1
|
Auwerx C, Kutalik Z, Reymond A. The pleiotropic spectrum of proximal 16p11.2 CNVs. Am J Hum Genet 2024:S0002-9297(24)00301-X. [PMID: 39332410 DOI: 10.1016/j.ajhg.2024.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 08/18/2024] [Accepted: 08/21/2024] [Indexed: 09/29/2024] Open
Abstract
Recurrent genomic rearrangements at 16p11.2 BP4-5 represent one of the most common causes of genomic disorders. Originally associated with increased risk for autism spectrum disorder, schizophrenia, and intellectual disability, as well as adiposity and head circumference, these CNVs have since been associated with a plethora of phenotypic alterations, albeit with high variability in expressivity and incomplete penetrance. Here, we comprehensively review the pleiotropy associated with 16p11.2 BP4-5 rearrangements to shine light on its full phenotypic spectrum. Illustrating this phenotypic heterogeneity, we expose many parallels between findings gathered from clinical versus population-based cohorts, which often point to the same physiological systems, and emphasize the role of the CNV beyond neuropsychiatric and anthropometric traits. Revealing the complex and variable clinical manifestations of this CNV is crucial for accurate diagnosis and personalized treatment strategies for carrier individuals. Furthermore, we discuss areas of research that will be key to identifying factors contributing to phenotypic heterogeneity and gaining mechanistic insights into the molecular pathways underlying observed associations, while demonstrating how diversity in affected individuals, cohorts, experimental models, and analytical approaches can catalyze discoveries.
Collapse
Affiliation(s)
- Chiara Auwerx
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
| |
Collapse
|
2
|
Yue F, Hao M, Jiang D, Liu R, Zhang H. Prenatal phenotypes and pregnancy outcomes of fetuses with 16p11.2 microdeletion/microduplication. BMC Pregnancy Childbirth 2024; 24:494. [PMID: 39039444 PMCID: PMC11265082 DOI: 10.1186/s12884-024-06702-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024] Open
Abstract
BACKGROUND Chromosomal 16p11.2 deletions and duplications are genomic disorders which are characterized by neurobehavioral abnormalities, obesity, congenital abnormalities. However, the prenatal phenotypes associated with 16p11.2 copy number variations (CNVs) have not been well characterized. This study aimed to provide an elaborate summary of intrauterine phenotypic features for these genomic disorders. METHODS Twenty prenatal amniotic fluid samples diagnosed with 16p11.2 microdeletions/microduplications were obtained from pregnant women who opted for invasive prenatal testing. Karyotypic analysis and chromosomal microarray analysis (CMA) were performed in parallel. The pregnancy outcomes and health conditions of all cases after birth were followed up. Meanwhile, we made a pooled analysis of the prenatal phenotypes in the published cases carrying 16p11.2 CNVs. RESULTS 20 fetuses (20/20,884, 0.10%) with 16p11.2 CNVs were identified: five had 16p11.2 BP2-BP3 deletions, 10 had 16p11.2 BP4-BP5 deletions and five had 16p11.2 BP4-BP5 duplications. Abnormal ultrasound findings were recorded in ten fetuses with 16p11.2 deletions, with various degrees of intrauterine phenotypic features observed. No ultrasound abnormalities were observed in any of the 16p11.2 duplications cases during the pregnancy period. Eleven cases with 16p11.2 deletions terminated their pregnancies. For 16p11.2 duplications, four cases gave birth to healthy neonates except for one case that was lost to follow-up. CONCLUSIONS Diverse prenatal phenotypes, ranging from normal to abnormal, were observed in cases with 16p11.2 CNVs. For 16p11.2 BP4-BP5 deletions, abnormalities of the vertebral column or ribs and thickened nuchal translucency were the most common structural and non-structural abnormalities, respectively. 16p11.2 BP2-BP3 deletions might be closely associated with fetal growth restriction and single umbilical artery. No characteristic ultrasound findings for 16p11.2 duplications have been observed to date. Given the variable expressivity and incomplete penetrance of 16p11.2 CNVs, long-term follow-up after birth should be conducted for these cases.
Collapse
Affiliation(s)
- Fagui Yue
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China
| | - Mengzhe Hao
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China
| | - Dandan Jiang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China
| | - Ruizhi Liu
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China
| | - Hongguo Zhang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China.
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China.
| |
Collapse
|
3
|
Szoszkiewicz A, Bukowska-Olech E, Jamsheer A. Molecular landscape of congenital vertebral malformations: recent discoveries and future directions. Orphanet J Rare Dis 2024; 19:32. [PMID: 38291488 PMCID: PMC10829358 DOI: 10.1186/s13023-024-03040-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/19/2024] [Indexed: 02/01/2024] Open
Abstract
Vertebral malformations (VMs) pose a significant global health problem, causing chronic pain and disability. Vertebral defects occur as isolated conditions or within the spectrum of various congenital disorders, such as Klippel-Feil syndrome, congenital scoliosis, spondylocostal dysostosis, sacral agenesis, and neural tube defects. Although both genetic abnormalities and environmental factors can contribute to abnormal vertebral development, our knowledge on molecular mechanisms of numerous VMs is still limited. Furthermore, there is a lack of resource that consolidates the current knowledge in this field. In this pioneering review, we provide a comprehensive analysis of the latest research on the molecular basis of VMs and the association of the VMs-related causative genes with bone developmental signaling pathways. Our study identifies 118 genes linked to VMs, with 98 genes involved in biological pathways crucial for the formation of the vertebral column. Overall, the review summarizes the current knowledge on VM genetics, and provides new insights into potential involvement of biological pathways in VM pathogenesis. We also present an overview of available data regarding the role of epigenetic and environmental factors in VMs. We identify areas where knowledge is lacking, such as precise molecular mechanisms in which specific genes contribute to the development of VMs. Finally, we propose future research avenues that could address knowledge gaps.
Collapse
Affiliation(s)
- Anna Szoszkiewicz
- Department of Medical Genetics, Poznan University of Medical Sciences, Rokietnicka 8, 60-806, Poznan, Poland.
| | - Ewelina Bukowska-Olech
- Department of Medical Genetics, Poznan University of Medical Sciences, Rokietnicka 8, 60-806, Poznan, Poland
| | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Rokietnicka 8, 60-806, Poznan, Poland.
- Centers for Medical Genetics GENESIS, Dąbrowskiego 77A, 60-529, Poznan, Poland.
| |
Collapse
|
4
|
Pollak RM, Tilmon JC, Murphy MM, Gambello MJ, Sanchez Russo R, Dormans JP, Mulle JG. Musculoskeletal phenotypes in 3q29 deletion syndrome. Am J Med Genet A 2023; 191:2749-2756. [PMID: 37691301 PMCID: PMC10662927 DOI: 10.1002/ajmg.a.63384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/20/2023] [Accepted: 08/10/2023] [Indexed: 09/12/2023]
Abstract
3q29 deletion syndrome (3q29del) is a rare genomic disorder caused by a 1.6 Mb deletion (hg19, chr3:195725000-197350000). 3q29del is associated with neurodevelopmental and psychiatric phenotypes, including an astonishing >40-fold increased risk for schizophrenia, but medical phenotypes are less well-described. We used the online 3q29 registry of 206 individuals (3q29deletion.org) to recruit 57 individuals with 3q29del (56.14% male) and requested information about musculoskeletal phenotypes with a custom questionnaire. 85.96% of participants with 3q29del reported at least one musculoskeletal phenotype. Congenital anomalies were most common (70.18%), with pes planus (40.35%), pectus excavatum (22.81%), and pectus carinatum (5.26%) significantly elevated relative to the pediatric general population. 49.12% of participants reported fatigue after 30 min or less of activity. Bone fractures (8.77%) were significantly elevated relative to the pediatric general population. Participants commonly report receiving medical care for musculoskeletal complaints (71.93%), indicating that these phenotypes impact quality of life for individuals with 3q29del. This is the most comprehensive description of musculoskeletal phenotypes in 3q29del to date, suggests ideas for clinical evaluation, and expands our understanding of the phenotypic spectrum of this syndrome.
Collapse
Affiliation(s)
- Rebecca M Pollak
- Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, USA
| | - Jacob C Tilmon
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Melissa M Murphy
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Michael J Gambello
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Rossana Sanchez Russo
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - John P Dormans
- Emeritus Professor of Orthopedic Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jennifer G Mulle
- Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, USA
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, USA
| |
Collapse
|
5
|
Chen Y, Zhang Z, Zhu Q. The effect of an exercise intervention on adolescent idiopathic scoliosis: a network meta-analysis. J Orthop Surg Res 2023; 18:655. [PMID: 37667353 PMCID: PMC10476432 DOI: 10.1186/s13018-023-04137-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/25/2023] [Indexed: 09/06/2023] Open
Abstract
PURPOSE To explore the effect of exercise intervention on adolescent idiopathic scoliosis (AIS), various exercise forms were compared and the sequence of the possibility of improving the effect of each exercise form was sorted out. We expect that our findings will provide clinicians and patients with more effective treatments and references. METHOD A thorough search was done on CNKI, Wanfang, WOS, Cochrane library, Embase, PubMed, Scopus and obtained the publication time from the database establishment to May 6, 2023. The relevant contents of the literature that passed the screening criteria were extracted, including relevant information about the sample, first author, intervention measures, intervention time, and outcome indicators. Analysis was performed by Review Manager 5.4 and Stata17.0. RESULT The study finally included 12 articles with 538 samples. After comparison, it was found that exercise interventions to reduce Cobb's angle were more effective than conventional therapies and reached a statistically significant difference. Compared with conventional therapy, core strength training, Physiotherapeutic Scoliosis-Specific Exercise (PSSE), yoga, Schroth, and sling reduced the Cobb angle by an average of 3.82 degrees, 3.79 degrees, 4.60 degrees, 3.63 degrees, and 3.30 degrees, respectively. However, the therapeutic effects on AIS did not show statistically significant differences between the exercise interventions. According to the SUCRA value and the cumulative probability, the MeanRank of improving the AIS effect by various sports intervention measures as follows: yoga (2.2), core strength training (2.8), PSSE (2.8), Schroth exercise (3.2), and sling exercise (4.0). CONCLUSION Exercise intervention can significantly improve AIS. There was no significant difference in the improvement effect of AIS among different exercise forms. Yoga may have the best effect on AIS improvement.
Collapse
Affiliation(s)
- Yonghuan Chen
- Department of Physical Education, Pukyong National University, Busan, South Korea
- School of Physical Education, Zhengzhou University, Zhengzhou, China
| | - Zhendong Zhang
- School of Physical Education, Zhengzhou Sias University, Zhengzhou, Henan, China
| | - Qiuhan Zhu
- School of Physical Education, Zhengzhou University, Zhengzhou, China.
| |
Collapse
|
6
|
Pollak RM, Tilmon JC, Murphy MM, Gambello MJ, Russo RS, Dormans JP, Mulle JG. Musculoskeletal phenotypes in 3q29 deletion syndrome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.03.23288084. [PMID: 37066183 PMCID: PMC10104205 DOI: 10.1101/2023.04.03.23288084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
3q29 deletion syndrome (3q29del) is a rare genomic disorder caused by a 1.6 Mb deletion (hg19, chr3:195725000â€"197350000). 3q29del is associated with neurodevelopmental and psychiatric phenotypes, including an astonishing >40-fold increased risk for schizophrenia, but medical phenotypes are less well-described. We used the online 3q29 registry ( 3q29deletion.org ) to recruit 57 individuals with 3q29del (56.14% male) and requested information about musculoskeletal phenotypes with a custom questionnaire. 85.96% of participants with 3q29del reported at least one musculoskeletal phenotype. Congenital anomalies were most common (70.18%), with pes planus (40.35%), pectus excavatum (22.81%), and pectus carinatum (5.26%) significantly elevated relative to the pediatric general population. 49.12% of participants reported fatigue after 30 minutes or less of activity. Bone fractures (8.77%) were significantly elevated relative to the pediatric general population, suggesting 3q29del impacts bone strength. Participants commonly report receiving medical care for musculoskeletal complaints (71.93%), indicating that these phenotypes impact quality of life for individuals with 3q29del. This is the most comprehensive description of musculoskeletal phenotypes in 3q29del to date, suggests ideas for clinical evaluation, and expands our understanding of the phenotypic spectrum of this syndrome.
Collapse
Affiliation(s)
- Rebecca M Pollak
- Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University
| | | | | | | | | | - John P Dormans
- Emeritus Professor of Orthopedic Surgery, University of Pennsylvania
| | - Jennifer G Mulle
- Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University
| |
Collapse
|
7
|
Liu N, Li H, Li M, Gao Y, Yan H. Prenatally diagnosed 16p11.2 copy number variations by SNP Array: A retrospective case series. Clin Chim Acta 2023; 538:15-21. [PMID: 36374846 DOI: 10.1016/j.cca.2022.10.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 01/12/2023]
Abstract
OBJECTIVE The 16p11.2 copy number variations (CNVs) are increasingly recognized as one of the most frequent genomic disorders, with a broad spectrum of phenotypes. The fetal phenotype associated with 16p11.2 CNVs is poorly described. The current study presents prenatal series of 16p11.2 CNVs and provides a better understanding of this submicroscopic imbalance in prenatal diagnosis. METHOD Retrospective case series were extracted from a single tertiary referral center performing prenatal single nucleotide polymorphism (SNP) array from April 2017 to December 2021. The maternal demographics, indication for amniocentesis, ultrasound findings, SNP array results, inheritance of the CNVs, and pregnancy outcomes were studied. RESULTS We indentified 30 fetuses carrying 16p11.2 CNVs, representing 0.35% (30/8578) of prenatal SNP array results. The series included 17 fetuses with a proximal deletion, 7 with a distal deletion, 4 with a proximal duplication, and 2 with a distal duplication. Prenatal ultrasound anomalies were reported in 80% of these cases. The most common presentation was vertebralanomalies (9/30). Other features noted in more than one fetus were increased nuchal translucency/nuchal fold (NT/NF) (5/30), absent/hypoplastic nasal bone (3/30), polyhydramnios (3/30), ventricular septal defect (VSD) (2/30), unilateral mild ventriculomegaly (2/30), fetal growth restriction (FGR) (2/30), right aortic arch (2/30). All the 9 vertebralanomalies were present in fetuses harboring proximal deletion (9/17). Familial transmission was confirmed in 44% of cases (11/25) and termination of pregnancy was requested in 62.1% (18/29) of cases. CONCLUSION The 16p11.2 CNVs can have variable prenatal phenotypes and these CNVs are frequently inherited from parents with a milder or normal phenotype. Our results underline that vertebral deformities were frequent in cases of 16p11.2 proximal deletion, and further demonstrate the incomplete penetrance of the CNVs.
Collapse
Affiliation(s)
- Nian Liu
- Department of Health Toxicology, MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Prenatal Diagnostic Center, Genetic Lab, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Li
- Prenatal Diagnostic Center, Genetic Lab, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Manman Li
- Prenatal Diagnostic Center, Genetic Lab, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanduo Gao
- Department of Ultrasound, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hong Yan
- Department of Health Toxicology, MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
8
|
Li G, Strong A, Wang H, Kim JS, Watson D, Zhao S, Vaccaro C, Hartung E, Hakonarson H, Zhang TJ, Giampietro PF, Wu N. TBX6 as a cause of a combined skeletal-kidney dysplasia syndrome. Am J Med Genet A 2022; 188:3469-3481. [PMID: 36161696 PMCID: PMC10473889 DOI: 10.1002/ajmg.a.62972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/24/2022] [Accepted: 08/06/2022] [Indexed: 01/31/2023]
Abstract
TBX6 encodes transcription-factor box 6, a transcription factor critical to paraxial mesoderm segmentation and somitogenesis during embryonic development. TBX6 haploinsufficiency is believed to drive the skeletal and kidney phenotypes associated with the 16p11.2 deletion syndrome. Heterozygous and biallelic variants in TBX6 are associated with vertebral and rib malformations (TBX6-associated congenital scoliosis) and spondylocostal dysostosis, and heterozygous TBX6 variants are associated with increased risk of genitourinary tract malformations. Combined skeletal and kidney phenotypes in individuals harboring heterozygous or biallelic TBX6 variants are rare. Here, we present seven individuals with vertebral and rib malformations and structural kidney differences associated with heterozygous TBX6 gene deletion in trans with a hypomorphic TBX6 allele or biallelic TBX6 variants. Our case series highlights the association between TBX6 and both skeletal and kidney disease.
Collapse
Affiliation(s)
- Guozhuang Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Alanna Strong
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Haojun Wang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Ji-Sun Kim
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical Center, New Brunswick, NJ
| | - Deborah Watson
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Courtney Vaccaro
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Erum Hartung
- Division of Nephrology, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Hakon Hakonarson
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Division of Pulmonary Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Philip F. Giampietro
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical Center, New Brunswick, NJ
- Department of Pediatrics, University of Illinois-Chicago, Chicago, IL
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| |
Collapse
|
9
|
Possible association of 16p11.2 copy number variation with altered lymphocyte and neutrophil counts. NPJ Genom Med 2022; 7:38. [PMID: 35715439 PMCID: PMC9205872 DOI: 10.1038/s41525-022-00308-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 05/23/2022] [Indexed: 11/09/2022] Open
Abstract
Recurrent copy-number variations (CNVs) at chromosome 16p11.2 are associated with neurodevelopmental diseases, skeletal system abnormalities, anemia, and genitourinary defects. Among the 40 protein-coding genes encompassed within the rearrangement, some have roles in leukocyte biology and immunodeficiency, like SPN and CORO1A. We therefore investigated leukocyte differential counts and disease in 16p11.2 CNV carriers. In our clinically-recruited cohort, we identified three deletion carriers from two families (out of 32 families assessed) with neutropenia and lymphopenia. They had no deleterious single-nucleotide or indel variant in known cytopenia genes, suggesting a possible causative role of the deletion. Noticeably, all three individuals had the lowest copy number of the human-specific BOLA2 duplicon (copy-number range: 3–8). Consistent with the lymphopenia and in contrast with the neutropenia associations, adult deletion carriers from UK biobank (n = 74) showed lower lymphocyte (Padj = 0.04) and increased neutrophil (Padj = 8.31e-05) counts. Mendelian randomization studies pinpointed to reduced CORO1A, KIF22, and BOLA2-SMG1P6 expressions being causative for the lower lymphocyte counts. In conclusion, our data suggest that 16p11.2 deletion, and possibly also the lowest dosage of the BOLA2 duplicon, are associated with low lymphocyte counts. There is a trend between 16p11.2 deletion with lower copy-number of the BOLA2 duplicon and higher susceptibility to moderate neutropenia. Higher numbers of cases are warranted to confirm the association with neutropenia and to resolve the involvement of the deletion coupled with deleterious variants in other genes and/or with the structure and copy number of segments in the CNV breakpoint regions.
Collapse
|
10
|
Identification of Copy Number Variants in a Southern Chinese Cohort of Patients with Congenital Scoliosis. Genes (Basel) 2021; 12:genes12081213. [PMID: 34440387 PMCID: PMC8391542 DOI: 10.3390/genes12081213] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/01/2021] [Accepted: 08/03/2021] [Indexed: 12/15/2022] Open
Abstract
Congenital scoliosis (CS) is a lateral curvature of the spine resulting from congenital vertebral malformations (CVMs) and affects 0.5–1/1000 live births. The copy number variant (CNV) at chromosome 16p11.2 has been implicated in CVMs and recent studies identified a compound heterozygosity of 16p11.2 microdeletion and TBX6 variant/haplotype causing CS in multiple cohorts, which explains about 5–10% of the affected cases. Here, we studied the genetic etiology of CS by analyzing CNVs in a cohort of 67 patients with congenital hemivertebrae and 125 family controls. We employed both candidate gene and family-based approaches to filter CNVs called from whole exome sequencing data. This identified 12 CNVs in four scoliosis-associated genes (TBX6, NOTCH2, DSCAM, and SNTG1) as well as eight recessive and 64 novel rare CNVs in 15 additional genes. Some candidates, such as DHX40, NBPF20, RASA2, and MYSM1, have been found to be associated with syndromes with scoliosis or implicated in bone/spine development. In particular, the MYSM1 mutant mouse showed spinal deformities. Our findings suggest that, in addition to the 16p11.2 microdeletion, other CNVs are potentially important in predisposing to CS.
Collapse
|
11
|
Chu C, Wu H, Xu F, Ray JW, Britt A, Robinson SS, Lupo PJ, Murphy CRC, Dreyer CF, Lee PDK, Hu PC, Dong J. Phenotypes Associated with 16p11.2 Copy Number Gains and Losses at a Single Institution. Lab Med 2021; 51:642-648. [PMID: 32537635 DOI: 10.1093/labmed/lmaa026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chromosome 16p11.2 is one of the susceptible sites for recurrent copy number variations (CNVs) due to flanking near-identical segmental duplications. Five segmental duplications, named breakpoints 1 to 5 (BP1-BP5), have been defined as recombination hotspots within 16p11.2. Common CNVs on 16p11.2 include a proximal ~593 kb between BP4 and BP5, and a distal ~220 kb between BP2 and BP3. We performed a search for patients carrying 16p11.2 CNVs, as detected using chromosome microarray (CMA), in the Molecular Diagnostic Laboratory at the University of Texas Medical Branch (UTMB), in Galveston. From March 2013 through April 2018, a total of 1200 CMA results were generated for germline testing, and 14 patients tested positive for 16p11.2 CNVs, of whom 7 had proximal deletion, 2 had distal deletion, 4 had proximal duplication, and 1 had distal duplication. Herein, we provide detailed phenotype data for these patients. Our study results show that developmental delay, abnormal body weight, behavioral problems, and hypotonia are common phenotypes associated with 16p11.2 CNVs.
Collapse
Affiliation(s)
- Caleb Chu
- School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Haotian Wu
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| | - Fangling Xu
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| | - Joseph W Ray
- Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas
| | - Allison Britt
- Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas
| | - Sally S Robinson
- Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas
| | - Pamela J Lupo
- Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas
| | | | - Charles F Dreyer
- Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas
| | - Phillip D K Lee
- Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas
| | - Peter C Hu
- School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianli Dong
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| |
Collapse
|
12
|
Giovanniello J, Ahrens S, Yu K, Li B. Sex-Specific Stress-Related Behavioral Phenotypes and Central Amygdala Dysfunction in a Mouse Model of 16p11.2 Microdeletion. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2021; 1:59-69. [PMID: 36324434 PMCID: PMC9616311 DOI: 10.1016/j.bpsgos.2021.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/08/2021] [Accepted: 01/26/2021] [Indexed: 12/27/2022] Open
Abstract
Background Substantial evidence indicates that a microdeletion on human chromosome 16p11.2 is linked to neurodevelopmental disorders, including autism spectrum disorder (ASD). Carriers of this deletion show divergent symptoms besides the core features of autism spectrum disorder, such as anxiety and emotional symptoms. The neural mechanisms underlying these symptoms are poorly understood. Methods We used mice heterozygous for a deletion allele of the genomic region corresponding to the human 16p11.2 microdeletion locus (i.e., 16p11.2 del/+ mice) and their sex-matched wild-type littermates for the study and examined their anxiety-related behaviors, auditory perception, and central amygdala circuit function using behavioral, circuit tracing, and electrophysiological techniques. Results Mice heterozygous for a deletion allele of the genomic region corresponding to the human 16p11.2 microdeletion locus (i.e., 16p11.2 del/+ mice) had sex-specific anxiety-related behavioral and neural circuit changes. Specifically, we found that female, but not male, 16p11.2 del/+ mice showed enhanced fear generalization-a hallmark of anxiety disorders-after auditory fear conditioning and displayed increased anxiety-like behaviors after physical restraint stress. Notably, such sex-specific behavioral changes were paralleled by an increase in activity in central amygdala neurons projecting to the globus pallidus in female, but not male, 16p11.2 del/+ mice. Conclusions Together, these results reveal female-specific anxiety phenotypes related to 16p11.2 microdeletion syndrome and a potential underlying neural circuit mechanism. Our study therefore identifies previously underappreciated sex-specific behavioral and neural changes in a genetic model of 16p11.2 microdeletion syndrome and highlights the importance of investigating female-specific aspects of this syndrome for targeted treatment strategies.
Collapse
Affiliation(s)
- Jacqueline Giovanniello
- School of Biological Sciences, Cold Spring Harbor, New York
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Sandra Ahrens
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Kai Yu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Bo Li
- School of Biological Sciences, Cold Spring Harbor, New York
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| |
Collapse
|
13
|
Cai M, Huang H, Xu L, Lin N. Clinical Utility and the Yield of Single Nucleotide Polymorphism Array in Prenatal Diagnosis of Fetal Central Nervous System Abnormalities. Front Mol Biosci 2021; 8:666115. [PMID: 34084776 PMCID: PMC8167038 DOI: 10.3389/fmolb.2021.666115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/05/2021] [Indexed: 11/22/2022] Open
Abstract
Applying single nucleotide polymorphism (SNP) array to identify the etiology of fetal central nervous system (CNS) abnormality, and exploring its association with chromosomal abnormalities, copy number variations, and obstetrical outcome. 535 fetuses with CNS abnormalities were analyzed using karyotype analysis and SNP array. Among the 535 fetuses with CNS abnormalities, chromosomal abnormalities were detected in 36 (6.7%) of the fetuses, which were consistent with karyotype analysis. Further, additional 41 fetuses with abnormal copy number variations (CNVs) were detected using SNP array (the detection rate of additional abnormal CNVs was 7.7%). The rate of chromosomal abnormalities, but not that of pathogenic CNVs in CNS abnormalities with other ultrasound abnormalities was significantly higher than that in isolated CNS abnormalities. The rates of chromosomal abnormalities and pathogenic CNVs in fetuses with spine malformation (50%), encephalocele (50%), subependymal cyst (20%), and microcephaly (16.7%) were higher than those with other isolated CNS abnormalities. The pregnancies for 36 cases with chromosomal abnormalities, 18 cases with pathogenic CNVs, and three cases with VUS CNVs were terminated. SNP array should be used in the prenatal diagnosis of fetuses with CNS abnormalities, which can enable better prenatal assessment and genetic counseling, and affect obstetrical outcomes.
Collapse
Affiliation(s)
| | | | - Liangpu Xu
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| |
Collapse
|
14
|
Verbitsky M, Krithivasan P, Batourina E, Khan A, Graham SE, Marasà M, Kim H, Lim TY, Weng PL, Sánchez-Rodríguez E, Mitrotti A, Ahram DF, Zanoni F, Fasel DA, Westland R, Sampson MG, Zhang JY, Bodria M, Kil BH, Shril S, Gesualdo L, Torri F, Scolari F, Izzi C, van Wijk JA, Saraga M, Santoro D, Conti G, Barton DE, Dobson MG, Puri P, Furth SL, Warady BA, Pisani I, Fiaccadori E, Allegri L, Degl'Innocenti ML, Piaggio G, Alam S, Gigante M, Zaza G, Esposito P, Lin F, Simões-e-Silva AC, Brodkiewicz A, Drozdz D, Zachwieja K, Miklaszewska M, Szczepanska M, Adamczyk P, Tkaczyk M, Tomczyk D, Sikora P, Mizerska-Wasiak M, Krzemien G, Szmigielska A, Zaniew M, Lozanovski VJ, Gucev Z, Ionita-Laza I, Stanaway IB, Crosslin DR, Wong CS, Hildebrandt F, Barasch J, Kenny EE, Loos RJ, Levy B, Ghiggeri GM, Hakonarson H, Latos-Bieleńska A, Materna-Kiryluk A, Darlow JM, Tasic V, Willer C, Kiryluk K, Sanna-Cherchi S, Mendelsohn CL, Gharavi AG. Copy Number Variant Analysis and Genome-wide Association Study Identify Loci with Large Effect for Vesicoureteral Reflux. J Am Soc Nephrol 2021; 32:805-820. [PMID: 33597122 PMCID: PMC8017540 DOI: 10.1681/asn.2020050681] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/04/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Vesicoureteral reflux (VUR) is a common, familial genitourinary disorder, and a major cause of pediatric urinary tract infection (UTI) and kidney failure. The genetic basis of VUR is not well understood. METHODS A diagnostic analysis sought rare, pathogenic copy number variant (CNV) disorders among 1737 patients with VUR. A GWAS was performed in 1395 patients and 5366 controls, of European ancestry. RESULTS Altogether, 3% of VUR patients harbored an undiagnosed rare CNV disorder, such as the 1q21.1, 16p11.2, 22q11.21, and triple X syndromes ((OR, 3.12; 95% CI, 2.10 to 4.54; P=6.35×10-8) The GWAS identified three study-wide significant and five suggestive loci with large effects (ORs, 1.41-6.9), containing canonical developmental genes expressed in the developing urinary tract (WDPCP, OTX1, BMP5, VANGL1, and WNT5A). In particular, 3.3% of VUR patients were homozygous for an intronic variant in WDPCP (rs13013890; OR, 3.65; 95% CI, 2.39 to 5.56; P=1.86×10-9). This locus was associated with multiple genitourinary phenotypes in the UK Biobank and eMERGE studies. Analysis of Wnt5a mutant mice confirmed the role of Wnt5a signaling in bladder and ureteric morphogenesis. CONCLUSIONS These data demonstrate the genetic heterogeneity of VUR. Altogether, 6% of patients with VUR harbored a rare CNV or a common variant genotype conferring an OR >3. Identification of these genetic risk factors has multiple implications for clinical care and for analysis of outcomes in VUR.
Collapse
Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Sarah E. Graham
- Department of Internal Medicine, Cardiology, University of Michigan, Ann Arbor, Michigan
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Hyunwoo Kim
- Department of Urology, Columbia University, New York, New York
| | - Tze Y. Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Patricia L. Weng
- Department of Pediatric Nephrology, University of California, Los Angeles Medical Center and University of California, Los Angeles Medical Center-Santa Monica, Los Angeles, California
| | | | - Adele Mitrotti
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Dina F. Ahram
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Francesca Zanoni
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - David A. Fasel
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Rik Westland
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Pediatric Nephrology, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Matthew G. Sampson
- Division of Nephrology, Boston Children’s Hospital, Boston, Massachusetts
| | - Jun Y. Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Monica Bodria
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Byum Hee Kil
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Shirlee Shril
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Fabio Torri
- Department of Pediatric Surgery, Spedali Civili Children’s Hospital of Brescia, Brescia, Italy
| | - Francesco Scolari
- Chair and Division of Nephrology, University and Spedali Civili Hospital, Brescia, Italy
| | - Claudia Izzi
- Division of Nephrology and Department of Obstetrics and Gynecology, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Joanna A.E. van Wijk
- Department of Pediatric Nephrology, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
| | - Domenico Santoro
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Giovanni Conti
- Department of Pediatric Nephrology, Azienda Ospedaliera Universitaria “G. Martino,” Messina, Italy
| | - David E. Barton
- University College Dublin School of Medicine, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Mark G. Dobson
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Prem Puri
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- Department of Pediatric Surgery, Beacon Hospital, University College Dublin, Dublin, Ireland
| | - Susan L. Furth
- Division of Nephrology, Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Bradley A. Warady
- Division of Nephrology, Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Children’s Mercy Kansas City, Kansas City, Missouri
| | - Isabella Pisani
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Enrico Fiaccadori
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Landino Allegri
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Maria Ludovica Degl'Innocenti
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Giorgio Piaggio
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Shumyle Alam
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, New York
| | - Maddalena Gigante
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Gianluigi Zaza
- Renal and Dialysis Unit, Department of Medicine, School of Medicine, University of Verona, Verona, Italy
| | - Pasquale Esposito
- Department of Internal Medicine, Nephrology, Dialysis and Transplantation Clinics, Genoa University and IRCCS Policlinico San Martino, Genova, Italy
| | - Fangming Lin
- Division of Pediatric Nephrology, Department of Pediatrics, Columbia University, New York, New York
| | - Ana Cristina Simões-e-Silva
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Andrzej Brodkiewicz
- Department of Pediatrics, Child Nephrology, Dialysotheraphy and Management of Acute Poisoning, Pomeranian Medical University, Szczecin, Poland
| | - Dorota Drozdz
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Zachwieja
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Maria Szczepanska
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Piotr Adamczyk
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Daria Tomczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology, Medical University of Lublin, Lublin, Poland
| | | | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Poland
| | | | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Vladimir J. Lozanovski
- University Clinic for General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Zoran Gucev
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | | | - Ian B. Stanaway
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Washington
| | - David R. Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Washington
| | - Craig S. Wong
- Division of Pediatric Nephrology, University of New Mexico Children’s Hospital, Albuquerque, New Mexico
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan Barasch
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Urology, Columbia University, New York, New York
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna Latos-Bieleńska
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - John M. Darlow
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Velibor Tasic
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Cristen Willer
- Department of Internal Medicine, Cardiology, University of Michigan, Ann Arbor, Michigan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, Ann Arbor, Michigan
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| |
Collapse
|
15
|
Ren X, Yang N, Wu N, Xu X, Chen W, Zhang L, Li Y, Du RQ, Dong S, Zhao S, Chen S, Jiang LP, Wang L, Zhang J, Wu Z, Jin L, Qiu G, Lupski JR, Shi J, Zhang F, Liu P. Increased TBX6 gene dosages induce congenital cervical vertebral malformations in humans and mice. J Med Genet 2020; 57:371-379. [PMID: 31888956 PMCID: PMC9179029 DOI: 10.1136/jmedgenet-2019-106333] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND Congenital vertebral malformations (CVMs) manifest with abnormal vertebral morphology. Genetic factors have been implicated in CVM pathogenesis, but the underlying pathogenic mechanisms remain unclear in most subjects. We previously reported that the human 16p11.2 BP4-BP5 deletion and its associated TBX6 dosage reduction caused CVMs. We aim to investigate the reciprocal 16p11.2 BP4-BP5 duplication and its potential genetic contributions to CVMs. METHODS AND RESULTS Patients who were found to carry the 16p11.2 BP4-BP5 duplication by chromosomal microarray analysis were retrospectively analysed for their vertebral phenotypes. The spinal assessments in seven duplication carriers showed that four (57%) presented characteristics of CVMs, supporting the contention that increased TBX6 dosage could induce CVMs. For further in vivo functional investigation in a model organism, we conducted genome editing of the upstream regulatory region of mouse Tbx6 using CRISPR-Cas9 and obtained three mouse mutant alleles (Tbx6up1 to Tbx6up3 ) with elevated expression levels of Tbx6. Luciferase reporter assays showed that the Tbx6up3 allele presented with the 160% expression level of that observed in the reference (+) allele. Therefore, the homozygous Tbx6up3/up3 mice could functionally mimic the TBX6 dosage of heterozygous carriers of 16p11.2 BP4-BP5 duplication (approximately 150%, ie, 3/2 gene dosage of the normal level). Remarkably, 60% of the Tbx6up3/up3 mice manifested with CVMs. Consistent with our observations in humans, the CVMs induced by increased Tbx6 dosage in mice mainly affected the cervical vertebrae. CONCLUSION Our findings in humans and mice consistently support that an increased TBX6 dosage contributes to the risk of developing cervical CVMs.
Collapse
Affiliation(s)
- Xiaojun Ren
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Nan Yang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ximing Xu
- Department of Orthopedic Surgery, Spine Center, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Weisheng Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ling Zhang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Yingping Li
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
| | - Ren-Qian Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Shuangshuang Dong
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Shuxia Chen
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
| | - Li-Ping Jiang
- State key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, China
| | - Lianlei Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Li Jin
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Jiangang Shi
- Department of Orthopedic Surgery, Spine Center, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics, Houston, Texas, USA
| |
Collapse
|
16
|
Liu G, Shen J, Chen C, Jiao Y, Li Z, Tan H, Lin Y, Rong T. Genome-Wide Analysis of circular RNAs and validation of hsa_circ_0006719 as a potential novel diagnostic biomarker in congenital scoliosis patients. J Cell Mol Med 2020; 24:7015-7022. [PMID: 32394619 PMCID: PMC7299707 DOI: 10.1111/jcmm.15370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/31/2020] [Accepted: 04/22/2020] [Indexed: 01/01/2023] Open
Abstract
Congenital scoliosis (CS) is a form of spinal curvature resulting from anomalous development of vertebrae. Recent studies demonstrated that circRNAs could serve as potential biomarkers of disease diagnosis. Genome‐wide circRNAs expression in seven CS patients and three healthy controls was initially detected. Bioinformatics analysis was conducted to explore the potential pathological pathway of CS. Quantitative PCR (qPCR) was performed to validate the selected circRNAs in the replication cohort with 32 CS patients and 30 healthy controls. Logistic regression controlling for gender was conducted to compare the expression difference. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic value. Twenty‐two differentially expressed circRNAs were filtered from genome‐wide circRNA sequencing. Seven circRNAs were validated by qPCR. Only hsa_circ_0006719 was confirmed to have a higher expression level in the CS group than the healthy control group (P = 0.036). Receiver operating characteristic curve also suggested that hsa_circ_0006719 had significant diagnostic value for CS (AUC = 0.739, P = 0.001). We described the first study of circRNAs in CS and validated hsa_circ_0006719 as a potential novel diagnostic biomarker of CS.
Collapse
Affiliation(s)
- Gang Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Jianxiong Shen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Chong Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Department of Spine Surgery, Orthopedics Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yang Jiao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zheng Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Haining Tan
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Youxi Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Tianhua Rong
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| |
Collapse
|
17
|
Karolak JA, Gambin T, Honey EM, Slavik T, Popek E, Stankiewicz P. A de novo 2.2 Mb recurrent 17q23.1q23.2 deletion unmasks novel putative regulatory non-coding SNVs associated with lethal lung hypoplasia and pulmonary hypertension: a case report. BMC Med Genomics 2020; 13:34. [PMID: 32143628 PMCID: PMC7060516 DOI: 10.1186/s12920-020-0701-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/27/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Application of whole genome sequencing (WGS) enables identification of non-coding variants that play a phenotype-modifying role and are undetectable by exome sequencing. Recently, non-coding regulatory single nucleotide variants (SNVs) have been reported in patients with lethal lung developmental disorders (LLDDs) or congenital scoliosis with recurrent copy-number variant (CNV) deletions at 17q23.1q23.2 or 16p11.2, respectively. CASE PRESENTATION Here, we report a deceased newborn with pulmonary hypertension and pulmonary interstitial emphysema with features suggestive of pulmonary hypoplasia, resulting in respiratory failure and neonatal death soon after birth. Using the array comparative genomic hybridization and WGS, two heterozygous recurrent CNV deletions: ~ 2.2 Mb on 17q23.1q23.2, involving TBX4, and ~ 600 kb on 16p11.2, involving TBX6, that both arose de novo on maternal chromosomes were identified. In the predicted lung-specific enhancer upstream to TBX4, we have detected seven novel putative regulatory non-coding SNVs that were absent in 13 control individuals with the overlapping deletions but without any structural lung anomalies. CONCLUSIONS Our findings further support a recently reported model of complex compound inheritance of LLDD in which both non-coding and coding heterozygous TBX4 variants contribute to the lung phenotype. In addition, this is the first report of a patient with combined de novo heterozygous recurrent 17q23.1q23.2 and 16p11.2 CNV deletions.
Collapse
Affiliation(s)
- Justyna A Karolak
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781, Poznan, Poland
| | - Tomasz Gambin
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Institute of Computer Science, Warsaw University of Technology, 00-665, Warsaw, Poland
| | - Engela M Honey
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Science, University of Pretoria, Pretoria, South Africa
| | - Tomas Slavik
- Ampath Pathology Laboratories, and Department of Anatomical Pathology, University of Pretoria, Pretoria, South Africa
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| |
Collapse
|
18
|
Lemire GT, Beauregard-Lacroix É, Campeau PM, Parent S, Roy-Beaudry M, Soglio DD, Grignon A, Rypens F, Wavrant S, Laberge AM, Delrue MA. Retrospective analysis of fetal vertebral defects: Associated anomalies, etiologies, and outcome. Am J Med Genet A 2019; 182:664-672. [PMID: 31880412 DOI: 10.1002/ajmg.a.61468] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/13/2019] [Accepted: 12/16/2019] [Indexed: 01/04/2023]
Abstract
Our objectives were to describe fetal cases of vertebral defects (VD), assess the diagnostic yield of fetal chromosomal analysis for VD and determine which investigations should be performed when evaluating fetal VD. We performed a retrospective chart review for fetuses with VD seen between 2006 and 2015. Cases were identified from CHU Sainte-Justine's prenatal clinic visits, postmortem fetal skeletal surveys, and medical records. Cases with neural tube defects were excluded. Sixty-six fetuses with VD were identified at a mean gestational age of 20 weeks. Forty-seven (71.2%) had associated antenatal anomalies, most commonly genitourinary, skeletal/limb, and cardiac anomalies. Thirteen mothers (19.7%) had pregestational diabetes (95% CI [10.1%-29.3%]). Fifty-three cases had chromosomal analysis. Three had abnormal results (5.6%): trisomy 13, trisomy 22, and 9q33.1q34.11 deletion. Thirty-four (51.5%) pregnancies were terminated, one led to intrauterine fetal demise and 31 (46.9%) continued to term. Of 27 children who survived the neonatal period, 21 had congenital scoliosis and 3 had spondylocostal dysostosis. Seven had developmental delay. In conclusion, prenatal evaluation of fetuses with VD should include detailed morphological assessment (including fetal echocardiogram), maternal diabetes screening, and chromosomal microarray if non-isolated. Our findings provide guidance about management and counseling after a diagnosis of fetal VD.
Collapse
Affiliation(s)
- Gabrielle T Lemire
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Éliane Beauregard-Lacroix
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Philippe M Campeau
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Stefan Parent
- Department of Surgery, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Marjolaine Roy-Beaudry
- Department of Surgery, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Dorothée Dal Soglio
- Department of Pathology, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada.,Integrated Prenatal Diagnosis Center, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Andrée Grignon
- Integrated Prenatal Diagnosis Center, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada.,Department of Medical Imaging, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Françoise Rypens
- Integrated Prenatal Diagnosis Center, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada.,Department of Medical Imaging, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Sandrine Wavrant
- Integrated Prenatal Diagnosis Center, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada.,Maternal-Fetal Medicine, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Anne-Marie Laberge
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada.,Integrated Prenatal Diagnosis Center, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Marie-Ange Delrue
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada.,Integrated Prenatal Diagnosis Center, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| |
Collapse
|
19
|
Sadler B, Haller G, Antunes L, Bledsoe X, Morcuende J, Giampietro P, Raggio C, Miller N, Kidane Y, Wise CA, Amarillo I, Walton N, Seeley M, Johnson D, Jenkins C, Jenkins T, Oetjens M, Tong RS, Druley TE, Dobbs MB, Gurnett CA. Distal chromosome 16p11.2 duplications containing SH2B1 in patients with scoliosis. J Med Genet 2019; 56:427-433. [PMID: 30803986 DOI: 10.1136/jmedgenet-2018-105877] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/18/2019] [Accepted: 01/25/2019] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Adolescent idiopathic scoliosis (AIS) is a common musculoskeletal disorder with strong evidence for a genetic contribution. CNVs play an important role in congenital scoliosis, but their role in idiopathic scoliosis has been largely unexplored. METHODS Exome sequence data from 1197 AIS cases and 1664 in-house controls was analysed using coverage data to identify rare CNVs. CNV calls were filtered to include only highly confident CNVs with >10 average reads per region and mean log-ratio of coverage consistent with single-copy duplication or deletion. The frequency of 55 common recurrent CNVs was determined and correlated with clinical characteristics. RESULTS Distal chromosome 16p11.2 microduplications containing the gene SH2B1 were found in 0.7% of AIS cases (8/1197). We replicated this finding in two additional AIS cohorts (8/1097 and 2/433), resulting in 0.7% (18/2727) of all AIS cases harbouring a chromosome 16p11.2 microduplication, compared with 0.06% of local controls (1/1664) and 0.04% of published controls (8/19584) (p=2.28×10-11, OR=16.15). Furthermore, examination of electronic health records of 92 455 patients from the Geisinger health system showed scoliosis in 30% (20/66) patients with chromosome 16p11.2 microduplications containing SH2B1 compared with 7.6% (10/132) of controls (p=5.6×10-4, OR=3.9). CONCLUSIONS Recurrent distal chromosome 16p11.2 duplications explain nearly 1% of AIS. Distal chromosome 16p11.2 duplications may contribute to scoliosis pathogenesis by directly impairing growth or by altering expression of nearby genes, such as TBX6. Individuals with distal chromosome 16p11.2 microduplications should be screened for scoliosis to facilitate early treatment.
Collapse
Affiliation(s)
- Brooke Sadler
- Department of Neurology, Washington University in Saint Louis School of Medicine, St. Louis, Missouri, USA
| | - Gabe Haller
- Department of Orthopedic Surgery, Washington University in Saint Louis School of Medicine, St. Louis, Missouri, USA
| | - Lilian Antunes
- Department of Neurology, Washington University in Saint Louis School of Medicine, St. Louis, Missouri, USA
| | - Xavier Bledsoe
- Department of Neurology, Washington University in Saint Louis School of Medicine, St. Louis, Missouri, USA
| | - Jose Morcuende
- Department of Orthopaedic Surgery and Rehabilitation, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, Iowa, USA
| | - Philip Giampietro
- Department of Genetics, St. Christopher's Hospital for Children, Philadelphia, Pennsylvania, USA
| | - Cathleen Raggio
- Orthopedic Surgery, Pediatrics, Hospital for Special Surgery, New York City, New York, USA
| | - Nancy Miller
- Department of Orthopedics, University of Colorado at Denver - Anschutz Medical Campus, Aurora, Colorado, USA
| | - Yared Kidane
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas, USA
| | - Carol A Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas, USA
| | - Ina Amarillo
- Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, St. Louis, Missouri, USA
| | - Nephi Walton
- Genomic Medicine, Geisinger Health System, Danville, Pennsylvania, USA
| | - Mark Seeley
- Genomic Medicine, Geisinger Health System, Danville, Pennsylvania, USA
| | - Darren Johnson
- Genomic Medicine, Geisinger Health System, Danville, Pennsylvania, USA
| | - Conner Jenkins
- Genomic Medicine, Geisinger Health System, Danville, Pennsylvania, USA
| | - Troy Jenkins
- Genomic Medicine, Geisinger Health System, Danville, Pennsylvania, USA
| | - Matthew Oetjens
- Genomic Medicine, Geisinger Health System, Danville, Pennsylvania, USA
| | - R Spencer Tong
- Department of Pediatrics, Washington University in Saint Louis School of Medicine, St. Louis, Missouri, USA
| | - Todd E Druley
- Department of Pediatrics, Washington University in Saint Louis School of Medicine, St. Louis, Missouri, USA
| | - Matthew B Dobbs
- Department of Orthopedic Surgery, Washington University in Saint Louis School of Medicine, St. Louis, Missouri, USA
| | - Christina A Gurnett
- Department of Neurology, Division of Pediatric Neurology, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| |
Collapse
|
20
|
Liu J, Wu N, Yang N, Takeda K, Chen W, Li W, Du R, Liu S, Zhou Y, Zhang L, Liu Z, Zuo Y, Zhao S, Blank R, Pehlivan D, Dong S, Zhang J, Shen J, Si N, Wang Y, Liu G, Li S, Zhao Y, Zhao H, Chen Y, Zhao Y, Song X, Hu J, Lin M, Tian Y, Yuan B, Yu K, Niu Y, Yu B, Li X, Chen J, Yan Z, Zhu Q, Meng X, Chen X, Su J, Zhao X, Wang X, Ming Y, Li X, Raggio CL, Zhang B, Weng X, Zhang S, Zhang X, Watanabe K, Matsumoto M, Jin L, Shen Y, Sobreira NL, Posey JE, Giampietro PF, Valle D, Liu P, Wu Z, Ikegawa S, Lupski JR, Zhang F, Qiu G. TBX6-associated congenital scoliosis (TACS) as a clinically distinguishable subtype of congenital scoliosis: further evidence supporting the compound inheritance and TBX6 gene dosage model. Genet Med 2019; 21:1548-1558. [PMID: 30636772 DOI: 10.1038/s41436-018-0377-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/09/2018] [Indexed: 02/07/2023] Open
Abstract
PURPOSE To characterize clinically measurable endophenotypes, implicating the TBX6 compound inheritance model. METHODS Patients with congenital scoliosis (CS) from China(N = 345, cohort 1), Japan (N = 142, cohort 2), and the United States (N = 10, cohort 3) were studied. Clinically measurable endophenotypes were compared according to the TBX6 genotypes. A mouse model for Tbx6 compound inheritance (N = 52) was investigated by micro computed tomography (micro-CT). A clinical diagnostic algorithm (TACScore) was developed to assist in clinical recognition of TBX6-associated CS (TACS). RESULTS In cohort 1, TACS patients (N = 33) were significantly younger at onset than the remaining CS patients (P = 0.02), presented with one or more hemivertebrae/butterfly vertebrae (P = 4.9 × 10‒8), and exhibited vertebral malformations involving the lower part of the spine (T8-S5, P = 4.4 × 10‒3); observations were confirmed in two replication cohorts. Simple rib anomalies were prevalent in TACS patients (P = 3.1 × 10‒7), while intraspinal anomalies were uncommon (P = 7.0 × 10‒7). A clinically usable TACScore was developed with an area under the curve (AUC) of 0.9 (P = 1.6 × 10‒15). A Tbx6-/mh (mild-hypomorphic) mouse model supported that a gene dosage effect underlies the TACS phenotype. CONCLUSION TACS is a clinically distinguishable entity with consistent clinically measurable endophenotypes. The type and distribution of vertebral column abnormalities in TBX6/Tbx6 compound inheritance implicate subtle perturbations in gene dosage as a cause of spine developmental birth defects responsible for about 10% of CS.
Collapse
Affiliation(s)
- Jiaqi Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China. .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China. .,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | | | - Nan Yang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Kazuki Takeda
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan.,Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Weisheng Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Weiyu Li
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai, China
| | - Renqian Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sen Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Yangzhong Zhou
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Internal Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ling Zhang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai, China
| | - Zhenlei Liu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yuzhi Zuo
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Robert Blank
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shuangshuang Dong
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai, China
| | - Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Jianxiong Shen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Nuo Si
- The McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yipeng Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Gang Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Shugang Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yanxue Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Hong Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yixin Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Yu Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jianhua Hu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Mao Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Ye Tian
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Keyi Yu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Bin Yu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jia Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Zihui Yan
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Qiankun Zhu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Xiaolu Meng
- The McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoli Chen
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, China
| | - Jianzhong Su
- College of Biomedical Engineering, The Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiuli Zhao
- The McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoyue Wang
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yue Ming
- PET-CT Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiao Li
- Department of Radiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Cathleen L Raggio
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Baozhong Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xisheng Weng
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuyang Zhang
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xue Zhang
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,The McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Kota Watanabe
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Morio Matsumoto
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | | | - Li Jin
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Yiping Shen
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Nara L Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Philip F Giampietro
- Department of Pediatrics, Drexel University College of Medicine, Philadelphia, PA, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Departments of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China. .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China. .,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China.
| |
Collapse
|
21
|
Verbitsky M, Westland R, Perez A, Kiryluk K, Liu Q, Krithivasan P, Mitrotti A, Fasel DA, Batourina E, Sampson MG, Bodria M, Werth M, Kao C, Martino J, Capone VP, Vivante A, Shril S, Kil BH, Marasà M, Zhang JY, Na YJ, Lim TY, Ahram D, Weng PL, Heinzen EL, Carrea A, Piaggio G, Gesualdo L, Manca V, Masnata G, Gigante M, Cusi D, Izzi C, Scolari F, van Wijk JAE, Saraga M, Santoro D, Conti G, Zamboli P, White H, Drozdz D, Zachwieja K, Miklaszewska M, Tkaczyk M, Tomczyk D, Krakowska A, Sikora P, Jarmoliński T, Borszewska-Kornacka MK, Pawluch R, Szczepanska M, Adamczyk P, Mizerska-Wasiak M, Krzemien G, Szmigielska A, Zaniew M, Dobson MG, Darlow JM, Puri P, Barton DE, Furth SL, Warady BA, Gucev Z, Lozanovski VJ, Tasic V, Pisani I, Allegri L, Rodas LM, Campistol JM, Jeanpierre C, Alam S, Casale P, Wong CS, Lin F, Miranda DM, Oliveira EA, Simões-E-Silva AC, Barasch JM, Levy B, Wu N, Hildebrandt F, Ghiggeri GM, Latos-Bielenska A, Materna-Kiryluk A, Zhang F, Hakonarson H, Papaioannou VE, Mendelsohn CL, Gharavi AG, Sanna-Cherchi S. The copy number variation landscape of congenital anomalies of the kidney and urinary tract. Nat Genet 2018; 51:117-127. [PMID: 30578417 PMCID: PMC6668343 DOI: 10.1038/s41588-018-0281-y] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/18/2018] [Indexed: 12/18/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are a major cause of pediatric kidney failure. We performed a genome-wide analysis of copy number variants (CNVs) in 2,824 cases and 21,498 controls. Affected individuals carried a significant burden of rare exonic (i.e. affecting coding regions) CNVs and were enriched for known genomic disorders (GD). Kidney anomaly (KA) cases were most enriched for exonic CNVs, encompassing GD-CNVs and novel deletions; obstructive uropathy (OU) had a lower CNV burden and an intermediate prevalence of GD-CNVs; vesicoureteral reflux (VUR) had the fewest GD-CNVs but was enriched for novel exonic CNVs, particularly duplications. Six loci (1q21, 4p16.1-p16.3, 16p11.2, 16p13.11, 17q12, and 22q11.2) accounted for 65% of patients with GD-CNVs. Deletions at 17q12, 4p16.1-p16.3, and 22q11.2 were specific for KA; the 16p11.2 locus showed extensive pleiotropy. Using a multidisciplinary approach, we identified TBX6 as a driver for the CAKUT subphenotypes in the 16p11.2 microdeletion syndrome.
Collapse
Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Rik Westland
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA.,Department of Pediatric Nephrology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Alejandra Perez
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Qingxue Liu
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Adele Mitrotti
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - David A Fasel
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Ekaterina Batourina
- Department of Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Matthew G Sampson
- University of Michigan School of Medicine, Department of Pediatrics-Nephrology, Ann Arbor, MI, USA
| | - Monica Bodria
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Max Werth
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Charlly Kao
- Center for Applied Genomics, The Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jeremiah Martino
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Valentina P Capone
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Asaf Vivante
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Pediatric Department B and Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer and the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Byum Hee Kil
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Jun Y Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Young-Ji Na
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Tze Y Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Dina Ahram
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Patricia L Weng
- Department of Pediatric Nephrology, UCLA Medical Center and UCLA Medical Center-Santa Monica, Los Angeles, CA, USA
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Alba Carrea
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Giorgio Piaggio
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Valeria Manca
- Department of Pediatric Urology, Azienda Ospedaliera Brotzu, Cagliari, Italy
| | - Giuseppe Masnata
- Department of Pediatric Urology, Azienda Ospedaliera Brotzu, Cagliari, Italy
| | - Maddalena Gigante
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Daniele Cusi
- National Research Council of Italy, Inst. Biomedical Technologies Milano Bio4dreams Scientific Unit, Milano, Italy
| | - Claudia Izzi
- Dipartimento Ostetrico-Ginecologico e Seconda Divisione di Nefrologia ASST, Spedali Civili e Presidio di Montichiari, Brescia, Italy
| | - Francesco Scolari
- Cattedra di Nefrologia, Università di Brescia, Seconda Divisione di Nefrologia, Azienda Ospedaliera Spedali Civili di Brescia Presidio di Montichiari, Brescia, Italy
| | - Joanna A E van Wijk
- Department of Pediatric Nephrology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split, Croatia.,School of Medicine, University of Split, Split, Croatia
| | - Domenico Santoro
- Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Messina, Messina, Italy
| | - Giovanni Conti
- Department of Pediatric Nephrology, Azienda Ospedaliera Universitaria "G. Martino", Messina, Italy
| | - Pasquale Zamboli
- Division of Nephrology, University of Campania "Luigi Vanvitell", Naples, Italy
| | - Hope White
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Dorota Drozdz
- Department of Pediatric Nephrology and Hypertension, Dialysis Unit, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Zachwieja
- Department of Pediatric Nephrology and Hypertension, Dialysis Unit, Jagiellonian University Medical College, Krakow, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology, Jagiellonian University Medical College, Krakow, Poland
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Daria Tomczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Anna Krakowska
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology Medical University of Lublin, Lublin, Poland
| | | | - Maria K Borszewska-Kornacka
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Robert Pawluch
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Maria Szczepanska
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Piotr Adamczyk
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | | | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Szmigielska
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Mark G Dobson
- Department of Clinical Genetics, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,National Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - John M Darlow
- Department of Clinical Genetics, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,National Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Prem Puri
- National Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,National Children's Hospital Tallaght, Dublin, Ireland
| | - David E Barton
- Department of Clinical Genetics, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,University College Dublin UCD School of Medicine, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Susan L Furth
- Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Division of Nephrology, Children's Hospital of Philadelphia (CHOP), Philadelphia, PA, USA
| | - Bradley A Warady
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Division of Nephrology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Zoran Gucev
- University Children's Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Vladimir J Lozanovski
- University Children's Hospital, Medical Faculty of Skopje, Skopje, Macedonia.,University Clinic for General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Velibor Tasic
- University Children's Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Isabella Pisani
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Landino Allegri
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Lida M Rodas
- Renal Division, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Josep M Campistol
- Renal Division, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Cécile Jeanpierre
- Laboratory of Hereditary Kidney Diseases, Inserm UMR 1163, Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Shumyle Alam
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Pasquale Casale
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA.,Mount Sinai Medical Center, Kravis Children's Hospital, New York, NY, USA
| | - Craig S Wong
- Division of Pediatric Nephrology, University of New Mexico Children's Hospital, Albuquerque, NM, USA
| | - Fangming Lin
- Division of Pediatric Nephrology, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Débora M Miranda
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Eduardo A Oliveira
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Ana Cristina Simões-E-Silva
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Jonathan M Barasch
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Nan Wu
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Medical Research Center of Orthopedics, all at Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Anna Latos-Bielenska
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Virginia E Papaioannou
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA.
| | - Cathy L Mendelsohn
- Department of Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA.
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA.
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA.
| |
Collapse
|
22
|
Lin S, Shi S, Zhou Y, Ji Y, Huang P, Wu J, Chen B, Luo Y. Intrauterine phenotypic features associated with 16p11.2 recurrent microdeletions. Prenat Diagn 2018. [PMID: 29514395 DOI: 10.1002/pd.5245] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To investigate the detection rate of 16p11.2 recurrent microdeletions in fetuses with abnormal ultrasound findings and determine the common abnormal ultrasound findings in fetuses carrying the deletion. METHODS This study reviewed 2262 consecutive fetuses with abnormal ultrasound findings who underwent prenatal chromosomal microarray analysis between October 2014 and December 2016. Cases carrying the 16p11.2 recurrent microdeletion were further genetically analyzed, and their clinical features were reviewed. RESULTS The 16p11.2 recurrent microdeletion was identified in 12 fetuses, who had skeletal malformations (5/12), cardiovascular malformations (4/12), or isolated ultrasound markers (3/12). Approximately 0.5% (12/2262) of the fetuses with abnormal ultrasound findings harbored the deletion. The 5 fetuses with skeletal malformations displayed vertebral defects, particularly in the hemivertebra and butterfly vertebra. The detection rate of the 16p11.2 recurrent microdeletion was statistically significant (P < .05) among fetuses with skeletal malformations (3.6%, 5/140), fetuses with cardiovascular malformations (1.1%, 4/367), and fetuses with isolated ultrasound markers (0.4%, 3/702). CONCLUSION The most frequent ultrasound findings in fetuses with 16p11.2 recurrent microdeletions are skeletal malformations (particularly vertebral malformations), followed by cardiovascular malformations, and isolated ultrasound markers.
Collapse
Affiliation(s)
- Shaobin Lin
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Shanshan Shi
- Fetal Medicine Center, The First Affiliated Hospital, Jinan University, Guangzhou, People's Republic of China
| | - Yi Zhou
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yuanjun Ji
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Peizhi Huang
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jianzhu Wu
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Baojiang Chen
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yanmin Luo
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| |
Collapse
|
23
|
Chen W, Liu J, Yuan D, Zuo Y, Liu Z, Liu S, Zhu Q, Qiu G, Huang S, Giampietro PF, Zhang F, Wu N, Wu Z. Progress and perspective of TBX6 gene in congenital vertebral malformations. Oncotarget 2018; 7:57430-57441. [PMID: 27437870 PMCID: PMC5302999 DOI: 10.18632/oncotarget.10619] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/16/2016] [Indexed: 02/05/2023] Open
Abstract
Congenital vertebral malformation is a series of significant health problems affecting a large number of populations. It may present as an isolated condition or as a part of an underlying syndromes occurring with other malformations and/or clinical features. Disruption of the genesis of paraxial mesoderm, somites or axial bones can result in spinal deformity. In the course of somitogenesis, the segmentation clock and the wavefront are the leading factors during the entire process in which TBX6 gene plays an important role. TBX6 is a member of the T-box gene family, and its important pathogenicity in spinal deformity has been confirmed. Several TBX6 gene variants and novel pathogenic mechanisms have been recently revealed, and will likely have significant impact in understanding the genetic basis for CVM. In this review, we describe the role which TBX6 plays during human spine development including its interaction with other key elements during the process of somitogenesis. We then systematically review the association between TBX6 gene variants and CVM associated phenotypes, highlighting an important and emerging role for TBX6 and human malformations.
Collapse
Affiliation(s)
- Weisheng Chen
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiaqi Liu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Breast Surgical Oncology, Cancer Hospital of Chinese Academy of Medical Sciences, Beijing, China
| | - Dongtang Yuan
- Department of Orthopaedics, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China
| | - Yuzhi Zuo
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhenlei Liu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Sen Liu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Qiankun Zhu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Guixing Qiu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Shishu Huang
- Department of Orthopaedic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Philip F Giampietro
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Nan Wu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopaedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong Wu
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| |
Collapse
|
24
|
Lefebvre M, Dieux-Coeslier A, Baujat G, Schaefer E, Judith SO, Bazin A, Pinson L, Attie-Bitach T, Baumann C, Fradin M, Pierquin G, Julia S, Quélin C, Doray B, Berg S, Vincent-Delorme C, Lambert L, Bachmann N, Lacombe D, Isidor B, Laurent N, Joelle R, Blanchet P, Odent S, Kervran D, Leporrier N, Abel C, Segers K, Guiliano F, Ginglinger-Fabre E, Selicorni A, Goldenberg A, El Chehadeh S, Francannet C, Demeer B, Duffourd Y, Thauvin-Robinet C, Verloes A, Cormier-Daire V, Riviere JB, Faivre L, Thevenon J. Diagnostic strategy in segmentation defect of the vertebrae: a retrospective study of 73 patients. J Med Genet 2018; 55:422-429. [DOI: 10.1136/jmedgenet-2017-104939] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 01/02/2018] [Accepted: 01/21/2018] [Indexed: 11/04/2022]
Abstract
BackgroundSegmentation defects of the vertebrae (SDV) are non-specific features found in various syndromes. The molecular bases of SDV are not fully elucidated due to the wide range of phenotypes and classification issues. The genes involved are in the Notch signalling pathway, which is a key system in somitogenesis. Here we report on mutations identified in a diagnosis cohort of SDV. We focused on spondylocostal dysostosis (SCD) and the phenotype of these patients in order to establish a diagnostic strategy when confronted with SDV.Patients and methodsWe used DNA samples from a cohort of 73 patients and performed targeted sequencing of the five known SCD-causing genes (DLL3, MESP2, LFNG, HES7 and TBX6) in the first 48 patients and whole-exome sequencing (WES) in 28 relevant patients.ResultsTen diagnoses, including four biallelic variants in TBX6, two biallelic variants in LFNG and DLL3, and one in MESP2 and HES7, were made with the gene panel, and two diagnoses, including biallelic variants in FLNB and one variant in MEOX1, were made by WES. The diagnostic yield of the gene panel was 10/73 (13.7%) in the global cohort but 8/10 (80%) in the subgroup meeting the SCD criteria; the diagnostic yield of WES was 2/28 (8%).ConclusionAfter negative array CGH, targeted sequencing of the five known SCD genes should only be performed in patients who meet the diagnostic criteria of SCD. The low proportion of candidate genes identified by WES in our cohort suggests the need to consider more complex genetic architectures in cases of SDV.
Collapse
|
25
|
McCammon JM, Blaker-Lee A, Chen X, Sive H. The 16p11.2 homologs fam57ba and doc2a generate certain brain and body phenotypes. Hum Mol Genet 2018; 26:3699-3712. [PMID: 28934389 PMCID: PMC5886277 DOI: 10.1093/hmg/ddx255] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/29/2017] [Indexed: 01/28/2023] Open
Abstract
Deletion of the 16p11.2 CNV affects 25 core genes and is associated with multiple symptoms affecting brain and body, including seizures, hyperactivity, macrocephaly, and obesity. Available data suggest that most symptoms are controlled by haploinsufficiency of two or more 16p11.2 genes. To identify interacting 16p11.2 genes, we used a pairwise partial loss of function antisense screen for embryonic brain morphology, using the accessible zebrafish model. fam57ba, encoding a ceramide synthase, was identified as interacting with the doc2a gene, encoding a calcium-sensitive exocytosis regulator, a genetic interaction not previously described. Using genetic mutants, we demonstrated that doc2a+/− fam57ba+/− double heterozygotes show hyperactivity and increased seizure susceptibility relative to wild-type or single doc2a−/− or fam57ba−/− mutants. Additionally, doc2a+/− fam57ba+/− double heterozygotes demonstrate the increased body length and head size. Single doc2a+/− and fam57ba+/− heterozygotes do not show a body size increase; however, fam57ba−/− homozygous mutants show a strongly increased head size and body length, suggesting a greater contribution from fam57ba to the haploinsufficient interaction between doc2a and fam57ba. The doc2a+/− fam57ba+/− interaction has not been reported before, nor has any 16p11.2 gene previously been linked to increased body size. These findings demonstrate that one pair of 16p11.2 homologs can regulate both brain and body phenotypes that are reflective of those in people with 16p11.2 deletion. Together, these findings suggest that dysregulation of ceramide pathways and calcium sensitive exocytosis underlies seizures and large body size associated with 16p11.2 homologs in zebrafish. The data inform consideration of mechanisms underlying human 16p11.2 deletion symptoms.
Collapse
Affiliation(s)
| | - Alicia Blaker-Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Xiao Chen
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hazel Sive
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
26
|
Myers L, Anderlid BM, Nordgren A, Willfors C, Kuja-Halkola R, Tammimies K, Bölte S. Minor physical anomalies in neurodevelopmental disorders: a twin study. Child Adolesc Psychiatry Ment Health 2017; 11:57. [PMID: 29209412 PMCID: PMC5706157 DOI: 10.1186/s13034-017-0195-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/19/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Minor physical anomalies (MPAs) are subtle anatomical deviations in one's appearance and may suggest altered embryogenesis. MPAs have been shown to be more common in neurodevelopmental disorders (NDDs) compared with typical development. Still, further studies are needed on MPAs in NDDs, especially using twins to adjust for confounding familial factors. METHODS Clinical assessments were conducted on 116 twins (61 NDD, 55 controls) from 51 monozygotic and 7 dizygotic pairs to examine MPAs and their association with DSM-5 defined NDDs. Additionally, the relationship between the number of MPAs within twins by zygosity was investigated. RESULTS Within the cohort sample, a specific association was found between MPAs and autism spectrum disorder (ASD) diagnosis (crude odds ratio = 1.29, p = .047; adjusted odds ratios = 1.26-1.33, adjusted p values = .032-.073) and autistic traits (crude β = 3.02, p = .002; adjusted β = 2.28, p = .019), but not NDDs in general or ADHD, nor within-pairs. Identified MPAs in ASD included overweight, hypermobility, pes planus, straight eyebrows, vision impairment, arachnodactyly/long toes, long eyelashes, and microtia. The number of MPAs within all monozygotic pairs was highly correlated (r = .88, p < .001). CONCLUSION MPAs are more frequent in participants with ASD and may be influenced by genetics. The value of MPAs for (early) detection should be further explored, as they might index individuals at increased risk for ASD in particular.
Collapse
Affiliation(s)
- Lynnea Myers
- 0000 0001 2326 2191grid.425979.4Department of Women’s and Children’s Health, Center of Neurodevelopmental Disorders (KIND), Karolinska Institutet & Center for Psychiatry Research, Stockholm County Council, Stockholm, Sweden
| | - Britt-Marie Anderlid
- 0000 0004 1937 0626grid.4714.6Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden ,0000 0000 9241 5705grid.24381.3cDepartment of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- 0000 0004 1937 0626grid.4714.6Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden ,0000 0000 9241 5705grid.24381.3cDepartment of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Charlotte Willfors
- 0000 0001 2326 2191grid.425979.4Department of Women’s and Children’s Health, Center of Neurodevelopmental Disorders (KIND), Karolinska Institutet & Center for Psychiatry Research, Stockholm County Council, Stockholm, Sweden
| | - Ralf Kuja-Halkola
- 0000 0004 1937 0626grid.4714.6Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kristiina Tammimies
- 0000 0001 2326 2191grid.425979.4Department of Women’s and Children’s Health, Center of Neurodevelopmental Disorders (KIND), Karolinska Institutet & Center for Psychiatry Research, Stockholm County Council, Stockholm, Sweden
| | - Sven Bölte
- 0000 0001 2326 2191grid.425979.4Department of Women’s and Children’s Health, Center of Neurodevelopmental Disorders (KIND), Karolinska Institutet & Child and Adolescent Psychiatry, Center for Psychiatry Research, Stockholm County Council, Gävlegatan 22B, 113 30 Stockholm, Sweden
| |
Collapse
|
27
|
Owen JP, Bukshpun P, Pojman N, Thieu T, Chen Q, Lee J, D'Angelo D, Glenn OA, Hunter JV, Berman JI, Roberts TP, Buckner R, Nagarajan SS, Mukherjee P, Sherr EH. Brain MR Imaging Findings and Associated Outcomes in Carriers of the Reciprocal Copy Number Variation at 16p11.2. Radiology 2017; 286:217-226. [PMID: 28786752 DOI: 10.1148/radiol.2017162934] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Purpose To identify developmental neuroradiologic findings in a large cohort of carriers who have deletion and duplication at 16p11.2 (one of the most common genetic causes of autism spectrum disorder [ASD]) and assess how these features are associated with behavioral and cognitive outcomes. Materials and Methods Seventy-nine carriers of a deletion at 16p11.2 (referred to as deletion carriers; age range, 1-48 years; mean age, 12.3 years; 42 male patients), 79 carriers of a duplication at 16p11.2 (referred to as duplication carriers; age range, 1-63 years; mean age, 24.8 years; 43 male patients), 64 unaffected family members (referred to as familial noncarriers; age range, 1-46 years; mean age, 11.7 years; 31 male participants), and 109 population control participants (age range, 6-64 years; mean age, 25.5 years; 64 male participants) were enrolled in this cross-sectional study. Participants underwent structural magnetic resonance (MR) imaging and completed cognitive and behavioral tests. MR images were reviewed for development-related abnormalities by neuroradiologists. Differences in frequency were assessed with a Fisher exact test corrected for multiple comparisons. Unsupervised machine learning was used to cluster radiologic features and an association between clusters and cognitive and behavioral scores from IQ testing, and parental measures of development were tested by using analysis of covariance. Volumetric analysis with automated segmentation was used to confirm radiologic interpretation. Results For deletion carriers, the most prominent features were dysmorphic and thicker corpora callosa compared with familial noncarriers and population control participants (16%; P < .001 and P < .001, respectively) and a greater likelihood of cerebellar tonsillar ectopia (30.7%; P < .002 and P < .001, respectively) and Chiari I malformations (9.3%; P < .299 and P < .002, respectively). For duplication carriers, the most salient findings compared with familial noncarriers and population control participants were reciprocally thinner corpora callosa (18.6%; P < .003 and P < .001, respectively), decreased white matter volume (22.9%; P < .001, and P < .001, respectively), and increased ventricular volume (24.3%; P < .001 and P < .001, respectively). By comparing cognitive assessments to imaging findings, the presence of any imaging feature associated with deletion carriers indicated worse daily living, communication, and social skills compared with deletion carriers without any radiologic abnormalities (P < .005, P < .002, and P < .004, respectively). For the duplication carriers, presence of decreased white matter, callosal volume, and/or increased ventricle size was associated with decreased full-scale and verbal IQ scores compared with duplication carriers without these findings (P < .007 and P < .004, respectively). Conclusion In two genetically related cohorts at high risk for ASD, reciprocal neuroanatomic abnormalities were found and determined to be associated with cognitive and behavioral impairments. © RSNA, 2017 Online supplemental material is available for this article.
Collapse
Affiliation(s)
- Julia P Owen
- From the Departments of Radiology (J.P.O., O.A.G., S.S.N., P.M.) and Neurology (P.B., N.P., T.T., E.H.S.), University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158; Department of Biostatistics, Columbia University, New York, NY (Q.C., J.L., D.D.); Department of Medicine and Pediatrics, Baylor School of Medicine, Houston, Tex (J.V.H.); Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pa (J.I.B., T.P.R.); and Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Mass (R.B.)
| | - Polina Bukshpun
- From the Departments of Radiology (J.P.O., O.A.G., S.S.N., P.M.) and Neurology (P.B., N.P., T.T., E.H.S.), University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158; Department of Biostatistics, Columbia University, New York, NY (Q.C., J.L., D.D.); Department of Medicine and Pediatrics, Baylor School of Medicine, Houston, Tex (J.V.H.); Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pa (J.I.B., T.P.R.); and Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Mass (R.B.)
| | - Nicholas Pojman
- From the Departments of Radiology (J.P.O., O.A.G., S.S.N., P.M.) and Neurology (P.B., N.P., T.T., E.H.S.), University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158; Department of Biostatistics, Columbia University, New York, NY (Q.C., J.L., D.D.); Department of Medicine and Pediatrics, Baylor School of Medicine, Houston, Tex (J.V.H.); Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pa (J.I.B., T.P.R.); and Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Mass (R.B.)
| | - Tony Thieu
- From the Departments of Radiology (J.P.O., O.A.G., S.S.N., P.M.) and Neurology (P.B., N.P., T.T., E.H.S.), University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158; Department of Biostatistics, Columbia University, New York, NY (Q.C., J.L., D.D.); Department of Medicine and Pediatrics, Baylor School of Medicine, Houston, Tex (J.V.H.); Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pa (J.I.B., T.P.R.); and Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Mass (R.B.)
| | - Qixuan Chen
- From the Departments of Radiology (J.P.O., O.A.G., S.S.N., P.M.) and Neurology (P.B., N.P., T.T., E.H.S.), University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158; Department of Biostatistics, Columbia University, New York, NY (Q.C., J.L., D.D.); Department of Medicine and Pediatrics, Baylor School of Medicine, Houston, Tex (J.V.H.); Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pa (J.I.B., T.P.R.); and Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Mass (R.B.)
| | - Jihui Lee
- From the Departments of Radiology (J.P.O., O.A.G., S.S.N., P.M.) and Neurology (P.B., N.P., T.T., E.H.S.), University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158; Department of Biostatistics, Columbia University, New York, NY (Q.C., J.L., D.D.); Department of Medicine and Pediatrics, Baylor School of Medicine, Houston, Tex (J.V.H.); Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pa (J.I.B., T.P.R.); and Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Mass (R.B.)
| | - Debra D'Angelo
- From the Departments of Radiology (J.P.O., O.A.G., S.S.N., P.M.) and Neurology (P.B., N.P., T.T., E.H.S.), University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158; Department of Biostatistics, Columbia University, New York, NY (Q.C., J.L., D.D.); Department of Medicine and Pediatrics, Baylor School of Medicine, Houston, Tex (J.V.H.); Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pa (J.I.B., T.P.R.); and Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Mass (R.B.)
| | - Orit A Glenn
- From the Departments of Radiology (J.P.O., O.A.G., S.S.N., P.M.) and Neurology (P.B., N.P., T.T., E.H.S.), University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158; Department of Biostatistics, Columbia University, New York, NY (Q.C., J.L., D.D.); Department of Medicine and Pediatrics, Baylor School of Medicine, Houston, Tex (J.V.H.); Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pa (J.I.B., T.P.R.); and Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Mass (R.B.)
| | - Jill V Hunter
- From the Departments of Radiology (J.P.O., O.A.G., S.S.N., P.M.) and Neurology (P.B., N.P., T.T., E.H.S.), University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158; Department of Biostatistics, Columbia University, New York, NY (Q.C., J.L., D.D.); Department of Medicine and Pediatrics, Baylor School of Medicine, Houston, Tex (J.V.H.); Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pa (J.I.B., T.P.R.); and Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Mass (R.B.)
| | - Jeffrey I Berman
- From the Departments of Radiology (J.P.O., O.A.G., S.S.N., P.M.) and Neurology (P.B., N.P., T.T., E.H.S.), University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158; Department of Biostatistics, Columbia University, New York, NY (Q.C., J.L., D.D.); Department of Medicine and Pediatrics, Baylor School of Medicine, Houston, Tex (J.V.H.); Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pa (J.I.B., T.P.R.); and Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Mass (R.B.)
| | - Timothy P Roberts
- From the Departments of Radiology (J.P.O., O.A.G., S.S.N., P.M.) and Neurology (P.B., N.P., T.T., E.H.S.), University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158; Department of Biostatistics, Columbia University, New York, NY (Q.C., J.L., D.D.); Department of Medicine and Pediatrics, Baylor School of Medicine, Houston, Tex (J.V.H.); Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pa (J.I.B., T.P.R.); and Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Mass (R.B.)
| | - Randy Buckner
- From the Departments of Radiology (J.P.O., O.A.G., S.S.N., P.M.) and Neurology (P.B., N.P., T.T., E.H.S.), University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158; Department of Biostatistics, Columbia University, New York, NY (Q.C., J.L., D.D.); Department of Medicine and Pediatrics, Baylor School of Medicine, Houston, Tex (J.V.H.); Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pa (J.I.B., T.P.R.); and Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Mass (R.B.)
| | - Srikantan S Nagarajan
- From the Departments of Radiology (J.P.O., O.A.G., S.S.N., P.M.) and Neurology (P.B., N.P., T.T., E.H.S.), University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158; Department of Biostatistics, Columbia University, New York, NY (Q.C., J.L., D.D.); Department of Medicine and Pediatrics, Baylor School of Medicine, Houston, Tex (J.V.H.); Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pa (J.I.B., T.P.R.); and Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Mass (R.B.)
| | - Pratik Mukherjee
- From the Departments of Radiology (J.P.O., O.A.G., S.S.N., P.M.) and Neurology (P.B., N.P., T.T., E.H.S.), University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158; Department of Biostatistics, Columbia University, New York, NY (Q.C., J.L., D.D.); Department of Medicine and Pediatrics, Baylor School of Medicine, Houston, Tex (J.V.H.); Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pa (J.I.B., T.P.R.); and Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Mass (R.B.)
| | - Elliott H Sherr
- From the Departments of Radiology (J.P.O., O.A.G., S.S.N., P.M.) and Neurology (P.B., N.P., T.T., E.H.S.), University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158; Department of Biostatistics, Columbia University, New York, NY (Q.C., J.L., D.D.); Department of Medicine and Pediatrics, Baylor School of Medicine, Houston, Tex (J.V.H.); Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pa (J.I.B., T.P.R.); and Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Mass (R.B.)
| |
Collapse
|
28
|
Lefebvre M, Duffourd Y, Jouan T, Poe C, Jean-Marçais N, Verloes A, St-Onge J, Riviere JB, Petit F, Pierquin G, Demeer B, Callier P, Thauvin-Robinet C, Faivre L, Thevenon J. Autosomal recessive variations of TBX6, from congenital scoliosis to spondylocostal dysostosis. Clin Genet 2017; 91:908-912. [PMID: 27861764 DOI: 10.1111/cge.12918] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/04/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022]
Abstract
Proximal 16p11.2 microdeletions are recurrent microdeletions with an overall prevalence of 0.03%. In patients with segmentation defects of the vertebra (SDV), a burden of this microdeletion was observed with TBX6 as a candidate gene for SDV. In a published cohort of patients with congenital scoliosis (CS), TBX6 haploinsufficiency was compound heterozygous with a common haplotype. Besides, a single three-generation family with spondylocostal dysostosis (SCD) was reported with a heterozygous stop-loss of TBX6. These observations questioned both on the inheritance mode and on the variable expressivity associated with TBX6-associated SDV. Based on a national recruitment of 56 patients with SDV, we describe four patients with variable SDV ranging from CS to SCD associated with biallelic variations of TBX6. Two patients with CS were carrying a proximal 16p11.2 microdeletion associated with the previously reported haplotype. One patient with extensive SDV was carrying a proximal 16p11.2 microdeletion associated with a TBX6 rare missense change. One patient with a clinical diagnosis of SCD was compound heterozygous for two TBX6 rare missense changes. The three rare variants were affecting the chromatin-binding domain. Our data illustrate the variable expressivity of recessive TBX6 ranging from CS to SCD.
Collapse
Affiliation(s)
- M Lefebvre
- GAD EA4271 «Génétique des Anomalies du Développement» (GAD), Université de Bourgogne, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Y Duffourd
- GAD EA4271 «Génétique des Anomalies du Développement» (GAD), Université de Bourgogne, Dijon, France
| | - T Jouan
- GAD EA4271 «Génétique des Anomalies du Développement» (GAD), Université de Bourgogne, Dijon, France
| | - C Poe
- GAD EA4271 «Génétique des Anomalies du Développement» (GAD), Université de Bourgogne, Dijon, France
| | - N Jean-Marçais
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - A Verloes
- Département de Génétique, Hôpital Robert Debré, APHP, Paris, France
| | - J St-Onge
- GAD EA4271 «Génétique des Anomalies du Développement» (GAD), Université de Bourgogne, Dijon, France
| | - J-B Riviere
- GAD EA4271 «Génétique des Anomalies du Développement» (GAD), Université de Bourgogne, Dijon, France
| | - F Petit
- Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHRU, Lille, France
| | - G Pierquin
- Service de Génétique Clinique, Hôpital Sart Tilman, Liège, Belgium
| | - B Demeer
- Service de génétique clinique, CLAD Nord de France, CHU Amiens, Amiens, France
| | - P Callier
- Service de Cytogénétique, Plateau technique de Biologie, CHU Dijon, Dijon, France
| | - C Thauvin-Robinet
- GAD EA4271 «Génétique des Anomalies du Développement» (GAD), Université de Bourgogne, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - L Faivre
- GAD EA4271 «Génétique des Anomalies du Développement» (GAD), Université de Bourgogne, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - J Thevenon
- GAD EA4271 «Génétique des Anomalies du Développement» (GAD), Université de Bourgogne, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| |
Collapse
|
29
|
D’Angelo D, Lebon S, Chen Q, Martin-Brevet S, Snyder LG, Hippolyte L, Hanson E, Maillard AM, Faucett WA, Macé A, Pain A, Bernier R, Chawner SJRA, David A, Andrieux J, Aylward E, Baujat G, Caldeira I, Conus P, Ferrari C, Forzano F, Gérard M, Goin-Kochel RP, Grant E, Hunter JV, Isidor B, Jacquette A, Jønch AE, Keren B, Lacombe D, Le Caignec C, Martin CL, Männik K, Metspalu A, Mignot C, Mukherjee P, Owen MJ, Passeggeri M, Rooryck-Thambo C, Rosenfeld JA, Spence SJ, Steinman KJ, Tjernagel J, Van Haelst M, Shen Y, Draganski B, Sherr EH, Ledbetter DH, van den Bree MBM, Beckmann JS, Spiro JE, Reymond A, Jacquemont S, Chung WK. Defining the Effect of the 16p11.2 Duplication on Cognition, Behavior, and Medical Comorbidities. JAMA Psychiatry 2016; 73:20-30. [PMID: 26629640 PMCID: PMC5894477 DOI: 10.1001/jamapsychiatry.2015.2123] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE The 16p11.2 BP4-BP5 duplication is the copy number variant most frequently associated with autism spectrum disorder (ASD), schizophrenia, and comorbidities such as decreased body mass index (BMI). OBJECTIVES To characterize the effects of the 16p11.2 duplication on cognitive, behavioral, medical, and anthropometric traits and to understand the specificity of these effects by systematically comparing results in duplication carriers and reciprocal deletion carriers, who are also at risk for ASD. DESIGN, SETTING, AND PARTICIPANTS This international cohort study of 1006 study participants compared 270 duplication carriers with their 102 intrafamilial control individuals, 390 reciprocal deletion carriers, and 244 deletion controls from European and North American cohorts. Data were collected from August 1, 2010, to May 31, 2015 and analyzed from January 1 to August 14, 2015. Linear mixed models were used to estimate the effect of the duplication and deletion on clinical traits by comparison with noncarrier relatives. MAIN OUTCOMES AND MEASURES Findings on the Full-Scale IQ (FSIQ), Nonverbal IQ, and Verbal IQ; the presence of ASD or other DSM-IV diagnoses; BMI; head circumference; and medical data. RESULTS Among the 1006 study participants, the duplication was associated with a mean FSIQ score that was lower by 26.3 points between proband carriers and noncarrier relatives and a lower mean FSIQ score (16.2-11.4 points) in nonproband carriers. The mean overall effect of the deletion was similar (-22.1 points; P < .001). However, broad variation in FSIQ was found, with a 19.4- and 2.0-fold increase in the proportion of FSIQ scores that were very low (≤40) and higher than the mean (>100) compared with the deletion group (P < .001). Parental FSIQ predicted part of this variation (approximately 36.0% in hereditary probands). Although the frequency of ASD was similar in deletion and duplication proband carriers (16.0% and 20.0%, respectively), the FSIQ was significantly lower (by 26.3 points) in the duplication probands with ASD. There also were lower head circumference and BMI measurements among duplication carriers, which is consistent with the findings of previous studies. CONCLUSIONS AND RELEVANCE The mean effect of the duplication on cognition is similar to that of the reciprocal deletion, but the variance in the duplication is significantly higher, with severe and mild subgroups not observed with the deletion. These results suggest that additional genetic and familial factors contribute to this variability. Additional studies will be necessary to characterize the predictors of cognitive deficits.
Collapse
Affiliation(s)
- Debra D’Angelo
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York
| | - Sébastien Lebon
- Pediatric Neurology Unit, Department of Pediatrics, Lausanne University Hospital, Lausanne, Switzerland
| | - Qixuan Chen
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York
| | - Sandra Martin-Brevet
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Loyse Hippolyte
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Ellen Hanson
- Department of Psychiatry, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Anne M. Maillard
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - W. Andrew Faucett
- Genomic Medicine Institute, Geisinger Clinic, Danville, Pennsylvania
| | - Aurélien Macé
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland7Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Aurélie Pain
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Science, University of Washington, Seattle
| | - Samuel J. R. A. Chawner
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, Wales
| | - Albert David
- Service de Génétique Médicale, Faculté de Médecine, Centre Hospitalier Universitaire (CHU) Nantes, Institut National de la Santé et de la Recherche Medicale (INSERM) Unités Mixtes de Recherche 957, Nantes, France
| | - Joris Andrieux
- Institut de Génétique Médicale, Hospital Jeanne de Flandre, Centre Hospitalier Régional Universitaire (CHRU) de Lille, Lille, France
| | - Elizabeth Aylward
- Center for Integrative Brain Research, Children’s Research Institute, Seattle, Washington
| | - Genevieve Baujat
- Département de Génétique, Hôpital Necker–Enfants Malades, Assistance Publique–Hôpitaux de Paris (AP-HP), Paris, France 14INSERM U1163, Hôpital Necker–Enfants Malades, Paris, France15Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, Paris
| | - Ines Caldeira
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Philippe Conus
- Department of Psychiatry, Cery Hospital, CHU Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Carrina Ferrari
- Department of Psychiatry, Cery Hospital, CHU Vaudois and University of Lausanne, Lausanne, Switzerland
| | | | - Marion Gérard
- Departement de Génétique, AP-HP, Hôpital Robert Debré, Université Paris VII-Paris Diderot, Paris, France
| | - Robin P. Goin-Kochel
- Section of Psychology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Ellen Grant
- Department of Radiology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jill V. Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas
| | - Bertrand Isidor
- Service de Génétique Médicale, Faculté de Médecine, Centre Hospitalier Universitaire (CHU) Nantes, Institut National de la Santé et de la Recherche Medicale (INSERM) Unités Mixtes de Recherche 957, Nantes, France
| | - Aurélia Jacquette
- Département de Génétique et de Cytogénétique, Unité fonctionnelle de Génétique Clinique, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France23Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France24Groupe de Recherche Clinique, Déficie
| | - Aia E. Jønch
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Boris Keren
- Department of Genetics and Cytogenetics, Groupe Hospitalier Pitié Salpêtrière, AP-HP, Paris, France
| | - Didier Lacombe
- Service de Génétique Médicale, Faculté de Médecine, Centre Hospitalier Universitaire (CHU) Nantes, Institut National de la Santé et de la Recherche Medicale (INSERM) Unités Mixtes de Recherche 957, Nantes, France26Service de Génétique Médicale, CHU de Bor
| | - Cédric Le Caignec
- Service de Génétique Médicale, Faculté de Médecine, Centre Hospitalier Universitaire (CHU) Nantes, Institut National de la Santé et de la Recherche Medicale (INSERM) Unités Mixtes de Recherche 957, Nantes, France
| | - Christa Lese Martin
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania
| | - Katrin Männik
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland29Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia30Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Cyril Mignot
- Department of Radiology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Pratik Mukherjee
- Department of Radiology and Biomedical Imaging, University of California, San Francisco
| | - Michael J. Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, Wales
| | - Marzia Passeggeri
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Caroline Rooryck-Thambo
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France32Laboratoire Maladies Rares: Génétique et Métabolisme, Université de Bordeaux, Bordeaux, France
| | | | - Sarah J. Spence
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kyle J. Steinman
- Department of Neurology, Seattle Children’s Research Institute and University of Washington, Seattle
| | | | - Mieke Van Haelst
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Yiping Shen
- Genetic Diagnostic Laboratory, Department of Laboratory Medicine, Children’s Hospital, Boston, Massachusetts
| | - Bogdan Draganski
- Laboratoire de Recherche en Neuroimagerie, Department for Clinical Neurosciences, Centre Hospitalo-Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Elliott H. Sherr
- Department of Neurology, University of California, San Francisco
| | - David H. Ledbetter
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania
| | - Marianne B. M. van den Bree
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, Wales
| | - Jacques S. Beckmann
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland7Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | | | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Sébastien Jacquemont
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland41CHU Sainte-Justine Research Center, Montreal, Canada42Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada
| | - Wendy K. Chung
- Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, New York44Department of Medicine, Columbia University, New York, New York
| | | | | | | |
Collapse
|
30
|
A highly penetrant form of childhood apraxia of speech due to deletion of 16p11.2. Eur J Hum Genet 2015; 24:302-6. [PMID: 26173965 DOI: 10.1038/ejhg.2015.149] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 05/07/2015] [Accepted: 05/26/2015] [Indexed: 02/07/2023] Open
Abstract
Individuals with heterozygous 16p11.2 deletions reportedly suffer from a variety of difficulties with speech and language. Indeed, recent copy-number variant screens of children with childhood apraxia of speech (CAS), a specific and rare motor speech disorder, have identified three unrelated individuals with 16p11.2 deletions. However, the nature and prevalence of speech and language disorders in general, and CAS in particular, is unknown for individuals with 16p11.2 deletions. Here we took a genotype-first approach, conducting detailed and systematic characterization of speech abilities in a group of 11 unrelated children ascertained on the basis of 16p11.2 deletions. To obtain the most precise and replicable phenotyping, we included tasks that are highly diagnostic for CAS, and we tested children under the age of 18 years, an age group where CAS has been best characterized. Two individuals were largely nonverbal, preventing detailed speech analysis, whereas the remaining nine met the standard accepted diagnostic criteria for CAS. These results link 16p11.2 deletions to a highly penetrant form of CAS. Our findings underline the need for further precise characterization of speech and language profiles in larger groups of affected individuals, which will also enhance our understanding of how genetic pathways contribute to human communication disorders.
Collapse
|
31
|
Zhang F, Lupski JR. Non-coding genetic variants in human disease. Hum Mol Genet 2015; 24:R102-10. [PMID: 26152199 DOI: 10.1093/hmg/ddv259] [Citation(s) in RCA: 389] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 07/03/2015] [Indexed: 01/16/2023] Open
Abstract
Genetic variants, including single-nucleotide variants (SNVs) and copy number variants (CNVs), in the non-coding regions of the human genome can play an important role in human traits and complex diseases. Most of the genome-wide association study (GWAS) signals map to non-coding regions and potentially point to non-coding variants, whereas their functional interpretation is challenging. In this review, we discuss the human non-coding variants and their contributions to human diseases in the following four parts. (i) Functional annotations of non-coding SNPs mapped by GWAS: we discuss recent progress revealing some of the molecular mechanisms for GWAS signals affecting gene function. (ii) Technical progress in interpretation of non-coding variants: we briefly describe some of the technologies for functional annotations of non-coding variants, including the methods for genome-wide mapping of chromatin interaction, computational tools for functional predictions and the new genome editing technologies useful for dissecting potential functional consequences of non-coding variants. (iii) Non-coding CNVs in human diseases: we review our emerging understanding the role of non-coding CNVs in human disease. (iv) Compound inheritance of large genomic deletions and non-coding variants: compound inheritance at a locus consisting of coding variants plus non-coding ones is described.
Collapse
Affiliation(s)
- Feng Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA and Texas Children's Hospital, Houston, TX 77030, USA
| |
Collapse
|
32
|
Abstract
STUDY DESIGN A hypothesis-driven study was conducted in a familial cohort to determine the potential association between variants within the TBX6 gene and Familial Idiopathic Scoliosis (FIS). OBJECTIVE To determine if variants within exons of the TBX6 gene segregate with the FIS phenotype within a sample of families with FIS. SUMMARY OF BACKGROUND DATA Idiopathic Scoliosis (IS) is a structural curvature of the spine whose underlying genetic etiology has not been established. IS has been reported to occur at a higher rate than expected in family members of individuals with congenital scoliosis (CS), suggesting that the two diseases might have a shared etiology. The TBX6 gene on chromosome 16p, essential to somite development, has been associated with CS in a Chinese population. Previous studies have identified linkage to this locus in families with FIS, and specifically with rs8060511, located in an intron of the TBX6 gene. METHODS Parent-offspring trios from 11 families (13 trios, 42 individuals) with FIS were selected for Sanger sequencing of the TBX6 gene. Trios were selected from a large population of families with FIS in which a genome-wide scan had resulted in linkage to 16p. RESULTS Sequencing analyses of the subset of families resulted in the identification of five coding variants. Three of the five variants were novel; the remaining two variants were previously characterized and account for 90% of the observed variants in these trios. In all cases, there was no correlation between transmission of the TBX6 variant allele and FIS phenotype. However, an analysis of regulatory markers in osteoblasts showed that rs8060511 is in a putative enhancer element. CONCLUSIONS Although this study did not identify any TBX6 coding variants that segregate with FIS, we identified a variant that is located in a potential TBX6 enhancer element. Therefore, further investigation of the region is needed.
Collapse
|
33
|
Wu N, Ming X, Xiao J, Wu Z, Chen X, Shinawi M, Shen Y, Yu G, Liu J, Xie H, Gucev ZS, Liu S, Yang N, Al-Kateb H, Chen J, Zhang J, Hauser N, Zhang T, Tasic V, Liu P, Su X, Pan X, Liu C, Wang L, Shen J, Shen J, Chen Y, Zhang T, Zhang J, Choy KW, Wang J, Wang Q, Li S, Zhou W, Guo J, Wang Y, Zhang C, Zhao H, An Y, Zhao Y, Wang J, Liu Z, Zuo Y, Tian Y, Weng X, Sutton VR, Wang H, Ming Y, Kulkarni S, Zhong TP, Giampietro PF, Dunwoodie SL, Cheung SW, Zhang X, Jin L, Lupski JR, Qiu G, Zhang F. TBX6 null variants and a common hypomorphic allele in congenital scoliosis. N Engl J Med 2015; 372:341-50. [PMID: 25564734 PMCID: PMC4326244 DOI: 10.1056/nejmoa1406829] [Citation(s) in RCA: 210] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Congenital scoliosis is a common type of vertebral malformation. Genetic susceptibility has been implicated in congenital scoliosis. METHODS We evaluated 161 Han Chinese persons with sporadic congenital scoliosis, 166 Han Chinese controls, and 2 pedigrees, family members of which had a 16p11.2 deletion, using comparative genomic hybridization, quantitative polymerase-chain-reaction analysis, and DNA sequencing. We carried out tests of replication using an additional series of 76 Han Chinese persons with congenital scoliosis and a multicenter series of 42 persons with 16p11.2 deletions. RESULTS We identified a total of 17 heterozygous TBX6 null mutations in the 161 persons with sporadic congenital scoliosis (11%); we did not observe any null mutations in TBX6 in 166 controls (P<3.8×10(-6)). These null alleles include copy-number variants (12 instances of a 16p11.2 deletion affecting TBX6) and single-nucleotide variants (1 nonsense and 4 frame-shift mutations). However, the discordant intrafamilial phenotypes of 16p11.2 deletion carriers suggest that heterozygous TBX6 null mutation is insufficient to cause congenital scoliosis. We went on to identify a common TBX6 haplotype as the second risk allele in all 17 carriers of TBX6 null mutations (P<1.1×10(-6)). Replication studies involving additional persons with congenital scoliosis who carried a deletion affecting TBX6 confirmed this compound inheritance model. In vitro functional assays suggested that the risk haplotype is a hypomorphic allele. Hemivertebrae are characteristic of TBX6-associated congenital scoliosis. CONCLUSIONS Compound inheritance of a rare null mutation and a hypomorphic allele of TBX6 accounted for up to 11% of congenital scoliosis cases in the series that we analyzed. (Funded by the National Basic Research Program of China and others.).
Collapse
Affiliation(s)
- N Wu
- The authors' affiliations are listed in the Appendix
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Are copy number variants associated with adolescent idiopathic scoliosis? Clin Orthop Relat Res 2014; 472:3216-25. [PMID: 25005481 PMCID: PMC4160470 DOI: 10.1007/s11999-014-3766-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/13/2014] [Indexed: 01/31/2023]
Abstract
BACKGROUND Adolescent idiopathic scoliosis (AIS) is a complex genetic disorder that causes spinal deformity in approximately 3% of the population. Candidate gene, linkage, and genome-wide association studies have sought to identify genetic variation that predisposes individuals to AIS, but the genetic basis remains unclear. Copy number variants are associated with several isolated skeletal phenotypes, but their role in AIS, to our knowledge, has not been assessed. QUESTIONS/PURPOSES We determined the frequency of recurrent copy number rearrangements, chromosome aneuploidy, and rare copy number variants in patients with AIS. METHODS Between January 2010 and August 2014, we evaluated 150 patients with isolated AIS and spinal curvatures measuring 10° or greater, and 148 agreed to participate. Genomic copy number analysis was performed on patients and 1079 control subjects using the Affymetrix(®) Genome-wide Human SNP Array 6.0. After removing poor quality samples, 143 (97%) patients with AIS were evaluated for copy number variation. RESULTS We identified a duplication of chromosome 1q21.1 in 2.1% (N = 3/143) of patients with AIS, which was enriched compared with 0.09% (N = 1/1079) of control subjects (p = 0.0057) and 0.07% (N = 6/8329) of a large published control cohort (p = 0.0004). Other notable findings include trisomy X, which was identified in 1.8% (N = 2/114) of female patients with AIS, and rearrangements of chromosome 15q11.2 and 16p11.2 that previously have been associated with spinal phenotypes. Finally, we report rare copy number variants that will be useful in future studies investigating candidate genes for AIS. CONCLUSIONS Copy number variation and chromosomal aneuploidy may contribute to the pathogenesis of adolescent idiopathic scoliosis. CLINICAL RELEVANCE Chromosomal microarray may reveal clinically useful abnormalities in some patients with AIS.
Collapse
|
35
|
Horn DL, DeMarre K, Parikh SR. Interarytenoid Sodium Carboxymethylcellulose Gel Injection for Management of Pediatric Aspiration. Ann Otol Rhinol Laryngol 2014; 123:852-8. [DOI: 10.1177/0003489414539129] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objective: This study aimed to investigate the role of interarytenoid injection laryngoplasty (IL) for the management of pediatric aspiration. Methods: Medical records of 30 patients, 9 female, with radiographically confirmed chronic aspiration who underwent intraoperative IL were retrospectively reviewed. Clinical improvement was defined as successful advancement of feeds to thinner consistencies. Results: Clinical improvement was observed in 57% of patients. Six children with type 1 posterior laryngeal cleft (PLC-1) were not significantly more likely to show improvement compared to the children without PLC-1. Type 1 posterior laryngeal cleft was associated with older age and higher prevalence of neurodevelopmental risk factors relative to absence of PLC-1. Patients with PLC-1 were more likely than noncleft patients to show recurrence of symptoms after initial improvement with IL. Five patients underwent endoscopic repair. Repair was successful in 3 patients who improved after IL but not in 2 patients who did not improve after IL. Conclusion: Chronic aspiration can improve after IL even in patients with normal anatomy. Injection laryngoplasty can be performed to improve selection of PLC-1 patients for definitive endoscopic repair. Further prospective research, with a randomized control group, is needed to understand whether interarytenoid incompetence plays a role in some patients with chronic aspiration, who do not have a PLC-1.
Collapse
Affiliation(s)
- David L. Horn
- Department of Otolaryngology–Head and Neck Surgery, University of Washington School of Medicine; Division of Pediatric Otolaryngology, Seattle Children’s Hospital, Seattle, Washington, USA
| | - Kim DeMarre
- Department of Speech and Language, Seattle Children’s Hospital, Seattle, Washington, USA
| | - Sanjay R. Parikh
- Department of Otolaryngology–Head and Neck Surgery, University of Washington School of Medicine; Division of Pediatric Otolaryngology, Seattle Children’s Hospital, Seattle, Washington, USA
| |
Collapse
|