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Guan J, Wu X, Zhang J, Li J, Wang H, Wang Q. Global research landscape on the contribution of de novo mutations to human genetic diseases over the past 20 years: bibliometric analysis. J Neurogenet 2024:1-10. [PMID: 38647210 DOI: 10.1080/01677063.2024.2335171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
As the contribution of de novo mutations (DNMs) to human genetic diseases has been gradually uncovered, analyzing the global research landscape over the past 20 years is essential. Because of the large and rapidly increasing number of publications in this field, understanding the current landscape of the contribution of DNMs in the human genome to genetic diseases remains a challenge. Bibliometric analysis provides an approach for visualizing these studies using information in published records in a specific field. This study aimed to illustrate the current global research status and explore trends in the field of DNMs underlying genetic diseases. Bibliometric analyses were performed using the Bibliometrix Package based on the R language version 4.1.3 and CiteSpace version 6.1.R2 software for publications from 2000 to 2021 indexed under the Web of Science Core Collection (WoSCC) about DNMs underlying genetic diseases on 17 September 2022. We identified 3435 records, which were published in 731 journals by 26,538 authors from 6052 institutes in 66 countries. There was an upward trend in the number of publications since 2013. The USA, China, and Germany contributed the majority of the records included. The University of Washington, Columbia University, and Baylor College of Medicine were the top-producing institutions. Evan E Eichler of the University of Washington, Stephan J Sanders of the Yale University School of Medicine, and Ingrid E Scheffer of the University of Melbourne were the most high-ranked authors. Keyword co-occurrence analysis suggested that DNMs in neurodevelopmental disorders and intellectual disabilities were research hotspots and trends. In conclusion, our data show that DNMs have a significant effect on human genetic diseases, with a noticeable increase in annual publications over the last 5 years. Furthermore, potential hotspots are shifting toward understanding the causative role and clinical interpretation of newly identified or low-frequency DNMs observed in patients.
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Affiliation(s)
- Jing Guan
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Xiaonan Wu
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Jiao Zhang
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Jin Li
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Hongyang Wang
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Qiuju Wang
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
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Yue X, Luo Y, Wang J, Huang D. Monogenic Diabetes with GATA6 Mutations: Characterization of a Novel Family and a Comprehensive Analysis of the GATA6 Clinical and Genetics Traits. Mol Biotechnol 2024; 66:467-474. [PMID: 37204622 PMCID: PMC10881634 DOI: 10.1007/s12033-023-00761-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/26/2023] [Indexed: 05/20/2023]
Abstract
Monogenic diabetes caused by GATA6 mutations were almost described as neonatal diabetes, and the phenotypic spectrum has expanded since then. Our study underscores the broad phenotypic spectrum by reporting a de novo GATA6 mutation in a family. Furthermore, we reviewed related literature to summarize the clinical and genetic characteristics of monogenic diabetes with GATA6 mutations (n = 39) in order to improve clinicians' understanding of the disease. We conclude that the GATA6 missense mutation (c. 749G > T, p. Gly250Val) is not reported presently, characterized by adult-onset diabetes with pancreatic dysplasia and located in transcriptional activation region. Carries with GATA6 mutations (n = 55) have a variable spectrum of diabetes, ranging from neonatal (72.7%), childhood-onset (20%) to adults-onset (7.5%). 83.5% of patients with abnormal pancreatic development. Heart and hepatobillary defects are the most common abnormalities of extrapancreatic features. Most mutations with GATA6 are loss of function (LOF, 71.8%) and located in functional region. Functional studies mostly support loss-of-function as the pathophysiological mechanism. In conclusion, there are various types of diabetes with GATA6 mutations, which can also occur in adult diabetes. Phenotypic defects with GATA6 mutations are most frequently malformations of pancreas and heart. This highlights the importance of comprehensive clinical evaluation of identified carriers to evaluate their full phenotypic spectrum.
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Affiliation(s)
- Xing Yue
- Department of Metabolism and Endocrinology, The Third Hospital of Changsha, Laodongxi Road #176, Changsha, 410011, Hunan, People's Republic of China.
| | - Yaheng Luo
- Department of Metabolism and Endocrinology, The Third Hospital of Changsha, Laodongxi Road #176, Changsha, 410011, Hunan, People's Republic of China
| | - Jing Wang
- Department of Metabolism and Endocrinology, The Third Hospital of Changsha, Laodongxi Road #176, Changsha, 410011, Hunan, People's Republic of China
| | - Debin Huang
- Department of Metabolism and Endocrinology, The Third Hospital of Changsha, Laodongxi Road #176, Changsha, 410011, Hunan, People's Republic of China.
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Liang Y, He S, Yang L, Li T, Zhao L, Sun C. CHARGE syndrome with early fetal ear abnormalities: A case report. Clin Case Rep 2024; 12:e8670. [PMID: 38505478 PMCID: PMC10948373 DOI: 10.1002/ccr3.8670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/06/2024] [Accepted: 03/07/2024] [Indexed: 03/21/2024] Open
Abstract
Key Clinical Message CHARGE syndrome is a rare genetic disorder characterized by several distinct features. The presence of fetal ear abnormalities could be the early indicator of CHARGE syndrome. Subsequent prenatal diagnosis is essential to confirm the disorder. This is significant because the patient may receive genetic counseling and appropriate disposal based on the accurate diagnosis. Abstract CHARGE syndrome is a rare genetic disorder with multiple specific clinical features. The prenatal diagnosis is crucial but rarely achieved. We report a fetus with fetal external ear abnormality detected by ultrasound at 22nd week of gestation. Postnatal examination revealed an external ear abnormality, a mild atrial septal defect, and other clinical signs of CHARGE syndrome. A de novo pathogenic nonsense mutation in the CHD7 gene (c.406C > T, p.Q136X in exon 2) was identified to cause the disorder. Our study demonstrated that prenatal diagnosis and genetic testing were recommended to obtain a solid diagnosis of CHARGE syndrome when fetal external ear abnormality was detected by ultrasound examination.
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Affiliation(s)
- Yu Liang
- Department of UltrasoundShijiazhuang Fourth Hospital, Hebei Key Laboratory of Maternal and Fetal MedicineShijiazhuangChina
| | - Sijie He
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI GenomicsShijiazhuangChina
| | - Liuqiao Yang
- BGI ResearchShenzhenChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Tao Li
- BGI ResearchShenzhenChina
| | | | - Cong‐xin Sun
- Department of UltrasoundShijiazhuang Fourth Hospital, Hebei Key Laboratory of Maternal and Fetal MedicineShijiazhuangChina
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Wang Y, Chang Y, Gao M, Zang W, Liu X. Genetic analysis of albinism caused by compound heterozygous mutations of the OCA2 gene in a Chinese family. Hereditas 2024; 161:8. [PMID: 38317267 PMCID: PMC10845747 DOI: 10.1186/s41065-024-00312-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/25/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Oculocutaneous albinism (OCA) is a group of rare genetic disorders characterized by a reduced or complete lack of melanin in the skin, hair, and eyes. Patients present with colorless retina, pale pink iris, and pupil, and fear of light. The skin, eyebrows, hair, and other body hair are white or yellowish-white. These conditions are caused by mutations in specific genes necessary for the production of melanin. OCA is divided into eight clinical types (OCA1-8), each with different clinical phenotypes and potential genetic factors. This study aimed to identify the genetic causes of non-syndromic OCA in a Chinese Han family. METHODS We performed a comprehensive clinical examination of family members, screened for mutation loci using whole exome sequencing (WES) technology, and predicted mutations using In silico tools. RESULTS The patient's clinical manifestations were white skin, yellow hair, a few freckles on the cheeks and bridge of the nose, decreased vision, blue iris, poorly defined optic disk borders, pigmentation of the fundus being insufficient, and significant vascular exposure. The WES test results indicate that the patient has compound heterozygous mutations in the OCA2 gene (c.1258G > A (p.G420R), c.1441G > A (p.A481T), and c.2267-2 A > C), respectively, originating from her parents. Among them, c.1258G > A (p.G420R) is a de novo mutation with pathogenic. Our analysis suggests that compound heterozygous mutations in the OCA2 gene are the primary cause of the disease in this patient. CONCLUSIONS The widespread application of next-generation sequencing technologies such as WES in clinical practice can effectively replace conventional detection methods and assist in the diagnosis of clinical diseases more quickly and accurately. The newly discovered c.1258G > A (p.G420R) mutation can update and expand the gene mutation spectrum of OCA2-type albinism.
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Affiliation(s)
- Yanan Wang
- Genetics and Prenatal Diagnosis Department, Luoyang Maternal and Child Health Hospital, Luoyang, China.
| | - Yujie Chang
- Genetics and Prenatal Diagnosis Department, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Mingya Gao
- Genetics and Prenatal Diagnosis Department, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Weiwei Zang
- Genetics and Prenatal Diagnosis Department, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Xiaofei Liu
- Genetics and Prenatal Diagnosis Department, Luoyang Maternal and Child Health Hospital, Luoyang, China
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Arango-Ibañez JP, Parra-Lara LG, Zambrano ÁR, Rodríguez-Rojas LX. Li-Fraumeni syndrome presenting with de novo TP53 mutation, severe phenotype and advanced paternal age: a case report. Hered Cancer Clin Pract 2024; 22:1. [PMID: 38238849 PMCID: PMC10797758 DOI: 10.1186/s13053-023-00272-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/04/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Li-Fraumeni syndrome (LFS) is an autosomal dominant hereditary cancer syndrome caused by pathogenic variants in the gene TP53. This gene codes for the P53 protein, a crucial player in genomic stability, which functions as a tumor suppressor gene. Individuals with LFS frequently develop multiple primary tumors at a young age, such as soft tissue sarcomas, breast cancer, and brain tumors. CASE PRESENTATION A 38 years-old female with a history of femur osteosarcoma, ductal carcinoma of the breast, high-grade breast sarcoma, pleomorphic sarcoma of the left upper limb, infiltrating lobular carcinoma of the breast, gastric adenocarcinoma, leiomyosarcoma of the right upper limb, and high-grade pleomorphic renal sarcoma. Complete molecular sequencing of the TP53 gene showed c.586 C > T (p.R196X) in exon 6, which is a nonsense mutation that produces a shorter and malfunctioning P53. Family history includes advanced father's age at the time of conception (75 years), which has been associated with an increased risk of de novo germline mutations. The patient had seven paternal half-siblings with no cancer history. The patient received multiple treatments including surgery, systemic therapy, and radiotherapy, but died at the age of 38. CONCLUSIONS Advanced paternal age is a risk factor to consider when hereditary cancer syndrome is suspected. Early detection of hereditary cancer syndromes and their multi-disciplinary surveillance and treatment is important to improve clinical outcomes for these patients. Further investigation of the relationship between the pathogenic variant of TP53 and its phenotype may guide the stratification of surveillance and treatment.
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Affiliation(s)
- Juan Pablo Arango-Ibañez
- Facultad de Ciencias de la Salud, Universidad Icesi, Cali, Colombia
- Centro de Investigaciones Clínicas (CIC), Fundación Valle del Lili, Cali, Colombia
| | - Luis Gabriel Parra-Lara
- Facultad de Ciencias de la Salud, Universidad Icesi, Cali, Colombia
- Centro de Investigaciones Clínicas (CIC), Fundación Valle del Lili, Cali, Colombia
| | - Ángela R Zambrano
- Servicio de Hematología & Oncología Clínica, Departamento de Medicina Interna, Fundación Valle del Lili, Cali, Colombia
| | - Lisa Ximena Rodríguez-Rojas
- Facultad de Ciencias de la Salud, Universidad Icesi, Cali, Colombia.
- Servicio de Genética, Fundación Valle del Lili, Cra. 98 #18-49, Cali, Valle del Cauca, 760032, Colombia.
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Lin J, Li N, Yao R, Yu T, Wang X, Wang J. Autosomal dominant neurodevelopmental disorders associated with KIF1A gene variants in 6 pediatric patients. Zhejiang Da Xue Xue Bao Yi Xue Ban 2023; 52:693-700. [PMID: 38105687 PMCID: PMC10764188 DOI: 10.3724/zdxbyxb-2023-0457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
OBJECTIVES To analyze the clinical and genetic characteristics of children with autosomal dominant neurodevelopmental disorders caused by kinesin family member 1A (KIF1A) gene variation. METHODS Clinical and genetic testing data of 6 children with KIF1A gene de novo heterozygous variation diagnosed in Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine from the year 2018 to 2020 were retrospectively analyzed. Pathogenic variants were identified based on whole exome sequencing, and verified by Sanger sequencing. Moreover, the effect of variants on three-dimensional structure and stability of protein was analyzed by bioinformatics. RESULTS Among 6 patients there were 4 males and 2 females, and the age of consultation varied from 7 months to 18 years. All cases had varying degrees of motor developmental delay since childhood, and 4 of them had gait abnormalities or fell easily. In addition, 2 children were accompanied by delayed mental development, epilepsy and abnormal eye development. Genetic tests showed that all 6 cases had heterozygous de novo variations of KIF1A gene, including 4 missense mutations c.296C>T (p.T99M), c.761G>A (p.R254Q), c.326G>T (p.G109V), c.745C>G (p.L249V) and one splicing mutation c.798+1G>A, among which the last three variants have not been previously reported. Bioinformatics analysis showed that G109V and L249V may impair their interaction with the neighboring amino acid residues, thereby impacting protein function and reducing protein stability, and were assessed as "likely pathogenic". Meanwhile, c.798+1G>A may damage an alpha helix in the motor domain of the KIF1A protein, and was assessed as "likely pathogenic". CONCLUSIONS KIF1A-associated neurological diseases are clinically heterogeneous, with motor developmental delay and abnormal gait often being the most common clinical features. The clinical symptoms in T99M carriers are more severe, while those in R254Q carriers are relatively mild.
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Affiliation(s)
- Jingqi Lin
- Central Laboratory, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China.
| | - Niu Li
- Central Laboratory, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Ru'en Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Tingting Yu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Xiumin Wang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center,Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Jian Wang
- Central Laboratory, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China.
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Liu X, Meng J, Liao X, Liu Y, Zhou Q, Xu Z, Yin S, Cao Q, Su G, He S, Li W, Wang X, Wang G, Li D, Yang P, Hou S. A de novo missense mutation in MPP2 confers an increased risk of Vogt-Koyanagi-Harada disease as shown by trio-based whole-exome sequencing. Cell Mol Immunol 2023; 20:1379-1392. [PMID: 37828081 PMCID: PMC10616125 DOI: 10.1038/s41423-023-01088-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023] Open
Abstract
Vogt-Koyanagi-Harada (VKH) disease is a leading cause of blindness in young and middle-aged people. However, the etiology of VKH disease remains unclear. Here, we performed the first trio-based whole-exome sequencing study, which enrolled 25 VKH patients and 50 controls, followed by a study of 2081 VKH patients from a Han Chinese population to uncover detrimental mutations. A total of 15 de novo mutations in VKH patients were identified, with one of the most important being the membrane palmitoylated protein 2 (MPP2) p.K315N (MPP2-N315) mutation. The MPP2-N315 mutation was highly deleterious according to bioinformatic predictions. Additionally, this mutation appears rare, being absent from the 1000 Genome Project and Genome Aggregation Database, and it is highly conserved in 10 species, including humans and mice. Subsequent studies showed that pathological phenotypes and retinal vascular leakage were aggravated in MPP2-N315 mutation knock-in or MPP2-N315 adeno-associated virus-treated mice with experimental autoimmune uveitis (EAU). In vitro, we used clustered regularly interspaced short palindromic repeats (CRISPR‒Cas9) gene editing technology to delete intrinsic MPP2 before overexpressing wild-type MPP2 or MPP2-N315. Levels of cytokines, such as IL-1β, IL-17E, and vascular endothelial growth factor A, were increased, and barrier function was destroyed in the MPP2-N315 mutant ARPE19 cells. Mechanistically, the MPP2-N315 mutation had a stronger ability to directly bind to ANXA2 than MPP2-K315, as shown by LC‒MS/MS and Co-IP, and resulted in activation of the ERK3/IL-17E pathway. Overall, our results demonstrated that the MPP2-K315N mutation may increase susceptibility to VKH disease.
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Affiliation(s)
- Xianyang Liu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, China
- Chongqing Eye Institute, Chongqing, China
| | - Jiayu Meng
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, China
- Chongqing Eye Institute, Chongqing, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Xingyun Liao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, China
- Chongqing Eye Institute, Chongqing, China
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Yusen Liu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, China
- Chongqing Eye Institute, Chongqing, China
| | - Qian Zhou
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, China
- Chongqing Eye Institute, Chongqing, China
| | - Zongren Xu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, China
- Chongqing Eye Institute, Chongqing, China
| | - Shuming Yin
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Qingfeng Cao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, China
- Chongqing Eye Institute, Chongqing, China
| | - Guannan Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, China
- Chongqing Eye Institute, Chongqing, China
| | - Siyuan He
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, China
- Chongqing Eye Institute, Chongqing, China
| | - Wanqian Li
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, China
- Chongqing Eye Institute, Chongqing, China
| | - Xiaotang Wang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, China
- Chongqing Eye Institute, Chongqing, China
| | - Guoqing Wang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, China
- Chongqing Eye Institute, Chongqing, China
| | - Dali Li
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
- Chongqing Key Laboratory of Ophthalmology, Chongqing, China.
- Chongqing Eye Institute, Chongqing, China.
| | - Shengping Hou
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
- Chongqing Key Laboratory of Ophthalmology, Chongqing, China.
- Chongqing Eye Institute, Chongqing, China.
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, 100730, China.
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Lee M, Lui ACY, Chan JCK, Doong PHL, Kwong AKY, Mak CCY, Li RHW, Kan ASY, Chung BHY. Revealing parental mosaicism: the hidden answer to the recurrence of apparent de novo variants. Hum Genomics 2023; 17:91. [PMID: 37798624 PMCID: PMC10557286 DOI: 10.1186/s40246-023-00535-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
Mosaicism refers to the presence of two or more populations of genetically distinct cells within an individual, all of which originate from a single zygote. Previous literature estimated the percentage of parental mosaicism ranged from 0.33 to 25.9%. In this study, parents whose children had previously been diagnosed with developmental disorders with an apparent de novo variant were recruited. Peripheral blood, buccal and semen samples were collected from these parents if available for the detection of potential parental mosaicism using droplet digital PCR, complemented with the method of blocker displacement amplification. Among the 20 families being analyzed, we report four families with parental mosaicism (4/20, 20%). Two families have maternal gonosomal mosaicism (EYA1 and EBF3) and one family has paternal gonadal mosaicism (CHD7) with a pathogenic/ likely pathogenic variant. One family has a paternal gonosomal mosaicism with a variant of uncertain significance (FLNC) with high clinical relevance. The detectable variant allele frequency in our cohort ranged from 8.7-35.9%, limit of detection 0.08-0.16% based on our in-house EBF3 assay. Detecting parental mosaicism not only informs family with a more accurate recurrence risk, but also facilitates medical teams to create appropriate plans for pregnancy and delivery, offering the most suitable care.
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Affiliation(s)
- Mianne Lee
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Adrian C Y Lui
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Joshua C K Chan
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Anna K Y Kwong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Christopher C Y Mak
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Raymond H W Li
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong SAR, China
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Anita S Y Kan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong SAR, China
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- Prenatal Diagnostic Laboratory, Department of Obstetrics and Gynaecology, Tsan Yuk Hospital, Sai Wan Ho, Hong Kong SAR, China
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China.
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Ngau Tau Kok, Hong Kong SAR, China.
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9
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Peng C, Chen H, Ren J, Zhou F, Li Y, Keqie Y, Ding T, Ruan J, Wang H, Chen X, Liu S. A long-read sequencing and SNP haplotype-based novel preimplantation genetic testing method for female ADPKD patient with de novo PKD1 mutation. BMC Genomics 2023; 24:521. [PMID: 37667185 PMCID: PMC10478289 DOI: 10.1186/s12864-023-09593-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 08/16/2023] [Indexed: 09/06/2023] Open
Abstract
The autosomal dominant form of polycystic kidney disease (ADPKD) is the most common hereditary disease that causes late-onset renal cyst development and end-stage renal disease. Preimplantation genetic testing for monogenic disease (PGT-M) has emerged as an effective strategy to prevent pathogenic mutation transmission rely on SNP linkage analysis between pedigree members. Yet, it remains challenging to establish reliable PGT-M methods for ADPKD cases or other monogenic diseases with de novo mutations or without a family history. Here we reported the application of long-read sequencing for direct haplotyping in a female patient with de novo PKD1 c.11,526 G > C mutation and successfully established the high-risk haplotype. Together with targeted short-read sequencing of SNPs for the couple and embryos, the carrier status for embryos was identified. A healthy baby was born without the PKD1 pathogenic mutation. Our PGT-M strategy based on long-read sequencing for direct haplotyping combined with targeted SNP haplotype can be widely applied to other monogenic disease carriers with de novo mutation.
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Affiliation(s)
- Cuiting Peng
- Center of prenatal diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, No17, Section 3, South Renmin Road, Chengdu, China
- Laboratory of birth defects and related diseases of women and children, Sichuan university, Ministry of Education, Sichuan, China
| | - Han Chen
- Center of prenatal diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, No17, Section 3, South Renmin Road, Chengdu, China
- Laboratory of birth defects and related diseases of women and children, Sichuan university, Ministry of Education, Sichuan, China
| | - Jun Ren
- Center of prenatal diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, No17, Section 3, South Renmin Road, Chengdu, China
- Laboratory of birth defects and related diseases of women and children, Sichuan university, Ministry of Education, Sichuan, China
| | - Fan Zhou
- Center of prenatal diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, No17, Section 3, South Renmin Road, Chengdu, China
- Laboratory of birth defects and related diseases of women and children, Sichuan university, Ministry of Education, Sichuan, China
| | - Yutong Li
- Center of prenatal diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, No17, Section 3, South Renmin Road, Chengdu, China
- Laboratory of birth defects and related diseases of women and children, Sichuan university, Ministry of Education, Sichuan, China
| | - Yuezhi Keqie
- Center of prenatal diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, No17, Section 3, South Renmin Road, Chengdu, China
- Laboratory of birth defects and related diseases of women and children, Sichuan university, Ministry of Education, Sichuan, China
| | | | | | - He Wang
- Center of prenatal diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, No17, Section 3, South Renmin Road, Chengdu, China
- Laboratory of birth defects and related diseases of women and children, Sichuan university, Ministry of Education, Sichuan, China
| | - Xinlian Chen
- Center of prenatal diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, No17, Section 3, South Renmin Road, Chengdu, China.
- Laboratory of birth defects and related diseases of women and children, Sichuan university, Ministry of Education, Sichuan, China.
| | - Shanling Liu
- Center of prenatal diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, No17, Section 3, South Renmin Road, Chengdu, China.
- Laboratory of birth defects and related diseases of women and children, Sichuan university, Ministry of Education, Sichuan, China.
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10
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Cheng CY, Zhang ZB. Reconstructing early transmission networks of SARS-CoV-2 using a genomic mutation model. Zool Res 2023; 44:494-504. [PMID: 36999549 DOI: 10.24272/j.issn.2095-8137.2022.535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has greatly damaged human society, but the origins and early transmission patterns of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen remain unclear. Here, we reconstructed the transmission networks of SARS-CoV-2 during the first three and six months since its first report based on ancestor-offspring relationships using BANAL-52-referenced mutations. We explored the position (i.e., root, middle, or tip) of early detected samples in the evolutionary tree of SARS-CoV-2. In total, 6 799 transmission chains and 1 766 transmission networks were reconstructed, with chain lengths ranging from 1-9 nodes. The root node samples of the 1 766 transmission networks were from 58 countries or regions and showed no common ancestor, indicating the occurrence of many independent or parallel transmissions of SARS-CoV-2 when first detected (i.e., all samples were located at the tip position of the evolutionary tree). No root node sample was found in any sample ( n=31, all from the Chinese mainland) collected in the first 15 days from 24 December 2019. Results using six-month data or RaTG13-referenced mutation data were similar. The reconstruction method was verified using a simulation approach. Our results suggest that SARS-CoV-2 may have already been spreading independently worldwide before the outbreak of COVID-19 in Wuhan, China. Thus, a comprehensive global survey of human and animal samples is essential to explore the origins of SARS-CoV-2 and its natural reservoirs and hosts.
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Affiliation(s)
- Chao-Yuan Cheng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-Bin Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China. E-mail:
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11
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Zhu W, Lo CW. Insights into the genetic architecture of congenital heart disease from animal modeling. Zool Res 2023; 44:577-590. [PMID: 37147909 PMCID: PMC10236297 DOI: 10.24272/j.issn.2095-8137.2022.463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/28/2023] [Indexed: 05/07/2023] Open
Abstract
Congenital heart disease (CHD) is observed in up to 1% of live births and is one of the leading causes of mortality from birth defects. While hundreds of genes have been implicated in the genetic etiology of CHD, their role in CHD pathogenesis is still poorly understood. This is largely a reflection of the sporadic nature of CHD, as well as its variable expressivity and incomplete penetrance. We reviewed the monogenic causes and evidence for oligogenic etiology of CHD, as well as the role of de novo mutations, common variants, and genetic modifiers. For further mechanistic insight, we leveraged single-cell data across species to investigate the cellular expression characteristics of genes implicated in CHD in developing human and mouse embryonic hearts. Understanding the genetic etiology of CHD may enable the application of precision medicine and prenatal diagnosis, thereby facilitating early intervention to improve outcomes for patients with CHD.
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Affiliation(s)
- Wenjuan Zhu
- Chinese University of Hong Kong, Hong Kong SAR, China
- Kunming Institute of Zoology-Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Hong Kong SAR, China
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201 USA. E-mail:
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12
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Steensma MJ, Lee YL, Bouwman AC, Pita Barros C, Derks MFL, Bink MCAM, Harlizius B, Huisman AE, Crooijmans RPMA, Groenen MAM, Mulder HA, Rochus CM. Identification and characterisation of de novo germline structural variants in two commercial pig lines using trio-based whole genome sequencing. BMC Genomics 2023; 24:208. [PMID: 37072725 PMCID: PMC10114323 DOI: 10.1186/s12864-023-09296-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/04/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND De novo mutations arising in the germline are a source of genetic variation and their discovery broadens our understanding of genetic disorders and evolutionary patterns. Although the number of de novo single nucleotide variants (dnSNVs) has been studied in a number of species, relatively little is known about the occurrence of de novo structural variants (dnSVs). In this study, we investigated 37 deeply sequenced pig trios from two commercial lines to identify dnSVs present in the offspring. The identified dnSVs were characterised by identifying their parent of origin, their functional annotations and characterizing sequence homology at the breakpoints. RESULTS We identified four swine germline dnSVs, all located in intronic regions of protein-coding genes. Our conservative, first estimate of the swine germline dnSV rate is 0.108 (95% CI 0.038-0.255) per generation (one dnSV per nine offspring), detected using short-read sequencing. Two detected dnSVs are clusters of mutations. Mutation cluster 1 contains a de novo duplication, a dnSNV and a de novo deletion. Mutation cluster 2 contains a de novo deletion and three de novo duplications, of which one is inverted. Mutation cluster 2 is 25 kb in size, whereas mutation cluster 1 (197 bp) and the other two individual dnSVs (64 and 573 bp) are smaller. Only mutation cluster 2 could be phased and is located on the paternal haplotype. Mutation cluster 2 originates from both micro-homology as well as non-homology mutation mechanisms, where mutation cluster 1 and the other two dnSVs are caused by mutation mechanisms lacking sequence homology. The 64 bp deletion and mutation cluster 1 were validated through PCR. Lastly, the 64 bp deletion and the 573 bp duplication were validated in sequenced offspring of probands with three generations of sequence data. CONCLUSIONS Our estimate of 0.108 dnSVs per generation in the swine germline is conservative, due to our small sample size and restricted possibilities of dnSV detection from short-read sequencing. The current study highlights the complexity of dnSVs and shows the potential of breeding programs for pigs and livestock species in general, to provide a suitable population structure for identification and characterisation of dnSVs.
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Affiliation(s)
- Marije J Steensma
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands.
| | - Y L Lee
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - A C Bouwman
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - C Pita Barros
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - M F L Derks
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
- Topigs Norsvin Research Center, Schoenaker 6, Beuningen, 6641 SZ, the Netherlands
| | - M C A M Bink
- Hendrix Genetics, P.O. Box 114, Boxmeer, 5830 AC, the Netherlands
| | - B Harlizius
- Topigs Norsvin Research Center, Schoenaker 6, Beuningen, 6641 SZ, the Netherlands
| | - A E Huisman
- Hendrix Genetics, P.O. Box 114, Boxmeer, 5830 AC, the Netherlands
| | - R P M A Crooijmans
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - M A M Groenen
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - H A Mulder
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - C M Rochus
- University of Guelph, Centre for Genetic Improvement of Livestock, 50 Stone Rd E, Guelph, O N, N1G 2W1, Canada
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13
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Chow JC, Hormozdiari F. Prediction of Neurodevelopmental Disorders Based on De Novo Coding Variation. J Autism Dev Disord 2023; 53:963-976. [PMID: 35596027 PMCID: PMC9986216 DOI: 10.1007/s10803-022-05586-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2022] [Indexed: 11/27/2022]
Abstract
The early detection of neurodevelopmental disorders (NDDs) can significantly improve patient outcomes. The differential burden of non-synonymous de novo mutation among NDD cases and controls indicates that de novo coding variation can be used to identify a subset of samples that will likely display an NDD phenotype. Thus, we have developed an approach for the accurate prediction of NDDs with very low false positive rate (FPR) using de novo coding variation for a small subset of cases. We use a shallow neural network that integrates de novo likely gene-disruptive and missense variants, measures of gene constraint, and conservation information to predict a small subset of NDD cases at very low FPR and prioritizes NDD risk genes for future clinical study.
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Affiliation(s)
- Julie C Chow
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
| | - Fereydoun Hormozdiari
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
- MIND Institute, University of California, Davis, 95817, USA.
- Biochemistry and Molecular Medicine, University of California, Davis, 95616, USA.
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14
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Lu LF, Wang J, Liu KZ, Yi XN, Ma ZJ, Li YQ, Feng RJ. Double-strand breaks induced by learning-like activity may increase risk of de novo mutations in schizophrenia. Asian J Psychiatr 2022; 78:103292. [PMID: 36252325 DOI: 10.1016/j.ajp.2022.103292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 11/20/2022]
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15
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Sun Y, Yuan F, Wang L, Dai D, Zhang Z, Liang F, Liu N, Long J, Zhao X, Xi Y. Recombination and mutation shape variations in the major histocompatibility complex. J Genet Genomics 2022; 49:1151-1161. [PMID: 35358716 DOI: 10.1016/j.jgg.2022.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 01/14/2023]
Abstract
The major histocompatibility complex (MHC) is closely associated with numerous diseases, but its high degree of polymorphism complicates the discovery of disease-associated variants. In principle, recombination and de novo mutations are two critical factors responsible for MHC polymorphisms. However, direct evidence for this hypothesis is lacking. Here, we report the generation of fine-scale MHC recombination and de novo mutation maps of ∼5 Mb by deep sequencing (> 100×) of the MHC genome for 17 MHC recombination and 30 non-recombination Han Chinese families (a total of 190 individuals). Recombination hotspots and Han-specific breakpoints are located in close proximity at haplotype block boundaries. The average MHC de novo mutation rate is higher than the genome-wide de novo mutation rate, particularly in MHC recombinant individuals. Notably, mutation and recombination generated polymorphisms are located within and outside linkage disequilibrium regions of the MHC, respectively, and evolution of the MHC locus was mainly controlled by positive selection. These findings provide insights on the evolutionary causes of the MHC diversity and may facilitate the identification of disease-associated genetic variants.
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Affiliation(s)
- Yuying Sun
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Institute of Beijing 307 Hospital, Anhui Medical University, Hefei, Anhui 230032, China.
| | - Fang Yuan
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Ling Wang
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Institute of Beijing 307 Hospital, Anhui Medical University, Hefei, Anhui 230032, China
| | - Dongfa Dai
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Institute of Beijing 307 Hospital, Anhui Medical University, Hefei, Anhui 230032, China
| | - Zhijian Zhang
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Institute of Beijing 307 Hospital, Anhui Medical University, Hefei, Anhui 230032, China
| | - Fei Liang
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Nan Liu
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Juan Long
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Xiao Zhao
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Yongzhi Xi
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China.
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16
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Khakzad M, Shahbazi Z, Naderi M, Karimipoor M. A de novo TINF2, R282C Mutation in a Case of Dyskeratosis Congenita Founded by Next-Generation Sequencing. Iran Biomed J 2022. [PMID: 37070599 DOI: 10.52547/ibj.3783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Affiliation(s)
- Motahareh Khakzad
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Zahra Shahbazi
- Pediatric Cell and Gene Therapy Research Center, Gene, Cell & Tissue Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Majid Naderi
- Ali Ebne Abitaleb Hospital, School of Medicine, University of Medical Sciences, Zahedan, Iran
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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17
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Hirao AS, Watanabe Y, Hasegawa Y, Takagi T, Ueno S, Kaneko S. Mutational effects of chronic gamma radiation throughout the life cycle of Arabidopsis thaliana: Insight into radiosensitivity in the reproductive stage. Sci Total Environ 2022; 838:156224. [PMID: 35644386 DOI: 10.1016/j.scitotenv.2022.156224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/17/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Organisms living on Earth have always been exposed to natural sources of ionizing radiation, but following recent nuclear disasters, these background levels have often increased regionally due to the addition of man-made sources of radiation. To assess the mutational effects of ubiquitously present radiation on plants, we performed a whole-genome resequencing analysis of mutations induced by chronic irradiation throughout the life cycle of Arabidopsis thaliana grown under controlled conditions. We obtained resequencing data from 36 second generation post-mutagenesis (M2) progeny derived from 12 first generation (M1) lines grown under gamma-irradiation conditions, ranging from 0.0 to 2.0 Gray per day (Gy/day), to identify de novo mutations, including single base substitutions (SBSs) and small insertions/deletions (INDELs). The relationship between de novo mutation frequency and radiation dose rate from 0.0 to 2.0 Gy/day was assessed by statistical modeling. The increase in de novo mutations in response to irradiation dose fit the negative binomial model, which accounted for the high variability of mutation frequency observed. Among the different types of mutations, SBSs were more prevalent than INDELs, and deletions were more frequent than insertions. Furthermore, we observed that the mutational effects of chronic radiation were greater during the reproductive stage. These results will provide valuable insights into practical strategies for analyzing mutational effects in wild plants growing in environments with various mutagens.
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Affiliation(s)
- Akira S Hirao
- Faculty of Symbiotic Systems Science, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima 960-1296, Japan; National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Yoshito Watanabe
- Fukushima Project Headquarters, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Yoichi Hasegawa
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki, Japan
| | - Toshihito Takagi
- Graduate School of Symbiotic Systems Science and Technology, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima, Japan
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki, Japan
| | - Shingo Kaneko
- Faculty of Symbiotic Systems Science, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima 960-1296, Japan; Institute of Environmental Radioactivity, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima, Japan.
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18
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Zheng S, Huang H, Ma L, Zhu T. RASopathies due to de novo pathogenic variants: clinical features, genetic findings and outcomes in nine neonates born with congenital heart defects. BMC Med Genomics 2022; 15:184. [PMID: 36002837 PMCID: PMC9400306 DOI: 10.1186/s12920-022-01336-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/11/2022] [Indexed: 12/04/2022] Open
Abstract
Background There are limited information available related to neonatal characteristics of RASopathies, a group of autosomal dominant syndromes with considerable phenotypic overlap. Methods The retrospective review revealed 9 neonates born with congenital heart defects (CHDs) and diagnosed as RASopathies due to de novo mutations (DNMs) by trio-based exome sequencing (ES) between January 2017 and December 2020. We report in details of the neonatal course, molecular analysis and 180-days of age follow-up in affected individuals. Results The early clinical spectrum included various types of CHDs, less noticeable multiple extracardiac anomalies and unspecific symptoms like poor feeding. Of the 8 variants identified from 6 genes, 2 in RASA1 were novel: (NM_002890.2: c.2828 T > C (p.Leu943Pro)) and (NM_002890.2: c.2001del (p.Pro668Leufs*10)), which functionally impaired the protein structure. There was a relatively high mortality rate of 33.33% (3/9) for all the defects combined. A RAF1-deficient male and a RASA1-deficient male survived from severe heart failure by surgical interventions in early life. Conclusions Our results revealed that family-based ES was useful in identifying DNMs and causal genes for sporadic diseases and screening Rasopathies shortly after birth. We recommended a family-based ES and a full phenotypic evaluation including echocardiogram, magnetic resonance imaging, ultrasonography and coagulation screening in neonates with CHDs and a suspected genetic etiology.
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Affiliation(s)
- Simin Zheng
- Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huanyang Huang
- Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Ma
- Department of Neonatology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianwen Zhu
- Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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19
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Zemet R, Van den Veyver IB, Stankiewicz P. Parental mosaicism for apparent de novo genetic variants: Scope, detection, and counseling challenges. Prenat Diagn 2022; 42:811-821. [PMID: 35394072 PMCID: PMC9995893 DOI: 10.1002/pd.6144] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 11/07/2022]
Abstract
The disease burden of de novo mutations (DNMs) has been evidenced only recently when the common application of next-generation sequencing technologies enabled their reliable and affordable detection through family-based clinical exome or genome sequencing. Implementation of exome sequencing into prenatal diagnostics revealed that up to 63% of pathogenic or likely pathogenic variants associated with fetal structural anomalies are apparently de novo, primarily for autosomal dominant disorders. Apparent DNMs have been considered to primarily occur as germline or zygotic events, with consequently negligible recurrence risks. However, there is now evidence that a considerable proportion of them are in fact inherited from a parent mosaic for the variant. Here, we review the burden of DNMs in prenatal diagnostics and the influence of parental mosaicism on the interpretation of apparent DNMs and discuss the challenges with detecting and quantifying parental mosaicism and its effect on recurrence risk. We also describe new bioinformatic and technological tools developed to assess mosaicism and discuss how they improve the accuracy of reproductive risk counseling when parental mosaicism is detected.
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Affiliation(s)
- Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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20
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Gu P, Wang G, Gao X, Kang D, Dai P, Huang S. Clinical and molecular findings in a Chinese family with a de novo mitochondrial A1555G mutation. BMC Med Genomics 2022; 15:121. [PMID: 35614445 PMCID: PMC9131558 DOI: 10.1186/s12920-022-01276-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/17/2022] [Indexed: 11/10/2022] Open
Abstract
Background The mitochondrial 12S rRNA A1555G mutation is the most prevalent deafness-causing mitochondrial DNA (mtDNA) mutation and is inherited maternally. Studies have suggested that A1555G mutations have multiple origins, although there is no direct evidence of this. Here, we identified a family with a de novo A1555G mutation. Method Based on detailed mtDNA analyses of the family members using next-generation sequencing with 1% sensitivity to mutated mtDNA, the level of heteroplasmy in terms of the A1555G mutation in blood DNA samples was quantified. Results An individual harbored a heterogeneous A1555G mutation, at 28.68% heteroplasmy. The individual’s son was also a heterogeneous carrier, with 7.25% heteroplasmy. The individual’s brother and mother did not carry the A1555G mutation, and both had less than 1% mitochondrial 12S rRNA A1555G heteroplasmy. Conclusion The A1555G mutation arose de novo in this family. This is the first report of a family with a de novo A1555G mutation, providing direct evidence of its multipoint origin. This is important for both diagnostic investigations and genetic counselling.
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Affiliation(s)
- Ping Gu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Do.28 Fuxing Road, Beijing, 100853, People's Republic of China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People's Republic of China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People's Republic of China.,Department of Otolaryngology, Shenzhen Children's Hospital, Shenzhen, 518038, People's Republic of China
| | - Guojian Wang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Do.28 Fuxing Road, Beijing, 100853, People's Republic of China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People's Republic of China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People's Republic of China
| | - Xue Gao
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Do.28 Fuxing Road, Beijing, 100853, People's Republic of China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People's Republic of China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People's Republic of China
| | - Dongyang Kang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Do.28 Fuxing Road, Beijing, 100853, People's Republic of China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People's Republic of China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People's Republic of China
| | - Pu Dai
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Do.28 Fuxing Road, Beijing, 100853, People's Republic of China. .,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People's Republic of China. .,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People's Republic of China.
| | - Shasha Huang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Do.28 Fuxing Road, Beijing, 100853, People's Republic of China. .,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People's Republic of China. .,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People's Republic of China.
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21
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Valera Ribera C, Martinez-Ferrer À, Flores Fernández E, Vázquez Gómez I, Orenes Vera A, Valls Pascual E, Ybáñez García D, Alegre Sancho JJ. Snyder-Robinson syndrome: differential diagnosis of osteogenesis imperfecta. Osteoporos Int 2022; 33:1177-1180. [PMID: 34741636 DOI: 10.1007/s00198-021-06228-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 11/01/2021] [Indexed: 10/19/2022]
Abstract
Snyder-Robinson syndrome is an extremely rare genetic disorder, caused by mutations of the spermine synthase gene. We report a novel case of Snyder-Robinson syndrome, caused by a de novo mutation and first misdiagnosed with osteogenesis imperfecta. Clinical features, course, and genetic analysis are presented. The patient was treated with bisphosphonates for a decade, until developing an atypical femoral fracture. Teriparatide was then administered for 2 years and then changed to denosumab every 6 months, improving his bone density mass and preventing further fractures.
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Affiliation(s)
- C Valera Ribera
- Rheumatology Department, Doctor Peset University Hospital, Valencia, Spain.
| | - À Martinez-Ferrer
- Rheumatology Department, Doctor Peset University Hospital, Valencia, Spain
| | - E Flores Fernández
- Rheumatology Department, Doctor Peset University Hospital, Valencia, Spain
| | - I Vázquez Gómez
- Rheumatology Department, Doctor Peset University Hospital, Valencia, Spain
| | - A Orenes Vera
- Rheumatology Department, Doctor Peset University Hospital, Valencia, Spain
| | - E Valls Pascual
- Rheumatology Department, Doctor Peset University Hospital, Valencia, Spain
| | - D Ybáñez García
- Rheumatology Department, Doctor Peset University Hospital, Valencia, Spain
| | - J J Alegre Sancho
- Rheumatology Department, Doctor Peset University Hospital, Valencia, Spain
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22
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Nicolas G, Sévigny M, Lecoquierre F, Marguet F, Deschênes A, del Pelaez MC, Feuillette S, Audebrand A, Lecourtois M, Rousseau S, Richard AC, Cassinari K, Deramecourt V, Duyckaerts C, Boland A, Deleuze JF, Meyer V, Clarimon Echavarria J, Gelpi E, Akiyama H, Hasegawa M, Kawakami I, Wong TH, Van Rooij JGJ, Van Swieten JC, Campion D, Dutchak PA, Wallon D, Lavoie-Cardinal F, Laquerrière A, Rovelet-Lecrux A, Sephton CF. A postzygotic de novo NCDN mutation identified in a sporadic FTLD patient results in neurochondrin haploinsufficiency and altered FUS granule dynamics. Acta Neuropathol Commun 2022; 10:20. [PMID: 35151370 PMCID: PMC8841087 DOI: 10.1186/s40478-022-01314-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/18/2022] [Indexed: 12/19/2022] Open
Abstract
Frontotemporal dementia (FTD) is a heterogeneous clinical disorder characterized by progressive abnormalities in behavior, executive functions, personality, language and/or motricity. A neuropathological subtype of FTD, frontotemporal lobar degeneration (FTLD)-FET, is characterized by protein aggregates consisting of the RNA-binding protein fused in sarcoma (FUS). The cause of FTLD-FET is not well understood and there is a lack of genetic evidence to aid in the investigation of mechanisms of the disease. The goal of this study was to identify genetic variants contributing to FTLD-FET and to investigate their effects on FUS pathology. We performed whole-exome sequencing on a 50-year-old FTLD patient with ubiquitin and FUS-positive neuronal inclusions and unaffected parents, and identified a de novo postzygotic nonsense variant in the NCDN gene encoding Neurochondrin (NCDN), NM_014284.3:c.1206G > A, p.(Trp402*). The variant was associated with a ~ 31% reduction in full-length protein levels in the patient’s brain, suggesting that this mutation leads to NCDN haploinsufficiency. We examined the effects of NCDN haploinsufficiency on FUS and found that depleting primary cortical neurons of NCDN causes a reduction in the total number of FUS-positive cytoplasmic granules. Moreover, we found that these granules were significantly larger and more highly enriched with FUS. We then examined the effects of a loss of FUS function on NCDN in neurons and found that depleting cells of FUS leads to a decrease in NCDN protein and mRNA levels. Our study identifies the NCDN protein as a likely contributor of FTLD-FET pathophysiology. Moreover, we provide evidence for a negative feedback loop of toxicity between NCDN and FUS, where loss of NCDN alters FUS cytoplasmic dynamics, which in turn has an impact on NCDN expression.
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23
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Klei L, McClain LL, Mahjani B, Panayidou K, De Rubeis S, Grahnat ACS, Karlsson G, Lu Y, Melhem N, Xu X, Reichenberg A, Sandin S, Hultman CM, Buxbaum JD, Roeder K, Devlin B. How rare and common risk variation jointly affect liability for autism spectrum disorder. Mol Autism 2021; 12:66. [PMID: 34615521 PMCID: PMC8495987 DOI: 10.1186/s13229-021-00466-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 09/02/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genetic studies have implicated rare and common variations in liability for autism spectrum disorder (ASD). Of the discovered risk variants, those rare in the population invariably have large impact on liability, while common variants have small effects. Yet, collectively, common risk variants account for the majority of population-level variability. How these rare and common risk variants jointly affect liability for individuals requires further study. METHODS To explore how common and rare variants jointly affect liability, we assessed two cohorts of ASD families characterized for rare and common genetic variations (Simons Simplex Collection and Population-Based Autism Genetics and Environment Study). We analyzed data from 3011 affected subjects, as well as two cohorts of unaffected individuals characterized for common genetic variation: 3011 subjects matched for ancestry to ASD subjects and 11,950 subjects for estimating allele frequencies. We used genetic scores, which assessed the relative burden of common genetic variation affecting risk of ASD (henceforth "burden"), and determined how this burden was distributed among three subpopulations: ASD subjects who carry a potentially damaging variant implicated in risk of ASD ("PDV carriers"); ASD subjects who do not ("non-carriers"); and unaffected subjects who are assumed to be non-carriers. RESULTS Burden harbored by ASD subjects is stochastically greater than that harbored by control subjects. For PDV carriers, their average burden is intermediate between non-carrier ASD and control subjects. Both carrier and non-carrier ASD subjects have greater burden, on average, than control subjects. The effects of common and rare variants likely combine additively to determine individual-level liability. LIMITATIONS Only 305 ASD subjects were known PDV carriers. This relatively small subpopulation limits this study to characterizing general patterns of burden, as opposed to effects of specific PDVs or genes. Also, a small fraction of subjects that are categorized as non-carriers could be PDV carriers. CONCLUSIONS Liability arising from common and rare risk variations likely combines additively to determine risk of any individual diagnosed with ASD. On average, ASD subjects carry a substantial burden of common risk variation, even if they also carry a rare PDV affecting risk.
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Affiliation(s)
- Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lora Lee McClain
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Behrang Mahjani
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Klea Panayidou
- Department of Health Sciences Department, School of Sciences, European University Cyprus, Nicosia, Cyprus
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anna-Carin Säll Grahnat
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Gun Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yangyi Lu
- Department of Statistics, University of Michigan, Ann Arbor, MI, USA
| | - Nadine Melhem
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Xinyi Xu
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Genebox, Beijing, China
| | - Abraham Reichenberg
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sven Sandin
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kathryn Roeder
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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24
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Niu Z, Lai Y, Tan S, Tang F, Tang X, Su Y, Liu L, Xie L, Fang Q, Xie M, Tang A. A de novo mutation of the SOX10 gene associated with inner ear malformation in a Guangxi family with Waardenburg syndrome type II. Int J Pediatr Otorhinolaryngol 2021; 145:110711. [PMID: 33865100 DOI: 10.1016/j.ijporl.2021.110711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/21/2021] [Accepted: 04/05/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVE Waardenburg syndrome type 2 (WS2) is a rare neural-crest disorder, characterized by heterochromic irides or blue eyes and sensorineural hearing loss. The aim of this study was to analyze the clinical features and investigate the genetic cause of WS2 in a small family from Guangxi Zhuang Autonomous region. METHODS Whole-exome sequencing and mutational analysis were used to identify disease-causing genes in this family. RESULTS A de novo missense mutation, C.355C > T (p. Arg119Cys), in exon 2 of SOX10 was related to inner ear malformation in the proband and identified by whole exon sequencing, but this mutation was absent in normal controls and any public databases. According to nucleic acid sequence and protein bioinformatic analysis, this mutation is considered the cause of WS2 without neurologic involvement in the proband. CONCLUSIONS Our findings provide an accurate genetic diagnosis, counseling, and rehabilitation for family members and may contribute to further genotype-phenotype correlation studies of the SOX10 gene.
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Affiliation(s)
- Zhijie Niu
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China.
| | - Yongjing Lai
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Songhua Tan
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Fen Tang
- The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Xianglong Tang
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Yupei Su
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Lei Liu
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Lihong Xie
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Qin Fang
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Mao Xie
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Anzhou Tang
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China; Regional Key Laboratory of Early Prevention and Treatment of High-Rise Tumors, Nanning, 530021, China.
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25
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Li K, Fang Z, Zhao G, Li B, Chen C, Xia L, Wang L, Luo T, Wang X, Wang Z, Zhang Y, Jiang Y, Pan Q, Hu Z, Guo H, Tang B, Liu C, Sun Z, Xia K, Li J. Cross-Disorder Analysis of De Novo Mutations in Neuropsychiatric Disorders. J Autism Dev Disord 2021; 52:1299-1313. [PMID: 33970367 PMCID: PMC8854168 DOI: 10.1007/s10803-021-05031-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 12/02/2022]
Abstract
The clinical similarity among different neuropsychiatric disorders (NPDs) suggested a shared genetic basis. We catalogued 23,109 coding de novo mutations (DNMs) from 6511 patients with autism spectrum disorder (ASD), 4,293 undiagnosed developmental disorder (UDD), 933 epileptic encephalopathy (EE), 1022 intellectual disability (ID), 1094 schizophrenia (SCZ), and 3391 controls. We evaluated that putative functional DNMs contribute to 38.11%, 34.40%, 33.31%, 10.98% and 6.91% of patients with ID, EE, UDD, ASD and SCZ, respectively. Consistent with phenotype similarity and heterogeneity in different NPDs, they show different degree of genetic association. Cross-disorder analysis of DNMs prioritized 321 candidate genes (FDR < 0.05) and showed that genes shared in more disorders were more likely to exhibited specific expression pattern, functional pathway, genetic convergence, and genetic intolerance.
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Affiliation(s)
- Kuokuo Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Zhenghuan Fang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Lu Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Lin Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Tengfei Luo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Xiaomeng Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Yi Zhang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Yi Jiang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Qian Pan
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Zhengmao Hu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Hui Guo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Beisha Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Chunyu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China. .,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China. .,School of Basic Medical Science, Central South University, Changsha, Hunan, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Shanghai, China.
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China. .,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China. .,Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.
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26
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Wang Y, Zhai F, Guan S, Yan Z, Zhu X, Kuo Y, Wang N, Zhi X, Lian Y, Huang J, Jia J, Liu P, Li R, Qiao J, Yan L. A comprehensive PGT-M strategy for ADPKD patients with de novo PKD1 mutations using affected embryo or gametes as proband. J Assist Reprod Genet 2021; 38:2425-2434. [PMID: 33939064 DOI: 10.1007/s10815-021-02188-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/04/2021] [Indexed: 10/21/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disease characterized by the development of renal cysts and progression to renal failure. Preimplantation genetic testing-monogenic disease (PGT-M) is an alternative option to obtain healthy babies. However, de novo PKD1 mutation of one of the spouses or the absence of a positive family history poses a serious challenge to PGT-M. Here, we described a comprehensive strategy which includes preimplantation genetic testing for aneuploidies (PGT-A) study and monogenic diagnosis study for ADPKD patients bearing de novo mutations. The innovation of our strategy is to use the gamete (polar body or single sperm) as proband for single-nucleotide polymorphism (SNP) linkage analysis to detect an embryo's carrier status. Nine ADPKD couples with either de novo mutation or without a positive family history were recruited and a total of 34 embryos from 13 PGT-M cycles were examined. Within these nine couples, two successfully delivered healthy babies had their genetic status confirmed by amniocentesis. This study provides a creative approach for embryo diagnosis of patients with de novo mutations or patients who lack essential family members for linkage analysis.
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Affiliation(s)
- Yuqian Wang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100191, China
| | - Fan Zhai
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Shuo Guan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Zhiqiang Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xiaohui Zhu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Ying Kuo
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Nan Wang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xu Zhi
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Ying Lian
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Jin Huang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Jialin Jia
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Ping Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100191, China.,Beijing Advanced Innovation Center for Genomics, Beijing, 100191, China
| | - Liying Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China. .,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China. .,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China. .,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
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Kitagawa K, Matsumura K, Baba M, Kondo M, Takemoto T, Nagayasu K, Ago Y, Seiriki K, Hayata-Takano A, Kasai A, Takuma K, Hashimoto R, Hashimoto H, Nakazawa T. Intranasal oxytocin administration ameliorates social behavioral deficits in a POGZ WT/Q1038R mouse model of autism spectrum disorder. Mol Brain 2021; 14:56. [PMID: 33726803 PMCID: PMC7962304 DOI: 10.1186/s13041-021-00769-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/10/2021] [Indexed: 11/10/2022] Open
Abstract
Autism spectrum disorder (ASD) is a highly prevalent neurodevelopmental disorder characterized by core symptoms of impaired social behavior and communication. Recent studies have suggested that the oxytocin system, which regulates social behavior in mammals, is potentially involved in ASD. Mouse models of ASD provide a useful system for understanding the associations between an impaired oxytocin system and social behavior deficits. However, limited studies have shown the involvement of the oxytocin system in the behavioral phenotypes in mouse models of ASD. We have previously demonstrated that a mouse model that carries the ASD patient-derived de novo mutation in the pogo transposable element derived with zinc finger domain (POGZWT/Q1038R mice), showed ASD-like social behavioral deficits. Here, we have explored whether oxytocin (OXT) administration improves impaired social behavior in POGZWT/Q1038R mice and found that intranasal oxytocin administration effectively restored the impaired social behavior in POGZWT/Q1038R mice. We also found that the expression level of the oxytocin receptor gene (OXTR) was low in POGZWT/Q1038R mice. However, we did not detect significant changes in the number of OXT-expressing neurons between the paraventricular nucleus of POGZWT/Q1038R mice and that of WT mice. A chromatin immunoprecipitation assay revealed that POGZ binds to the promoter region of OXTR and is involved in the transcriptional regulation of OXTR. In summary, our study demonstrate that the pathogenic mutation in the POGZ, a high-confidence ASD gene, impairs the oxytocin system and social behavior in mice, providing insights into the development of oxytocin-based therapeutics for ASD.
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Affiliation(s)
- Kohei Kitagawa
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kensuke Matsumura
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masayuki Baba
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Momoka Kondo
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tomoya Takemoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kazuki Nagayasu
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan.,Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yukio Ago
- Department of Cellular and Molecular Pharmacology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Minami-ku, Hiroshima, 734-8553, Japan
| | - Kaoru Seiriki
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan.,Interdisciplinary Program for Biomedical Sciences, Institute for Transdisciplinary Graduate Degree Programs, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Atsuko Hayata-Takano
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan.,Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Suita, Osaka, 565-0871, Japan
| | - Atsushi Kasai
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kazuhiro Takuma
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Suita, Osaka, 565-0871, Japan.,Department of Pharmacology, Graduate School of Dentistry, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Tokyo, 187-8553, Japan.,Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hitoshi Hashimoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan. .,Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Suita, Osaka, 565-0871, Japan. .,Division of Bioscience, Institute for Datability Science, Osaka University, Suita, Osaka, 565-0871, Japan. .,Transdimensional Life Imaging Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, 565-0871, Japan. .,Department of Molecular Pharmaceutical Science, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Takanobu Nakazawa
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan. .,Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan.
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28
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Ricci C, Cerase A, Riolo G, Manasse G, Battistini S. KRIT1 Gene in Patients with Cerebral Cavernous Malformations: Clinical Features and Molecular Characterization of Novel Variants. J Mol Neurosci 2021; 71:1876-1883. [PMID: 33651268 PMCID: PMC8421287 DOI: 10.1007/s12031-021-01814-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/09/2021] [Indexed: 11/24/2022]
Abstract
Cerebral cavernous malformations (CCMs) are vascular malformations that may result in headaches, seizures, focal neurological deficits, and hemorrhage. CCMs occur sporadically (80%) or in familial form (20%), with autosomal dominant inheritance. Among the three CCM-related genes, mutations in KRIT1 account for 53–65% of familial cases and more than 100 different mutations have been identified so far. In the present work, we describe the clinical, neuroradiological, and genetic findings of sixteen CCM Italian patients, 13 belonging to 4 unrelated families and 3 sporadic cases. Six distinct KRIT1 gene variants, two novel (c.1730+1_1730+3del, c.1664 C>T) and four previously described (c.966G>A, c.1255-1G>A c.1197_1200del, c.1255-1_1256del), were identified, including a possible de novo mutation. All the variants resulted in a premature stop codon. Cerebral 1.5 T magnetic resonance imaging showed multiple CCMs in all the mutation carriers for whom it was available, including sporadic cases. One patient had also cutaneous angiomas. Among the mutation carriers, symptomatic patients constituted 66% and a variable phenotypic expression was observed. Our data confirms phenotypic variability and incomplete penetrance of neurological symptoms in KRIT1-positive families, expands the mutational spectrum of this gene, and highlights how sporadic cases with multiple lesions need an approach similar to individuals with familial CCM.
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Affiliation(s)
- Claudia Ricci
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | - Alfonso Cerase
- Neuroimaging Unit - Diagnostic and Functional Neuroradiology, Department of Neurological and Motor Sciences, Azienda ospedaliero-universitaria Senese University Hospital, Siena, Italy
| | - Giulia Riolo
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | - Giuditta Manasse
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | - Stefania Battistini
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy.
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29
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Luo T, Li K, Ling Z, Zhao G, Li B, Wang Z, Wang X, Han Y, Xia L, Zhang Y, Zhou Q, Fang Z, Wang Y, Chen Q, Zhou X, Pan H, Zhao Y, Wang Y, Dong L, Huang Y, Hu Z, Pan Q, Xia K, Li J. De novo mutations in folate-related genes associated with common developmental disorders. Comput Struct Biotechnol J 2021; 19:1414-1422. [PMID: 33777337 PMCID: PMC7966843 DOI: 10.1016/j.csbj.2021.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/14/2021] [Accepted: 02/16/2021] [Indexed: 01/23/2023] Open
Abstract
Folate deficiency is an environmental risk factor for several developmental disorders. De novo mutations (DNMs) also play important etiological roles in various developmental disorders. However, it remains unclear whether DNMs in folate-related genes (FRGs) contribute to developmental disorders. We obtained a list of 1,821 FRGs from folate metabolism pathways and the Comparative Toxicogenomics Database, along with data concerning DNMs in 15,404 cases and 3,391 controls from the Gene4Denovo database. We used a TADA-Denovo model to prioritize candidate disease-associated FRGs, and characterized these genes in terms of genic intolerance, functional networks, and expression patterns. Compared with the controls, FRGs were significantly enriched in likely damaging DNMs (ldDNMs) in patients with developmental disorders (1.54 ≤ odds ratio ≤ 3.39, Padj ≤ 0.0075). Furthermore, FRGs with ldDNMs rather than with likely non-damaging DNMs (lndDNMs) overlapped significantly among the five developmental disorders included in the datasets. The TADA-Denovo model prioritized 96 candidate disease-associated FRGs, which were intolerant to genetic variants. Their functional networks mainly involved pathways associated with chromatin modification, organ development, and signal transduction pathways. DNMT3A, KMT2B, KMT2C, and YY1 emerged as hub FRGs from the protein–protein interaction network. These candidate disease-associated FRGs are preferentially expressed in the excitatory neurones during embryonic development, and in the cortex, cerebellum, striatum, and amygdala during foetal development. Overall, these findings show that DNMs in FRGs are associated with the risk of developmental disorders. Further research on these DNMs may facilitate the discovery of developmental disorder biomarkers and therapeutic targets, enabling detailed, personalized, and precise folate treatment plan.
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Key Words
- ADD, all five developmental disorders
- ASD, autism spectrum disorder
- CHD, congenital heart disease
- Candidate disease-associated genes
- DNMs, De novo mutations
- De novo mutation
- Developmental disorders
- Dmis, deleterious missense variants
- EE, epileptic encephalopathy
- Expression patterns
- FRGs, folate-related genes
- Folate-related gene
- ID, intellectual disability
- PPI, Protein–protein interaction
- PTV, protein-truncating variants
- RVIS, residual variation intolerance scores
- SNPs, single nucleotide polymorphisms
- TADA, Transmitted And De novo Association
- Tmis, tolerant missense variants
- UDD, undiagnosed developmental disorder
- ldDNMs, likely damaging DNMs
- lndDNMs, likely non-damaging DNMs
- pLI, probability of loss-of-function intolerance
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Affiliation(s)
- Tengfei Luo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Kuokuo Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, China
| | - Zhengbao Ling
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaomeng Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Ying Han
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lu Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yi Zhang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiao Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhenghuan Fang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yijing Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qian Chen
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xun Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongxu Pan
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuwen Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yige Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lijie Dong
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yuanfeng Huang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhengmao Hu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qian Pan
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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30
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Peterson K, Coffman S, Zehri A, Anzalone A, Xiang Z, Wolfe S. Somatic Mosaicism in the Pathogenesis of de novo Cerebral Arteriovenous Malformations: A Paradigm Shift Implicating the RAS-MAPK Signaling Cascade. Cerebrovasc Dis 2021; 50:231-238. [PMID: 33556951 DOI: 10.1159/000512800] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 10/28/2020] [Indexed: 11/19/2022] Open
Abstract
Cerebral arteriovenous malformations (AVMs) are leading causes of lesional hemorrhagic stroke in both the pediatric and young adult population, with sporadic AVMs accounting for the majority of cases. Recent evidence has identified somatic mosaicism in key proximal components of the RAS-MAPK signaling cascade within endothelial cells collected from human sporadic cerebral AVMs, with early preclinical models supporting a potential causal role for these mutations in the pathogenesis of these malformations. Germline mutations that predispose to deregulation of the RAS-MAPK signaling axis have also been identified in hereditary vascular malformation syndromes, highlighting the key role of this signaling axis in global AVM development. Herein, we review the most recent genomic and preclinical evidence implicating somatic mosaicism in the RAS-MAPK signaling pathway in the pathogenesis of sporadic cerebral AVMs. Also, we review evidence for RAS-MAPK dysregulation in hereditary vascular malformation syndromes and present a hypothesis suggesting that this pathway is central for the development of both sporadic and syndrome-associated AVMs. Finally, we examine the clinical implications of these recent discoveries and highlight potential therapeutic targets within this signaling pathway.
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Affiliation(s)
- Keyan Peterson
- Department of Neurosurgery, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA,
| | - Stephanie Coffman
- Department of Neurosurgery, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Aqib Zehri
- Department of Neurosurgery, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Anthony Anzalone
- Department of Neurosurgery, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Zhidan Xiang
- Department of Neurosurgery, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Stacey Wolfe
- Department of Neurosurgery, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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31
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Martins L, Dos Santos EL, de Almeida AB, Machado RA, Lyrio AM, Foster BL, Kantovitz KR, Coletta RD, Nociti FH. A novel de novo heterozygous ALPL nonsense mutation associated with adult hypophosphatasia. Osteoporos Int 2020; 31:2251-2257. [PMID: 32572521 PMCID: PMC8214176 DOI: 10.1007/s00198-020-05490-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022]
Abstract
UNLABELLED Using genetic, clinical, biochemical, and radiographic assessment and bioinformatic approaches, we present an unusual case of adult HPP caused by a novel de novo heterozygous nonsense mutation in the alkaline phosphatase (ALPL). INTRODUCTION Hypophosphatasia (HPP) is caused by genetic alterations of the ALPL gene, encoding the tissue-nonspecific isozyme of alkaline phosphatase (TNSALP). Here, the purpose was to perform clinical and molecular investigation in a 36-year-old Caucasian woman suspected to present adult HPP. METHODS Medical and dental histories were obtained for the proposita and family members, including biochemical, radiographic, and dental assessments. ALPL mutational analysis was performed by the Sanger sequencing method, and the functional impact prediction of the identified mutations was assessed by bioinformatic methods. RESULTS We identified a novel heterozygous nonsense mutation in the ALPL gene (NM_000478.6:c.768G>A; W[TGG]>*[TGA]) associated with spontaneous vertebral fracture, severe back pain, musculoskeletal pain, low bone density, and short-rooted permanent teeth loss. Functional prediction analysis revealed that the Trp256Ter mutation led to a complete loss of TNSALP crown domain and extensive loss of other functional domains (calcium-binding domain, active site vicinity, and zinc-binding site) and over 60% loss of homodimer interface residues, suggesting that the mutant TNSALP molecules are nonfunctional and form unstable homodimers. Genotyping of the ALPL in the proposita's parents, sister, and niece revealed that in this case, HPP occurred due to a de novo mutation. CONCLUSION The present study describes a novel genotype-phenotype and structure-function relationship for HPP, contributing to a better molecular comprehension of HPP etiology and pathophysiology.
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Affiliation(s)
- L Martins
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, State University of Campinas - UNICAMP, Av. Limeira, 901, Piracicaba, SP, 13414-903, Brazil
| | - E L Dos Santos
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, State University of Campinas - UNICAMP, Av. Limeira, 901, Piracicaba, SP, 13414-903, Brazil
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - A B de Almeida
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, State University of Campinas - UNICAMP, Av. Limeira, 901, Piracicaba, SP, 13414-903, Brazil
| | - R A Machado
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas - UNICAMP, Piracicaba, SP, Brazil
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo (HRAC/USP), Bauru, SP, Brazil
| | - A M Lyrio
- Pontifical Catholic University of Campinas, Campinas, SP, Brazil
| | - B L Foster
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - K R Kantovitz
- Department of Dental Materials, São Leopoldo Research Center, Campinas, SP, Brazil
| | - R D Coletta
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas - UNICAMP, Piracicaba, SP, Brazil
| | - F H Nociti
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, State University of Campinas - UNICAMP, Av. Limeira, 901, Piracicaba, SP, 13414-903, Brazil.
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32
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Li B, Li K, Tian D, Zhou Q, Xie Y, Fang Z, Wang X, Luo T, Wang Z, Zhang Y, Wang Y, Chen Q, Meng Q, Zhao G, Li J. De novo mutation of cancer-related genes associates with particular neurodevelopmental disorders. J Mol Med (Berl) 2020; 98:1701-1712. [PMID: 33047154 DOI: 10.1007/s00109-020-01991-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 10/01/2020] [Accepted: 10/07/2020] [Indexed: 12/31/2022]
Abstract
Epidemiological studies have shown an increased prevalence of cancer in some patients with neurodevelopmental disorder (NDD); however, the genetic mechanisms regarding how cancer-related genes (CRGs) contribute to NDD remain unclear. We performed bioinformatic analyses on 219 CRGs from OMIM and de novo mutations (DNMs) from 16,498 patients with different NDDs and 3391 controls. Our results showed that autism spectrum disorder, undiagnosed neurodevelopmental disorder, congenital heart disease and intellectual disability, but not epileptic encephalopathy and schizophrenia, harboured significantly more putative functional DNMs in CRGs, compared with controls, providing genetic evidence supporting previous epidemiological surveys. We further detected 26 CRGs with recurrent putative functional DNMs that showed high expression in the human brain during the prenatal stage and in non-brain organs in adults. The proteins coded by the 26 CRGs and known NDD candidate genes formed a functional network that is involved in brain development and tumorigenesis. Overall, we proposed 39 cancer-targeting drugs that could be investigated for treating patients with NDD, which would be potentially cost-effective. In conclusion, DNMs contribute to specific NDDs and there may be a shared genetic basis between NDDs and cancer, highlighting the importance of considering cancer-targeting drugs with potential curative effects in patients with NDDs. KEY MESSAGES: • The contribution of DNMs in NDD is consistent with epidemiological surveys. • We highlighted 26 CRGs, including nine genes with more than five functional DNMs. • Specific expression patterns underlie the genetic mechanism of CRGs in NDD. • Specific functional networks underlie the genetic mechanism of CRGs in NDD. • The shared genetic aetiology suggests potential mutual treatment strategies.
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Affiliation(s)
- Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, 87 #, Xiangya Road, Changsha, 410008, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Kuokuo Li
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, Hunan, China
| | - Di Tian
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, Hunan, China
| | - Qiao Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, 87 #, Xiangya Road, Changsha, 410008, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yali Xie
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, 87 #, Xiangya Road, Changsha, 410008, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Zhenghuan Fang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, Hunan, China
| | - Xiaomeng Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, Hunan, China
| | - Tengfei Luo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, Hunan, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, 87 #, Xiangya Road, Changsha, 410008, Hunan, China
| | - Yi Zhang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, 87 #, Xiangya Road, Changsha, 410008, Hunan, China
| | - Yijing Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, Hunan, China
| | - Qian Chen
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, 87 #, Xiangya Road, Changsha, 410008, Hunan, China
| | - Qingtuan Meng
- Guangxi Clinical Research Center for Neurological Diseases, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, 87 #, Xiangya Road, Changsha, 410008, Hunan, China. .,Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, 87 #, Xiangya Road, Changsha, 410008, Hunan, China. .,Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. .,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, Hunan, China.
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Takagi T, Higashi Y, Asai M, Ishii S. Introduction of a de novo Creb-binding protein gene mutation in sperm to produce a Rubinstein-Taybi syndrome model using inbred C57BL/6 mice. Brain Res 2020; 1749:147140. [PMID: 33022214 DOI: 10.1016/j.brainres.2020.147140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/07/2020] [Accepted: 09/28/2020] [Indexed: 02/02/2023]
Abstract
Neurodevelopmental disorders, including intellectual disability and autism spectrum disorder, are often caused by de novo autosomal dominant mutations. While mouse models are frequently used to investigate these disorders, the genetic background sometimes affects the appearance or severity of mutant phenotypes. In a previous report, we developed a system to produce de novo heterozygous mutant mice using the Cre-LoxP system without the need to maintain the heterozygous mutant line itself (Takagi et al. 2015). To further verify the applicability of the de novo mutation system in sperm, we used this system to produce a mouse model for Rubinstein-Taybi syndrome, using a Cbp heterozygous mutant, which has been reported to be difficult to maintain on a C57BL/6 background. Here, we show that de novo Cbp- loss-of-function heterozygous mutant mice with a C57BL/6 background, present with a clear craniofacial phenotype and reduced locomotor activity in the open field test, which was not observed in the loss-of-function of Cbp heterozygous mutant line mice with a mixed genetic background, but was observed in the dominant negative Cbp heterozygous mutant line with a mixed genetic background. Meanwhile, the de novo heterozygous Cbp mutant mice still showed great variability in survival rates despite their inbred background. These results further confirmed that the de novo mutation system used in germ cells is effective for stable production and analysis of an autosomal dominant disorder mouse model, which is often difficult to maintain as a mutant mouse line.
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Affiliation(s)
- Tsuyoshi Takagi
- Department of Disease Model, Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kagiya-cho, Kasugai, Aichi 480-0392, Japan.
| | - Yujiro Higashi
- Department of Disease Model, Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kagiya-cho, Kasugai, Aichi 480-0392, Japan
| | - Masato Asai
- Department of Disease Model, Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kagiya-cho, Kasugai, Aichi 480-0392, Japan
| | - Shunsuke Ishii
- Cluster for Pioneering Research, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
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Yuan P, Xia J, Ou S, Liu P, Du T, Zheng L, Yin X, Xie L, Zhang S, Yan H, Gao Y, Zhang Q, Jiang H, Chen F, Wang W. A whole-genome sequencing-based novel preimplantation genetic testing method for de novo mutations combined with chromosomal balanced translocations. J Assist Reprod Genet 2020; 37:2525-2533. [PMID: 32783137 DOI: 10.1007/s10815-020-01921-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/06/2020] [Indexed: 12/28/2022] Open
Abstract
PURPOSE To explore a new preimplantation genetic testing (PGT) method for de novo mutations (DNMs) combined with chromosomal balanced translocations by whole-genome sequencing (WGS) using the MGISEQ-2000 sequencer. METHODS Two families, one with maternal Olmsted syndrome caused by DNM (c.1246C>T) in TRPV3 and a paternal Robertsonian translocation and one with paternal Marfan syndrome caused by DNM (c.4952_4955delAATG) in FBN1 and a maternal reciprocal translocation, underwent PGT for monogenetic disease (PGT-M), chromosomal aneuploidy, and structural rearrangement. WGS of embryos and family members were performed. Bioinformatics analysis based on gradient sequencing depth was performed, and parent-embryo haplotyping was conducted for DNM diagnosis. Sanger sequencing, karyotyping, and chromosomal microarray analysis were performed using an amniotic fluid sample to confirm the PGT results. RESULTS After 1 PGT cycle, WGS of 2 embryos from the Olmsted syndrome family revealed euploid embryos without DNMs; after 2 cycles, the 11 embryos from the Marfan syndrome family showed only 1 normal embryo without DNM, copy number variations (CNVs), or aneuploidy. Moreover, 1 blastocyst from the Marfan syndrome family was transferred back to the uterus; the amniocentesis test results were confirmed by PGT and a healthy infant was born. CONCLUSIONS WGS based on parent-embryo haplotypes was an effective strategy for PGT of DNMs combined with a chromosomal balanced translocation. Our results indicate this is a reliable and effective diagnostic method that is useful for clinical application in PGT of patients with DNMs.
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Affiliation(s)
- Ping Yuan
- IVF Center, Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
| | - Jun Xia
- MGI, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Songbang Ou
- IVF Center, Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
| | - Ping Liu
- MGI, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Tao Du
- Department of Obstetrics, Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
| | - Lingyan Zheng
- IVF Center, Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
| | - Xuyang Yin
- MGI, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Lin Xie
- MGI, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Sijia Zhang
- MGI, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Huijuan Yan
- MGI, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Qingxue Zhang
- IVF Center, Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
| | - Hui Jiang
- MGI, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, Guangdong, China
| | - Fang Chen
- MGI, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China.
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, Guangdong, China.
| | - Wenjun Wang
- IVF Center, Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China.
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Long K, Wang H, Song Z, Yin X, Wang Y. EEF1A2 mutations in epileptic encephalopathy/intellectual disability: Understanding the potential mechanism of phenotypic variation. Epilepsy Behav 2020; 105:106955. [PMID: 32062104 DOI: 10.1016/j.yebeh.2020.106955] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/27/2020] [Accepted: 01/27/2020] [Indexed: 10/25/2022]
Abstract
EEF1A2 encodes protein elongation factor 1-alpha 2, which is involved in Guanosine triphosphate (GTP)-dependent binding of aminoacyl-transfer RNA (tRNA) to the A-site of ribosomes during protein biosynthesis and is highly expressed in the central nervous system. De novo mutations in EEF1A2 have been identified in patients with extensive neurological deficits, including intractable epilepsy, globe developmental delay, and severe intellectual disability. However, the mechanism underlying phenotype variation is unknown. Using next-generation sequencing, we identified a novel and a recurrent de novo mutation, c.294C>A; p.(Phe98Leu) and c.208G>A; p.(Gly70Ser), in patients with Lennox-Gastaut syndrome. The further systematic analysis revealed that all EEF1A2 mutations were associated with epilepsy and intellectual disability, suggesting its critical role in neurodevelopment. Missense mutations with severe molecular alteration in the t-RNA binding sites or GTP hydrolysis domain were associated with early-onset severe epilepsy, indicating that the clinical expression was potentially determined by the location of mutations and alteration of molecular effects. This study highlights the potential genotype-phenotype relationship in EEF1A2 and facilitates the evaluation of the pathogenicity of EEF1A2 mutations in clinical practice.
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Affiliation(s)
- Kexin Long
- Institute of Medical Sciences, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hua Wang
- Maternal and Child Health Hospital of Hunan Province, Changsha, Hunan 410008, China; Key Laboratory of Birth Defects Research and Prevention, Changsha, Hunan 410008, China
| | - Zhanyi Song
- Med Department of Pediatric Neurology, Chenzhou No.1 People's Hospital (Children's Hospital), Chenzhou, Hunan 423000, China
| | - Xiaomeng Yin
- Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
| | - Yaqin Wang
- Department of Health Management Centre, the Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China.
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Joob B, Wiwanitkit V. G130V de novo mutation in case with nonsyndromic hearing loss without palmoplantar keratoderma. Int J Pediatr Otorhinolaryngol 2020; 129:109793. [PMID: 31785923 DOI: 10.1016/j.ijporl.2019.109793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/19/2019] [Indexed: 10/25/2022]
Affiliation(s)
- Beuy Joob
- Sanitation 1 Medical Academic Center, Bangkok, Thailand.
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Lin GN, Guo S, Tan X, Wang W, Qian W, Song W, Wang J, Yu S, Wang Z, Cui D, Wang H. PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders. Genomics Proteomics Bioinformatics 2019; 17:453-64. [PMID: 31809863 DOI: 10.1016/j.gpb.2019.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 10/14/2019] [Accepted: 10/23/2019] [Indexed: 01/21/2023]
Abstract
De novo variants (DNVs) are one of the most significant contributors to severe early-onset genetic disorders such as autism spectrum disorder, intellectual disability, and other developmental and neuropsychiatric (DNP) disorders. Presently, a plethora of DNVs have been identified using next-generation sequencing, and many efforts have been made to understand their impact at the gene level. However, there has been little exploration of the effects at the isoform level. The brain contains a high level of alternative splicing and regulation, and exhibits a more divergent splicing program than other tissues. Therefore, it is crucial to explore variants at the transcriptional regulation level to better interpret the mechanisms underlying DNP disorders. To facilitate a better usage and improve the isoform-level interpretation of variants, we developed NeuroPsychiatric Mutation Knowledge Base (PsyMuKB). It contains a comprehensive, carefully curated list of DNVs with transcriptional and translational annotations to enable identification of isoform-specific mutations. PsyMuKB allows a flexible search of genes or variants and provides both table-based descriptions and associated visualizations, such as expression, transcript genomic structures, protein interactions, and the mutation sites mapped on the protein structures. It also provides an easy-to-use web interface, allowing users to rapidly visualize the locations and characteristics of mutations and the expression patterns of the impacted genes and isoforms. PsyMuKB thus constitutes a valuable resource for identifying tissue-specific DNVs for further functional studies of related disorders. PsyMuKB is freely accessible at http://psymukb.net.
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Abstract
PURPOSE OF REVIEW To summarize the molecular and clinical findings of KMT2B-related dystonia (DYT-KMT2B), a newly identified genetic dystonia syndrome. RECENT FINDINGS Since first described in 2016, 66 different KMT2B-affecting variants, encompassing a set of frameshift, nonsense, splice-site, missense, and deletion mutations, have been reported in 76 patients. Most mutations are de novo and expected to mediate epigenetic dysregulation by inducing KMT2B haploinsufficiency. DYT-KMT2B is characterized phenotypically by limb-onset childhood dystonia that tends to spread progressively, resulting in generalized dystonia with cranio-cervical involvement. Co-occuring signs such as intellectual disability are frequently observed. Sustained response to deep brain stimulation (DBS), including restoration of independent ambulation, is seen in 93% (27/29) of patients. DYT-KMT2B is emerging as a prevalent monogenic dystonia. Childhood-onset dystonia presentations should prompt a search for KMT2B mutations, preferentially via next-generation-sequencing and genomic-array technologies, to enable specific counseling and treatment. Prospective multicenter studies are desirable to establish KMT2B mutational status as a DBS outcome predictor.
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Affiliation(s)
- Michael Zech
- Institut für Neurogenomik, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Munich, Neuherberg, Germany.,Institut für Humangenetik, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Daniel D Lam
- Institut für Neurogenomik, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Munich, Neuherberg, Germany
| | - Juliane Winkelmann
- Institut für Neurogenomik, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Munich, Neuherberg, Germany. .,Institut für Humangenetik, Klinikum rechts der Isar, Technische Universität München, Munich, Germany. .,Lehrstuhl für Neurogenetik, Technische Universität München, Munich, Germany. .,Munich Cluster for Systems Neurology, SyNergy, Munich, Germany.
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Tatsi P, Papanikolaou GE, Chartomatsidou T, Papoulidis I, Athanasiadis A, Najdecki R, Timotheou E. Lowe syndrome identified in the offspring of an oocyte donor who was an unknown carrier of a de novo mutation: a case report and review of the literature. J Med Case Rep 2019; 13:325. [PMID: 31676009 DOI: 10.1186/s13256-019-2263-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/22/2019] [Indexed: 11/30/2022] Open
Abstract
Background Oculocerebrorenal syndrome of Lowe is an X-linked disorder with very low prevalence in the general population. The OCRL gene encodes the protein phosphatidylinositol 4,5-bisphosphate-5-phosphatase, a lipid phosphatase, located in the trans-Golgi network. Point mutations in the OCRL gene cause Lowe syndrome and Dent disease, which are characterized as a multisystemic disorder. The symptoms of Lowe syndrome are expressed primarily as dysfunction of the eyes, kidneys, and the central nervous system. Case presentation This report describes a case of a 31-year-old Georgian woman with a de novo pathogenic mutation causing oculocerebrorenal syndrome of Lowe, who was a volunteer in an oocyte donation program for in vitro fertilization purposes, and the outcome of the treatments of this particular donor’s oocyte receivers, describing the implications of the mutation for the children born as a result of the treatments. It raises important medical and ethical issues about the necessity of genetic testing of oocyte donors and the possibility of rare genetic disorders being inherited by the offspring of donors. Conclusion This particular case indicates the legal, medical, and emotional risks of utilizing donor oocytes from phenotypically healthy women, whose genetic constitution is unknown in terms of being silent carriers of rare diseases. In addition, all the necessary actions were followed; the further examinations that are required are mentioned. The donor and the offspring should be further tested. The remaining cryopreserved embryos should be destroyed or preimplantation genetic testing should be performed before they are utilized. Finally, all the people involved, the treated couples and the donor, alongside her family, should follow genetic and psychological counselling.
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Chow J, Jensen M, Amini H, Hormozdiari F, Penn O, Shifman S, Girirajan S, Hormozdiari F. Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders. Genome Med 2019; 11:65. [PMID: 31653223 DOI: 10.1186/s13073-019-0678-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 10/15/2019] [Indexed: 12/22/2022] Open
Abstract
Background Neurodevelopmental disorders (NDDs) such as autism spectrum disorder, intellectual disability, developmental disability, and epilepsy are characterized by abnormal brain development that may affect cognition, learning, behavior, and motor skills. High co-occurrence (comorbidity) of NDDs indicates a shared, underlying biological mechanism. The genetic heterogeneity and overlap observed in NDDs make it difficult to identify the genetic causes of specific clinical symptoms, such as seizures. Methods We present a computational method, MAGI-S, to discover modules or groups of highly connected genes that together potentially perform a similar biological function. MAGI-S integrates protein-protein interaction and co-expression networks to form modules centered around the selection of a single “seed” gene, yielding modules consisting of genes that are highly co-expressed with the seed gene. We aim to dissect the epilepsy phenotype from a general NDD phenotype by providing MAGI-S with high confidence NDD seed genes with varying degrees of association with epilepsy, and we assess the enrichment of de novo mutation, NDD-associated genes, and relevant biological function of constructed modules. Results The newly identified modules account for the increased rate of de novo non-synonymous mutations in autism, intellectual disability, developmental disability, and epilepsy, and enrichment of copy number variations (CNVs) in developmental disability. We also observed that modules seeded with genes strongly associated with epilepsy tend to have a higher association with epilepsy phenotypes than modules seeded at other neurodevelopmental disorder genes. Modules seeded with genes strongly associated with epilepsy (e.g., SCN1A, GABRA1, and KCNB1) are significantly associated with synaptic transmission, long-term potentiation, and calcium signaling pathways. On the other hand, modules found with seed genes that are not associated or weakly associated with epilepsy are mostly involved with RNA regulation and chromatin remodeling. Conclusions In summary, our method identifies modules enriched with de novo non-synonymous mutations and can capture specific networks that underlie the epilepsy phenotype and display distinct enrichment in relevant biological processes. MAGI-S is available at https://github.com/jchow32/magi-s.
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Lee YH, Shim KY, Park SB, Kim YC. Ocular manifestations in a patient with de novo Fabry disease. Yeungnam Univ J Med 2019; 35:232-235. [PMID: 31620600 PMCID: PMC6784698 DOI: 10.12701/yujm.2018.35.2.232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/05/2018] [Accepted: 04/10/2018] [Indexed: 11/10/2022] Open
Abstract
Fabry disease (FD) is an X-linked, recessively inherited, rare, progressive, disorder of glycosphingolipid metabolism affecting multiple organs resulting in organ dysfunction. It is rare to find only one FD affected subject with a de novo mutation. Here we report a case of a 41-year-old Asian male diagnosed with de novo FD. Comprehensive ophthalmological evaluation was performed using slit lamp, color fundus photography, optical coherence tomography, fluorescein angiography, and indocyanine green angiography. On slit lamp examination, cornea verticillata and slightly tortuous, and aneurysmal dilatation of inferior bulbar conjunctival vessels were observed. Other imaging modalities showed unremarkable findings. Cornea verticillata and inferior bulbar conjunctival vascular abnormalities may be detected earlier than other ocular abnormalities in de novo FDs like hereditary FDs.
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Affiliation(s)
- You Hyun Lee
- Department of Ophthalmology, Keimyung University School of Medicine, Daegu, Korea
| | - Kyu Young Shim
- Department of Ophthalmology, Keimyung University School of Medicine, Daegu, Korea
| | - Sung Bae Park
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Yu Cheol Kim
- Department of Ophthalmology, Keimyung University School of Medicine, Daegu, Korea
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Li J, Lin H, Hou R, Shen J, Li X, Xing J, He F, Wu X, Zhao X, Sun L, Fan X, Niu X, Liu Y, Liu R, An P, Qu T, Chang W, Wang Q, Zhou L, Li J, Wang Z, Jiao J, Wang Y, Wang G, Liang N, Liang J, Liang Y, Hou H, Shi Y, Yang X, Li J, Dang E, Yin G, Yang X, Zhang G, Gao Q, Fang X, Li X, Zhang K. Multi-omics study in monozygotic twins confirm the contribution of de novo mutation to psoriasis. J Autoimmun 2019; 106:102349. [PMID: 31629629 DOI: 10.1016/j.jaut.2019.102349] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/03/2019] [Accepted: 10/07/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND Genome-wide association studies have identified over 120 risk loci for psoriasis. However, most of the variations are located in non-coding region with high frequency and small effect size. Pathogenetic variants are rarely reported except HLA-C*0602 with the odds ratio being approximately 4.0 in Chinese population. Although rare variations still account for a small proportion of phenotypic variances in complex diseases, their effect on phenotypes is large. Recently, more and more studies focus on the low-frequency functional variants and have achieved a certain amount of success. METHOD Whole genome sequencing and sanger sequencing was performed on 8 MZ twin pairs discordant for psoriasis to scan and verified the de novo mutations (DNMs). Additionally, 665 individuals with about 20 years' medical history versus 2054 healthy controls and two published large population studies which had about 8 years' medical history (including 10,727 cases versus 10,582 controls) were applied to validate the enrichment of rare damaging mutations in two DNMs genes. Besides, to verify the pathogenicity of candidate DNM in C3, RNA-sequencing for CD4+, CD8+ T cells of twins and lesion, non-lesion skin of psoriasis patients were carried out. Meanwhile, the enzyme-linked immunosorbent assay kit was used to detect the level of C3, C3b in the supernatant of peripheral blood. RESULT A total of 27 DNMs between co-twins were identified. We found six of eight twins carry HLA-C∗0602 allele which have large effects on psoriasis. And it is interesting that a missense mutation in SPRED1 and a splice region mutation in C3 are found in the psoriasis individuals in the other two MZ twin pairs without carrying HLA-C*0602 allele. In the replication stage, we found 2 loss-of-function (LOF) variants of C3 only in 665 cases with about 20 years' medical history and gene-wise analysis in 665 cases and 2054 controls showed that the rare missense mutations in C3 were enriched in cases (OR = 1.91, P = 0.0028). We further scanned the LOF mutations of C3 in two published studies (about 8 years' medical history), and found one LOF mutation in the case without carrying HLA-C*0602. In the individual with DNM in C3, RNA sequencing showed the expression level of C3 in skin was significant higher than healthy samples in public database (TPM fold change = 1.40, P = 0.000181) and ELISA showed protein C3 in peripheral blood was higher (~2.2-fold difference) than the other samples of twins without DNM in C3. CONCLUSION To the best of our knowledge, this is the first report that DNM in C3 is the likely pathological mutations, and it provided a better understanding of the genetic etiology of psoriasis and additional treatments for this disease.
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Affiliation(s)
- Junqin Li
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Haoxiang Lin
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Ruixia Hou
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Juan Shen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xiaofang Li
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Jianxiao Xing
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Fusheng He
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Xueli Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xincheng Zhao
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Liangdan Sun
- Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, 230032, China.
| | - Xing Fan
- Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, 230032, China.
| | - Xuping Niu
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Yanmin Liu
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Ruifeng Liu
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Peng An
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Tong Qu
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Wenjuan Chang
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Qiang Wang
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Ling Zhou
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Jiao Li
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Ziyuan Wang
- Shanxi Medical University, No. 56 Xinjian South Road, Taiyuan, 030001, China.
| | - Juanjuan Jiao
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Ying Wang
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Gang Wang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, No. 15 Changle Road West, Xi'an, 710032, China.
| | - Nannan Liang
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Jiannan Liang
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Yanyang Liang
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Hui Hou
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Yu Shi
- Department of Hematology, Oncology and Tumor Immunology Charité University Medicine Berlin, Campus Virchow Hospital, Berlin, Germany.
| | - Xiaohong Yang
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Juan Li
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Erle Dang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, No. 15 Changle Road West, Xi'an, 710032, China.
| | - Guohua Yin
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Xukui Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Guiping Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xiaodong Fang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xinhua Li
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
| | - Kaiming Zhang
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, No. 5 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, China.
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Matsumura K, Baba M, Nagayasu K, Yamamoto K, Kondo M, Kitagawa K, Takemoto T, Seiriki K, Kasai A, Ago Y, Hayata-Takano A, Shintani N, Kuriu T, Iguchi T, Sato M, Takuma K, Hashimoto R, Hashimoto H, Nakazawa T. Autism-associated protein kinase D2 regulates embryonic cortical neuron development. Biochem Biophys Res Commun 2019; 519:626-632. [PMID: 31540692 DOI: 10.1016/j.bbrc.2019.09.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 09/12/2019] [Indexed: 12/26/2022]
Abstract
Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder, characterized by impaired social interaction, repetitive behavior and restricted interests. Although the molecular etiology of ASD remains largely unknown, recent studies have suggested that de novo mutations are significantly involved in the risk of ASD. We and others recently identified spontaneous de novo mutations in PKD2, a protein kinase D family member, in sporadic ASD cases. However, the biological significance of the de novo PKD2 mutations and the role of PKD2 in brain development remain unclear. Here, we performed functional analysis of PKD2 in cortical neuron development using in utero electroporation. PKD2 is highly expressed in cortical neural stem cells in the developing cortex and regulates cortical neuron development, including the neuronal differentiation of neural stem cells and migration of newborn neurons. Importantly, we determined that the ASD-associated de novo mutations impair the kinase activity of PKD2, suggesting that the de novo PKD2 mutations can be a risk factor for the disease by loss of function of PKD2. Our current findings provide novel insight into the molecular and cellular pathogenesis of ASD.
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Affiliation(s)
- Kensuke Matsumura
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan; Interdisciplinary Program for Biomedical Sciences, Institute for Transdisciplinary Graduate Degree Programs, Osaka University, Suita, Osaka, 565-0871, Japan; Research Fellowships for Young Scientists of the Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo, 102-0083, Japan
| | - Masayuki Baba
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kazuki Nagayasu
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kana Yamamoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Momoka Kondo
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kohei Kitagawa
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tomoya Takemoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kaoru Seiriki
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan; Interdisciplinary Program for Biomedical Sciences, Institute for Transdisciplinary Graduate Degree Programs, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Atsushi Kasai
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yukio Ago
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan; Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Atsuko Hayata-Takano
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan; United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Suita, Osaka, 565-0871, Japan
| | - Norihito Shintani
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Toshihiko Kuriu
- Osaka Medical College, Research and Development Center, Takatsuki, Osaka, 569-8686, Japan
| | - Tokuichi Iguchi
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Makoto Sato
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Suita, Osaka, 565-0871, Japan; Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan; Research Center for Child Mental Development, University of Fukui, Yoshida-gun, Fukui, 910-1193, Japan
| | - Kazuhiro Takuma
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Suita, Osaka, 565-0871, Japan; Department of Pharmacology, Graduate School of Dentistry, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Tokyo, 187-8553, Japan; Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hitoshi Hashimoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan; United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Suita, Osaka, 565-0871, Japan; Division of Bioscience, Institute for Datability Science, Osaka University, Suita, Osaka, 565-0871, Japan; Transdimensional Life Imaging Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, 565-0871, Japan; Department of Molecular Pharmaceutical Science, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Takanobu Nakazawa
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan; Department of Pharmacology, Graduate School of Dentistry, Osaka University, Suita, Osaka, 565-0871, Japan.
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Wang SH, Hsiao PC, Yeh LL, Liu CM, Liu CC, Hwang TJ, Hsieh MH, Chien YL, Lin YT, Huang YT, Chen CY, Chandler SD, Faraone SV, Neale B, Glatt SJ, Tsuang MT, Hwu HG, Chen WJ. Advanced Paternal Age and Early Onset of Schizophrenia in Sporadic Cases: Not Confounded by Parental Polygenic Risk for Schizophrenia. Biol Psychiatry 2019; 86:56-64. [PMID: 30926130 DOI: 10.1016/j.biopsych.2019.01.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 01/24/2019] [Accepted: 01/24/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND Whether paternal age effect on schizophrenia is a causation or just an association due to confounding by selection into late parenthood is still debated. We investigated the association between paternal age and early onset of schizophrenia in offspring, controlling for both paternal and maternal predisposition to schizophrenia as empirically estimated using polygenic risk score (PRS) derived from the Psychiatric Genomics Consortium. METHODS Among 2923 sporadic schizophrenia cases selected from the Schizophrenia Trio Genomic Research in Taiwan project, 1649 had parents' genotyping data. The relationships of paternal schizophrenia PRS to paternal age at first birth (AFB) and of maternal schizophrenia PRS to maternal AFB were examined. A logistic regression model of patients' early onset of schizophrenia (≤18 years old) on paternal age was conducted. RESULTS Advanced paternal age over 20 years exhibited a trend of an increasing proportion of early onset of schizophrenia (odds ratio per 10-year increase in paternal age = 1.28, p = .007) after adjusting for maternal age, sex, and age. Older paternal AFB also exhibited an increasing trend of paternal schizophrenia PRS. Additionally, a U-shaped relationship between maternal AFB and maternal schizophrenia PRS was observed. After adjusting for both paternal and maternal schizophrenia PRS, the association of paternal age with patients' early onset of schizophrenia remained (odds ratio = 1.29, p = .04). CONCLUSIONS The association between paternal age and early onset of schizophrenia was not confounded by parental PRS for schizophrenia, which partially captures parental genetic vulnerability to schizophrenia. Our findings support an independent role of paternal age per se in increased risk of early onset of schizophrenia in offspring.
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Affiliation(s)
- Shi-Heng Wang
- Departments of Public Health and Occupational Safety and Health, College of Public Health, China Medical University, Taichung, Taiwan
| | - Po-Chang Hsiao
- Institute of Epidemiology and Preventive Medicine, College of Public Health, Taipei, Taiwan
| | - Ling-Ling Yeh
- Department of Healthcare Administration, College of Medical and Health Science, Asia University, Taichung, Taiwan
| | - Chih-Min Liu
- Department of Psychiatry, College of Medicine and National Taiwan University Hospital, Taipei, Taiwan
| | - Chen-Chung Liu
- Department of Psychiatry, College of Medicine and National Taiwan University Hospital, Taipei, Taiwan
| | - Tzung-Jeng Hwang
- Department of Psychiatry, College of Medicine and National Taiwan University Hospital, Taipei, Taiwan
| | - Ming H Hsieh
- Department of Psychiatry, College of Medicine and National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Ling Chien
- Department of Psychiatry, College of Medicine and National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Ting Lin
- Department of Psychiatry, College of Medicine and National Taiwan University Hospital, Taipei, Taiwan
| | - Yen-Tsung Huang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Chia-Yen Chen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sharon D Chandler
- Center for Behavioral Genomics, Department of Psychiatry and Institute for Genomic Medicine, University of California San Diego, La Jolla, California
| | - Stephen V Faraone
- Departments of Psychiatry and Behavioral Sciences and Neuroscience and Physiology, Medical Genetics Research Center, State University of New York Upstate Medical University, Syracuse, New York
| | - Benjamin Neale
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Stephen J Glatt
- Departments of Psychiatry and Behavioral Sciences and Neuroscience and Physiology, Medical Genetics Research Center, State University of New York Upstate Medical University, Syracuse, New York
| | - Ming T Tsuang
- Center for Behavioral Genomics, Department of Psychiatry and Institute for Genomic Medicine, University of California San Diego, La Jolla, California
| | - Hai-Gwo Hwu
- Department of Psychiatry, College of Medicine and National Taiwan University Hospital, Taipei, Taiwan; Institute of Brain and Mind Sciences, College of Medicine, Taipei, Taiwan
| | - Wei J Chen
- Institute of Epidemiology and Preventive Medicine, College of Public Health, Taipei, Taiwan; Department of Public Health, College of Public Health, Taipei, Taiwan; Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.
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Chen M, Liu R, Wu C, Li X, Wang Y. A novel de novo mutation (p.Pro1310Glnfs*46) in KMT2A caused Wiedemann-Steiner Syndrome in a Chinese boy with postnatal growth retardation: a case report. Mol Biol Rep 2019; 46:5555-5559. [PMID: 31250358 DOI: 10.1007/s11033-019-04936-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/20/2019] [Indexed: 12/19/2022]
Abstract
Wiedemann-Steiner Syndrome (WSS) is a very rare autosomal dominant disease. Mutations in the KMT2A gene have been shown to cause this disease. A 1-year-old Chinese boy exhibited growth delay, psychomotor retardation, limb hypotonia and facial dysmorphism that was consistent with WSS. His body weight started to drop below the normal range at 3 months old, and the decline persisted. Whole-exome sequencing showed a novel de novo mutation (p.Pro1310Glnfs*46) in KMT2A, which confirmed the diagnosis of WSS. We diagnosed a Chinese boy who presented postnatal growth retardation with WSS caused by a novel de novo mutation in KMT2A. Our findings expand the mutational and phenotypic spectra of WSS and will be valuable for the mutation-based pre- and postnatal screening for and genetic diagnosis of WSS.
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Affiliation(s)
- Minghui Chen
- Center for Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Ruihong Liu
- United Laboratory of the Fifth Affiliated Hospital and BGI, Department of Experimental Medicine, Guangdong Provincial Engineering Research Center of Molecular Imaging, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Chao Wu
- Department of Neurology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Xunhua Li
- Department of Neurology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yiming Wang
- United Laboratory of the Fifth Affiliated Hospital and BGI, Department of Experimental Medicine, Guangdong Provincial Engineering Research Center of Molecular Imaging, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China. .,Xinhua College, Sun Yat-sen University, 19 Long Dong Mei Hua Road, Tianhe District, Guangzhou, 510520, China.
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Kuroda Y, Murakami H, Yokoi T, Kumaki T, Enomoto Y, Tsurusaki Y, Kurosawa K. Two unrelated girls with intellectual disability associated with a truncating mutation in the PPM1D penultimate exon. Brain Dev 2019; 41:538-541. [PMID: 30795918 DOI: 10.1016/j.braindev.2019.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 01/21/2019] [Accepted: 02/12/2019] [Indexed: 01/07/2023]
Abstract
PPM1D truncating mutations in the last and penultimate exons of the gene have been associated with intellectual disability (ID) syndrome. Only 15 affected patients to-date have been reported with mild-to-severe ID, autistic behavior, anxiety and dysmorphic features. Here, we describe the clinical characteristics and underlying genetics of two unrelated girls with moderate developmental delay and dysmorphic features associated with novel mutations in PPM1D exon 5. The dysmorphic features demonstrated by these two patients are consistent with previously reported patients, including broad forehead, thin upper lip, brachydactyly, and hypoplastic nails. We identified a de novo PPM1D mutation in exon 5 of each patient (c.1250_1251insACCA p.V419Tfs*16 and c.1256_1257insCAAG p.S421Qfs*14) by panel sequencing for 4,813 disease-related genes. Both patients also had frameshift mutations (at different positions) that resulted in the same estimated termination codon at 434. These additional reports add to the growing literature on PPM1D-associated ID syndrome and help delineate the clinical phenotype and genetic basis.
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Affiliation(s)
- Yukiko Kuroda
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan.
| | - Hiroaki Murakami
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Takayuki Yokoi
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Tatsuro Kumaki
- Division of Neurology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yumi Enomoto
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yoshinori Tsurusaki
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan.
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Kim S, Park AK, Cho J. Early emergence of de novo EGFR T790M gatekeeper mutations during erlotinib treatment in PC9 non-small cell lung cancer cells. Biochem Biophys Res Commun 2018; 503:710-714. [PMID: 29909007 DOI: 10.1016/j.bbrc.2018.06.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 06/13/2018] [Indexed: 10/28/2022]
Abstract
The emergence of the T790M gatekeeper mutation in the Epidermal Growth Factor Receptor (EGFR) gene is an important mechanism that can lead to the acquired resistance to EGFR-targeted tyrosine kinase inhibitors such as erlotinib or gefitinib. These drugs have been used in treating a subset of non-small cell lung cancer (NSCLC) patients harboring EGFR activating mutations. Here we investigated the paths leading to the acquisition of the T790M mutation by establishing an erlotinib resistant PC9 cell model harboring ectopically introduced EGFR cDNA. We detected the emergence of T790M mutation within the EGFR cDNA in a subset of erlotinib resistant PC9 cell models through Sanger sequencing and droplet digital PCR-based methods, demonstrating that T790M mutation can emerge via de novo events following treatment with erlotinib. In addition, we show that the de novo T790M bearing erlotinib resistant PC9 cells are sensitive to the 3rd generation EGFR-targeted drug, WZ4002. Furthermore, GFP-based competition cell proliferation assays reveal that PC9 cells ectopically expressing EGFR mutant become more rapidly resistant to erlotinib than parental PC9 cells through the acquisition of the T790M mutation. Taken together, we believe that our findings expand upon the previous notion of evolutionary paths of T790M development, providing an important clue to designing a therapeutic strategy to overcome drug resistance.
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Affiliation(s)
- Sujin Kim
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea
| | - Angela Kj Park
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea
| | - Jeonghee Cho
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea.
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Munné S. Status of preimplantation genetic testing and embryo selection. Reprod Biomed Online 2018; 37:393-6. [PMID: 30232021 DOI: 10.1016/j.rbmo.2018.08.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/04/2018] [Accepted: 08/07/2018] [Indexed: 11/22/2022]
Abstract
At the recent 2018 PGDIS congress, a review of randomized controlled trials of preimplantation genetic testing for aneuploidies (PGT-A) showed improved ongoing pregnancy rates per transfer in experienced centres and in women aged 35 years and older. Young women produce 40% abnormal embryos (20-60% range), but not all centres see a selection advantage; this indicates the need for more emphasis in improving biopsy and case management. Some chromosome abnormalities are iatrogenic; PGT-A could, therefore, be used as assisted reproductive technology (ART) quality control. Great improvements in non-invasive PGT by testing spent media have been reported, ranging from 80-95% concordance with trophectoderm biopsy, probably precluding the need for biopsy soon. Mosaicism was widely discussed, with PGDIS agreeing to update their guidelines, but continuing to recommend prioritizing euploid, followed by mosaic embryos. Techniques to allow simultaneous single sample analysis of aneuploidy and inherited mutations are improving, but this does not extend to de-novo mutations. Convincing data were presented on the efficacy of using endometrial receptivity tests to improve ART outcomes adjuvant or independently of PGT-A. Imprinting, CRISPR and cloning were also discussed, with a concluding presentation on the first extensive data (aneuploidy and morphology) on in-vivo conceived embryos.
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Feng Y, Chen R, Da M, Qian B, Mo X. Identification of rare heterozygous missense mutations in FANCA in esophageal atresia patients using next-generation sequencing. Gene 2018; 661:182-8. [PMID: 29621589 DOI: 10.1016/j.gene.2018.03.097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/12/2018] [Accepted: 03/29/2018] [Indexed: 11/23/2022]
Abstract
Esophageal atresia and tracheoesophageal fistula (EA/TEF) are relatively common malformations in newborns, but the etiology of EA/TEF remains unknown. Fanconi anemia (FA) complementation group A (FANCA) is a key component of the FA core complex and is essential for the activation of the DNA repair pathway. The middle region (amino acids 674-1208) of FANCA is required for its interaction with FAAP20. We performed targeted sequencing of this binding region of FANCA (exons 23-36) in 40 EA/TEF patients. We also investigated the effect of the p.A958V mutation on the protein-protein interaction between FANCA and FAAP20 using an in vitro binding assay and co-immunoprecipitation. Immunolocalization analysis was performed to investigate the subcellular localization of FANCA, and tissue sections and immunohistochemistry were used to explore the expression of FANCA. We identified four rare missense variants in the FANCA binding region. FANCA mutations were significantly overrepresented in EA/TEF patients compared with 4300 control subjects from the NHLBI-ESP project (Fisher's exact p = 2.17 × 10-5, odds ratio = 31.75). p.A958V, a novel de novo mutation in the FANCA gene, was identified in one patient with EA/TEF. We provide further evidence that the p.A958V mutation reduces the binding affinity of FANCA for FAAP20. Interestingly, the p.A958V mutation impaired the nuclear localization of the FANCA protein expressed in HeLa cells. We found that FANCA was more highly expressed in stratified squamous epithelium than in smooth muscle. In conclusion, mutations in the FANCA gene are associated with EA/TEF in humans.
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Zhou X, Batzoglou S, Sidow A, Zhang L. HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data. BMC Genomics 2018; 19:467. [PMID: 29914369 PMCID: PMC6006847 DOI: 10.1186/s12864-018-4867-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 06/13/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND De novo mutations (DNMs) are associated with neurodevelopmental and congenital diseases, and their detection can contribute to understanding disease pathogenicity. However, accurate detection is challenging because of their small number relative to the genome-wide false positives in next generation sequencing (NGS) data. Software such as DeNovoGear and TrioDeNovo have been developed to detect DNMs, but at good sensitivity they still produce many false positive calls. RESULTS To address this challenge, we develop HAPDeNovo, a program that leverages phasing information from linked read sequencing, to remove false positive DNMs from candidate lists generated by DNM-detection tools. Short reads from each phasing block are allocated to each of the two haplotypes followed by generating a haploid genotype for each putative DNM. HAPDeNovo removes variants that are called as heterozygous in one of the haplotypes because they are almost certainly false positives. Our experiments on 10X Chromium linked read sequencing trio data reveal that HAPDeNovo eliminates 80 to 99% of false positives regardless of how large the candidate DNM set is. CONCLUSIONS HAPDeNovo leverages the haplotype information from linked read sequencing to remove spurious false positive DNMs effectively, and it increases accuracy of DNM detection dramatically without sacrificing sensitivity.
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Affiliation(s)
- Xin Zhou
- Department of Computer Science, Stanford University, Stanford, California, 94305, USA
| | - Serafim Batzoglou
- Department of Computer Science, Stanford University, Stanford, California, 94305, USA
| | - Arend Sidow
- Department of Pathology, Stanford University School of Medicine, Stanford, California, 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Lu Zhang
- Department of Computer Science, Stanford University, Stanford, California, 94305, USA. .,Department of Pathology, Stanford University School of Medicine, Stanford, California, 94305, USA.
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