1
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He J, Meng M, Zhou X, Gao R, Wang H. Isolation of single cells from human hepatoblastoma tissues for whole-exome sequencing. STAR Protoc 2023; 4:102052. [PMID: 36853859 PMCID: PMC9876968 DOI: 10.1016/j.xpro.2023.102052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/02/2022] [Accepted: 01/03/2023] [Indexed: 01/22/2023] Open
Abstract
By combining single-cell processing with whole-exome sequencing, we have developed single-cell whole-exome sequencing to investigate the mechanisms of hepatoblastoma development and to provide potential targets and therapeutic approaches for clinical treatment. In the following protocol, we outline the steps involved in single-cell sorting, whole-genome amplification, amplification uniformity estimation, and whole-exome library construction. In addition to the cells we use, this protocol is also suitable for other cell lines and cell types.
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Affiliation(s)
- Jian He
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Mei Meng
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xianchao Zhou
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Rui Gao
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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2
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Salman DO, Mahfouz R, Bitar ER, Samaha J, Karam PE. Challenges of genetic diagnosis of inborn errors of metabolism in a major tertiary care center in Lebanon. Front Genet 2022; 13:1029947. [PMID: 36468010 PMCID: PMC9715967 DOI: 10.3389/fgene.2022.1029947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/08/2022] [Indexed: 01/25/2023] Open
Abstract
Background: Inborn errors of metabolism are rare genetic disorders; however, these are prevalent in countries with high consanguinity rates, like Lebanon. Patients are suspected, based on a combination of clinical and biochemical features; however, the final confirmation relies on genetic testing. Using next generation sequencing, as a new genetic investigational tool, carries several challenges for the physician, the geneticist, and the families. Methods: In this retrospective study, we analyzed the clinical, biochemical, and genetic profile of inborn errors of metabolism suspected patients, seen at a major tertiary care center in Lebanon, between 2015 and 2018. Genetic testing was performed using next generation sequencing. Genotype-phenotype correlation and diagnostic yield of each testing modality were studied. Results: Out of 211 patients genetically tested, 126 were suspected to have an inborn error of metabolism. The diagnostic yield of next generation sequencing reached 64.3%. Single gene testing was requested in 53%, whole exome sequencing in 36% and gene panels in 10%. Aminoacid disorders were mostly diagnosed followed by storage disorders, organic acidemias and mitochondrial diseases. Targeted testing was performed in 77% of aminoacid and organic acid disorders and half of suspected storage disorders. Single gene sequencing was positive in 75%, whereas whole exome sequencing diagnostic yield for complex cases, like mitochondrial disorders, reached 49%. Good clinical and biochemical correlation allowed the interpretation of variants of unknown significance and negative mutations as well as therapeutic management of most patients. Conclusion: Tailoring the choice of test modality, by next generation sequencing, to the category of suspected inborn errors of metabolism may lead to rapid diagnosis, shortcutting the cost of repeated testing. Whole exome sequencing as a first-tier investigation may be considered mainly for suspected mitochondrial diseases, whereas targeted sequencing can be offered upon suspicion of a specific enzyme deficiency. Timing and modality of gene test remain challenging, in view of the cost incurred by families.
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Affiliation(s)
- Doaa O. Salman
- Department of Pediatrics and Adolescent Medicine, American University of Beirut, Beirut, Lebanon
| | - Rami Mahfouz
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Elio R. Bitar
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Jinane Samaha
- Department of Pediatrics and Adolescent Medicine, American University of Beirut, Beirut, Lebanon,Inherited Metabolic Diseases Program, American University of Beirut Medical Center, Beirut, Lebanon
| | - Pascale E. Karam
- Department of Pediatrics and Adolescent Medicine, American University of Beirut, Beirut, Lebanon,Inherited Metabolic Diseases Program, American University of Beirut Medical Center, Beirut, Lebanon,*Correspondence: Pascale E. Karam,
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3
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Ritter A, Leonard J, Gray C, Izumi K, Levinson K, Nair DR, O'Connor M, Rossano J, Shankar V, Chowns J, Marzolf A, Owens A, Ahrens-Nicklas RC. MYH7 variants cause complex congenital heart disease. Am J Med Genet A 2022; 188:2772-2776. [PMID: 35491958 DOI: 10.1002/ajmg.a.62766] [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: 09/16/2021] [Revised: 02/01/2022] [Accepted: 04/09/2022] [Indexed: 01/25/2023]
Abstract
MYH7, encoding the myosin heavy chain sarcomeric β-myosin heavy chain, is a common cause of both hypertrophic and dilated cardiomyopathy. Additionally, families with left ventricular noncompaction cardiomyopathy (LVNC) and congenital heart disease (CHD), typically septal defects or Ebstein anomaly, have been identified to have heterozygous pathogenic variants in MHY7. One previous case of single ventricle CHD with heart failure due to a MYH7 variant has been identified. Herein, we present a single center's experience of complex CHD due to MYH7 variants. Three probands with a history of CHD, LVNC, and/or arrhythmias were identified to have MYH7 variants through multigene panel testing or exome sequencing. These three patients collectively had 12 affected family members, four with a history of Ebstein anomaly and seven with a history of LVNC. These findings suggest a wider phenotypic spectrum in MYH7-related CHD than previously understood. Further investigation into the possible role of MYH7 in CHD and mechanism of disease is necessary to fully delineate the phenotypic spectrum of MYH7-related cardiac disease. MYH7 should be considered for families with multiple individuals with complex CHD in the setting of a family history of LVNC or arrhythmias.
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Affiliation(s)
- Alyssa Ritter
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jacqueline Leonard
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christopher Gray
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katharine Levinson
- Division of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Divya R Nair
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Matthew O'Connor
- Division of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Joseph Rossano
- Division of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Venkat Shankar
- Division of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jessica Chowns
- Center for Inherited Cardiovascular Disease, Division of Cardiology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Amy Marzolf
- Center for Inherited Cardiovascular Disease, Division of Cardiology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Anjali Owens
- Center for Inherited Cardiovascular Disease, Division of Cardiology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Rebecca C Ahrens-Nicklas
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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4
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Robertson AJ, Tan NB, Spurdle AB, Metke-Jimenez A, Sullivan C, Waddell N. Re-analysis of genomic data: An overview of the mechanisms and complexities of clinical adoption. Genet Med 2022; 24:798-810. [PMID: 35065883 DOI: 10.1016/j.gim.2021.12.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022] Open
Abstract
Re-analyzing genomic information from a patient suspected of having an underlying genetic condition can improve the diagnostic yield of sequencing tests, potentially providing significant benefits to the patient and to the health care system. Although a significant number of studies have shown the clinical potential of re-analysis, less work has been performed to characterize the mechanisms responsible for driving the increases in diagnostic yield. Complexities surrounding re-analysis have also emerged. The terminology itself represents a challenge because "re-analysis" can refer to a range of different concepts. Other challenges include the increased workload that re-analysis demands of curators, adequate reimbursement pathways for clinical and diagnostic services, and the development of systems to handle large volumes of data. Re-analysis also raises ethical implications for patients and families, most notably when re-classification of a variant alters diagnosis, treatment, and prognosis. This review highlights the possibilities and complexities associated with the re-analysis of existing clinical genomic data. We propose a terminology that builds on the foundation presented in a recent statement from the American College of Medical Genetics and Genomics and describes each re-analysis process. We identify mechanisms for increasing diagnostic yield and provide perspectives on the range of challenges that must be addressed by health care systems and individual patients.
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Affiliation(s)
- Alan J Robertson
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; Queensland Digital Health Research Network, Global Change Institute, The University of Queensland, Brisbane, Queensland, Australia; The Genomic Institute, Department of Health, Queensland Government, Brisbane, Queensland, Australia
| | - Natalie B Tan
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Paediatrics, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Clair Sullivan
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Queensland Digital Health Research Network, Global Change Institute, The University of Queensland, Brisbane, Queensland, Australia; Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Metro North Hospital and Health Service, Department of Health, Queensland Government, Brisbane, Queensland, Australia
| | - Nicola Waddell
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
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5
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Molecular Diagnostic Outcomes from 700 Cases: What Can We Learn from a Retrospective Analysis of Clinical Exome Sequencing? J Mol Diagn 2022; 24:274-286. [PMID: 35065284 PMCID: PMC9904168 DOI: 10.1016/j.jmoldx.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 11/29/2021] [Accepted: 12/10/2021] [Indexed: 01/19/2023] Open
Abstract
Clinical exome sequencing (CES) aids in the diagnosis of rare genetic disorders. Herein, we report the molecular diagnostic yield and spectrum of genetic alterations contributing to disease in 700 pediatric cases analyzed at the Children's Hospital of Philadelphia. The overall diagnostic yield was 23%, with three cases having more than one molecular diagnosis and 2.6% having secondary/additional findings. A candidate gene finding was reported in another 8.4% of cases. The clinical indications with the highest diagnostic yield were neurodevelopmental disorders (including seizures), whereas immune- and oncology-related indications were negatively associated with molecular diagnosis. The rapid expansion of knowledge regarding the genome's role in human disease necessitates reanalysis of CES samples. To capture these new discoveries, a subset of cases (n = 240) underwent reanalysis, with an increase in diagnostic yield. We describe our experience reporting CES results in a pediatric setting, including reporting of secondary findings, reporting newly discovered genetic conditions, and revisiting negative test results. Finally, we highlight the challenges associated with implementing critical updates to the CES workflow. Although these updates are necessary, they demand an investment of time and resources from the laboratory. In summary, these data demonstrate the clinical utility of exome sequencing and reanalysis, while highlighting the critical considerations for continuous improvement of a CES test in a clinical laboratory.
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6
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Bedoukian EC, Rentas S, Skraban C, Shao Q, Treat J, Laird DW, Sullivan KE. Palmoplantar keratoderma with deafness phenotypic variability in a patient with an inherited GJB2 frameshift variant and novel missense variant. Mol Genet Genomic Med 2021; 9:e1574. [PMID: 33443819 PMCID: PMC8077155 DOI: 10.1002/mgg3.1574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/06/2020] [Accepted: 11/20/2020] [Indexed: 11/20/2022] Open
Abstract
Background Variants in the GJB2 gene encoding the gap junction protein connexin‐26 (Cx26) can cause autosomal recessive nonsyndromic hearing loss or a variety of phenotypically variable autosomal dominant disorders that effect skin and hearing, such as palmoplantar keratoderma (PPK) with deafness and keratitis–ichthyosis–deafness (KID) syndrome. Here, we report a patient with chronic mucocutaneous candidiasis, hyperkeratosis with resorption of the finger tips, profound bilateral sensorineural hearing loss, and normal hair and ocular examination. Exome analysis identified a novel missense variant in GJB2 (NM_004004.5:c.101T>A, p.Met34Lys) that was inherited from a mosaic unaffected parent in the setting of a well‐reported GJB2 loss of function variant (NM_004004.5:c.35delG, p.Gly12Valfs*2) on the other allele. Method Rat epidermal keratinocytes were transfected with cDNA encoding wildtype Cx26 and/or the Met34Lys mutant of Cx26. Fixed cells were immunolabeled in order to assess the subcellular location of the Cx26 mutant and cell images were captured. Results Expression in rat epidermal keratinocytes revealed that the Met34Lys mutant was retained in the endoplasmic reticulum, unlike wildtype Cx26, and failed to reach the plasma membrane to form gap junctions. Additionally, the Met34Lys mutant acted dominantly to wildtype Cx26, restricting its delivery to the cell surface. Conclusion Overall, we show the p.Met34Lys variant is a novel dominant acting variant causing PPK with deafness. The presence of a loss a function variant on the other allele creates a more severe clinical phenotype, with some features reminiscent of KID syndrome.
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Affiliation(s)
- Emma C. Bedoukian
- Roberts Individualized Medical Genetics CenterChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
| | - Stefan Rentas
- Division of Genomic DiagnosticsChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
| | - Cara Skraban
- Roberts Individualized Medical Genetics CenterChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
| | - Qing Shao
- Department of Anatomy and Cell BiologyUniversity of Western OntarioLondonONCanada
| | - James Treat
- Department of DermatologyChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
| | - Dale W. Laird
- Department of Anatomy and Cell BiologyUniversity of Western OntarioLondonONCanada
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7
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Lassmann T, Francis RW, Weeks A, Tang D, Jamieson SE, Broley S, Dawkins HJS, Dreyer L, Goldblatt J, Groza T, Kamien B, Kiraly-Borri C, McKenzie F, Murphy L, Pachter N, Pathak G, Poulton C, Samanek A, Skoss R, Slee J, Townshend S, Ward M, Baynam GS, Blackwell JM. A flexible computational pipeline for research analyses of unsolved clinical exome cases. NPJ Genom Med 2020; 5:54. [PMID: 33303739 PMCID: PMC7730424 DOI: 10.1038/s41525-020-00161-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/12/2020] [Indexed: 12/25/2022] Open
Abstract
Exome sequencing has enabled molecular diagnoses for rare disease patients but often with initial diagnostic rates of ~25-30%. Here we develop a robust computational pipeline to rank variants for reassessment of unsolved rare disease patients. A comprehensive web-based patient report is generated in which all deleterious variants can be filtered by gene, variant characteristics, OMIM disease and Phenolyzer scores, and all are annotated with an ACMG classification and links to ClinVar. The pipeline ranked 21/34 previously diagnosed variants as top, with 26 in total ranked ≤7th, 3 ranked ≥13th; 5 failed the pipeline filters. Pathogenic/likely pathogenic variants by ACMG criteria were identified for 22/145 unsolved cases, and a previously undefined candidate disease variant for 27/145. This open access pipeline supports the partnership between clinical and research laboratories to improve the diagnosis of unsolved exomes. It provides a flexible framework for iterative developments to further improve diagnosis.
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Affiliation(s)
- Timo Lassmann
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia.
| | - Richard W Francis
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Alexia Weeks
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Dave Tang
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Sarra E Jamieson
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Stephanie Broley
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Hugh J S Dawkins
- Office of Population Health Genomics, Public Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Lauren Dreyer
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Jack Goldblatt
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Tudor Groza
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Benjamin Kamien
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Cathy Kiraly-Borri
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Fiona McKenzie
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
- Faculty of Health and Medical Sciences, Division of Pediatrics, University of Western Australia, Perth, WA, Australia
| | | | - Nicholas Pachter
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Gargi Pathak
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Cathryn Poulton
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Amanda Samanek
- GaRDN Genetics and Rare Diseases Network, Booragoon, WA, Australia
| | - Rachel Skoss
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Jennie Slee
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Sharron Townshend
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Michelle Ward
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Gareth S Baynam
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
- Faculty of Health and Medical Sciences, Division of Pediatrics, University of Western Australia, Perth, WA, Australia
- Western Australian Register of Developmental Anomalies, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Jenefer M Blackwell
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia.
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8
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Ritter A, Berger JH, Deardorff M, Izumi K, Lin KY, Medne L, Ahrens-Nicklas RC. Variants in NAA15 cause pediatric hypertrophic cardiomyopathy. Am J Med Genet A 2020; 185:228-233. [PMID: 33103328 DOI: 10.1002/ajmg.a.61928] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/01/2020] [Accepted: 10/04/2020] [Indexed: 01/28/2023]
Abstract
The NatA N-acetyltransferase complex is important for cotranslational protein modification and regulation of multiple cellular processes. The NatA complex includes the core components of NAA10, the catalytic subunit, and NAA15, the auxiliary component. Both NAA10 and NAA15 have been associated with neurodevelopmental disorders with overlapping clinical features, including variable intellectual disability, dysmorphic facial features, and, less commonly, congenital anomalies such as cleft lip or palate. Cardiac arrhythmias, including long QT syndrome, ventricular tachycardia, and ventricular fibrillation were among the first reported cardiac manifestations in patients with NAA10-related syndrome. Recently, three individuals with NAA10-related syndrome have been reported to also have hypertrophic cardiomyopathy (HCM). The general and cardiac phenotypes of NAA15-related syndrome are not as well described as NAA10-related syndrome. Congenital heart disease, including ventricular septal defects, and arrhythmias, such as ectopic atrial tachycardia, have been reported in a small proportion of patients with NAA15-related syndrome. Given the relationship between NAA10 and NAA15, we propose that HCM is also likely to occur in NAA15-related disorder. We present two patients with pediatric HCM found to have NAA15-related disorder via exome sequencing, providing the first evidence that variants in NAA15 can cause HCM.
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Affiliation(s)
- Alyssa Ritter
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Divison of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Justin H Berger
- Divison of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew Deardorff
- Department of Pathology and Laboratory Medicine and Pediatrics, Children's Hospital Los Angeles, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kimberly Y Lin
- Divison of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Livija Medne
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rebecca C Ahrens-Nicklas
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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9
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JARID2 haploinsufficiency is associated with a clinically distinct neurodevelopmental syndrome. Genet Med 2020; 23:374-383. [PMID: 33077894 DOI: 10.1038/s41436-020-00992-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/15/2020] [Accepted: 09/23/2020] [Indexed: 11/08/2022] Open
Abstract
PURPOSE JARID2, located on chromosome 6p22.3, is a regulator of histone methyltransferase complexes that is expressed in human neurons. So far, 13 individuals sharing clinical features including intellectual disability (ID) were reported with de novo heterozygous deletions in 6p22-p24 encompassing the full length JARID2 gene (OMIM 601594). However, all published individuals to date have a deletion of at least one other adjoining gene, making it difficult to determine if JARID2 is the critical gene responsible for the shared features. We aim to confirm JARID2 as a human disease gene and further elucidate the associated clinical phenotype. METHODS Chromosome microarray analysis, exome sequencing, and an online matching platform (GeneMatcher) were used to identify individuals with single-nucleotide variants or deletions involving JARID2. RESULTS We report 16 individuals in 15 families with a deletion or single-nucleotide variant in JARID2. Several of these variants are likely to result in haploinsufficiency due to nonsense-mediated messenger RNA (mRNA) decay. All individuals have developmental delay and/or ID and share some overlapping clinical characteristics such as facial features with those who have larger deletions involving JARID2. CONCLUSION We report that JARID2 haploinsufficiency leads to a clinically distinct neurodevelopmental syndrome, thus establishing gene-disease validity for the purpose of diagnostic reporting.
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10
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Zaman T, Helbig KL, Clatot J, Thompson CH, Kang SK, Stouffs K, Jansen AE, Verstraete L, Jacquinet A, Parrini E, Guerrini R, Fujiwara Y, Miyatake S, Ben‐Zeev B, Bassan H, Reish O, Marom D, Hauser N, Vu T, Ackermann S, Spencer CE, Lippa N, Srinivasan S, Charzewska A, Hoffman‐Zacharska D, Fitzpatrick D, Harrison V, Vasudevan P, Joss S, Pilz DT, Fawcett KA, Helbig I, Matsumoto N, Kearney JA, Fry AE, Goldberg EM. SCN3A
‐Related Neurodevelopmental Disorder: A Spectrum of Epilepsy and Brain Malformation. Ann Neurol 2020; 88:348-362. [DOI: 10.1002/ana.25809] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 05/05/2020] [Accepted: 05/25/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Tariq Zaman
- Division of Neurology, Department of Pediatrics Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Katherine L. Helbig
- Division of Neurology, Department of Pediatrics Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
- Epilepsy NeuroGenetics Initiative Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Jérôme Clatot
- Division of Neurology, Department of Pediatrics Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
- Epilepsy NeuroGenetics Initiative Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Christopher H. Thompson
- Department of Pharmacology Northwestern University Feinberg School of Medicine Chicago Illinois USA
| | - Seok Kyu Kang
- Department of Pharmacology Northwestern University Feinberg School of Medicine Chicago Illinois USA
| | - Katrien Stouffs
- Center for Medical Genetics/Research Center for Reproduction and Genetics University Hospital Brussels, Free University of Brussels Brussels Belgium
| | - Anna E. Jansen
- Pediatric Neurology Unit, Department of Pediatrics University Hospital Brussels Brussels Belgium
- Neurogenetics Research Group Free University of Brussels Brussels Belgium
| | | | - Adeline Jacquinet
- Human Genetics Service Sart Tilman University Hospital Center Liege Belgium
| | - Elena Parrini
- Pediatric Neurology, Neurogenetics, and Neurobiology Unit and Laboratories, Department of Neuroscience A. Meyer Children's Hospital, University of Florence Florence Italy
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics, and Neurobiology Unit and Laboratories, Department of Neuroscience A. Meyer Children's Hospital, University of Florence Florence Italy
| | - Yuh Fujiwara
- Department of Pediatrics Yokohama City University Medical Center Yokohama Japan
| | - Satoko Miyatake
- Department of Human Genetics Yokohama City University Graduate School of Medicine Yokohama Japan
| | - Bruria Ben‐Zeev
- Pediatric Neurology Unit Edmond and Lili Safra Children's Hospital, Haim Sheba Medical Center Ramat Gan Israel
- Sackler School of Medicine Tel Aviv University Tel Aviv Israel
| | - Haim Bassan
- Sackler School of Medicine Tel Aviv University Tel Aviv Israel
- Pediatric Neurology & Development Center Shamir Medical Center (Assaf Harofe) Zerifin Israel
| | - Orit Reish
- Sackler School of Medicine Tel Aviv University Tel Aviv Israel
- Genetics Institute Shamir Medical Center (Assaf Harofe) Zerifin Zerifin Israel
| | - Daphna Marom
- Sackler School of Medicine Tel Aviv University Tel Aviv Israel
- Genetics Institute Shamir Medical Center (Assaf Harofe) Zerifin Zerifin Israel
| | - Natalie Hauser
- Inova Translational Medicine Institute Inova Health System Fairfax Virginia USA
| | - Thuy‐Anh Vu
- Department of Pediatric Neurology Children's National Medical Center, Washington, District of Columbia, and Pediatric Specialists of Virginia Fairfax Virginia USA
| | - Sally Ackermann
- Division of Paediatric Neurology, Department of Paediatrics and Child Health Red Cross War Memorial Children's Hospital, University of Cape Town Cape Town South Africa
| | - Careni E. Spencer
- Division of Human Genetics, Department of Medicine University of Cape Town, South Africa and Groote Schuur Hospital Cape Town South Africa
| | - Natalie Lippa
- Institute for Genomic Medicine Columbia University Medical Center New York New York USA
| | - Shraddha Srinivasan
- Department of Neurology Columbia University Medical Center New York New York USA
| | | | | | - David Fitzpatrick
- Medical Research Council Human Genetics Unit Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh United Kingdom
| | - Victoria Harrison
- Wessex Clinical Genetics Service Princess Anne Hospital Southampton United Kingdom
| | - Pradeep Vasudevan
- Department of Clinical Genetics University Hospitals Leicester National Health Service Trust Leicester United Kingdom
| | - Shelagh Joss
- West of Scotland Clinical Genetics Service Queen Elizabeth University Hospital Glasgow United Kingdom
| | - Daniela T. Pilz
- West of Scotland Clinical Genetics Service Queen Elizabeth University Hospital Glasgow United Kingdom
- Division of Cancer and Genetics School of Medicine, Cardiff University Cardiff United Kingdom
| | - Katherine A. Fawcett
- Medical Research Council (MRC) Computational Genomics Analysis and Training Programme, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital Oxford United Kingdom
| | - Ingo Helbig
- Division of Neurology, Department of Pediatrics Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
- Epilepsy NeuroGenetics Initiative Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
- Department of Neurology, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
- Department of Biomedical and Health Informatics Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Naomichi Matsumoto
- Department of Human Genetics Yokohama City University Graduate School of Medicine Yokohama Japan
| | - Jennifer A. Kearney
- Department of Pharmacology Northwestern University Feinberg School of Medicine Chicago Illinois USA
| | - Andrew E. Fry
- Division of Cancer and Genetics School of Medicine, Cardiff University Cardiff United Kingdom
- Institute of Medical Genetics University Hospital of Wales Cardiff United Kingdom
| | - Ethan M. Goldberg
- Division of Neurology, Department of Pediatrics Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
- Epilepsy NeuroGenetics Initiative Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
- Department of Neurology, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
- Department of Neuroscience Perelman School of Medicine, University of Pennsylvania Philadelphia Pennsylvania USA
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11
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Pranckeviciene E, Racacho L, Ghani M, Nfonsam L, Potter R, Sinclair-Bourque E, Mettler G, Smith A, Bronicki L, Huang L, Jarinova O. Interplay between probe design and test performance: overlap between genomic regions of interest, capture regions and high quality reference calls influence performance of WES-based assays. Hum Genet 2020; 140:289-297. [PMID: 32627054 DOI: 10.1007/s00439-020-02201-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/25/2020] [Indexed: 11/25/2022]
Abstract
Whole exome sequencing (WES)-based assays undergo rigorous validation before being implemented in diagnostic laboratories. This validation process generates experimental evidence that allows laboratories to predict the performance of the intended assay. The NA12878 Genome in a Bottle (GIAB) HapMap reference sample is commonly used for validation in diagnostic laboratories. We investigated what data points should be taken into consideration when validating WES-based assays using the GIAB reference in a diagnostic setting. We delineate specific factors that require special consideration and identify OMIM genes associated with diseases that may 'bypass' validation. Four replicates of the NA12878 sample were sequenced at the CHEO Genetics Diagnostic Laboratory on a NextSeq 500; the data were analyzed using the bcbio_nexgen v1.1.2 pipeline. The hap.py validation engine, Real Time Genomics vcfeval tool, and high confidence (HC) variant calls in HC regions available for the GIAB sample were used to validate the obtained variant calls. The same validation process was then used to evaluate variant calls obtained for the same sample by two other clinical diagnostic laboratories. We showed that variant calls in NA12878 can be confidently measured only in the regions that intersect between the GIAB HC regions and the target regions of exome capture. Of the 4139 (as of October 2019) OMIM genes associated with a phenotype and having a known molecular basis of disease, 84 were fully outside of the GIAB HC regions and many of the remaining OMIM genes were only partially covered by the HC regions. A significant proportion of variants identified in the NA12878 sample outside of the HC regions have unknown (UNK) status due to the absence of HC reference alleles. Verification of such calls is possible either by an alternative truth set or by orthogonal testing. Similarly, many variants outside of exome capture regions, if not accounted for, will be deemed false negatives due to insufficient probe coverage. Our results demonstrate the importance of the intersection between genomic regions of interest, capture regions, and the high confidence regions. If not considered, false and ambiguous variant calls could have a negative impact on diagnostic accuracy of the intended WES-based diagnostic assay and increase the need for confirmatory testing. To enable laboratories to identify 'problematic' regions and optimize validation efforts, we have made our VCF and BED files available in UCSC Genome Browser: NA12878 WES Benchmark. Relevant genes and genome annotations are evolving, we implemented a general purpose algorithm to cross-reference OMIM genes with the genomic regions of interest that can be applied to capture genes/regions outside HC regions (see repository of data material section).
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Affiliation(s)
- Erinija Pranckeviciene
- Department of Genetics, CHEO, Ottawa, ON, Canada.
- Department of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Vilnius, Lithuania.
| | - Lemuel Racacho
- Department of Genetics, CHEO, Ottawa, ON, Canada
- Department of Newborn Screening, CHEO, Ottawa, ON, Canada
| | - Mahdi Ghani
- Department of Genetics, CHEO, Ottawa, ON, Canada
| | | | - Ryan Potter
- Department of Genetics, CHEO, Ottawa, ON, Canada
| | | | | | - Amanda Smith
- Department of Genetics, CHEO, Ottawa, ON, Canada
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Lucas Bronicki
- Department of Genetics, CHEO, Ottawa, ON, Canada
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Lijia Huang
- Department of Genetics, CHEO, Ottawa, ON, Canada
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Olga Jarinova
- Department of Genetics, CHEO, Ottawa, ON, Canada.
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON, Canada.
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12
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Pritchard AB, Kanai SM, Krock B, Schindewolf E, Oliver-Krasinski J, Khalek N, Okashah N, Lambert NA, Tavares ALP, Zackai E, Clouthier DE. Loss-of-function of Endothelin receptor type A results in Oro-Oto-Cardiac syndrome. Am J Med Genet A 2020; 182:1104-1116. [PMID: 32133772 PMCID: PMC7202054 DOI: 10.1002/ajmg.a.61531] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 01/14/2023]
Abstract
Craniofacial morphogenesis is regulated in part by signaling from the Endothelin receptor type A (EDNRA). Pathogenic variants in EDNRA signaling pathway components EDNRA, GNAI3, PCLB4, and EDN1 cause Mandibulofacial Dysostosis with Alopecia (MFDA), Auriculocondylar syndrome (ARCND) 1, 2, and 3, respectively. However, cardiovascular development is normal in MFDA and ARCND individuals, unlike Ednra knockout mice. One explanation may be that partial EDNRA signaling remains in MFDA and ARCND, as mice with reduced, but not absent, EDNRA signaling also lack a cardiovascular phenotype. Here we report an individual with craniofacial and cardiovascular malformations mimicking the Ednra -/- mouse phenotype, including a distinctive micrognathia with microstomia and a hypoplastic aortic arch. Exome sequencing found a novel homozygous missense variant in EDNRA (c.1142A>C; p.Q381P). Bioluminescence resonance energy transfer assays revealed that this amino acid substitution in helix 8 of EDNRA prevents recruitment of G proteins to the receptor, abrogating subsequent receptor activation by its ligand, Endothelin-1. This homozygous variant is thus the first reported loss-of-function EDNRA allele, resulting in a syndrome we have named Oro-Oto-Cardiac Syndrome. Further, our results illustrate that EDNRA signaling is required for both normal human craniofacial and cardiovascular development, and that limited EDNRA signaling is likely retained in ARCND and MFDA individuals. This work illustrates a straightforward approach to identifying the functional consequence of novel genetic variants in signaling molecules associated with malformation syndromes.
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Affiliation(s)
- Amanda Barone Pritchard
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Stanley M Kanai
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Bryan Krock
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Erica Schindewolf
- Center for Fetal Diagnosis and Treatment, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Nahla Khalek
- Center for Fetal Diagnosis and Treatment, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Najeah Okashah
- Department of Pharmacology and Toxicology, Medical College of Georgia-Augusta University, Augusta, Georgia, USA
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of Georgia-Augusta University, Augusta, Georgia, USA
| | - Andre L P Tavares
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Elaine Zackai
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - David E Clouthier
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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13
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Ritter A, Werner P, Latney B, Krock BL, Santani A, Bedoukian E, Skraban CM, Deardorff MA, Goldmuntz E. NKX2-6 related congenital heart disease: Biallelic homeodomain-disrupting variants and truncus arteriosus. Am J Med Genet A 2020; 182:1454-1459. [PMID: 32198970 DOI: 10.1002/ajmg.a.61550] [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: 12/09/2019] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 11/11/2022]
Abstract
Congenital heart defects (CHD) are the most common birth defect and are both clinically and genetically heterogeneous. Truncus arteriosus (TA), characterized by a single arterial vessel arising from both ventricles giving rise to the coronary, pulmonary and systemic arteries, is rare and only responsible for 1% of all CHD. Two consanguineous families with TA were previously identified to have homozygous nonsense variants within the gene NKX2-6. NKX2-6 is a known downstream target of TBX1, an important transcriptional regulator implicated in the cardiac phenotype of 22q11.2 microdeletion syndrome. Herein, we report two siblings with TA presumably caused by compound heterozygous NKX2-6 variants without a history of consanguinity. Two in-house cohorts with conotruncal defects (CTD) were sequenced for variants in NKX2-6 and no additional cases of biallelic NKX2-6 variants were identified. The similar phenotype of these cases, and the clustering of variants that likely result in a truncated protein that disrupts the homeobox domain, suggest that biallelic loss of function for NKX2-6 is a rare genetic etiology for TA in particular, and possibly other types of CHD.
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Affiliation(s)
- Alyssa Ritter
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Pennsylvania, USA.,Divison of Cardiology, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA
| | - Petra Werner
- Divison of Cardiology, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA
| | - Brande Latney
- Divison of Cardiology, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA
| | - Bryon L Krock
- ARUP Institute for Clinical and Experimental Pathology®, ARUP Laboratories, Salt Lake City, Utah, USA.,University of Utah School of Medicine, Department of Pathology, Salt Lake City, Utah, USA
| | - Avni Santani
- Division of Molecular Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Pennsylvania, USA
| | - Emma Bedoukian
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Pennsylvania, USA.,The Roberts Individualized Medical Genetics Center, Children's Hospital of Philadelphia, Pennsylvania, USA
| | - Cara M Skraban
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Pennsylvania, USA.,The Roberts Individualized Medical Genetics Center, Children's Hospital of Philadelphia, Pennsylvania, USA
| | - Matthew A Deardorff
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Pennsylvania, USA.,The Roberts Individualized Medical Genetics Center, Children's Hospital of Philadelphia, Pennsylvania, USA
| | - Elizabeth Goldmuntz
- Divison of Cardiology, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA
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14
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Burdick KJ, Cogan JD, Rives LC, Robertson AK, Koziura ME, Brokamp E, Duncan L, Hannig V, Pfotenhauer J, Vanzo R, Paul MS, Bican A, Morgan T, Duis J, Newman JH, Hamid R, Phillips JA. Limitations of exome sequencing in detecting rare and undiagnosed diseases. Am J Med Genet A 2020; 182:1400-1406. [PMID: 32190976 DOI: 10.1002/ajmg.a.61558] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/28/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
Abstract
While exome sequencing (ES) is commonly the final diagnostic step in clinical genetics, it may miss diagnoses. To clarify the limitations of ES, we investigated the diagnostic yield of genetic tests beyond ES in our Undiagnosed Diseases Network (UDN) participants. We reviewed the yield of additional genetic testing including genome sequencing (GS), copy number variant (CNV), noncoding variant (NCV), repeat expansion (RE), or methylation testing in UDN cases with nondiagnostic ES results. Overall, 36/54 (67%) of total diagnoses were based on clinical findings and coding variants found by ES and 3/54 (6%) were based on clinical findings only. The remaining 15/54 (28%) required testing beyond ES. Of these, 7/15 (47%) had NCV, 6/15 (40%) CNV, and 2/15 (13%) had a RE or a DNA methylation disorder. Thus 18/54 (33%) of diagnoses were not solved exclusively by ES. Several methods were needed to detect and/or confirm the functional effects of the variants missed by ES, and in some cases by GS. These results indicate that tests to detect elusive variants should be considered after nondiagnostic preliminary steps. Further studies are needed to determine the cost-effectiveness of tests beyond ES that provide diagnoses and insights to possible treatment.
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Affiliation(s)
- Kendall J Burdick
- University of Massachusetts of Medical School, Worcester, Massachusetts, USA
| | - Joy D Cogan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lynette C Rives
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Amy K Robertson
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mary E Koziura
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Elly Brokamp
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Laura Duncan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Vickie Hannig
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jean Pfotenhauer
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rena Vanzo
- Lineagen Inc., Salt Lake City, Utah, USA
| | | | - Anna Bican
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Thomas Morgan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jessica Duis
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John H Newman
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rizwan Hamid
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John A Phillips
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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15
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Imprinted genes in clinical exome sequencing: Review of 538 cases and exploration of mouse-human conservation in the identification of novel human disease loci. Eur J Med Genet 2020; 63:103903. [PMID: 32169557 DOI: 10.1016/j.ejmg.2020.103903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 01/20/2020] [Accepted: 03/09/2020] [Indexed: 01/01/2023]
Abstract
Human imprinting disorders cause a range of dysmorphic and neurocognitive phenotypes, and they may elude traditional molecular diagnosis such exome sequencing. The discovery of novel disorders related to imprinted genes has lagged behind traditional Mendelian disorders because current diagnostic technology, especially unbiased testing, has limited utility in their discovery. To identify novel imprinting disorders, we reviewed data for every human gene hypothesized to be imprinted, identified each mouse ortholog, determined its imprinting status in the mouse, and analyzed its function in humans and mice. We identified 17 human genes that are imprinted in both humans and mice, and have functional data in mice or humans to suggest that dysregulated expression would lead to an abnormal phenotype in humans. These 17 genes, along with known imprinted genes, were preferentially flagged 538 clinical exome sequencing tests. The identified genes were: DIRAS3 [1p31.3], TP73 [1p36.32], SLC22A3 [6q25.3], GRB10 [7p12.1], DDC [7p12.2], MAGI2 [7q21.11], PEG10 [7q21.3], PPP1R9A [7q21.3], CALCR [7q21.3], DLGAP2 [8p23.3], GLIS3 [9p24.2], INPP5F [10q26.11], ANO1 [11q13.3], SLC38A4 [12q13.11], GATM [15q21.1], PEG3 [19q13.43], and NLRP2 [19q13.42]. In the 538 clinical cases, eight cases (1.7%) reported variants in a causative known imprinted gene. There were 367/758 variants (48.4%) in imprinted genes that were not known to cause disease, but none of those variants met the criteria for clinical reporting. Imprinted disorders play a significant role in human disease, and additional human imprinted disorders remain to be discovered. Therefore, evolutionary conservation is a potential tool to identify novel genes involved in human imprinting disorders and to identify them in clinical testing.
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16
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Rajagopalan R, Murrell JR, Luo M, Conlin LK. A highly sensitive and specific workflow for detecting rare copy-number variants from exome sequencing data. Genome Med 2020; 12:14. [PMID: 32000839 PMCID: PMC6993336 DOI: 10.1186/s13073-020-0712-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/13/2020] [Indexed: 12/12/2022] Open
Abstract
Background Exome sequencing (ES) is a first-tier diagnostic test for many suspected Mendelian disorders. While it is routine to detect small sequence variants, it is not a standard practice in clinical settings to detect germline copy-number variants (CNVs) from ES data due to several reasons relating to performance. In this work, we comprehensively characterized one of the most sensitive ES-based CNV tools, ExomeDepth, against SNP array, a standard of care test in clinical settings to detect genome-wide CNVs. Methods We propose a modified ExomeDepth workflow by excluding exons with low mappability prior to variant calling to drastically reduce the false positives originating from the repetitive regions of the genome, and an iterative variant calling framework to assess the reproducibility. We used a cohort of 307 individuals with clinical ES data and clinical SNP array to estimate the sensitivity and false discovery rate of the CNV detection using exome sequencing. Further, we performed targeted testing of the STRC gene in 1972 individuals. To reduce the number of variants for downstream analysis, we performed a large-scale iterative variant calling process with random control cohorts to assess the reproducibility of the CNVs. Results The modified workflow presented in this paper reduced the number of total variants identified by one third while retaining a higher sensitivity of 97% and resulted in an improved false discovery rate of 11.4% compared to the default ExomeDepth pipeline. The exclusion of exons with low mappability removes 4.5% of the exons, including a subset of exons (0.6%) in disease-associated genes which are intractable by short-read next-generation sequencing (NGS). Results from the reproducibility analysis showed that the clinically reported variants were reproducible 100% of the time and that the modified workflow can be used to rank variants from high to low confidence. Targeted testing of 30 CNVs identified in STRC, a challenging gene to ascertain by NGS, showed a 100% validation rate. Conclusions In summary, we introduced a modification to the default ExomeDepth workflow to reduce the false positives originating from the repetitive regions of the genome, created a large-scale iterative variant calling framework for reproducibility, and provided recommendations for implementation in clinical settings.
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Affiliation(s)
- Ramakrishnan Rajagopalan
- Division of Genomic Diagnostics, Department of Pathology and Laboaratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Jill R Murrell
- Division of Genomic Diagnostics, Department of Pathology and Laboaratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Minjie Luo
- Division of Genomic Diagnostics, Department of Pathology and Laboaratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura K Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboaratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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17
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Sun Y, Xiang J, Liu Y, Chen S, Yu J, Peng J, Liu Z, Chen L, Sun J, Yang Y, Yang Y, Zhou Y, Peng Z. Increased diagnostic yield by reanalysis of data from a hearing loss gene panel. BMC Med Genomics 2019; 12:76. [PMID: 31138263 PMCID: PMC6540452 DOI: 10.1186/s12920-019-0531-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/14/2019] [Indexed: 12/30/2022] Open
Abstract
Background Congenital hearing loss affects approximately 1–2 infants out of every 1000, with 50% of the cases resulting from genetic factors. Targeted gene panels have been widely used for genetic diagnosis of hearing loss. This study aims to reveal new diagnoses via reanalyzing historical data of a multigene panel, and exam the reasons for new diagnoses. Methods A total of 210 samples were enlisted, including clinical reports and sequencing data of patients with congenital/prelingual hearing loss who were referred to clinical genetic testing from October 2014 to June 2017. All variants listed on the original clinical reports were reinterpreted according to the standards and guidelines recommended by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP). Expanded analysis of raw data were performed in undiagnosed cases. Results Re-analysis resulted in nine new diagnoses, improving the overall diagnostic rate from 39 to 43%. New diagnoses were attributed to newly published clinical evidence in the literature, adoption of new interpretation guidelines and expanded analysis range. Conclusion This work demonstrates benefits of reanalysis of targeted gene panel data, indicating that periodical reanalysis should be performed in clinical practice. Electronic supplementary material The online version of this article (10.1186/s12920-019-0531-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu Sun
- Department of Otorhinolaryngology, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jiale Xiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yidong Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sen Chen
- Department of Otorhinolaryngology, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jintao Yu
- Department of Otorhinolaryngology, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jiguang Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zijing Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Lisha Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yun Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,AiLife Diagnostics, 1920 Country Place Pkwy, Pearland, TX, 77584, USA
| | - Yulin Zhou
- United Diagnostic and Research Center for Clinical Genetics, School of Public Health of Xiamen University, Xiamen, Fujian, 361003, China. .,Xiamen Maternal and Child Health Hospital, Xiamen, Fujian, 361003, China.
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
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18
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Kernohan KD, Hartley T, Naumenko S, Armour CM, Graham GE, Nikkel SM, Lines M, Geraghty MT, Richer J, Mears W, Boycott KM, Dyment DA. Diagnostic clarity of exome sequencing following negative comprehensive panel testing in the neonatal intensive care unit. Am J Med Genet A 2019; 176:1688-1691. [PMID: 30160830 DOI: 10.1002/ajmg.a.38838] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Sergey Naumenko
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christine M Armour
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gail E Graham
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | - Sarah M Nikkel
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew Lines
- Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael T Geraghty
- Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | - Julie Richer
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | - Wendy Mears
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | - David A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
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19
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Wu C, Devkota B, Evans P, Zhao X, Baker SW, Niazi R, Cao K, Gonzalez MA, Jayaraman P, Conlin LK, Krock BL, Deardorff MA, Spinner NB, Krantz ID, Santani AB, Tayoun ANA, Sarmady M. Rapid and accurate interpretation of clinical exomes using Phenoxome: a computational phenotype-driven approach. Eur J Hum Genet 2019; 27:612-620. [PMID: 30626929 PMCID: PMC6460638 DOI: 10.1038/s41431-018-0328-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/10/2018] [Accepted: 12/11/2018] [Indexed: 01/26/2023] Open
Abstract
Clinical exome sequencing (CES) has become the preferred diagnostic platform for complex pediatric disorders with suspected monogenic etiologies. Despite rapid advancements, the major challenge still resides in identifying the casual variants among the thousands of variants detected during CES testing, and thus establishing a molecular diagnosis. To improve the clinical exome diagnostic efficiency, we developed Phenoxome, a robust phenotype-driven model that adopts a network-based approach to facilitate automated variant prioritization. Phenoxome dissects the phenotypic manifestation of a patient in concert with their genomic profile to filter and then prioritize variants that are likely to affect the function of the gene (potentially pathogenic variants). To validate our method, we have compiled a clinical cohort of 105 positive patient samples that represent a wide range of genetic heterogeneity. Phenoxome identifies the causative variants within the top 5, 10, or 25 candidates in more than 50%, 71%, or 88% of these exomes, respectively. Furthermore, we show that our method is optimized for clinical testing by outperforming the current state-of-art method. We have demonstrated the performance of Phenoxome using a clinical cohort and showed that it enables rapid and accurate interpretation of clinical exomes. Phenoxome is available at https://phenoxome.chop.edu/ .
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Affiliation(s)
- Chao Wu
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Batsal Devkota
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Perry Evans
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiaonan Zhao
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Samuel W Baker
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rojeen Niazi
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kajia Cao
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael A Gonzalez
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Pushkala Jayaraman
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura K Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bryan L Krock
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew A Deardorff
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics, Department of Pediatrics, Roberts individualized Medical Genetics Center, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nancy B Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian D Krantz
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics, Department of Pediatrics, Roberts individualized Medical Genetics Center, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Avni B Santani
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ahmad N Abou Tayoun
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Mahdi Sarmady
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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20
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Shashi V, Schoch K, Spillmann R, Cope H, Tan QKG, Walley N, Pena L, McConkie-Rosell A, Jiang YH, Stong N, Need AC, Goldstein DB. A comprehensive iterative approach is highly effective in diagnosing individuals who are exome negative. Genet Med 2019; 21:161-172. [PMID: 29907797 PMCID: PMC6295275 DOI: 10.1038/s41436-018-0044-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/09/2018] [Indexed: 01/01/2023] Open
Abstract
PURPOSE Sixty to seventy-five percent of individuals with rare and undiagnosed phenotypes remain undiagnosed after exome sequencing (ES). With standard ES reanalysis resolving 10-15% of the ES negatives, further approaches are necessary to maximize diagnoses in these individuals. METHODS In 38 ES negative patients an individualized genomic-phenotypic approach was employed utilizing (1) phenotyping; (2) reanalyses of FASTQ files, with innovative bioinformatics; (3) targeted molecular testing; (4) genome sequencing (GS); and (5) conferring of clinical diagnoses when pathognomonic clinical findings occurred. RESULTS Certain and highly likely diagnoses were made in 18/38 (47%) individuals, including identifying two new developmental disorders. The majority of diagnoses (>70%) were due to our bioinformatics, phenotyping, and targeted testing identifying variants that were undetected or not prioritized on prior ES. GS diagnosed 3/18 individuals with structural variants not amenable to ES. Additionally, tentative diagnoses were made in 3 (8%), and in 5 individuals (13%) candidate genes were identified. Overall, diagnoses/potential leads were identified in 26/38 (68%). CONCLUSIONS Our comprehensive approach to ES negatives maximizes the ES and clinical data for both diagnoses and candidate gene identification, without GS in the majority. This iterative approach is cost-effective and is pertinent to the current conundrum of ES negatives.
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Affiliation(s)
- Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA.
| | - Kelly Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Rebecca Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Heidi Cope
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Queenie K-G Tan
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicole Walley
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Loren Pena
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Allyn McConkie-Rosell
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Yong-Hui Jiang
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Anna C Need
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
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21
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Baker SW, Murrell JR, Nesbitt AI, Pechter KB, Balciuniene J, Zhao X, Yu Z, Denenberg EH, DeChene ET, Wilkens AB, Bhoj EJ, Guan Q, Dulik MC, Conlin LK, Abou Tayoun AN, Luo M, Wu C, Cao K, Sarmady M, Bedoukian EC, Tarpinian J, Medne L, Skraban CM, Deardorff MA, Krantz ID, Krock BL, Santani AB. Automated Clinical Exome Reanalysis Reveals Novel Diagnoses. J Mol Diagn 2019; 21:38-48. [DOI: 10.1016/j.jmoldx.2018.07.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/19/2018] [Accepted: 07/30/2018] [Indexed: 10/27/2022] Open
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22
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Ritter AL, McDougall C, Skraban C, Medne L, Bedoukian EC, Asher SB, Balciuniene J, Campbell CD, Baker SW, Denenberg EH, Mazzola S, Fiordaliso SK, Krantz ID, Kaplan P, Ierardi‐Curto L, Santani AB, Zackai EH, Izumi K. Variable Clinical Manifestations of Xia‐Gibbs syndrome: Findings of Consecutively Identified Cases at a Single Children's Hospital. Am J Med Genet A 2018; 176:1890-1896. [DOI: 10.1002/ajmg.a.40380] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 05/31/2018] [Accepted: 06/04/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Alyssa L. Ritter
- Division of Human Genetics, Department of PediatricsThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
| | - Carey McDougall
- Division of Human Genetics, Department of PediatricsThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
| | - Cara Skraban
- Division of Human Genetics, Department of PediatricsThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
- Department of PediatricsPerelman School of Medicine at the University of Pennsylvania, Philadelphia Pennsylvania Philadelphia USA
| | - Livija Medne
- Division of Human Genetics, Department of PediatricsThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
| | - Emma C. Bedoukian
- Division of Human Genetics, Department of PediatricsThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
| | - Stephanie B. Asher
- Division of Human Genetics, Department of PediatricsThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
| | - Jorune Balciuniene
- Division of Genomic Diagnostics, Department of Pathology and Laboratory MedicineThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
| | - Colleen D. Campbell
- Division of Genomic Diagnostics, Department of Pathology and Laboratory MedicineThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
| | - Samuel W. Baker
- Division of Genomic Diagnostics, Department of Pathology and Laboratory MedicineThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
| | - Elizabeth H. Denenberg
- Division of Genomic Diagnostics, Department of Pathology and Laboratory MedicineThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
| | - Sarah Mazzola
- Division of Human Genetics, Department of PediatricsThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
| | - Sarah K. Fiordaliso
- Division of Human Genetics, Department of PediatricsThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
| | - Ian D. Krantz
- Division of Human Genetics, Department of PediatricsThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
- Department of PediatricsPerelman School of Medicine at the University of Pennsylvania, Philadelphia Pennsylvania Philadelphia USA
| | - Paige Kaplan
- Division of Human Genetics, Department of PediatricsThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
- Department of PediatricsPerelman School of Medicine at the University of Pennsylvania, Philadelphia Pennsylvania Philadelphia USA
| | - Lynne Ierardi‐Curto
- Division of Human Genetics, Department of PediatricsThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
- Department of PediatricsPerelman School of Medicine at the University of Pennsylvania, Philadelphia Pennsylvania Philadelphia USA
| | - Avni B. Santani
- Division of Genomic Diagnostics, Department of Pathology and Laboratory MedicineThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
- Department of Pathology and Laboratory MedicinePerelman School of Medicine at the University of Pennsylvania, Philadelphia Pennsylvania Philadelphia USA
| | - Elaine H. Zackai
- Division of Human Genetics, Department of PediatricsThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
- Department of PediatricsPerelman School of Medicine at the University of Pennsylvania, Philadelphia Pennsylvania Philadelphia USA
| | - Kosuke Izumi
- Division of Human Genetics, Department of PediatricsThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
- Department of PediatricsPerelman School of Medicine at the University of Pennsylvania, Philadelphia Pennsylvania Philadelphia USA
- Division of Genomic Diagnostics, Department of Pathology and Laboratory MedicineThe Children's Hospital of Philadelphia Pennsylvania Philadelphia USA
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