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Dardas Z, Marafi D, Duan R, Fatih JM, El-Rashidy OF, Grochowski CM, Carvalho CMB, Jhangiani SN, Bi W, Du H, Gibbs RA, Posey JE, Calame DG, Zaki MS, Lupski JR. Genomic Balancing Act: deciphering DNA rearrangements in the complex chromosomal aberration involving 5p15.2, 2q31.1, and 18q21.32. Eur J Hum Genet 2024:10.1038/s41431-024-01680-1. [PMID: 39256534 DOI: 10.1038/s41431-024-01680-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 05/15/2024] [Accepted: 08/01/2024] [Indexed: 09/12/2024] Open
Abstract
Despite extensive research into the genetic underpinnings of neurodevelopmental disorders (NDD), many clinical cases remain unresolved. We studied a female proband with a NDD, mildly dysmorphic facial features, and brain stem hypoplasia on neuroimaging. Comprehensive genomic analyses revealed a terminal 5p loss and a terminal 18q gain in the proband while a diploid copy number for chromosomes 5 and 18 in both parents. Genomic investigations in the proband identified an unbalanced translocation t(5;18) with additional genetic material from chromosome 2 (2q31.3) inserted at the breakpoint, pointing to a complex chromosomal rearrangement (CCR) involving 5p15.2, 2q31.3, and 18q21.32. Breakpoint junction analyses enabled by long-read genome sequencing unveiled the presence of four distinct junctions in the father, who is a carrier of a balanced CCR. The proband inherited from the father both the abnormal chromosome 5 resulting in segmental aneusomies of chr5 (loss) and chr18 (gain) and a der(2) homologue. Evidences suggest a chromoplexy mechanism for this CCR derivation, involving double-strand breaks (DSBs) repaired by non-homologous end joining (NHEJ) or alternative end joining (alt-EJ). The complexity of the CCR and the segregation of homologues elucidate the genetic model for this family. This study demonstrates the importance of combining multiple genomic technologies to uncover genetic causes of complex neurodevelopmental syndromes and to better understand genetic disease mechanisms.
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Affiliation(s)
- Zain Dardas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Omnia F El-Rashidy
- Department of Pediatrics, Faculty of Medicine Ain Shams University, Cairo, Egypt
| | | | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
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2
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Schrauwen I, Rajendran Y, Acharya A, Öhman S, Arvio M, Paetau R, Siren A, Avela K, Granvik J, Leal SM, Määttä T, Kokkonen H, Järvelä I. Optical genome mapping unveils hidden structural variants in neurodevelopmental disorders. Sci Rep 2024; 14:11239. [PMID: 38755281 PMCID: PMC11099145 DOI: 10.1038/s41598-024-62009-y] [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: 01/04/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
While short-read sequencing currently dominates genetic research and diagnostics, it frequently falls short of capturing certain structural variants (SVs), which are often implicated in the etiology of neurodevelopmental disorders (NDDs). Optical genome mapping (OGM) is an innovative technique capable of capturing SVs that are undetectable or challenging-to-detect via short-read methods. This study aimed to investigate NDDs using OGM, specifically focusing on cases that remained unsolved after standard exome sequencing. OGM was performed in 47 families using ultra-high molecular weight DNA. Single-molecule maps were assembled de novo, followed by SV and copy number variant calling. We identified 7 variants of interest, of which 5 (10.6%) were classified as likely pathogenic or pathogenic, located in BCL11A, OPHN1, PHF8, SON, and NFIA. We also identified an inversion disrupting NAALADL2, a gene which previously was found to harbor complex rearrangements in two NDD cases. Variants in known NDD genes or candidate variants of interest missed by exome sequencing mainly consisted of larger insertions (> 1kbp), inversions, and deletions/duplications of a low number of exons (1-4 exons). In conclusion, in addition to improving molecular diagnosis in NDDs, this technique may also reveal novel NDD genes which may harbor complex SVs often missed by standard sequencing techniques.
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Affiliation(s)
- Isabelle Schrauwen
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA.
| | - Yasmin Rajendran
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA
| | - Anushree Acharya
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA
| | | | - Maria Arvio
- Päijät-Häme Wellbeing Services, Neurology, Lahti, Finland
| | - Ritva Paetau
- Department of Child Neurology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Auli Siren
- Kanta-Häme Central Hospital, Hämeenlinna, Finland
| | - Kristiina Avela
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Johanna Granvik
- The Wellbeing Services County of Ostrobothnia, Kokkola, Finland
| | - Suzanne M Leal
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Tuomo Määttä
- The Wellbeing Services County of Kainuu, Kajaani, Finland
| | - Hannaleena Kokkonen
- Northern Finland Laboratory Centre NordLab and Medical Research Centre, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Irma Järvelä
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
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3
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Hoff FW, Xing C, Garg A. A Novel Subtype of Acquired Generalized Lipodystrophy Associated With Subcutaneous Panniculitis-Like T-cell Lymphoma. JCEM CASE REPORTS 2024; 2:luae069. [PMID: 38681964 PMCID: PMC11055395 DOI: 10.1210/jcemcr/luae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Indexed: 05/01/2024]
Abstract
Acquired generalized lipodystrophy (AGL) is an extremely rare disease that is characterized by loss of body fat affecting nearly all parts of the body. It is often associated with autoimmune diseases or panniculitis, whereas in other patients the underlying etiology is unclear. We report a 52-year-old male individual who was diagnosed with subcutaneous panniculitis-like T-cell lymphoma (SPTCL) that spontaneously went into remission. Years later he developed new subcutaneous nodules most concerning for relapse SPTCL or lupus panniculitis, followed by onset of hemophagocytic lymphohistiocytosis (HLH) that was treated with allogeneic stem cell transplantation. Notably, around the same time, he also developed generalized subcutaneous fat loss of both upper and lower extremities, chest, abdomen, and face that persisted after treatment of the HLH. Whole exome sequencing was performed to search for pathogenic variants that are associated with SPTCL, including those in hepatitis A virus cellular receptor 2 (HAVCR2), but did not detect any potential disease-causing variant. Our report brings to the attention a novel subtype of panniculitis-variety of AGL. Whether generalized loss of subcutaneous fat in this patient is due to lymphoma-associated panniculitis or due to development of adipose tissue-directed autoantibodies as a paraneoplastic "autoimmune" manifestation of SPTCL remains unclear.
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Affiliation(s)
- Fieke W Hoff
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chao Xing
- McDermott Center for Human Growth and Development, Department of Bioinformatics, O’Donnell School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Abhimanyu Garg
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Section of Nutrition and Metabolic Diseases, Division of Endocrinology, Department of Internal Medicine and the Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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4
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Dardas Z, Fatih JM, Jolly A, Dawood M, Du H, Grochowski CM, Jones EG, Jhangiani SN, Wehrens XHT, Liu P, Bi W, Boerwinkle E, Posey JE, Muzny DM, Gibbs RA, Lupski JR, Coban-Akdemir Z, Morris SA. NODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy. Genome Med 2024; 16:53. [PMID: 38570875 PMCID: PMC10988827 DOI: 10.1186/s13073-024-01312-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND NODAL signaling plays a critical role in embryonic patterning and heart development in vertebrates. Genetic variants resulting in perturbations of the TGF-β/NODAL signaling pathway have reproducibly been shown to cause laterality defects in humans. To further explore this association and improve genetic diagnosis, the study aims to identify and characterize a broader range of NODAL variants in a large number of individuals with laterality defects. METHODS We re-analyzed a cohort of 321 proband-only exomes of individuals with clinically diagnosed laterality congenital heart disease (CHD) using family-based, rare variant genomic analyses. To this cohort we added 12 affected subjects with known NODAL variants and CHD from institutional research and clinical cohorts to investigate an allelic series. For those with candidate contributory variants, variant allele confirmation and segregation analysis were studied by Sanger sequencing in available family members. Array comparative genomic hybridization and droplet digital PCR were utilized for copy number variants (CNV) validation and characterization. We performed Human Phenotype Ontology (HPO)-based quantitative phenotypic analyses to dissect allele-specific phenotypic differences. RESULTS Missense, nonsense, splice site, indels, and/or structural variants of NODAL were identified as potential causes of heterotaxy and other laterality defects in 33 CHD cases. We describe a recurrent complex indel variant for which the nucleic acid secondary structure predictions implicate secondary structure mutagenesis as a possible mechanism for formation. We identified two CNV deletion alleles spanning NODAL in two unrelated CHD cases. Furthermore, 17 CHD individuals were found (16/17 with known Hispanic ancestry) to have the c.778G > A:p.G260R NODAL missense variant which we propose reclassification from variant of uncertain significance (VUS) to likely pathogenic. Quantitative HPO-based analyses of the observed clinical phenotype for all cases with p.G260R variation, including heterozygous, homozygous, and compound heterozygous cases, reveal clustering of individuals with biallelic variation. This finding provides evidence for a genotypic-phenotypic correlation and an allele-specific gene dosage model. CONCLUSION Our data further support a role for rare deleterious variants in NODAL as a cause for sporadic human laterality defects, expand the repertoire of observed anatomical complexity of potential cardiovascular anomalies, and implicate an allele specific gene dosage model.
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Affiliation(s)
- Zain Dardas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Edward G Jones
- Division of Cardiology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xander H T Wehrens
- Division of Cardiology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, 77030, USA
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Shaine A Morris
- Division of Cardiology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, 77030, USA.
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5
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Louw N, Carstens N, Lombard Z. Incorporating CNV analysis improves the yield of exome sequencing for rare monogenic disorders-an important consideration for resource-constrained settings. Front Genet 2023; 14:1277784. [PMID: 38155715 PMCID: PMC10753787 DOI: 10.3389/fgene.2023.1277784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
Exome sequencing (ES) is a recommended first-tier diagnostic test for many rare monogenic diseases. It allows for the detection of both single-nucleotide variants (SNVs) and copy number variants (CNVs) in coding exonic regions of the genome in a single test, and this dual analysis is a valuable approach, especially in limited resource settings. Single-nucleotide variants are well studied; however, the incorporation of copy number variant analysis tools into variant calling pipelines has not been implemented yet as a routine diagnostic test, and chromosomal microarray is still more widely used to detect copy number variants. Research shows that combined single and copy number variant analysis can lead to a diagnostic yield of up to 58%, increasing the yield with as much as 18% from the single-nucleotide variant only pipeline. Importantly, this is achieved with the consideration of computational costs only, without incurring any additional sequencing costs. This mini review provides an overview of copy number variant analysis from exome data and what the current recommendations are for this type of analysis. We also present an overview on rare monogenic disease research standard practices in resource-limited settings. We present evidence that integrating copy number variant detection tools into a standard exome sequencing analysis pipeline improves diagnostic yield and should be considered a significantly beneficial addition, with relatively low-cost implications. Routine implementation in underrepresented populations and limited resource settings will promote generation and sharing of CNV datasets and provide momentum to build core centers for this niche within genomic medicine.
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Affiliation(s)
- Nadja Louw
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Alabdulrazzaq F, Alanzi T, Al‐Balool HH, Gardham A, Wakeling E, Leitch HG, AlSayed M, Abdulrahim M, Aladwani A, Romito A, Kampe K, Ferdinandusse S, Aboelanine AH, Abdullah A, Alwadani A, Bastaki L, Vaz FM, Bertoli‐Avella AM, Marafi D. Expanding the allelic spectrum of ELOVL4-related autosomal recessive neuro-ichthyosis. Mol Genet Genomic Med 2023; 11:e2256. [PMID: 37592902 PMCID: PMC10724518 DOI: 10.1002/mgg3.2256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/27/2023] [Accepted: 07/14/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Very long-chain fatty acids (VLCFAs) composed of more than 20 carbon atoms are essential in the biosynthesis of cell membranes in the brain, skin, and retina. VLCFAs are elongated beyond 28 carbon atoms by ELOVL4 enzyme. Variants in ELOVL4 are associated with three Mendelian disorders: autosomal dominant (AD) Stargardt-like macular dystrophy type 3, AD spinocerebellar ataxia, and autosomal recessive disorder congenital ichthyosis, spastic quadriplegia and impaired intellectual development (ISQMR). Only seven subjects from five unrelated families with ISQMR have been described, all of which have biallelic single-nucleotide variants. METHODS We performed clinical exome sequencing on probands from four unrelated families with neuro-ichthyosis. RESULTS We identified three novel homozygous ELOVL4 variants. Two of the families originated from the same Saudi tribe and had the exact homozygous exonic deletion in ELOVL4, while the third and fourth probands had two different novel homozygous missense variants. Seven out of the eight affected subjects had profound developmental delay, epilepsy, axial hypotonia, peripheral hypertonia, and ichthyosis. Delayed myelination and corpus callosum hypoplasia were seen in two of five subjects with brain magnetic rosonance imaging and cerebral atrophy in three. CONCLUSION Our study expands the allelic spectrum of ELOVL4-related ISQMR. The detection of the same exonic deletion in two unrelated Saudi family from same tribe suggests a tribal founder mutation.
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Affiliation(s)
- Fatima Alabdulrazzaq
- Department of PediatricsAdan Hospital, Ministry of HealthHadiyaKuwait
- Kuwait Institute of Medical SpecializationSulaibkikhatKuwait
| | - Talal Alanzi
- Division Medical Genetics and Metabolic, Department of PediatricsPrince Sultan Military Medical CityRiyadhSaudi Arabia
| | | | - Alice Gardham
- North West Thames Regional Genetics Service, Northwick Park HospitalHarrowUK
| | - Emma Wakeling
- North East Thames Regional Genetics ServiceGreat Ormond Street HospitalLondonUK
| | - Harry G. Leitch
- North West Thames Regional Genetics Service, Northwick Park HospitalHarrowUK
- Medical Research CouncilLondon Institute of Medical SciencesLondonUK
- Institute of Clinical Sciences, Faculty of MedicineImperial College LondonLondonUK
| | - Moeenaldeen AlSayed
- Department of Medical GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Faculty of MedicineAlfaisal UniversityRiyadhSaudi Arabia
| | - Maha Abdulrahim
- King Abdullah Bin Abdulaziz University Hospital, Princess Nourah Bint Abdulrahman UniversityRiyadhSaudi Arabia
| | | | | | | | - Sacha Ferdinandusse
- Amsterdam UMC Location University of Amsterdam, Department of Clinical Chemistry and PediatricsLaboratory Genetic Metabolic Diseases, Emma Children's HospitalAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of MetabolismAmsterdamThe Netherlands
| | | | - Amira Abdullah
- Department of PediatricsAdan Hospital, Ministry of HealthHadiyaKuwait
| | - Amal Alwadani
- Kuwait Medical Genetics Centre, Ministry of HealthSulaibikhatKuwait
| | - Laila Bastaki
- Kuwait Medical Genetics Centre, Ministry of HealthSulaibikhatKuwait
| | - Frédéric M. Vaz
- Amsterdam UMC Location University of Amsterdam, Department of Clinical Chemistry and PediatricsLaboratory Genetic Metabolic Diseases, Emma Children's HospitalAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of MetabolismAmsterdamThe Netherlands
| | | | - Dana Marafi
- Department of PediatricsAdan Hospital, Ministry of HealthHadiyaKuwait
- Kuwait Medical Genetics Centre, Ministry of HealthSulaibikhatKuwait
- Department of Pediatrics, Faculty of MedicineKuwait UniversitySafatKuwait
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7
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Salah S, Jaber H, Frumkin A, Harel T. Homozygous 22q11.2 distal type II microdeletion is associated with syndromic neurodevelopmental delay. Am J Med Genet A 2023; 191:2623-2630. [PMID: 37365930 DOI: 10.1002/ajmg.a.63326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 05/19/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023]
Abstract
Genomic disorders result from heterozygous copy number variants (CNVs). Homozygous deletions spanning numerous genes are rare, despite the potential contribution of consanguinity to such instances. CNVs in the 22q11.2 region are mediated by nonallelic homologous recombination between pairs of low copy repeats (LCRs), from amongst eight LCRs designated A-H. Heterozygous distal type II deletions (LCR-E to LCR-F) have incomplete penetrance and variable expressivity, and can lead to neurodevelopmental issues, minor craniofacial anomalies, and congenital abnormalities. We report siblings with global developmental delay, hypotonia, minor craniofacial anomalies, ocular abnormalities, and minor skeletal issues, in whom chromosomal microarray identified a homozygous distal type II deletion. The deletion was brought to homozygosity as a result of a consanguineous marriage between two heterozygous carriers of the deletion. The phenotype of the children was strikingly more severe and complex than that of the parents. This report suggests that the distal type II deletion harbors a dosage-sensitive gene or regulatory element, which leads to a more severe phenotype when deleted on both chromosomes.
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Affiliation(s)
- Somaya Salah
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Hiba Jaber
- Pediatric Neurology Unit, Hadassah Medical Center, Jerusalem, Israel
| | - Ayala Frumkin
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Israel
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8
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Jolly A, Du H, Borel C, Chen N, Zhao S, Grochowski CM, Duan R, Fatih JM, Dawood M, Salvi S, Jhangiani SN, Muzny DM, Koch A, Rouskas K, Glentis S, Deligeoroglou E, Bacopoulou F, Wise CA, Dietrich JE, Van den Veyver IB, Dimas AS, Brucker S, Sutton VR, Gibbs RA, Antonarakis SE, Wu N, Coban-Akdemir ZH, Zhu L, Posey JE, Lupski JR. Rare variant enrichment analysis supports GREB1L as a contributory driver gene in the etiology of Mayer-Rokitansky-Küster-Hauser syndrome. HGG ADVANCES 2023; 4:100188. [PMID: 37124138 PMCID: PMC10130500 DOI: 10.1016/j.xhgg.2023.100188] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is characterized by aplasia of the female reproductive tract; the syndrome can include renal anomalies, absence or dysgenesis, and skeletal anomalies. While functional models have elucidated several candidate genes, only WNT4 (MIM: 603490) variants have been definitively associated with a subtype of MRKH with hyperandrogenism (MIM: 158330). DNA from 148 clinically diagnosed MRKH probands across 144 unrelated families and available family members from North America, Europe, and South America were exome sequenced (ES) and by family-based genomics analyzed for rare likely deleterious variants. A replication cohort consisting of 442 Han Chinese individuals with MRKH was used to further reproduce GREB1L findings in diverse genetic backgrounds. Proband and OMIM phenotypes annotated using the Human Phenotype Ontology were analyzed to quantitatively delineate the phenotypic spectrum associated with GREB1L variant alleles found in our MRKH cohort and those previously published. This study reports 18 novel GREB1L variant alleles, 16 within a multiethnic MRKH cohort and two within a congenital scoliosis cohort. Cohort-wide analyses for a burden of rare variants within a single gene identified likely damaging variants in GREB1L (MIM: 617782), a known disease gene for renal hypoplasia and uterine abnormalities (MIM: 617805), in 16 of 590 MRKH probands. GREB1L variant alleles, including a CNV null allele, were found in 8 MRKH type 1 probands and 8 MRKH type II probands. This study used quantitative phenotypic analyses in a worldwide multiethnic cohort to identify and strengthen the association of GREB1L to isolated uterine agenesis (MRKH type I) and syndromic MRKH type II.
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Affiliation(s)
- Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | | | - Na Chen
- Department of Obstetrics and Gynaecology, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases and Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Sejal Salvi
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Shalini N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - André Koch
- University of Tübingen, Department of Obstetrics and Gynecology, Tübingen, Germany
| | - Konstantinos Rouskas
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Stavros Glentis
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
| | - Efthymios Deligeoroglou
- Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, Athens 11527, Greece
| | - Flora Bacopoulou
- Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, Athens 11527, Greece
| | - Carol A. Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
- McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Jennifer E. Dietrich
- Department of Obstetrics and Gynecology, Houston, TX, USA
- Department of Pediatrics, BCM, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Ignatia B. Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Obstetrics and Gynecology, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Antigone S. Dimas
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
| | - Sara Brucker
- University of Tübingen, Department of Obstetrics and Gynecology, Tübingen, Germany
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Stylianos E. Antonarakis
- University of Geneva Medical School, 1211 Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, 1205 Geneva, Switzerland
- Medigenome, the Swiss Institute of Genomic Medicine, 1207 Geneva, Switzerland
| | - Nan Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases and Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zeynep H. Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Lan Zhu
- Department of Obstetrics and Gynaecology, Beijing 100730, China
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Pediatrics, BCM, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
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9
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Zhang XR, Ren H, Yao F, Liu Y, Song CL. Study of pathogenic genes in a pedigree with familial dilated cardiomyopathy. World J Clin Cases 2023; 11:2412-2422. [PMID: 37123301 PMCID: PMC10130982 DOI: 10.12998/wjcc.v11.i11.2412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 02/22/2023] [Accepted: 03/15/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Dilated cardiomyopathy (DCM) is a genetically heterogeneous cardiac disorder characterized by left ventricular dilation and contractile dysfunction. The substantial genetic heterogeneity evident in patients with DCM contributes to variable disease severity and complicates overall prognosis, which can be very poor.
AIM To identify pathogenic genes in DCM through pedigree analysis.
METHODS Our research team identified a patient with DCM in the clinic. Through investigation, we found that the family of this patient has a typical DCM pedigree. High-throughput sequencing technology, next-generation sequencing, was used to sequence the whole exomes of seven samples in the pedigree.
RESULTS A novel and potentially pathogenic gene mutation-ANK2p.F3067L-was discovered. The mutation was completely consistent with the clinical information for this DCM pedigree. Sanger sequencing was used to further verify the locus of the mutation in pedigree samples. These results were consistent with those of high-throughput sequencing.
CONCLUSIONS ANK2p.F3067L is considered a novel and potentially pathogenic gene mutation in DCM.
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Affiliation(s)
- Xin-Ru Zhang
- Department of Pharmacy, The Second Hospital of Jilin University, Changchun 130000, Jilin Province, China
| | - Hang Ren
- Department of Cardiovascular Medicine, The Second Hospital of Jilin University, Changchun 130000, Jilin Province, China
| | - Fang Yao
- Department of Cardiovascular Medicine, The Second Hospital of Jilin University, Changchun 130000, Jilin Province, China
| | - Yang Liu
- Department of Cardiovascular Medicine, The Second Hospital of Jilin University, Changchun 130000, Jilin Province, China
| | - Chun-Li Song
- Department of Cardiovascular Medicine, The Second Hospital of Jilin University, Changchun 130000, Jilin Province, China
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10
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Penon-Portmann M, Hodoglugil U, Arun P W, Yip T, Slavotinek A, Tenney JL. TRAPPC9-related neurodevelopmental disorder: Report of a homozygous deletion in TRAPPC9 due to paternal uniparental isodisomy. Am J Med Genet A 2023; 191:1077-1082. [PMID: 36574751 DOI: 10.1002/ajmg.a.63100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/24/2022] [Accepted: 12/11/2022] [Indexed: 12/28/2022]
Abstract
TRAPPC9 loss-of-function biallelic variants are associated with an autosomal recessive intellectual disability syndrome (Online Mendelian Inheritance of Man no. 613192), also characterized by microcephaly, hypertelorism, obesity, growth delay, and behavioral differences. Here, we describe an 8-year-old Hispanic female with neurodevelopmental disorder, partial epilepsy, microcephaly, bilateral cleft lip and alveolus, growth delay, and dysmorphic features. She had abnormal myelination, mega cisterna magna, and colpocephaly on brain magnetic resonance imaging (MRI). Microarray showed a single ~146 Mb region of homozygosity (ROH) encompassing all of Chromosome 8, consistent with uniparental isodisomy (UPD). Exome sequencing performed in-house did not identify single nucleotide variants to explain her phenotype. Algorithms developed in-house and further evaluation of BAM files revealed a homozygous deletion overlapping Exon 2 in TRAPPC9 within the ROH. Subsequent del/dup analyses with exon-level oligo array confirmed a likely pathogenic deletion in TRAPPC9 (NM_031466.5): arr[GRCh37] 8q24.3(141460661_141461780)x0. Our case highlights the implications of downstream analyses from UPD/ROH given the increased risk for AR conditions, the strengths of combining orthologous molecular methods to establish a diagnosis and further delineates the TRAPPC9-related phenotype in an individual of Hispanic ancestry.
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Affiliation(s)
- Monica Penon-Portmann
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA.,Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Ugur Hodoglugil
- Genomic Medicine Laboratory, University of California San Francisco, San Francisco, California, USA
| | - Wiita Arun P
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Tiffany Yip
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA.,Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jessica L Tenney
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
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11
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Dawood M, Akay G, Mitani T, Marafi D, Fatih JM, Gezdirici A, Najmabadi H, Kahrizi K, Punetha J, Grochowski CM, Du H, Jolly A, Li H, Coban-Akdemir Z, Sedlazeck FJ, Hunter JV, Jhangiani SN, Muzny D, Pehlivan D, Posey JE, Carvalho CM, Gibbs RA, Lupski JR. A biallelic frameshift indel in PPP1R35 as a cause of primary microcephaly. Am J Med Genet A 2023; 191:794-804. [PMID: 36598158 PMCID: PMC9928800 DOI: 10.1002/ajmg.a.63080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/05/2022] [Accepted: 12/01/2022] [Indexed: 01/05/2023]
Abstract
Protein phosphatase 1 regulatory subunit 35 (PPP1R35) encodes a centrosomal protein required for recruiting microtubule-binding elongation machinery. Several proteins in this centriole biogenesis pathway correspond to established primary microcephaly (MCPH) genes, and multiple model organism studies hypothesize PPP1R35 as a candidate MCPH gene. Here, using exome sequencing (ES) and family-based rare variant analyses, we report a homozygous, frameshifting indel deleting the canonical stop codon in the last exon of PPP1R35 [Chr7: c.753_*3delGGAAGCGTAGACCinsCG (p.Trp251Cysfs*22)]; the variant allele maps in a 3.7 Mb block of absence of heterozygosity (AOH) in a proband with severe MCPH (-4.3 SD at birth, -6.1 SD by 42 months), pachygyria, and global developmental delay from a consanguineous Turkish kindred. Droplet digital PCR (ddPCR) confirmed mutant mRNA expression in fibroblasts. In silico prediction of the translation of mutant PPP1R35 is expected to be elongated by 18 amino acids before encountering a downstream stop codon. This complex indel allele is absent in public databases (ClinVar, gnomAD, ARIC, 1000 genomes) and our in-house database of 14,000+ exomes including 1800+ Turkish exomes supporting predicted pathogenicity. Comprehensive literature searches for PPP1R35 variants yielded two probands affected with severe microcephaly (-15 SD and -12 SD) with the same homozygous indel from a single, consanguineous, Iranian family from a cohort of 404 predominantly Iranian families. The lack of heterozygous cases in two large cohorts representative of the genetic background of these two families decreased our suspicion of a founder allele and supports the contention of a recurrent mutation. We propose two potential secondary structure mutagenesis models for the origin of this variant allele mediated by hairpin formation between complementary GC rich segments flanking the stop codon via secondary structure mutagenesis.
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Affiliation(s)
- Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul 34480, Turkey
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | | | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - He Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Fritz J. Sedlazeck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill V. Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas, 77030, USA
- E.B. Singleton Department of Pediatric Radiology, Texas Children’s Hospital, Houston, Texas, 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Shalini N. Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Claudia M.B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Pacific Northwest Research Institute, Seattle, WA, 98122, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030
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12
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Garg T, Weiss CR, Sheth RA. Techniques for Profiling the Cellular Immune Response and Their Implications for Interventional Oncology. Cancers (Basel) 2022; 14:3628. [PMID: 35892890 PMCID: PMC9332307 DOI: 10.3390/cancers14153628] [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: 07/08/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 12/07/2022] Open
Abstract
In recent years there has been increased interest in using the immune contexture of the primary tumors to predict the patient's prognosis. The tumor microenvironment of patients with cancers consists of different types of lymphocytes, tumor-infiltrating leukocytes, dendritic cells, and others. Different technologies can be used for the evaluation of the tumor microenvironment, all of which require a tissue or cell sample. Image-guided tissue sampling is a cornerstone in the diagnosis, stratification, and longitudinal evaluation of therapeutic efficacy for cancer patients receiving immunotherapies. Therefore, interventional radiologists (IRs) play an essential role in the evaluation of patients treated with systemically administered immunotherapies. This review provides a detailed description of different technologies used for immune assessment and analysis of the data collected from the use of these technologies. The detailed approach provided herein is intended to provide the reader with the knowledge necessary to not only interpret studies containing such data but also design and apply these tools for clinical practice and future research studies.
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Affiliation(s)
- Tushar Garg
- Division of Vascular and Interventional Radiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (T.G.); (C.R.W.)
| | - Clifford R. Weiss
- Division of Vascular and Interventional Radiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (T.G.); (C.R.W.)
| | - Rahul A. Sheth
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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13
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Xiao T, Chen X, Xu Y, Chen H, Dong X, Yang L, Wu B, Chen L, Li L, Zhuang D, Chen D, Zhou Y, Wang H, Zhou W. Clinical Study of 30 Novel KCNQ2 Variants/Deletions in KCNQ2-Related Disorders. Front Mol Neurosci 2022; 15:809810. [PMID: 35557555 PMCID: PMC9088225 DOI: 10.3389/fnmol.2022.809810] [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: 11/05/2021] [Accepted: 03/02/2022] [Indexed: 11/24/2022] Open
Abstract
Background KCNQ2-related disorder is typically characterized as neonatal onset seizure and epileptic encephalopathy. The relationship between its phenotype and genotype is still elusive. This study aims to provide clinical features, management, and prognosis of patients with novel candidate variants of the KCNQ2 gene. Methods We enrolled patients with novel variants in the KCNQ2 gene from the China Neonatal Genomes Project between January 2018 and January 2021. All patients underwent next-generation sequencing tests and genetic data were analyzed by an in-house pipeline. The pathogenicity of variants was classified according to the guideline of the American College of Medical Genetics. Each case was evaluated by two geneticists back to back. Patients' information was acquired from clinical records. Results A total of 30 unrelated patients with novel variants in the KCNQ2 gene were identified, including 19 patients with single-nucleotide variants (SNVs) and 11 patients with copy number variants (CNVs). For the 19 SNVs, 12 missense variants and 7 truncating variants were identified. Of them, 36.8% (7/19) of the KCNQ2 variants were located in C-terminal regions, 15.7% (3/19) in segment S2, and 15.7% (3/19) in segment S4. Among them, 18 of 19 patients experienced seizures in the early neonatal period. However, one patient presented neurodevelopmental delay (NDD) as initial phenotype when he was 2 months old, and he had severe NDD when he was 3 years old. This patient did not present seizure but had abnormal electrographic background activity and brain imaging. Moreover, for the 11 patients with CNVs, 20q13.3 deletions involving EEF1A2, KCNQ2, and CHRNA4 genes were detected. All of them presented neonatal-onset seizures, responded to antiepileptic drugs, and had normal neurological development. Conclusion In this study, patients with novel KCNQ2 variants have variable phenotypes, whereas patients with 20q13.3 deletion involving EEF1A2, KCNQ2, and CHRNA4 genes tend to have normal neurological development.
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Affiliation(s)
- Tiantian Xiao
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Xiang Chen
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Yan Xu
- Division of Neurology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Huiyao Chen
- Center for Molecular Medicine, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Lin Yang
- Department of Endocrinology and Inherited Metabolic Diseases, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Liping Chen
- Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Long Li
- Department of Neonatology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | | | - Dongmei Chen
- Quanzhou Women and Children's Hospital, Quanzhou, China
| | - Yuanfeng Zhou
- Division of Neurology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
- *Correspondence: Yuanfeng Zhou
| | - Huijun Wang
- Center for Molecular Medicine, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
- Huijun Wang
| | - Wenhao Zhou
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
- Center for Molecular Medicine, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
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14
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Mahmud S, Biswas S, Afrose S, Mita MA, Hasan MR, Shimu MSS, Paul GK, Chung S, Saleh MA, Alshehri S, Ghoneim MM, Alruwaily M, Kim B. Use of Next-Generation Sequencing for Identifying Mitochondrial Disorders. Curr Issues Mol Biol 2022; 44:1127-1148. [PMID: 35723297 PMCID: PMC8947152 DOI: 10.3390/cimb44030074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 12/06/2022] Open
Abstract
Mitochondria are major contributors to ATP synthesis, generating more than 90% of the total cellular energy production through oxidative phosphorylation (OXPHOS): metabolite oxidation, such as the β-oxidation of fatty acids, and the Krebs's cycle. OXPHOS inadequacy due to large genetic lesions in mitochondrial as well as nuclear genes and homo- or heteroplasmic point mutations in mitochondrially encoded genes is a characteristic of heterogeneous, maternally inherited genetic disorders known as mitochondrial disorders that affect multisystemic tissues and organs with high energy requirements, resulting in various signs and symptoms. Several traditional diagnostic approaches, including magnetic resonance imaging of the brain, cardiac testing, biochemical screening, variable heteroplasmy genetic testing, identifying clinical features, and skeletal muscle biopsies, are associated with increased risks, high costs, a high degree of false-positive or false-negative results, or a lack of precision, which limits their diagnostic abilities for mitochondrial disorders. Variable heteroplasmy levels, mtDNA depletion, and the identification of pathogenic variants can be detected through genetic sequencing, including the gold standard Sanger sequencing. However, sequencing can be time consuming, and Sanger sequencing can result in the missed recognition of larger structural variations such as CNVs or copy-number variations. Although each sequencing method has its own limitations, genetic sequencing can be an alternative to traditional diagnostic methods. The ever-growing roster of possible mutations has led to the development of next-generation sequencing (NGS). The enhancement of NGS methods can offer a precise diagnosis of the mitochondrial disorder within a short period at a reasonable expense for both research and clinical applications.
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Affiliation(s)
- Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Mst. Sharmin Sultana Shimu
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Gobindo Kumar Paul
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Sanghyun Chung
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea;
| | - Md. Abu Saleh
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Sultan Alshehri
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Momammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia; (M.M.G.); (M.A.)
| | - Maha Alruwaily
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia; (M.M.G.); (M.A.)
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea;
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15
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Zhang C, Jolly A, Shayota BJ, Mazzeu JF, Du H, Dawood M, Soper PC, Ramalho de Lima A, Ferreira BM, Coban-Akdemir Z, White J, Shears D, Thomson FR, Douglas SL, Wainwright A, Bailey K, Wordsworth P, Oldridge M, Lester T, Calder AD, Dumic K, Banka S, Donnai D, Jhangiani SN, Potocki L, Chung WK, Mora S, Northrup H, Ashfaq M, Rosenfeld JA, Mason K, Pollack LC, McConkie-Rosell A, Kelly W, McDonald M, Hauser NS, Leahy P, Powell CM, Boy R, Honjo RS, Kok F, Martelli LR, Filho VO, Genomics England Research Consortium, Muzny DM, Gibbs RA, Posey JE, Liu P, Lupski JR, Sutton VR, Carvalho CM. Novel pathogenic variants and quantitative phenotypic analyses of Robinow syndrome: WNT signaling perturbation and phenotypic variability. HGG ADVANCES 2022; 3:100074. [PMID: 35047859 PMCID: PMC8756549 DOI: 10.1016/j.xhgg.2021.100074] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/24/2021] [Indexed: 11/20/2022] Open
Abstract
Robinow syndrome (RS) is a genetically heterogeneous disorder with six genes that converge on the WNT/planar cell polarity (PCP) signaling pathway implicated (DVL1, DVL3, FZD2, NXN, ROR2, and WNT5A). RS is characterized by skeletal dysplasia and distinctive facial and physical characteristics. To further explore the genetic heterogeneity, paralog contribution, and phenotypic variability of RS, we investigated a cohort of 22 individuals clinically diagnosed with RS from 18 unrelated families. Pathogenic or likely pathogenic variants in genes associated with RS or RS phenocopies were identified in all 22 individuals, including the first variant to be reported in DVL2. We retrospectively collected medical records of 16 individuals from this cohort and extracted clinical descriptions from 52 previously published cases. We performed Human Phenotype Ontology (HPO) based quantitative phenotypic analyses to dissect allele-specific phenotypic differences. Individuals with FZD2 variants clustered into two groups with demonstrable phenotypic differences between those with missense and truncating alleles. Probands with biallelic NXN variants clustered together with the majority of probands carrying DVL1, DVL2, and DVL3 variants, demonstrating no phenotypic distinction between the NXN-autosomal recessive and dominant forms of RS. While phenotypically similar diseases on the RS differential matched through HPO analysis, clustering using phenotype similarity score placed RS-associated phenotypes in a unique cluster containing WNT5A, FZD2, and ROR2 apart from non-RS-associated paralogs. Through human phenotype analyses of this RS cohort and OMIM clinical synopses of Mendelian disease, this study begins to tease apart specific biologic roles for non-canonical WNT-pathway proteins.
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Affiliation(s)
- Chaofan Zhang
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Medical Scientist Training Program, BCM, Houston, TX 77030, USA
| | - Brian J. Shayota
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Juliana F. Mazzeu
- University of Brasilia, Brasilia 70050, Brazil
- Robinow Syndrome Foundation, Anoka, MN 55303, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Medical Scientist Training Program, BCM, Houston, TX 77030, USA
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | | | | | | | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, UTHealth, Houston, TX 77030, USA
| | - Janson White
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Deborah Shears
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7HE, UK
| | - Fraser Robert Thomson
- Cardiothoracic Surgery, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7HE, UK
| | | | - Andrew Wainwright
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7HE, UK
| | - Kathryn Bailey
- Pediatric Rheumatology, Nuffield Orthopedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7HE, UK
| | - Paul Wordsworth
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, Oxford OX3 7LD, UK
| | - Mike Oldridge
- Oxford Regional Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Tracy Lester
- Oxford Regional Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Alistair D. Calder
- Radiology Department, Great Ormond Street Hospital NHS Foundation Trust, London WC1N 3JH, UK
| | - Katja Dumic
- Department of Pediatric Endocrinology and Diabetes, University Clinical Center Zagreb, Zagreb 10000, Croatia
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9WL, UK
- Manchester Center for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Dian Donnai
- Manchester Center for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | | | - Lorraine Potocki
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Wendy K. Chung
- Department of Pediatrics and Medicine, Columbia University, NY 10032, USA
| | - Sara Mora
- GeneDx Inc., Gaithersburg, MD 20878, USA
| | - Hope Northrup
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston) and Children’s Memorial Hermann Hospital, Houston, TX 77030, USA
| | - Myla Ashfaq
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston) and Children’s Memorial Hermann Hospital, Houston, TX 77030, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Kati Mason
- GeneDx Inc., Gaithersburg, MD 20878, USA
- Arnold Palmer Hospital for Children, Orlando, FL 32806, USA
| | | | | | - Wei Kelly
- Division of Medical Genetics, Duke University Medical Center, Durham, NC 27708, USA
| | - Marie McDonald
- Division of Medical Genetics, Duke University Medical Center, Durham, NC 27708, USA
| | - Natalie S. Hauser
- Medical Genetics, Inova Fairfax Hospital, Falls Church, VA 22042, USA
| | - Peter Leahy
- Cook Children's Hospital, Fort Worth, TX 76104, USA
| | - Cynthia M. Powell
- Division of Pediatric Genetics and Metabolism, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Raquel Boy
- State University of Rio de Janeiro, Rio de Janeiro 21941, Brazil
| | - Rachel Sayuri Honjo
- Unidade de Genética, Instituto da Criança - Hospital das Clinicas HCFMUSP, Faculdade de Medicina, University of Sao Paulo, São Paulo 05508, Brasil
| | - Fernando Kok
- Mendelics Análise Genômica, São Paulo 04013, Brasil
| | - Lucia R. Martelli
- Department of Genetics, Ribeirao Preto Medical School, University of Sao Paulo, São Paulo 05508, Brazil
| | - Vicente Odone Filho
- Instituto de Tratamento do Câncer Infantil, São Paulo University Medical School, Hospital Israelita Albert Einstein, São Paulo 05508, Brasil
| | | | - Donna M. Muzny
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Baylor Genetics, Houston, TX 77021, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
- Department of Pediatrics, BCM, Houston, TX 77030, USA
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Claudia M.B. Carvalho
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Pacific Northwest Research Institute (PNRI), Seattle, WA 98122, USA
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16
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Musacchia F, Karali M, Torella A, Laurie S, Policastro V, Pizzo M, Beltran S, Casari G, Nigro V, Banfi S. VarGenius-HZD Allows Accurate Detection of Rare Homozygous or Hemizygous Deletions in Targeted Sequencing Leveraging Breadth of Coverage. Genes (Basel) 2021; 12:genes12121979. [PMID: 34946927 PMCID: PMC8701221 DOI: 10.3390/genes12121979] [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: 11/11/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022] Open
Abstract
Homozygous deletions (HDs) may be the cause of rare diseases and cancer, and their discovery in targeted sequencing is a challenging task. Different tools have been developed to disentangle HD discovery but a sensitive caller is still lacking. We present VarGenius-HZD, a sensitive and scalable algorithm that leverages breadth-of-coverage for the detection of rare homozygous and hemizygous single-exon deletions (HDs). To assess its effectiveness, we detected both real and synthetic rare HDs in fifty exomes from the 1000 Genomes Project obtaining higher sensitivity in comparison with state-of-the-art algorithms that each missed at least one event. We then applied our tool on targeted sequencing data from patients with Inherited Retinal Dystrophies and solved five cases that still lacked a genetic diagnosis. We provide VarGenius-HZD either stand-alone or integrated within our recently developed software, enabling the automated selection of samples using the internal database. Hence, it could be extremely useful for both diagnostic and research purposes.
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Affiliation(s)
- Francesco Musacchia
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy; (M.K.); (M.P.); (G.C.); (V.N.); (S.B.)
- Center for Human Technologies, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Correspondence:
| | - Marianthi Karali
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy; (M.K.); (M.P.); (G.C.); (V.N.); (S.B.)
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania ‘Luigi Vanvitelli’, 80138 Naples, Italy
| | - Annalaura Torella
- Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, 80138 Naples, Italy;
| | - Steve Laurie
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; (S.L.); (S.B.)
| | - Valeria Policastro
- Institute for Applied Mathematics “Mauro Picone” (IAC), National Research Council, 80131 Naples, Italy;
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania ‘Luigi Vanvitelli’, 81100 Caserta, Italy
| | - Mariateresa Pizzo
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy; (M.K.); (M.P.); (G.C.); (V.N.); (S.B.)
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; (S.L.); (S.B.)
- Universitat Pompeu Fabra (UPF), 08017 Barcelona, Spain
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona (UB), 08028 Barcelona, Spain
| | - Giorgio Casari
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy; (M.K.); (M.P.); (G.C.); (V.N.); (S.B.)
- Neurogenomics Unit, Center for Genomics, Bioinformatics and Biostatistics, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy; (M.K.); (M.P.); (G.C.); (V.N.); (S.B.)
- Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, 80138 Naples, Italy;
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy; (M.K.); (M.P.); (G.C.); (V.N.); (S.B.)
- Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, 80138 Naples, Italy;
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17
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Atlas G, Sreenivasan R, Sinclair A. Targeting the Non-Coding Genome for the Diagnosis of Disorders of Sex Development. Sex Dev 2021; 15:392-410. [PMID: 34634785 DOI: 10.1159/000519238] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/12/2021] [Indexed: 11/19/2022] Open
Abstract
Disorders of sex development (DSD) are a complex group of conditions with highly variable clinical phenotypes, most often caused by failure of gonadal development. DSD are estimated to occur in around 1.7% of all live births. Whilst the understanding of genes involved in gonad development has increased exponentially, approximately 50% of patients with a DSD remain without a genetic diagnosis, possibly implicating non-coding genomic regions instead. Here, we review how variants in the non-coding genome of DSD patients can be identified using techniques such as array comparative genomic hybridization (CGH) to detect copy number variants (CNVs), and more recently, whole genome sequencing (WGS). Once a CNV in a patient's non-coding genome is identified, putative regulatory elements such as enhancers need to be determined within these vast genomic regions. We will review the available online tools and databases that can be used to refine regions with potential enhancer activity based on chromosomal accessibility, histone modifications, transcription factor binding site analysis, chromatin conformation, and disease association. We will also review the current in vitro and in vivo techniques available to demonstrate the functionality of the identified enhancers. The review concludes with a clinical update on the enhancers linked to DSD.
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Affiliation(s)
- Gabby Atlas
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia, .,Department of Endocrinology and Diabetes, Royal Children's Hospital, Melbourne, Victoria, Australia, .,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia,
| | - Rajini Sreenivasan
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew Sinclair
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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18
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Mitani T, Isikay S, Gezdirici A, Gulec EY, Punetha J, Fatih JM, Herman I, Akay G, Du H, Calame DG, Ayaz A, Tos T, Yesil G, Aydin H, Geckinli B, Elcioglu N, Candan S, Sezer O, Erdem HB, Gul D, Demiral E, Elmas M, Yesilbas O, Kilic B, Gungor S, Ceylan AC, Bozdogan S, Ozalp O, Cicek S, Aslan H, Yalcintepe S, Topcu V, Bayram Y, Grochowski CM, Jolly A, Dawood M, Duan R, Jhangiani SN, Doddapaneni H, Hu J, Muzny DM, Marafi D, Akdemir ZC, Karaca E, Carvalho CMB, Gibbs RA, Posey JE, Lupski JR, Pehlivan D. High prevalence of multilocus pathogenic variation in neurodevelopmental disorders in the Turkish population. Am J Hum Genet 2021; 108:1981-2005. [PMID: 34582790 PMCID: PMC8546040 DOI: 10.1016/j.ajhg.2021.08.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/20/2021] [Indexed: 02/06/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) are clinically and genetically heterogenous; many such disorders are secondary to perturbation in brain development and/or function. The prevalence of NDDs is > 3%, resulting in significant sociocultural and economic challenges to society. With recent advances in family-based genomics, rare-variant analyses, and further exploration of the Clan Genomics hypothesis, there has been a logarithmic explosion in neurogenetic "disease-associated genes" molecular etiology and biology of NDDs; however, the majority of NDDs remain molecularly undiagnosed. We applied genome-wide screening technologies, including exome sequencing (ES) and whole-genome sequencing (WGS), to identify the molecular etiology of 234 newly enrolled subjects and 20 previously unsolved Turkish NDD families. In 176 of the 234 studied families (75.2%), a plausible and genetically parsimonious molecular etiology was identified. Out of 176 solved families, deleterious variants were identified in 218 distinct genes, further documenting the enormous genetic heterogeneity and diverse perturbations in human biology underlying NDDs. We propose 86 candidate disease-trait-associated genes for an NDD phenotype. Importantly, on the basis of objective and internally established variant prioritization criteria, we identified 51 families (51/176 = 28.9%) with multilocus pathogenic variation (MPV), mostly driven by runs of homozygosity (ROHs) - reflecting genomic segments/haplotypes that are identical-by-descent. Furthermore, with the use of additional bioinformatic tools and expansion of ES to additional family members, we established a molecular diagnosis in 5 out of 20 families (25%) who remained undiagnosed in our previously studied NDD cohort emanating from Turkey.
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Affiliation(s)
- Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sedat Isikay
- Department of Pediatric Neurology, Faculty of Medicine, University of Gaziantep, Gaziantep 27310, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul 34480, Turkey
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, 34303 Istanbul, Turkey
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Isabella Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Akif Ayaz
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey; Departments of Medical Genetics, School of Medicine, Istanbul Medipol University, Istanbul 34810, Turkey
| | - Tulay Tos
- University of Health Sciences Zubeyde Hanim Research and Training Hospital of Women's Health and Diseases, Department of Medical Genetics, Ankara 06080, Turkey
| | - Gozde Yesil
- Istanbul Faculty of Medicine, Department of Medical Genetics, Istanbul University, Istanbul 34093, Turkey
| | - Hatip Aydin
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey; Private Reyap Istanbul Hospital, Istanbul 34515, Turkey
| | - Bilgen Geckinli
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey; Department of Medical Genetics, School of Medicine, Marmara University, Istanbul 34722, Turkey
| | - Nursel Elcioglu
- Department of Pediatric Genetics, School of Medicine, Marmara University, Istanbul 34722, Turkey; Eastern Mediterranean University Medical School, Magosa, Mersin 10, Turkey
| | - Sukru Candan
- Medical Genetics Section, Balikesir Ataturk Public Hospital, Balikesir 10100, Turkey
| | - Ozlem Sezer
- Department of Medical Genetics, Samsun Education and Research Hospital, Samsun 55100, Turkey
| | - Haktan Bagis Erdem
- Department of Medical Genetics, University of Health Sciences, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara 06110, Turkey
| | - Davut Gul
- Department of Medical Genetics, Gulhane Military Medical School, Ankara 06010, Turkey
| | - Emine Demiral
- Department of Medical Genetics, School of Medicine, University of Inonu, Malatya 44280, Turkey
| | - Muhsin Elmas
- Department of Medical Genetics, Afyon Kocatepe University, School of Medicine, Afyon 03218, Turkey
| | - Osman Yesilbas
- Division of Critical Care Medicine, Department of Pediatrics, School of Medicine, Bezmialem Foundation University, Istanbul 34093, Turkey; Department of Pediatrics, Division of Pediatric Critical Care Medicine, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Betul Kilic
- Department of Pediatrics and Pediatric Neurology, Faculty of Medicine, Inonu University, Malatya 34218, Turkey
| | - Serdal Gungor
- Department of Pediatrics and Pediatric Neurology, Faculty of Medicine, Inonu University, Malatya 34218, Turkey
| | - Ahmet C Ceylan
- Department of Medical Genetics, University of Health Sciences, Ankara Training and Research Hospital, Ankara 06110, Turkey
| | - Sevcan Bozdogan
- Department of Medical Genetics, Cukurova University Faculty of Medicine, Adana 01330, Turkey
| | - Ozge Ozalp
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey
| | - Salih Cicek
- Department of Medical Genetics, Konya Training and Research Hospital, Konya 42250, Turkey
| | - Huseyin Aslan
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey
| | - Sinem Yalcintepe
- Department of Medical Genetics, School of Medicine, Trakya University, Edirne 22130, Turkey
| | - Vehap Topcu
- Department of Medical Genetics, Ankara City Hospital, Ankara 06800, Turkey
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA.
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19
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Vorsteveld EE, Hoischen A, van der Made CI. Next-Generation Sequencing in the Field of Primary Immunodeficiencies: Current Yield, Challenges, and Future Perspectives. Clin Rev Allergy Immunol 2021; 61:212-225. [PMID: 33666867 PMCID: PMC7934351 DOI: 10.1007/s12016-021-08838-5] [Citation(s) in RCA: 3] [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] [Accepted: 01/07/2021] [Indexed: 12/18/2022]
Abstract
Primary immunodeficiencies comprise a group of inborn errors of immunity that display significant clinical and genetic heterogeneity. Next-generation sequencing techniques and predominantly whole exome sequencing have revolutionized the understanding of the genetic and molecular basis of genetic diseases, thereby also leading to a sharp increase in the discovery of new genes associated with primary immunodeficiencies. In this review, we discuss the current diagnostic yield of this generic diagnostic approach by evaluating the studies that have employed next-generation sequencing techniques in cohorts of patients with primary immunodeficiencies. The average diagnostic yield for primary immunodeficiencies is determined to be 29% (range 10-79%) and 38% specifically for whole-exome sequencing (range 15-70%). The significant variation between studies is mainly the result of differences in clinical characteristics of the studied cohorts but is also influenced by varying sequencing approaches and (in silico) gene panel selection. We further discuss other factors contributing to the relatively low yield, including the inherent limitations of whole-exome sequencing, challenges in the interpretation of novel candidate genetic variants, and promises of exploring the non-coding part of the genome. We propose strategies to improve the diagnostic yield leading the way towards expanded personalized treatment in PIDs.
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Affiliation(s)
- Emil E Vorsteveld
- Department of Human Genetics, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases (RCI), Radboudumc, Nijmegen, The Netherlands.
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Caspar I van der Made
- Department of Human Genetics, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases (RCI), Radboudumc, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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20
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Calame DG, Fatih JM, Herman I, Coban‐Akdemir Z, Du H, Mitani T, Jhangiani SN, Marafi D, Gibbs RA, Posey JE, Mehta VP, Mohila CA, Abid F, Lotze TE, Pehlivan D, Adesina AM, Lupski JR. Deep clinicopathological phenotyping identifies a previously unrecognized pathogenic EMD splice variant. Ann Clin Transl Neurol 2021; 8:2052-2058. [PMID: 34524739 PMCID: PMC8528454 DOI: 10.1002/acn3.51454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/12/2021] [Accepted: 09/02/2021] [Indexed: 12/05/2022] Open
Abstract
Exome sequencing (ES) has revolutionized rare disease management, yet only ~25%-30% of patients receive a molecular diagnosis. A limiting factor is the quality of available phenotypic data. Here, we describe how deep clinicopathological phenotyping yielded a molecular diagnosis for a 19-year-old proband with muscular dystrophy and negative clinical ES. Deep phenotypic analysis identified two critical data points: (1) the absence of emerin protein in muscle biopsy and (2) clinical features consistent with Emery-Dreifuss muscular dystrophy. Sequencing data analysis uncovered an ultra-rare, intronic variant in EMD, the gene encoding emerin. The variant, NM_000117.3: c.188-6A > G, is predicted to impact splicing by in silico tools. This case thus illustrates how better integration of clinicopathologic data into ES analysis can enhance diagnostic yield with implications for clinical practice.
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Affiliation(s)
- Daniel G. Calame
- Division of Neurology and Developmental NeuroscienceDepartment of PediatricsBaylor College of MedicineHoustonTexas77030USA
- Texas Children’s HospitalHoustonTexas77030USA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
| | - Jawid M. Fatih
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
| | - Isabella Herman
- Division of Neurology and Developmental NeuroscienceDepartment of PediatricsBaylor College of MedicineHoustonTexas77030USA
- Texas Children’s HospitalHoustonTexas77030USA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
| | - Zeynep Coban‐Akdemir
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
| | - Haowei Du
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
| | - Tadahiro Mitani
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
| | | | - Dana Marafi
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
- Department of PediatricsFaculty of MedicineKuwait UniversitySafat13110Kuwait
| | - Richard A. Gibbs
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
- Human Genome Sequencing CenterBaylor College of MedicineHoustonTexas77030USA
| | - Jennifer E. Posey
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
| | - Vidya P. Mehta
- Department of PathologyTexas Children's HospitalBaylor College of MedicineHoustonTexas77030USA
| | - Carrie A. Mohila
- Department of PathologyTexas Children's HospitalBaylor College of MedicineHoustonTexas77030USA
| | - Farida Abid
- Division of Neurology and Developmental NeuroscienceDepartment of PediatricsBaylor College of MedicineHoustonTexas77030USA
- Texas Children’s HospitalHoustonTexas77030USA
| | - Timothy E. Lotze
- Division of Neurology and Developmental NeuroscienceDepartment of PediatricsBaylor College of MedicineHoustonTexas77030USA
- Texas Children’s HospitalHoustonTexas77030USA
| | - Davut Pehlivan
- Division of Neurology and Developmental NeuroscienceDepartment of PediatricsBaylor College of MedicineHoustonTexas77030USA
- Texas Children’s HospitalHoustonTexas77030USA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
| | - Adekunle M. Adesina
- Department of PathologyTexas Children's HospitalBaylor College of MedicineHoustonTexas77030USA
| | - James R. Lupski
- Texas Children’s HospitalHoustonTexas77030USA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
- Human Genome Sequencing CenterBaylor College of MedicineHoustonTexas77030USA
- Department of PediatricsBaylor College of MedicineHoustonTexas77030USA
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21
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Bastard P, Manry J, Chen J, Rosain J, Seeleuthner Y, AbuZaitun O, Lorenzo L, Khan T, Hasek M, Hernandez N, Bigio B, Zhang P, Lévy R, Shrot S, Reino EJG, Lee YS, Boucherit S, Aubart M, Gijsbers R, Béziat V, Li Z, Pellegrini S, Rozenberg F, Marr N, Meyts I, Boisson B, Cobat A, Bustamante J, Zhang Q, Jouangy E, Abel L, Somech R, Casanova JL, Zhang SY. Herpes simplex encephalitis in a patient with a distinctive form of inherited IFNAR1 deficiency. J Clin Invest 2021; 131:139980. [PMID: 32960813 DOI: 10.1172/jci139980] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/17/2020] [Indexed: 12/16/2022] Open
Abstract
Inborn errors of TLR3-dependent IFN-α/β- and IFN-λ-mediated immunity in the CNS can underlie herpes simplex virus 1 (HSV-1) encephalitis (HSE). The respective contributions of IFN-α/β and IFN-λ are unknown. We report a child homozygous for a genomic deletion of the entire coding sequence and part of the 3'-UTR of the last exon of IFNAR1, who died of HSE at the age of 2 years. An older cousin died following vaccination against measles, mumps, and rubella at 12 months of age, and another 17-year-old cousin homozygous for the same variant has had other, less severe, viral illnesses. The encoded IFNAR1 protein is expressed on the cell surface but is truncated and cannot interact with the tyrosine kinase TYK2. The patient's fibroblasts and EBV-B cells did not respond to IFN-α2b or IFN-β, in terms of STAT1, STAT2, and STAT3 phosphorylation or the genome-wide induction of IFN-stimulated genes. The patient's fibroblasts were susceptible to viruses, including HSV-1, even in the presence of exogenous IFN-α2b or IFN-β. HSE is therefore a consequence of inherited complete IFNAR1 deficiency. This viral disease occurred in natural conditions, unlike those previously reported in other patients with IFNAR1 or IFNAR2 deficiency. This experiment of nature indicates that IFN-α/β are essential for anti-HSV-1 immunity in the CNS.
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Affiliation(s)
- Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, USA
| | - Jeremy Manry
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France
| | - Jie Chen
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, USA
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France
| | | | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France
| | | | - Mary Hasek
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, USA
| | - Nicholas Hernandez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, USA
| | - Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, USA
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, USA
| | - Romain Lévy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France.,Pediatric Immunology-Hematology Unit, Assistance Publique-Hôpitaux de Paris (AP-HP), Necker Hospital for Sick Children, Paris, France
| | - Shai Shrot
- Department of Diagnostic Imaging, Sheba Medical Center, Ramat Gan, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eduardo J Garcia Reino
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, USA
| | - Yoon-Seung Lee
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, USA
| | - Soraya Boucherit
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France
| | - Mélodie Aubart
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Department of Pediatric Neurology, Necker Hospital for Sick Children, University of Paris, Paris, France
| | - Rik Gijsbers
- Laboratory of Viral Vector Technology and Gene Therapy and Leuven Viral Vector Core, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
| | - Zhi Li
- Unit of Cytokine Signaling, Pasteur Institute, INSERM U1221, Paris, France
| | - Sandra Pellegrini
- Unit of Cytokine Signaling, Pasteur Institute, INSERM U1221, Paris, France
| | - Flore Rozenberg
- Laboratory of Virology, University of Paris, AP-HP, Cochin Hospital, Paris, France
| | - Nico Marr
- Research Branch, Sidra Medicine, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Isabelle Meyts
- Laboratory of Inborn Errors of Immunity, Department of Immunology, Microbiology and Transplantation, KU Leuven, Leuven, Belgium.,Department of Pediatrics, Jeffrey Modell Diagnostic and Research Network Center, University Hospitals Leuven, Leuven, Belgium.,Precision Immunology Institute and Mindich Child Health and Development Institute at the Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bertrand Boisson
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, USA.,Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, USA
| | - Emmanuelle Jouangy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, USA
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, USA
| | - Raz Somech
- Pediatric Department and Immunology Unit, Edmond and Lily Safra Children's Hospital, Jeffrey Modell Foundation Center, Sheba Medical Center, Tel HaShomer, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, USA.,Pediatric Immunology-Hematology Unit, Assistance Publique-Hôpitaux de Paris (AP-HP), Necker Hospital for Sick Children, Paris, France.,Howard Hughes Medical Institute, New York, New York, USA
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, USA
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22
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Gordeeva V, Sharova E, Babalyan K, Sultanov R, Govorun VM, Arapidi G. Benchmarking germline CNV calling tools from exome sequencing data. Sci Rep 2021; 11:14416. [PMID: 34257369 PMCID: PMC8277855 DOI: 10.1038/s41598-021-93878-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Whole-exome sequencing is an attractive alternative to microarray analysis because of the low cost and potential ability to detect copy number variations (CNV) of various sizes (from 1-2 exons to several Mb). Previous comparison of the most popular CNV calling tools showed a high portion of false-positive calls. Moreover, due to a lack of a gold standard CNV set, the results are limited and incomparable. Here, we aimed to perform a comprehensive analysis of tools capable of germline CNV calling available at the moment using a single CNV standard and reference sample set. Compiling variants from previous studies with Bayesian estimation approach, we constructed an internal standard for NA12878 sample (pilot National Institute of Standards and Technology Reference Material) including 110,050 CNV or non-CNV exons. The standard was used to evaluate the performance of 16 germline CNV calling tools on the NA12878 sample and 10 correlated exomes as a reference set with respect to length distribution, concordance, and efficiency. Each algorithm had a certain range of detected lengths and showed low concordance with other tools. Most tools are focused on detection of a limited number of CNVs one to seven exons long with a false-positive rate below 50%. EXCAVATOR2, exomeCopy, and FishingCNV focused on detection of a wide range of variations but showed low precision. Upon unified comparison, the tools were not equivalent. The analysis performed allows choosing algorithms or ensembles of algorithms most suitable for a specific goal, e.g. population studies or medical genetics.
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Affiliation(s)
- Veronika Gordeeva
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia.
| | - Elena Sharova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Konstantin Babalyan
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Rinat Sultanov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, Russia
| | - Vadim M Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Georgij Arapidi
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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23
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Bigio B, Seeleuthner Y, Kerner G, Migaud M, Rosain J, Boisson B, Nasca C, Puel A, Bustamante J, Casanova JL, Abel L, Cobat A. Detection of homozygous and hemizygous complete or partial exon deletions by whole-exome sequencing. NAR Genom Bioinform 2021; 3:lqab037. [PMID: 34046589 PMCID: PMC8140739 DOI: 10.1093/nargab/lqab037] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 03/19/2021] [Accepted: 05/03/2021] [Indexed: 12/11/2022] Open
Abstract
The detection of copy number variations (CNVs) in whole-exome sequencing (WES) data is important, as CNVs may underlie a number of human genetic disorders. The recently developed HMZDelFinder algorithm can detect rare homozygous and hemizygous (HMZ) deletions in WES data more effectively than other widely used tools. Here, we present HMZDelFinder_opt, an approach that outperforms HMZDelFinder for the detection of HMZ deletions, including partial exon deletions in particular, in WES data from laboratory patient collections that were generated over time in different experimental conditions. We show that using an optimized reference control set of WES data, based on a PCA-derived Euclidean distance for coverage, strongly improves the detection of HMZ complete exon deletions both in real patients carrying validated disease-causing deletions and in simulated data. Furthermore, we develop a sliding window approach enabling HMZDelFinder_opt to identify HMZ partial deletions of exons that are undiscovered by HMZDelFinder. HMZDelFinder_opt is a timely and powerful approach for detecting HMZ deletions, particularly partial exon deletions, in WES data from inherently heterogeneous laboratory patient collections.
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Affiliation(s)
- Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
| | - Gaspard Kerner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Carla Nasca
- Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY 10065, USA
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Aurelie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
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24
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Xiao T, Wu B, Cao Y, Liu R, Cheng G, Wang L, Zhuang D, Zhao Z, Wang H, Zhou W. Genetic identification of pathogenic variations of the DMD gene: a retrospective study from 10,481 neonatal patients based on next-generation sequencing data. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:766. [PMID: 34268379 PMCID: PMC8246177 DOI: 10.21037/atm-20-7102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/07/2021] [Indexed: 12/20/2022]
Abstract
Background An elevated level of creatine kinase (CK) is usually the primary screening marker for Duchenne muscular dystrophy (DMD)/Becker muscular dystrophy (BMD). This study investigated the clinical application of next-generation sequencing (NGS) in newborns with a possible diagnosis of DMD/BMD in the neonatal intensive care unit (NICU). Methods NGS data from the NICU between June 1, 2016, and June 30, 2020, were reanalyzed by an in-house pipeline. Other methods confirmed the genetic findings, and clinical follow-up was performed until August 1, 2020. Results Of the 10,481 newborns, 19 (0.18%, 19/10,481) cases with pathogenic variations of the DMD gene were identified, including 13 (68.4%, 13/19) deletions, 4 (21.1%, 4/19) duplications, and 2 (10.5%, 2/19) nonsense mutations. Eight of the cases were diagnosed with DMD. Therapeutic strategies were modified for these patients. Six cases were diagnosed with BMD. Five patients except for 1 deceased patient were further followed-up, and clinical management was adjusted based on the clinical symptoms. The remaining 5 cases were indeterminate for DMD and BMD. Genetic counseling and further follow-up were performed or suggested. Conclusions Our study showed that DMD/BMD could be diagnosed earlier in the neonatal stage before the typical clinical symptoms appear. Early diagnosis may provide an opportunity for guiding the care and treatment of patients. However, ethical issues need to be kept in mind in the process of genetic counseling.
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Affiliation(s)
- Tiantian Xiao
- Department of Neonates, Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Department of Neonatology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yun Cao
- Department of Neonates, Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Renchao Liu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Guoqiang Cheng
- Department of Neonates, Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Laishuan Wang
- Department of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Deyi Zhuang
- Department of Pediatrics, Xiamen Children's Hospital, Xiamen, China
| | - Zhengyan Zhao
- Department of Child Health Care, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Wenhao Zhou
- Department of Neonates, Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
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25
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Prasad A, Bhargava H, Gupta A, Shukla N, Rajagopal S, Gupta S, Sharma A, Valadi J, Nigam V, Suravajhala P. Next Generation Sequencing. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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26
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Tang X, Liu C, Liu X, Chen J, Fan X, Liu J, Ma D, Cao G, Chen Z, Xu D, Zhu Y, Jiang X, Cheng L, Wu Y, Hou L, Li Y, Shao X, Zheng S, Zhang A, Zheng B, Jian S, Rong Z, Su Q, Gao X, Rao J, Shen Q, Xu H. Phenotype and genotype spectra of a Chinese cohort with nephronophthisis-related ciliopathy. J Med Genet 2020; 59:147-154. [PMID: 33323469 DOI: 10.1136/jmedgenet-2020-107184] [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: 05/14/2020] [Revised: 10/23/2020] [Accepted: 11/11/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND Nephronophthisis-related ciliopathies (NPHP-RC) account for the majority of cases of monogenetically caused end-stage renal disease (ESRD) in children. Exploring the correlation between the phenotype and genotype of NPHP-RC is helpful for early diagnosis and management. We investigated the phenotype and genotype spectra of NPHP-RC in a Chinese multicentre cohort. METHODS Crosss-ectional and longitudinal data of 60 patients from 57 families with pathogenic NPHP-RC gene mutations distributed in 22 regions of China were collected into a unified, anonymous database. The mean observation time of this cohort was 3.5±3.1 years. RESULTS Mutations in NPHP1 and NPHP3 were the most common genetic defects. Overall, 45% of patients presented with isolated nephronophthisis (NPH), and 55% exhibited the extrarenal phenotype, which frequently involved the liver (41.7%, n=25), central nervous system (26.7%, n=16), eyes (26.7%, n=16) and skeletal system (11.7%, n=7). Accidental detection of elevated serum creatinine and non-specific symptoms caused by chronic kidney disease occurred in 65% of patients. Patients carrying NPHP1 mutations mainly presented with isolated NPH (90%, 18/20) and progressed to ESRD at a mean age of 12.9±0.5 years. The mean age of ESRD onset in the non-NPHP1 group was lower than that in the NPHP1 group (6.2±1.4 years, p<0.001), especially for patients carrying NPHP3 mutations (3.1±1.2 years), showing a heterogeneous phenotype characterised by Bardet-Biedl syndrome (12.5%, n=5), Joubert syndrome (7.5%, n=3), COACH syndrome (2.5%, n=1), Mainzer-Saldino syndrome (2.5%, n=1), short-rib thoracic dysplasia (2.5%, n=1) and unclassified symptoms (32.5%, n=13). CONCLUSIONS The Chinese Children Genetic Kidney Disease Database registry characterised the spectrum of the phenotype and genotype of NPHP-RC in the Chinese population. NPHP1 and NPHP3 were the most common pathogenic genes. Rapid progression to ESRD and liver involvement were noted in patients with NPHP3 mutations.
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Affiliation(s)
- Xiaoshan Tang
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Cuihua Liu
- Nephrology and Rheumatology, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Xiaorong Liu
- Nephrology, Bejing Children's Hospital, Beijing, China.,Beijing Children's Key Laboratory of Chronic Kidney Disease and Blood Purification, Beijing Children's Hospital, Beijing, China
| | - Jing Chen
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Xiaoyan Fan
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Jialu Liu
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institutes of Biomedical Sciences, Fudan University School of Basic Medical Sciences, Shanghai, China
| | - Guanghai Cao
- Nephrology and Rheumatology, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Zhi Chen
- Nephrology, Bejing Children's Hospital, Beijing, China.,Beijing Children's Key Laboratory of Chronic Kidney Disease and Blood Purification, Beijing Children's Hospital, Beijing, China
| | - Daliang Xu
- Nephrology, Anhui Provincial Children's Hospital, Hefei, China
| | - Ying Zhu
- Nephrology, Anhui Provincial Children's Hospital, Hefei, China
| | - Xiaoyun Jiang
- Pediatric, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
| | - Lizhi Cheng
- Pediatric, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
| | - Yubing Wu
- Pediatric Nephrology and Rheumatology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ling Hou
- Pediatric Nephrology and Rheumatology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yuhong Li
- Nephrology and Rheumatology, Guiyang Children's Hospital, Guiyang, China
| | - Xiaoshan Shao
- Nephrology and Rheumatology, Guiyang Children's Hospital, Guiyang, China
| | - Shasha Zheng
- Nephrology and Rheumatology, Guiyang Children's Hospital, Guiyang, China
| | - Aihua Zhang
- Nephrology, Nanjing Medical University Affiliated Nanjing Children's Hospital, Nanjing, China
| | - Bixia Zheng
- Nanjing Key Laboratory of Pediatrics, Nanjing Medical University Affiliated Nanjing Children's Hospital, Nanjing, Jiangsu, China
| | - Shan Jian
- Pediatrics, Peking Union Medical College Hospital, Beijing, China
| | - Zanhua Rong
- Pediatrics, Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Qingxiao Su
- Pediatrics, Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xia Gao
- Nephrology, Guangzhou Children's Hospital, Guangzhou, China
| | - Jia Rao
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China .,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and School of Basic Medical Science,Fudan University, Shanghai, China.,Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China, Shanghai, China
| | - Qian Shen
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China .,Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Hong Xu
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China .,Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China, Shanghai, China
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27
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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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28
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Kanzi AM, San JE, Chimukangara B, Wilkinson E, Fish M, Ramsuran V, de Oliveira T. Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance. Front Genet 2020; 11:544162. [PMID: 33193618 PMCID: PMC7649788 DOI: 10.3389/fgene.2020.544162] [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: 03/20/2020] [Accepted: 09/21/2020] [Indexed: 12/29/2022] Open
Abstract
Mendelian and complex genetic trait diseases continue to burden and affect society both socially and economically. The lack of effective tests has hampered diagnosis thus, the affected lack proper prognosis. Mendelian diseases are caused by genetic mutations in a singular gene while complex trait diseases are caused by the accumulation of mutations in either linked or unlinked genomic regions. Significant advances have been made in identifying novel diseases associated mutations especially with the introduction of next generation and third generation sequencing. Regardless, some diseases are still without diagnosis as most tests rely on SNP genotyping panels developed from population based genetic analyses. Analysis of family genetic inheritance using whole genomes, whole exomes or a panel of genes has been shown to be effective in identifying disease-causing mutations. In this review, we discuss next generation and third generation sequencing platforms, bioinformatic tools and genetic resources commonly used to analyze family based genomic data with a focus on identifying inherited or novel disease-causing mutations. Additionally, we also highlight the analytical, ethical and regulatory challenges associated with analyzing personal genomes which constitute the data used for family genetic inheritance.
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Affiliation(s)
- Aquillah M. Kanzi
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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29
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Zhang Q, Bastard P, Liu Z, Le Pen J, Moncada-Velez M, Chen J, Ogishi M, Sabli IKD, Hodeib S, Korol C, Rosain J, Bilguvar K, Ye J, Bolze A, Bigio B, Yang R, Arias AA, Zhou Q, Zhang Y, Onodi F, Korniotis S, Karpf L, Philippot Q, Chbihi M, Bonnet-Madin L, Dorgham K, Smith N, Schneider WM, Razooky BS, Hoffmann HH, Michailidis E, Moens L, Han JE, Lorenzo L, Bizien L, Meade P, Neehus AL, Ugurbil AC, Corneau A, Kerner G, Zhang P, Rapaport F, Seeleuthner Y, Manry J, Masson C, Schmitt Y, Schlüter A, Le Voyer T, Khan T, Li J, Fellay J, Roussel L, Shahrooei M, Alosaimi MF, Mansouri D, Al-Saud H, Al-Mulla F, Almourfi F, Al-Muhsen SZ, Alsohime F, Al Turki S, Hasanato R, van de Beek D, Biondi A, Bettini LR, D'Angio' M, Bonfanti P, Imberti L, Sottini A, Paghera S, Quiros-Roldan E, Rossi C, Oler AJ, Tompkins MF, Alba C, Vandernoot I, Goffard JC, Smits G, Migeotte I, Haerynck F, Soler-Palacin P, Martin-Nalda A, Colobran R, Morange PE, Keles S, Çölkesen F, Ozcelik T, Yasar KK, Senoglu S, Karabela ŞN, Rodríguez-Gallego C, Novelli G, Hraiech S, Tandjaoui-Lambiotte Y, Duval X, Laouénan C, Snow AL, Dalgard CL, Milner JD, Vinh DC, Mogensen TH, Marr N, Spaan AN, Boisson B, Boisson-Dupuis S, Bustamante J, Puel A, Ciancanelli MJ, Meyts I, Maniatis T, Soumelis V, Amara A, Nussenzweig M, García-Sastre A, Krammer F, Pujol A, Duffy D, Lifton RP, Zhang SY, Gorochov G, Béziat V, Jouanguy E, Sancho-Shimizu V, Rice CM, Abel L, Notarangelo LD, Cobat A, Su HC, Casanova JL. Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science 2020; 370:eabd4570. [PMID: 32972995 PMCID: PMC7857407 DOI: 10.1126/science.abd4570] [Citation(s) in RCA: 1523] [Impact Index Per Article: 380.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/16/2020] [Indexed: 12/15/2022]
Abstract
Clinical outcome upon infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ranges from silent infection to lethal coronavirus disease 2019 (COVID-19). We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern Toll-like receptor 3 (TLR3)- and interferon regulatory factor 7 (IRF7)-dependent type I interferon (IFN) immunity to influenza virus in 659 patients with life-threatening COVID-19 pneumonia relative to 534 subjects with asymptomatic or benign infection. By testing these and other rare variants at these 13 loci, we experimentally defined LOF variants underlying autosomal-recessive or autosomal-dominant deficiencies in 23 patients (3.5%) 17 to 77 years of age. We show that human fibroblasts with mutations affecting this circuit are vulnerable to SARS-CoV-2. Inborn errors of TLR3- and IRF7-dependent type I IFN immunity can underlie life-threatening COVID-19 pneumonia in patients with no prior severe infection.
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Affiliation(s)
- Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Zhiyong Liu
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jérémie Le Pen
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Marcela Moncada-Velez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jie Chen
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Ira K D Sabli
- Department of Paediatric Infectious Diseases & Virology, Imperial College London, London, UK
| | - Stephanie Hodeib
- Department of Paediatric Infectious Diseases & Virology, Imperial College London, London, UK
| | - Cecilia Korol
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Kaya Bilguvar
- Yale Center for Genome Analysis and Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Junqiang Ye
- Zukerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | | | - Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Rui Yang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Andrés Augusto Arias
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Primary Immunodeficiencies Group, University of Antioquia UdeA, Medellin, Colombia
- School of Microbiology, University of Antioquia UdeA, Medellin, Colombia
| | - Qinhua Zhou
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Bethesda, MD, USA
| | - Fanny Onodi
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Hôpital Saint-Louis, Paris, France
| | - Sarantis Korniotis
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Hôpital Saint-Louis, Paris, France
| | - Léa Karpf
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Hôpital Saint-Louis, Paris, France
| | - Quentin Philippot
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Marwa Chbihi
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Lucie Bonnet-Madin
- Laboratory of Genomes & Cell Biology of Disease, INSERM U944, CNRS UMR 7212, Université de Paris, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, Paris, France
| | - Karim Dorgham
- Sorbonne Université, Inserm, Centre d'Immunologie et des Maladies Infectieuses-Paris (CIMI PARIS), Assistance Publique-Hôpitaux de Paris (AP-HP) Hôpital Pitié-Salpêtrière, Paris, France
| | - Nikaïa Smith
- Translational Immunology Lab, Institut Pasteur, Paris, France
| | - William M Schneider
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Brandon S Razooky
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Leen Moens
- Laboratory for Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, Department of Pediatrics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Ji Eun Han
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Philip Meade
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anna-Lena Neehus
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Aileen Camille Ugurbil
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Aurélien Corneau
- Sorbonne Université, UMS037, PASS, Plateforme de Cytométrie de la Pitié-Salpêtrière CyPS, Paris, France
| | - Gaspard Kerner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Franck Rapaport
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Jeremy Manry
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Cecile Masson
- Bioinformatics Platform, Structure Fédérative de Recherche Necker, INSERM UMR1163, Université de Paris, Imagine Institute, Paris, France
| | - Yohann Schmitt
- Bioinformatics Platform, Structure Fédérative de Recherche Necker, INSERM UMR1163, Université de Paris, Imagine Institute, Paris, France
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, IDIBELL-Hospital Duran i Reynals, CIBERER U759, and Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Tom Le Voyer
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Taushif Khan
- Department of Immunology, Research Branch, Sidra Medicine, Doha, Qatar
| | - Juan Li
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jacques Fellay
- School of Life sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Swiss Institue of Bioinformatics, Lausanne, Switzerland
| | - Lucie Roussel
- Infectious Disease Susceptibility Program, Research Institute, McGill University Health Centre, Montréal, Québec, Canada
| | - Mohammad Shahrooei
- Specialized Immunology Laboratory of Dr. Shahrooei, Sina Medical Complex, Ahvaz, Iran
- Department of Microbiology and Immunology, Clinical and Diagnostic Immunology, KU Leuven, Leuven, Belgium
| | - Mohammed F Alosaimi
- Department of Pathology and Laboratory Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Davood Mansouri
- Department of Clinical Immunology and Infectious Diseases, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- The Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of, Tuberculosis and Lung Diseases (NRITLD), Masih Daneshvari Hospital, Shahid Beheshti, University of Medical Sciences, Tehran, Iran
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti, Iran
| | - Haya Al-Saud
- National Center of Genomics Technology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fahd Al-Mulla
- Dasman Diabetes Institute, Department of Genetics and Bioinformatics, Kuwait
| | - Feras Almourfi
- National Center of Genomics Technology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Saleh Zaid Al-Muhsen
- Immunology Research Laboratory, Department of Pediatrics, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Fahad Alsohime
- Department of Pathology and Laboratory Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Saeed Al Turki
- Translational Pathology, Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Misery of National Guard Health Affairs, Riyadh, Saudi Arabia
- Cancer & Blood Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Rana Hasanato
- Department of Pathology and Laboratory Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Diederik van de Beek
- Amsterdam UMC, Department of Neurology, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Andrea Biondi
- Pediatric Departement and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale, San Gerardo, Monza, Italy
| | - Laura Rachele Bettini
- Pediatric Departement and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale, San Gerardo, Monza, Italy
| | - Mariella D'Angio'
- Pediatric Departement and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale, San Gerardo, Monza, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
| | - Luisa Imberti
- CREA Laboratory, Diagnostic Laboratory, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Alessandra Sottini
- CREA Laboratory, Diagnostic Laboratory, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Simone Paghera
- CREA Laboratory, Diagnostic Laboratory, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali di Brescia, Brescia, Italy
| | - Camillo Rossi
- Chief Medical Officer, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, MD, USA
| | - Miranda F Tompkins
- PRIMER, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Camille Alba
- PRIMER, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Isabelle Vandernoot
- Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-Christophe Goffard
- Department of Internal Medicine, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Guillaume Smits
- Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Isabelle Migeotte
- Fonds de la Recherche Scientifique (FNRS) and Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Filomeen Haerynck
- Department of Paediatric Immunology and Pulmonology, Centre for Primary Immunodeficiency Ghent (CPIG), PID Research Lab, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium
| | - Pere Soler-Palacin
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), Barcelona, Catalonia, Spain
| | - Andrea Martin-Nalda
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), Barcelona, Catalonia, Spain
| | - Roger Colobran
- Immunology Division, Genetics Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Vall d'Hebron Barcelona Hospital Campus, UAB, Barcelona, Catalonia, Spain
| | | | - Sevgi Keles
- Necmettin Erbakan University, Meram Medical Faculty, Division of Pediatric Allergy and Immunology, Konya, Turkey
| | - Fatma Çölkesen
- Department of Infectious Diseases and Clinical Microbiology, Konya Training and Research Hospital, Konya, Turkey
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, Bilkent University, Bilkent-Ankara, Turkey
| | - Kadriye Kart Yasar
- Departments of Infectious Diseases and Clinical Microbiology, Bakirkoy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Sevtap Senoglu
- Departments of Infectious Diseases and Clinical Microbiology, Bakirkoy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Şemsi Nur Karabela
- Departments of Infectious Diseases and Clinical Microbiology, Bakirkoy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Carlos Rodríguez-Gallego
- Department of Immunology, Hospital Universitario de G.C. Dr. Negrín, Canarian Health System, Las Palmas de Gran Canaria, Spain
- University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata," Rome, Italy
| | | | - Yacine Tandjaoui-Lambiotte
- Avicenne Hospital Intensive Care Unit, APHP, Bobigny, INSERM U1272 Hypoxia & Lung, Paris, France
- PH Réanimation CHU Avicenne, Bobigny, INSERM U1272 Hypoxie & Poumon, Paris, France
| | - Xavier Duval
- Université de Paris, IAME UMR-S 1137, INSERM, Paris, France
- Inserm CIC 1425, Paris, France
| | - Cédric Laouénan
- Université de Paris, IAME UMR-S 1137, INSERM, Paris, France
- Inserm CIC 1425, Paris, France
- AP-HP, Département Epidémiologie Biostatistiques et Recherche Clinique, Hôpital Bichat, Paris, France
| | - Andrew L Snow
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Clifton L Dalgard
- PRIMER, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Joshua D Milner
- Division of Pediatric Allergy, Immunology and Rheumatology, Columbia University, New York, USA
| | - Donald C Vinh
- Infectious Disease Susceptibility Program, Research Institute, McGill University Health Centre, Montréal, Québec, Canada
| | - Trine H Mogensen
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Nico Marr
- Department of Immunology, Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - András N Spaan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Department of Medical Microbiology, Utrecht UMC, Utrecht, Netherlands
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, Paris, France
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Michael J Ciancanelli
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Turnstone Biologics, New York, NY, USA
| | - Isabelle Meyts
- Laboratory for Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, Department of Pediatrics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
- Department of Pediatrics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Tom Maniatis
- Zukerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Vassili Soumelis
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Hôpital Saint-Louis, Paris, France
- AP-HP, Hôpital Saint-Louis, Laboratoire d'Immunologie, Paris, France
| | - Ali Amara
- Laboratory of Genomes & Cell Biology of Disease, INSERM U944, CNRS UMR 7212, Université de Paris, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, Paris, France
| | - Michel Nussenzweig
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, IDIBELL-Hospital Duran i Reynals, CIBERER U759, and Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Darragh Duffy
- Translational Immunology Lab, Institut Pasteur, Paris, France
| | - Richard P Lifton
- Laboratory of Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Guy Gorochov
- Sorbonne Université, Inserm, Centre d'Immunologie et des Maladies Infectieuses-Paris (CIMI PARIS), Assistance Publique-Hôpitaux de Paris (AP-HP) Hôpital Pitié-Salpêtrière, Paris, France
| | - Vivien Béziat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Vanessa Sancho-Shimizu
- Department of Paediatric Infectious Diseases & Virology, Imperial College London, London, UK
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Bethesda, MD, USA
| | - Aurélie Cobat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Bethesda, MD, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
- Pediatric Hematology and Immunology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
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30
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Lupski JR, Liu P, Stankiewicz P, Carvalho CMB, Posey JE. Clinical genomics and contextualizing genome variation in the diagnostic laboratory. Expert Rev Mol Diagn 2020; 20:995-1002. [PMID: 32954863 DOI: 10.1080/14737159.2020.1826312] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION The human genome contains the instructions for the development and biological homeostasis of the human organism and the genetic transmission of traits. Genome variation in human populations is the basis of evolution; individual or personal genomes vary tremendously, making each of us truly unique. AREAS COVERED Assaying this individual variation using genomic technologies has many applications in clinical medicine, from elucidating the biology of disease to designing strategies to ameliorate perturbations from homeostasis. Detecting pathogenic rare variation in a genome may provide a molecular diagnosis that can be informative for patient management and family healthcare. EXPERT OPINION Despite the increasing clinical use of unbiased genomic testing, including chromosome microarray analysis (CMA) with array comparative genomic hybridization (aCGH) or SNP arrays, clinical exome sequencing (cES), and whole-genome sequencing (WGS), to survey genome-wide for molecular aberrations, clinical acumen paired with an understanding of the limitations of each testing type will be needed to achieve molecular diagnoses. Potential opportunities for improving case solved rates, functionally annotating the majority of genes in the human genome, and further understanding genetic contributions to disease will empower clinical genomics and the precision medicine initiative.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine , Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine , Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX, USA.,Baylor Genetics, Baylor College of Medicine , Houston, TX, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX, USA
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31
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Saad AK, Marafi D, Mitani T, Jolly A, Du H, Elbendary HM, Jhangiani SN, Akdemir ZC, Gibbs RA, Hunter JV, Carvalho CMBC, Pehlivan D, Posey JE, Zaki MS, Lupski JR. Biallelic in-frame deletion in TRAPPC4 in a family with developmental delay and cerebellar atrophy. Brain 2020; 143:e83. [PMID: 33011761 PMCID: PMC7586085 DOI: 10.1093/brain/awaa256] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Ahmed K Saad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- MD/PhD Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Hasnaa M Elbendary
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | | | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill V Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas, 77030, USA
- E.B. Singleton Department of Pediatric Radiology, Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Claudia M B C Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
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32
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Beecroft SJ, Lamont PJ, Edwards S, Goullée H, Davis MR, Laing NG, Ravenscroft G. The Impact of Next-Generation Sequencing on the Diagnosis, Treatment, and Prevention of Hereditary Neuromuscular Disorders. Mol Diagn Ther 2020; 24:641-652. [PMID: 32997275 DOI: 10.1007/s40291-020-00495-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2020] [Indexed: 12/13/2022]
Abstract
The impact of high-throughput sequencing in genetic neuromuscular disorders cannot be overstated. The ability to rapidly and affordably sequence multiple genes simultaneously has enabled a second golden age of Mendelian disease gene discovery, with flow-on impacts for rapid genetic diagnosis, evidence-based treatment, tailored therapy development, carrier-screening, and prevention of disease recurrence in families. However, there are likely many more neuromuscular disease genes and mechanisms to be discovered. Many patients and families remain without a molecular diagnosis following targeted panel sequencing, clinical exome sequencing, or even genome sequencing. Here we review how massively parallel, or next-generation, sequencing has changed the field of genetic neuromuscular disorders, and anticipate future benefits of recent technological innovations such as RNA-seq implementation and detection of tandem repeat expansions from short-read sequencing.
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Affiliation(s)
- Sarah J Beecroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | | | - Samantha Edwards
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Hayley Goullée
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Mark R Davis
- Neurogenetic Unit, Department of Diagnostic Genomics, PP Block, QEII Medical Centre, Nedlands, WA, Australia
| | - Nigel G Laing
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia.,Neurogenetic Clinic, Royal Perth Hospital, Perth, Australia
| | - Gianina Ravenscroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia.
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Clinical Utility of Next-Generation Sequencing for Developmental Disorders in the Rehabilitation Department: Experiences from a Single Chinese Center. J Mol Neurosci 2020; 71:845-853. [PMID: 32959227 DOI: 10.1007/s12031-020-01707-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 09/07/2020] [Indexed: 02/05/2023]
Abstract
This study investigated the clinical and genetic characteristics of developmental disorders (DDs) in children attending a rehabilitation department. A total of 94 children with suspected rare and undiagnosed DDs were included in this study. All patients were subjected to next-generation sequencing by means of proband single whole-exome sequencing (Pro-WES) or trio whole-exome sequencing (Trio-WES). To investigate the copy number variations (CNVs), 63 patients were subjected to the trio strategy, and 17 cases were subjected to the proband single strategy. The patients developed early and suffered from severe symptoms. WES reached a high diagnostic rate (48.7%, 46/94), and de novo (48.3%, 28/58) was the main pathogenic form. Most identified single-nucleotide variations (SNVs)/small insertions and deletions (indels) were found only in one patient. The number of uncertain significant locus in the patients taking Trio-WES was significantly lower than that in patients taking Pro-WES (2.1% vs 2.8%). Compared with hereditary mutations passed from parents, pathogenicity was more obvious in de novo mutations. The diagnostic rate of WES accompanied by CNVseq (57.5%, 46/80) was significantly higher (p = 0.016) than WES alone. Next-generation sequencing exhibited a satisfactory diagnostic rate for DDs patients in the rehabilitation department. Compared with the proband-only model, the family trio strategy should be employed more frequently because it can reduce the number of uncertain significant sites and help to identify de novo pathogenic mutations.
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Robak LA, Du R, Yuan B, Gu S, Alfradique-Dunham I, Kondapalli V, Hinojosa E, Stillwell A, Young E, Zhang C, Song X, Du H, Gambin T, Jhangiani SN, Coban Akdemir Z, Muzny DM, Tejomurtula A, Ross OA, Shaw C, Jankovic J, Bi W, Posey JE, Lupski JR, Shulman JM. Integrated sequencing and array comparative genomic hybridization in familial Parkinson disease. NEUROLOGY-GENETICS 2020; 6:e498. [PMID: 32802956 PMCID: PMC7413630 DOI: 10.1212/nxg.0000000000000498] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 06/15/2020] [Indexed: 12/16/2022]
Abstract
Objective To determine how single nucleotide variants (SNVs) and copy number variants (CNVs) contribute to molecular diagnosis in familial Parkinson disease (PD), we integrated exome sequencing (ES) and genome-wide array-based comparative genomic hybridization (aCGH) and further probed CNV structure to reveal mutational mechanisms. Methods We performed ES on 110 subjects with PD and a positive family history; 99 subjects were also evaluated using genome-wide aCGH. We interrogated ES and aCGH data for pathogenic SNVs and CNVs at Mendelian PD gene loci. We confirmed SNVs via Sanger sequencing and further characterized CNVs with custom-designed high-density aCGH, droplet digital PCR, and breakpoint sequencing. Results Using ES, we discovered individuals with known pathogenic SNVs in GBA (p.Glu365Lys, p.Thr408Met, p.Asn409Ser, and p.Leu483Pro) and LRRK2 (p.Arg1441Gly and p.Gly2019Ser). Two subjects were each double heterozygotes for variants in GBA and LRRK2. Based on aCGH, we additionally discovered cases with an SNCA duplication and heterozygous intragenic GBA deletion. Five additional subjects harbored both SNVs (p.Asn52Metfs*29, p.Thr240Met, p.Pro437Leu, and p.Trp453*) and likely disrupting CNVs at the PRKN locus, consistent with compound heterozygosity. In nearly all cases, breakpoint sequencing revealed microhomology, a mutational signature consistent with CNV formation due to DNA replication errors. Conclusions Integrated ES and aCGH yielded a genetic diagnosis in 19.3% of our familial PD cohort. Our analyses highlight potential mechanisms for SNCA and PRKN CNV formation, uncover multilocus pathogenic variation, and identify novel SNVs and CNVs for further investigation as potential PD risk alleles.
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Affiliation(s)
- Laurie A Robak
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Renqian Du
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Bo Yuan
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Shen Gu
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Isabel Alfradique-Dunham
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Vismaya Kondapalli
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Evelyn Hinojosa
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Amanda Stillwell
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Emily Young
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Chaofan Zhang
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Xiaofei Song
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Haowei Du
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Tomasz Gambin
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Donna M Muzny
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Anusha Tejomurtula
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Owen A Ross
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Chad Shaw
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Joseph Jankovic
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Weimin Bi
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Jennifer E Posey
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - James R Lupski
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Joshua M Shulman
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
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Yuan B, Wang L, Liu P, Shaw C, Dai H, Cooper L, Zhu W, Anderson SA, Meng L, Wang X, Wang Y, Xia F, Xiao R, Braxton A, Peacock S, Schmitt E, Ward PA, Vetrini F, He W, Chiang T, Muzny D, Gibbs RA, Beaudet AL, Breman AM, Smith J, Cheung SW, Bacino CA, Eng CM, Yang Y, Lupski JR, Bi W. CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels. Genet Med 2020; 22:1633-1641. [PMID: 32576985 DOI: 10.1038/s41436-020-0864-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Improved resolution of molecular diagnostic technologies enabled detection of smaller sized exonic level copy-number variants (CNVs). The contribution of CNVs to autosomal recessive (AR) conditions may be better recognized using a large clinical cohort. METHODS We retrospectively investigated the CNVs' contribution to AR conditions in cases subjected to chromosomal microarray analysis (CMA, N = ~70,000) and/or clinical exome sequencing (ES, N = ~12,000) at Baylor Genetics; most had pediatric onset neurodevelopmental disorders. RESULTS CNVs contributed to biallelic variations in 87 cases, including 81 singletons and three affected sibling pairs. Seventy cases had CNVs affecting both alleles, and 17 had a CNV and a single-nucleotide variant (SNV)/indel in trans. In total, 94.3% of AR-CNVs affected one gene; among these 41.4% were single-exon and 35.0% were multiexon partial-gene events. Sixty-nine percent of homozygous AR-CNVs were embedded in homozygous genomic intervals. Five cases had large deletions unmasking an SNV/indel on the intact allele for a recessive condition, resulting in multiple molecular diagnoses. CONCLUSIONS AR-CNVs are often smaller in size, transmitted through generations, and underrecognized due to limitations in clinical CNV detection methods. Our findings from a large clinical cohort emphasized integrated CNV and SNV/indel analyses for precise clinical and molecular diagnosis especially in the context of genomic disorders.
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Affiliation(s)
- Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics Laboratory, Houston, TX, USA.
| | - Lei Wang
- Baylor Genetics Laboratory, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | | | - Wenmiao Zhu
- Baylor Genetics Laboratory, Houston, TX, USA
| | | | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Yue Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Alicia Braxton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Sandra Peacock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Eric Schmitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Francesco Vetrini
- Baylor Genetics Laboratory, Houston, TX, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Weimin He
- Baylor Genetics Laboratory, Houston, TX, USA
| | - Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Janice Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics Laboratory, Houston, TX, USA.
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36
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Dong X, Liu B, Yang L, Wang H, Wu B, Liu R, Chen H, Chen X, Yu S, Chen B, Wang S, Xu X, Zhou W, Lu Y. Clinical exome sequencing as the first-tier test for diagnosing developmental disorders covering both CNV and SNV: a Chinese cohort. J Med Genet 2020; 57:558-566. [PMID: 32005694 PMCID: PMC7418612 DOI: 10.1136/jmedgenet-2019-106377] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 01/08/2020] [Accepted: 01/11/2020] [Indexed: 12/12/2022]
Abstract
Background Developmental disorders (DDs) are early onset disorders affecting 5%–10% of children worldwide. Chromosomal microarray analysis detecting CNVs is currently recommended as the first-tier test for DD diagnosis. However, this analysis omits a high percentage of disease-causing single nucleotide variations (SNVs) that warrant further sequencing. Currently, next-generation sequencing can be used in clinical scenarios detecting CNVs, and the use of exome sequencing in the DD cohort ahead of the microarray test has not been evaluated. Methods Clinical exome sequencing (CES) was performed on 1090 unrelated Chinese DD patients who were classified into five phenotype subgroups. CNVs and SNVs were both detected and analysed based on sequencing data. Results An overall diagnostic rate of 41.38% was achieved with the combinational analysis of CNV and SNV. Over 12.02% of patients were diagnosed based on CNV, which was comparable with the published CMA diagnostic rate, while 0.74% were traditionally elusive cases who had dual diagnosis or apparently homozygous mutations that were clarified. The diagnostic rates among subgroups ranged from 21.82% to 50.32%. The top three recurrent cytobands with diagnostic CNVs were 15q11.2-q13.1, 22q11.21 and 7q11.23. The top three genes with diagnostic SNVs were: MECP2, SCN1A and SCN2A. Both the diagnostic rate and spectrums of CNVs and SNVs showed differences among the phenotype subgroups. Conclusion With a higher diagnostic rate, more comprehensive observation of variations and lower cost compared with conventional strategies, simultaneous analysis of CNVs and SNVs based on CES showed potential as a new first-tier choice to diagnose DD.
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Affiliation(s)
- Xinran Dong
- Center for Molecular Medicine of Children's Hospital of Fudan University, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Bo Liu
- Center for Molecular Medicine of Children's Hospital of Fudan University, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lin Yang
- Shanghai Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Huijun Wang
- Shanghai Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Shanghai Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China.,Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China
| | - Renchao Liu
- Shanghai Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Hongbo Chen
- Shanghai Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Xiang Chen
- Shanghai Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Sha Yu
- Shanghai Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Bin Chen
- Shanghai Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Sujuan Wang
- Department of Rehabilitation, Children's Hospital of Fudan University, Shanghai, China
| | - Xiu Xu
- Division of Child Health Care, Children's Hospital of Fudan University, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine of Children's Hospital of Fudan University, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine of Children's Hospital of Fudan University, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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Sirbu IO, Chiş AR, Moise AR. Role of carotenoids and retinoids during heart development. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158636. [PMID: 31978553 DOI: 10.1016/j.bbalip.2020.158636] [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: 12/03/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 02/08/2023]
Abstract
The nutritional requirements of the developing embryo are complex. In the case of dietary vitamin A (retinol, retinyl esters and provitamin A carotenoids), maternal derived nutrients serve as precursors to signaling molecules such as retinoic acid, which is required for embryonic patterning and organogenesis. Despite variations in the composition and levels of maternal vitamin A, embryonic tissues need to generate a precise amount of retinoic acid to avoid congenital malformations. Here, we summarize recent findings regarding the role and metabolism of vitamin A during heart development and we survey the association of genes known to affect retinoid metabolism or signaling with various inherited disorders. A better understanding of the roles of vitamin A in the heart and of the factors that affect retinoid metabolism and signaling can help design strategies to meet nutritional needs and to prevent birth defects and disorders associated with altered retinoid metabolism. This article is part of a Special Issue entitled Carotenoids recent advances in cell and molecular biology edited by Johannes von Lintig and Loredana Quadro.
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Affiliation(s)
- Ioan Ovidiu Sirbu
- Biochemistry Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, 300041 Timisoara, Romania; Timisoara Institute of Complex Systems, V. Lucaciu 18, 300044 Timisoara, Romania.
| | - Aimée Rodica Chiş
- Biochemistry Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
| | - Alexander Radu Moise
- Medical Sciences Division, Northern Ontario School of Medicine, Sudbury, ON P3E 2C6, Canada; Department of Chemistry and Biochemistry, Biology and Biomolecular Sciences Program, Laurentian University, Sudbury, ON P3E 2C6, Canada.
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38
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Arora V, Setia N, Dalal A, Vanaja MC, Gupta D, Razdan T, Phadke SR, Saxena R, Rohtagi A, Verma IC, Puri RD. Sialidosis type II: Expansion of phenotypic spectrum and identification of a common mutation in seven patients. Mol Genet Metab Rep 2020; 22:100561. [PMID: 31956508 PMCID: PMC6957780 DOI: 10.1016/j.ymgmr.2019.100561] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 12/25/2019] [Accepted: 12/25/2019] [Indexed: 12/18/2022] Open
Abstract
Sialidosis, an autosomal recessive disorder, is characterized by progressive lysosomal storage of sialylated glycopeptides and oligosaccharides. It occurs as a result of biallelic mutations in the NEU1 gene. Sialidosis is traditionally classified as a milder, late-onset type I and a severe early-onset type II disease. The presence of a cherry-red spot is a well-established ophthalmological clue to the disorder. We present a clinical-radiological report of seven unrelated patients with molecularly confirmed sialidosis type II. To the best of our knowledge, This is the largest reported series of patients with Sialidosis type II. A novel, previously unreported ophthalmic phenotype of bulls-eye maculopathy, is described. All seven phenotypically heterogeneous patients had the same pathogenic variant (c.679G > A; p.Gly227Arg) at a homozygous level in the NEU1 gene. We propose that this is a common mutation in north Indians for this rare disorder. We also observed an overlap of symptoms and a continuum of phenotypes in type I and II Sialidosis.
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Affiliation(s)
- Veronica Arora
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi 110060, India
| | - Nitika Setia
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi 110060, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | - Deepti Gupta
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi 110060, India
| | - Tinku Razdan
- Department of Ophthalmology, Sir Ganga Ram Hospital, New Delhi 110060, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Renu Saxena
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi 110060, India
| | - Anshu Rohtagi
- Department of Neurology, Sir Ganga Ram Hospital, New Delhi 110060, India
| | - Ishwar C Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi 110060, India
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi 110060, India
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39
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Van Bergen NJ, Guo Y, Al-Deri N, Lipatova Z, Stanga D, Zhao S, Murtazina R, Gyurkovska V, Pehlivan D, Mitani T, Gezdirici A, Antony J, Collins F, Willis MJH, Coban Akdemir ZH, Liu P, Punetha J, Hunter JV, Jhangiani SN, Fatih JM, Rosenfeld JA, Posey JE, Gibbs RA, Karaca E, Massey S, Ranasinghe TG, Sleiman P, Troedson C, Lupski JR, Sacher M, Segev N, Hakonarson H, Christodoulou J. Deficiencies in vesicular transport mediated by TRAPPC4 are associated with severe syndromic intellectual disability. Brain 2020; 143:112-130. [PMID: 31794024 PMCID: PMC6935753 DOI: 10.1093/brain/awz374] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/20/2019] [Accepted: 10/07/2019] [Indexed: 12/11/2022] Open
Abstract
The conserved transport protein particle (TRAPP) complexes regulate key trafficking events and are required for autophagy. TRAPPC4, like its yeast Trs23 orthologue, is a core component of the TRAPP complexes and one of the essential subunits for guanine nucleotide exchange factor activity for Rab1 GTPase. Pathogenic variants in specific TRAPP subunits are associated with neurological disorders. We undertook exome sequencing in three unrelated families of Caucasian, Turkish and French-Canadian ethnicities with seven affected children that showed features of early-onset seizures, developmental delay, microcephaly, sensorineural deafness, spastic quadriparesis and progressive cortical and cerebellar atrophy in an effort to determine the genetic aetiology underlying neurodevelopmental disorders. All seven affected subjects shared the same identical rare, homozygous, potentially pathogenic variant in a non-canonical, well-conserved splice site within TRAPPC4 (hg19:chr11:g.118890966A>G; TRAPPC4: NM_016146.5; c.454+3A>G). Single nucleotide polymorphism array analysis revealed there was no haplotype shared between the tested Turkish and Caucasian families suggestive of a variant hotspot region rather than a founder effect. In silico analysis predicted the variant to cause aberrant splicing. Consistent with this, experimental evidence showed both a reduction in full-length transcript levels and an increase in levels of a shorter transcript missing exon 3, suggestive of an incompletely penetrant splice defect. TRAPPC4 protein levels were significantly reduced whilst levels of other TRAPP complex subunits remained unaffected. Native polyacrylamide gel electrophoresis and size exclusion chromatography demonstrated a defect in TRAPP complex assembly and/or stability. Intracellular trafficking through the Golgi using the marker protein VSVG-GFP-ts045 demonstrated significantly delayed entry into and exit from the Golgi in fibroblasts derived from one of the affected subjects. Lentiviral expression of wild-type TRAPPC4 in these fibroblasts restored trafficking, suggesting that the trafficking defect was due to reduced TRAPPC4 levels. Consistent with the recent association of the TRAPP complex with autophagy, we found that the fibroblasts had a basal autophagy defect and a delay in autophagic flux, possibly due to unsealed autophagosomes. These results were validated using a yeast trs23 temperature sensitive variant that exhibits constitutive and stress-induced autophagic defects at permissive temperature and a secretory defect at restrictive temperature. In summary we provide strong evidence for pathogenicity of this variant in a member of the core TRAPP subunit, TRAPPC4 that associates with vesicular trafficking and autophagy defects. This is the first report of a TRAPPC4 variant, and our findings add to the growing number of TRAPP-associated neurological disorders.
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Affiliation(s)
- Nicole J Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Yiran Guo
- Center for Applied Genomics (CAG) at the Children’s Hospital of Philadelphia (CHOP), Philadelphia, USA
| | - Noraldin Al-Deri
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Zhanna Lipatova
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Daniela Stanga
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Sarah Zhao
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Rakhilya Murtazina
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Valeriya Gyurkovska
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, 34303, Turkey
| | - Jayne Antony
- TY Nelson Department of Neurology and Neurosurgery, Children’s Hospital at Westmead, Sydney, Australia
| | - Felicity Collins
- Western Sydney Genetics Program, Children’s Hospital at Westmead, Sydney, Australia
- Medical Genomics Department, Royal Prince Alfred Hospital, Sydney, Australia
| | - Mary J H Willis
- Department of Pediatrics, Naval Medical Center San Diego, San Diego, California, USA
| | - Zeynep H Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill V Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Ender Karaca
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Thisara G Ranasinghe
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Patrick Sleiman
- Center for Applied Genomics (CAG) at the Children’s Hospital of Philadelphia (CHOP), Philadelphia, USA
| | - Chris Troedson
- TY Nelson Department of Neurology and Neurosurgery, Children’s Hospital at Westmead, Sydney, Australia
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Michael Sacher
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Nava Segev
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Hakon Hakonarson
- Center for Applied Genomics (CAG) at the Children’s Hospital of Philadelphia (CHOP), Philadelphia, USA
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, VIC, Australia
- Kids Research, The Children’s Hospital at Westmead, Sydney, NSW, Australia
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40
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Ngo KJ, Rexach JE, Lee H, Petty LE, Perlman S, Valera JM, Deignan JL, Mao Y, Aker M, Posey JE, Jhangiani SN, Coban-Akdemir ZH, Boerwinkle E, Muzny D, Nelson AB, Hassin-Baer S, Poke G, Neas K, Geschwind MD, Grody WW, Gibbs R, Geschwind DH, Lupski JR, Below JE, Nelson SF, Fogel BL. A diagnostic ceiling for exome sequencing in cerebellar ataxia and related neurological disorders. Hum Mutat 2019; 41:487-501. [PMID: 31692161 DOI: 10.1002/humu.23946] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/25/2019] [Accepted: 11/01/2019] [Indexed: 12/30/2022]
Abstract
Genetic ataxias are associated with mutations in hundreds of genes with high phenotypic overlap complicating the clinical diagnosis. Whole-exome sequencing (WES) has increased the overall diagnostic rate considerably. However, the upper limit of this method remains ill-defined, hindering efforts to address the remaining diagnostic gap. To further assess the role of rare coding variation in ataxic disorders, we reanalyzed our previously published exome cohort of 76 predominantly adult and sporadic-onset patients, expanded the total number of cases to 260, and introduced analyses for copy number variation and repeat expansion in a representative subset. For new cases (n = 184), our resulting clinically relevant detection rate remained stable at 47% with 24% classified as pathogenic. Reanalysis of the previously sequenced 76 patients modestly improved the pathogenic rate by 7%. For the combined cohort (n = 260), the total observed clinical detection rate was 52% with 25% classified as pathogenic. Published studies of similar neurological phenotypes report comparable rates. This consistency across multiple cohorts suggests that, despite continued technical and analytical advancements, an approximately 50% diagnostic rate marks a relative ceiling for current WES-based methods and a more comprehensive genome-wide assessment is needed to identify the missing causative genetic etiologies for cerebellar ataxia and related neurodegenerative diseases.
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Affiliation(s)
- Kathie J Ngo
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Jessica E Rexach
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Lauren E Petty
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Susan Perlman
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Juliana M Valera
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Yuanming Mao
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Mamdouh Aker
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shalini N Jhangiani
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | | | - Eric Boerwinkle
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Human Genetics Center, University of Texas Health Science Center, Houston, Texas
| | - Donna Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Alexandra B Nelson
- Department of Neurology, UCSF Memory and Aging Center, University of California, San Francisco, California
| | - Sharon Hassin-Baer
- Department of Neurology, Chaim Sheba Medical Center, Movement Disorders Institute, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gemma Poke
- Genetic Health Service NZ, Central Hub, Wellington Hospital, Wellington, New Zealand
| | - Katherine Neas
- Genetic Health Service NZ, Central Hub, Wellington Hospital, Wellington, New Zealand
| | - Michael D Geschwind
- Department of Neurology, UCSF Memory and Aging Center, University of California, San Francisco, California
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Richard Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Daniel H Geschwind
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Jennifer E Below
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Stanley F Nelson
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Brent L Fogel
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Clinical Neurogenomics Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
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41
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Bartha Á, Győrffy B. Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology. Cancers (Basel) 2019; 11:E1725. [PMID: 31690036 PMCID: PMC6895801 DOI: 10.3390/cancers11111725] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 12/17/2022] Open
Abstract
Whole exome sequencing (WES) enables the analysis of all protein coding sequences in the human genome. This technology enables the investigation of cancer-related genetic aberrations that are predominantly located in the exonic regions. WES delivers high-throughput results at a reasonable price. Here, we review analysis tools enabling utilization of WES data in clinical and research settings. Technically, WES initially allows the detection of single nucleotide variants (SNVs) and copy number variations (CNVs), and data obtained through these methods can be combined and further utilized. Variant calling algorithms for SNVs range from standalone tools to machine learning-based combined pipelines. Tools for CNV detection compare the number of reads aligned to a dedicated segment. Both SNVs and CNVs help to identify mutations resulting in pharmacologically druggable alterations. The identification of homologous recombination deficiency enables the use of PARP inhibitors. Determining microsatellite instability and tumor mutation burden helps to select patients eligible for immunotherapy. To pave the way for clinical applications, we have to recognize some limitations of WES, including its restricted ability to detect CNVs, low coverage compared to targeted sequencing, and the missing consensus regarding references and minimal application requirements. Recently, Galaxy became the leading platform in non-command line-based WES data processing. The maturation of next-generation sequencing is reinforced by Food and Drug Administration (FDA)-approved methods for cancer screening, detection, and follow-up. WES is on the verge of becoming an affordable and sufficiently evolved technology for everyday clinical use.
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Affiliation(s)
- Áron Bartha
- Semmelweis University, Department of Bioinformatics and 2nd Department of Pediatrics, H-1094 Budapest, Hungary.
- TTK Cancer Biomarker Research Group, Institute of Enzymology, Magyar tudósokkörútja 2., H-1117 Budapest, Hungary.
| | - Balázs Győrffy
- Semmelweis University, Department of Bioinformatics and 2nd Department of Pediatrics, H-1094 Budapest, Hungary.
- TTK Cancer Biomarker Research Group, Institute of Enzymology, Magyar tudósokkörútja 2., H-1117 Budapest, Hungary.
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42
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Hoyos-Bachiloglu R, Gallo S, Vizcaya C, Zuñiga P, Valbuena JR, Casanova JL, Bustamante J, Borzutzky A. Disseminated Mycobacterial Disease in a Patient with 22q11.2 Deletion Syndrome: Case Report and Review of the Literature. J Clin Immunol 2019; 39:743-746. [PMID: 31385124 PMCID: PMC7159191 DOI: 10.1007/s10875-019-00678-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/28/2019] [Indexed: 10/26/2022]
Affiliation(s)
- Rodrigo Hoyos-Bachiloglu
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362 octavo piso, 8330077, Santiago, Chile
| | - Silvanna Gallo
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362 octavo piso, 8330077, Santiago, Chile
| | - Cecilia Vizcaya
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362 octavo piso, 8330077, Santiago, Chile
| | - Pamela Zuñiga
- Pediatric Hematology and Oncology Section, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - José R Valbuena
- Department of Pathology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jean Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Paris University, Paris, France
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Pediatric Hematology-Immunology Unit, AP-HP, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Paris University, Paris, France
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Study Center for Primary Immunodeficiencies, Assistance Publique-Hôpitaux de Paris (AP-HP), Necker Children Hospital, Paris, France
| | - Arturo Borzutzky
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362 octavo piso, 8330077, Santiago, Chile.
- Millennium Institute on Immunology and Immunotherapy, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile.
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43
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Oswiecimska J, Dawidziuk M, Gambin T, Ziora K, Marek M, Rzonca S, Guilbride DL, Jhangiani SN, Obuchowicz A, Sikora A, Lupski JR, Wiszniewski W, Gawlinski P. A Patient with Berardinelli-Seip Syndrome, Novel AGPAT2 Splicesite Mutation and Concomitant Development of Non-diabetic Polyneuropathy. J Clin Res Pediatr Endocrinol 2019; 11:319-326. [PMID: 30563316 PMCID: PMC6745459 DOI: 10.4274/jcrpe.galenos.2018.2018.0227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/17/2018] [Indexed: 12/01/2022] Open
Abstract
Primary polyneuropathy in the context of Seip-Berardinelli type 1 seipinopathy, or congenital generalized lipodystrophy type 1 (CGL1) has not been previously reported. We report the case history of a 27 year old female CGL1 patient presenting with an unusual additional development of non-diabetic peripheral neuropathy and learning disabilities in early adolescence. Whole exome sequencing (WES) of the patient genome identified a novel variant, homozygous for a 52 bp intronic deletion in the AGPAT2 locus, coding for 1-acylglycerol-3-phosphate O-acyltransferase 2, which is uniquely associated with CGL1 seipinopathies, with no molecular evidence for dual diagnosis. Functional studies using RNA isolated from patient peripheral blood leucocytes showed abnormal RNA splicing resulting in the loss of 25 amino acids from the patient AGPAT2 protein coding sequence. Stability and transcription levels for the misspliced AGPAT2 mRNA in our patient nonetheless remained normal. Any AGPAT2 protein produced in our patient is therefore likely to be dysfunctional. However, formal linkage of this deletion to the neuropathy observed remains to be shown. The classical clinical presentation of a patient with AGPAT2-associated lipodystrophy shows normal cognition and no development of polyneuropathy. Cognitive disabilities and polyneuropathy are features associated exclusively with clinical CGL type 2 arising from seipin (BSCL2) gene mutations. This case study suggests that in some genetic contexts, AGPAT2 mutations can also produce phenotypes with primary polyneuropathy.
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Affiliation(s)
- Joanna Oswiecimska
- Medical University of Silesia in Katowice, Department of Pediatrics in Zabrze, Silesia, Poland
| | - Mateusz Dawidziuk
- Institute of Mother and Child, Department of Medical Genetics, Warsaw, Poland
| | - Tomasz Gambin
- Institute of Mother and Child, Department of Medical Genetics, Warsaw, Poland
- Warsaw University of Technology, Institute of Computer Science, Warsaw, Poland
- Baylor College of Medicine, Department of Molecular and Human Genetics, Texas, USA
| | - Katarzyna Ziora
- Medical University of Silesia in Katowice, Department of Pediatrics in Zabrze, Silesia, Poland
| | - Marta Marek
- Medical University of Silesia in Katowice, Department of Pediatrics in Bytom, Silesia, Poland
| | - Sylwia Rzonca
- Institute of Mother and Child, Department of Medical Genetics, Warsaw, Poland
| | | | | | - Anna Obuchowicz
- Medical University of Silesia in Katowice, Department of Pediatrics in Bytom, Silesia, Poland
| | - Alicja Sikora
- Medical University of Silesia in Katowice, Department of Pediatrics in Bytom, Silesia, Poland
| | - James R. Lupski
- Baylor College of Medicine, Department of Molecular and Human Genetics, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Texas, USA
- Baylor College of Medicine, Department of Pediatrics, Texas, USA
- Texas Children’s Hospital, Texas, USA
| | - Wojciech Wiszniewski
- Institute of Mother and Child, Department of Medical Genetics, Warsaw, Poland
- Oregon Health and Science University, Department of Molecular and Medical Genetics, Portland, USA
| | - Pawel Gawlinski
- Institute of Mother and Child, Department of Medical Genetics, Warsaw, Poland
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Wiewiórka M, Szmurło A, Kuśmirek W, Gambin T. SeQuiLa-cov: A fast and scalable library for depth of coverage calculations. Gigascience 2019; 8:giz094. [PMID: 31378808 PMCID: PMC6680061 DOI: 10.1093/gigascience/giz094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/24/2019] [Accepted: 07/10/2019] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Depth of coverage calculation is an important and computationally intensive preprocessing step in a variety of next-generation sequencing pipelines, including the analysis of RNA-sequencing data, detection of copy number variants, or quality control procedures. RESULTS Building upon big data technologies, we have developed SeQuiLa-cov, an extension to the recently released SeQuiLa platform, which provides efficient depth of coverage calculations, reaching >100× speedup over the state-of-the-art tools. The performance and scalability of our solution allow for exome and genome-wide calculations running locally or on a cluster while hiding the complexity of the distributed computing with Structured Query Language Application Programming Interface. CONCLUSIONS SeQuiLa-cov provides significant performance gain in depth of coverage calculations streamlining the widely used bioinformatic processing pipelines.
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Affiliation(s)
- Marek Wiewiórka
- Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, 00-665 Warsaw, Poland
| | - Agnieszka Szmurło
- Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, 00-665 Warsaw, Poland
| | - Wiktor Kuśmirek
- Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, 00-665 Warsaw, Poland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, 00-665 Warsaw, Poland
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45
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Jolly A, Bayram Y, Turan S, Aycan Z, Tos T, Abali ZY, Hacihamdioglu B, Coban Akdemir ZH, Hijazi H, Bas S, Atay Z, Guran T, Abali S, Bas F, Darendeliler F, Colombo R, Barakat TS, Rinne T, White JJ, Yesil G, Gezdirici A, Gulec EY, Karaca E, Pehlivan D, Jhangiani SN, Muzny DM, Poyrazoglu S, Bereket A, Gibbs RA, Posey JE, Lupski JR. Exome Sequencing of a Primary Ovarian Insufficiency Cohort Reveals Common Molecular Etiologies for a Spectrum of Disease. J Clin Endocrinol Metab 2019; 104:3049-3067. [PMID: 31042289 PMCID: PMC6563799 DOI: 10.1210/jc.2019-00248] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/25/2019] [Indexed: 12/15/2022]
Abstract
CONTEXT Primary ovarian insufficiency (POI) encompasses a spectrum of premature menopause, including both primary and secondary amenorrhea. For 75% to 90% of individuals with hypergonadotropic hypogonadism presenting as POI, the molecular etiology is unknown. Common etiologies include chromosomal abnormalities, environmental factors, and congenital disorders affecting ovarian development and function, as well as syndromic and nonsyndromic single gene disorders suggesting POI represents a complex trait. OBJECTIVE To characterize the contribution of known disease genes to POI and identify molecular etiologies and biological underpinnings of POI. DESIGN, SETTING, AND PARTICIPANTS We applied exome sequencing (ES) and family-based genomics to 42 affected female individuals from 36 unrelated Turkish families, including 31 with reported parental consanguinity. RESULTS This analysis identified likely damaging, potentially contributing variants and molecular diagnoses in 16 families (44%), including 11 families with likely damaging variants in known genes and five families with predicted deleterious variants in disease genes (IGSF10, MND1, MRPS22, and SOHLH1) not previously associated with POI. Of the 16 families, 2 (13%) had evidence for potentially pathogenic variants at more than one locus. Absence of heterozygosity consistent with identity-by-descent mediated recessive disease burden contributes to molecular diagnosis in 15 of 16 (94%) families. GeneMatcher allowed identification of additional families from diverse genetic backgrounds. CONCLUSIONS ES analysis of a POI cohort further characterized locus heterogeneity, reaffirmed the association of genes integral to meiotic recombination, demonstrated the likely contribution of genes involved in hypothalamic development, and documented multilocus pathogenic variation suggesting the potential for oligogenic inheritance contributing to the development of POI.
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Affiliation(s)
- Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Serap Turan
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Zehra Aycan
- Department of Pediatric Endocrinology, Sami Ulus Children’s Hospital, Ankara, Turkey
| | - Tulay Tos
- Department of Medical Genetics, Sami Ulus Children’s Hospital, Ankara, Turkey
| | - Zehra Yavas Abali
- Department of Pediatric Endocrinology, İstanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | | | | | - Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Serpil Bas
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Zeynep Atay
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Tulay Guran
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Saygin Abali
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Firdevs Bas
- Department of Pediatric Endocrinology, İstanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Feyza Darendeliler
- Department of Pediatric Endocrinology, İstanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Roberto Colombo
- Center for the Study of Rare Inherited Diseases (CeSMER), Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy
- Faculty of Medicine, Catholic University, IRCCS Policlinico Gemelli University Hospital, Rome, Italy
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Tuula Rinne
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Gozde Yesil
- Department of Medical Genetics, Bezmialem University, Istanbul, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Ender Karaca
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | | | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Sukran Poyrazoglu
- Department of Pediatric Endocrinology, İstanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Abdullah Bereket
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Correspondence and Reprint Requests: James R. Lupski, MD, PhD, DSc (Hon), FAAP, FACMG, FANA, FAAAS, FAAS, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, Texas 77030. E-mail: ; or Jennifer E. Posey, MD, PhD, FACMG, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room T603, Houston, Texas 77030. E-mail:
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, Texas
- Correspondence and Reprint Requests: James R. Lupski, MD, PhD, DSc (Hon), FAAP, FACMG, FANA, FAAAS, FAAS, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, Texas 77030. E-mail: ; or Jennifer E. Posey, MD, PhD, FACMG, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room T603, Houston, Texas 77030. E-mail:
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Paine I, Posey JE, Grochowski CM, Jhangiani SN, Rosenheck S, Kleyner R, Marmorale T, Yoon M, Wang K, Robison R, Cappuccio G, Pinelli M, Magli A, Coban Akdemir Z, Hui J, Yeung WL, Wong BKY, Ortega L, Bekheirnia MR, Bierhals T, Hempel M, Johannsen J, Santer R, Aktas D, Alikasifoglu M, Bozdogan S, Aydin H, Karaca E, Bayram Y, Ityel H, Dorschner M, White JJ, Wilichowski E, Wortmann SB, Casella EB, Kitajima JP, Kok F, Monteiro F, Muzny DM, Bamshad M, Gibbs RA, Sutton VR, Van Esch H, Brunetti-Pierri N, Hildebrandt F, Brautbar A, Van den Veyver IB, Glass I, Lessel D, Lyon GJ, Lupski JR. Paralog Studies Augment Gene Discovery: DDX and DHX Genes. Am J Hum Genet 2019; 105:302-316. [PMID: 31256877 PMCID: PMC6698803 DOI: 10.1016/j.ajhg.2019.06.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/31/2019] [Indexed: 12/24/2022] Open
Abstract
Members of a paralogous gene family in which variation in one gene is known to cause disease are eight times more likely to also be associated with human disease. Recent studies have elucidated DHX30 and DDX3X as genes for which pathogenic variant alleles are involved in neurodevelopmental disorders. We hypothesized that variants in paralogous genes encoding members of the DExD/H-box RNA helicase superfamily might also underlie developmental delay and/or intellectual disability (DD and/or ID) disease phenotypes. Here we describe 15 unrelated individuals who have DD and/or ID, central nervous system (CNS) dysfunction, vertebral anomalies, and dysmorphic features and were found to have probably damaging variants in DExD/H-box RNA helicase genes. In addition, these individuals exhibit a variety of other tissue and organ system involvement including ocular, outer ear, hearing, cardiac, and kidney tissues. Five individuals with homozygous (one), compound-heterozygous (two), or de novo (two) missense variants in DHX37 were identified by exome sequencing. We identified ten total individuals with missense variants in three other DDX/DHX paralogs: DHX16 (four individuals), DDX54 (three individuals), and DHX34 (three individuals). Most identified variants are rare, predicted to be damaging, and occur at conserved amino acid residues. Taken together, these 15 individuals implicate the DExD/H-box helicases in both dominantly and recessively inherited neurodevelopmental phenotypes and highlight the potential for more than one disease mechanism underlying these disorders.
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Affiliation(s)
- Ingrid Paine
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah Rosenheck
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Robert Kleyner
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Taylor Marmorale
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Margaret Yoon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Reid Robison
- Utah Foundation for Biomedical Research, Salt Lake City, UT 84107, USA
| | - Gerarda Cappuccio
- Department of Translational Medicine, University of Naples "Federico II," 80131 Napoli, Italy; Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Michele Pinelli
- Department of Translational Medicine, University of Naples "Federico II," 80131 Napoli, Italy; Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Adriano Magli
- Department of Pediatric Ophthalmology, University of Salerno, 84081 Baronissi SA, Italy
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joannie Hui
- Department of Pediatrics, Prince of Wales Hospital, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wai Lan Yeung
- Department of Pediatrics and Adolescent Medicine, Alice Ho Miu Ling Nethersole Hospital, Hong Kong SAR, China
| | - Bibiana K Y Wong
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; The Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Lucia Ortega
- Medical Genetics Department, Cook Children's Hospital, Fort Worth, TX 76104, USA
| | - Mir Reza Bekheirnia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Section of Pediatric Renal, Baylor College of Medicine, Houston, TX 77030, USA; Department of Genetics, Texas Children's Hospital, Houston, TX 76104, USA
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jessika Johannsen
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - René Santer
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Dilek Aktas
- DAMAGEN Genetic Diagnostic Center, 06690 Ankara, Turkey
| | | | - Sevcan Bozdogan
- Department of Medical Genetics, Cukurova University Faculty of Medicine, 01330 Adana, Turkey
| | - Hatip Aydin
- Department of Medical Genetics, Medical Faculty of Namik Kemal University, Tekirdag 59100, Turkey
| | - Ender Karaca
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yavuz Bayram
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Hadas Ityel
- Division of Nephrology, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Dorschner
- Center for Precision Diagnostics, University of Washington, Seattle, WA 98195, USA
| | - Janson J White
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Ekkehard Wilichowski
- Department of Pediatrics and Pediatric Neurology, Georg-August-Universität Göttingen, 37075 Göttingen, Germany
| | - Saskia B Wortmann
- Institute of Human Genetics, Technical University München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum Munchen, 85764 Neuherberg, Germany; University Children's Hospital, Paracelsus Medical University, 5020 Salsburg, Austria
| | - Erasmo B Casella
- Children's Institute, Hospital das Clinicas, University of Sao Paulo, 05405-000 Sao Paulo, Brazil
| | | | - Fernando Kok
- Mendelics Genomic Analysis, 04013-000 Sao Paulo, Brazil; Department of Neurology, University of Sao Paulo School of Medicine, 01246-903 Sao Paulo, Brazil
| | | | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, University of Naples "Federico II," 80131 Napoli, Italy; Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Ariel Brautbar
- Medical Genetics Department, Cook Children's Hospital, Fort Worth, TX 76104, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; The Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Ian Glass
- Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, NY 11724, USA; Utah Foundation for Biomedical Research, Salt Lake City, UT 84107, USA; Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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47
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Pehlivan D, Bayram Y, Gunes N, Coban Akdemir Z, Shukla A, Bierhals T, Tabakci B, Sahin Y, Gezdirici A, Fatih JM, Gulec EY, Yesil G, Punetha J, Ocak Z, Grochowski CM, Karaca E, Albayrak HM, Radhakrishnan P, Erdem HB, Sahin I, Yildirim T, Bayhan IA, Bursali A, Elmas M, Yuksel Z, Ozdemir O, Silan F, Yildiz O, Yesilbas O, Isikay S, Balta B, Gu S, Jhangiani SN, Doddapaneni H, Hu J, Muzny DM, Boerwinkle E, Gibbs RA, Tsiakas K, Hempel M, Girisha KM, Gul D, Posey JE, Elcioglu NH, Tuysuz B, Lupski JR. The Genomics of Arthrogryposis, a Complex Trait: Candidate Genes and Further Evidence for Oligogenic Inheritance. Am J Hum Genet 2019; 105:132-150. [PMID: 31230720 PMCID: PMC6612529 DOI: 10.1016/j.ajhg.2019.05.015] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/21/2019] [Indexed: 01/29/2023] Open
Abstract
Arthrogryposis is a clinical finding that is present either as a feature of a neuromuscular condition or as part of a systemic disease in over 400 Mendelian conditions. The underlying molecular etiology remains largely unknown because of genetic and phenotypic heterogeneity. We applied exome sequencing (ES) in a cohort of 89 families with the clinical sign of arthrogryposis. Additional molecular techniques including array comparative genomic hybridization (aCGH) and Droplet Digital PCR (ddPCR) were performed on individuals who were found to have pathogenic copy number variants (CNVs) and mosaicism, respectively. A molecular diagnosis was established in 65.2% (58/89) of families. Eleven out of 58 families (19.0%) showed evidence for potential involvement of pathogenic variation at more than one locus, probably driven by absence of heterozygosity (AOH) burden due to identity-by-descent (IBD). RYR3, MYOM2, ERGIC1, SPTBN4, and ABCA7 represent genes, identified in two or more families, for which mutations are probably causative for arthrogryposis. We also provide evidence for the involvement of CNVs in the etiology of arthrogryposis and for the idea that both mono-allelic and bi-allelic variants in the same gene cause either similar or distinct syndromes. We were able to identify the molecular etiology in nine out of 20 families who underwent reanalysis. In summary, our data from family-based ES further delineate the molecular etiology of arthrogryposis, yielded several candidate disease-associated genes, and provide evidence for mutational burden in a biological pathway or network. Our study also highlights the importance of reanalysis of individuals with unsolved diagnoses in conjunction with sequencing extended family members.
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Affiliation(s)
- Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nilay Gunes
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa Medical Faculty, Istanbul 34096, Turkey
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg 20246, Germany
| | - Burcu Tabakci
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul 34854, Turkey
| | - Yavuz Sahin
- Department of Medical Genetics, Necip Fazıl City Hospital, Kahramanmaras 46050, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | - Gozde Yesil
- Department of Medical Genetics, Bezmi Alem Vakif University Faculty of Medicine, Istanbul 34093, Turkey
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Ocak
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | | | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hatice Mutlu Albayrak
- Department of Pediatrics, Division of Pediatric Genetics, Faculty of Medicine, Ondokuz Mayıs University, Samsun 55270, Turkey
| | - Periyasamy Radhakrishnan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Haktan Bagis Erdem
- Department of Medical Genetics, University of Health Sciences, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara 06110, Turkey
| | - Ibrahim Sahin
- Department of Medical Genetics, University of Erzurum, School of Medicine, Erzurum 25240, Turkey
| | - Timur Yildirim
- Department of Orthopedics and Traumatology, Baltalimani Bone Diseases Training and Research Hospital, Istanbul 34470, Turkey
| | - Ilhan A Bayhan
- Department of Orthopedics and Traumatology, Baltalimani Bone Diseases Training and Research Hospital, Istanbul 34470, Turkey
| | - Aysegul Bursali
- Department of Orthopedics and Traumatology, Baltalimani Bone Diseases Training and Research Hospital, Istanbul 34470, Turkey
| | - Muhsin Elmas
- Department of Medical Genetics, Afyon Kocatepe University, School of Medicine, Afyon 03218, Turkey
| | - Zafer Yuksel
- Medical Genetics Clinic, Mersin Women and Children Hospital, Mersin 33330, Turkey
| | - Ozturk Ozdemir
- Department of Medical Genetics, Faculty of Medicine, Onsekiz Mart University, Canakkale 17000, Turkey
| | - Fatma Silan
- Department of Medical Genetics, Faculty of Medicine, Onsekiz Mart University, Canakkale 17000, Turkey
| | - Onur Yildiz
- Department of Medical Genetics, Faculty of Medicine, Onsekiz Mart University, Canakkale 17000, Turkey
| | - Osman Yesilbas
- Division of Critical Care Medicine, Department of Pediatrics, University of Health Sciences, Van Training and Research Hospital, Van 65130, Turkey
| | - Sedat Isikay
- Department of Physiotherapy and Rehabilitation, Hasan Kalyoncu University, School of Health Sciences, Gaziantep 27000, Turkey
| | - Burhan Balta
- Department of Medical Genetics, Kayseri Training and Research Hospital, Kayseri 38080, Turkey
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genetics Center, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Konstantinos Tsiakas
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg 20246, Germany
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Davut Gul
- Department of Medical Genetics, Gulhane Military Medical School, Ankara 06010, Turkey
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nursel H Elcioglu
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul 34854, Turkey; Eastern Mediterranean University School of Medicine, Cyprus, Mersin 10, Turkey
| | - Beyhan Tuysuz
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa Medical Faculty, Istanbul 34096, Turkey
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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48
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Abstract
The practice of genomic medicine stands to revolutionize our approach to medical care, and to realize this goal will require discovery of the relationship between rare variation at each of the ~ 20,000 protein-coding genes and their consequent impact on individual health and expression of Mendelian disease. The step-wise evolution of broad-based, genome-wide cytogenetic and molecular genomic testing approaches (karyotyping, chromosomal microarray [CMA], exome sequencing [ES]) has driven much of the rare disease discovery to this point, with genome sequencing representing the newest member of this team. Each step has brought increased sensitivity to interrogate individual genomic variation in an unbiased method that does not require clinical prediction of the locus or loci involved. Notably, each step has also brought unique limitations in variant detection, for example, the low sensitivity of ES for detection of triploidy, and of CMA for detection of copy neutral structural variants. The utility of genome sequencing (GS) as a clinical molecular diagnostic test, and the increased sensitivity afforded by addition of long-read sequencing or other -omics technologies such as RNAseq or metabolomics, are not yet fully explored, though recent work supports improved sensitivity of variant detection, at least in a subset of cases. The utility of GS will also rely upon further elucidation of the complexities of genetic and allelic heterogeneity, multilocus rare variation, and the impact of rare and common variation at a locus, as well as advances in functional annotation of identified variants. Much discovery remains to be done before the potential utility of GS is fully appreciated.
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Affiliation(s)
- Jennifer E Posey
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, T603, Houston, TX, 77030, USA.
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49
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Arts P, Simons A, AlZahrani MS, Yilmaz E, AlIdrissi E, van Aerde KJ, Alenezi N, AlGhamdi HA, AlJubab HA, Al-Hussaini AA, AlManjomi F, Alsaad AB, Alsaleem B, Andijani AA, Asery A, Ballourah W, Bleeker-Rovers CP, van Deuren M, van der Flier M, Gerkes EH, Gilissen C, Habazi MK, Hehir-Kwa JY, Henriet SS, Hoppenreijs EP, Hortillosa S, Kerkhofs CH, Keski-Filppula R, Lelieveld SH, Lone K, MacKenzie MA, Mensenkamp AR, Moilanen J, Nelen M, Ten Oever J, Potjewijd J, van Paassen P, Schuurs-Hoeijmakers JHM, Simon A, Stokowy T, van de Vorst M, Vreeburg M, Wagner A, van Well GTJ, Zafeiropoulou D, Zonneveld-Huijssoon E, Veltman JA, van Zelst-Stams WAG, Faqeih EA, van de Veerdonk FL, Netea MG, Hoischen A. Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies. Genome Med 2019; 11:38. [PMID: 31203817 PMCID: PMC6572765 DOI: 10.1186/s13073-019-0649-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/17/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Diagnosis of primary immunodeficiencies (PIDs) is complex and cumbersome yet important for the clinical management of the disease. Exome sequencing may provide a genetic diagnosis in a significant number of patients in a single genetic test. METHODS In May 2013, we implemented exome sequencing in routine diagnostics for patients suffering from PIDs. This study reports the clinical utility and diagnostic yield for a heterogeneous group of 254 consecutively referred PID patients from 249 families. For the majority of patients, the clinical diagnosis was based on clinical criteria including rare and/or unusual severe bacterial, viral, or fungal infections, sometimes accompanied by autoimmune manifestations. Functional immune defects were interpreted in the context of aberrant immune cell populations, aberrant antibody levels, or combinations of these factors. RESULTS For 62 patients (24%), exome sequencing identified pathogenic variants in well-established PID genes. An exome-wide analysis diagnosed 10 additional patients (4%), providing diagnoses for 72 patients (28%) from 68 families altogether. The genetic diagnosis directly indicated novel treatment options for 25 patients that received a diagnosis (34%). CONCLUSION Exome sequencing as a first-tier test for PIDs granted a diagnosis for 28% of patients. Importantly, molecularly defined diagnoses indicated altered therapeutic options in 34% of cases. In addition, exome sequencing harbors advantages over gene panels as a truly generic test for all genetic diseases, including in silico extension of existing gene lists and re-analysis of existing data.
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Affiliation(s)
- Peer Arts
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Annet Simons
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mofareh S AlZahrani
- Department of Pediatrics, Children's specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Elanur Yilmaz
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Biology, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Eman AlIdrissi
- Department of Pediatrics, Children's specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Koen J van Aerde
- Department of Pediatric immunology, Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Njood Alenezi
- Department of Pediatrics, Children's specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Hamza A AlGhamdi
- Department of Pediatrics, Children's specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Hadeel A AlJubab
- Department of Pediatrics, Children's specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Abdulrahman A Al-Hussaini
- Department of Pediatrics, Children's specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Fahad AlManjomi
- Department of Pediatric Hematology and Oncology, Comprehensive Cancer center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Alaa B Alsaad
- Department of Pediatrics, Children's specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Badr Alsaleem
- Department of Pediatrics, Children's specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Abdulrahman A Andijani
- Department of Pediatrics, Children's specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ali Asery
- Department of Pediatrics, Children's specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Walid Ballourah
- Department of Pediatric Hematology and Oncology, Comprehensive Cancer center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Chantal P Bleeker-Rovers
- Radboud Expertise Center for Immunodeficiency and Autoinflammation, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marcel van Deuren
- Radboud Expertise Center for Immunodeficiency and Autoinflammation, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michiel van der Flier
- Department of Pediatric immunology, Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Erica H Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Murad K Habazi
- Department of Pediatrics, Children's specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Jayne Y Hehir-Kwa
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Stefanie S Henriet
- Department of Pediatric immunology, Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Esther P Hoppenreijs
- Department of Pediatric Rheumatology, Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sarah Hortillosa
- Department of Pediatrics, Children's specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Chantal H Kerkhofs
- Department of Clinical Genetics, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Riikka Keski-Filppula
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland
- Department of Clinical Genetics, Oulu University Hospital, Oulu, Finland
| | - Stefan H Lelieveld
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Khurram Lone
- Department of Pediatrics, Children's specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Marius A MacKenzie
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jukka Moilanen
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland
- Department of Clinical Genetics, Oulu University Hospital, Oulu, Finland
| | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jaap Ten Oever
- Radboud Expertise Center for Immunodeficiency and Autoinflammation, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Judith Potjewijd
- Department of Clinical Immunology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Pieter van Paassen
- Department of Clinical Immunology, Maastricht University Medical Center, Maastricht, The Netherlands
| | | | - Anna Simon
- Radboud Expertise Center for Immunodeficiency and Autoinflammation, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tomasz Stokowy
- Department of Clinical Science, Department of Informatics, Computational Biology Unit, University of Bergen, 5020, Bergen, Norway
| | - Maartje van de Vorst
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maaike Vreeburg
- Department of Clinical Genetics, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Gijs T J van Well
- Department of Pediatrics, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht University, Maastricht, The Netherlands
| | - Dimitra Zafeiropoulou
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | | | - Eissa A Faqeih
- Department of Pediatrics, Children's specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Frank L van de Veerdonk
- Radboud Expertise Center for Immunodeficiency and Autoinflammation, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Radboud Expertise Center for Immunodeficiency and Autoinflammation, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
- Radboud Expertise Center for Immunodeficiency and Autoinflammation, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.
- Department of Human Genetics and Department of Internal Medicine, Radboud University Medical Center, P.O. Box 9101, 6500, HB, Nijmegen, The Netherlands.
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50
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Gao C, Wang X, Mei S, Li D, Duan J, Zhang P, Chen B, Han L, Gao Y, Yang Z, Li B, Yang XA. Diagnostic Yields of Trio-WES Accompanied by CNVseq for Rare Neurodevelopmental Disorders. Front Genet 2019; 10:485. [PMID: 31178897 PMCID: PMC6542989 DOI: 10.3389/fgene.2019.00485] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 05/06/2019] [Indexed: 01/20/2023] Open
Abstract
Objective This study is to investigate the diagnostic yield of the combination of trio whole exome sequencing (Trio-WES) and copy number variation sequencing (CNVseq) for rare neurodevelopmental disorders (NDDs). Methods Clinical data from consecutive pediatric patients who were diagnosed with rare NDDs that were suspected to be monogenic disorders, who were admitted to our hospital from April 2017 to March 2019, and who underwent next generation sequencing (NGS) were extracted from the medical records. Patients for whom Trio-WES and CNVseq data were available were enrolled in this study. Sanger sequencing was applied for the validation of the variants identified by Trio-WES. Sequence alignment and structural modeling were conducted for analyzing the possibility of the variants in the onset of the NDDs. Results In total, 54 patients were enrolled in this study, with the median age of 15 (8–26) months. A total of 242 phenotypic abnormalities belonging to 20 different systems were identified in the cohort. Twenty-four patients were diagnosed by Trio-WES, eight patients were diagnosed by CNVseq, and one case was identified by both WES and CNVseq. Compared with Trio-WES, the diagnosis rate of Trio-WES accompanied by CNVseq was significantly higher (P = 0.016). Trio-WES identified 36 variants in 26 different genes, among which 27 variants were novel. CNVseq detected four duplications and eight deletions, ranging from 310 kb to 23.27 Mb. Our case examples demonstrated the high heterogeneity of NDDs and showed the challenges of rare NDDs for physicians. Conclusion The significantly higher diagnosis rate of Trio-WES accompanied by CNVseq makes this strategy a potential alternative to the most widely used approaches for pediatric children with rare and undiagnosed NDDs.
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Affiliation(s)
- Chao Gao
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China.,Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Xiaona Wang
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Shiyue Mei
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Dongxiao Li
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Jiali Duan
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Pei Zhang
- Department of Pediatric Neurology and Rehabilitation, First People's Hospital of Shangqiu, Shangqiu, China
| | - Baiyun Chen
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Liang Han
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Yang Gao
- Graduate School of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Yang
- Third People's Hospital of Qingdao West Coast New District, Qingdao, China
| | - Bing Li
- Central Laboratory, Jinshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Xiu-An Yang
- School of Basic Medical Science, Chengde Medical University, Chengde, China
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