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Yu K, Dou J, Huang W, Wang F, Wu Y. Expanding the genetic spectrum of tooth agenesis using whole-exome sequencing. Clin Genet 2022; 102:503-516. [PMID: 36071541 DOI: 10.1111/cge.14225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Tooth agenesis is a high genetic heterogeneous disorder with more than eighty genes identified as associated molecular causes. The present study aimed to detect the possible pathogenic variants in a cohort of well-characterized probands with a clinical diagnosis of tooth agenesis. METHODS We performed whole-exome sequencing (WES) in 131 tooth agenesis patients with no previously identified molecular diagnosis. All the potential pathogenic variants were verified by Sanger sequencing in patients and their family members. Results Seventy-three patients were genetically diagnosed in 131 unrelated Chinese patients with tooth agenesis, providing a positive molecular diagnostic rate of 55.7%, including 53.8% (49/91) in the non-syndromic tooth agenesis (NSTA) group, and 60.0% (24/40) in syndromic tooth agenesis (STA) group. A total of 75 variants from 13 different genes were identified, including 33 novel variants, and WNT10A and EDA are the most common causative genes associated with non-syndromic and syndromic tooth agenesis, respectively. CONCLUSIONS This study further extends the variant spectrum and clinical profiles of tooth agenesis, which has a positive significance for clinical practice, genetic diagnosis, prenatal counseling and future treatment.
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Affiliation(s)
- Kang Yu
- Department of Second Dental Center, Ninth People's Hospital Affiliated with Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Jiaqi Dou
- Department of Second Dental Center, Ninth People's Hospital Affiliated with Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Wei Huang
- Department of Second Dental Center, Ninth People's Hospital Affiliated with Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Feng Wang
- Department of Oral Implantology, Ninth People's Hospital Affiliated with Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Yiqun Wu
- Department of Second Dental Center, Ninth People's Hospital Affiliated with Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
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2
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Qiu L, Li C, Zheng G, Yang T, Yang F. Microduplication of BTRC detected in a Chinese family with split hand/foot malformation type 3. Clin Genet 2022; 102:451-456. [PMID: 35908152 DOI: 10.1111/cge.14204] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/24/2022] [Accepted: 07/25/2022] [Indexed: 01/08/2023]
Abstract
Split hand/foot malformation (SHFM) is a clinically heterogeneous genetic disorder, which is mainly characterized by median clefts of the hand/feet due to the absence of the central digital rays. Several subgroups of SHFM have been identified, including SHFM1 to SHFM6. SHFM3 is an autosomal dominant disease, which has been identified to associate with a 500 kb microduplication at 10q24. The duplication involved several genes, including LBX1, BTRC, POLL, FBXW4, etc. In the study, using trio clinical exome sequencing, a 120 kb microduplication containing only BTRC were identified in a Chinese family affected with SHFM3. Further confirmation was performed using qRT-PCR assay, which showed that the 120 kb duplication was co-segregated with SHFM phenotypes in the family. It is the smallest duplication which has ever been reported relating to SHFM3. Furthermore, the transcription levels of BTRC mRNA in lymphocyte of the proband was significantly higher than that in the healthy control. The study provided evidence for the limb malformation caused by abnormal BTRC expression, and suggested that next generation sequencing could provide more precise diagnosis to SHFM3 patients. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Liyan Qiu
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Caimin Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Guiyun Zheng
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Tuyin Yang
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Fang Yang
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Nanfang Hospital of Southern Medical University, Guangzhou, China
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3
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Zhang P, Xiao F, Li X, Liang Y, Yi H, Hou M, Mou Y, Chen Z. Familial episodic pain syndrome: a case report and literature review. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:238. [PMID: 35280382 PMCID: PMC8908130 DOI: 10.21037/atm-22-102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/27/2022] [Indexed: 11/06/2022]
Abstract
The purpose of this case report and literature review is to show that familial episodic pain syndrome (FEPS) is a non-inflammatory genetically inherited pain syndrome. A 3-year-old boy presented at our hospital with pain in both his forearms and lower limbs below the knees for more than 3 years. There were no abnormalities in the blood tests, blood smears, liver and kidney function tests, trace elements tests, cellular immunity test, humoral immunity test, autoantibody tests, C-reactive protein (CRP) test, erythrocyte sedimentation rate (ESR) test, and tumor-related and bone marrow cytology examinations. Additionally, the imaging examination results showed no abnormalities. From the patient's medical history, we found that the mother of the child had a family history of a similar disease. To date, only 21 cases of FEPS3 caused by the sodium voltage-gated channel alpha subunit 11A (SCN11A) gene mutation have been reported. Although the age of onset is different, most of them are inherited in families. The results of the genetic examination revealed that the pain mainly came from the genetic inheritance of the maternal family line. The whole exon gene test revealed that the pain was caused by 2 heterozygous mutations of c.674G > T and c.671T > C in the SCN11A gene.
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Affiliation(s)
- Pingping Zhang
- Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Feng Xiao
- Department of Stomatology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaofeng Li
- Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ying Liang
- Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Huan Yi
- Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Minghui Hou
- Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yikun Mou
- Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhuanggui Chen
- Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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4
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Sicko RJ, Romitti PA, Browne ML, Brody LC, Stevens CF, Mills JL, Caggana M, Kay DM. Rare Variants in RPPH1 Real-Time Quantitative PCR Control Assay Binding Sites Result in Incorrect Copy Number Calls. J Mol Diagn 2022; 24:33-40. [PMID: 34656763 PMCID: PMC8802765 DOI: 10.1016/j.jmoldx.2021.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/21/2021] [Accepted: 09/15/2021] [Indexed: 01/03/2023] Open
Abstract
Real-time quantitative PCR (qPCR) using RPPH1 as a reference gene is a standard method for assessment and validation of genomic copy number variations. However, variants in the reference amplicon may cause errors, which was investigated herein. While conducting copy number variation validations for birth defects research studies, 13 of 1634 specimens with multiple loci that appeared to be present as three copies were unexpectedly detected. This apparent trisomy was hypothesized to be an amplification artifact caused by a variant in the RPPH1 amplicon. Sequencing revealed all 13 individuals carried one of the four different variants within the RPPH1 amplicon. These variants could produce allelic dropout or altered reaction efficiency, causing an inaccurate measurement of copy number. Additional genotyping predicted a low frequency of the most common variant (rs3093876; 14/3562 alleles; minor allele frequency, 0.39%). Laboratories should recognize the potential for inaccurate results when using a single qPCR control assay. Overestimated CFTR and SMN2 copy numbers identified during newborn screening that otherwise would have been incorrectly called were also detected. Variants in reference loci may produce false-negative normal results for test loci when real deletions are present. For clinical laboratories screening for heterozygous deletions for diagnostic testing or prenatal/carrier screening via qPCR, the most cost-effective solution to maximize sensitivity is to run triplex reactions targeting the region of interest with two control genes.
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Affiliation(s)
- Robert J Sicko
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, Iowa
| | - Marilyn L Browne
- Birth Defects Registry, New York State Department of Health, Albany, New York; University at Albany School of Public Health, Rensselaer, New York
| | - Lawrence C Brody
- Genetics and Environment Interaction Section, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Colleen F Stevens
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - James L Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland
| | - Michele Caggana
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Denise M Kay
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York.
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5
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Markova ZG, Minzhenkova ME, Bessonova LA, Shilova NV. A new case of 17p13.3p13.1 microduplication resulted from unbalanced translocation: clinical and molecular cytogenetic characterization. Mol Cytogenet 2021; 14:41. [PMID: 34465353 PMCID: PMC8408977 DOI: 10.1186/s13039-021-00562-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 07/29/2021] [Indexed: 11/30/2022] Open
Abstract
Copy number gain 17 p13.3p13.1 was detected by chromosomal microarray (CMA) in a girl with developmental/speech delay and facial dysmorphism. FISH studies made it possible to establish that the identified genomic imbalance is the unbalanced t(9;17) translocation of maternal origin. Clinical features of the patient are also discussed. The advisability of using the combination of CMA and FISH analysis is shown. Copy number gains detected by clinical CMA should be confirmed using FISH analysis in order to determine the physical location of the duplicated segment. Parental follow-up studies is an important step to determine the origin of genomic imbalance. This approach not only allows a most comprehensive characterization of an identified chromosomal/genomic imbalance but also provision of an adequate medical and genetic counseling for a family taking into account a balanced chromosomal rearrangement.
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Affiliation(s)
- Zhanna G Markova
- Research Centre for Medical Genetics, Moskvorechye St., 1, Moscow, Russia, 115522.
| | - Marina E Minzhenkova
- Research Centre for Medical Genetics, Moskvorechye St., 1, Moscow, Russia, 115522
| | - Lyudmila A Bessonova
- Research Centre for Medical Genetics, Moskvorechye St., 1, Moscow, Russia, 115522
| | - Nadezda V Shilova
- Research Centre for Medical Genetics, Moskvorechye St., 1, Moscow, Russia, 115522
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6
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McClendon-Weary B, Putnick DL, Robinson S, Yeung E. Little to Give, Much to Gain-What Can You Do With a Dried Blood Spot? Curr Environ Health Rep 2021; 7:211-221. [PMID: 32851603 DOI: 10.1007/s40572-020-00289-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW Technological advances have allowed dried blood spots (DBS) to be utilized for various measurements, helpful in population-based studies. The following is a review of the literature highlighting the advantages and disadvantages of DBS and describing their use in multiple areas of research. RECENT FINDINGS DBS can track pollutant exposure to understand their impact on health. DBS can also be used for (epi-)genetic studies, to measure clinical biomarkers, and to monitor drug adherence. Advantages of DBS include being minimally invasive, requiring low blood volume, and being cost-effective to collect, transport, and store. Disadvantages of DBS include the hematocrit effect, which is related to the viscosity of the blood affecting its spread on to the filter paper, causing a major source of error when assessing concentrations, and the possibility of low DNA volume. Numerous uses for DBS make them an important source of biomaterial but they require additional validation for accuracy and reproducibility.
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Affiliation(s)
- Bryttany McClendon-Weary
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 6710B Rockledge Dr, MSC 7004, Bethesda, MD, 20817, USA
| | - Diane L Putnick
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 6710B Rockledge Dr, MSC 7004, Bethesda, MD, 20817, USA
| | - Sonia Robinson
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 6710B Rockledge Dr, MSC 7004, Bethesda, MD, 20817, USA
| | - Edwina Yeung
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 6710B Rockledge Dr, MSC 7004, Bethesda, MD, 20817, USA.
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7
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Lewiecki EM, Bilezikian JP, Kagan R, Krakow D, McClung MR, Miller PD, Rush ET, Shuhart CR, Watts NB, Yu EW. Proceedings of the 2019 Santa Fe Bone Symposium: New Concepts in the Care of Osteoporosis and Rare Bone Diseases. J Clin Densitom 2020; 23:1-20. [PMID: 31685420 DOI: 10.1016/j.jocd.2019.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 02/08/2023]
Abstract
The 20th annual Santa Fe Bone Symposium was held August 9-10, 2019, in Santa Fe, New Mexico, USA. This is an annual meeting devoted to clinical applications of recent advances in skeletal research that impact the care of patients with osteoporosis, metabolic bone diseases, and inherited bone diseases. Participants included practicing and academic physicians, fellows, advanced practice providers, fracture liaison service (FLS) coordinators, clinical researchers, and bone density technologists. The symposium consisted of lectures, case presentations, and panel discussions, with an emphasis on learning through interaction of all attendees. Topics included new approaches in the use of anabolic agents for the treatment osteoporosis, a review of important events in skeletal health over the past year, new and emerging treatments for rare bone diseases, the use of genetic testing for bone diseases in clinical practice, medication-associated causes of osteoporosis, new concepts in the use of estrogen therapy for osteoporosis, new Official Positions of the International Society for Clinical Densitometry, skeletal consequences of bariatric surgery, and update on the progress and potential of Bone Health TeleECHO, a virtual community of practice using videoconferencing technology to link healthcare professionals for advancing the care of osteoporosis worldwide. Sessions on rare bone diseases were developed in collaboration with the Rare Bone Disease Alliance. Symposium premeetings included an FLS workshop by the National Osteoporosis Foundation and others devoted to the use of new therapeutic agents for the care of osteoporosis and related disorders.
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Affiliation(s)
- E Michael Lewiecki
- New Mexico Clinical Research & Osteoporosis Center, Albuquerque, NM, USA.
| | - John P Bilezikian
- Columbia University College of Physicians and Surgeons, NYC, NY, USA
| | - Risa Kagan
- UCSF and Sutter East Bay Medical Foundation, Berkeley, CA, USA
| | - Deborah Krakow
- University of California Los Angeles, Los Angeles, CA, USA
| | - Michael R McClung
- Oregon Osteoporosis Center, Portland, OR, USA; Mary MacKillop Center for Health Research, Australian Catholic University, Melbourne, VIC, Australia
| | - Paul D Miller
- University of Colorado Health Sciences Center, Denver, CO, USA
| | - Eric T Rush
- University of Kansas Medical Center, Kansas City, MO, USA; Children's Mercy Hospital, Kansas City, MO, USA; University of Missouri - Kansas City, Kansas City, MO, USA
| | | | - Nelson B Watts
- Mercy Health Osteoporosis and Bone Health Services, Cincinnati, OH, USA
| | - Elaine W Yu
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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8
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Ruaud L, Flöttmann R, Spielmann M, Escande F, Van Maldergem L, Mundlos S, Piard J. Split hand/foot malformation associated with 20p12.1 deletion: A case report. Eur J Med Genet 2019; 63:103805. [PMID: 31698100 DOI: 10.1016/j.ejmg.2019.103805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 11/02/2019] [Indexed: 11/17/2022]
Abstract
Split hand/foot malformation (SHFM) or ectrodactyly is a rare congenital disorder affecting limb development characterized by clinical and genetic heterogeneity. SHFM is usually inherited as an autosomal dominant trait with incomplete penetrance. Isolated and syndromic forms are described. The extent of associated malformations is highly variable and multiple syndromes with clinical and genetic overlap have been described. We report here a 28 year-old man presenting with SHFM, sparse hair and widespread freckles. Array-CGH identified a 450 kb de novo 20p12.1 microdeletion encompassing three exons (exon 6 to 8) of MACROD2. Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. Additionally, the deletion encompassed a histone modification H3K27ac mark, known as a provider of quantitative readout of promoter and enhancer activity during human limb development. Altogether, these findings suggest that the 20p12.1 CNV is causative of SHFM in the present case through disturbance of regulatory elements functioning.
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Affiliation(s)
- Lyse Ruaud
- Centre de Génétique Humaine, CHU Besançon, Université de Franche -Comté, Besançon, France; Université de Paris, NeuroDiderot, INSERM, F-75019 Paris, France; Service de génétique clinique, APHP, Hôpital Robert Debré, F-75019 Paris, France
| | - Ricarda Flöttmann
- Charité - Universitätsmedizin Berlin, Institut für Medizinische Genetik, Germany
| | - Malte Spielmann
- Charité - Universitätsmedizin Berlin, Institut für Medizinische Genetik, Germany
| | - Fabienne Escande
- Laboratoire de Biochimie et Biologie Moléculaire, CHU Lille, F-59000 Lille, France; EA7364 RADEME, Univiversité de Lille, F-59000 Lille, France
| | - Lionel Van Maldergem
- Centre de Génétique Humaine, CHU Besançon, Université de Franche -Comté, Besançon, France
| | - Stefan Mundlos
- Charité - Universitätsmedizin Berlin, Institut für Medizinische Genetik, Germany
| | - Juliette Piard
- Centre de Génétique Humaine, CHU Besançon, Université de Franche -Comté, Besançon, France.
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9
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Jourdain A, Petit F, Odou M, Balduyck M, Brunelle P, Dufour W, Boussion S, Brischoux‐Boucher E, Colson C, Dieux A, Gérard M, Ghoumid J, Giuliano F, Goldenberg A, Khau Van Kien P, Lehalle D, Morin G, Moutton S, Smol T, Vanlerberghe C, Manouvrier‐Hanu S, Escande F. Multiplex targeted high‐throughput sequencing in a series of 352 patients with congenital limb malformations. Hum Mutat 2019; 41:222-239. [DOI: 10.1002/humu.23912] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/31/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Anne‐Sophie Jourdain
- Service de Biochimie et Biologie MoléculaireCHU LilleLille France
- EA7364 RADEMEUniv. LilleLille France
| | - Florence Petit
- EA7364 RADEMEUniv. LilleLille France
- Clinique de Génétique Guy FontaineCHU LilleLille France
| | - Marie‐Françoise Odou
- Service de Biochimie et Biologie MoléculaireCHU LilleLille France
- Faculty of Pharmacy, UMR995, LIRIC (Lille Inflammation Research International Center)University of LilleLille France
| | - Malika Balduyck
- Service de Biochimie et Biologie MoléculaireCHU LilleLille France
- EA7364 RADEMEUniv. LilleLille France
| | - Perrine Brunelle
- Service de Biochimie et Biologie MoléculaireCHU LilleLille France
- Clinique de Génétique Guy FontaineCHU LilleLille France
| | | | | | | | | | - Anne Dieux
- Clinique de Génétique Guy FontaineCHU LilleLille France
| | | | - Jamal Ghoumid
- EA7364 RADEMEUniv. LilleLille France
- Clinique de Génétique Guy FontaineCHU LilleLille France
| | | | | | | | - Daphné Lehalle
- Reference Center for Developmental Anomalies, Department of Medical GeneticsDijon University HospitalDijon France
| | - Gilles Morin
- Centre d'activité de Génétique et d'OncogénétiqueCHU Amiens PicardieAmiens France
| | - Sébastien Moutton
- Reference Center for Developmental Anomalies, Department of Medical GeneticsDijon University HospitalDijon France
| | - Thomas Smol
- EA7364 RADEMEUniv. LilleLille France
- Institut de Génétique MédicaleCHU LilleLille France
| | - Clémence Vanlerberghe
- EA7364 RADEMEUniv. LilleLille France
- Clinique de Génétique Guy FontaineCHU LilleLille France
| | - Sylvie Manouvrier‐Hanu
- EA7364 RADEMEUniv. LilleLille France
- Clinique de Génétique Guy FontaineCHU LilleLille France
| | - Fabienne Escande
- Service de Biochimie et Biologie MoléculaireCHU LilleLille France
- EA7364 RADEMEUniv. LilleLille France
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10
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Holt RJ, Young RM, Crespo B, Ceroni F, Curry CJ, Bellacchio E, Bax DA, Ciolfi A, Simon M, Fagerberg CR, van Binsbergen E, De Luca A, Memo L, Dobyns WB, Mohammed AA, Clokie SJ, Zazo Seco C, Jiang YH, Sørensen KP, Andersen H, Sullivan J, Powis Z, Chassevent A, Smith-Hicks C, Petrovski S, Antoniadi T, Shashi V, Gelb BD, Wilson SW, Gerrelli D, Tartaglia M, Chassaing N, Calvas P, Ragge NK. De Novo Missense Variants in FBXW11 Cause Diverse Developmental Phenotypes Including Brain, Eye, and Digit Anomalies. Am J Hum Genet 2019; 105:640-657. [PMID: 31402090 PMCID: PMC6731360 DOI: 10.1016/j.ajhg.2019.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022] Open
Abstract
The identification of genetic variants implicated in human developmental disorders has been revolutionized by second-generation sequencing combined with international pooling of cases. Here, we describe seven individuals who have diverse yet overlapping developmental anomalies, and who all have de novo missense FBXW11 variants identified by whole exome or whole genome sequencing and not reported in the gnomAD database. Their phenotypes include striking neurodevelopmental, digital, jaw, and eye anomalies, and in one individual, features resembling Noonan syndrome, a condition caused by dysregulated RAS signaling. FBXW11 encodes an F-box protein, part of the Skp1-cullin-F-box (SCF) ubiquitin ligase complex, involved in ubiquitination and proteasomal degradation and thus fundamental to many protein regulatory processes. FBXW11 targets include β-catenin and GLI transcription factors, key mediators of Wnt and Hh signaling, respectively, critical to digital, neurological, and eye development. Structural analyses indicate affected residues cluster at the surface of the loops of the substrate-binding domain of FBXW11, and the variants are predicted to destabilize the protein and/or its interactions. In situ hybridization studies on human and zebrafish embryonic tissues demonstrate FBXW11 is expressed in the developing eye, brain, mandibular processes, and limb buds or pectoral fins. Knockdown of the zebrafish FBXW11 orthologs fbxw11a and fbxw11b resulted in embryos with smaller, misshapen, and underdeveloped eyes and abnormal jaw and pectoral fin development. Our findings support the role of FBXW11 in multiple developmental processes, including those involving the brain, eye, digits, and jaw.
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11
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Yamoto K, Saitsu H, Nishimura G, Kosaki R, Takayama S, Haga N, Tonoki H, Okumura A, Horii E, Okamoto N, Suzumura H, Ikegawa S, Kato F, Fujisawa Y, Nagata E, Takada S, Fukami M, Ogata T. Comprehensive clinical and molecular studies in split-hand/foot malformation: identification of two plausible candidate genes (LRP6 and UBA2). Eur J Hum Genet 2019; 27:1845-1857. [PMID: 31332306 DOI: 10.1038/s41431-019-0473-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/27/2019] [Accepted: 07/02/2019] [Indexed: 12/18/2022] Open
Abstract
Split-hand/foot malformation (SHFM) is a clinically and genetically heterogeneous condition. We sequentially performed screening of the previously identified Japanese founder 17p13.3 duplication/triplication involving BHLHA9, array comparative genomic hybridization, and whole exome sequencing (WES) in newly recruited 41 Japanese families with non-syndromic and syndromic SHFM. We also carried out WES in seven families with nonsyndromic and syndromic SHFM in which underlying genetic causes including pathogenic copy-number variants (CNVs) remained undetected in our previous studies of 56 families. Consequently, we identified not only known pathogenic CNVs (17p13.3 duplications/triplications [n = 21], 2q31 deletion [n = 1], and 10q24 duplications [n = 3]) and rare variants in known causative genes (TP63 [n = 3], DLX5 [n = 1], IGF2 [n = 1], WNT10B [n = 3], WNT10B/PORCN [n = 1], and PORCN [n = 1]), but also a de novo 19q13.11 deletion disrupting UBA2 (n = 1) and variants that probably affect function in LRP6 (n = 1) and UBA2 (n = 1). Thus, together with our previous data based on testing of 56 families, molecular studies for a total of 97 families with SHFM revealed underlying genetic causes in 75 families, and clinical studies for the 75 families indicated a certain degree of correlation between genetic causes and phenotypes. The results imply that SHFM primarily occurs as a genetic disorder with genotype-phenotype correlations. Furthermore, the results together with previous data such as the development of SHFM in Lrp6 knockout mice, the presence of SHFM in two subjects with 19q13 deletions involving UBA2, and strong mouse Uba2 expression in the developing limb buds, imply that LRP6 and UBA2 represent plausible candidate genes for SHFM.
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Affiliation(s)
- Kaori Yamoto
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Gen Nishimura
- Center for Intractable Diseases, Saitama Medical University Hospital, Iruma, Japan
| | - Rika Kosaki
- Division of Medical Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Shinichiro Takayama
- Division of Orthopedic Surgery, National Center for Child Health and Development, Tokyo, Japan
| | - Nobuhiko Haga
- Department of Rehabilitation Medicine, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Hidefumi Tonoki
- Department of Pediatrics, Sapporo Tenshi Hospital, Sapporo, Japan
| | - Akihisa Okumura
- Department of Pediatrics, Aichi Medical University, Nagakute, Japan
| | - Emiko Horii
- Department of Orthopedic Surgery, Nagoya First Red Cross Hospital, Nagoya, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Hiroshi Suzumura
- Department of Pediatrics, Dokkyo Medical University School of Medicine, Mibu, Japan
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
| | - Fumiko Kato
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yasuko Fujisawa
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Eiko Nagata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan. .,Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.
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12
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Paththinige CS, Sirisena ND, Escande F, Manouvrier S, Petit F, Dissanayake VHW. Split hand/foot malformation with long bone deficiency associated with BHLHA9 gene duplication: a case report and review of literature. BMC MEDICAL GENETICS 2019; 20:108. [PMID: 31200655 PMCID: PMC6570964 DOI: 10.1186/s12881-019-0839-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/03/2019] [Indexed: 12/11/2022]
Abstract
Background Split hand/foot malformation (SHFM) is a group of congenital skeletal disorders which may occur either as an isolated abnormality or in syndromic forms with extra-limb manifestations. Chromosomal micro-duplication or micro-triplication involving 17p13.3 region has been described as the most common cause of split hand/foot malformation with long bone deficiency (SHFLD) in several different Caucasian and Asian populations. Gene dosage effect of the extra copies of BHLHA9 gene at this locus has been implicated in the pathogenesis of SHFLD. Case presentation The proband was a female child born to non-consanguineous parents. She was referred for genetic evaluation of bilateral asymmetric ectrodactyly involving both hands and right foot along with right tibial hemimelia. The right foot had fixed clubfoot deformity with only 2 toes. The mother had bilateral ectrodactyly involving both hands, but the rest of the upper limbs and both lower limbs were normal. Neither of them had any other congenital malformations or neurodevelopmental abnormalities. Genetic testing for rearrangement of BHLHA9 gene by quantitative polymerase chain reaction confirmed the duplication of the BHLHA9 gene in both the proband and the mother. Conclusions We report the first Sri Lankan family with genetic diagnosis of BHLHA9 duplication causing SHFLD. This report along with the previously reported cases corroborate the possible etiopathogenic role of BHLHA9 gene dosage imbalances in SHFM and SHFLD across different populations.
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Affiliation(s)
- Chamara Sampath Paththinige
- Human Genetics Unit, Faculty of Medicine, University of Colombo, Kynsey Road, Colombo, 00800, Sri Lanka. .,Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Anuradhapura, 50008, Sri Lanka.
| | | | - Fabienne Escande
- Laboratoire de Biochimie et Oncologie Moléculaire, CHU Lille, F-59000, Lille, France
| | - Sylvie Manouvrier
- Clinique de Génétique Guy Fontaine, CHU Lille, F-59000, Lille, France
| | - Florence Petit
- Clinique de Génétique Guy Fontaine, CHU Lille, F-59000, Lille, France
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13
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Duplication of 10q24 locus: broadening the clinical and radiological spectrum. Eur J Hum Genet 2019; 27:525-534. [PMID: 30622331 DOI: 10.1038/s41431-018-0326-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/25/2017] [Accepted: 12/04/2018] [Indexed: 01/21/2023] Open
Abstract
Split-hand-split-foot malformation (SHFM) is a rare condition that occurs in 1 in 8500-25,000 newborns and accounts for 15% of all limb reduction defects. SHFM is heterogeneous and can be isolated, associated with other malformations, or syndromic. The mode of inheritance is mostly autosomal dominant with incomplete penetrance, but can be X-linked or autosomal recessive. Seven loci are currently known: SHFM1 at 7q21.2q22.1 (DLX5 gene), SHFM2 at Xq26, SHFM3 at 10q24q25, SHFM4 at 3q27 (TP63 gene), SHFM5 at 2q31 and SHFM6 as a result of variants in WNT10B (chromosome 12q13). Duplications at 17p13.3 are seen in SHFM when isolated or associated with long bone deficiency. Tandem genomic duplications at chromosome 10q24 involving at least the DACTYLIN gene are associated with SHFM3. No point variant in any of the genes residing within the region has been identified so far, but duplication of exon 1 of the BTRC gene may explain the phenotype, with likely complex alterations of gene regulation mechanisms that would impair limb morphogenesis. We report on 32 new index cases identified by array-CGH and/or by qPCR, including some prenatal ones, leading to termination for the most severe. Twenty-two cases were presenting with SHFM and 7 with monodactyly only. Three had an overlapping phenotype. Additional findings were identified in 5 (renal dysplasia, cutis aplasia, hypogonadism and agenesis of corpus callosum with hydrocephalus). We present their clinical and radiological findings and review the literature on this rearrangement that seems to be one of the most frequent cause of SHFM.
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14
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Pasińska M, Łazarczyk E, Jułga K, Bartnik-Głaska M, Nowakowska B, Haus O. Multiple occurrence of psychomotor retardation and recurrent miscarriages in a family with a submicroscopic reciprocal translocation t(7;17)(p22;p13.2). BMC Med Genomics 2018; 11:69. [PMID: 30126420 PMCID: PMC6102823 DOI: 10.1186/s12920-018-0384-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 08/02/2018] [Indexed: 11/24/2022] Open
Abstract
Background Balanced reciprocal chromosomal translocations (RCTs) are the ones of the most common structural aberrations in the population, with an incidence of 1:625. RCT carriers usually do not demonstrate changes in phenotype, except when the translocation results in gene interruption. However, these people are at risk of production of unbalanced gametes during meiosis, as a result of various forms of chromosome segregation. This may cause infertility, non-implantation of the embryo, shorter embryo or foetus survival, as well as congenital defects and developmental disorders in children after birth. The increasing popularity of cytogenetic molecular techniques, such as microarray-based CGH (aCGH), contributed to the improved detection of chromosomal abnormalities in patients with intellectual disability, however, these modern techniques do not allow the identification of the balanced in potential carriers. Therefore, classical chromosome analysis with GTG technique still plays an important role in the identification of balanced rearrangements in every case of procreation failure. Case presentation In this article, a family with multiple occurrences of 17p13.3 duplication syndrome in the offspring and multiple miscarriages resulting from carrying of the balanced reciprocal translocation t(7;17)(p22;p13.2) by proband father is presented. The aCGH diagnostics allowed the identification of an unbalanced fragment responsible for the occurrence of clinical signs in the female patient, while karyotyping and FISH using specific probes allowed the localization of the additional material in the patient chromosomes, and identified the type of this translocation in the carriers. Conclusions Identification of a balanced structural aberration in one of the partners allows direct diagnostics for the exclusion or confirmation of genetic imbalance in the foetus via traditional invasive prenatal diagnostics. It is also possible to use an alternative method, Preimplantation Genetic Diagnosis (PGD) after in vitro fertilization, which prevents initiating pregnancy if genetic imbalance is detected in the embryo.
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Affiliation(s)
- Magdalena Pasińska
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Skłodowskiej - Curie 9, 85-094, Bydgoszcz, Poland.
| | - Ewelina Łazarczyk
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Skłodowskiej - Curie 9, 85-094, Bydgoszcz, Poland
| | - Katarzyna Jułga
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Skłodowskiej - Curie 9, 85-094, Bydgoszcz, Poland
| | - Magdalena Bartnik-Głaska
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland
| | - Beata Nowakowska
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland
| | - Olga Haus
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Skłodowskiej - Curie 9, 85-094, Bydgoszcz, Poland
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15
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Bedard T, Lowry RB, Sibbald B, Crawford S, Kiefer GN. Congenital limb deficiencies and major associated anomalies in Alberta for the years 1980-2012. Am J Med Genet A 2017; 176:19-28. [PMID: 29168277 DOI: 10.1002/ajmg.a.38513] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/23/2017] [Accepted: 09/26/2017] [Indexed: 12/11/2022]
Abstract
There is a wide range of the proportion of congenital anomalies associated with limb deficiencies reported in the literature. This variation is primarily attributed to methodology and classification differences. The distribution of associated anomalies among cases with congenital limb deficiencies in Alberta born between January 1, 1980 and December 31, 2012 is described. Of the 170 cases identified, most were live born (75.3%), male (61.8%), had longitudinal limb deficiencies (78.8%), and had associated anomalies outside the musculoskeletal system (77.6%). Significant associations between the preaxial longitudinal group and the central nervous, gastrointestinal, and cardiovascular systems are reported as well as between the postaxial longitudinal group and congenital hip and foot anomalies. Probable and possible syndrome diagnoses are described for cases with recognized malformation patterns.
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Affiliation(s)
- Tanya Bedard
- Alberta Congenital Anomalies Surveillance System, Alberta Health, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - R Brian Lowry
- Alberta Congenital Anomalies Surveillance System, Alberta Health, Alberta Children's Hospital, Calgary, Alberta, Canada.,Departments of Pediatrics and Medical Genetics, University of Calgary, Alberta Children's Hospital, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
| | - Barbara Sibbald
- Alberta Congenital Anomalies Surveillance System, Alberta Health, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Susan Crawford
- Alberta Perinatal Health Program, Calgary, Alberta, Canada
| | - Gerhard N Kiefer
- Alberta Congenital Anomalies Surveillance System, Alberta Health, Alberta Children's Hospital, Calgary, Alberta, Canada.,Department of Surgery, University of Calgary, Alberta Children's Hospital, Calgary, Alberta, Canada
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