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Zeng B, Liu DC, Huang JG, Xia XB, Qin B. PdmIRD: missense variants pathogenicity prediction for inherited retinal diseases in a disease-specific manner. Hum Genet 2024; 143:331-342. [PMID: 38478153 DOI: 10.1007/s00439-024-02645-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/17/2024] [Indexed: 04/25/2024]
Abstract
Accurate discrimination of pathogenic and nonpathogenic variation remains an enormous challenge in clinical genetic testing of inherited retinal diseases (IRDs) patients. Computational methods for predicting variant pathogenicity are the main solutions for this dilemma. The majority of the state-of-the-art variant pathogenicity prediction tools disregard the differences in characteristics among different genes and treat all types of mutations equally. Since missense variants are the most common type of variation in the coding region of the human genome, we developed a novel missense mutation pathogenicity prediction tool, named Prediction of Deleterious Missense Mutation for IRDs (PdmIRD) in this study. PdmIRD was tailored for IRDs-related genes and constructed with the conditional random forest model. Population frequencies and a newly available prediction tool were incorporated into PdmIRD to improve the performance of the model. The evaluation of PdmIRD demonstrated its superior performance over nonspecific tools (areas under the curves, 0.984 and 0.910) and an existing eye abnormalities-specific tool (areas under the curves, 0.975 and 0.891). We also demonstrated the submodel that used a smaller gene panel further slightly improved performance. Our study provides evidence that a disease-specific model can enhance the prediction of missense mutation pathogenicity, especially when new and important features are considered. Additionally, this study provides guidance for exploring the characteristics and functions of the mutated proteins in a greater number of Mendelian disorders.
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Affiliation(s)
- Bing Zeng
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, 518031, Guangdong, China
- Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, 518031, Guangdong, China
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Dong Cheng Liu
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, 518031, Guangdong, China
- Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, 518031, Guangdong, China
| | - Jian Guo Huang
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, 518031, Guangdong, China
- Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, 518031, Guangdong, China
| | - Xiao Bo Xia
- Eye Center of Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Bo Qin
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, 518031, Guangdong, China.
- Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, 518031, Guangdong, China.
- Aier School of Ophthalmology, Central South University, Changsha, Hunan, China.
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2
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Deng M, Chen W, Qi Y. High-throughput Second-generation Sequencing Technology Assisted Diagnosis of Familial Partial Lipodystrophy (Type 2 Kobberling-Dunnigan Syndrome): A Case Report. Comb Chem High Throughput Screen 2024; 27:346-351. [PMID: 37231758 DOI: 10.2174/1386207326666230523112454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Whole exome sequencing (WES) provides support for clinical diagnosis and treatment of genetically related diseases based on specific probe capture and high-throughput second-generation sequencing technology. Familial partial lipodystrophy 2 (FPLD2; OMIM # 151660) or type 2 Köbberling-Dunnigan syndrome with insulin resistance syndrome is uncommon in mainland China and elsewhere. AIMS We report the case in order to have a further understanding of FPLD2 or type 2 Kobberling- Dunnigan syndrome) with the assistance of WES and improve the clinical and genetic understanding and diagnosis of this disease. CASE REPORT A 30-year-old woman was admitted to the cadre department of our hospital at 14:00 on July 11, 2021, because of hyperglycemia, a rapid heart rate, and excessive sweating during pregnancy. An oral glucose tolerance test (OGTT) showed that insulin and C-peptide increased slowly after glucose stimulation, and the peak value was extended backward (Table 1). It was suggested that the patient had developed insulin antibodies, resulting in insulin resistance. Her clinical features and familial inheritance were consistent with FPLD2 (type 2 Kobberling-Dunnigan syndrome). The results of WES indicated that a heterozygous mutation occurred in exon 8 of the LMNA gene, because the base C at position 1444 was mutated into T during transcription. This mutation changed the amino acid position 482 of the encoded protein from Arg to Trp. Type 2 Kobberling- Dunnigan syndrome is associated with an LMNA gene mutation. According to the patient's clinical manifestations, hypoglycemic and lipid-lowering therapy is recommended. CONCLUSION WES can assist in the simultaneous clinical investigation or confirmation of FPLD2 and help identify diseases with similar clinical phenotypes. This case demonstrates that familial partial lipodystrophy is associated with an LMNA gene mutation on chromosome 1q21-22. This is one of the few cases of familial partial lipodystrophy diagnosed by WES.
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Affiliation(s)
- Mingling Deng
- Department of Cadre Ward Two, Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumchi, 830000, China
| | - Wen Chen
- Department of Cadre Ward Two, Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumchi, 830000, China
| | - Yan Qi
- Department of Cadre Ward Two, Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumchi, 830000, China
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3
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Kumaran M, Devarajan B. eyeVarP: A computational framework for the identification of pathogenic variants specific to eye disease. Genet Med 2023; 25:100862. [PMID: 37092535 DOI: 10.1016/j.gim.2023.100862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/25/2023] Open
Abstract
PURPOSE Disease-specific pathogenic variant prediction tools that differentiate pathogenic variants from benign have been improved through disease specificity recently. However, they have not been evaluated on disease-specific pathogenic variants compared with other diseases, which would help to prioritize disease-specific variants from several genes or novel genes. Thus, we hypothesize that features of pathogenic variants alone would provide a better model. METHODS We developed an eye disease-specific variant prioritization tool (eyeVarP), which applied the random forest algorithm to the data set of pathogenic variants of eye diseases and other diseases. We also developed the VarP tool and generalized pipeline to filter missense and insertion-deletion variants and predict their pathogenicity from exome or genome sequencing data, thus we provide a complete computational procedure. RESULTS eyeVarP outperformed pan disease-specific tools in identifying eye disease-specific pathogenic variants under the top 10. VarP outperformed 12 pathogenicity prediction tools with an accuracy of 95% in correctly identifying the pathogenicity of missense and insertion-deletion variants. The complete pipeline would help to develop disease-specific tools for other genetic disorders. CONCLUSION eyeVarP performs better in identifying eye disease-specific pathogenic variants using pathogenic variant features and gene features. Implementing such complete computational procedure would significantly improve the clinical variant interpretation for specific diseases.
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Affiliation(s)
- Manojkumar Kumaran
- Department of Bioinformatics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India; School of Chemical and Biotechnology, SASTRA (Deemed to be a university), Thanjavur, Tamil Nadu, India
| | - Bharanidharan Devarajan
- Department of Bioinformatics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India.
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4
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Henry OJ, Stödberg T, Båtelson S, Rasi C, Stranneheim H, Wedell A. Individualised human phenotype ontology gene panels improve clinical whole exome and genome sequencing analytical efficacy in a cohort of developmental and epileptic encephalopathies. Mol Genet Genomic Med 2023; 11:e2167. [PMID: 36967109 PMCID: PMC10337286 DOI: 10.1002/mgg3.2167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/21/2023] [Accepted: 03/01/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND The majority of genetic epilepsies remain unsolved in terms of specific genotype. Phenotype-based genomic analyses have shown potential to strengthen genomic analysis in various ways, including improving analytical efficacy. METHODS We have tested a standardised phenotyping method termed 'Phenomodels' for integrating deep-phenotyping information with our in-house developed clinical whole exome/genome sequencing analytical pipeline. Phenomodels includes a user-friendly epilepsy phenotyping template and an objective measure for selecting which template terms to include in individualised Human Phenotype Ontology (HPO) gene panels. In a pilot study of 38 previously solved cases of developmental and epileptic encephalopathies, we compared the sensitivity and specificity of the individualised HPO gene panels with the clinical epilepsy gene panel. RESULTS The Phenomodels template showed high sensitivity for capturing relevant phenotypic information, where 37/38 individuals' HPO gene panels included the causative gene. The HPO gene panels also had far fewer variants to assess than the epilepsy gene panel. CONCLUSION We have demonstrated a viable approach for incorporating standardised phenotype information into clinical genomic analyses, which may enable more efficient analysis.
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Affiliation(s)
- Olivia J. Henry
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
| | - Tommy Stödberg
- Department of Women's and Children's HealthKarolinska InstitutetStockholmSweden
- Department of Pediatric NeurologyKarolinska University HospitalStockholmSweden
| | - Sofia Båtelson
- Department of Pediatric NeurologyKarolinska University HospitalStockholmSweden
| | - Chiara Rasi
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Henrik Stranneheim
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell BiologyKarolinska InstitutetStockholmSweden
- Centre for Inherited Metabolic DiseasesKarolinska University HospitalStockholmSweden
| | - Anna Wedell
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
- Centre for Inherited Metabolic DiseasesKarolinska University HospitalStockholmSweden
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5
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Cruz Marino T, Leblanc J, Pratte A, Tardif J, Thomas MJ, Fortin CA, Girard L, Bouchard L. Portrait of autosomal recessive diseases in the French-Canadian founder population of Saguenay-Lac-Saint-Jean. Am J Med Genet A 2023; 191:1145-1163. [PMID: 36786328 DOI: 10.1002/ajmg.a.63147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/16/2023] [Accepted: 01/30/2023] [Indexed: 02/15/2023]
Abstract
The population of the Saguenay-Lac-Saint-Jean (SLSJ) region, located in the province of Quebec, Canada, is recognized as a founder population, where some rare autosomal recessive diseases show a high prevalence. Through the clinical and molecular study of 82 affected individuals from 60 families, this study outlines 12 diseases identified as recurrent in SLSJ. Their carrier frequency was estimated with the contribution of 1059 healthy individuals, increasing the number of autosomal recessive diseases with known carrier frequency in this region from 14 to 25. We review the main clinical and molecular features previously reported for these disorders. Five of the studied diseases have a potential lethal effect and three are associated with intellectual deficiency. Therefore, we believe that the provincial program for carrier screening should be extended to include these eight disorders. The high-carrier frequency, together with the absence of consanguinity in most of these unrelated families, suggest a founder effect and genetic drift for the 12 recurrent variants. We recommend further studies to validate this hypothesis, as well as to extend the present study to other regions in the province of Quebec, since some of these disorders could also be present in other French-Canadian families.
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Affiliation(s)
- Tania Cruz Marino
- Department of Laboratory Medicine, CIUSSS Saguenay-Lac-St-Jean, Quebec, Canada
| | - Josianne Leblanc
- Department of Laboratory Medicine, CIUSSS Saguenay-Lac-St-Jean, Quebec, Canada
| | - Annabelle Pratte
- Department of Laboratory Medicine, CIUSSS Saguenay-Lac-St-Jean, Quebec, Canada
| | - Jessica Tardif
- Department of Laboratory Medicine, CIUSSS Saguenay-Lac-St-Jean, Quebec, Canada
| | | | - Carol-Ann Fortin
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Quebec, Canada
| | - Lysanne Girard
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Quebec, Canada
| | - Luigi Bouchard
- Department of Laboratory Medicine, CIUSSS Saguenay-Lac-St-Jean, Quebec, Canada.,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Quebec, Canada
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6
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Seo GH, Kim T, Choi IH, Park JY, Lee J, Kim S, Won DG, Oh A, Lee Y, Choi J, Lee H, Kang HG, Cho HY, Cho MH, Kim YJ, Yoon YH, Eun BL, Desnick RJ, Keum C, Lee BH. Diagnostic yield and clinical utility of whole exome sequencing using an automated variant prioritization system, EVIDENCE. Clin Genet 2020; 98:562-570. [PMID: 32901917 PMCID: PMC7756481 DOI: 10.1111/cge.13848] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 01/14/2023]
Abstract
EVIDENCE, an automated variant prioritization system, has been developed to facilitate whole exome sequencing analyses. This study investigated the diagnostic yield of EVIDENCE in patients with suspected genetic disorders. DNA from 330 probands (age range, 0‐68 years) with suspected genetic disorders were subjected to whole exome sequencing. Candidate variants were identified by EVIDENCE and confirmed by testing family members and/or clinical reassessments. EVIDENCE reported a total 228 variants in 200 (60.6%) of the 330 probands. The average number of organs involved per patient was 4.5 ± 5.0. After clinical reassessment and/or family member testing, 167 variants were identified in 141 probands (42.7%), including 105 novel variants. These variants were confirmed as being responsible for 121 genetic disorders. A total of 103 (61.7%) of the 167 variants in 95 patients were classified as pathogenic or probably to be pathogenic before, and 161 (96.4%) variants in 137 patients (41.5%) after, clinical assessment and/or family member testing. Factor associated with a variant being regarded as causative includes similar symptom scores of a gene variant to the phenotype of the patient. This new, automated variant interpretation system facilitated the diagnosis of various genetic diseases with a 42.7% diagnostic yield.
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Affiliation(s)
- Go Hun Seo
- Division of Medical genetics, 3billion Inc., Seoul, South Korea
| | - Taeho Kim
- Biomedical Research Center, Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul, South Korea
| | - In Hee Choi
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jung-Young Park
- Division of Medical genetics, 3billion Inc., Seoul, South Korea
| | - Jungsul Lee
- Division of Medical genetics, 3billion Inc., Seoul, South Korea
| | - Sehwan Kim
- Division of Medical genetics, 3billion Inc., Seoul, South Korea
| | - Dhong-Gun Won
- Division of Medical genetics, 3billion Inc., Seoul, South Korea
| | - Arum Oh
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Yena Lee
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jeongmin Choi
- Biomedical Research Center, Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul, South Korea
| | - Hajeong Lee
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Hee Gyung Kang
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Hee Yeon Cho
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Min Hyun Cho
- Department of Pediatrics, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Yoon Jeon Kim
- Department of Ophthalmology, Asan Medical Center, University of Ulsan, Seoul, South Korea
| | - Young Hee Yoon
- Department of Ophthalmology, Asan Medical Center, University of Ulsan, Seoul, South Korea
| | - Baik-Lin Eun
- Department of Pediatrics, Korea University College of Medicine, Seoul, South Korea
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai Medical Center, New York, New York, USA
| | - Changwon Keum
- Division of Medical genetics, 3billion Inc., Seoul, South Korea
| | - Beom Hee Lee
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea.,Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
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7
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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: 31] [Impact Index Per Article: 7.8] [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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8
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Deisseroth CA, Birgmeier J, Bodle EE, Kohler JN, Matalon DR, Nazarenko Y, Genetti CA, Brownstein CA, Schmitz-Abe K, Schoch K, Cope H, Signer R, Martinez-Agosto JA, Shashi V, Beggs AH, Wheeler MT, Bernstein JA, Bejerano G. ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis. Genet Med 2018; 21:1585-1593. [PMID: 30514889 DOI: 10.1038/s41436-018-0381-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 11/13/2018] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Diagnosing monogenic diseases facilitates optimal care, but can involve the manual evaluation of hundreds of genetic variants per case. Computational tools like Phrank expedite this process by ranking all candidate genes by their ability to explain the patient's phenotypes. To use these tools, busy clinicians must manually encode patient phenotypes from lengthy clinical notes. With 100 million human genomes estimated to be sequenced by 2025, a fast alternative to manual phenotype extraction from clinical notes will become necessary. METHODS We introduce ClinPhen, a fast, high-accuracy tool that automatically converts clinical notes into a prioritized list of patient phenotypes using Human Phenotype Ontology (HPO) terms. RESULTS ClinPhen shows superior accuracy and 20× speedup over existing phenotype extractors, and its novel phenotype prioritization scheme improves the performance of gene-ranking tools. CONCLUSION While a dedicated clinician can process 200 patient records in a 40-hour workweek, ClinPhen does the same in 10 minutes. Compared with manual phenotype extraction, ClinPhen saves an additional 3-5 hours per Mendelian disease diagnosis. Providers can now add ClinPhen's output to each summary note attached to a filled testing laboratory request form. ClinPhen makes a substantial contribution to improvements in efficiency critically needed to meet the surging demand for clinical diagnostic sequencing.
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Affiliation(s)
- Cole A Deisseroth
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | - Ethan E Bodle
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
| | | | - Dena R Matalon
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
| | - Yelena Nazarenko
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Casie A Genetti
- The Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Catherine A Brownstein
- The Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Klaus Schmitz-Abe
- The Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kelly Schoch
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Heidi Cope
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Rebecca Signer
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | | | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Department of Pediatrics, Division of Medical Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Department of Psychiatry, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Alan H Beggs
- The Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew T Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford, CA, USA.,Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | | | - Gill Bejerano
- Department of Computer Science, Stanford University, Stanford, CA, USA. .,Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA. .,Department of Biomedical Data Science, Stanford University, Stanford, CA, USA. .,Department of Developmental Biology, Stanford University, Stanford, CA, USA.
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9
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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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10
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Rodenburg RJ. The functional genomics laboratory: functional validation of genetic variants. J Inherit Metab Dis 2018; 41:297-307. [PMID: 29445992 PMCID: PMC5959958 DOI: 10.1007/s10545-018-0146-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/10/2018] [Accepted: 01/18/2018] [Indexed: 02/06/2023]
Abstract
Currently, one of the main challenges in human molecular genetics is the interpretation of rare genetic variants of unknown clinical significance. A conclusive diagnosis is of importance for the patient to obtain certainty about the cause of the disease, for the clinician to be able to provide optimal care to the patient and to predict the disease course, and for the clinical geneticist for genetic counseling of the patient and family members. Conclusive evidence for pathogenicity of genetic variants is therefore crucial. This review gives an introduction to the problem of the interpretation of genetic variants of unknown clinical significance in view of the recent advances in genetic screening, and gives an overview of the possibilities for functional tests that can be performed to answer questions about the function of genes and the functional consequences of genetic variants ("functional genomics") in the field of inborn errors of metabolism (IEM), including several examples of functional genomics studies of mitochondrial disorders and several other IEM.
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Affiliation(s)
- Richard J Rodenburg
- Radboudumc, Radboud Center for Mitochondrial Medicine, 774 Translational Metabolic Laboratory, Department of Pediatrics, PO Box 9101, 6500HB, Nijmegen, The Netherlands.
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11
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Clinical validity of phenotype-driven analysis software PhenoVar as a diagnostic aid for clinical geneticists in the interpretation of whole-exome sequencing data. Genet Med 2018; 20:942-949. [PMID: 29388948 DOI: 10.1038/gim.2017.239] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/20/2017] [Indexed: 12/12/2022] Open
Abstract
PURPOSE We sought to determine the diagnostic yield of whole-exome sequencing (WES) combined with phenotype-driven analysis of variants in patients with suspected genetic disorders. METHODS WES was performed on a cohort of 51 patients presenting dysmorphisms with or without neurodevelopmental disorders of undetermined etiology. For each patient, a clinical geneticist reviewed the phenotypes and used the phenotype-driven analysis software PhenoVar (http://phenovar.med.usherbrooke.ca/) to analyze WES variants. The prioritized list of potential diagnoses returned was reviewed by the clinical geneticist, who selected candidate variants to be confirmed by segregation analysis. Conventional analysis of the individual variants was performed in parallel. The resulting candidate variants were subsequently reviewed by the same geneticist, to identify any additional potential diagnoses. RESULTS A molecular diagnosis was identified in 35% of the patients using the conventional analysis, and 17 of these 18 diagnoses were independently identified using PhenoVar. The only diagnosis initially missed by PhenoVar was rescued when the optional "minimal phenotypic cutoff" filter was omitted. PhenoVar reduced by half the number of potential diagnoses per patient compared with the conventional analysis. CONCLUSION Phenotype-driven software prioritizes WES variants, provides an efficient diagnostic aid to clinical geneticists and laboratories, and should be incorporated in clinical practice.
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12
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Zarate Y, Kalsner L, Basinger A, Jones J, Li C, Szybowska M, Xu Z, Vergano S, Caffrey A, Gonzalez C, Dubbs H, Zackai E, Millan F, Telegrafi A, Baskin B, Person R, Fish J, Everman D. Genotype and phenotype in 12 additional individuals with SATB2
-associated syndrome. Clin Genet 2017; 92:423-429. [DOI: 10.1111/cge.12982] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/24/2017] [Accepted: 01/25/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Y.A. Zarate
- Section of Genetics and Metabolism; University of Arkansas for Medical Sciences; Little Rock Arkansas
| | - L. Kalsner
- Department of Pediatrics; Connecticut Children's Medical Center; Hartford Connecticut
| | - A. Basinger
- Department of Pediatrics; Cook Children's Physician Network; Fort Worth Texas
| | - J.R. Jones
- Department of Genetics; Greenwood Genetic Center; Greenwood South Carolina
| | - C. Li
- Clinical Genetics program; McMaster University Medical Center; Hamilton Ontario Canada
| | - M. Szybowska
- Clinical Genetics program; McMaster University Medical Center; Hamilton Ontario Canada
| | - Z.L. Xu
- Faculty of Health Sciences; McMaster University; Hamilton Ontario Canada
| | - S. Vergano
- Division of Medical Genetics and Metabolism; Children's Hospital of The King's Daughters; Norfolk Virginia
| | - A.R. Caffrey
- Health Outcomes, Collage of pharmacy; University of Rhode Island; Kingston Rhode Island
| | - C.V. Gonzalez
- Biostatistics Program, Department of Pediatrics; University of Arkansas for Medical Sciences; Little Rock Arkansas
| | - H. Dubbs
- Department of Genetics; Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - E. Zackai
- Department of Genetics; Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - F. Millan
- Department of Molecular Genetics; GeneDx; Gaithersburg Maryland
| | - A. Telegrafi
- Department of Molecular Genetics; GeneDx; Gaithersburg Maryland
| | - B. Baskin
- Department of Molecular Genetics; GeneDx; Gaithersburg Maryland
| | - R. Person
- Department of Molecular Genetics; GeneDx; Gaithersburg Maryland
| | - J.L. Fish
- Department of Biological Sciences; University of Massachusetts Lowell; Lowell Massachusetts
| | - D.B. Everman
- Department of Genetics; Greenwood Genetic Center; Greenwood South Carolina
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13
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Marino TC, Maranda B, Leblanc J, Pratte A, Barabas M, Dupéré A, Lévesque S. Novel founder mutation in French-Canadian families with Naxos disease. Clin Genet 2017; 92:451-453. [DOI: 10.1111/cge.12971] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 11/26/2022]
Affiliation(s)
- T. Cruz Marino
- Department of Medical Biology; CIUSSS Saguenay Lac-St-Jean; Chicoutimi Quebec Canada
| | - B. Maranda
- Department of Pediatrics, Division of Medical Genetics; Centre Hospitalier Universitaire de Sherbrooke and Université de Sherbrooke; Sherbrooke Quebec Canada
| | - J. Leblanc
- Department of Medical Biology; CIUSSS Saguenay Lac-St-Jean; Chicoutimi Quebec Canada
| | - A. Pratte
- Department of Medical Biology; CIUSSS Saguenay Lac-St-Jean; Chicoutimi Quebec Canada
| | - M. Barabas
- Department of Cardiology; CIUSSS Saguenay Lac-St-Jean; Chicoutimi Quebec Canada
| | - A. Dupéré
- Department of Dermatology; CIUSSS Saguenay Lac-St-Jean; Chicoutimi Quebec Canada
| | - S. Lévesque
- Department of Pediatrics, Division of Medical Genetics; Centre Hospitalier Universitaire de Sherbrooke and Université de Sherbrooke; Sherbrooke Quebec Canada
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14
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Schwartz E, Wilkens A, Noon SE, Krantz ID, Wu Y. A de novo SATB2
mutation in monozygotic twins with cleft palate, dental anomalies, and developmental delay. Am J Med Genet A 2017; 173:809-812. [DOI: 10.1002/ajmg.a.38071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 11/14/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Emily Schwartz
- Division of Human Genetics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Alisha Wilkens
- Division of Human Genetics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Sarah E. Noon
- Division of Human Genetics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Ian D. Krantz
- Division of Human Genetics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
- The Perelman School of Medicine at the University of Pennsylvania; Philadelphia Pennsylvania
| | - Yaning Wu
- Division of Human Genetics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
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15
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Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJS, DeMare LE, Devereau AD, de Vries BBA, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jähn JA, James R, Krause R, F Laulederkind SJ, Lochmüller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MWM, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Züchner S, Zemojtel T, Jacobsen JOB, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN. The Human Phenotype Ontology in 2017. Nucleic Acids Res 2016; 45:D865-D876. [PMID: 27899602 PMCID: PMC5210535 DOI: 10.1093/nar/gkw1039] [Citation(s) in RCA: 501] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/28/2016] [Indexed: 12/14/2022] Open
Abstract
Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.
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Affiliation(s)
- Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Nicole A Vasilevsky
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Mark Engelstad
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Erin Foster
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Julie McMurry
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ségolène Aymé
- Institut du Cerveau et de la Moelle épinière-ICM, CNRS UMR 7225-Inserm U 1127-UPMC-P6 UMR S 1127, Hôpital Pitié-Salpêtrière, 47, bd de l'Hôpital, 75013 Paris, France
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, King Edward Memorial Hospital Department of Health, Government of Western Australia, Perth, WA 6008, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6008, Australia
| | - Susan M Bello
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Cornelius F Boerkoel
- Imagenetics Research, Sanford Health, PO Box 5039, Route 5001, Sioux Falls, SD 57117-5039, USA
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Orion J Buske
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.,NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Valentina Cipriani
- UCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.,UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | | | - Hugh J S Dawkins
- Office of Population Health Genomics, Public Health Division, Health Department of Western Australia, 189 Royal Street, Perth, WA, 6004 Australia
| | - Laura E DeMare
- Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA
| | - Andrew D Devereau
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University, University Medical Centre, Nijmegen, The Netherlands
| | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Daniel Greene
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.,Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ingo Helbig
- Division of Neurology, The Children's Hospital of Philadelphia, 3501 Civic Center Blvd, Philadelphia, PA 19104, USA.,Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Courtney Hum
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON M5G 1H3, Canada
| | - Johanna A Jähn
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Roger James
- NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.,Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Roland Krause
- LuxembourgCentre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | | | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, New York, NY 11797, USA
| | - Soichi Ogishima
- Dept of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University, Tohoku Medical Megabank Organization Bldg 7F room #741,736, Seiryo 2-1, Aoba-ku, Sendai Miyagi 980-8573 Japan
| | - Annie Olry
- Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France
| | - Willem H Ouwehand
- Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Nikolas Pontikos
- UCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.,UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Ana Rath
- Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France
| | - Franz Schaefer
- Division of Pediatric Nephrology and KFH Children's Kidney Center, Center for Pediatrics and Adolescent Medicine, 69120 Heidelberg, Germany
| | - Richard H Scott
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Michael Segal
- SimulConsult Inc., 27 Crafts Road, Chestnut Hill, MA 02467, USA
| | | | - Richard Sever
- Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA
| | - Cynthia L Smith
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Rachel Thompson
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Catherine Turner
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Ernest Turro
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.,Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Marijcke W M Veltman
- NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Tom Vulliamy
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Jing Yu
- Nuffield Department of Clinical Neurosciences, University of Oxford, Level 6, West Wing, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Julie von Ziegenweidt
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK
| | - Andreas Zankl
- Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, Australia.,Academic Department of Medical Genetics, Sydney Childrens Hospitals Network (Westmead), Australia
| | - Stephan Züchner
- JD McDonald Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Tomasz Zemojtel
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Julius O B Jacobsen
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Tudor Groza
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Australia
| | - Damian Smedley
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Melissa Haendel
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA .,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA
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16
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Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, Flynn ED, Girdea M, Godfrey R, Golas G, Groden C, Jacobsen J, Köhler S, Lee EMJ, Links AE, Markello TC, Mungall CJ, Nehrebecky M, Robinson PN, Sincan M, Soldatos AG, Tifft CJ, Toro C, Trang H, Valkanas E, Vasilevsky N, Wahl C, Wolfe LA, Boerkoel CF, Brudno M, Haendel MA, Gahl WA, Smedley D. Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency. Genet Med 2016; 18:608-17. [PMID: 26562225 PMCID: PMC4916229 DOI: 10.1038/gim.2015.137] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 08/27/2015] [Indexed: 01/18/2023] Open
Abstract
PURPOSE Medical diagnosis and molecular or biochemical confirmation typically rely on the knowledge of the clinician. Although this is very difficult in extremely rare diseases, we hypothesized that the recording of patient phenotypes in Human Phenotype Ontology (HPO) terms and computationally ranking putative disease-associated sequence variants improves diagnosis, particularly for patients with atypical clinical profiles. METHODS Using simulated exomes and the National Institutes of Health Undiagnosed Diseases Program (UDP) patient cohort and associated exome sequence, we tested our hypothesis using Exomiser. Exomiser ranks candidate variants based on patient phenotype similarity to (i) known disease-gene phenotypes, (ii) model organism phenotypes of candidate orthologs, and (iii) phenotypes of protein-protein association neighbors. RESULTS Benchmarking showed Exomiser ranked the causal variant as the top hit in 97% of known disease-gene associations and ranked the correct seeded variant in up to 87% when detectable disease-gene associations were unavailable. Using UDP data, Exomiser ranked the causative variant(s) within the top 10 variants for 11 previously diagnosed variants and achieved a diagnosis for 4 of 23 cases undiagnosed by clinical evaluation. CONCLUSION Structured phenotyping of patients and computational analysis are effective adjuncts for diagnosing patients with genetic disorders.Genet Med 18 6, 608-617.
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Affiliation(s)
- William P. Bone
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Nicole L. Washington
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Orion J. Buske
- Centre for Computational Medicine Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - David R. Adams
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
- Medical Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Joie Davis
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - David Draper
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Elise D. Flynn
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Marta Girdea
- Centre for Computational Medicine Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Rena Godfrey
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Gretchen Golas
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Catherine Groden
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Julius Jacobsen
- Skarnes Faculty group, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Elizabeth M. J. Lee
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Amanda E. Links
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas C. Markello
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Michele Nehrebecky
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter N. Robinson
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Murat Sincan
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Ariane G. Soldatos
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Cynthia J. Tifft
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
- Medical Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Camilo Toro
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Heather Trang
- Centre for Computational Medicine Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Elise Valkanas
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Nicole Vasilevsky
- Library; and Department of Medical Informatics and Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
| | - Colleen Wahl
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Lynne A. Wolfe
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Cornelius F. Boerkoel
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Brudno
- Centre for Computational Medicine Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Melissa A. Haendel
- Library; and Department of Medical Informatics and Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
| | - William A. Gahl
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
- Medical Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Damian Smedley
- Skarnes Faculty group, Wellcome Trust Sanger Institute, Hinxton, UK
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17
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Srour M, Caron V, Pearson T, Nielsen SB, Lévesque S, Delrue MA, Becker TA, Hamdan FF, Kibar Z, Sattler SG, Schneider MC, Bitoun P, Chassaing N, Rosenfeld JA, Xia F, Desai S, Roeder E, Kimonis V, Schneider A, Littlejohn RO, Douzgou S, Tremblay A, Michaud JL. Gain-of-Function Mutations inRARBCause Intellectual Disability with Progressive Motor Impairment. Hum Mutat 2016; 37:786-93. [DOI: 10.1002/humu.23004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/04/2016] [Accepted: 04/12/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Myriam Srour
- CHU Sainte-Justine Research Center; Montréal H3T 1C5 Canada
- Department of Pediatrics; Neurology and Neurosurgery; McGill University; Montreal H3A 1A4 Canada
| | | | - Toni Pearson
- Department of Neurology; Icahn School of Medicine at Mount Sinai; New York New York 10029
| | | | - Sébastien Lévesque
- Division of Medical Genetics; Department of Pediatrics; Centre Hospitalier Universitaire de Sherbrooke; Sherbrooke J1H 5N4 Canada
| | - Marie-Ange Delrue
- Department of Pediatrics; Université de Montréal; Montreal H3T 1J4 Canada
| | - Troy A. Becker
- Division of Genetics and Metabolism; All Children's Hospital; St-Petersburg Florida 33701
| | - Fadi F. Hamdan
- CHU Sainte-Justine Research Center; Montréal H3T 1C5 Canada
| | - Zoha Kibar
- CHU Sainte-Justine Research Center; Montréal H3T 1C5 Canada
- Department of Neurosciences; Université de Montréal; Montreal H3T 1J4 Canada
| | | | | | - Pierre Bitoun
- Génétique Médicale; Hôpital Jean Verdier AP-HP; C.H.U. Paris Nord Bondy 93140 France
| | - Nicolas Chassaing
- Service de Génétique Médicale; Hôpital Purpan; CHU Toulouse Toulouse 31059 France
- Université Paul-Sabatier; Toulouse III, EA-4555 and Inserm U1056 Toulouse 31000 France
| | | | - Fan Xia
- Baylor College of Medicine; Houston Texas 77030
| | - Sonal Desai
- Department of Neurogenetics; Kennedy Krieger Institute; Baltimore Maryland 21205
| | | | - Virginia Kimonis
- Division of Genetics and Genomic Medicine; Univerity of California-Irvine Medical Center; Orange California 92868
| | - Adele Schneider
- Division of Genetics and Genomic Medicine; Univerity of California-Irvine Medical Center; Orange California 92868
| | | | - Sofia Douzgou
- Manchester Centre for Genomic Medicine; Central Manchester University Hospitals NHS Foundation Trust; MAHSC; Saint Mary's Hospital; Manchester M13 9WL UK
| | - André Tremblay
- CHU Sainte-Justine Research Center; Montréal H3T 1C5 Canada
- Department of Obstetrics and Gynecology; Université de Montréal; Montreal H3T 1J4 Canada
- Department of Biochemistry and Molecular Medicine; Université de Montréal; Montreal H3T 1J4 Canada
| | - Jacques L. Michaud
- CHU Sainte-Justine Research Center; Montréal H3T 1C5 Canada
- Department of Pediatrics; Université de Montréal; Montreal H3T 1J4 Canada
- Department of Neurosciences; Université de Montréal; Montreal H3T 1J4 Canada
- Department of Biochemistry and Molecular Medicine; Université de Montréal; Montreal H3T 1J4 Canada
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