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Migliavacca MP, Fock RA, Almeida N, Cavalcanti T, Villela D, Perez ABA, Valle D, Wohler E, Sobreira NLDM, Raskin S. A Brazilian case of IFAP syndrome with severe congenital ichthyosis and limb malformations caused by a rare variant in MBTPS2. REVISTA PAULISTA DE PEDIATRIA : ORGAO OFICIAL DA SOCIEDADE DE PEDIATRIA DE SAO PAULO 2023; 41:e2022057. [PMID: 37042943 PMCID: PMC10108828 DOI: 10.1590/1984-0462/2023/41/2022057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 09/11/2022] [Indexed: 04/13/2023]
Abstract
OBJECTIVE The classic triad, which defines IFAP syndrome, is ichthyosis follicularis, alopecia, and photophobia. It is a rare X-linked genetic disorder characterized by multiple congenital anomalies with variable severity, caused by pathogenic variants in the MBTPS2 gene, which encodes a zinc metalloprotease that is essential for normal development. This study aimed to report a case of a Brazilian patient with IFAP syndrome presenting skeletal anomalies, which is a rare finding among patients from different families. CASE DESCRIPTION We describe a male proband with IFAP syndrome showing severe ichthyosis congenita, cryptorchidism, limb malformation, and comprising the BRESHECK syndrome features. Using whole-exome sequencing, we identified a rare missense variant in hemizygosity in the MBTPS2 gene, which had not been identified in other family members. COMMENTS This is the first diagnosis of IFAP syndrome in Brazil with a molecular investigation. The present case study thus expands our knowledge on the mutational spectrum of MBPTS2 associated with IFAP syndrome.
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Affiliation(s)
- Michele Patricia Migliavacca
- Universidade Federal de São Paulo, São Paulo, SP, Brazil
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Nadia Almeida
- Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil
| | | | | | | | - David Valle
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | - Salmo Raskin
- Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil
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2
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Phenotype-aware prioritisation of rare Mendelian disease variants. Trends Genet 2022; 38:1271-1283. [PMID: 35934592 PMCID: PMC9950798 DOI: 10.1016/j.tig.2022.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/06/2022] [Accepted: 07/05/2022] [Indexed: 01/24/2023]
Abstract
A molecular diagnosis from the analysis of sequencing data in rare Mendelian diseases has a huge impact on the management of patients and their families. Numerous patient phenotype-aware variant prioritisation (VP) tools have been developed to help automate this process, and shorten the diagnostic odyssey, but performance statistics on real patient data are limited. Here we identify, assess, and compare the performance of all up-to-date, freely available, and programmatically accessible tools using a whole-exome, retinal disease dataset from 134 individuals with a molecular diagnosis. All tools were able to identify around two-thirds of the genetic diagnoses as the top-ranked candidate, with LIRICAL performing best overall. Finally, we discuss the challenges to overcome most cases remaining undiagnosed after current, state-of-the-art practices.
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Ghafoor S, Silveira KDC, Qamar R, Azam M, Kannu P. Exome Sequencing Identifies a Biallelic GALNS Variant (p.Asp233Asn) Causing Mucopolysaccharidosis Type IVA in a Pakistani Consanguineous Family. Genes (Basel) 2022; 13:genes13101743. [PMID: 36292628 PMCID: PMC9602411 DOI: 10.3390/genes13101743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 01/02/2023] Open
Abstract
Mucopolysaccharidoses (MPS) type IVA is a lysosomal storage disease that mainly affects the skeletal system and is caused by a deficiency of the enzyme N-acetylgalactosamine-6-sulfatase (GALNS). The condition can mistakenly be diagnosed as a primary skeletal dysplasia such as spondylo-epiphyseal dysplasia, which shares many similar phenotypic features. Here, we utilised whole exome sequencing to make the diagnosis of MPS IVA in a resource poor country. We report for the first time the identification of a biallelic GALNS missense variant (c.697G>A, p.Asp233Asn) in the Pakistani population and highlight the potential contribution that academic institutions can make in rare disease diagnosis in the absence of a developed clinical genetic service.
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Affiliation(s)
- Saima Ghafoor
- Translational Genomics Laboratory, COMSATS University Islamabad, Islamabad 45550, Pakistan
| | | | - Raheel Qamar
- Pakistan Academy of Sciences, Islamabad 44000, Pakistan
- Science and Technology Sector, ICESCO, Rabat 10104, Morocco
| | - Maleeha Azam
- Translational Genomics Laboratory, COMSATS University Islamabad, Islamabad 45550, Pakistan
- Correspondence: or (M.A.); (P.K.); Tel.: +92-(51)-9235033 (M.A.); +1-(780)-492-9044 (P.K.)
| | - Peter Kannu
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Correspondence: or (M.A.); (P.K.); Tel.: +92-(51)-9235033 (M.A.); +1-(780)-492-9044 (P.K.)
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Yan S, Luo L, Lai PT, Veltri D, Oler AJ, Xirasagar S, Ghosh R, Similuk M, Robinson PN, Lu Z. PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology. J Biomed Inform 2022; 129:104059. [PMID: 35351638 PMCID: PMC11040548 DOI: 10.1016/j.jbi.2022.104059] [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: 09/20/2021] [Revised: 02/23/2022] [Accepted: 03/22/2022] [Indexed: 11/29/2022]
Abstract
The study aims at developing a neural network model to improve the performance of Human Phenotype Ontology (HPO) concept recognition tools. We used the terms, definitions, and comments about the phenotypic concepts in the HPO database to train our model. The document to be analyzed is first split into sentences and annotated with a base method to generate candidate concepts. The sentences, along with the candidate concepts, are then fed into the pre-trained model for re-ranking. Our model comprises the pre-trained BlueBERT and a feature selection module, followed by a contrastive loss. We re-ranked the results generated by three robust HPO annotation tools and compared the performance against most of the existing approaches. The experimental results show that our model can improve the performance of the existing methods. Significantly, it boosted 3.0% and 5.6% in F1 score on the two evaluated datasets compared with the base methods. It removed more than 80% of the false positives predicted by the base methods, resulting in up to 18% improvement in precision. Our model utilizes the descriptive data in the ontology and the contextual information in the sentences for re-ranking. The results indicate that the additional information and the re-ranking model can significantly enhance the precision of HPO concept recognition compared with the base method.
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Affiliation(s)
- Shankai Yan
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Ling Luo
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Po-Ting Lai
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Daniel Veltri
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sandhya Xirasagar
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rajarshi Ghosh
- Centralized Sequencing Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Morgan Similuk
- Centralized Sequencing Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Zhiyong Lu
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA.
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Slavotinek A, Prasad H, Yip T, Rego S, Hoban H, Kvale M. Predicting genes from phenotypes using human phenotype ontology (HPO) terms. Hum Genet 2022; 141:1749-1760. [PMID: 35357580 DOI: 10.1007/s00439-022-02449-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/16/2022] [Indexed: 11/28/2022]
Abstract
The interpretation of genomic variants following whole exome sequencing (WES) can be aided using human phenotype ontology (HPO) terms to standardize clinical features and predict causative genes. We performed WES on 453 patients diagnosed prior to 18 years of age and identified 114 pathogenic (P) or likely pathogenic (LP) variants in 112 patients. We utilized PhenoDB to extract HPO terms from provider notes and then used Phen2Gene to generate a gene score and gene ranking from each list of HPO terms. We assigned Phen2Gene gene rankings to 6 rank classes, with class 1 covering raw gene rankings of 1 to 10 and class 2 covering rankings from 11 to 50 out of a total of 17,126 possible gene rankings. Phen2Gene ranked causative genes into rank class 1 or 2 in 27.7% of cases and the genes in rank class 1 were all associated with well-characterized phenotypes. We found significant associations between the gene score and the number of years, since the gene was first published, the number of HPO terms with an hierarchical depth greater or equal to 11, and the number of Online Mendelian Inheritance in Man terms associated with the phenotype and gene. We conclude that genes associated with recognizable phenotypes and terms deep in the HPO hierarchy have the best chance of producing a high gene score and ranking in class 1 to 2 using Phen2Gene software with HPO terms. Clinicians and laboratory staff should consider these results when HPO terms are employed to prioritize candidate genes.
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Affiliation(s)
- Anne Slavotinek
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
| | - Hannah Prasad
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Tiffany Yip
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Shannon Rego
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Hannah Hoban
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Mark Kvale
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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Hamosh A, Wohler E, Martin R, Griffith S, da S Rodrigues E, Antonescu C, Doheny KF, Valle D, Sobreira N. The impact of GeneMatcher on international data sharing and collaboration. Hum Mutat 2022; 43:668-673. [PMID: 35170833 PMCID: PMC9133194 DOI: 10.1002/humu.24350] [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: 10/14/2021] [Revised: 02/03/2022] [Accepted: 02/11/2022] [Indexed: 11/30/2022]
Abstract
GeneMatcher (genematcher.org) is a tool designed to connect individuals with an interest in the same gene. Now used around the world to create collaborations and generate the evidence needed to support novel disease gene identification, GeneMatcher is a founding member of the Matchmaker Exchange (MME; matchmakerexchange.org) and strongest possible advocate for global data sharing including those in resource‐limited environments. As of October 1, 2021, there are 12,531 submitters from 94 countries who have submitted 58,134 submissions with 13,498 unique genes in the database. Among these genes, 8970 (64%) have matched at least once and the total number of matches is 378,806, growing by about 10,000 per month. GeneMatcher submitters increase by 80–120 each month and submissions grow by >800 per month, while unique genes and gene matches continue to grow steadily at rate of about 80 per month. The number of genes without a match peaked at 4371 in February of 2019 and despite the increase in the number of new submissions, the number of unique genes without a match continues to slowly decline, currently standing at 4,016. All submissions in GeneMatcher are available for matching across the MME.
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Affiliation(s)
- Ada Hamosh
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - Elizabeth Wohler
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - Renan Martin
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - Sean Griffith
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - Eliete da S Rodrigues
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - Corina Antonescu
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - Kimberly F Doheny
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - David Valle
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - Nara Sobreira
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
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de Mello LEB, Carneiro TNR, Araujo AN, Alves CX, Galante PAF, Buzatto VC, das Graças de Almeida M, Vermeulen-Serpa KM, de Lima Vale SH, José de Pinto Paiva F, Brandão-Neto J, Cerutti JM. Identification of NID1 as a novel candidate susceptibility gene for familial non-medullary thyroid carcinoma using whole-exome sequencing. Endocr Connect 2022; 11:EC-21-0406.R2. [PMID: 34941562 PMCID: PMC8859953 DOI: 10.1530/ec-21-0406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/22/2021] [Indexed: 11/15/2022]
Abstract
The genetics underlying non-syndromic familial non-medullary thyroid carcinoma (FNMTC) is still poorly understood. To identify susceptibility genes for FNMTC, we performed whole-exome sequencing (WES) in a Brazilian family affected by papillary thyroid carcinoma (PTC) in three consecutive generations. WES was performed in four affected and two unaffected family members. Manual inspection in over 100 previously reported susceptibility genes for FNMTC showed that no variants in known genes co-segregated with disease phenotype in this family. Novel candidate genes were investigated using PhenoDB and filtered using Genome Aggregation (gnomAD) and Online Archive of Brazilian Mutations (ABraOM) population databases. The missense variant p.Ile657Met in the NID1 gene was the only variant that co-segregated with the disease, while absent in unaffected family members and controls. The allele frequency for this variant was <0.0001 in the gnomAD and ABbraOM databases. In silico analysis predicted the variant to be deleterious or likely damaging to the protein function. Somatic mutations in NID1 gene were found in nearly 500 cases of different cancer subtypes in the intOGen platform. Immunohistochemistry analysis showed NID1 expression in PTC cells, while it was absent in normal thyroid tissue. Our findings were corroborated using data from the TCGA cohort. Moreover, higher expression of NID1 was associated with higher likelihood of relapse after treatment and N1b disease in PTCs from the TCGA cohort. Although replication studies are needed to better understand the role of this variant in the FNMTC susceptibility, the NID1 variant (c.1971T>G) identified in this study fulfills several criteria that suggest it as a new FNMTC predisposing gene.
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Affiliation(s)
- Luis Eduardo Barbalho de Mello
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Postgraduate Program in Health Sciences, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Thaise Nayane Ribeiro Carneiro
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Aline Neves Araujo
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Camila Xavier Alves
- Postgraduate Program in Health Sciences, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | | | - Maria das Graças de Almeida
- Postgraduate Program in Health Sciences, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
- Department of Clinical and Toxicological Analyses, Natal, Rio Grande do Norte, Brazil
| | - Karina Marques Vermeulen-Serpa
- Postgraduate Program in Health Sciences, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Sancha Helena de Lima Vale
- Department of Clinical and Toxicological Analyses, Natal, Rio Grande do Norte, Brazil
- Department of Nutrition, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Fernando José de Pinto Paiva
- Postgraduate Program in Health Sciences, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - José Brandão-Neto
- Postgraduate Program in Health Sciences, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Janete Maria Cerutti
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Correspondence should be addressed to J M Cerutti:
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Wohler E, Martin R, Griffith S, Rodrigues EDS, Antonescu C, Posey JE, Coban-Akdemir Z, Jhangiani SN, Doheny KF, Lupski JR, Valle D, Hamosh A, Sobreira N. PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data. Orphanet J Rare Dis 2021; 16:365. [PMID: 34407837 PMCID: PMC8371856 DOI: 10.1186/s13023-021-01916-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/13/2021] [Indexed: 12/02/2022] Open
Abstract
Background With the advent of whole exome (ES) and genome sequencing (GS) as tools for disease gene discovery, rare variant filtering, prioritization and data sharing have become essential components of the search for disease genes and variants potentially contributing to disease phenotypes. The computational storage, data manipulation, and bioinformatic interpretation of thousands to millions of variants identified in ES and GS, respectively, is a challenging task. To aid in that endeavor, we constructed PhenoDB, GeneMatcher and VariantMatcher. Results PhenoDB is an accessible, freely available, web-based platform that allows users to store, share, analyze and interpret their patients’ phenotypes and variants from ES/GS data. GeneMatcher is accessible to all stakeholders as a web-based tool developed to connect individuals (researchers, clinicians, health care providers and patients) around the globe with interest in the same gene(s), variant(s) or phenotype(s). Finally, VariantMatcher was developed to enable public sharing of variant-level data and phenotypic information from individuals sequenced as part of multiple disease gene discovery projects. Here we provide updates on PhenoDB and GeneMatcher applications and implementation and introduce VariantMatcher. Conclusion Each of these tools has facilitated worldwide data sharing and data analysis and improved our ability to connect genes to phenotypic traits. Further development of these platforms will expand variant analysis, interpretation, novel disease-gene discovery and facilitate functional annotation of the human genome for clinical genomics implementation and the precision medicine initiative. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-01916-z.
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Affiliation(s)
- Elizabeth Wohler
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Renan Martin
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sean Griffith
- Center for Inherited Disease Research - CIDR, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Eliete da S Rodrigues
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Corina Antonescu
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Kimberly F Doheny
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Center for Inherited Disease Research - CIDR, Johns Hopkins School of Medicine, Baltimore, MD, 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.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - David Valle
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nara Sobreira
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Perrone E, Perez ABA, D'Almeida V, de Mello CB, Jacobina MAA, Loureiro RM, Burlin S, Migliavacca M, do Amaral Virmond L, Graziadio C, Pedroso JL, Mendes EL, Gomy I, de Macena Sobreira NL. Clinical and molecular evaluation of 13 Brazilian patients with Gomez-López-Hernández syndrome. Am J Med Genet A 2020; 185:1047-1058. [PMID: 33381921 DOI: 10.1002/ajmg.a.62059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 01/21/2023]
Abstract
We aim to characterize patients with Gomez-López-Hernández syndrome (GLHS) clinically and to investigate them molecularly. A clinical protocol, including a morphological and neuropsychological assessment, was applied to 13 patients with GLHS. Single-nucleotide polymorphism (SNP) array and whole-exome sequencing were undertaken; magnetic resonance imaging was performed in 12 patients, including high-resolution, heavily T2-weighted sequences (HRT2) in 6 patients to analyze the trigeminal nerves. All patients presented alopecia; two did not present rhombencephalosynapsis (RES); trigeminal anesthesia was present in 5 of the 11 patients (45.4%); brachycephaly/brachyturricephaly and mid-face retrusion were found in 84.6 and 92.3% of the patients, respectively. One patient had intellectual disability. HRT2 sequences showed trigeminal nerve hypoplasia in four of the six patients; all four had clinical signs of trigeminal anesthesia. No common candidate gene was found to explain GLHS phenotype. RES does not seem to be an obligatory finding in respect of GLHS diagnosis. We propose that a diagnosis of GLHS should be considered in patients with at least two of the following criteria: focal non-scarring alopecia, rhombencephalosynapsis, craniofacial anomalies (brachyturrycephaly, brachycephaly or mid-face retrusion), trigeminal anesthesia or anatomic abnormalities of the trigeminal nerve. Studies focusing on germline whole genome sequencing or DNA and/or RNA sequencing of the alopecia tissue may be the next step for the better understanding of GLHS etiology.
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Affiliation(s)
- Eduardo Perrone
- Clinical Genetics Department, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Vânia D'Almeida
- Psychobiology Department, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | | | | | - Rafael Maffei Loureiro
- Department of Radiology, Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
| | - Stênio Burlin
- Department of Radiology, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Luiza do Amaral Virmond
- Clinical Genetics Department, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Carla Graziadio
- Department of Clinical Genetics, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA) and Complexo Hospitalar Santa Casa de Porto Alegre (CHSCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - José Luiz Pedroso
- Ataxia Unit, Department of Neurology, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Israel Gomy
- Departament of Pediatrics, Universidade Federal do Paraná, Paraná, Brazil
| | - Nara Lygia de Macena Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Schaaf J, Sedlmayr M, Schaefer J, Storf H. Diagnosis of Rare Diseases: a scoping review of clinical decision support systems. Orphanet J Rare Dis 2020; 15:263. [PMID: 32972444 PMCID: PMC7513302 DOI: 10.1186/s13023-020-01536-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 09/07/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Rare Diseases (RDs), which are defined as diseases affecting no more than 5 out of 10,000 people, are often severe, chronic and life-threatening. A main problem is the delay in diagnosing RDs. Clinical decision support systems (CDSSs) for RDs are software systems to support clinicians in the diagnosis of patients with RDs. Due to their clinical importance, we conducted a scoping review to determine which CDSSs are available to support the diagnosis of RDs patients, whether the CDSSs are available to be used by clinicians and which functionalities and data are used to provide decision support. METHODS We searched PubMed for CDSSs in RDs published between December 16, 2008 and December 16, 2018. Only English articles, original peer reviewed journals and conference papers describing a clinical prototype or a routine use of CDSSs were included. For data charting, we used the data items "Objective and background of the publication/project", "System or project name", "Functionality", "Type of clinical data", "Rare Diseases covered", "Development status", "System availability", "Data entry and integration", "Last software update" and "Clinical usage". RESULTS The search identified 636 articles. After title and abstracting screening, as well as assessing the eligibility criteria for full-text screening, 22 articles describing 19 different CDSSs were identified. Three types of CDSSs were classified: "Analysis or comparison of genetic and phenotypic data," "machine learning" and "information retrieval". Twelve of nineteen CDSSs use phenotypic and genetic data, followed by clinical data, literature databases and patient questionnaires. Fourteen of nineteen CDSSs are fully developed systems and therefore publicly available. Data can be entered or uploaded manually in six CDSSs, whereas for four CDSSs no information for data integration was available. Only seven CDSSs allow further ways of data integration. thirteen CDSS do not provide information about clinical usage. CONCLUSIONS Different CDSS for various purposes are available, yet clinicians have to determine which is best for their patient. To allow a more precise usage, future research has to focus on CDSSs RDs data integration, clinical usage and updating clinical knowledge. It remains interesting which of the CDSSs will be used and maintained in the future.
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Affiliation(s)
- Jannik Schaaf
- Medical Informatics Group (MIG), University Hospital Frankfurt, Frankfurt, Germany.
| | - Martin Sedlmayr
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine Technische Universität Dresden, Dresden, Germany
| | - Johanna Schaefer
- Medical Informatics Group (MIG), University Hospital Frankfurt, Frankfurt, Germany
| | - Holger Storf
- Medical Informatics Group (MIG), University Hospital Frankfurt, Frankfurt, Germany
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11
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Gaysinskaya V, Stanley SE, Adam S, Armanios M. Synonymous Mutation in DKC1 Causes Telomerase RNA Insufficiency Manifesting as Familial Pulmonary Fibrosis. Chest 2020; 158:2449-2457. [PMID: 32710892 DOI: 10.1016/j.chest.2020.07.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is the most common of short telomere phenotypes. Familial clustering of IPF is common, but the genetic basis remains unknown in more than one-half of cases. We identified a 65-year-old man with familial IPF, short telomere length, and low telomerase RNA levels. He was diagnosed with a short telomere syndrome after developing hematologic complications post-lung transplantation, but no mutations were identified in a clinical testing pipeline. RESEARCH QUESTION What is the molecular basis underlying the familial IPF and low telomerase RNA levels in this patient? STUDY DESIGN AND METHODS We analyzed whole-genome sequence data and performed functional molecular studies on cells derived from the patient and his family. RESULTS We identified a previously unreported synonymous variant c.942G>A p.K314K in DKC1, the gene encoding the dyskerin ribonucleoprotein, which is required for telomerase RNA biogenesis. The mutation created a competing de novo exonic splicing enhancer, and the misspliced product was degraded by nonsense-mediated decay causing an overall dyskerin deficiency in mutation carriers. In silico tools identified other rare silent DKC1 variants that warrant functional evaluation if found in patients with short telomere-mediated disease. INTERPRETATION Our data point to silent mutation in telomere maintenance genes as a mechanism of familial pulmonary fibrosis. In contrast to DKC1 missense mutations, which primarily manifest in children as dyskeratosis congenita, hypomorphic mutations affecting dyskerin levels likely have a predilection to presenting in adults as pulmonary fibrosis.
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Affiliation(s)
- Valeriya Gaysinskaya
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD; Telomere Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Susan E Stanley
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD; Telomere Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Soheir Adam
- Department of Medicine, Duke University School of Medicine, Durham, NC
| | - Mary Armanios
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD; Sidney Kimmel Comprehensive Cancer, Johns Hopkins University School of Medicine, Baltimore, MD.
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12
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Cipriani V, Pontikos N, Arno G, Sergouniotis PI, Lenassi E, Thawong P, Danis D, Michaelides M, Webster AR, Moore AT, Robinson PN, Jacobsen JO, Smedley D. An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data. Genes (Basel) 2020; 11:E460. [PMID: 32340307 PMCID: PMC7230372 DOI: 10.3390/genes11040460] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/08/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing has revolutionized rare disease diagnostics, but many patients remain without a molecular diagnosis, particularly because many candidate variants usually survive despite strict filtering. Exomiser was launched in 2014 as a Java tool that performs an integrative analysis of patients' sequencing data and their phenotypes encoded with Human Phenotype Ontology (HPO) terms. It prioritizes variants by leveraging information on variant frequency, predicted pathogenicity, and gene-phenotype associations derived from human diseases, model organisms, and protein-protein interactions. Early published releases of Exomiser were able to prioritize disease-causative variants as top candidates in up to 97% of simulated whole-exomes. The size of the tested real patient datasets published so far are very limited. Here, we present the latest Exomiser version 12.0.1 with many new features. We assessed the performance using a set of 134 whole-exomes from patients with a range of rare retinal diseases and known molecular diagnosis. Using default settings, Exomiser ranked the correct diagnosed variants as the top candidate in 74% of the dataset and top 5 in 94%; not using the patients' HPO profiles (i.e., variant-only analysis) decreased the performance to 3% and 27%, respectively. In conclusion, Exomiser is an effective support tool for rare Mendelian phenotype-driven variant prioritization.
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Affiliation(s)
- Valentina Cipriani
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.O.B.J.); (D.S.)
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- UCL Genetics Institute, University College London, London WC1E 6AA, UK
| | - Nikolas Pontikos
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- North East Thames Regional Genetics Laboratory, Great Ormond Street Hospital NHS Trust, London WC1N 3BH, UK
| | | | - Eva Lenassi
- Manchester Royal Eye Hospital & University of Manchester, Manchester M13 9WL, UK; (P.I.S.); (E.L.)
| | - Penpitcha Thawong
- Department of Medical Sciences, Medical Genetics Section, National Institute of Health, Ministry of Public Health, Nonthaburi 11000, Thailand;
| | - Daniel Danis
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; (D.D.); (P.N.R.)
| | - Michel Michaelides
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
| | - Andrew R. Webster
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
| | - Anthony T. Moore
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- Ophthalmology Department, UCSF School of Medicine, San Francisco, CA 94143-0644, USA
| | - Peter N. Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; (D.D.); (P.N.R.)
| | - Julius O.B. Jacobsen
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.O.B.J.); (D.S.)
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.O.B.J.); (D.S.)
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13
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Jelin AC, Sobreira N, Wohler E, Solomon B, Sparks T, Sagaser KG, Forster KR, Miller J, Witmer PD, Hamosh A, Valle D, Blakemore K. The utility of exome sequencing for fetal pleural effusions. Prenat Diagn 2020; 40:590-595. [PMID: 31994743 DOI: 10.1002/pd.5650] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 01/23/2023]
Abstract
OBJECTIVE We sought to evaluate the performance of exome sequencing (ES) in determining an underlying genetic etiology for cases of fetal pleural effusions. STUDY DESIGN We examined a prospective cohort series of fetal pleural effusions visualized sonographically between 1 April 2016 and 31 August 2017. Fetal pleural effusions attributed to twin sharing, anemia, or structural anomalies were excluded, as were all cases with a genetic diagnosis established by karyotype or chromosomal microarray analysis. The remaining cases with pleural effusions of unclear etiology were offered ES. ES was performed by clinical sequencing and/or sequencing under the Baylor-Hopkins Center for Mendelian Genomics' (BHCMG) research platform. All cases were evaluated for novel genes or phenotypic expansion of disease-causing genes. RESULTS ES was performed on six probands affected by pleural effusions. A pathogenic variant was identified in one case (16.7%). Four additional cases had variants of uncertain significance (VUS) in candidate genes of pathological interest. Neither clinical nor candidate genes were evident in the final case. CONCLUSION ES should be considered in the evaluation of prenatally detected idiopathic pleural effusions when other diagnostic workup for a genetic etiology has failed.
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Affiliation(s)
- Angie C Jelin
- Department of Gynecology and Obstetrics, Division of Maternal Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.,Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD, USA
| | - Elizabeth Wohler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.,Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD, USA
| | | | - Teresa Sparks
- Department of Obstetrics, Gynecology & Reproductive Sciences, Division of Maternal Fetal Medicine, University of California, San Francisco, CA, USA
| | - Katelynn G Sagaser
- Department of Gynecology and Obstetrics, Division of Maternal Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Katherine R Forster
- Department of Gynecology and Obstetrics, Center for Fetal Therapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jena Miller
- Department of Gynecology and Obstetrics, Center for Fetal Therapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - P Dane Witmer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.,Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.,Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.,Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD, USA
| | - Karin Blakemore
- Department of Gynecology and Obstetrics, Division of Maternal Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
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14
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Gable DL, Gaysinskaya V, Atik CC, Talbot CC, Kang B, Stanley SE, Pugh EW, Amat-Codina N, Schenk KM, Arcasoy MO, Brayton C, Florea L, Armanios M. ZCCHC8, the nuclear exosome targeting component, is mutated in familial pulmonary fibrosis and is required for telomerase RNA maturation. Genes Dev 2019; 33:1381-1396. [PMID: 31488579 PMCID: PMC6771387 DOI: 10.1101/gad.326785.119] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/15/2019] [Indexed: 11/25/2022]
Abstract
In this study, Gable et al. follow a family with early onset pulmonary fibrosis and report the discovery of a new genetic cause of pulmonary fibrosis. They use multidimensional analysis methods, involving molecular studies, mouse model, and transcriptome-wide studies to show that heterozygous loss-of-function of the exosomal targeting protein ZCCHC8 to identify a novel cause of telomerase insufficiency in human disease. Short telomere syndromes manifest as familial idiopathic pulmonary fibrosis; they are the most common premature aging disorders. We used genome-wide linkage to identify heterozygous loss of function of ZCCHC8, a zinc-knuckle containing protein, as a cause of autosomal dominant pulmonary fibrosis. ZCCHC8 associated with TR and was required for telomerase function. In ZCCHC8 knockout cells and in mutation carriers, genomically extended telomerase RNA (TR) accumulated at the expense of mature TR, consistent with a role for ZCCHC8 in mediating TR 3′ end targeting to the nuclear RNA exosome. We generated Zcchc8-null mice and found that heterozygotes, similar to human mutation carriers, had TR insufficiency but an otherwise preserved transcriptome. In contrast, Zcchc8−/− mice developed progressive and fatal neurodevelopmental pathology with features of a ciliopathy. The Zcchc8−/− brain transcriptome was highly dysregulated, showing accumulation and 3′ end misprocessing of other low-abundance RNAs, including those encoding cilia components as well as the intronless replication-dependent histones. Our data identify a novel cause of human short telomere syndromes-familial pulmonary fibrosis and uncover nuclear exosome targeting as an essential 3′ end maturation mechanism that vertebrate TR shares with replication-dependent histones.
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Affiliation(s)
- Dustin L Gable
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Valeriya Gaysinskaya
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Christine C Atik
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Byunghak Kang
- Department of Comparative and Molecular Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Susan E Stanley
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Elizabeth W Pugh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Nuria Amat-Codina
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Kara M Schenk
- Osler Medical Housestaff Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Murat O Arcasoy
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27708, USA
| | - Cory Brayton
- Department of Comparative and Molecular Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Liliana Florea
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Mary Armanios
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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15
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Nellåker C, Alkuraya FS, Baynam G, Bernier RA, Bernier FP, Boulanger V, Brudno M, Brunner HG, Clayton-Smith J, Cogné B, Dawkins HJ, deVries BB, Douzgou S, Dudding-Byth T, Eichler EE, Ferlaino M, Fieggen K, Firth HV, FitzPatrick DR, Gration D, Groza T, Haendel M, Hallowell N, Hamosh A, Hehir-Kwa J, Hitz MP, Hughes M, Kini U, Kleefstra T, Kooy RF, Krawitz P, Küry S, Lees M, Lyon GJ, Lyonnet S, Marcadier JL, Meyn S, Moslerová V, Politei JM, Poulton CC, Raymond FL, Reijnders MR, Robinson PN, Romano C, Rose CM, Sainsbury DC, Schofield L, Sutton VR, Turnovec M, Van Dijck A, Van Esch H, Wilkie AO. Enabling Global Clinical Collaborations on Identifiable Patient Data: The Minerva Initiative. Front Genet 2019; 10:611. [PMID: 31417602 PMCID: PMC6681681 DOI: 10.3389/fgene.2019.00611] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 06/12/2019] [Indexed: 01/25/2023] Open
Abstract
The clinical utility of computational phenotyping for both genetic and rare diseases is increasingly appreciated; however, its true potential is yet to be fully realized. Alongside the growing clinical and research availability of sequencing technologies, precise deep and scalable phenotyping is required to serve unmet need in genetic and rare diseases. To improve the lives of individuals affected with rare diseases through deep phenotyping, global big data interrogation is necessary to aid our understanding of disease biology, assist diagnosis, and develop targeted treatment strategies. This includes the application of cutting-edge machine learning methods to image data. As with most digital tools employed in health care, there are ethical and data governance challenges associated with using identifiable personal image data. There are also risks with failing to deliver on the patient benefits of these new technologies, the biggest of which is posed by data siloing. The Minerva Initiative has been designed to enable the public good of deep phenotyping while mitigating these ethical risks. Its open structure, enabling collaboration and data sharing between individuals, clinicians, researchers and private enterprise, is key for delivering precision public health.
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Affiliation(s)
- Christoffer Nellåker
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
- Institute for Biomedical Engineering, University of Oxford, Oxford, United Kingdom
| | - Fowzan S. Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, and Genetic Services of Western Australia, King Edward Memorial, Subiaco, WA, Australia
- Telethon Kids Institute and School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
- Spatial Sciences, Science and Engineering, Curtin University, Perth, WA, Australia
| | - Raphael A. Bernier
- Department of Psychiatry & Behavioral Science, University of Washington School of Medicine, Seattle, WA, United States
| | | | - Vanessa Boulanger
- National Organization for Rare Disorders, Danbury, CT, United States
| | - Michael Brudno
- Department of Computer Science, University of Toronto and the Hospital for Sick Children, Toronto, Canada
| | - Han G. Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Saint Mary’s Hospital, Manchester, United Kingdom
| | - Benjamin Cogné
- CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Hugh J.S. Dawkins
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health Government of Western Australia, Perth, WA, Australia
- Sir Walter Murdoch School of Policy and International Affairs, Murdoch University
- Centre for Population Health Research, Curtin University of Technology, Perth, WA, Australia
| | - Bert B.A. deVries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sofia Douzgou
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Saint Mary’s Hospital, Manchester, United Kingdom
| | | | - Evan E. Eichler
- Department of Genome Science, University of Washington School of Medicine, Seattle, WA, United States
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, United States
| | - Michael Ferlaino
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Karen Fieggen
- Division of Human Genetics, Level 3, Wernher and Beit North, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Helen V. Firth
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - David R. FitzPatrick
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Dylan Gration
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Tudor Groza
- The Garvan Institute, Sydney, NSW, Australia
| | - Melissa Haendel
- Oregon Health & Science University, Portland, OR, United States
| | - Nina Hallowell
- Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Ethics and Humanities, University of Oxford, Oxford, United Kingdom
- Ethox Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Jayne Hehir-Kwa
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Marc-Phillip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein–Campus Kiel, Kiel, Germany
| | - Mark Hughes
- Department of Clinical Neurosciences, Western General Hospital, Edinburgh, United Kingdom
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford, United Kingdom
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Peter Krawitz
- Institut für Genomische Statistik und Bioinformatik, Universitätsklinikum Bonn, Rheinische-Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Melissa Lees
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Gholson J. Lyon
- George A. Jervis Clinic and Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, NY, United States
| | | | | | - Stephen Meyn
- Department of Computer Science, University of Toronto and the Hospital for Sick Children, Toronto, Canada
| | - Veronika Moslerová
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and University Hospital, Prague, Czechia
| | - Juan M. Politei
- Laboratorio Chamoles, Errores Congénitos del Metabolismo, Buenos Aires, Argentina
| | - Cathryn C. Poulton
- Department of Paediatrics and Neonates, Fiona Stanley Hospital, Perth, WA, Australia
| | - F Lucy Raymond
- CIMR (Wellcome Trust/MRC Building), Cambridge, United Kingdom
| | - Margot R.F. Reijnders
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | | | | | - Catherine M. Rose
- Victorian Clinical Genetics Service and Murdoch Childrens Research Institute, The Royal Children’s Hospital, Parkville, VIC, Australia
| | - David C.G. Sainsbury
- Northern & Yorkshire Cleft Lip and Palate Service, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Lyn Schofield
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Vernon R. Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Marek Turnovec
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and University Hospital, Prague, Czechia
| | - Anke Van Dijck
- Department of Medical Genetics, University and University Hospital Antwerp, Antwerp, Belgium
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Andrew O.M. Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
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16
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Posey JE, O'Donnell-Luria AH, Chong JX, Harel T, Jhangiani SN, Coban Akdemir ZH, Buyske S, Pehlivan D, Carvalho CMB, Baxter S, Sobreira N, Liu P, Wu N, Rosenfeld JA, Kumar S, Avramopoulos D, White JJ, Doheny KF, Witmer PD, Boehm C, Sutton VR, Muzny DM, Boerwinkle E, Günel M, Nickerson DA, Mane S, MacArthur DG, Gibbs RA, Hamosh A, Lifton RP, Matise TC, Rehm HL, Gerstein M, Bamshad MJ, Valle D, Lupski JR. Insights into genetics, human biology and disease gleaned from family based genomic studies. Genet Med 2019; 21:798-812. [PMID: 30655598 PMCID: PMC6691975 DOI: 10.1038/s41436-018-0408-7] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022] Open
Abstract
Identifying genes and variants contributing to rare disease phenotypes and Mendelian conditions informs biology and medicine, yet potential phenotypic consequences for variation of >75% of the ~20,000 annotated genes in the human genome are lacking. Technical advances to assess rare variation genome-wide, particularly exome sequencing (ES), enabled establishment in the United States of the National Institutes of Health (NIH)-supported Centers for Mendelian Genomics (CMGs) and have facilitated collaborative studies resulting in novel "disease gene" discoveries. Pedigree-based genomic studies and rare variant analyses in families with suspected Mendelian conditions have led to the elucidation of hundreds of novel disease genes and highlighted the impact of de novo mutational events, somatic variation underlying nononcologic traits, incompletely penetrant alleles, phenotypes with high locus heterogeneity, and multilocus pathogenic variation. Herein, we highlight CMG collaborative discoveries that have contributed to understanding both rare and common diseases and discuss opportunities for future discovery in single-locus Mendelian disorder genomics. Phenotypic annotation of all human genes; development of bioinformatic tools and analytic methods; exploration of non-Mendelian modes of inheritance including reduced penetrance, multilocus variation, and oligogenic inheritance; construction of allelic series at a locus; enhanced data sharing worldwide; and integration with clinical genomics are explored. Realizing the full contribution of rare disease research to functional annotation of the human genome, and further illuminating human biology and health, will lay the foundation for the Precision Medicine Initiative.
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Affiliation(s)
- Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Anne H O'Donnell-Luria
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Tamar Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Shalini N Jhangiani
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep H Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Steven Buyske
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
- Department of Statistics, Rutgers University, Piscataway, NJ, USA
| | - Davut Pehlivan
- 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
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
| | - Nan Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sushant Kumar
- Computational Biology and Bioinformatics Program, Yale University Medical School, New Haven, CT, USA
| | - Dimitri Avramopoulos
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Kimberly F Doheny
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - P Dane Witmer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Corinne Boehm
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric Boerwinkle
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Human Genetics Center, University of Texas Health Science Center, Houston, TX, USA
| | - Murat Günel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Shrikant Mane
- Yale Center for Genome Analysis, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Richard P Lifton
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - Heidi L Rehm
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark Gerstein
- Computational Biology and Bioinformatics Program, Yale University Medical School, New Haven, CT, USA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
- Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA.
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17
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Coban-Akdemir Z, White JJ, Song X, Jhangiani SN, Fatih JM, Gambin T, Bayram Y, Chinn IK, Karaca E, Punetha J, Poli C, Boerwinkle E, Shaw CA, Orange JS, Gibbs RA, Lappalainen T, Lupski JR, Carvalho CM, Carvalho CMB. Identifying Genes Whose Mutant Transcripts Cause Dominant Disease Traits by Potential Gain-of-Function Alleles. Am J Hum Genet 2018; 103:171-187. [PMID: 30032986 DOI: 10.1016/j.ajhg.2018.06.009] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/14/2018] [Indexed: 12/14/2022] Open
Abstract
Premature termination codon (PTC)-bearing transcripts are often degraded by nonsense-mediated decay (NMD) resulting in loss-of-function (LoF) alleles. However, not all PTCs result in LoF mutations, i.e., some such transcripts escape NMD and are translated to truncated peptide products that result in disease due to gain-of-function (GoF) effects. Since the location of the PTC is a major factor determining transcript fate, we hypothesized that depletion of protein-truncating variants (PTVs) within the gene region predicted to escape NMD in control databases could provide a rank for genic susceptibility for disease through GoF versus LoF. We developed an NMD escape intolerance score to rank genes based on the depletion of PTVs that would render them able to escape NMD using the Atherosclerosis Risk in Communities Study (ARIC) and the Exome Aggregation Consortium (ExAC) control databases, which was further used to screen the Baylor-Center for Mendelian Genomics disease database. This analysis revealed 1,996 genes significantly depleted for PTVs that are predicted to escape from NMD, i.e., PTVesc; further studies provided evidence that revealed a subset as candidate genes underlying Mendelian phenotypes. Importantly, these genes have characteristically low pLI scores, which can cause them to be overlooked as candidates for dominant diseases. Collectively, we demonstrate that this NMD escape intolerance score is an effective and efficient tool for gene discovery in Mendelian diseases due to production of truncated or altered proteins. More importantly, we provide a complementary analytical tool to aid identification of genes associated with dominant traits through a mechanism distinct from LoF.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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18
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Sisk RA, Hufnagel RB, Laham A, Wohler ES, Sobreira N, Ahmed ZM. Peripheral Cone Dystrophy: Expanded Clinical Spectrum, Multimodal and Ultrawide-Field Imaging, and Genomic Analysis. J Ophthalmol 2018; 2018:2984934. [PMID: 30116628 PMCID: PMC6079493 DOI: 10.1155/2018/2984934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/19/2018] [Accepted: 05/02/2018] [Indexed: 12/30/2022] Open
Abstract
PURPOSE To present new clinical features, multimodal and ultrawide-field imaging characteristics of peripheral cone dystrophy (PCD), and results of laboratory and genetic investigation to decipher the etiology. METHODS Retrospective observational case-series. RESULTS Three patients with PCD presented with bilateral paracentral scotomas and a mean visual acuity of 20/25. All exhibited confluent macular hyperautofluorescence with a central bull's eye lesion. Spectral-domain optical coherence tomography revealed loss of outer retinal elements, particularly the inner segment ellipsoid band and external limiting membrane, within the area of macular hyperautofluorescence. This area corresponded with a lightened fundus appearance and variable retinal pigment epithelium (RPE) abnormalities. Full field and multifocal electroretinography distinguished PCD from other photoreceptor dystrophies. Ultrawide-field imaging revealed irregular peripheral retinal lesions in a distribution greater nasally than temporally and not contiguous with the macular lesion. Functional and anatomic testing remained stable over a mean follow-up of 3 years. Laboratory investigation for causes of uveitis was negative. Whole exome sequencing identified rare variants in genes associated with macular or cone dystrophy or degeneration. CONCLUSIONS In contrast to the original description, the funduscopic and fluorescein angiographic appearance of PCD is abnormal, although the defects are subtle. Peripheral lesions may be observed in some patients. Bilateral, symmetric, macular hyperautofluorescence associated with outer retinal atrophy that spares the fovea is a characteristic of PCD. Pathogenic variants in the same gene were not shared across the cohort, suggesting genetic heterogeneity. Further evaluation is warranted.
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Affiliation(s)
- Robert A. Sisk
- Department of Ophthalmology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Cincinnati Eye Institute, Cincinnati, OH, USA
- Division of Pediatric Ophthalmology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Robert B. Hufnagel
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ailee Laham
- Department of Ophthalmology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Elizabeth S. Wohler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology, School of Medicine, University of Maryland, Baltimore, MD, USA
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19
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Faber I, Martinez ARM, de Rezende TJR, Martins CR, Martins MP, Lourenço CM, Marques W, Montecchiani C, Orlacchio A, Pedroso JL, Barsottini OGP, Lopes-Cendes Í, França MC. SPG11 mutations cause widespread white matter and basal ganglia abnormalities, but restricted cortical damage. Neuroimage Clin 2018; 19:848-857. [PMID: 29946510 PMCID: PMC6008284 DOI: 10.1016/j.nicl.2018.05.031] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 05/20/2018] [Accepted: 05/22/2018] [Indexed: 12/12/2022]
Abstract
SPG11 mutations are the major cause of autosomal recessive Hereditary Spastic Paraplegia. The disease has a wide phenotypic variability indicating many regions of the nervous system besides the corticospinal tract are affected. Despite this, anatomical and phenotypic characterization is restricted. In the present study, we investigate the anatomical abnormalities related to SPG11 mutations and how they relate to clinical and cognitive measures. Moreover, we aim to depict how the disease course influences the regions affected, unraveling different susceptibility of specific neuronal populations. We performed clinical and paraclinical studies encompassing neuropsychological, neuroimaging, and neurophysiological tools in a cohort of twenty-five patients and age matched controls. We assessed cortical thickness (FreeSurfer software), deep grey matter volumes (T1-MultiAtlas tool), white matter microstructural damage (DTI-MultiAtlas) and spinal cord morphometry (Spineseg software) on a 3 T MRI scan. Mean age and disease duration were 29 and 13.2 years respectively. Sixty-four percent of the patients were wheelchair bound while 84% were demented. We were able to unfold a diffuse pattern of white matter integrity loss as well as basal ganglia and spinal cord atrophy. Such findings contrasted with a restricted pattern of cortical thinning (motor, limbic and parietal cortices). Electromyography revealed motor neuronopathy affecting 96% of the probands. Correlations with disease duration pointed towards a progressive degeneration of multiple grey matter structures and spinal cord, but not of the white matter. SPG11-related hereditary spastic paraplegia is characterized by selective neuronal vulnerability, in which a precocious and widespread white matter involvement is later followed by a restricted but clearly progressive grey matter degeneration.
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Key Words
- ACE-R, Addenbrooke's Cognitive Examination Revised
- ALS, amyotrophic lateral sclerosis
- CA, cord area
- CE, cord eccentricity
- CMAP, compound muscle action potential
- CST, corticospinal tract
- Complicated hereditary spastic paraplegia
- DTI, diffusion tensor imaging
- FA, fractional anisotropy
- GM, grey matter
- Grey matter
- HSP, hereditary spastic paraplegia
- LH, left hemisphere
- MD, mean diffusivity
- MOCA, Montreal cognitive assessment
- Motor neuron disorder
- NPI, neuropsychiatric inventory
- PNP, sensory-motor polyneuropathy
- PNS, peripheral nervous system
- RH, right hemisphere
- ROI, region of interest
- SC, spinal cord
- SNAP, sensory nerve action potential
- SPG11
- SPRS, Spastic Paraplegia Rating Scale
- STS, cortex adjacent to the superior temporal sulcus
- Spinal cord
- Thinning of the corpus callosum
- WES, whole exome sequencing
- WM, white matter
- White matter
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Affiliation(s)
- Ingrid Faber
- Department of Neurology, University of Campinas (UNICAMP), Campinas, Brazil
| | | | | | | | | | | | - Wilson Marques
- Department of Neurology, University of São Paulo (USP-RP), Ribeirão Preto, Brazil
| | - Celeste Montecchiani
- Laboratorio di Neurogenetica, Centro Europeo di Ricerca sul Cervello (CERC) - Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia, Rome, Italy
| | - Antonio Orlacchio
- Laboratorio di Neurogenetica, Centro Europeo di Ricerca sul Cervello (CERC) - Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia, Rome, Italy; Dipartimento di Scienze Chirurgiche e Biomediche, Università di Perugia, Perugia, Italy
| | - Jose Luiz Pedroso
- Department of Neurology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | | | - Íscia Lopes-Cendes
- Department of Medical Genetics, University of Campinas (UNICAMP), Campinas, Brazil
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20
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Gong X, Jiang J, Duan Z, Lu H. A new method to measure the semantic similarity from query phenotypic abnormalities to diseases based on the human phenotype ontology. BMC Bioinformatics 2018; 19:162. [PMID: 29745853 PMCID: PMC5998886 DOI: 10.1186/s12859-018-2064-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background Although rapid developed sequencing technologies make it possible for genotype data to be used in clinical diagnosis, it is still challenging for clinicians to understand the results of sequencing and make correct judgement based on them. Before this, diagnosis based on clinical features held a leading position. With the establishment of the Human Phenotype Ontology (HPO) and the enrichment of phenotype-disease annotations, there throws much more attention to the improvement of phenotype-based diagnosis. Results In this study, we presented a novel method called RelativeBestPair to measure similarity from the query terms to hereditary diseases based on HPO and then rank the candidate diseases. To evaluate the performance, we simulated a set of patients based on 44 complex diseases. Besides, by adding noise or imprecision or both, cases closer to real clinical conditions were generated. Thus, four simulated datasets were used to make comparison among RelativeBestPair and seven existing semantic similarity measures. RelativeBestPair ranked the underlying disease as top 1 on 93.73% of the simulated dataset without noise and imprecision, 93.64% of the simulated dataset with noise and without imprecision, 39.82% of the simulated dataset without noise and with imprecision, and 33.64% of the simulated dataset with both noise and imprecision. Conclusion Compared with the seven existing semantic similarity measures, RelativeBestPair showed similar performance in two datasets without imprecision. While RelativeBestPair appeared to be equal to Resnik and better than other six methods in the simulated dataset without noise and with imprecision, it significantly outperformed all other seven methods in the simulated dataset with both noise and imprecision. It can be indicated that RelativeBestPair might be of great help in clinical setting.
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Affiliation(s)
- Xiaofeng Gong
- Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Jianping Jiang
- Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Zhongqu Duan
- Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Lu
- Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China.
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21
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Patients with a Kabuki syndrome phenotype demonstrate DNA methylation abnormalities. Eur J Hum Genet 2017; 25:1335-1344. [PMID: 29255178 DOI: 10.1038/s41431-017-0023-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 09/20/2017] [Accepted: 09/22/2017] [Indexed: 01/05/2023] Open
Abstract
Kabuki syndrome is a monogenic disorder caused by loss of function variants in either of two genes encoding histone-modifying enzymes. We performed targeted sequencing in a cohort of 27 probands with a clinical diagnosis of Kabuki syndrome. Of these, 12 had causative variants in the two known Kabuki syndrome genes. In 2, we identified presumptive loss of function de novo variants in KMT2A (missense and splice site variants), a gene that encodes another histone modifying enzyme previously exclusively associated with Wiedermann-Steiner syndrome. Although Kabuki syndrome is a disorder of histone modification, we also find alterations in DNA methylation among individuals with a Kabuki syndrome diagnosis relative to matched normal controls, regardless of whether they carry a variant in KMT2A or KMT2D or not. Furthermore, we observed characteristic global abnormalities of DNA methylation that distinguished patients with a loss of function variant in KMT2D or missense or splice site variants in either KMT2D or KMT2A from normal controls. Our results provide new insights into the relationship of genotype to epigenotype and phenotype and indicate cross-talk between histone and DNA methylation machineries exposed by inborn errors of the epigenetic apparatus.
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22
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Eilbeck K, Quinlan A, Yandell M. Settling the score: variant prioritization and Mendelian disease. Nat Rev Genet 2017; 18:599-612. [PMID: 28804138 PMCID: PMC5935497 DOI: 10.1038/nrg.2017.52] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
When investigating Mendelian disease using exome or genome sequencing, distinguishing disease-causing genetic variants from the multitude of candidate variants is a complex, multidimensional task. Many prioritization tools and online interpretation resources exist, and professional organizations have offered clinical guidelines for review and return of prioritization results. In this Review, we describe the strengths and weaknesses of widely used computational approaches, explain their roles in the diagnostic and discovery process and discuss how they can inform (and misinform) expert reviewers. We place variant prioritization in the wider context of gene prioritization, burden testing and genotype-phenotype association, and we discuss opportunities and challenges introduced by whole-genome sequencing.
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Affiliation(s)
- Karen Eilbeck
- Department of Biomedical Informatics, School of Medicine, University of Utah, 421 Wakara Way, Suite 120, Salt Lake City, Utah 84108, USA
| | - Aaron Quinlan
- Department of Biomedical Informatics, School of Medicine, University of Utah, 421 Wakara Way, Suite 120, Salt Lake City, Utah 84108, USA
- Department of Human Genetics, Eccles Institute of Human Genetics, School of Medicine, University of Utah, 15 S 2030 E, Salt Lake City, Utah 84112, USA
| | - Mark Yandell
- Department of Human Genetics, Eccles Institute of Human Genetics, School of Medicine, University of Utah, 15 S 2030 E, Salt Lake City, Utah 84112, USA
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23
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Wangler MF, Yamamoto S, Chao HT, Posey JE, Westerfield M, Postlethwait J, Hieter P, Boycott KM, Campeau PM, Bellen HJ. Model Organisms Facilitate Rare Disease Diagnosis and Therapeutic Research. Genetics 2017; 207:9-27. [PMID: 28874452 PMCID: PMC5586389 DOI: 10.1534/genetics.117.203067] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/06/2017] [Indexed: 12/29/2022] Open
Abstract
Efforts to identify the genetic underpinnings of rare undiagnosed diseases increasingly involve the use of next-generation sequencing and comparative genomic hybridization methods. These efforts are limited by a lack of knowledge regarding gene function, and an inability to predict the impact of genetic variation on the encoded protein function. Diagnostic challenges posed by undiagnosed diseases have solutions in model organism research, which provides a wealth of detailed biological information. Model organism geneticists are by necessity experts in particular genes, gene families, specific organs, and biological functions. Here, we review the current state of research into undiagnosed diseases, highlighting large efforts in North America and internationally, including the Undiagnosed Diseases Network (UDN) (Supplemental Material, File S1) and UDN International (UDNI), the Centers for Mendelian Genomics (CMG), and the Canadian Rare Diseases Models and Mechanisms Network (RDMM). We discuss how merging human genetics with model organism research guides experimental studies to solve these medical mysteries, gain new insights into disease pathogenesis, and uncover new therapeutic strategies.
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Affiliation(s)
- Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Pediatrics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Neuroscience, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Hsiao-Tuan Chao
- Department of Pediatrics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Department of Pediatrics, Section of Child Neurology, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Monte Westerfield
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4C, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ontario K1H 8L1, Canada
| | - Philippe M Campeau
- Department of Pediatrics, University of Montreal, Quebec H3T 1C5, Canada
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Neuroscience, Baylor College of Medicine (BCM), Houston, Texas 77030
- Howard Hughes Medical Institute, Baylor College of Medicine (BCM), Houston, Texas 77030
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24
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Telegrafi A, Webb BD, Robbins SM, Speck-Martins CE, FitzPatrick D, Fleming L, Redett R, Dufke A, Houge G, van Harssel JJT, Verloes A, Robles A, Manoli I, Engle EC, Jabs EW, Valle D, Carey J, Hoover-Fong JE, Sobreira NLM. Identification of STAC3 variants in non-Native American families with overlapping features of Carey-Fineman-Ziter syndrome and Moebius syndrome. Am J Med Genet A 2017; 173:2763-2771. [PMID: 28777491 DOI: 10.1002/ajmg.a.38375] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/26/2017] [Accepted: 07/01/2017] [Indexed: 11/07/2022]
Abstract
Horstick et al. (2013) previously reported a homozygous p.Trp284Ser variant in STAC3 as the cause of Native American myopathy (NAM) in 5 Lumbee Native American families with congenital hypotonia and weakness, cleft palate, short stature, ptosis, kyphoscoliosis, talipes deformities, and susceptibility to malignant hyperthermia (MH). Here we present two non-Native American families, who were found to have STAC3 pathogenic variants. The first proband and her affected older sister are from a consanguineous Qatari family with a suspected clinical diagnosis of Carey-Fineman-Ziter syndrome (CFZS) based on features of hypotonia, myopathic facies with generalized weakness, ptosis, normal extraocular movements, cleft palate, growth delay, and kyphoscoliosis. We identified the homozygous c.851G>C;p.Trp284Ser variant in STAC3 in both sisters. The second proband and his affected sister are from a non-consanguineous, Puerto Rican family who was evaluated for a possible diagnosis of Moebius syndrome (MBS). His features included facial and generalized weakness, minimal limitation of horizontal gaze, cleft palate, and hypotonia, and he has a history of MH. The siblings were identified to be compound heterozygous for STAC3 variants c.851G>C;p.Trp284Ser and c.763_766delCTCT;p.Leu255IlefsX58. Given the phenotypic overlap of individuals with CFZS, MBS, and NAM, we screened STAC3 in 12 individuals diagnosed with CFZS and in 50 individuals diagnosed with MBS or a congenital facial weakness disorder. We did not identify any rare coding variants in STAC3. NAM should be considered in patients presenting with facial and generalized weakness, normal or mildly abnormal extraocular movement, hypotonia, cleft palate, and scoliosis, particularly if there is a history of MH.
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Affiliation(s)
| | - Bryn D Webb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sarah M Robbins
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - David FitzPatrick
- Human Genetics Unit, Medical and Developmental Genetics, University of Edinburgh Western General Hospital, Edinburgh, United Kingdom
| | - Leah Fleming
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Richard Redett
- Department of Plastic & Reconstructive Surgery, Johns Hopkins Hospital University School of Medicine, Baltimore, Maryland
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Rare Disease Center, University of Tübingen, Tübingen, Germany
| | - Gunnar Houge
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Jeske J T van Harssel
- Department of Clinical Genetics, University Medical Center, University of Utrecht, Utrecht, The Netherlands
| | - Alain Verloes
- Department of Genetics-Hospital Robert DEBRE, Paris, France
| | - Angela Robles
- Dr. Angela Robles Pediatrics Private Practice, San Sebastian, Puerto Rico
| | - Irini Manoli
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Elizabeth C Engle
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts.,Department of Ophthalmology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts.,Howard Hughes Medical Institution, Chevy Chase, Maryland
| | | | - Ethylin W Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - John Carey
- Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Julie E Hoover-Fong
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Greenberg Center for Skeletal Dysplasias, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nara L M Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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25
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Boycott KM, Rath A, Chong JX, Hartley T, Alkuraya FS, Baynam G, Brookes AJ, Brudno M, Carracedo A, den Dunnen JT, Dyke SOM, Estivill X, Goldblatt J, Gonthier C, Groft SC, Gut I, Hamosh A, Hieter P, Höhn S, Hurles ME, Kaufmann P, Knoppers BM, Krischer JP, Macek M, Matthijs G, Olry A, Parker S, Paschall J, Philippakis AA, Rehm HL, Robinson PN, Sham PC, Stefanov R, Taruscio D, Unni D, Vanstone MR, Zhang F, Brunner H, Bamshad MJ, Lochmüller H. International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases. Am J Hum Genet 2017; 100:695-705. [PMID: 28475856 PMCID: PMC5420351 DOI: 10.1016/j.ajhg.2017.04.003] [Citation(s) in RCA: 245] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Provision of a molecularly confirmed diagnosis in a timely manner for children and adults with rare genetic diseases shortens their "diagnostic odyssey," improves disease management, and fosters genetic counseling with respect to recurrence risks while assuring reproductive choices. In a general clinical genetics setting, the current diagnostic rate is approximately 50%, but for those who do not receive a molecular diagnosis after the initial genetics evaluation, that rate is much lower. Diagnostic success for these more challenging affected individuals depends to a large extent on progress in the discovery of genes associated with, and mechanisms underlying, rare diseases. Thus, continued research is required for moving toward a more complete catalog of disease-related genes and variants. The International Rare Diseases Research Consortium (IRDiRC) was established in 2011 to bring together researchers and organizations invested in rare disease research to develop a means of achieving molecular diagnosis for all rare diseases. Here, we review the current and future bottlenecks to gene discovery and suggest strategies for enabling progress in this regard. Each successful discovery will define potential diagnostic, preventive, and therapeutic opportunities for the corresponding rare disease, enabling precision medicine for this patient population.
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Affiliation(s)
- Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada.
| | - Ana Rath
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Research Center, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Gareth Baynam
- Genetic Services of Western Australia, Perth, WA 6008, Australia
| | - Anthony J Brookes
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto M5S 1A1, Canada
| | - Angel Carracedo
- Genomic Medicine Group, Galician Foundation of Genomic Medicine and University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Johan T den Dunnen
- Departments of Human Genetics and Clinical Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Stephanie O M Dyke
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3A 1A4, Canada
| | - Xavier Estivill
- Experimental Division, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar; Genetics Unit, Dexeus Woman's Health, 08028 Barcelona, Spain
| | - Jack Goldblatt
- Genetic Services of Western Australia, Perth, WA 6008, Australia
| | - Catherine Gonthier
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Stephen C Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-4874, USA
| | - Ivo Gut
- Centre Nacional d'Anàlisi Genòmica, Center for Genomic Regulation, Barcelona Institute of Science and Technology, Universitat Pompeu Fabra, 08028 Barcelona, Spain
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21286, USA
| | - Philip Hieter
- Michael Smith Laboratories, Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sophie Höhn
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Petra Kaufmann
- Office of Rare Diseases Research, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-4874, USA
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3A 1A4, Canada
| | - Jeffrey P Krischer
- University of South Florida Health Informatics Institute, Tampa, FL 33620, USA
| | - Milan Macek
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, 150 06 Prague 5, Czech Republic
| | - Gert Matthijs
- Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Annie Olry
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | | | - Justin Paschall
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | | | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter N Robinson
- Institut für Medizinische Genetik und Humangenetik, Charité Universitätsmdizin Berlin, 13353 Berlin, Germany; Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Pak-Chung Sham
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong, China
| | - Rumen Stefanov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv 4002, Bulgaria
| | - Domenica Taruscio
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome 299-00161, Italy
| | - Divya Unni
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Megan R Vanstone
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Feng Zhang
- WuXi AppTec, Waigaoqiao Free Trade Zone, Shanghai 200131, China; WuXi NextCODE, Cambridge, MA 02142, USA
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Maastricht University Medical Center, Department of Clinical Genetics, 6229 GT Maastricht, the Netherlands
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
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26
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Eldomery MK, Coban-Akdemir Z, Harel T, Rosenfeld JA, Gambin T, Stray-Pedersen A, Küry S, Mercier S, Lessel D, Denecke J, Wiszniewski W, Penney S, Liu P, Bi W, Lalani SR, Schaaf CP, Wangler MF, Bacino CA, Lewis RA, Potocki L, Graham BH, Belmont JW, Scaglia F, Orange JS, Jhangiani SN, Chiang T, Doddapaneni H, Hu J, Muzny DM, Xia F, Beaudet AL, Boerwinkle E, Eng CM, Plon SE, Sutton VR, Gibbs RA, Posey JE, Yang Y, Lupski JR. Lessons learned from additional research analyses of unsolved clinical exome cases. Genome Med 2017; 9:26. [PMID: 28327206 PMCID: PMC5361813 DOI: 10.1186/s13073-017-0412-6] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 02/08/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease. Pilot project data included 74 families, consisting mostly of parent-offspring trios. Analyses performed on a research basis employed both WES from additional family members and complementary bioinformatics approaches and protocols. RESULTS Analysis of all possible modes of Mendelian inheritance, focusing on both single nucleotide variants (SNV) and copy number variant (CNV) alleles, yielded a likely contributory variant in 36% (27/74) of cases. If one includes candidate genes with variants identified within a single family, a potential contributory variant was identified in a total of ~51% (38/74) of cases enrolled in this pilot study. The molecular diagnosis was achieved in 30/63 trios (47.6%). Besides this, the analysis workflow yielded evidence for pathogenic variants in disease-associated genes in 4/6 singleton cases (66.6%), 1/1 multiplex family involving three affected siblings, and 3/4 (75%) quartet families. Both the analytical pipeline and the collaborative efforts between the diagnostic and research laboratories provided insights that allowed recent disease gene discoveries (PURA, TANGO2, EMC1, GNB5, ATAD3A, and MIPEP) and increased the number of novel genes, defined in this study as genes identified in more than one family (DHX30 and EBF3). CONCLUSION An efficient genomics pipeline in which clinical sequencing in a diagnostic laboratory is followed by the detailed reanalysis of unsolved cases in a research environment, supplemented with WES data from additional family members, and subject to adjuvant bioinformatics analyses including relaxed variant filtering parameters in informatics pipelines, can enhance the molecular diagnostic yield and provide mechanistic insights into Mendelian disorders. Implementing these approaches requires collaborative clinical molecular diagnostic and research efforts.
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Affiliation(s)
- Mohammad K. Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Present Address: Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, 350 W. 11th Street, Indianapolis, IN 46202 USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Institute of Computer Science, Warsaw University of Technology, 00-665 Warsaw, Poland
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Women and Children’s Division, Oslo University Hospital, 0424 Oslo, Norway
| | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, CEDEX 1 France
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, CEDEX 1 France
- Atlantic Gene Therapies, UMR1089, Nantes, France
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Wojciech Wiszniewski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Samantha Penney
- Department of Molecular and Human Genetics, 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, Baylor College of Medicine, Houston, TX 77030 USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Christian P. Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030 USA
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Richard Alan Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030 USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Brett H. Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - John W. Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Jordan S. Orange
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital Center for Human Immuno-Biology, Houston, TX USA
| | - Shalini N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Theodore Chiang
- 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
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, 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, Houston, TX 77030 USA
| | - Christine M. Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Sharon E. Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Cancer Center, Texas Children’s Hospital, Houston, TX 7703 USA
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, 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
- Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor 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
- Texas Children’s Hospital, 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
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX 77030-3498 USA
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27
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Fiallos K, Applegate C, Mathews DJ, Bollinger J, Bergner AL, James CA. Choices for return of primary and secondary genomic research results of 790 members of families with Mendelian disease. Eur J Hum Genet 2017; 25:530-537. [PMID: 28272539 DOI: 10.1038/ejhg.2017.21] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 01/26/2017] [Accepted: 02/01/2017] [Indexed: 01/12/2023] Open
Abstract
Although consensus is building that primary (PR) and secondary findings (SF) from genomic research should be offered to participants under some circumstances, data describing (1) actual choices of study participants and (2) factors associated with these choices are limited, hampering study planning. We conducted a cross-sectional analysis of choices made for return of PR and SF during informed consent by members of the first 247 families (790 individuals) enrolled in the Baylor-Hopkins Center for Mendelian Genomics, a genome sequencing study. Most (619; 78.3%) chose to receive SF and PR, 66 (8.4%) chose PR only, 65 (8.2%) wanted no results, and 40 (5.1%) chose SF only. Choosing SF was associated with an established clinical diagnosis in the proband (87.8 vs 79%, P=0.009) and European ancestry (EA) (87.7 vs 73%, P<0.008). Participants of non-European ancestry (NEA) were as likely as those of EA to choose SF when consented by a genetic counselor (GC) (82% NEA vs 88.3% EA, P=0.09) but significantly less likely when consented by a physician (67.4% NEA vs 85.4% EA, P=0.001). Controlling for proband diagnosis, individuals of NEA were 2.13-fold (95% CI: 1.11-4.08) more likely to choose SF when consented by a GC rather than a physician. Participants of NEA were 3-fold more likely than those of EA to decline all study results (14.7% NEA vs 5.4% EA, P<0.008). In this ethnically diverse population, whereas most participants desired PR and SF, more than 20% declined some or all results, highlighting the importance of research participant choice.
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Affiliation(s)
- Katie Fiallos
- National Human Genome Research Institute, NIH, Bethesda, MD, USA.,Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Carolyn Applegate
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Debra Jh Mathews
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.,Berman Institute of Bioethics, Johns Hopkins University, Baltimore, MD, USA
| | - Juli Bollinger
- Berman Institute of Bioethics, Johns Hopkins University, Baltimore, MD, USA
| | - Amanda L Bergner
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.,Ambry Genetics, Inc., Aliso Viejo, CA, USA
| | - Cynthia A James
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, USA
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28
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Orenstein N, Weiss K, Oprescu SN, Shapira R, Kidron D, Vanagaite-Basel L, Antonellis A, Muenke M. Bi-allelic IARS mutations in a child with intra-uterine growth retardation, neonatal cholestasis, and mild developmental delay. Clin Genet 2017; 91:913-917. [PMID: 27891590 DOI: 10.1111/cge.12930] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 12/14/2022]
Abstract
Recently, bi-allelic mutations in cytosolic isoleucyl-tRNA synthetase (IARS) have been described in three individuals with growth delay, hepatic dysfunction, and neurodevelopmental disabilities. Here we report an additional subject with this condition identified by whole-exome sequencing. Our findings support the association between this disorder and neonatal cholestasis with distinct liver pathology. Furthermore, we provide functional data on two novel missense substitutions and expand the phenotype to include mild developmental delay, skin hyper-elasticity, and hypervitaminosis D.
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Affiliation(s)
- N Orenstein
- Department of Pediatric Genetics, Schneider Children Medical Center of Israel, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - K Weiss
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - S N Oprescu
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - R Shapira
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - D Kidron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Pathology, Meir Hospital, Kfar Saba, Israel
| | - L Vanagaite-Basel
- Department of Pediatric Genetics, Schneider Children Medical Center of Israel, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Raphael Recanati Genetics Institute, Rabin Medical Center, Petah Tikva, Israel.,Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikvay, Israel
| | - A Antonellis
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - M Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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29
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Schossig A, Bloch-Zupan A, Lussi A, Wolf NI, Raskin S, Cohen M, Giuliano F, Jurgens J, Krabichler B, Koolen DA, de Macena Sobreira NL, Maurer E, Muller-Bolla M, Penzien J, Zschocke J, Kapferer-Seebacher I. SLC13A5 is the second gene associated with Kohlschütter-Tönz syndrome. J Med Genet 2016; 54:54-62. [PMID: 27600704 DOI: 10.1136/jmedgenet-2016-103988] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/12/2016] [Accepted: 08/01/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND Kohlschütter-Tönz syndrome (KTZS) is a rare autosomal-recessive disease characterised by epileptic encephalopathy, intellectual disability and amelogenesis imperfecta (AI). It is frequently caused by biallelic mutations in ROGDI. Here, we report on individuals with ROGDI-negative KTZS carrying biallelic SLC13A5 mutations. METHODS In the present cohort study, nine individuals from four families with the clinical diagnosis of KTZS and absence of ROGDI mutations as well as one patient with unexplained epileptic encephalopathy were investigated by clinical and dental evaluation, parametric linkage analysis (one family), and exome and/or Sanger sequencing. Dental histological investigations were performed on teeth from individuals with SLC13A5-associated and ROGDI-associated KTZS. RESULTS Biallelic mutations in SLC13A5 were identified in 10 affected individuals. Epileptic encephalopathy usually presents in the neonatal and (less frequently) early infantile period. Yellowish to orange discolouration of both deciduous and permanent teeth, as well as wide interdental spaces and abnormal crown forms are major clinical signs of individuals with biallelic SLC13A5 mutations. Histological dental investigations confirmed the clinical diagnosis of hypoplastic AI. In comparison, the histological evaluation of a molar assessed from an individual with ROGDI-associated KTZS revealed hypocalcified AI. CONCLUSIONS We conclude that SLC13A5 is the second major gene associated with the clinical diagnosis of KTZS, characterised by neonatal epileptic encephalopathy and hypoplastic AI. Careful clinical and dental delineation provides clues whether ROGDI or SLC13A5 is the causative gene. Hypersensitivity of teeth as well as high caries risk requires individual dental prophylaxis and attentive dental management.
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Affiliation(s)
- Anna Schossig
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Agnès Bloch-Zupan
- Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France.,Pôle de Médecine et Chirurgie Bucco-dentaires, Centre de Référence des Manifestations Odontologiques des Maladies Rares, Hôpitaux Universitaires de Strasbourg (HUS), Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire and Cellulaire-Centre Européen de Recherche en Biologie et en Médecine, Université de Strasbourg, IGBMC-CERBM CNRS UMR7104, INSERM U964, Illkirch, France
| | - Adrian Lussi
- Department of Preventive, Restorative and Pediatric Dentistry, School of Dental Medicine, University of Bern, Bern, Switzerland
| | - Nicole I Wolf
- Department of Child Neurology, VU University Medical Center, Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
| | - Salmo Raskin
- Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Brazil.,Genetika-Centro de Aconselhamento e Laboratório de Genética, Curitiba, Brazil
| | - Monika Cohen
- kbo-Kinderzentrum München gGmbH, Munich, Germany
| | - Fabienne Giuliano
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs PACA, Service de Génétique Médicale, CHU Nice, Nice, France
| | - Julie Jurgens
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Birgit Krabichler
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - David A Koolen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nara Lygia de Macena Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elisabeth Maurer
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Michèle Muller-Bolla
- UFR Odontologie, Département d'Odontologie Pédiatrique, Université de Nice Sophia-Antipolis, UCA, Nice, France.,CHU de Nice, Pôle Odontologie, UF soins pour enfants; Laboratory URB2i-EA 4462, Paris Descartes, France
| | - Johann Penzien
- Department of Neuropaediatrics, Klinikum Augsburg, Augsburg, Germany
| | - Johannes Zschocke
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Ines Kapferer-Seebacher
- Department of Operative and Restorative Dentistry, Medical University of Innsbruck, Innsbruck, Austria
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30
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Charng WL, Karaca E, Coban Akdemir Z, Gambin T, Atik MM, Gu S, Posey JE, Jhangiani SN, Muzny DM, Doddapaneni H, Hu J, Boerwinkle E, Gibbs RA, Rosenfeld JA, Cui H, Xia F, Manickam K, Yang Y, Faqeih EA, Al Asmari A, Saleh MAM, El-Hattab AW, Lupski JR. Exome sequencing in mostly consanguineous Arab families with neurologic disease provides a high potential molecular diagnosis rate. BMC Med Genomics 2016; 9:42. [PMID: 27435318 PMCID: PMC4950750 DOI: 10.1186/s12920-016-0208-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/08/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Neurodevelopment is orchestrated by a wide range of genes, and the genetic causes of neurodevelopmental disorders are thus heterogeneous. We applied whole exome sequencing (WES) for molecular diagnosis and in silico analysis to identify novel disease gene candidates in a cohort from Saudi Arabia with primarily Mendelian neurologic diseases. METHODS We performed WES in 31 mostly consanguineous Arab families and analyzed both single nucleotide and copy number variants (CNVs) from WES data. Interaction/expression network and pathway analyses, as well as paralog studies were utilized to investigate potential pathogenicity and disease association of novel candidate genes. Additional cases for candidate genes were identified through the clinical WES database at Baylor Miraca Genetics Laboratories and GeneMatcher. RESULTS We found known pathogenic or novel variants in known disease genes with phenotypic expansion in 6 families, disease-associated CNVs in 2 families, and 12 novel disease gene candidates in 11 families, including KIF5B, GRM7, FOXP4, MLLT1, and KDM2B. Overall, a potential molecular diagnosis was provided by variants in known disease genes in 17 families (54.8 %) and by novel candidate disease genes in an additional 11 families, making the potential molecular diagnostic rate ~90 %. CONCLUSIONS Molecular diagnostic rate from WES is improved by exome-predicted CNVs. Novel candidate disease gene discovery is facilitated by paralog studies and through the use of informatics tools and available databases to identify additional evidence for pathogenicity. TRIAL REGISTRATION Not applicable.
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Affiliation(s)
- Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA
| | - Mehmed M Atik
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA
| | - Shalini N Jhangiani
- The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Harsha Doddapaneni
- The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jianhong Hu
- The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA.,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, Houston, TX, 77030, USA
| | - Richard A Gibbs
- The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX, 77030, USA
| | - Hong Cui
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX, 77030, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX, 77030, USA
| | - Kandamurugu Manickam
- Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX, 77030, USA
| | - Eissa A Faqeih
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Ali Al Asmari
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed A M Saleh
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Department of Pediatrics, Tawam Hospital, Al-Ain, United Arab Emirates
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. .,The Baylor-Hopkins Center for Mendelian Genomics, 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. .,Department of Pediatrics, Texas Children's Hospital, Houston, TX, 77030, USA.
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Lelieveld SH, Veltman JA, Gilissen C. Novel bioinformatic developments for exome sequencing. Hum Genet 2016; 135:603-14. [PMID: 27075447 PMCID: PMC4883269 DOI: 10.1007/s00439-016-1658-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/15/2016] [Indexed: 01/19/2023]
Abstract
With the widespread adoption of next generation sequencing technologies by the genetics community and the rapid decrease in costs per base, exome sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers standard solutions for the analysis of exome sequencing data, many challenges still remain; especially the increasing scale at which exome data are now being generated has given rise to novel challenges in how to efficiently store, analyze and interpret exome data of this magnitude. In this review we discuss some of the recent developments in bioinformatics for exome sequencing and the directions that this is taking us to. With these developments, exome sequencing is paving the way for the next big challenge, the application of whole genome sequencing.
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Affiliation(s)
- Stefan H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
- Department of Clinical Genetics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
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32
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Robinson PN, Mungall CJ, Haendel M. Capturing phenotypes for precision medicine. Cold Spring Harb Mol Case Stud 2016; 1:a000372. [PMID: 27148566 PMCID: PMC4850887 DOI: 10.1101/mcs.a000372] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Deep phenotyping followed by integrated computational analysis of genotype and phenotype is becoming ever more important for many areas of genomic diagnostics and translational research. The overwhelming majority of clinical descriptions in the medical literature are available only as natural language text, meaning that searching, analysis, and integration of medically relevant information in databases such as PubMed is challenging. The new journal Cold Spring Harbor Molecular Case Studies will require authors to select Human Phenotype Ontology terms for research papers that will be displayed alongside the manuscript, thereby providing a foundation for ontology-based indexing and searching of articles that contain descriptions of phenotypic abnormalities-an important step toward improving the ability of researchers and clinicians to get biomedical information that is critical for clinical care or translational research.
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Affiliation(s)
- Peter N Robinson
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany;; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;; Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany;; Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | | | - Melissa Haendel
- Oregon Health and Science University, Portland, Oregon 97239, USA
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33
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Siu LL, Lawler M, Haussler D, Knoppers BM, Lewin J, Vis DJ, Liao RG, Andre F, Banks I, Barrett JC, Caldas C, Camargo AA, Fitzgerald RC, Mao M, Mattison JE, Pao W, Sellers WR, Sullivan P, Teh BT, Ward R, ZenKlusen JC, Sawyers CL, Voest EE. Facilitating a culture of responsible and effective sharing of cancer genome data. Nat Med 2016; 22:464-71. [PMID: 27149219 PMCID: PMC4995884 DOI: 10.1038/nm.4089] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 03/21/2016] [Indexed: 12/17/2022]
Abstract
Rapid and affordable tumor molecular profiling has led to an explosion of clinical and genomic data poised to enhance the diagnosis, prognostication and treatment of cancer. A critical point has now been reached at which the analysis and storage of annotated clinical and genomic information in unconnected silos will stall the advancement of precision cancer care. Information systems must be harmonized to overcome the multiple technical and logistical barriers to data sharing. Against this backdrop, the Global Alliance for Genomic Health (GA4GH) was established in 2013 to create a common framework that enables responsible, voluntary and secure sharing of clinical and genomic data. This Perspective from the GA4GH Clinical Working Group Cancer Task Team highlights the data-aggregation challenges faced by the field, suggests potential collaborative solutions and describes how GA4GH can catalyze a harmonized data-sharing culture.
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Affiliation(s)
- Lillian L. Siu
- Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - Mark Lawler
- Centre for Cancer Research and Cell Biology, Queen’s University, Belfast, UK
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | - Jeremy Lewin
- Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - Daniel J. Vis
- The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Rachel G. Liao
- The Global Alliance for Genomics and Health, Toronto, Canada and the Broad Institute, Cambridge, MA, USA
| | - Fabrice Andre
- Gustave Roussy and Université Paris Sud, Villejuif, France
| | - Ian Banks
- Patient’s Advocacy Committee, European Cancer Organization, Brussels, Belgium
| | - J. Carl Barrett
- Translational Sciences, Oncology iMED, AstraZeneca, Waltham, MA, USA
| | | | | | | | - Mao Mao
- Yonsei Cancer Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | | | - William Pao
- Roche Innovation Center Basel, Pharma Research and Early Development, Roche, Basel, Switzerland
| | | | - Patrick Sullivan
- Advocacy for Canadian Children Oncology Network, Vancouver, Canada
| | | | - Robyn Ward
- University of Queensland, St. Lucia, Australia
| | - Jean Claude ZenKlusen
- The Cancer Genome Atlas, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Emile E. Voest
- The Netherlands Cancer Institute, Amsterdam, the Netherlands
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34
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Lelieveld SH, Veltman JA, Gilissen C. Novel bioinformatic developments for exome sequencing. Hum Genet 2016. [PMID: 27075447 DOI: 10.1007/s00439‐016‐1658‐6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
With the widespread adoption of next generation sequencing technologies by the genetics community and the rapid decrease in costs per base, exome sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers standard solutions for the analysis of exome sequencing data, many challenges still remain; especially the increasing scale at which exome data are now being generated has given rise to novel challenges in how to efficiently store, analyze and interpret exome data of this magnitude. In this review we discuss some of the recent developments in bioinformatics for exome sequencing and the directions that this is taking us to. With these developments, exome sequencing is paving the way for the next big challenge, the application of whole genome sequencing.
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Affiliation(s)
- Stefan H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.,Department of Clinical Genetics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
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35
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James RA, Campbell IM, Chen ES, Boone PM, Rao MA, Bainbridge MN, Lupski JR, Yang Y, Eng CM, Posey JE, Shaw CA. A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics. Genome Med 2016; 8:13. [PMID: 26838676 PMCID: PMC4736244 DOI: 10.1186/s13073-016-0261-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/05/2016] [Indexed: 12/22/2022] Open
Abstract
Background Genome-wide data are increasingly important in the clinical evaluation of human disease. However, the large number of variants observed in individual patients challenges the efficiency and accuracy of diagnostic review. Recent work has shown that systematic integration of clinical phenotype data with genotype information can improve diagnostic workflows and prioritization of filtered rare variants. We have developed visually interactive, analytically transparent analysis software that leverages existing disease catalogs, such as the Online Mendelian Inheritance in Man database (OMIM) and the Human Phenotype Ontology (HPO), to integrate patient phenotype and variant data into ranked diagnostic alternatives. Methods Our tool, “OMIM Explorer” (http://www.omimexplorer.com), extends the biomedical application of semantic similarity methods beyond those reported in previous studies. The tool also provides a simple interface for translating free-text clinical notes into HPO terms, enabling clinical providers and geneticists to contribute phenotypes to the diagnostic process. The visual approach uses semantic similarity with multidimensional scaling to collapse high-dimensional phenotype and genotype data from an individual into a graphical format that contextualizes the patient within a low-dimensional disease map. The map proposes a differential diagnosis and algorithmically suggests potential alternatives for phenotype queries—in essence, generating a computationally assisted differential diagnosis informed by the individual’s personal genome. Visual interactivity allows the user to filter and update variant rankings by interacting with intermediate results. The tool also implements an adaptive approach for disease gene discovery based on patient phenotypes. Results We retrospectively analyzed pilot cohort data from the Baylor Miraca Genetics Laboratory, demonstrating performance of the tool and workflow in the re-analysis of clinical exomes. Our tool assigned to clinically reported variants a median rank of 2, placing causal variants in the top 1 % of filtered candidates across the 47 cohort cases with reported molecular diagnoses of exome variants in OMIM Morbidmap genes. Our tool outperformed Phen-Gen, eXtasy, PhenIX, PHIVE, and hiPHIVE in the prioritization of these clinically reported variants. Conclusions Our integrative paradigm can improve efficiency and, potentially, the quality of genomic medicine by more effectively utilizing available phenotype information, catalog data, and genomic knowledge. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0261-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Regis A James
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ian M Campbell
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Edward S Chen
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Philip M Boone
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mitchell A Rao
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew N Bainbridge
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Department of Molecular & 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.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chad A Shaw
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Department of Statistics, Rice University, Houston, TX, 77005, USA.
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36
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Sobreira N, Schiettecatte F, Boehm C, Valle D, Hamosh A. New tools for Mendelian disease gene identification: PhenoDB variant analysis module; and GeneMatcher, a web-based tool for linking investigators with an interest in the same gene. Hum Mutat 2015; 36:425-31. [PMID: 25684268 DOI: 10.1002/humu.22769] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 02/09/2015] [Indexed: 01/10/2023]
Abstract
Identifying the causative variant from among the thousands identified by whole-exome sequencing or whole-genome sequencing is a formidable challenge. To make this process as efficient and flexible as possible, we have developed a Variant Analysis Module coupled to our previously described Web-based phenotype intake tool, PhenoDB (http://researchphenodb.net and http://phenodb.org). When a small number of candidate-causative variants have been identified in a study of a particular patient or family, a second, more difficult challenge becomes proof of causality for any given variant. One approach to this problem is to find other cases with a similar phenotype and mutations in the same candidate gene. Alternatively, it may be possible to develop biological evidence for causality, an approach that is assisted by making connections to basic scientists studying the gene of interest, often in the setting of a model organism. Both of these strategies benefit from an open access, online site where individual clinicians and investigators could post genes of interest. To this end, we developed GeneMatcher (http://genematcher.org), a freely accessible Website that enables connections between clinicians and researchers across the world who share an interest in the same gene(s).
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Affiliation(s)
- Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
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Human genotype–phenotype databases: aims, challenges and opportunities. Nat Rev Genet 2015; 16:702-15. [DOI: 10.1038/nrg3932] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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38
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Jurgens J, Ling H, Hetrick K, Pugh E, Schiettecatte F, Doheny K, Hamosh A, Avramopoulos D, Valle D, Sobreira N. Assessment of incidental findings in 232 whole-exome sequences from the Baylor-Hopkins Center for Mendelian Genomics. Genet Med 2015; 17:782-8. [PMID: 25569433 PMCID: PMC4496331 DOI: 10.1038/gim.2014.196] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 12/01/2014] [Indexed: 12/30/2022] Open
Abstract
PURPOSE In March 2013 the American College of Medical Genetics and Genomics published a list of 56 genes with the recommendation that pathogenic and likely pathogenic variants detected incidentally by clinical sequencing be reported to patients. As an initial step in determining the practical consequences of this recommendation in the research setting, we searched for variants in these genes in 232 whole-exome sequences from the Baylor-Hopkins Center for Mendelian Genomics. METHODS We identified rare, nonsynonymous, and splicing single-nucleotide variants and insertions/deletions and assessed variant classification using the Human Gene Mutation, Emory, and ClinVar databases. We analyzed the burden of mutation in each of the 56 genes and determined which variants should be reported to patients. RESULTS Our filtering resulted in 249 distinct variants, with a mean of 1.69 variants per individual. Half of these were novel missense mutations not classified by any of the three reference databases. Of 101 variants listed in the Human Gene Mutation Database, 48 were also in ClinVar and 3 were also in Emory; half of these shared variants were classified discordantly between databases. Some genes consistently had greater variation than others. In total, 0.86% of individuals had a reportable incidental variant. CONCLUSION These observations demonstrate some current challenges of assessing phenotypic consequences of incidental variants for counseling patients.
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Affiliation(s)
- Julie Jurgens
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hua Ling
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Kurt Hetrick
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Elizabeth Pugh
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | | | - Kimberly Doheny
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dimitri Avramopoulos
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Sobreira N, Schiettecatte F, Valle D, Hamosh A. GeneMatcher: a matching tool for connecting investigators with an interest in the same gene. Hum Mutat 2015. [PMID: 26220891 DOI: 10.1002/humu.22844] [Citation(s) in RCA: 1012] [Impact Index Per Article: 112.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Here, we describe an overview and update on GeneMatcher (http://www.genematcher.org), a freely accessible Web-based tool developed as part of the Baylor-Hopkins Center for Mendelian Genomics. We created GeneMatcher with the goal of identifying additional individuals with rare phenotypes who had variants in the same candidate disease gene. We also wanted to facilitate connections to basic scientists working on orthologous genes in model systems with the goal of connecting their work to human Mendelian phenotypes. Meeting these goals will enhance the identification of novel Mendelian genes. Launched in September, 2013, GeneMatcher now has 2,178 candidate genes from 486 submitters spread across 38 countries entered in the database (June 1, 2015). GeneMatcher is also part of the Matchmaker Exchange (http://matchmakerexchange.org/) with an Application Programing Interface enabling submitters to query other databases of genetic variants and phenotypes without having to create accounts and data entries in multiple systems.
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Affiliation(s)
- Nara Sobreira
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - David Valle
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ada Hamosh
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Chong J, Buckingham K, Jhangiani S, Boehm C, Sobreira N, Smith J, Harrell T, McMillin M, Wiszniewski W, Gambin T, Coban Akdemir Z, Doheny K, Scott A, Avramopoulos D, Chakravarti A, Hoover-Fong J, Mathews D, Witmer P, Ling H, Hetrick K, Watkins L, Patterson K, Reinier F, Blue E, Muzny D, Kircher M, Bilguvar K, López-Giráldez F, Sutton V, Tabor H, Leal S, Gunel M, Mane S, Gibbs R, Boerwinkle E, Hamosh A, Shendure J, Lupski J, Lifton R, Valle D, Nickerson D, Bamshad M, Bamshad MJ. The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities. Am J Hum Genet 2015; 97:199-215. [PMID: 26166479 DOI: 10.1016/j.ajhg.2015.06.009] [Citation(s) in RCA: 445] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Indexed: 01/06/2023] Open
Abstract
Discovering the genetic basis of a Mendelian phenotype establishes a causal link between genotype and phenotype, making possible carrier and population screening and direct diagnosis. Such discoveries also contribute to our knowledge of gene function, gene regulation, development, and biological mechanisms that can be used for developing new therapeutics. As of February 2015, 2,937 genes underlying 4,163 Mendelian phenotypes have been discovered, but the genes underlying ∼50% (i.e., 3,152) of all known Mendelian phenotypes are still unknown, and many more Mendelian conditions have yet to be recognized. This is a formidable gap in biomedical knowledge. Accordingly, in December 2011, the NIH established the Centers for Mendelian Genomics (CMGs) to provide the collaborative framework and infrastructure necessary for undertaking large-scale whole-exome sequencing and discovery of the genetic variants responsible for Mendelian phenotypes. In partnership with 529 investigators from 261 institutions in 36 countries, the CMGs assessed 18,863 samples from 8,838 families representing 579 known and 470 novel Mendelian phenotypes as of January 2015. This collaborative effort has identified 956 genes, including 375 not previously associated with human health, that underlie a Mendelian phenotype. These results provide insight into study design and analytical strategies, identify novel mechanisms of disease, and reveal the extensive clinical variability of Mendelian phenotypes. Discovering the gene underlying every Mendelian phenotype will require tackling challenges such as worldwide ascertainment and phenotypic characterization of families affected by Mendelian conditions, improvement in sequencing and analytical techniques, and pervasive sharing of phenotypic and genomic data among researchers, clinicians, and families.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Michael J 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, Seattle Children's Hospital, Seattle, WA 98105, USA.
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Rehm HL, Berg JS, Brooks LD, Bustamante CD, Evans JP, Landrum MJ, Ledbetter DH, Maglott DR, Martin CL, Nussbaum RL, Plon SE, Ramos EM, Sherry ST, Watson MS. ClinGen--the Clinical Genome Resource. N Engl J Med 2015; 372:2235-42. [PMID: 26014595 PMCID: PMC4474187 DOI: 10.1056/nejmsr1406261] [Citation(s) in RCA: 810] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
On autopsy, a patient is found to have hypertrophic cardiomyopathy. The patient’s family pursues genetic testing that shows a “likely pathogenic” variant for the condition on the basis of a study in an original research publication. Given the dominant inheritance of the condition and the risk of sudden cardiac death, other family members are tested for the genetic variant to determine their risk. Several family members test negative and are told that they are not at risk for hypertrophic cardiomyopathy and sudden cardiac death, and those who test positive are told that they need to be regularly monitored for cardiomyopathy on echocardiography. Five years later, during a routine clinic visit of one of the genotype-positive family members, the cardiologist queries a database for current knowledge on the genetic variant and discovers that the variant is now interpreted as “likely benign” by another laboratory that uses more recently derived population-frequency data. A newly available testing panel for additional genes that are implicated in hypertrophic cardiomyopathy is initiated on an affected family member, and a different variant is found that is determined to be pathogenic. Family members are retested, and one member who previously tested negative is now found to be positive for this new variant. An immediate clinical workup detects evidence of cardiomyopathy, and an intracardiac defibrillator is implanted to reduce the risk of sudden cardiac death.
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Affiliation(s)
- Heidi L Rehm
- From Harvard Medical School and Brigham and Women's Hospital and Partners HealthCare - all in Boston (H.L.R.); University of North Carolina, Chapel Hill (J.S.B., J.P.E.); National Human Genome Research Institute, National Institutes of Health (NIH) (L.D.B., E.M.R.), National Center for Biotechnology Information, National Library of Medicine, NIH (M.J.L., D.R.M., S.T.S.), and American College of Medical Genetics and Genomics (M.S.W.) - all in Bethesda, MD; Stanford University School of Medicine, Stanford (C.D.B.), and University of California, San Francisco, San Francisco (R.L.N.) - both in California; Geisinger Health System, Danville, PA (D.H.L., C.L.M.); and Baylor College of Medicine, Houston (S.E.P.)
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Gripp KW, Robbins KM, Sobreira NL, Witmer PD, Bird LM, Avela K, Makitie O, Alves D, Hogue JS, Zackai EH, Doheny KF, Stabley DL, Sol-Church K. Truncating mutations in the last exon of NOTCH3 cause lateral meningocele syndrome. Am J Med Genet A 2015; 167A:271-81. [PMID: 25394726 PMCID: PMC5589071 DOI: 10.1002/ajmg.a.36863] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 10/15/2014] [Indexed: 12/30/2022]
Abstract
Lateral meningocele syndrome (LMS, OMIM%130720), also known as Lehman syndrome, is a very rare skeletal disorder with facial anomalies, hypotonia and meningocele-related neurologic dysfunction. The characteristic lateral meningoceles represent the severe end of the dural ectasia spectrum and are typically most severe in the lower spine. Facial features of LMS include hypertelorism and telecanthus, high arched eyebrows, ptosis, midfacial hypoplasia, micrognathia, high and narrow palate, low-set ears and a hypotonic appearance. Hyperextensibility, hernias and scoliosis reflect a connective tissue abnormality, and aortic dilation, a high-pitched nasal voice, wormian bones and osteolysis may be present. Lateral meningocele syndrome has phenotypic overlap with Hajdu-Cheney syndrome. We performed exome resequencing in five unrelated individuals with LMS and identified heterozygous truncating NOTCH3 mutations. In an additional unrelated individual Sanger sequencing revealed a deleterious variant in the same exon 33. In total, five novel de novo NOTCH3 mutations were identified in six unrelated patients. One had a 26 bp deletion (c.6461_6486del, p.G2154fsTer78), two carried the same single base pair insertion (c.6692_93insC, p.P2231fsTer11), and three individuals had a nonsense point mutation at c.6247A > T (pK2083*), c.6663C > G (p.Y2221*) or c.6732C > A, (p.Y2244*). All mutations cluster into the last coding exon, resulting in premature termination of the protein and truncation of the negative regulatory proline-glutamate-serine-threonine rich PEST domain. Our results suggest that mutant mRNA products escape nonsense mediated decay. The truncated NOTCH3 may cause gain-of-function through decreased clearance of the active intracellular product, resembling NOTCH2 mutations in the clinically related Hajdu-Cheney syndrome and contrasting the NOTCH3 missense mutations causing CADASIL.
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Affiliation(s)
- Karen W. Gripp
- Division of Medical Genetics, A.I. duPont Hospital for Children, Wilmington, Delaware, and Sidney Kimmel Medical School at T. Jefferson University, Philadelphia, Pennsylvania
| | - Katherine M. Robbins
- Department of Biomedical Research, A.I. duPont Hospital for Children, Wilmington, Delaware
- Department of Biological Sciences, University of Delaware, Newark, Delaware
| | - Nara L. Sobreira
- Johns Hopkins University School of Medicine, Institute of Genetic Medicine, Baltimore, Maryland
| | - P. Dane Witmer
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lynne M. Bird
- University of California San Diego and Rady Children's Hospital, San Diego, California
| | - Kristiina Avela
- Department of Clinical Genetics, Helsinki University Central Hospital, Helsinki, Finland
| | - Outi Makitie
- Children's Hospital, Helsinki University Central Hospital and University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Daniela Alves
- Neurogenetics Unit, Department of Medical Genetics, Centro Hospitalar de São João, Porto, Portugal
| | | | - Elaine H. Zackai
- Division of Human Genetics and Molecular Biology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kimberly F. Doheny
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Deborah L. Stabley
- Department of Biomedical Research, A.I. duPont Hospital for Children, Wilmington, Delaware
| | - Katia Sol-Church
- Department of Biomedical Research, A.I. duPont Hospital for Children, Wilmington, Delaware
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Amberger JS, Bocchini CA, Schiettecatte F, Scott AF, Hamosh A. OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders. Nucleic Acids Res 2014; 43:D789-98. [PMID: 25428349 PMCID: PMC4383985 DOI: 10.1093/nar/gku1205] [Citation(s) in RCA: 1386] [Impact Index Per Article: 138.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Online Mendelian Inheritance in Man, OMIM®, is a comprehensive, authoritative and timely research resource of curated descriptions of human genes and phenotypes and the relationships between them. The new official website for OMIM, OMIM.org (http://omim.org), was launched in January 2011. OMIM is based on the published peer-reviewed biomedical literature and is used by overlapping and diverse communities of clinicians, molecular biologists and genome scientists, as well as by students and teachers of these disciplines. Genes and phenotypes are described in separate entries and are given unique, stable six-digit identifiers (MIM numbers). OMIM entries have a structured free-text format that provides the flexibility necessary to describe the complex and nuanced relationships between genes and genetic phenotypes in an efficient manner. OMIM also has a derivative table of genes and genetic phenotypes, the Morbid Map. OMIM.org has enhanced search capabilities such as genome coordinate searching and thesaurus-enhanced search term options. Phenotypic series have been created to facilitate viewing genetic heterogeneity of phenotypes. Clinical synopsis features are enhanced with UMLS, Human Phenotype Ontology and Elements of Morphology terms and image links. All OMIM data are available for FTP download and through an API. MIMmatch is a novel outreach feature to disseminate updates and encourage collaboration.
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Affiliation(s)
- Joanna S Amberger
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Carol A Bocchini
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | - Alan F Scott
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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Rodríguez-López R, Reyes-Palomares A, Sánchez-Jiménez F, Medina MÁ. PhenUMA: a tool for integrating the biomedical relationships among genes and diseases. BMC Bioinformatics 2014; 15:375. [PMID: 25420641 PMCID: PMC4260198 DOI: 10.1186/s12859-014-0375-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 11/04/2014] [Indexed: 01/04/2023] Open
Abstract
Background Several types of genetic interactions in humans can be directly or indirectly associated with the causal effects of mutations. These interactions are usually based on their co-associations to biological processes, coexistence in cellular locations, coexpression in cell lines, physical interactions and so on. In addition, pathological processes can present similar phenotypes that have mutations either in the same genomic location or in different genomic regions. Therefore, integrative resources for all of these complex interactions can help us prioritize the relationships between genes and diseases that are most deserving to be studied by researchers and physicians. Results PhenUMA is a web application that displays biological networks using information from biomedical and biomolecular data repositories. One of its most innovative features is to combine the benefits of semantic similarity methods with the information taken from databases of genetic diseases and biological interactions. More specifically, this tool is useful in studying novel pathological relationships between functionally related genes, merging diseases into clusters that share specific phenotypes or finding diseases related to reported phenotypes. Conclusions This framework builds, analyzes and visualizes networks based on both functional and phenotypic relationships. The integration of this information helps in the discovery of alternative pathological roles of genes, biological functions and diseases. PhenUMA represents an advancement toward the use of new technologies for genomics and personalized medicine. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0375-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rocío Rodríguez-López
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Andalucía Tech, Facultad de Ciencias, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain. .,CIBER de Enfermedades Raras (CIBERER), E-29071, Málaga, Spain.
| | - Armando Reyes-Palomares
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Andalucía Tech, Facultad de Ciencias, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain. .,CIBER de Enfermedades Raras (CIBERER), E-29071, Málaga, Spain.
| | - Francisca Sánchez-Jiménez
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Andalucía Tech, Facultad de Ciencias, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain. .,CIBER de Enfermedades Raras (CIBERER), E-29071, Málaga, Spain.
| | - Miguel Ángel Medina
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Andalucía Tech, Facultad de Ciencias, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain. .,CIBER de Enfermedades Raras (CIBERER), E-29071, Málaga, Spain.
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Yamamoto S, Jaiswal M, Charng WL, Gambin T, Karaca E, Mirzaa G, Wiszniewski W, Sandoval H, Haelterman NA, Xiong B, Zhang K, Bayat V, David G, Li T, Chen K, Gala U, Harel T, Pehlivan D, Penney S, Vissers LELM, de Ligt J, Jhangiani SN, Xie Y, Tsang SH, Parman Y, Sivaci M, Battaloglu E, Muzny D, Wan YW, Liu Z, Lin-Moore AT, Clark RD, Curry CJ, Link N, Schulze KL, Boerwinkle E, Dobyns WB, Allikmets R, Gibbs RA, Chen R, Lupski JR, Wangler MF, Bellen HJ. A drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases. Cell 2014; 159:200-214. [PMID: 25259927 PMCID: PMC4298142 DOI: 10.1016/j.cell.2014.09.002] [Citation(s) in RCA: 257] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 06/04/2014] [Accepted: 09/02/2014] [Indexed: 12/31/2022]
Abstract
Invertebrate model systems are powerful tools for studying human disease owing to their genetic tractability and ease of screening. We conducted a mosaic genetic screen of lethal mutations on the Drosophila X chromosome to identify genes required for the development, function, and maintenance of the nervous system. We identified 165 genes, most of whose function has not been studied in vivo. In parallel, we investigated rare variant alleles in 1,929 human exomes from families with unsolved Mendelian disease. Genes that are essential in flies and have multiple human homologs were found to be likely to be associated with human diseases. Merging the human data sets with the fly genes allowed us to identify disease-associated mutations in six families and to provide insights into microcephaly associated with brain dysgenesis. This bidirectional synergism between fly genetics and human genomics facilitates the functional annotation of evolutionarily conserved genes involved in human health.
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Affiliation(s)
- Shinya Yamamoto
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA
| | - Manish Jaiswal
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA
| | - Wu-Lin Charng
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Institute of Computer Science, Warsaw University of Technology, 00-661 Warsaw, Poland
| | - Ender Karaca
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Ghayda Mirzaa
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Wojciech Wiszniewski
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Hector Sandoval
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Nele A Haelterman
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Bo Xiong
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Ke Zhang
- Program in Structural and Computational Biology and Molecular Biophysics, BCM, Houston, TX 77030, USA
| | - Vafa Bayat
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Gabriela David
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Tongchao Li
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Kuchuan Chen
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Upasana Gala
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Samantha Penney
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Joep de Ligt
- Department of Human Genetics, Radboudumc, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | | | - Yajing Xie
- Department of Ophthalmology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yesim Parman
- Neurology Department and Neuropathology Laboratory, Istanbul University Medical School, Istanbul 34390, Turkey
| | - Merve Sivaci
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul 34342, Turkey
| | - Esra Battaloglu
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul 34342, Turkey
| | - Donna Muzny
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA; Department of Obstetrics and Gynecology, BCM, Houston, TX 77030, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA; Department of Pediatrics, BCM, Houston, TX 77030, USA
| | | | - Robin D Clark
- Division of Medical Genetics, Department of Pediatrics, Loma Linda University Medical Center, Loma Linda, CA 92354, USA
| | - Cynthia J Curry
- Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA; Genetic Medicine Central California, Fresno, CA 93701, USA
| | - Nichole Link
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Karen L Schulze
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA; Human Genetics Center, University of Texas, Health Science Center, Houston, TX 77030, USA
| | - William B Dobyns
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Neurology, University of Washington, Seattle WA 98195, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Rui Chen
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, 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
| | - Michael F Wangler
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA; Program in Structural and Computational Biology and Molecular Biophysics, BCM, Houston, TX 77030, USA; Department of Neuroscience, BCM, Houston, TX 77030, USA.
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Trakadis YJ, Buote C, Therriault JF, Jacques PÉ, Larochelle H, Lévesque S. PhenoVar: a phenotype-driven approach in clinical genomics for the diagnosis of polymalformative syndromes. BMC Med Genomics 2014; 7:22. [PMID: 24884844 PMCID: PMC4030287 DOI: 10.1186/1755-8794-7-22] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 04/24/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND We propose a phenotype-driven analysis of encrypted exome data to facilitate the widespread implementation of exome sequencing as a clinical genetic screening test.Twenty test-patients with varied syndromes were selected from the literature. For each patient, the mutation, phenotypic data, and genetic diagnosis were available. Next, control exome-files, each modified to include one of these twenty mutations, were assigned to the corresponding test-patients. These data were used by a geneticist blinded to the diagnoses to test the efficiency of our software, PhenoVar. The score assigned by PhenoVar to any genetic diagnosis listed in OMIM (Online Mendelian Inheritance in Man) took into consideration both the patient's phenotype and all variations present in the corresponding exome. The physician did not have access to the individual mutations. PhenoVar filtered the search using a cut-off phenotypic match threshold to prevent undesired discovery of incidental findings and ranked the OMIM entries according to diagnostic score. RESULTS When assigning the same weight to all variants in the exome, PhenoVar predicted the correct diagnosis in 10/20 patients, while in 15/20 the correct diagnosis was among the 4 highest ranked diagnoses. When assigning a higher weight to variants known, or bioinformatically predicted, to cause disease, PhenoVar's yield increased to 14/20 (18/20 in top 4). No incidental findings were identified using our cut-off phenotypic threshold. CONCLUSION The phenotype-driven approach described could render widespread use of ES more practical, ethical and clinically useful. The implications about novel disease identification, advancement of complex diseases and personalized medicine are discussed.
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Affiliation(s)
- Yannis J Trakadis
- Department of Medical Genetics, McGill University Health Centre, Montreal, Canada.
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Prada CE, Gonzaga-Jauregui C, Tannenbaum R, Penney S, Lupski JR, Hopkin RJ, Sutton VR. Clinical utility of whole-exome sequencing in rare diseases: Galactosialidosis. Eur J Med Genet 2014; 57:339-344. [PMID: 24769197 DOI: 10.1016/j.ejmg.2014.04.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 04/13/2014] [Indexed: 10/25/2022]
Abstract
Rare genetic disorders can go undiagnosed for years as the entire spectrum of phenotypic variation is not well characterized given the reduced number of patients reported in the literature and the low frequency at which these occur. Moreover, the current paradigm for clinical diagnostics defines disease diagnosis by a specified spectrum of phenotypic findings; when such parameters are either missing, or other findings not usually observed are seen, the phenotype driven approach to diagnosis may result in a specific etiological diagnosis not even being considered within the differential diagnosis. The novel implementation of genomic sequencing approaches to investigate rare genetic disorders is allowing not only the discovery of new genes, but also the phenotypic expansion of known Mendelian genetic disorders. Here we report the detailed clinical assessment of a patient with a rare genetic disorder with undefined molecular diagnosis. We applied whole-exome sequencing to this patient and unaffected parents in order to identify the molecular cause of her disorder. We identified compound heterozygous mutations in the CTSA gene, responsible for causing galactosialidosis; the molecular diagnosis was further confirmed by biochemical studies. This report expands on the clinical spectrum of this rare lysosomal disorder and exemplifies how genomic approaches are further elucidating the characterization and understanding of genetic diseases.
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Affiliation(s)
- Carlos E Prada
- Division of Human Genetics. Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Center for Genomic Medicine and Metabolism. Cardiovascular Foundation of Colombia, Floridablanca, Colombia
| | | | - Rebecca Tannenbaum
- Division of Human Genetics. Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Samantha Penney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Centers for Mendelian Genomics, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Centers for Mendelian Genomics, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Robert J Hopkin
- Division of Human Genetics. Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Centers for Mendelian Genomics, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
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Danielsson K, Mun LJ, Lordemann A, Mao J, Lin CHJ. Next-generation sequencing applied to rare diseases genomics. Expert Rev Mol Diagn 2014; 14:469-87. [PMID: 24702023 DOI: 10.1586/14737159.2014.904749] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genomics has revolutionized the study of rare diseases. In this review, we overview the latest technological development, rare disease discoveries, implementation obstacles and bioethical challenges. First, we discuss the technology of genome and exome sequencing, including the different next-generation platforms and exome enrichment technologies. Second, we survey the pioneering centers and discoveries for rare diseases, including few of the research institutions that have contributed to the field, as well as an overview survey of different types of rare diseases that have had new discoveries due to next-generation sequencing. Third, we discuss the obstacles and challenges that allow for clinical implementation, including returning of results, informed consent and privacy. Last, we discuss possible outlook as clinical genomics receives wider adoption, as third-generation sequencing is coming onto the horizon, and some needs in informatics and software to further advance the field.
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Affiliation(s)
- Krissi Danielsson
- Rare Genomics Institute, 4100 Forest Park Ave, Suite 204, St. Louis, MO 63108, USA
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Kassahn KS, Scott HS, Caramins MC. Integrating massively parallel sequencing into diagnostic workflows and managing the annotation and clinical interpretation challenge. Hum Mutat 2014; 35:413-23. [PMID: 24510514 DOI: 10.1002/humu.22525] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 01/30/2014] [Indexed: 11/07/2022]
Abstract
Massively parallel sequencing has become a powerful tool for the clinical management of patients with applications in diagnosis, guidance of treatment, prediction of drug response, and carrier screening. A considerable challenge for the clinical implementation of these technologies is the management of the vast amount of sequence data generated, in particular the annotation and clinical interpretation of genomic variants. Here, we describe annotation steps that can be automated and common strategies employed for variant prioritization. The definition of best practice standards for variant annotation and prioritization is still ongoing; at present, there is limited consensus regarding an optimal clinical sequencing pipeline. We provide considerations to help define these. For the first time, clinical genetics and genomics is not limited by our ability to sequence, but our ability to clinically interpret and use genomic information in health management. We argue that the development of standardized variant annotation and interpretation approaches and software tools implementing these warrants further support. As we gain a better understanding of the significance of genomic variation through research, patients will be able to benefit from the full scope that these technologies offer.
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Affiliation(s)
- Karin S Kassahn
- Genetic and Molecular Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, South Australia, 5006, Australia; School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, 5000, Australia
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50
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Migliavacca MP, Sobreira NLM, Antonialli GPM, Oliveira MM, Melaragno MISA, Casteels I, de Ravel T, Brunoni D, Valle D, Perez ABA. Sclerocornea in a patient with van den Ende-Gupta syndrome homozygous for a SCARF2 microdeletion. Am J Med Genet A 2014; 164A:1170-4. [PMID: 24478002 DOI: 10.1002/ajmg.a.36425] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 11/30/2013] [Indexed: 11/11/2022]
Abstract
Van den Ende-Gupta Syndrome (VDEGS) is an autosomal recessive disorder characterized by blepharophimosis, distinctive nose, hypoplastic maxilla, and skeletal abnormalities. Using homozygosity mapping in four VDEGS patients from three consanguineous families, Anastacio et al. [Anastacio et al. (2010); Am J Hum Genet 87:553-559] identified homozygous mutations in SCARF2, located at 22q11.2. Bedeschi et al. [2010] described a VDEGS patient with sclerocornea and cataracts with compound heterozygosity for the common 22q11.2 microdeletion and a hemizygous SCARF2 mutation. Because sclerocornea had been described in DiGeorge-velo-cardio-facial syndrome but not in VDEGS, they suggested that the ocular abnormalities were caused by the 22q11.2 microdeletion. We report on a 23-year-old male who presented with bilateral sclerocornea and the VDGEGS phenotype who was subsequently found to be homozygous for a 17 bp deletion in exon 4 of SCARF2. The occurrence of bilateral sclerocornea in our patient together with that of Bedeschi et al., suggests that the full VDEGS phenotype may include sclerocornea resulting from homozygosity or compound heterozygosity for loss of function variants in SCARF2.
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Affiliation(s)
- Michele P Migliavacca
- Clinical Genetics, Department of Morphology and Genetics, UNIFESP, São Paulo, Brazil
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