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Sun G, Huang W, Wang L, Wu J, Zhao G, Ren H, Liu L, Kong X. Molecular findings in patients for whole exome sequencing and mitochondrial genome assessment. Clin Chim Acta 2024; 561:119774. [PMID: 38852791 DOI: 10.1016/j.cca.2024.119774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/20/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
OBJECTIVE Whole exome sequencing (WES) is becoming more widely used as a diagnostic tool in the field of medicine. In this article, we reported the diagnostic yield of WES and mitochondrial genome assessment in 2226 consecutive cases in a single clinical laboratory. MATERIALS AND METHODS We retrospectively analyzed consecutive WES reports from 2226 patients with various genetic disorders. WES-process was focused exclusively on the probands and aimed at a higher diagnostic capacity. We determined the diagnostic rate of WES overall and by phenotypic category, mode of inheritance, mitochondrial genome variant, and copy number variants (CNVs). RESULTS Among the 2226 patients who had diagnostic WES proband-only, the overall diagnostic yield of WES was 34.59% (770/2226). The highest diagnostic yield was observed in autosomal dominant disorders, at 45.58% (351/770), followed by autosomal recessive at 31.95%(246/770), X-linked disorder at 9.61%(74/770), and mitochondrial diseases at a notably lower 0.65%(5/770). The 12.21% (94/770) diagnoses were based on a total of 94 copy number variants reported from WES data. CNVs in children accounted for 67.02% of the total CNVs. While majority of the molecular diagnoses were related to nuclear genes, the inclusion of mitochondrial genome sequencing in the WES test contributed to five diagnoses. all mitochondrial diseases were identified in adults. CONCLUSIONS The proband-only WES provided a definitive molecular diagnosis for 34.59% of a large cohort of patients while analysis of WES simultaneously analyzed the SNVs, exons, mitochondrial genome, and CNVs, thereby improving the diagnostic yield significantly compared to the single-detection WES method; and facilitating the identification of novel candidate genes.
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Affiliation(s)
- Gege Sun
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Huang
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Li Wang
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinlin Wu
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ganye Zhao
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huanan Ren
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lina Liu
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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Su H, Liu S, Xu H, Shen C, Xu M, Zhang J, Li D. A rapid PCR-free next-generation sequencing method for comprehensive diagnosis of chromosome disease syndromes in prenatal samples. Medicine (Baltimore) 2024; 103:e37610. [PMID: 38552051 PMCID: PMC10977541 DOI: 10.1097/md.0000000000037610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 02/23/2024] [Indexed: 04/02/2024] Open
Abstract
The aim of this study is to investigate the application performance of rapid copy number variation sequencing (rCNV-seq) technology for the detection of chromosomal abnormalities during prenatal diagnosis. Samples were collected from 424 pregnant women who were at high-risk for noninvasive prenatal screening in Kunming Maternal and Child Care Hospital from January 2018 to May 2022. rCNV-seq technique was used to detect fetal chromosome abnormalities and compare the results with that of chromosomal karyotype analysis. The Result showed that 330 (77.83%, 330/424) cases indicated chromosomal abnormalities among 424 high-risk pregnant women who underwent rCNV-seq. Moreover, 94 (22.17%, 94/424) cases were discovered to have copy number variations. Among the 330 fetuses with chromosomal abnormalities, common autosomal aneuploidy was observed in 203 cases (47.87%, 203/424) and sex chromosome aneuploidy was observed in 91 cases (21.46%, 91/424). Moreover, the abnormalities in multiple chromosomes were discovered in 33 cases (7.78%, 33/424), and the rare autosomal aneuploidy was observed in 3 cases (0.71%, 3/424). There were 63 fetuses (14.86%, 63/424) with pathogenic CNVs among the 94 fetuses with variable copy numbers. Of the 245 pregnant women who voluntarily selected G-band karyotyping, 1 fetus with copy number variation had normal karyotype results, and the remaining women were consistent with rCNV-seq. Our study revealed that rCNV-seq has higher accuracy in detecting common trisomy and can also detect chromosomal microdeletions or microduplications that cannot be detected by G-banding karyotype analysis. There is no effective treatment for chromosomal diseases, so it is particularly important to prevent chromosomal diseases through genetic counseling and prenatal diagnosis of chromosomal diseases.
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Affiliation(s)
- Hong Su
- Department of Obstetrics, Kunming Maternal and Child Care Hospital, Kunming, Yunnan, China
| | - Shengni Liu
- BSc(Hons) Biomedical Science, University of Bristol, Bristol, England
| | - Hongxia Xu
- Department of Reproductive Medicine, The First People’s Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China, National Health Commission Key Laboratory of Preconception Health Birth in Western China, Kunming, Yunnan, China
| | - Cuihua Shen
- Department of Obstetrics, Kunming Maternal and Child Care Hospital, Kunming, Yunnan, China
| | - Min Xu
- Department of Obstetrics, Kunming Maternal and Child Care Hospital, Kunming, Yunnan, China
| | - Jing Zhang
- Department of Obstetrics, Kunming Maternal and Child Care Hospital, Kunming, Yunnan, China
| | - Dongyun Li
- Department of Obstetrics, Kunming Maternal and Child Care Hospital, Kunming, Yunnan, China
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Wu J, Cui Y, Liu T, Gu C, Ma X, Yu C, Cai Y, Shu J, Wang W, Cai C. Whole exome sequencing approach for identification of the molecular etiology in pediatric patients with hematuria. Clin Chim Acta 2024; 554:117795. [PMID: 38262496 DOI: 10.1016/j.cca.2024.117795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/25/2023] [Accepted: 01/20/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND Hematuria is a common condition in clinical practice of pediatric patients. It is related to a wide spectrum of disorders and has high heterogeneity both clinically and genetically, which contributes to challenges of diagnosis and lead many pediatric patients with hematuria not to receive accurate diagnosis and early management. METHODS In this single center study, 42 children with hematuria were included in Tianjin Children's Hospital between 2019 and 2020. We analyzed the clinical information and performed WES (Whole exome sequencing) for all cases. Then the classification of identified variants was performed according to the American College of Medical Genetics and Genomics (ACMG) guidelines for interpreting sequence variants. For the fragment deletion, qPCR was performed to validate and confirm the inherited pattern. RESULTS For the 42 patients, 16 cases had gross hematuria and 26 had microscopic hematuria. Molecular genetic causes were uncovered in 9 (21.4%) children, including 7 with Alport syndrome (AS), one with polycystic nephropathy and one with lipoprotein glomerulopathy. The genetic causes for other patients were not related with hematuria. CONCLUSIONS WES is a rapid and effective way to evaluate patients with hematuria. The analysis of genotype-phenotype correlations of patients with AS indicated that severe variants were associated with early kidney failure. Secondary findings were not rare in Chinese children, thus the clinician should pay more attention to the clinical interpretation of sequencing results and properly interaction with patients and their family.
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Affiliation(s)
- Jinying Wu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China
| | - Yaqiong Cui
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China
| | - Tao Liu
- The department of nephrology, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin 300134, China
| | - Chunyu Gu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China
| | - Ximeng Ma
- Basic Medical College, Tianjin Medical University, Tianjin 30070, China
| | - Changshun Yu
- Tianjin KingMed Center for Clinical Laboratory Co. Ltd., Tianjin 300392, China
| | - Yingzi Cai
- Department of Medicine,Tianjin University, Tianjin 300110, China
| | - Jianbo Shu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China.
| | - Wenhong Wang
- The department of nephrology, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin 300134, China.
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China.
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Tang C, Tang F, Cai Y, Tan M, Liu S, Xie T, Jiang X, Huang Y. A pilot study of newborn screening for X-linked adrenoleukodystrophy based on liquid chromatography-tandem mass spectrometry method for detection of C26:0-lysophosphatidylcholine in dried blood spots: Results from 43,653 newborns in a southern Chinese population. Clin Chim Acta 2024; 552:117653. [PMID: 37977233 DOI: 10.1016/j.cca.2023.117653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND X-linked adrenoleukodystrophy (X-ALD) is a rare X-linked disease caused by mutations of the ABCD1 gene. C26:0-lysophosphatidylcholine (C26:0-LPC) has been proved to be an accurate biomarker for X-ALD. This study aims to propose an effective method for screening of X-ALD and to evaluate the performance of the newborn screening (NBS) assay for X-ALD in Guangzhou. METHODS C26:0-LPC in dried blood spots (DBS) was extracted by methanol solution containing isotope-labelled internal standard (C26:0-d4-LPC) and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The sensitivity of the method was assessed in eight male X-ALD patients, two female carriers and 583 healthy controls. The method was conducted on 43,653 newborns. Next generation sequencing was performed on screen-positive samples. Plasma analysis of very long-chain fatty acids and genetic counselling were performed by way of follow-up. RESULTS Elevated C26:0-LPC were 100% sensitive for screening of X-ALD. Of 43,653 newborns, 32 (18 males, 14 females) screened positive. Of these, 14 (43.7%) were identified ABCD1 variants, including seven hemizygous males and seven heterozygous females, and two (6.3%) were diagnosed with other peroxisomal disorders. CONCLUSION The LC-MS/MS method for screening of X-ALD can identify males, heterozygous females and other peroxisomal disorders. The incidence of X-ALD in Guangzhou is not low.
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Affiliation(s)
- Chengfang Tang
- Guangzhou Newborn Screening Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Fang Tang
- Guangzhou Newborn Screening Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Yanna Cai
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Minyi Tan
- Guangzhou Newborn Screening Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Sichi Liu
- Guangzhou Newborn Screening Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Ting Xie
- Guangzhou Newborn Screening Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Xiang Jiang
- Guangzhou Newborn Screening Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Yonglan Huang
- Guangzhou Newborn Screening Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, Guangdong, China.
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Rosina E, Pezzani L, Apuril E, Pezzoli L, Marchetti D, Bellini M, Lucca C, Meossi C, Massimello M, Mariani M, Scatigno A, Cattaneo E, Colombo L, Maitz S, Cereda A, Milani D, Spaccini L, Bedeschi MF, Selicorni A, Iascone M. Comparison of first-tier whole-exome sequencing with a multi-step traditional approach for diagnosing paediatric outpatients: An Italian prospective study. Mol Genet Genomic Med 2024; 12:e2316. [PMID: 38041506 PMCID: PMC10767581 DOI: 10.1002/mgg3.2316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND The recent guidelines suggest the use of genome-wide analyses, such as whole exome sequencing (WES), at the beginning of the diagnostic approach for cases with suspected genetic conditions. However, in many realities it still provides for the execution of a multi-step pathway, thus requiring several genetic tests to end the so-called 'diagnostic odyssey'. METHODS We reported the results of GENE Project (Genomic analysis Evaluation NEtwork): a multicentre prospective cohort study on 125 paediatric outpatients with a suspected genetic disease in which we performed first-tier trio-WES, including exome-based copy number variation analysis, in parallel to a 'traditional approach' of two/three sequential genetic tests. RESULTS First-tier trio-WES detected a conclusive diagnosis in 41.6% of patients, way above what was found with routine genetic testing (25%), with a time-to-result of about 50 days. Notably, the study showed that 44% of WES-reached diagnoses would be missed with the traditional approach. The diagnostic rate (DR) of the two approaches varied in relation to the phenotypic class of referral and to the proportion of cases with a defined diagnostic suspect, proving the major difference for neurodevelopmental disorders. Moreover, trio-WES analysis detected variants in candidate genes of unknown significance (EPHA4, DTNA, SYNCRIP, NCOR1, TFDP1, SPRED3, EDA2R, PHF12, PPP1R12A, WDR91, CDC42BPG, CSNK1D, EIF3H, TMEM63B, RIPPLY3) in 19.4% of undiagnosed cases. CONCLUSION Our findings represent real-practice evidence of how first-tier genome-wide sequencing tests significantly improve the DR for paediatric outpatients with a suspected underlying genetic aetiology, thereby allowing a time-saving setting of the correct management, follow-up and family planning.
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Affiliation(s)
- Erica Rosina
- Laboratory of Medical GeneticsASST Papa Giovanni XXIIIBergamoItaly
| | | | - Erika Apuril
- Laboratory of Medical GeneticsASST Papa Giovanni XXIIIBergamoItaly
| | - Laura Pezzoli
- Laboratory of Medical GeneticsASST Papa Giovanni XXIIIBergamoItaly
| | | | - Matteo Bellini
- Laboratory of Medical GeneticsASST Papa Giovanni XXIIIBergamoItaly
| | - Camilla Lucca
- Laboratory of Medical GeneticsASST Papa Giovanni XXIIIBergamoItaly
| | - Camilla Meossi
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore PoliclinicoMilanItaly
| | - Marta Massimello
- Department of PediatricsFondazione IRCCS San Gerardo dei TintoriMonzaItaly
| | - Milena Mariani
- Department of PediatricsASST Lariana Sant' Anna HospitalComoItaly
| | | | - Elisa Cattaneo
- Clinical Genetics Unit, Department of Obstetrics and GynecologyV. Buzzi Children's Hospital, University of MilanMilanItaly
| | - Lorenzo Colombo
- Neonatal Intensive Care Unit (NICU)Fondazione IRCCS Ca' Granda Ospedale Maggiore PoliclinicoMilanItaly
| | - Silvia Maitz
- Medical Genetics ServiceIOSI, Ente Ospedaliero CantonaleLuganoSwitzerland
| | - Anna Cereda
- Paediatric UnitASST Papa Giovanni XXIIIBergamoItaly
| | - Donatella Milani
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore PoliclinicoMilanItaly
| | - Luigina Spaccini
- Clinical Genetics Unit, Department of Obstetrics and GynecologyV. Buzzi Children's Hospital, University of MilanMilanItaly
| | | | - Angelo Selicorni
- Department of PediatricsASST Lariana Sant' Anna HospitalComoItaly
| | - Maria Iascone
- Laboratory of Medical GeneticsASST Papa Giovanni XXIIIBergamoItaly
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6
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James KN, Chowdhury S, Ding Y, Batalov S, Watkins K, Kwon YH, Van Der Kraan L, Ellsworth K, Kingsmore SF, Guidugli L. Genome sequencing detects a wide range of clinically relevant copy-number variants and other genomic alterations. Genet Med 2024; 26:101006. [PMID: 37869996 DOI: 10.1016/j.gim.2023.101006] [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: 04/04/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
PURPOSE Copy-number variants (CNVs) and other non-single nucleotide variant/indel variant types contribute an important proportion of diagnoses in individuals with suspected genetic disease. This study describes the range of such variants detected by genome sequencing (GS). METHODS For a pediatric cohort of 1032 participants undergoing clinical GS, we characterize the CNVs and other non-single nucleotide variant/indel variant types that were reported, including aneuploidies, mobile element insertions, and uniparental disomies, and we describe the bioinformatic pipeline used to detect these variants. RESULTS Together, these genetic alterations accounted for 15.8% of reported variants. Notably, 67.9% of these were deletions, 32.9% of which overlapped a single gene, and many deletions were reported together with a second variant in the same gene in cases of recessive disease. A retrospective medical record review in a subset of this cohort revealed that up to 6 additional genetic tests were ordered in 68% (26/38) of cases, some of which failed to report the CNVs/rare variants reported on GS. CONCLUSION GS detected a broad range of reported variant types, including CNVs ranging in size from 1 Kb to 46 Mb.
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Affiliation(s)
- Kiely N James
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Kelly Watkins
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Yong Hyun Kwon
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | | | | | - Lucia Guidugli
- Rady Children's Institute for Genomic Medicine, San Diego, CA.
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7
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Pande S, Majethia P, Nair K, Rao LP, Mascarenhas S, Kaur N, do Rosario MC, Neethukrishna K, Chaurasia A, Hunakunti B, Jadhav N, Xavier S, Kumar J, Bhat V, Bhavani GS, Narayanan DL, Yatheesha BL, Patil SJ, Nampoothiri S, Kamath N, Aroor S, Bhat Y R, Lewis LE, Sharma S, Bajaj S, Sankhyan N, Siddiqui S, Nayak SS, Bielas S, Girisha KM, Shukla A. De novo variants underlying monogenic syndromes with intellectual disability in a neurodevelopmental cohort from India. Eur J Hum Genet 2023:10.1038/s41431-023-01513-7. [PMID: 38114583 DOI: 10.1038/s41431-023-01513-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/21/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023] Open
Abstract
The contribution of de novo variants as a cause of intellectual disability (ID) is well established in several cohorts reported from the developed world. However, the genetic landscape as well as the appropriate testing strategies for identification of de novo variants of these disorders remain largely unknown in low-and middle-income countries like India. In this study, we delineate the clinical and genotypic spectrum of 54 families (55 individuals) with syndromic ID harboring rare de novo variants. We also emphasize on the effectiveness of singleton exome sequencing as a valuable tool for diagnosing these disorders in resource limited settings. Overall, 46 distinct disorders were identified encompassing 46 genes with 51 single-nucleotide variants and/or indels and two copy-number variants. Pathogenic variants were identified in CREBBP, TSC2, KMT2D, MECP2, IDS, NIPBL, NSD1, RIT1, SOX10, BRWD3, FOXG1, BCL11A, KDM6B, KDM5C, SETD5, QRICH1, DCX, SMARCD1, ASXL1, ASXL3, AKT3, FBN2, TCF12, WASF1, BRAF, SMARCA4, SMARCA2, TUBG1, KMT2A, CTNNB1, DLG4, MEIS2, GATAD2B, FBXW7, ANKRD11, ARID1B, DYNC1H1, HIVEP2, NEXMIF, ZBTB18, SETD1B, DYRK1A, SRCAP, CASK, L1CAM, and KRAS. Twenty-four of these monogenic disorders have not been previously reported in the Indian population. Notably, 39 out of 53 (74%) disease-causing variants are novel. These variants were identified in the genes mainly encoding transcriptional and chromatin regulators, serine threonine kinases, lysosomal enzymes, molecular motors, synaptic proteins, neuronal migration machinery, adhesion molecules, structural proteins and signaling molecules.
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Affiliation(s)
- Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Purvi Majethia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Karthik Nair
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Lakshmi Priya Rao
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Selinda Mascarenhas
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Namanpreet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Michelle C do Rosario
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Kausthubham Neethukrishna
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ankur Chaurasia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Bhagesh Hunakunti
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Nalesh Jadhav
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Sruthy Xavier
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Jeevan Kumar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Vivekananda Bhat
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - B L Yatheesha
- Dheemahi Child Neurology and Development Center, Shivamogga, India
| | - Siddaramappa J Patil
- Division of Medical Genetics, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, India
| | - Nutan Kamath
- Department of Paediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Shrikiran Aroor
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ramesh Bhat Y
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Leslie E Lewis
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Suvasini Sharma
- Neurology Division, Department of Pediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India
| | | | - Naveen Sankhyan
- Pediatric Neurology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Shahyan Siddiqui
- Department of Neuro and Vascular Interventional Radiology, Yashoda Hospitals, Secunderabad, Hyderabad, India
| | - Shalini S Nayak
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States of America
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Suma Genomics Private Limited, Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
- Department of Genetics, College of Medicine & Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
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8
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Louw N, Carstens N, Lombard Z. Incorporating CNV analysis improves the yield of exome sequencing for rare monogenic disorders-an important consideration for resource-constrained settings. Front Genet 2023; 14:1277784. [PMID: 38155715 PMCID: PMC10753787 DOI: 10.3389/fgene.2023.1277784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
Exome sequencing (ES) is a recommended first-tier diagnostic test for many rare monogenic diseases. It allows for the detection of both single-nucleotide variants (SNVs) and copy number variants (CNVs) in coding exonic regions of the genome in a single test, and this dual analysis is a valuable approach, especially in limited resource settings. Single-nucleotide variants are well studied; however, the incorporation of copy number variant analysis tools into variant calling pipelines has not been implemented yet as a routine diagnostic test, and chromosomal microarray is still more widely used to detect copy number variants. Research shows that combined single and copy number variant analysis can lead to a diagnostic yield of up to 58%, increasing the yield with as much as 18% from the single-nucleotide variant only pipeline. Importantly, this is achieved with the consideration of computational costs only, without incurring any additional sequencing costs. This mini review provides an overview of copy number variant analysis from exome data and what the current recommendations are for this type of analysis. We also present an overview on rare monogenic disease research standard practices in resource-limited settings. We present evidence that integrating copy number variant detection tools into a standard exome sequencing analysis pipeline improves diagnostic yield and should be considered a significantly beneficial addition, with relatively low-cost implications. Routine implementation in underrepresented populations and limited resource settings will promote generation and sharing of CNV datasets and provide momentum to build core centers for this niche within genomic medicine.
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Affiliation(s)
- Nadja Louw
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Yan L, He Y, Zhang Y, Liu Y, Xu L, Han C, Zhao Y, Li H. A novel 268 kb deletion combined with a splicing variant in IL7R causes of severe combined immunodeficiency in a Chinese family: a case report. BMC Med Genomics 2023; 16:323. [PMID: 38082310 PMCID: PMC10712040 DOI: 10.1186/s12920-023-01765-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Severe combined immunodeficiency (SCID) is a group of fatal primary immunodeficiencies characterized by the severe impairment of T-cell differentiation. IL7R deficiency is a rare form of SCID that usually presents in the first months of life with severe and opportunistic infections, failure to thrive, and a high risk of mortality unless treated. Although recent improvements in early diagnosis have been achieved through newborn screening, few IL7R-related SCID patients had been reported in the Chinese population. CASE PRESENTATION Here, we retrospectively analyzed a case of SCID in a 5-month-old girl with symptoms, including severe T-cell depletion, recurrent fever, oral ulcers, pneumonia, hepatosplenomegaly, bone marrow hemophagocytosis, and bacterial and viral infections. Whole-exome sequencing (WES), quantitative PCR (qPCR), and chromosome microarray analysis (CMA) were performed to identify the patient's genetic etiology. We identified a 268 kb deletion and a splicing variant, c.221 + 1G > A, in the proband. These two variants of IL7R were inherited from the father and mother. CONCLUSIONS To our knowledge, this is the first report of whole IL7R gene deletion in combination with a pathogenic splicing variant in a patient with SCID. This deletion also expands the pathogenic variation spectrum of SCID caused by IL7R. The incorporation of exome-based copy number variant analysis makes WES a powerful molecular diagnostic technique for the clinical diagnosis of pediatric patients.
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Affiliation(s)
- Lulu Yan
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China
| | - Yan He
- Department of Pediatrics, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China
| | - Yuxin Zhang
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China
| | - Yingwen Liu
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China
| | - Limin Xu
- Department of Pediatrics, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China
| | - Chunxiao Han
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China
| | - Yudan Zhao
- Department of Pediatrics, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China
| | - Haibo Li
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China.
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10
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Xie M, Xue J, Zhang Y, Zhou Y, Yu Q, Li H, Li Q. Combination of trio-based whole exome sequencing and optical genome mapping reveals a cryptic balanced translocation that causes unbalanced chromosomal rearrangements in a family with multiple anomalies. Front Genet 2023; 14:1248544. [PMID: 37745854 PMCID: PMC10512417 DOI: 10.3389/fgene.2023.1248544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023] Open
Abstract
Background: Balanced translocation (BT) carriers can produce imbalanced gametes and experience recurrent spontaneous abortions (RSAs) and even give birth to a child with complex chromosomal disorders. Here, we report a cryptic BT, t(5; 6) (p15.31; p25.1), in the proband's grandmother, which caused unbalanced chromosomal rearrangements and various anomalies in the two subsequent generations. We also provide a thorough overview of the application of optical genome mapping (OGM) to identify chromosomal structural variants (SVs). Methods: Trio-based whole exome sequencing (Trio-WES) was conducted to explore the genetic basis of the phenotype of the proband and her mother. High-resolution karyotype analysis and OGM detection were performed on the proband's grandparents to trace the origin of the unbalanced rearrangements between chromosomes 5 and 6. A PubMed search was conducted with the following keywords: "OGM" and "SVs." Then, relevant studies were collected and systematically reviewed. Results: The proband and her mother presented with various anomalies, whereas the grandmother was healthy but had a history of four abnormal pregnancies. Trio-WES revealed a heterozygous duplication on the terminal region of chromosome 5p and a heterozygous deletion on the proximal end of chromosome 6p in the proband and her mother. High-resolution karyotype analysis revealed no aberrant karyotypes in either grandparent, whereas OGM detection revealed a cryptic BT, t(5; 6)(p15.31; p25.1), in the proband's grandmother. An overwhelming majority of research publications have verified the clinical utility of OGM in detecting SVs. Conclusion: The results of this study revealed that the unbalanced chromosomal rearrangements and many anomalies observed in multiple members of the family were attributable to the cryptic BT carried by the proband's grandmother. This study supports that OGM has a unique advantage for detecting cryptic BTs, and can be used as a first-tier genetic test for the etiological diagnosis of infertility, RSAs, and other complex genetic disorders.
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Affiliation(s)
- Min Xie
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children’s Hospital, Ningbo, Zhejiang, China
| | - Jiangyang Xue
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children’s Hospital, Ningbo, Zhejiang, China
| | - Yuxin Zhang
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children’s Hospital, Ningbo, Zhejiang, China
| | - Ying Zhou
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children’s Hospital, Ningbo, Zhejiang, China
| | - Qi Yu
- Neonatal Screening Center, Ningbo Women and Children’s Hospital, Ningbo, Zhejiang, China
| | - Haibo Li
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children’s Hospital, Ningbo, Zhejiang, China
| | - Qiong Li
- Neonatal Screening Center, Ningbo Women and Children’s Hospital, Ningbo, Zhejiang, China
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Yu L, Ding H, Liu M, Liu L, Zhang Q, Lu J, Guo F, Zhang Y. A novel 1p13.2 deletion associates with neurodevelopmental disorders in a three-generation pedigree. BMC Med Genomics 2023; 16:114. [PMID: 37221554 DOI: 10.1186/s12920-023-01534-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 05/05/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND A multitude of studies have highlighted that copy number variants (CNVs) are associated with neurodevelopmental disorders (NDDs) characterized by a wide range of clinical characteristics. Benefiting from CNV calling from WES data, WES has emerged as a more powerful and cost-effective molecular diagnostic tool, which has been widely used for the diagnosis of genetic diseases, especially NDDs. To our knowledge, isolated deletions on chromosome 1p13.2 are rare. To date, only a few patients were reported with 1p13.2 deletions and most of them were sporadic. Besides, the correlation between 1p13.2 deletions and NDDs remained unclear. CASE PRESENTATION Here, we first reported five members in a three-generation Chinese family who presented with NDDs and carried a novel 1.41 Mb heterozygous 1p13.2 deletion with precise breakpoints. The diagnostic deletion contained 12 protein-coding genes and was observed to segregate with NDDs among the members of our reported family. Whether those genes contribute to the patient's phenotypes is still inconclusive. CONCLUSIONS We hypothesized that the NDD phenotype of our patients was caused by the diagnostic 1p13.2 deletion. However, further in-depth functional experiments are still needed to establish a 1p13.2 deletion-NDDs relationship. Our study might supplement the spectrum of 1p13.2 deletion-NDDs.
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Affiliation(s)
- Lihua Yu
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Hongke Ding
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Min Liu
- Prenatal diagnostic center, Huizhou No2 Maternal and Children's Healthcare Hospital, Huizhou, China
| | - Ling Liu
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Qi Zhang
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Jian Lu
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Fangfang Guo
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Yan Zhang
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.
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Yao L, Zhu Z, Zhang C, Tian W, Cao L. PLP1 gene mutations cause spastic paraplegia type 2 in three families. Ann Clin Transl Neurol 2023; 10:328-338. [PMID: 36622199 PMCID: PMC10014006 DOI: 10.1002/acn3.51722] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVE Spastic paraplegia type 2 (SPG2) is an X-linked recessive (XLR) form of hereditary spastic paraplegia (HSP) caused by mutations in proteolipid protein 1 (PLP1) gene. We described the clinical and genetic features of three unrelated families with PLP1 mutations and reviewed PLP1-related cases worldwide to summarize the genotype-phenotype correlations. METHODS The three probands were 23, 26, and 27 years old, respectively, with progressively aggravated walking difficulty as well as lower limb spasticity. Detailed physical examination showed elevated muscle tone, hyperreflexia, and Babinski signs in lower limbs. Brain MRI examinations were investigated for all cases. PLP1 mutations were identified by whole exome sequencing, followed by Sanger sequencing, family co-segregation, and phenotypic reevaluation. RESULTS A total of eight patients with SPG2 were identified in these three families. The probands additionally had cognitive impairment, urinary or fecal incontinence, ataxia, and white matter lesions (WML) in periventricular regions, with or without kinetic tremor. Three hemizygous mutations in PLP1 were identified, including c.453+159G>A, c.834A>T (p.*278C), and c.434G>A (p.W145*), of which c.834A>T was first associated with HSP. INTERPRETATION We identified three families with complicated SPG2 due to three PLP1 mutations. Our study supports the clinically inter-and intra-family heterogeneity of SPG2. The periventricular region WML and cognitive impairment are the most common characteristics. The kinetic tremor in upper limbs was observed in 2/3 families, suggesting the spectrum of PLP1-related disorders is still expanding.
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Affiliation(s)
- Li Yao
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.,Suzhou Hospital of Anhui Medical University, Suzhou Municipal Hospital of Anhui Province, Suzhou, 234000, China
| | - Zeyu Zhu
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Chao Zhang
- Suzhou Hospital of Anhui Medical University, Suzhou Municipal Hospital of Anhui Province, Suzhou, 234000, China
| | - Wotu Tian
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Li Cao
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
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Evaluation of Individuals with Non-Syndromic Global Developmental Delay and Intellectual Disability. CHILDREN 2023; 10:children10030414. [PMID: 36979972 PMCID: PMC10047567 DOI: 10.3390/children10030414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/11/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
Global Developmental Delay (GDD) and Intellectual Disability (ID) are two of the most common presentations encountered by physicians taking care of children. GDD/ID is classified into non-syndromic GDD/ID, where GDD/ID is the sole evident clinical feature, or syndromic GDD/ID, where there are additional clinical features or co-morbidities present. Careful evaluation of children with GDD and ID, starting with detailed history followed by a thorough examination, remain the cornerstone for etiologic diagnosis. However, when initial history and examination fail to identify a probable underlying etiology, further genetic testing is warranted. In recent years, genetic testing has been shown to be the single most important diagnostic modality for clinicians evaluating children with non-syndromic GDD/ID. In this review, we discuss different genetic testing currently available, review common underlying copy-number variants and molecular pathways, explore the recent evidence and recommendations for genetic evaluation and discuss an approach to the diagnosis and management of children with non-syndromic GDD and ID.
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14
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Gupta N. Deciphering Intellectual Disability. Indian J Pediatr 2023; 90:160-167. [PMID: 36441387 DOI: 10.1007/s12098-022-04345-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/05/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022]
Abstract
Intellectual disability (ID) is a common cause of referral to the pediatricians, geneticists, and pediatric neurologists. A thorough clinical evaluation and a stepwise investigative approach using a combination of traditional genetic techniques and appropriate latest genomic technologies can help in arriving at a diagnosis. In the current "omics" era, adopting a multiomics approach would further assist in solving the undiagnosed cases with intellectual disability.
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Affiliation(s)
- Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, Ansari Nagar, Old OT Block, New Delhi, 110029, India.
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15
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Liu CQ, Qu XC, He MF, Liang DH, Xie SM, Zhang XX, Lin YM, Zhang WJ, Wu KC, Qiao JD. Efficient strategies based on behavioral and electrophysiological methods for epilepsy-related gene screening in the Drosophila model. Front Mol Neurosci 2023; 16:1121877. [PMID: 37152436 PMCID: PMC10157486 DOI: 10.3389/fnmol.2023.1121877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction With the advent of trio-based whole-exome sequencing, the identification of epilepsy candidate genes has become easier, resulting in a large number of potential genes that need to be validated in a whole-organism context. However, conducting animal experiments systematically and efficiently remains a challenge due to their laborious and time-consuming nature. This study aims to develop optimized strategies for validating epilepsy candidate genes using the Drosophila model. Methods This study incorporate behavior, morphology, and electrophysiology for genetic manipulation and phenotypic examination. We utilized the Gal4/UAS system in combination with RNAi techniques to generate loss-of-function models. We performed a range of behavioral tests, including two previously unreported seizure phenotypes, to evaluate the seizure behavior of mutant and wild-type flies. We used Gal4/UAS-mGFP flies to observe the morphological alterations in the brain under a confocal microscope. We also implemented patch-clamp recordings, including a novel electrophysiological method for studying synapse function and improved methods for recording action potential currents and spontaneous EPSCs on targeted neurons. Results We applied different techniques or methods mentioned above to investigate four epilepsy-associated genes, namely Tango14, Klp3A, Cac, and Sbf, based on their genotype-phenotype correlation. Our findings showcase the feasibility and efficiency of our screening system for confirming epilepsy candidate genes in the Drosophila model. Discussion This efficient screening system holds the potential to significantly accelerate and optimize the process of identifying epilepsy candidate genes, particularly in conjunction with trio-based whole-exome sequencing.
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Affiliation(s)
- Chu-Qiao Liu
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
- The Second Clinical Medicine School of Guangzhou Medical University, Guangzhou, China
| | - Xiao-Chong Qu
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ming-Feng He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - De-Hai Liang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Shi-Ming Xie
- The First Clinical Medicine School of Guangzhou Medical University, Guangzhou, China
| | - Xi-Xing Zhang
- The Second Clinical Medicine School of Guangzhou Medical University, Guangzhou, China
| | - Yong-Miao Lin
- The Second Clinical Medicine School of Guangzhou Medical University, Guangzhou, China
| | - Wen-Jun Zhang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ka-Chun Wu
- School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jing-Da Qiao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Jing-Da Qiao, ; orcid.org/0000-0002-4693-8390
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The exploration of genetic aetiology and diagnostic strategy for 321 Chinese individuals with intellectual disability. Clin Chim Acta 2023; 538:94-103. [PMID: 36368352 DOI: 10.1016/j.cca.2022.10.023] [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: 08/31/2022] [Revised: 10/08/2022] [Accepted: 10/28/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Intellectual disability is a heterogeneous neurodevelopmental disorder with complex genetic architectures. Different sequential methodologies are usually applied to identify the genetic aetiologies of ID patients. METHODS We collected 321 consecutive ID patients. All patients underwent karyotyping, while 293 and 164 cases further received copy number variation sequencing (CNV-seq) and whole-exome sequencing (WES). The updated WES technology can detect CNVs simultaneously. The diagnostic data from 137 patients who received WES and CNV-seq were used to define the approach that could be recommended as the first-tier test. RESULTS WES obtains the highest diagnostic yield of 50% (82/164), compared with karyotyping (7.79%, 25/321) and CNV-seq (19.80%, 58/293). Among the variants detected by WES, 66.67% (44/66) de novo and 57.58% (38/66) novel pathogenic/likely pathogenic (P/LP) variants were identified in patients with ID. Besides, 24 out of 25P/LP CNVs discovered by CNV-seq can also be accurately identified using WES in 137 patients who received WES and CNV-seq. Thus, genetic abnormalities found through karyotyping, CNV-seq, and WES can be completely detected by combined karyotyping and WES. CONCLUSIONS This study illustrates the genetic aberrations of a Chinese ID cohort and expands the mutation spectrum of ID-related genes. Compared with the conventional diagnostic strategy, a combination of karyotype analysis and WES could be recommended as the first-tier diagnostic strategy for ID patients.
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Zhu X, Gao Z, Wang Y, Huang W, Li Q, Jiao Z, Liu N, Kong X. Utility of trio-based prenatal exome sequencing incorporating splice-site and mitochondrial genome assessment in pregnancies with fetal ultrasound anomalies: prospective cohort study. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2022; 60:780-792. [PMID: 35726512 DOI: 10.1002/uog.24974] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVE To evaluate the utility of trio-based prenatal exome sequencing (pES), incorporating splice-site and mitochondrial genome assessment, in the prenatal diagnosis of fetuses with ultrasound anomalies and normal copy-number variant sequencing (CNV-seq) results. METHODS This was a prospective study of 90 ongoing pregnancies with ultrasound anomalies that underwent trio-based pES after receiving normal CNV-seq results, from September 2020 to November 2021, in a single center in China. By using pES with a panel encompassing exome coding and splicing regions as well as mitochondrial genome for fetuses and parents, we identified the underlying genetic causes of fetal anomalies, incidental fetal findings and parental carrier status. Information on pregnancy outcome and the impact of pES findings on parental decision-making was collected. RESULTS Of the 90 pregnancies included, 28 (31.1%) received a diagnostic result that could explain the fetal ultrasound anomalies. The highest diagnostic yield was noted for brain abnormalities (3/6 (50.0%)), followed by hydrops (4/9 (44.4%)) and skeletal abnormalities (13/34 (38.2%)). Collectively, 34 variants of 20 genes were detected in the 28 diagnosed cases, with 55.9% (19/34) occurring de novo. Variants of uncertain significance (VUS) associated with fetal phenotypes were detected in six (6.7%) fetuses. Interestingly, fetal (n = 4) and parental (n = 3) incidental findings (IFs) were detected in seven (7.8%) cases. These included two fetuses carrying a de-novo likely pathogenic (LP) variant of the CIC and FBXO11 genes, respectively, associated with neurodevelopmental disorders, and one fetus with a LP variant in a mitochondrial gene. The remaining fetus presented with unilateral renal dysplasia and was incidentally found to carry a pathogenic PKD1 gene variant resulting in adult-onset polycystic kidney, which was later confirmed to be inherited from the mother. In addition, parental heterozygous variants associated with autosomal recessive diseases were detected in three families, including one with additional fetal diagnostic findings. Diagnostic results or fetal IFs contributed to parental decision-making about termination of the pregnancy in 26 families (26/72 (36.1%)), while negative pES results or identification of VUS encouraged 40 families (40/72 (55.6%)) to continue their pregnancy, which ended in a live birth in all cases. CONCLUSION Trio-based pES can provide additional genetic information for pregnancies with fetal ultrasound anomalies without a CNV-seq diagnosis. The incidental findings and parental carrier status reported by trio-based pES with splice-site and mitochondrial genome analysis extend its clinical application, but careful genetic counseling is warranted. © 2022 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- X Zhu
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Z Gao
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Y Wang
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - W Huang
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Q Li
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Z Jiao
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - N Liu
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - X Kong
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Li L, Liu Z, Yang H, Li Y, Zeng Q, Chen L, Liu Y, Chen Y, Zhu F, Cao D, Hu J, Shen X. Investigation of novel de novo KCNC2 variants causing severe developmental and early-onset epileptic encephalopathy. Seizure 2022; 101:218-224. [PMID: 36087422 DOI: 10.1016/j.seizure.2022.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/01/2022] [Accepted: 09/03/2022] [Indexed: 10/14/2022] Open
Abstract
Purpose The voltage-gated potassium channel Kv3.2, encoded by KCNC2, facilitates fast-spiking GABAergic interneurons to fire action potentials at high frequencies. It is pivotal to maintaining excitation/inhibition balance in mammalian brains. This study identified two novel de novo KCNC2 variants, p.Pro470Ser (P470S) and p.Phe382Leu (F382L), in patients with early onset developmental and epileptic encephalopathy (DEE). Methods To examine the molecular basis of DEE, we studied the functional characteristics of variant channels using patch-clamp techniques and computational modeling. Results Whole-cell patch clamp recordings from infected HEK293 cells revealed that channel activation and deactivation kinetics strongly decreased in both Kv3.2 P470S and F382L variant channels. This decrease also occurred in Kv3.2 p.Val471Leu (V471L) channels, known to be associated with DEE. In addition, Kv3.2 F382L and V471L variants exhibited a significant increase in channel conductance and a ∼20 mV negative shift in the threshold for voltage-dependent activation. Simulations of model GABAergic interneurons revealed that all variants decreased neuronal firing frequency. Thus, the variants' net loss-of-function effects disinhibited neural networks. Conclusion Our findings provide compelling evidence supporting the role of KCNC2 as a disease-causing gene in human neurodevelopmental delay and epilepsy.
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Affiliation(s)
- Lin Li
- Surgery Division, Epilepsy Center, Shenzhen Children's Hospital, Shenzhen, Guangdong 518038, China
| | - Zili Liu
- The Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong 518055, China
| | - Haiyang Yang
- The Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong 518055, China; Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Center for Excellence in Brain Science and Intelligence Technology, Shenzhen, Guangdong 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Li
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, CAS, Beijing 100101, China
| | - Qi Zeng
- Department of Neurology, Shenzhen Children's Hospital, Shenzhen, Guangdong 518038, China
| | - Li Chen
- Department of Neurology, Shenzhen Children's Hospital, Shenzhen, Guangdong 518038, China
| | - Yidi Liu
- Department of Neurology, Shenzhen Children's Hospital, Shenzhen, Guangdong 518038, China
| | - Yan Chen
- Surgery Division, Epilepsy Center, Shenzhen Children's Hospital, Shenzhen, Guangdong 518038, China
| | - Fengjun Zhu
- Surgery Division, Epilepsy Center, Shenzhen Children's Hospital, Shenzhen, Guangdong 518038, China
| | - Dezhi Cao
- Surgery Division, Epilepsy Center, Shenzhen Children's Hospital, Shenzhen, Guangdong 518038, China; Department of Neurology, Shenzhen Children's Hospital, Shenzhen, Guangdong 518038, China
| | - Jun Hu
- Department of Pediatrics, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, China.
| | - Xuefeng Shen
- The Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong 518055, China.
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19
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Bai Y, Liu J, Xu J, Sun Y, Li J, Gao Y, Liu L, Jia C, Kong X, Wang L. Long-Read Sequencing Revealed Extragenic and Intragenic Duplications of Exons 56-61 in DMD in an Asymptomatic Male and a DMD Patient. Front Genet 2022; 13:878806. [PMID: 35615378 PMCID: PMC9125615 DOI: 10.3389/fgene.2022.878806] [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: 02/18/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Expanded carrier screening (ECS) has become an increasingly common technique to assess the genetic risks of individuals in the prenatal or preconception period. Unexpected variants unrelated to referral are being increasingly detected in asymptomatic individuals through ECS. In this study, we reported an asymptomatic male with duplication of exons 56-61 in the DMD gene through ECS using whole-exome sequencing (WES), which was also detected in a male patient diagnosed with typical Duchenne muscular dystrophy (DMD). Breakpoint analysis was then performed to explore the potential mechanisms of phenotypic differences using long-read sequencing (LRS), PacBio single-molecule real-time (PacBio SMRT) target sequencing, and Sanger sequencing. Complex structural variations (SVs) on chromosome X were identified in the asymptomatic male, which revealed that the duplication occurred outside the DMD gene; whereas, the duplication in the patient with DMD was a tandem repeat. The phenotypic differences between the two men could be explained by the different breakpoint junctions. To the best of our knowledge, this is the first report of a breakpoint analysis of DMD duplication in two men with different phenotypes. Breakpoint analysis is necessary when the clinical phenotypes are inconsistent with genotypes, and it applies to prenatal testing.
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Affiliation(s)
- Ying Bai
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ju Liu
- Department of Neurology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinghan Xu
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yue Sun
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jingjing Li
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yong Gao
- GrandOmics Biosciences, Beijing, China
| | - Lina Liu
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | | | - Xiangdong Kong
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Li Wang
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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20
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Mastromoro G, Guadagnolo D, Khaleghi Hashemian N, Marchionni E, Traversa A, Pizzuti A. Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis. Diagnostics (Basel) 2022; 12:575. [PMID: 35328129 PMCID: PMC8947110 DOI: 10.3390/diagnostics12030575] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.
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Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (N.K.H.); (E.M.); (A.T.); (A.P.)
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21
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Duan J, Chen Y, Hu Z, Ye Y, Zhang T, Li C, Zeng Q, Zhao X, Mai J, Sun Y, Liu C, Zheng W, Xiao Y, Liao J, Chen L. Non-convulsive Status Epilepticus in SEMA6B-Related Progressive Myoclonic Epilepsy: A Case Report With Literature Review. Front Pediatr 2022; 10:859183. [PMID: 35573939 PMCID: PMC9096209 DOI: 10.3389/fped.2022.859183] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Progressive myoclonic epilepsy (PME) is a group of rare diseases characterized by progressive myoclonus, cognitive impairment, ataxia, and other neurologic deficits. PME has high genetic heterogeneity, and more than 40 genes are reportedly associated with this disorder. SEMA6B encodes a member of the semaphorin family and was first reported to cause PME in 2020. Herein, we present a rare case of PME due to a novel SEMA6B gene mutation in a 6-year-old boy born to healthy non-consanguineous Chinese parents. His developmental milestones were delayed, and he developed recurrent atonic seizures and myoclonic seizures without fever at 3 years and 11 months of age. He experienced recurrent myoclonic seizures, non-convulsive status epilepticus (NCSE), atonic seizures, and atypical absence seizures during the last 2 years. At different time points since onset, valproic acid, levetiracetam, piracetam, and clobazam were used to control the intractable seizures. Notably, NCSE was controlled by a combination of piracetam with clobazam and valproic acid instead of intravenous infusion of midazolam and phenobarbital. Due to the limited number of cases reported to date, the clinical description of our case provides a better understanding of the genotype-phenotype correlations associated with PME and indicate that piracetam may be effective against NCSE in patients with SEMA6B-related PME.
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Affiliation(s)
- Jing Duan
- Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Yan Chen
- Department of Epilepsy Surgery, Shenzhen Children’s Hospital, Shenzhen, China
| | - Zhanqi Hu
- Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Yuanzhen Ye
- Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Tian Zhang
- Department of Epilepsy Surgery, Shenzhen Children’s Hospital, Shenzhen, China
| | - Cong Li
- Department of Epilepsy Surgery, Shenzhen Children’s Hospital, Shenzhen, China
| | - Qi Zeng
- Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Xia Zhao
- Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Jiahui Mai
- Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Yang Sun
- Department of Epilepsy Surgery, Shenzhen Children’s Hospital, Shenzhen, China
| | - Chao Liu
- Department of Bioinformatics, Berry Genomics Co., Ltd., Beijing, China
| | - Wenxin Zheng
- Department of Bioinformatics, Berry Genomics Co., Ltd., Beijing, China
| | - Yuhan Xiao
- Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Jianxiang Liao
- Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Li Chen
- Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, China
- *Correspondence: Li Chen,
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22
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Li Q, Chen Z, Xiong H, Li R, Yu C, Meng J, Shi P, Kong X. Novel Partial Exon 51 Deletion in the Duchenne Muscular Dystrophy Gene Identified via Whole Exome Sequencing and Long-Read Whole-Genome Sequencing. Front Genet 2021; 12:762987. [PMID: 34899847 PMCID: PMC8662377 DOI: 10.3389/fgene.2021.762987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/28/2021] [Indexed: 01/07/2023] Open
Abstract
Duchenne muscular dystrophy (DMD), one of the most common progressive and severely disabling neuromuscular diseases in children, can be largely attributed to the loss of function of the DMD gene on chromosome Xp21.2-p21.1. This paper describes the case of a 10-year-old boy diagnosed with DMD. Whole exome sequencing confirmed the hypothesized large partial exonic deletion of c.7310-11543_7359del (chrX:g.31792260_31803852del) spanning exon 51 and intron 50 in DMD. This large deletion was verified to be de novo by PCR, and the two breakpoints were further confirmed by Sanger sequencing and long-read whole-genome sequencing. Notably, this partial exonic deletion was the only complex variation in the deep intron regions or intron–exon junction regions in DMD. In addition, the case study demonstrates the clinical importance of using multiple molecular genetic testing methods for the diagnosis of rare diseases.
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Affiliation(s)
- Qianqian Li
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhanni Chen
- Genokon Institute of Medical Science and Laboratory, Xiamen, China
| | - Hui Xiong
- Genokon Institute of Medical Science and Laboratory, Xiamen, China
| | - Ranran Li
- School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Chenguang Yu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Cardio-X Center, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Jingjing Meng
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Panlai Shi
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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23
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Tao X, Che Y, Li C, Ruan W, Xu J, Yu Y, Yang F, Wang J, Li H. Novel SNX13 Frameshift Variant in an Individual with Developmental Delay. Cytogenet Genome Res 2021; 161:514-519. [PMID: 34879376 DOI: 10.1159/000520296] [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: 07/26/2021] [Accepted: 10/13/2021] [Indexed: 11/19/2022] Open
Abstract
Recently, an increasing number of genes have been associated with global developmental delay (GDD) and intellectual disability (ID). The sorting nexin (SNX) protein family plays multiple roles in protein trafficking and intracellular signaling. SNXs have been reported to be associated with several disorders, including Alzheimer disease and Down syndrome. Despite the growing evidence of an association of SNXs with neurodegeneration, SNX13 deficiency has not been associated with GDD or ID. In this study, we present the case of a 4-year-old boy with brain dysplasia and GDD, including language delay, cognitive delay, and dyskinesia. Exome sequencing revealed a 1-bp homozygous deletion in SNX13 (NM_015132.5: exon8: c.742_743del; p.Tyr248Leufs*20), which caused a frameshift and predicted early termination. Sanger sequencing confirmed that the variant was inherited from his parents respectively. Our findings associate SNX13 variation with GDD for the first time and provide a new GDD candidate gene.
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Affiliation(s)
- Xicheng Tao
- Department of Rehabilitation, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yueping Che
- Department of Rehabilitation, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chenxi Li
- Department of Rehabilitation, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wencong Ruan
- Department of Rehabilitation, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jialu Xu
- Department of Rehabilitation, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yonglin Yu
- Department of Rehabilitation, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Fan Yang
- Cipher Gene, LLC, Beijing, China
| | - Jia Wang
- Cipher Gene, LLC, Beijing, China
| | - Haifeng Li
- Department of Rehabilitation, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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24
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Xiang J, Ding Y, Yang F, Gao A, Zhang W, Tang H, Mao J, He Q, Zhang Q, Wang T. Genetic Analysis of Children With Unexplained Developmental Delay and/or Intellectual Disability by Whole-Exome Sequencing. Front Genet 2021; 12:738561. [PMID: 34858471 PMCID: PMC8631448 DOI: 10.3389/fgene.2021.738561] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/07/2021] [Indexed: 11/25/2022] Open
Abstract
Background: Whole-exome sequencing (WES) has been recommended as a first-tier clinical diagnostic test for individuals with neurodevelopmental disorders (NDDs). We aimed to identify the genetic causes of 17 children with developmental delay (DD) and/or intellectual disability (ID). Methods: WES and exome-based copy number variation (CNV) analysis were performed for 17 patients with unexplained DD/ID. Results: Single-nucleotide variant (SNV)/small insertion or deletion (Indel) analysis and exome-based CNV calling yielded an overall diagnostic rate of 58.8% (10/17), of which diagnostic SNVs/Indels accounted for 41.2% (7/17) and diagnostic CNVs accounted for 17.6% (3/17). Conclusion: Our findings expand the known mutation spectrum of genes related to DD/ID and indicate that exome-based CNV analysis could improve the diagnostic yield of patients with DD/ID.
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Affiliation(s)
- Jingjing Xiang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Yang Ding
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Fei Yang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Ang Gao
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Wei Zhang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Hui Tang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Jun Mao
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Quanze He
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Qin Zhang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Ting Wang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
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