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Xu K, Li G, Niu Y, Wu Z, Zhang TJ, Zhang S, Wu N. First copy number variant in trans with single nucleotide variant in CCN6 causing progressive pseudorheumatoid dysplasia revealed by genome sequencing and deep phenotyping in monozygotic twins. Am J Med Genet A 2024:e63801. [PMID: 38958524 DOI: 10.1002/ajmg.a.63801] [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: 02/12/2024] [Revised: 05/21/2024] [Accepted: 06/14/2024] [Indexed: 07/04/2024]
Abstract
Biallelic pathogenic variants in CCN6 cause progressive pseudorheumatoid dysplasia (PPD), a rare skeletal dysplasia. The predominant features include noninflammatory progressive joint stiffness and enlargement, which are not unique to this condition. Nearly 100% of the reported variants are single nucleotide variants or small indels, and missing of a second variant has been reported. Genome sequencing (GS) covers various types of variants and deep phenotyping (DP) provides detailed and precise information facilitating genetic data interpretation. The combination of GS and DP improves diagnostic yield, especially in rare and undiagnosed diseases. We identified a novel compound heterozygote involving a disease-causing copy number variant (g.112057664_112064205del) in trans with a single nucleotide variant (c.624dup(p.Cys209MetfsTer21)) in CCN6 in a pair of monozygotic twins, through the methods of GS and DP. The twins had received three nondiagnostic results before. The g.112057664_112064205del variant was missed by all the tests, and the recorded phenotypes were inaccurate or even misleading. The twins were diagnosed with PPD, ending a 13-year diagnostic odyssey. There may be other patients with PPD experiencing underdiagnosis and misdiagnosis due to inadequate genetic testing or phenotyping methods. This case highlights the critical role of GS and DP in facilitating an accurate and timely diagnosis.
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Affiliation(s)
- Kexin Xu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Key Laboratory of Big Data for spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Guozhuang Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Key Laboratory of Big Data for spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuchen Niu
- Clinical Biobank, Medical Research Center, National Science and Technology Key Infrastructure on Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Key Laboratory of Big Data for spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Key Laboratory of Big Data for spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Shuyang Zhang
- State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Department of Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Key Laboratory of Big Data for spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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Xu K, Li G, Wu Z, Zhang TJ, Wu N. Diagnosis and treatment of the Ehlers-Danlos syndromes in China: synopsis of the first guidelines. Orphanet J Rare Dis 2024; 19:194. [PMID: 38741208 DOI: 10.1186/s13023-024-03121-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/03/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND The Ehlers-Danlos syndromes (EDS) are a group of rare hereditary connective tissue disorders. EDS is clinically and genetically heterogeneous and usually involves multiple systems. There are 14 subtypes of EDS with hallmark features including joint hypermobility, skin hyperextensibility, and tissue fragility. The clinical manifestations and their severity differ among the subtypes, encompassing recurrent joint dislocations, scoliosis, arterial aneurysm and dissection, and organ rupture. Challenges in diagnosis and management arise from the complexity of the disease, which is further complicated by its rarity. The development of clinical guidelines and implementation of coordinated multi-disciplinary team (MDT) approaches have emerged as global priorities. MAIN BODY Chinese Multi-Disciplinary Working Group on the Ehlers-Danlos Syndromes was therefore established. Healthcare professionals were recruited from 25 top hospitals across China. The experts are specialized in 24 fields, including genetics, vascular surgery, dermatology, and orthopedics, as well as nursing care, rehabilitation, psychology, and nutrition. Based on GRADE methodology, the Guidelines were written by the Group supervised by methodologists, following a systemic review of all 4453 articles in PubMed published before August 9, 2023, using the search term "Ehlers Danlos". A coordinated MDT approach for the diagnosis and management of EDS is highly recommended by the Group, along with 29 specific recommendations addressing key clinical questions. In addition to the treatment plan, the Guidelines also emphasize integrating support from nursing care, rehabilitation, psychology, and nutrition. This integration not only facilitates recovery in hospital settings, but most importantly, the transition from an illness-defined life to a more "normalized" life. CONCLUSION The first guidelines on EDS will shorten the diagnostic odyssey and solve the unmet medical needs of the patients. This article is a synopsis of the full guidelines.
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Affiliation(s)
- Kexin Xu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Guozhuang Li
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Terry Jianguo Zhang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Beijing, 100730, China.
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
| | - Nan Wu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Beijing, 100730, China.
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
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Zhou Z, Huang X, Tang X, Chen W, Chen Q, Zhang C, Li Y, Zhao D, Zheng Z, Hu S, Wang J, Kullo IJ, Ding K. Heterozygous nonsense variants in laminin subunit 3α resulting in Ebstein's anomaly. HGG ADVANCES 2023; 4:100227. [PMID: 37635785 PMCID: PMC10450520 DOI: 10.1016/j.xhgg.2023.100227] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023] Open
Abstract
Ebstein's anomaly is a rare congenital heart disease characterized by tricuspid valve downward displacement and is associated with additional cardiac phenotypes such as left ventricle non-compaction. The genetic basis of Ebstein's anomaly has yet to be fully elucidated, although several genes (e.g., NKX2-5, MYH7, TPM1, and FLNA) may contribute to Ebstein's anomaly. Here, in two Ebstein's anomaly families (a three-generation family and a trio), we identified independent heterozygous nonsense variants in laminin subunit 3 α (LAMA3), cosegregated with phenotypes in families with reduced penetrance. Furthermore, knocking out Lama3 in mice revealed that haploinsufficiency of Lama3 led to Ebstein's malformation of the tricuspid valve and an abnormal basement membrane structure. In conclusion, we identified a novel gene-disease association of LAMA3 implicated in Ebstein's anomaly, and the findings extended our understanding of the role of the extracellular matrix in Ebstein's anomaly etiology.
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Affiliation(s)
- Zhou Zhou
- Department of Laboratory Medicine, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, P.R. China
| | - Xumei Huang
- Department of Cardiovascular Diseases, Wenzhou Central Hospital, Wenzhou, Zhejiang 325000, P.R. China
| | - Xia Tang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Wen Chen
- Department of Laboratory Medicine, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, P.R. China
| | - Qianlong Chen
- Department of Laboratory Medicine, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, P.R. China
| | - Chaohui Zhang
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
| | - Yuxin Li
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
| | - Dachun Zhao
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Zhe Zheng
- Department of Laboratory Medicine, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, P.R. China
| | - Shengshou Hu
- Department of Laboratory Medicine, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, P.R. China
| | - Jikui Wang
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
| | - Iftikhar J. Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Keyue Ding
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
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Ye B, Tang X, Liao S, Ding K. A comparison of algorithms for identifying copy number variants in family-based whole-exome sequencing data and its implications in inheritance pattern analysis. Gene 2023; 861:147237. [PMID: 36731620 DOI: 10.1016/j.gene.2023.147237] [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: 08/17/2022] [Revised: 12/27/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
There remain challenges in accurately identifying constitutional or germline copy number variants (gCNVs) based on whole-exome sequencing data that have implications for genetic diagnosis for 'rare undiagnosed disease' in the clinical setting. Although multiple algorithms have been proposed, a systematic comparison of these algorithms for calling gCNVs and analyzing inherited pattern have yet to be fully conducted. Therefore, we empirically compared seven exome-based algorithms, including XHMM, CLAMMS, CODEX2, ExomeDepth, DECoN, CN.MOPS, and GATK gCNV, for calling gCNVs in 151 individuals from 44 pedigrees, together with the gold standard of genotyping-derived gCNVs in the same cohort for the performance assessment. These algorithms demonstrated varied powers in identifying gCNVs, although the distribution of gCNVs size was similar. The number of shared gCNVs across these algorithms was limited (e.g., only four gCNVs shared among seven algorithms); however, several algorithms showed varying degrees of consistency (e.g., 1,843 gCNVs shared between DECoN and ExomeDepth). CLAMMS and CODEX2 outperformed the remaining algorithms according to a relatively higher F-score (i.e., 0.145 and 0.152, respectively). In addition, these algorithms exhibited different Mendelian inconsistencies of gCNVs and significant challenges remained in inheritance pattern analysis. In conclusion, selecting good algorithms may have important implications in gCNVs-based inheritance pattern analysis for family-based studies.
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Affiliation(s)
- Bo Ye
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Xia Tang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Shixiu Liao
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, Henan Province 450003, PR China.
| | - Keyue Ding
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, Henan Province 450003, PR China; Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, United States.
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Pranav Chand R, Vinit W, Vaidya V, Iyer AS, Shelke M, Aggarwal S, Magar S, Danda S, Moirangthem A, Phadke SR, Goyal M, Ranganath P, Mistri M, Shah P, Shah N, Kotecha UH. Proband only exome sequencing in 403 Indian children with neurodevelopmental disorders: Diagnostic yield, utility and challenges in a resource-limited setting. Eur J Med Genet 2023; 66:104730. [PMID: 36801247 DOI: 10.1016/j.ejmg.2023.104730] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023]
Abstract
Whole exome sequencing is recommended as the first tier test for neurodevelopmental disorders (NDDs) with trio being an ideal option for the detection of de novo variants. Cost constraints have led to adoption of sequential testing i.e. proband-only whole exome followed by targeted testing of parents. The reported diagnostic yield for proband exome approach ranges between 31 and 53%. Typically, these study designs have aptly incorporated targeted parental segregation before concluding a genetic diagnosis to be confirmed. The reported estimates however do not accurately reflect the yield of proband only standalone whole -exome, a question commonly posed to the referring clinician in self pay medical systems like India. To assess the utility of standalone proband exome (without follow up targeted parental testing), we retrospectively evaluated 403 cases of neurodevelopmental disorders referred for proband-only whole exome sequencing at Neuberg Centre for Genomic Medicine (NCGM), Ahmedabad during the period of January 2019 and December 2021. A diagnosis was considered confirmed only upon the detection of Pathogenic/Likely Pathogenic variants in concordance with patient's phenotype as well as established inheritance pattern. Targeted parental/familial segregation analysis was recommended as a follow up test where applicable. The diagnostic yield of the proband-only standalone whole exome was 31.5%. Only 20 families submitted samples for follow up targeted testing, and a genetic diagnosis was confirmed in twelve cases increasing the yield to 34.5%. To understand factors leading to poor uptake of sequential parental testing, we focused on cases where an ultra-rare variant was detected in hitherto described de novo dominant neurodevelopmental disorder. A total of 40 novel variants in genes associated with de novo autosomal dominant disorders could not be reclassified as parental segregation was denied. Semi-structured telephonic interviews were conducted upon informed consent to comprehend reasons for denial. Major factors influencing decision making included lack of definitive cure in the detected disorders; especially when couples not planning further conception and financial constraints to fund further targeted testing. Our study thus depicts the utility and challenges of proband-only exome approach and highlights the need for larger studies to understand factors influencing decision making in sequential testing.
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Affiliation(s)
| | - Wankhede Vinit
- Kids Neuro Clinic and Child Rehabilitation Center, Nagpur, Maharashtra, India
| | - Varsha Vaidya
- Kpond Children Super Specialty Hospital, Aurangabad, Maharashtra, India
| | | | - Madhavi Shelke
- Integrated Centre for Child Neurodevelopment, Aurangabad, Maharashtra, India
| | | | - Suvarna Magar
- MGM Medical College and Hospitals, Aurangabad, India
| | - Sumita Danda
- Christian Medical College and Hospital, Vellore, India
| | - Amita Moirangthem
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | | | | | | | - Mehul Mistri
- Neuberg Centre for Genomic Medicine, Ahmedabad, 380059, Gujarat, India
| | - Parth Shah
- Neuberg Centre for Genomic Medicine, Ahmedabad, 380059, Gujarat, India
| | - Nidhi Shah
- Neuberg Centre for Genomic Medicine, Ahmedabad, 380059, Gujarat, India
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A Formative Study of the Implementation of Whole Genome Sequencing in Northern Ireland. Genes (Basel) 2022; 13:genes13071104. [PMID: 35885887 PMCID: PMC9316942 DOI: 10.3390/genes13071104] [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: 05/16/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 02/05/2023] Open
Abstract
Background: The UK 100,000 Genomes Project was a transformational research project which facilitated whole genome sequencing (WGS) diagnostics for rare diseases. We evaluated experiences of introducing WGS in Northern Ireland, providing recommendations for future projects. Methods: This formative evaluation included (1) an appraisal of the logistics of implementing and delivering WGS, (2) a survey of participant self-reported views and experiences, (3) semi-structured interviews with healthcare staff as key informants who were involved in the delivery of WGS and (4) a workshop discussion about interprofessional collaboration with respect to molecular diagnostics. Results: We engaged with >400 participants, with detailed reflections obtained from 74 participants including patients, caregivers, key National Health Service (NHS) informants, and researchers (patient survey n = 42; semi-structured interviews n = 19; attendees of the discussion workshop n = 13). Overarching themes included the need to improve rare disease awareness, education, and support services, as well as interprofessional collaboration being central to an effective, mainstreamed molecular diagnostic service. Conclusions: Recommendations for streamlining precision medicine for patients with rare diseases include administrative improvements (e.g., streamlining of the consent process), educational improvements (e.g., rare disease training provided from undergraduate to postgraduate education alongside genomics training for non-genetic specialists) and analytical improvements (e.g., multidisciplinary collaboration and improved computational infrastructure).
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