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Siddiqi S, Ain NU, Kauser M, Mukhtar Z, Ansar M, Umair M. Variants in FREM1 and trisomy 18 identified in a neonatal progeria patient. Mol Biol Rep 2023; 50:7935-7939. [PMID: 37470964 DOI: 10.1007/s11033-023-08595-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/14/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Neonatal progeroid disorders are rare disorders with clinical features including low body mass index, proptosis, aged and dysmorphic facial features at the time of birth, prominent veins, sparse scalp hairs, and severe growth retardation. Very few cases have been identified with an unknown genetic cause. Here, we report clinical and genetic findings of a proband with hallmark features of neonatal progeria. METHODS Microarray comparative genomic hybridization, whole exome sequencing (WES) and Sanger sequencing were performed using standard methods. RESULTS Array combined genome hybridization data revealed trisomy 18 in the proband (II-1), and WES data identified novel compound heterozygous variants (c.247 C > T; p.H83Y and c.14769868InsA) in the FREM1 gene. CONCLUSION We report a novel complex case of neonatal progeria with atrial septal defects, trisomy 18 without typical features of Edward syndrome. The phenotype of the patient was more consistent with neonatal progeria, thus we speculate it to be caused by the FREM1 variants.
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Affiliation(s)
- Saima Siddiqi
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan.
| | - Noor Ul Ain
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan
| | - Mehran Kauser
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan
- Department of Animal Sciences/MLT, Faculty of life sciences, Karakoram International University (KIU), Gilgit, GB, Pakistan
| | - Zahra Mukhtar
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan
- PMAS arid Agriculture University, Rawalpindi, Pakistan
| | - Muhammad Ansar
- Laboratory of Genetic medicine and Development, University of Geneva, Geneva, Switzerland
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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Lyraki M, Hibbert A, Langley-Hobbs S, Lait P, Buckley RM, Warren WC, Lyons LA. CTSK variant implicated in suspected pyknodysostosis in a domestic cat. JFMS Open Rep 2022; 8:20551169221137536. [DOI: 10.1177/20551169221137536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Case summary A 9-month-old entire male domestic longhair cat presented with a history of pathological fractures, chronic musculoskeletal pain and poor growth. Multiple facial and skeletal abnormalities were identified on physical examination and advanced imaging (CT and radiographs). A variant in CTSK was identified in the affected cat following whole-exome sequencing (WES). The cat was managed symptomatically with diet, environmental modifications and analgesia. Relevance and novel information This is the first report of a cat with a similar clinical presentation and genetic variant to the hereditary human genetic disorder pyknodysostosis. In this case, WES was performed, which often facilitates the diagnosis of various hereditary disorders (ie, a conceptual framework for practicing feline genomic medicine). Despite the severe skeletal and appendicular abnormalities described, the cat was alive more than 2 years after its initial presentation.
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Affiliation(s)
- Maria Lyraki
- The Feline Centre, Langford Vets, Langford, Bristol, UK
| | - Angie Hibbert
- The Feline Centre, Langford Vets, Langford, Bristol, UK
| | | | - Philippa Lait
- Molecular Diagnostic Unit, Diagnostic Laboratories, Langford Vets, Langford, Bristol, UK
| | - Reuben M Buckley
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA
| | - Wesley C Warren
- Department of Animal Sciences, Department of Surgery, Institute of Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA
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CNV Detection from Exome Sequencing Data in Routine Diagnostics of Rare Genetic Disorders: Opportunities and Limitations. Genes (Basel) 2021; 12:genes12091427. [PMID: 34573409 PMCID: PMC8472439 DOI: 10.3390/genes12091427] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/15/2022] Open
Abstract
To assess the potential of detecting copy number variations (CNVs) directly from exome sequencing (ES) data in diagnostic settings, we developed a CNV-detection pipeline based on ExomeDepth software and applied it to ES data of 450 individuals. Initially, only CNVs affecting genes in the requested diagnostic gene panels were scored and tested against arrayCGH results. Pathogenic CNVs were detected in 18 individuals. Most detected CNVs were larger than 400 kb (11/18), but three individuals had small CNVs impacting one or a few exons only and were thus not detectable by arrayCGH. Conversely, two pathogenic CNVs were initially missed, as they impacted genes not included in the original gene panel analysed, and a third one was missed as it was in a poorly covered region. The overall combined diagnostic rate (SNVs + CNVs) in our cohort was 36%, with wide differences between clinical domains. We conclude that (1) the ES-based CNV pipeline detects efficiently large and small pathogenic CNVs, (2) the detection of CNV relies on uniformity of sequencing and good coverage, and (3) in patients who remain unsolved by the gene panel analysis, CNV analysis should be extended to all captured genes, as diagnostically relevant CNVs may occur everywhere in the genome.
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A domestic cat whole exome sequencing resource for trait discovery. Sci Rep 2021; 11:7159. [PMID: 33785770 PMCID: PMC8009874 DOI: 10.1038/s41598-021-86200-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/17/2021] [Indexed: 12/13/2022] Open
Abstract
Over 94 million domestic cats are susceptible to cancers and other common and rare diseases. Whole exome sequencing (WES) is a proven strategy to study these disease-causing variants. Presented is a 35.7 Mb exome capture design based on the annotated Felis_catus_9.0 genome assembly, covering 201,683 regions of the cat genome. Whole exome sequencing was conducted on 41 cats with known and unknown genetic diseases and traits, of which ten cats had matching whole genome sequence (WGS) data available, used to validate WES performance. At 80 × mean exome depth of coverage, 96.4% of on-target base coverage had a sequencing depth > 20-fold, while over 98% of single nucleotide variants (SNVs) identified by WGS were also identified by WES. Platform-specific SNVs were restricted to sex chromosomes and a small number of olfactory receptor genes. Within the 41 cats, we identified 31 previously known causal variants and discovered new gene candidate variants, including novel missense variance for polycystic kidney disease and atrichia in the Peterbald cat. These results show the utility of WES to identify novel gene candidate alleles for diseases and traits for the first time in a feline model.
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Macnamara EF, D’Souza P, Tifft CJ. The undiagnosed diseases program: Approach to diagnosis. TRANSLATIONAL SCIENCE OF RARE DISEASES 2020; 4:179-188. [PMID: 32477883 PMCID: PMC7250153 DOI: 10.3233/trd-190045] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Undiagnosed and rare conditions are collectively common and affect millions of people worldwide. The NIH Undiagnosed Diseases Program (UDP) strives to achieve both a comprehensive diagnosis and a better understanding of the mechanisms of disease for many of these individuals. Through the careful review of records, a well-orchestrated inpatient evaluation, genomic sequencing and testing, and with the use of emerging strategies such as matchmaking programs, the UDP succeeds nearly 30 percent of the time for these highly selective cases. Although the UDP process is built on a unique set of resources, case examples demonstrate steps genetic professionals can take, in both clinical and research settings, to arrive at a diagnosis for their most challenging cases.
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Affiliation(s)
- Ellen F. Macnamara
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, MD, USA
| | - Precilla D’Souza
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, MD, USA
| | - Undiagnosed Diseases Network
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, MD, USA
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J. Tifft
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, MD, USA
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Cho A, Lima de Carvalho JR, Tanaka AJ, Jauregui R, Levi SR, Bassuk AG, Mahajan VB, Tsang SH. Fundoscopy-directed genetic testing to re-evaluate negative whole exome sequencing results. Orphanet J Rare Dis 2020; 15:32. [PMID: 32000842 PMCID: PMC6993391 DOI: 10.1186/s13023-020-1312-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/21/2020] [Indexed: 01/01/2023] Open
Abstract
Background Whole exome sequencing (WES) allows for an unbiased search of the genetic cause of a disease. Employing it as a first-tier genetic testing can be favored due to the associated lower incremental cost per diagnosis compared to when using it later in the diagnostic pathway. However, there are technical limitations of WES that can lead to inaccurate negative variant callings. Our study presents these limitations through a re-evaluation of negative WES results using subsequent tests primarily driven by fundoscopic findings. These tests included targeted gene testing, inherited retinal gene panels, whole genome sequencing (WGS), and array comparative genomic hybridization. Results Subsequent genetic testing guided by fundoscopy findings identified the following variant types causing retinitis pigmentosa that were not detected by WES: frameshift deletion and nonsense variants in the RPGR gene, 353-bp Alu repeat insertions in the MAK gene, and large exonic deletion variants in the EYS and PRPF31 genes. Deep intronic variants in the ABCA4 gene causing Stargardt disease and the GUCY2D gene causing Leber congenital amaurosis were also identified. Conclusions Negative WES analyses inconsistent with the phenotype should raise clinical suspicion. Subsequent genetic testing may detect genetic variants missed by WES and can make patients eligible for gene replacement therapy and upcoming clinical trials. When phenotypic findings support a genetic etiology, negative WES results should be followed by targeted gene sequencing, array based approach or whole genome sequencing.
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Affiliation(s)
- Ahra Cho
- Department of Ophthalmology, Columbia University, New York, NY, USA.,Institute of Human Nutrition, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.,Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, New York-Presbyterian Hospital, Edward S. Harkness Eye Institute, New York, NY, USA
| | - Jose Ronaldo Lima de Carvalho
- Department of Ophthalmology, Columbia University, New York, NY, USA.,Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, New York-Presbyterian Hospital, Edward S. Harkness Eye Institute, New York, NY, USA.,Department of Ophthalmology, Empresa Brasileira de Servicos Hospitalares (EBSERH) - Hospital das Clinicas de Pernambuco (HCPE), Federal University of Pernambuco (UFPE), Recife, Brazil.,Department of Ophthalmology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Akemi J Tanaka
- Department of Pathology & Cell Biology, and Columbia Stem Cell Initiative, Columbia University Medical Center, New York, NY, USA
| | - Ruben Jauregui
- Department of Ophthalmology, Columbia University, New York, NY, USA.,Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, New York-Presbyterian Hospital, Edward S. Harkness Eye Institute, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Sarah R Levi
- Department of Ophthalmology, Columbia University, New York, NY, USA.,Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, New York-Presbyterian Hospital, Edward S. Harkness Eye Institute, New York, NY, USA
| | | | - Vinit B Mahajan
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA.,Veterans Affairs Palo Alto Health Care Systems, Palo Alto, CA, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University, New York, NY, USA. .,Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, New York-Presbyterian Hospital, Edward S. Harkness Eye Institute, New York, NY, USA. .,Department of Pathology & Cell Biology, and Columbia Stem Cell Initiative, Columbia University Medical Center, New York, NY, USA.
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Gu F, Wu A, Gordon MG, Vlahos L, Macnamara S, Burke E, Malicdan MC, Adams DR, Tifft CJ, Toro C, Gahl WA, Markello TC. A suite of automated sequence analyses reduces the number of candidate deleterious variants and reveals a difference between probands and unaffected siblings. Genet Med 2019; 21:1772-1780. [PMID: 30700791 PMCID: PMC6669106 DOI: 10.1038/s41436-019-0434-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 01/03/2019] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Develop an automated exome analysis workflow that can produce a very small number of candidate variants yet still detect different numbers of deleterious variants between probands and unaffected siblings. METHODS Ninety-seven outbred nuclear families from the Undiagnosed Diseases Program/Network included single probands and the corresponding unaffected sibling(s). Single-nucleotide polymorphism (SNP) chip and exome analyses were performed on all, with proband and unaffected sibling considered independently as the target. The total burden of candidate genetic variants was summed for probands and siblings over all considered disease models. RESULTS Exome analysis workflow include automated programs for ethnicity-matched genotype calling, salvage pathway for Mendelian inconsistency, compound heterozygous recessive detection, BAM file regional curation, population frequency filtering, pedigree-aware BAM file noise evaluation, and exon deletion filtration. This workflow relied heavily on BAM file analysis. A greater average pathogenic variant number was found compared with unaffected siblings. This was significant (p < 0.05) when using published recommended thresholds, and implies that causal variants are retained in many probands' lists. CONCLUSION Using Mendelian and non-Mendelian models, this agnostic exome analysis shows a difference between a small group of probands and their unaffected siblings. This workflow produces candidate lists small enough to pursue with laboratory validation.
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Affiliation(s)
- Fangning Gu
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Anchi Wu
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - M Grace Gordon
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Lukas Vlahos
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Shane Macnamara
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth Burke
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - May C Malicdan
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J Tifft
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Camilo Toro
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - William A Gahl
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Thomas C Markello
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA.
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Chiereghin C, Robusto M, Mastrangelo A, Castorina P, Montini G, Giani M, Duga S, Asselta R, Soldà G. Alport syndrome cold cases: Missing mutations identified by exome sequencing and functional analysis. PLoS One 2017; 12:e0178630. [PMID: 28570636 PMCID: PMC5453569 DOI: 10.1371/journal.pone.0178630] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/16/2017] [Indexed: 12/30/2022] Open
Abstract
Alport syndrome (AS) is an inherited progressive renal disease caused by mutations in COL4A3, COL4A4, and COL4A5 genes. Despite simultaneous screening of these genes being widely available, mutation detection still remains incomplete in a non-marginal portion of patients. Here, we applied whole-exome sequencing (WES) in 3 Italian families negative after candidate-gene analyses. In Family 1, we identified a novel heterozygous intronic variant (c.2245-40A>G) -outside the conventionally screened candidate region for diagnosis- potentially disrupting COL4A5 exon29 splicing. Using a minigene-based approach in HEK293 cells we demonstrated that this variant abolishes exon29 branch site, causing exon skipping. Moreover, skewed X-inactivation of the c.2245-40A>G allele correlated with disease severity in heterozygous females. In Family 2, WES highlighted a novel COL4A5 hemizygous missense mutation (p.Gly491Asp), which segregates with the phenotype and impacts on a highly-conserved residue. Finally, in Family 3, we detected a homozygous 24-bp in-frame deletion in COL4A3 exon1 (NM_000091.4:c.30_53del:p.Val11_Leu18del or c.40_63del24:p.Leu14_Leu21del), which is ambiguously annotated in databases, although it corresponds to a recurrent AS mutation. Functional analyses showed that this deletion disrupts COL4A3 signal peptide, possibly altering protein secretion. In conclusion, WES -together with functional studies- was fundamental for molecular diagnosis in 3 AS families, highlighting pathogenic variants that escaped previous screenings.
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Affiliation(s)
- Chiara Chiereghin
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Michela Robusto
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Antonio Mastrangelo
- UOC Nefrologia Pediatrica, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Pierangela Castorina
- UO Audiologia, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
- Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano, Milan, Italy
| | - Giovanni Montini
- UOC Nefrologia Pediatrica, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Marisa Giani
- UOC Nefrologia Pediatrica, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
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