics. We demonstrate that this genome-wide constraint map improves the identification and interpretation of functional human genetic variation.
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Affiliation(s)
- Siwei Chen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
| | - Laurent C Francioli
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Julia K Goodrich
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan L Collins
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Masahiro Kanai
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Qingbo Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Jessica Alföldi
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Nicholas A Watts
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher Vittal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Laura D Gauthier
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Timothy Poterba
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael W Wilson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Yekaterina Tarasova
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William Phu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Riley Grant
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mary T Yohannes
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zan Koenig
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yossi Farjoun
- Richards Lab, Lady Davis Institute, Montreal, Quebec, Canada
| | - Eric Banks
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Stacey Gabriel
- Broad Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Broad Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven Ferriera
- Broad Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charlotte Tolonen
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sam Novod
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Louis Bergelson
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Roazen
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Miguel Covarrubias
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nikelle Petrillo
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gordon Wade
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Thibault Jeandet
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ruchi Munshi
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathleen Tibbetts
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Matthew Solomonson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Cotton Seed
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alicia R Martin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael E Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mark J Daly
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
| | - Grace Tiao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Benjamin M Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Goh CJ, Kwon HJ, Kim Y, Jung S, Park J, Lee IK, Park BR, Kim MJ, Kim MJ, Lee MS. Improving CNV Detection Performance in Microarray Data Using a Machine Learning-Based Approach. Diagnostics (Basel) 2023; 14:84. [PMID: 38201393 PMCID: PMC10871075 DOI: 10.3390/diagnostics14010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Copy number variation (CNV) is a primary source of structural variation in the human genome, leading to several disorders. Therefore, analyzing neonatal CNVs is crucial for managing CNV-related chromosomal disabilities. However, genomic waves can hinder accurate CNV analysis. To mitigate the influences of the waves, we adopted a machine learning approach and developed a new method that uses a modified log R ratio instead of the commonly used log R ratio. Validation results using samples with known CNVs demonstrated the superior performance of our method. We analyzed a total of 16,046 Korean newborn samples using the new method and identified CNVs related to 39 genetic disorders were identified in 342 cases. The most frequently detected CNV-related disorder was Joubert syndrome 4. The accuracy of our method was further confirmed by analyzing a subset of the detected results using NGS and comparing them with our results. The utilization of a genome-wide single nucleotide polymorphism array with wave offset was shown to be a powerful method for identifying CNVs in neonatal cases. The accurate screening and the ability to identify various disease susceptibilities offered by our new method could facilitate the identification of CNV-associated chromosomal disease etiologies.
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Affiliation(s)
- Chul Jun Goh
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Hyuk-Jung Kwon
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
- Department of Computer Science and Engineering, Incheon National University (INU), Incheon 22012, Republic of Korea
| | - Yoonhee Kim
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Seunghee Jung
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Jiwoo Park
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Isaac Kise Lee
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
- Department of Computer Science and Engineering, Incheon National University (INU), Incheon 22012, Republic of Korea
- NGENI Foundation, San Diego, CA 92127, USA
| | - Bo-Ram Park
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Myeong-Ji Kim
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Min-Jeong Kim
- Diagnomics, Inc., 5795 Kearny Villa Rd., San Diego, CA 92123, USA;
| | - Min-Seob Lee
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
- Diagnomics, Inc., 5795 Kearny Villa Rd., San Diego, CA 92123, USA;
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Detera-Wadleigh SD, Kassem L, Besancon E, Lopes F, Akula N, Sung H, Blattner M, Sheridan L, Lacbawan LN, Garcia J, Gordovez F, Hosey K, Donner C, Salvini C, Schulze T, Chen DTW, England B, Cross J, Jiang X, Corona W, Russ J, Mallon B, Dutra A, Pak E, Steiner J, Malik N, de Guzman T, Horato N, Mallmann MB, Mendes V, Dűck AL, Nardi AE, McMahon FJ. A resource of induced pluripotent stem cell (iPSC) lines including clinical, genomic, and cellular data from genetically isolated families with mood and psychotic disorders. Transl Psychiatry 2023; 13:397. [PMID: 38104115 PMCID: PMC10725500 DOI: 10.1038/s41398-023-02641-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 10/05/2023] [Accepted: 10/30/2023] [Indexed: 12/19/2023] Open
Abstract
Genome-wide (GWAS) and copy number variant (CNV) association studies have reproducibly identified numerous risk alleles associated with bipolar disorder (BD), major depressive disorder (MDD), and schizophrenia (SCZ), but biological characterization of these alleles lags gene discovery, owing to the inaccessibility of live human brain cells and inadequate animal models for human psychiatric conditions. Human-derived induced pluripotent stem cells (iPSCs) provide a renewable cellular reagent that can be differentiated into living, disease-relevant cells and 3D brain organoids carrying the full complement of genetic variants present in the donor germline. Experimental studies of iPSC-derived cells allow functional characterization of risk alleles, establishment of causal relationships between genes and neurobiology, and screening for novel therapeutics. Here we report the creation and availability of an iPSC resource comprising clinical, genomic, and cellular data obtained from genetically isolated families with BD and related conditions. Results from the first 324 study participants, 61 of whom have validated pluripotent clones, show enrichment of rare single nucleotide variants and CNVs overlapping many known risk genes and pathogenic CNVs. This growing iPSC resource is available to scientists pursuing functional genomic studies of BD and related conditions.
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Affiliation(s)
- Sevilla D Detera-Wadleigh
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA.
| | - Layla Kassem
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA.
| | - Emily Besancon
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Fabiana Lopes
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, 02903, USA
| | - Nirmala Akula
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Heejong Sung
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Meghan Blattner
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Laura Sheridan
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Ley Nadine Lacbawan
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Joshua Garcia
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Francis Gordovez
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Katherine Hosey
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Cassandra Donner
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Claudio Salvini
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Thomas Schulze
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
- Institute of Psychiatric Phenomics and Genomics, LMU Munich, 80336, München, Germany
- Department of Psychiatry and Behavioral Sciences, Upstate University Hospital, Syracuse, NY, 13210, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - David T W Chen
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Bryce England
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Joanna Cross
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Xueying Jiang
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Winston Corona
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Jill Russ
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Barbara Mallon
- Center for Scientific Review, Neurotechnology and Vision Branch, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Joe Steiner
- Neurotherapeutics Development Unit, NINDS, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nasir Malik
- Neurotherapeutics Development Unit, NINDS, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Theresa de Guzman
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Natia Horato
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Mariana B Mallmann
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Victoria Mendes
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Amanda L Dűck
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Antonio E Nardi
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Francis J McMahon
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
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Schmilovich Z, Bourque VR, Douard E, Huguet G, Poulain C, Ross JP, Alipour P, Castonguay CÉ, Younis N, Jean-Louis M, Saci Z, Pausova Z, Paus T, Schuman G, Porteous D, Davies G, Redmond P, Harris SE, Deary IJ, Whalley H, Hayward C, Dion PA, Jacquemont S, Rouleau GA. Copy-number variants and polygenic risk for intelligence confer risk for autism spectrum disorder irrespective of their effects on cognitive ability. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.29.23299190. [PMID: 38076919 PMCID: PMC10705642 DOI: 10.1101/2023.11.29.23299190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Rare copy number variants (CNVs) and polygenic risk for intelligence (PRS-IQ) both confer risk for autism spectrum disorder (ASD) but have opposing effects on cognitive ability. The field has struggled to disentangle the effects of these two classes of genomic variants on cognitive ability from their effects on ASD risk, in part because previous studies did not include controls with cognitive measures. We aim to investigate the impact of these genomic variants on ASD risk while adjusting for their known effects on cognitive ability. In a cohort of 8,426 subjects with ASD and 169,804 controls with cognitive assessments, we found that rare coding CNVs and PRS-IQ increased ASD risk, even after adjusting for their effects on cognitive ability. Bottom decile PRS-IQ and CNVs both decreased cognitive ability but had opposing effects on ASD risk. Models combining both classes of variants showed that the effects of rare CNVs and PRS-IQ on ASD risk and cognitive ability were largely additive, further suggesting that risk for ASD is conferred independently from its effects on cognitive ability. Despite imparting mostly additive effects on ASD risk, rare CNVs and PRS-IQ showed opposing effects on core and associated features and developmental history among subjects with ASD. Our findings suggest that cognitive ability itself may not be the factor driving the underlying risk for ASD conferred by these two classes of genomic variants. In other words, ASD risk and cognitive ability may be two distinct manifestations of CNVs and PRS-IQ. This study also highlights the challenge of understanding how genetic risk for ASD maps onto its dimensional traits.
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Affiliation(s)
- Zoe Schmilovich
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Vincent-Raphaël Bourque
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Elise Douard
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Guillaume Huguet
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Cécile Poulain
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jay P. Ross
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Paria Alipour
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Charles-Étienne Castonguay
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Nadine Younis
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Martineau Jean-Louis
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Zohra Saci
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Tomas Paus
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Departments of Psychiatry of Neuroscience, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Departments of Psychology and Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Gunter Schuman
- Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, London, England
| | - David Porteous
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, UK
| | - Gail Davies
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
| | - Paul Redmond
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
| | - Sarah E. Harris
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
| | - Ian J. Deary
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
| | - Heather Whalley
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, UK
| | - Caroline Hayward
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, UK
| | - Patrick A. Dion
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, Canada
| | - Sébastien Jacquemont
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Guy A. Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, Canada
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Carlisle SG, Albasha H, Michelena H, Sabate-Rotes A, Bianco L, De Backer J, Mosquera LM, Yetman AT, Bissell MM, Andreassi MG, Foffa I, Hui DS, Caffarelli A, Kim YY, Guo DC, Citro R, De Marco M, Tretter JT, McBride KL, Milewicz DM, Body SC, Prakash SK. Rare Genomic Copy Number Variants Implicate New Candidate Genes for Bicuspid Aortic Valve. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.23.23297397. [PMID: 37961530 PMCID: PMC10635161 DOI: 10.1101/2023.10.23.23297397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Bicuspid aortic valve (BAV), the most common congenital heart defect, is a major cause of aortic valve disease requiring valve interventions and thoracic aortic aneurysms predisposing to acute aortic dissections. The spectrum of BAV ranges from early onset valve and aortic complications (EBAV) to sporadic late onset disease. Rare genomic copy number variants (CNVs) have previously been implicated in the development of BAV and thoracic aortic aneurysms. We determined the frequency and gene content of rare CNVs in EBAV probands (n = 272) using genome-wide SNP microarray analysis and three complementary CNV detection algorithms (cnvPartition, PennCNV, and QuantiSNP). Unselected control genotypes from the Database of Genotypes and Phenotypes were analyzed using identical methods. We filtered the data to select large genic CNVs that were detected by multiple algorithms. Findings were replicated in cohorts with late onset sporadic disease (n = 5040). We identified 34 large and rare (< 1:1000 in controls) CNVs in EBAV probands. The burden of CNVs intersecting with genes known to cause BAV when mutated was increased in case-control analysis. CNVs intersecting with GATA4 and DSCAM were enriched in cases, recurrent in other datasets, and segregated with disease in families. In total, we identified potentially pathogenic CNVs in 8% of EBAV cases, implicating alterations of candidate genes at these loci in the pathogenesis of BAV.
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Affiliation(s)
- Steven G Carlisle
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Hasan Albasha
- UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Hector Michelena
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Anna Sabate-Rotes
- Department of Pediatric Cardiology, Hospital Vall d'Hebron, Facultad de Medicina, Universidad Autònoma Barcelona, Barcelona, Spain
| | - Lisa Bianco
- Department of Pediatric Cardiology, Hospital Vall d'Hebron, Facultad de Medicina, Universidad Autònoma Barcelona, Barcelona, Spain
| | - Julie De Backer
- Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium; VASCERN HTAD European Reference Centre, Belgium; Department of Pediatrics, Division of Pediatric Cardiology, Ghent University Hospital, Ghent, Belgium; Department of Cardiology, Ghent University Hospital, Ghent, Belgium
| | | | - Anji T Yetman
- Children's Hospital and Medical Center, University of Nebraska, Omaha, Nebraska
| | - Malenka M Bissell
- Deparmentt of Biomedical Imaging Science, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | | | - Ilenia Foffa
- Consiglio Nazionale delle Richerche (CNR), Instituto di Fisiologia Clinica, Pisa, Italy
| | - Dawn S Hui
- Department of Cardiothoracic Surgery, University of Texas Health Science Center San Antonio, Texas
| | - Anthony Caffarelli
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Yuli Y Kim
- Division of Cardiovascular Medicine, The Hospital of the University of Pennsylvania, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania; Philadelphia Adult Congenital Heart Center, The Children's Hospital of Philadelphia, Perelman Center for Advanced Medicine, Penn Medicine, Philadelphia, Pennsylvania
| | - Dong-Chuan Guo
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Rodolfo Citro
- Cardio-Thoracic and Vascular Department, University Hospital "San Giovanni di Dio e Ruggi d'Aragona," Salerno, Italy
| | - Margot De Marco
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Italy
| | - Justin T Tretter
- Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kim L McBride
- Division of Human Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Dianna M Milewicz
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Simon C Body
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts
| | - Siddharth K Prakash
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas
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36
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Liu Z, Huang YF. Deep multiple-instance learning accurately predicts gene haploinsufficiency and deletion pathogenicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555384. [PMID: 37693607 PMCID: PMC10491176 DOI: 10.1101/2023.08.29.555384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Copy number losses (deletions) are a major contributor to the etiology of severe genetic disorders. Although haploinsufficient genes play a critical role in deletion pathogenicity, current methods for deletion pathogenicity prediction fail to integrate multiple lines of evidence for haploinsufficiency at the gene level, limiting their power to pinpoint deleterious deletions associated with genetic disorders. Here we introduce DosaCNV, a deep multiple-instance learning framework that, for the first time, models deletion pathogenicity jointly with gene haploinsufficiency. By integrating over 30 gene-level features potentially predictive of haploinsufficiency, DosaCNV shows unmatched performance in prioritizing pathogenic deletions associated with a broad spectrum of genetic disorders. Furthermore, DosaCNV outperforms existing methods in predicting gene haploinsufficiency even though it is not trained on known haploinsufficient genes. Finally, DosaCNV leverages a state-of-the-art technique to quantify the contributions of individual gene-level features to haploinsufficiency, allowing for human-understandable explanations of model predictions. Altogether, DosaCNV is a powerful computational tool for both fundamental and translational research.
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Affiliation(s)
- Zhihan Liu
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Molecular, Cellular, and Integrative Biosciences Program, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
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37
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Forrest MP, Penzes P. Mechanisms of copy number variants in neuropsychiatric disorders: From genes to therapeutics. Curr Opin Neurobiol 2023; 82:102750. [PMID: 37515924 PMCID: PMC10529795 DOI: 10.1016/j.conb.2023.102750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/01/2023] [Accepted: 06/27/2023] [Indexed: 07/31/2023]
Abstract
Copy number variants (CNVs) are genomic imbalances strongly linked to the aetiology of neuropsychiatric disorders such as schizophrenia and autism. By virtue of their large size, CNVs often contain many genes, providing a multi-genic view of disease processes that can be dissected in model systems. Thus, CNV research provides an important stepping stone towards understanding polygenic disease mechanisms, positioned between monogenic and polygenic risk models. In this review, we will outline hypothetical models for gene interactions occurring within CNVs and discuss different approaches used to study rodent and stem cell disease models. We highlight recent work showing that genetic and pharmacological strategies can be used to rescue important aspects of CNV-mediated pathophysiology, which often converges onto synaptic pathways. We propose that using a rescue approach in complete CNV models provides a new path forward for precise mechanistic understanding of complex disorders and a tangible route towards therapeutic development.
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Affiliation(s)
- Marc P Forrest
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Autism and Neurodevelopment, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
| | - Peter Penzes
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Autism and Neurodevelopment, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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38
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Caseras X, Legge SE, Bracher-Smith M, Anney R, Owen MJ, Escott-Price V, Kirov G. Copy Number Variants Increasing Risk for Schizophrenia: Shared and Distinct Effects on Brain Morphometry and Cognitive Performance. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2023; 3:902-911. [PMID: 37881570 PMCID: PMC10593876 DOI: 10.1016/j.bpsgos.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Background Copy number variations (CNVs) conferring risk for mental disorders are associated with brain changes and cognitive deficits. However, whether these effects are shared or distinct across CNVs remains untested. Here we compared the effects on brain morphometry and cognitive performance across CNVs with shared psychiatric liability. Methods Unaffected and unrelated participants of White British and Irish ancestry were drawn from the UK Biobank. After quality control, we retained 31,941 participants not carrying any damaging CNVs and 202 participants carrying one CNV increasing risk for schizophrenia. Using regression analyses, we tested the association between brain morphometry and cognitive performance with CNV carrying status and compared these effect sizes across CNVs using z test for the equality of regression coefficients. Equation modeling was used to examine the mediation of brain phenotypes on the association between CNVs and cognitive performance. Results We detected different patterns of association between CNVs and brain morphometry and cognitive abilities. Comparing across CNVs, 1q21.1 deletion showed the strongest association with surface area in frontal lobe (β = -1.03, p = 4 × 10-8; β = -0.81, p = .00001) and performance in digit memory (β = -1.58, p = .00003), while 1q21.1 duplication showed the strongest association with volume of the putamen (β = -0.70, p = .0004) and reaction time (β = -1.14, p = .000002). We also showed that even when 2 CNVs were associated with performance in the same cognitive ability, these associations were mediated by different brain changes. Conclusions Despite sharing similar psychiatric liability, the CNVs under study appeared to have different effects on brain morphometry and on performance in cognitive abilities, suggesting the existence of distinctive neurobiological pathways into the same clinical phenotypes.
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Affiliation(s)
- Xavier Caseras
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Sophie E. Legge
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Matthew Bracher-Smith
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Richard Anney
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Michael J. Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Valentina Escott-Price
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - George Kirov
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
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39
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Allou L, Mundlos S. Disruption of regulatory domains and novel transcripts as disease-causing mechanisms. Bioessays 2023; 45:e2300010. [PMID: 37381881 DOI: 10.1002/bies.202300010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 06/30/2023]
Abstract
Deletions, duplications, insertions, inversions, and translocations, collectively called structural variations (SVs), affect more base pairs of the genome than any other sequence variant. The recent technological advancements in genome sequencing have enabled the discovery of tens of thousands of SVs per human genome. These SVs primarily affect non-coding DNA sequences, but the difficulties in interpreting their impact limit our understanding of human disease etiology. The functional annotation of non-coding DNA sequences and methodologies to characterize their three-dimensional (3D) organization in the nucleus have greatly expanded our understanding of the basic mechanisms underlying gene regulation, thereby improving the interpretation of SVs for their pathogenic impact. Here, we discuss the various mechanisms by which SVs can result in altered gene regulation and how these mechanisms can result in rare genetic disorders. Beyond changing gene expression, SVs can produce novel gene-intergenic fusion transcripts at the SV breakpoints.
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Affiliation(s)
- Lila Allou
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Mundlos
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
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40
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Mollon J, Schultz LM, Huguet G, Knowles EEM, Mathias SR, Rodrigue A, Alexander-Bloch A, Saci Z, Jean-Louis M, Kumar K, Douard E, Almasy L, Jacquemont S, Glahn DC. Impact of Copy Number Variants and Polygenic Risk Scores on Psychopathology in the UK Biobank. Biol Psychiatry 2023; 94:591-600. [PMID: 36764568 PMCID: PMC10409883 DOI: 10.1016/j.biopsych.2023.01.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
BACKGROUND Our understanding of the impact of copy number variants (CNVs) on psychopathology and their joint influence with polygenic risk scores (PRSs) remains limited. METHODS The UK Biobank recruited 502,534 individuals ages 37 to 73 years living in the United Kingdom between 2006 and 2010. After quality control, genotype data from 459,855 individuals were available for CNV calling. A total of 61 commonly studied recurrent neuropsychiatric CNVs were selected for analyses and examined individually and in aggregate (any CNV, deletion, or duplication). CNV risk scores were used to quantify intolerance of CNVs to haploinsufficiency. Major depressive disorder and generalized anxiety disorder PRSs were generated for White British individuals (N = 408,870). Mood/anxiety factor scores were generated using item-level questionnaire data (N = 501,289). RESULTS CNV carriers showed higher mood/anxiety scores than noncarriers, with the largest effects seen for intolerant deletions. A total of 11 individual deletions and 8 duplications were associated with higher mood/anxiety. Carriers of the 9p24.3 (DMRT1) duplication showed lower mood/anxiety. Associations remained significant for most CNVs when excluding individuals with psychiatric diagnoses. Nominally significant CNV × PRS interactions provided preliminary evidence that associations between select individual CNVs, but not CNVs in aggregate, and mood/anxiety may be modulated by PRSs. CONCLUSIONS CNVs associated with risk for psychiatric disorders showed small to large effects on dimensional mood/anxiety scores in a general population cohort, even when excluding individuals with psychiatric diagnoses. CNV × PRS interactions showed that associations between select CNVs and mood/anxiety may be modulated by PRSs.
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Affiliation(s)
- Josephine Mollon
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Laura M Schultz
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Guillaume Huguet
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada; Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Emma E M Knowles
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Samuel R Mathias
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amanda Rodrigue
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Aaron Alexander-Bloch
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Neurodevelopment and Psychosis Section, Department of Psychiatry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zohra Saci
- Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Martineau Jean-Louis
- Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Kuldeep Kumar
- Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Elise Douard
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada; Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Laura Almasy
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Genetics, Perelman School of Medicine, Penn-CHOP Lifespan Brain Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sebastien Jacquemont
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada; Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; Olin Neuropsychiatry Research Center, Institute of Living, Hartford, Connecticut
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Pan L, Wu J, Liang D, Yuan J, Wang J, Shen Y, Lu J, Xia A, Li J, Wu L. Association analysis between chromosomal abnormalities and fetal ultrasonographic soft markers based on 15,263 fetuses. Am J Obstet Gynecol MFM 2023; 5:101072. [PMID: 37393030 DOI: 10.1016/j.ajogmf.2023.101072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/03/2023]
Abstract
BACKGROUND Soft markers are common prenatal ultrasonographic findings that indicate an increased risk for fetal aneuploidy. However, the association between soft markers and pathogenic or likely pathogenic copy number variations is still unclear, and clinicians lack clarity on which soft markers warrant a recommendation for invasive prenatal genetic testing of the fetus. OBJECTIVE This study aimed to provide guidance on ordering prenatal genetic testing for fetuses with different soft markers and to elucidate the association between specific types of chromosomal abnormalities and specific ultrasonographic soft markers. STUDY DESIGN Low-pass genome sequencing was performed for 15,263 fetuses, including 9123 with ultrasonographic soft markers and 6140 with normal ultrasonographic findings. The detection rate of pathogenic or likely pathogenic copy number variants among fetuses with various ultrasonographic soft markers were compared with that of fetuses with normal ultrasonography. The association of soft markers with aneuploidy and pathogenic or likely pathogenic copy number variants were investigated using Fisher exact tests with Bonferroni correction. RESULTS The detection rate of aneuploidy and pathogenic or likely pathogenic copy number variants was 3.04% (277/9123) and 3.40% (310/9123), respectively, in fetuses with ultrasonographic soft markers. An absent or a hypoplastic nasal bone was the soft marker in the second trimester with the highest diagnostic rate for aneuploidy of 5.22% (83/1591) among all isolated groups. Four types of isolated ultrasonographic soft markers, namely a thickened nuchal fold, single umbilical artery, mild ventriculomegaly, and absent or hypoplastic nasal bone, had higher diagnostic rates for pathogenic or likely pathogenic copy number variants (P<.05; odds ratio, 1.69-3.31). Furthermore, this study found that the 22q11.2 deletion was associated with an aberrant right subclavian artery, whereas the 16p13.11 deletion, 10q26.13-q26.3 deletion, and 8p23.3-p23.1 deletion were associated with a thickened nuchal fold, and the 16p11.2 deletion and 17p11.2 deletion were associated with mild ventriculomegaly (P<.05). CONCLUSION Ultrasonographic phenotype-based genetic testing should be considered in clinical consultations. Copy number variant analysis is recommended for fetuses with an isolated thickened nuchal fold, a single umbilical artery, mild ventriculomegaly, and an absent or a hypoplastic nasal bone. A comprehensive definition of genotype-phenotype correlations in aneuploidy and pathogenic or likely pathogenic copy number variants could provide better information for genetic counseling.
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Affiliation(s)
- Lijuan Pan
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China (Drs Pan, J Wu, Liang, and L Wu); Department of Obstetrics, Xiangya Hospital, Central South University, Changsha, Hunan, China (Dr Pan)
| | - Jiayu Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China (Drs Pan, J Wu, Liang, and L Wu)
| | - Desheng Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China (Drs Pan, J Wu, Liang, and L Wu)
| | - Jing Yuan
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China (Dr Yuan)
| | - Jue Wang
- Department of Obstetrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China (Dr Wang)
| | - Yinchen Shen
- Department of Maternity Care, Nanning Maternity and Child Health Hospital, Nanning, Guangxi, China (Dr Shen)
| | - Junjie Lu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China (Dr Lu)
| | - Aihua Xia
- Department of Obstetrics, Beihai People's Hospital, Beihai, Guangxi, China (Dr Xia)
| | - Jinchen Li
- Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China (Dr Li).
| | - Lingqian Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China (Drs Pan, J Wu, Liang, and L Wu).
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Wu D, Wu Y, Lan Y, Lan S, Zhong Z, Li D, Zheng Z, Wang H, Ma L. Chromosomal Aberrations in Pediatric Patients With Moderate/Severe Developmental Delay/Intellectual Disability With Abundant Phenotypic Heterogeneities: A Single-Center Study. Pediatr Neurol 2023; 147:72-81. [PMID: 37566956 DOI: 10.1016/j.pediatrneurol.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/26/2023] [Accepted: 06/06/2023] [Indexed: 08/13/2023]
Abstract
BACKGROUND This study aimed to examine the clinical usefulness of chromosome microarray (CMA) for selective implementation in patients with unexplained moderate or severe developmental delay/intellectual disability (DD/ID) and/or combined with different dysphonic features in the Han Chinese population. METHODS We retrospectively analyzed data on 122 pediatric patients with unexplained isolated moderate/severe DD/ID with or without autism spectrum disorders, epilepsy, dystonia, and congenital abnormalities from a single-center neurorehabilitation clinic in southern China. RESULTS A total of 46 probands (37.7%) had abnormal CMA results among the 122 study patients. With the exclusion of aneuploidies, uniparental disomies, and multiple homozygotes, 37 patients harbored 39 pathogenic copy number variations (pCNVs) (median [interquartile range] size: 3.57 [1.6 to 7.1] Mb; 33 deletions and 6 duplications), enriched in chromosomes 5, 7, 15, 17, and 22, with a markedly high prevalence of Angelman/Prader-Willi syndrome (24.3% [nine of 37]). Three rare deletions in the regions 5q33.2q34, 17p13.2, and 13q33.2 were reported, with specific delineation of clinical phenotypes. The frequencies of pCNVs were 18%, 33.3%, 38.89%, 41.67%, and 100% for patients with 1, 2, 3, 4, and 5 study phenotypes, respectively; patients with more concomitant abnormalities in the heart, brain, craniofacial region, and/or other organs had a higher CMA diagnostic yield and pCNV prevalence (P < 0.05). CONCLUSIONS Clinical application of CMA as a first-tier test among patients with moderate/severe DD/ID combined with congenital structural anomalies improved diagnostic yields and the quality of clinical management in this series of patients.
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Affiliation(s)
- Dan Wu
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China; Centre for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia
| | - Yi Wu
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yulong Lan
- Centre for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia; Department of Cardiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Shaocong Lan
- Guangdong Medical College, Zhanjiang, Guangdong, China
| | - Zhiwei Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Duo Li
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zexin Zheng
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Hongwu Wang
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China.
| | - Lian Ma
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China; Department of Hematology and Oncology, Shenzhen Children's Hospital of China Medical University, Shenzhen, Guangdong, China; Shenzhen Public Service Platform of Molecular Medicine in Pediatric Hematology and Oncology, Shenzhen, Guangdong, China; Department of Pediatrics, The Third Affiliated Hospital of Guangzhou Medical University (The Women and Children's Hospital of Guangzhou Medical University), Guangzhou, Guangdong, China.
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Yang X, Mao Y, Wang XK, Ma DN, Xu Z, Gong N, Henning B, Zhang X, He G, Shi YY, Eichler EE, Li ZQ, Takahashi E, Li WD. Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing. Zool Res 2023; 44:837-847. [PMID: 37501399 PMCID: PMC10559097 DOI: 10.24272/j.issn.2095-8137.2022.514] [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: 04/23/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023] Open
Abstract
The common marmoset ( Callithrix jacchus) has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies. Epileptic marmosets have been independently reported in two Asian primate research centers. Nevertheless, the population genetics within these primate centers and the specific genetic variants associated with epilepsy in marmosets have not yet been elucidated. Here, we characterized the genetic relationships and risk variants for epilepsy in 41 samples from two epileptic marmoset pedigrees using whole-genome sequencing. We identified 14 558 184 single nucleotide polymorphisms (SNPs) from the 41 samples and found higher chimerism levels in blood samples than in fingernail samples. Genetic analysis showed fourth-degree of relatedness among marmosets at the primate centers. In addition, SNP and copy number variation (CNV) analyses suggested that the WW domain-containing oxidoreductase ( WWOX) and Tyrosine-protein phosphatase nonreceptor type 21 ( PTPN21) genes may be associated with epilepsy in marmosets. Notably, KCTD18-like gene deletion was more common in epileptic marmosets than control marmosets. This study provides valuable population genomic resources for marmosets in two Asian primate centers. Genetic analyses identified a reasonable breeding strategy for genetic diversity maintenance in the two centers, while the case-control study revealed potential risk genes/variants associated with epilepsy in marmosets.
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Affiliation(s)
- XiangYu Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Psychology and Behavioral Science, Shanghai Jiao Tong University, Shanghai 200030, China
- WLA Laboratories, World Laureates Association, Shanghai 201203, China
| | - YaFei Mao
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Genome Sciences, University of Washington School of Medicine, Seattle WA 98195, USA
| | - Xuan-Kai Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dong-Ni Ma
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- WLA Laboratories, World Laureates Association, Shanghai 201203, China
| | - Zhen Xu
- Institute of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Neng Gong
- Institute of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Barbara Henning
- Department of Genome Sciences, University of Washington School of Medicine, Seattle WA 98195, USA
| | - Xu Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- WLA Laboratories, World Laureates Association, Shanghai 201203, China
| | - Guang He
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong-Yong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Affiliated Hospital of Qingdao University & Biomedical Sciences Institute of Qingdao University, Qingdao Branch of SJTU Bio-X Institutes, Qingdao University, Qingdao, Shandong 266003, China
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle WA 98195, USA
| | - Zhi-Qiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Affiliated Hospital of Qingdao University & Biomedical Sciences Institute of Qingdao University, Qingdao Branch of SJTU Bio-X Institutes, Qingdao University, Qingdao, Shandong 266003, China. E-mail:
| | - Eiki Takahashi
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Biomedicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan. E-mail:
| | - Wei-Dong Li
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Psychology and Behavioral Science, Shanghai Jiao Tong University, Shanghai 200030, China
- WLA Laboratories, World Laureates Association, Shanghai 201203, China
- Global Institute of Future Technology, Shanghai Jiao Tong University, Shanghai 200240, China. E-mail:
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Li C, Chen L, Pan G, Zhang W, Li SC. Deciphering complex breakage-fusion-bridge genome rearrangements with Ambigram. Nat Commun 2023; 14:5528. [PMID: 37684230 PMCID: PMC10491683 DOI: 10.1038/s41467-023-41259-w] [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: 10/13/2022] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Breakage-fusion-bridge (BFB) is a complex rearrangement that leads to tumor malignancy. Existing models for detecting BFBs rely on the ideal BFB hypothesis, ruling out the possibility of BFBs entangled with other structural variations, that is, complex BFBs. We propose an algorithm Ambigram to identify complex BFB and reconstruct the rearranged structure of the local genome during the cancer subclone evolution process. Ambigram handles data from short, linked, long, and single-cell sequences, and optical mapping technologies. Ambigram successfully deciphers the gold- or silver-standard complex BFBs against the state-of-the-art in multiple cancers. Ambigram dissects the intratumor heterogeneity of complex BFB events with single-cell reads from melanoma and gastric cancer. Furthermore, applying Ambigram to liver and cervical cancer data suggests that the BFB mechanism may mediate oncovirus integrations. BFB also exists in noncancer genomics. Investigating the complete human genome reference with Ambigram suggests that the BFB mechanism may be involved in two genome reorganizations of Homo Sapiens during evolution. Moreover, Ambigram discovers the signals of recurrent foldback inversions and complex BFBs in whole genome data from the 1000 genome project, and congenital heart diseases, respectively.
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Affiliation(s)
- Chaohui Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Lingxi Chen
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Guangze Pan
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Wenqian Zhang
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China.
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45
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Wang D, Peng H, Wang Y, Hou Y, Guo F, Zhu J, Hu T, Yang J. Performance of noninvasive prenatal testing for twin pregnancies in South China. J Assist Reprod Genet 2023; 40:2219-2231. [PMID: 37480419 PMCID: PMC10440307 DOI: 10.1007/s10815-023-02881-1] [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: 03/01/2023] [Accepted: 07/03/2023] [Indexed: 07/24/2023] Open
Abstract
OBJECTIVE The purpose of this study was to evaluate the performance of noninvasive prenatal testing (NIPT) for the detection of chromosomal aneuploidies and copy number variations (CNVs) in twin pregnancies. METHOD A cohort of 2010 women with twin pregnancies was recruited. 1331 patients opted for NIPT, and 679 patients opted for expanded NIPT (NIPT-plus). All high-risk patients were advised to undergo invasive prenatal diagnosis. All participants were followed up until 6 months after birth. RESULTS Twenty-two cases were predicted to have a high risk of chromosome abnormalities by NIPT, of which 14 pregnant women underwent invasive prenatal diagnosis. The 14 cases included 3 cases of trisomy 21, 1 case of trisomy 18, 1 case of trisomy 7, 2 cases of sex chromosome aneuploidies (SCAs), and 7 cases of CNVs, of which the confirmed cases numbered 2, 1, 0, 1, and 0, respectively. Twenty cases were predicted to have a high risk of chromosome abnormalities by NIPT-plus, of which 16 pregnant women underwent invasive prenatal diagnosis. The 16 cases included 1 case of trisomy 21, 1 case of trisomy 7, 7 cases of SCAs, and 7 cases of CNVs, of which were confirmed in 1, 0, 3, and 2, respectively. No false-negative result was reported during the follow-up period. CONCLUSION The NIPT/NIPT-plus has excellent performance in the detection of chromosome aneuploidies in twin pregnancies. But for CNVs, the effectiveness of NIPT is poor, and the NIPT-plus have a certain detection efficiency. It is worth noting that pre- and post-genetic counseling is especially important, and the chorionicity, mode of conception, clinical indications, and fetal fraction should be considered as influencing factors.
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Affiliation(s)
- Dongmei Wang
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Haishan Peng
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Yixia Wang
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Yaping Hou
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Fangfang Guo
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Juan Zhu
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Tingting Hu
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Jiexia Yang
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China.
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Liu J, Xie M, Duan X, Liu F, Luo P, Liu Q. Upregulation of the Four and a Half LIM Domains 1 linked with familial venous dysplasia in a familial genetic examination. Am J Transl Res 2023; 15:5035-5046. [PMID: 37692954 PMCID: PMC10492050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/31/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND This study aimed to analyze the mutation site in a family diagnosed with venous dysplasia to identify possible pathogenic genes. METHODS A 15-year-old female presented with lower extremity venous tortuosity aggravated by ulceration. Only the young sister exhibited similar symptoms within the immediate family of the proband. Whole genome sequencing (WGS) was used to evaluate the mutation sites and chromosome copy number variations (CNV) within the family. The possible pathogenic genes located in the region with CNVs were identified, and the expression of the possible pathogenic genes was verified via quantitative polymerase chain reaction (Q-PCR) and western blotting (WB) analysis. In-vitro models were used to verify the role of possible pathogenic genes linked with the development of venous dysplasia. RESULTS The high-resolution karyotype analysis of the chromosomes found no abnormalities. The results of the WGS indicated that the proband and her sister shared the CNV events, including a microdeletion on chromosomes X: 13580000-1358555000 and microduplications of chromosome X: 136055000-136290000, chromosome X: 136475000-13671000. The results of the Q-PCR and WB showed that FHL1 was highly expressed in the proband and her sister, indicating that mutations of the FHL1 may have an important role in the development of vein malformations. The results of the in vitro experiments showed that FHL1 overexpression could inhibit venous development. CONCLUSION The CNV in the Xq26 region (136054501-136288300) was found to be linked with the development of venous malformations in this family. However, further studies are required to evaluate the genetic mechanisms involved in the development of venous malformations.
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Affiliation(s)
- Jianping Liu
- Suzhou Medical College of Soochow UniversitySuzhou, Jiangsu, China
- Jiangxi Provincial Clinical Research Center for Vascular Anomalies, The First Affiliated Hospital of Gannan Medical UniversityGanzhou, Jiangxi, China
| | - Mingfeng Xie
- Jiangxi Provincial Clinical Research Center for Vascular Anomalies, The First Affiliated Hospital of Gannan Medical UniversityGanzhou, Jiangxi, China
- Chinese & Western Integrative Medicine Discipline, Jiangxi University of Chinese MedicineNanchang, Jiangxi, China
- Jiangxi Key Laboratory of TCM for Prevention and Treatment on HemangiomaNanchang, Jiangxi, China
| | - Xunhong Duan
- Jiangxi Provincial Clinical Research Center for Vascular Anomalies, The First Affiliated Hospital of Gannan Medical UniversityGanzhou, Jiangxi, China
| | - Fengen Liu
- Jiangxi Provincial Clinical Research Center for Vascular Anomalies, The First Affiliated Hospital of Gannan Medical UniversityGanzhou, Jiangxi, China
| | - Pan Luo
- Chinese & Western Integrative Medicine Discipline, Jiangxi University of Chinese MedicineNanchang, Jiangxi, China
| | - Qian Liu
- Suzhou Medical College of Soochow UniversitySuzhou, Jiangsu, China
- Jiangxi Provincial Clinical Research Center for Vascular Anomalies, The First Affiliated Hospital of Gannan Medical UniversityGanzhou, Jiangxi, China
- Chinese & Western Integrative Medicine Discipline, Jiangxi University of Chinese MedicineNanchang, Jiangxi, China
- Jiangxi Key Laboratory of TCM for Prevention and Treatment on HemangiomaNanchang, Jiangxi, China
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47
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Papageorgiou E, Athanasiadis A, Fidani S, Papoulidis I, Manolakos E, Siomou E, Chatzakis C, Sotiriadis A. The Effect of Resolution Level and Targeted Design in the Diagnostic Performance of Prenatal Chromosomal Microarray Analysis. Fetal Diagn Ther 2023; 50:397-405. [PMID: 37549642 DOI: 10.1159/000533137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 07/10/2023] [Indexed: 08/09/2023]
Abstract
INTRODUCTION This study was performed to assess the optimal resolution for prenatal testing by array comparative genomic hybridization (aCGH), aiming to balance between maximum diagnostic yield and minimal detection of variants of uncertain significance (VOUS). METHODS This was a prospective study using data of 2,336 fetuses that underwent invasive prenatal diagnosis, and the samples were analyzed by aCGH. In total, six different aCGH platforms were studied; four different resolutions (0.18 Mb, 0.5 Mb, 1 Mb, and 2 Mb) and two platform designs (whole-genome [WG] and targeted). The results of these designs were compared based on their diagnostic yield and VOUS rate. The performance of the different designs was further analyzed according to indication for invasive testing. RESULTS The diagnostic yield of copy number variants increased with increasing level of analysis. The detection rates of clinically significant chromosomal abnormalities were almost the same across our targeted array designs; 7.2% with 0.18 Mb backbone/0.05 Mb versus 7.1% with 0.5 Mb backbone/0.05 Mb (p >0.05). However, a significant difference in the rate of VOUS was observed; 9.4% with 0.18 Mb backbone/0.05 Mb versus 6% with 0.5 Mb backbone/0.05 Mb (p <0.001). After analyzing the results across different indications for testing, we found that the application of non-targeted platform designs and lower levels of resolution analysis (such as 1 Mb WG or 0.5 MbL/1 MbG WG) would offer similar diagnostic yield in most cases with major congenital anomalies, with lower VOUS rates. However, the sample size for many indication groups was too small to extract robust associations. CONCLUSION It appears that the targeted array platform with 0.5 Mb backbone resolution and 0.05 Mb on targeted gene-rich regions is optimal for routine chromosomal microarray analysis use in prenatal diagnosis. It may be beneficial to individualize the minimum resolution in specific referral indications as the indications for invasive prenatal testing may be quite heterogeneous.
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Affiliation(s)
- Elena Papageorgiou
- Second Department of Obstetrics and Gynecology, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Apostolos Athanasiadis
- Third Department of Obstetrics and Gynecology, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Stiliani Fidani
- Department of General Biology, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | | | | | - Christos Chatzakis
- Second Department of Obstetrics and Gynecology, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Alexandros Sotiriadis
- Second Department of Obstetrics and Gynecology, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
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48
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Bouassida M, Egloff M, Levy J, Chatron N, Bernardini L, Le Guyader G, Tabet AC, Schluth-Bolard C, Brancati F, Giuffrida MG, Dard R, Clorennec J, Coursimault J, Vialard F, Hervé B. 2p25.3 microduplications involving MYT1L: further phenotypic characterization through an assessment of 16 new cases and a literature review. Eur J Hum Genet 2023; 31:895-904. [PMID: 37188826 PMCID: PMC10400587 DOI: 10.1038/s41431-023-01379-9] [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: 10/02/2022] [Revised: 04/03/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
Microduplications involving the MYT1L gene have mostly been described in series of patients with isolated schizophrenia. However, few reports have been published, and the phenotype has still not been well characterized. We sought to further characterize the phenotypic spectrum of this condition by describing the clinical features of patients with a pure 2p25.3 microduplication that includes all or part of MYT1L. We assessed 16 new patients with pure 2p25.3 microduplications recruited through a French national collaboration (n = 15) and the DECIPHER database (n = 1). We also reviewed 27 patients reported in the literature. For each case, we recorded clinical data, the microduplication size, and the inheritance pattern. The clinical features were variable and included developmental and speech delays (33%), autism spectrum disorder (ASD, 23%), mild-to-moderate intellectual disability (ID, 21%), schizophrenia (23%), or behavioral disorders (16%). Eleven patients did not have an obvious neuropsychiatric disorder. The microduplications ranged from 62.4 kb to 3.8 Mb in size and led to duplication of all or part of MYT1L; seven of these duplications were intragenic. The inheritance pattern was available for 18 patients: the microduplication was inherited in 13 cases, and all parents but one had normal phenotype. Our comprehensive review and expansion of the phenotypic spectrum associated with 2p25.3 microduplications involving MYT1L should help clinicians to better assess, counsel and manage affected individuals. MYT1L microduplications are characterized by a spectrum of neuropsychiatric phenotypes with incomplete penetrance and variable expressivity, which are probably due to as-yet unknown genetic and nongenetic modifiers.
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Affiliation(s)
- Malek Bouassida
- Département de Génétique, Laboratoire de Biologie Médicale, CHI de Poissy-St Germain en Laye, F-78300, Poissy, France.
| | - Matthieu Egloff
- Service de Génétique, Centre Hospitalier Universitaire de Poitiers, F-86021, Poitiers, France
| | - Jonathan Levy
- Département de Génétique, Hôpital Robert Debré, APHP, F-75019, Paris, France
| | - Nicolas Chatron
- Service de cytogénétique, Groupement Hospitalier Est, Hospices Civils de Lyon, F-69500, Bron, France
| | | | - Gwenaël Le Guyader
- Service de Génétique, Centre Hospitalier Universitaire de Poitiers, F-86021, Poitiers, France
| | - Anne-Claude Tabet
- Département de Génétique, Hôpital Robert Debré, APHP, F-75019, Paris, France
| | - Caroline Schluth-Bolard
- Service de cytogénétique, Groupement Hospitalier Est, Hospices Civils de Lyon, F-69500, Bron, France
| | - Francesco Brancati
- Department of Life, Health and Environmental Sciences, University of L'Aquila Piazzale Salvatore Tommasi, It-67100, Coppito - L'Aquila, Italy
- San Raffaele Roma, IRCCS, It-00163, Roma, Italy
| | | | - Rodolphe Dard
- Département de Génétique, Laboratoire de Biologie Médicale, CHI de Poissy-St Germain en Laye, F-78300, Poissy, France
- RHuMA Team, UMR-BREED, INRA-UVSQ-ENVA, UFR Simone Veil Santé, F-78380, Montigny-le-Bretonneux, France
| | - Juliette Clorennec
- Département de Génétique, Laboratoire de Biologie Médicale, CHI de Poissy-St Germain en Laye, F-78300, Poissy, France
- RHuMA Team, UMR-BREED, INRA-UVSQ-ENVA, UFR Simone Veil Santé, F-78380, Montigny-le-Bretonneux, France
| | - Juliette Coursimault
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, F-76000, Rouen, France
| | - François Vialard
- Département de Génétique, Laboratoire de Biologie Médicale, CHI de Poissy-St Germain en Laye, F-78300, Poissy, France.
- RHuMA Team, UMR-BREED, INRA-UVSQ-ENVA, UFR Simone Veil Santé, F-78380, Montigny-le-Bretonneux, France.
| | - Bérénice Hervé
- Département de Génétique, Laboratoire de Biologie Médicale, CHI de Poissy-St Germain en Laye, F-78300, Poissy, France
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49
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Kawaguchi YW, Tsuchikane Y, Tanaka K, Taji T, Suzuki Y, Toyoda A, Ito M, Watano Y, Nishiyama T, Sekimoto H, Tsuchimatsu T. Extensive Copy Number Variation Explains Genome Size Variation in the Unicellular Zygnematophycean Alga, Closterium peracerosum-strigosum-littorale Complex. Genome Biol Evol 2023; 15:evad115. [PMID: 37348049 PMCID: PMC10407611 DOI: 10.1093/gbe/evad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/17/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023] Open
Abstract
Genome sizes are known to vary within and among closely related species, but the knowledge about genomic factors contributing to the variation and their impacts on gene functions is limited to only a small number of species. This study identified a more than 2-fold heritable genome size variation among the unicellular Zygnematophycean alga, Closterium peracerosum-strigosum-littorale (C. psl.) complex, based on short-read sequencing analysis of 22 natural strains and F1 segregation analysis. Six de novo assembled genomes revealed that genome size variation is largely attributable to genome-wide copy number variation (CNV) among strains rather than mating type-linked genomic regions or specific repeat sequences such as rDNA. Notably, about 30% of genes showed CNV even between strains that can mate with each other. Transcriptome and gene ontology analysis demonstrated that CNV is distributed nonrandomly in terms of gene functions, such that CNV was more often observed in the gene set with stage-specific expression. Furthermore, in about 30% of these genes with CNV, the expression level does not increase proportionally with the gene copy number, suggesting presence of dosage compensation, which was overrepresented in genes involved in basic biological functions, such as translation. Nonrandom patterns in gene duplications and corresponding expression changes in terms of gene functions may contribute to maintaining the high level of CNV associated with extensive genome size variation in the C. psl. complex, despite its possible detrimental effects.
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Affiliation(s)
- Yawako W Kawaguchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Graduate School of Science and Engineering, Chiba University, Chiba, Chiba, Japan
| | - Yuki Tsuchikane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Bunkyo-ku, Tokyo, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Teruaki Taji
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Motomi Ito
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Yasuyuki Watano
- Graduate School of Science, Chiba University, Chiba, Chiba, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Hiroyuki Sekimoto
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Bunkyo-ku, Tokyo, Japan
| | - Takashi Tsuchimatsu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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50
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Tilemis FN, Marinakis NM, Veltra D, Svingou M, Kekou K, Mitrakos A, Tzetis M, Kosma K, Makrythanasis P, Traeger-Synodinos J, Sofocleous C. Germline CNV Detection through Whole-Exome Sequencing (WES) Data Analysis Enhances Resolution of Rare Genetic Diseases. Genes (Basel) 2023; 14:1490. [PMID: 37510394 PMCID: PMC10379589 DOI: 10.3390/genes14071490] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Whole-Exome Sequencing (WES) has proven valuable in the characterization of underlying genetic defects in most rare diseases (RDs). Copy Number Variants (CNVs) were initially thought to escape detection. Recent technological advances enabled CNV calling from WES data with the use of accurate and highly sensitive bioinformatic tools. Amongst 920 patients referred for WES, 454 unresolved cases were further analysed using the ExomeDepth algorithm. CNVs were called, evaluated and categorized according to ACMG/ClinGen recommendations. Causative CNVs were identified in 40 patients, increasing the diagnostic yield of WES from 50.7% (466/920) to 55% (506/920). Twenty-two CNVs were available for validation and were all confirmed; of these, five were novel. Implementation of the ExomeDepth tool promoted effective identification of phenotype-relevant and/or novel CNVs. Among the advantages of calling CNVs from WES data, characterization of complex genotypes comprising both CNVs and SNVs minimizes cost and time to final diagnosis, while allowing differentiation between true or false homozygosity, as well as compound heterozygosity of variants in AR genes. The use of a specific algorithm for calling CNVs from WES data enables ancillary detection of different types of causative genetic variants, making WES a critical first-tier diagnostic test for patients with RDs.
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Affiliation(s)
- Faidon-Nikolaos Tilemis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Nikolaos M Marinakis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Danai Veltra
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Maria Svingou
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Kyriaki Kekou
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Anastasios Mitrakos
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Maria Tzetis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Konstantina Kosma
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Periklis Makrythanasis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Department of Genetic Medicine and Development, Medical School, University of Geneva, 1211 Geneva, Switzerland
- Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Joanne Traeger-Synodinos
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Christalena Sofocleous
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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