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Wang A, Liu C, Yang J, Weng C. Fine-tuning Large Language Models for Rare Disease Concept Normalization. bioRxiv 2024:2023.12.28.573586. [PMID: 38234802 PMCID: PMC10793431 DOI: 10.1101/2023.12.28.573586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Objective We aim to develop a novel method for rare disease concept normalization by fine-tuning Llama 2, an open-source large language model (LLM), using a domain-specific corpus sourced from the Human Phenotype Ontology (HPO). Methods We developed an in-house template-based script to generate two corpora for fine-tuning. The first (NAME) contains standardized HPO names, sourced from the HPO vocabularies, along with their corresponding identifiers. The second (NAME+SYN) includes HPO names and half of the concept's synonyms as well as identifiers. Subsequently, we fine-tuned Llama2 (Llama2-7B) for each sentence set and conducted an evaluation using a range of sentence prompts and various phenotype terms. Results When the phenotype terms for normalization were included in the fine-tuning corpora, both models demonstrated nearly perfect performance, averaging over 99% accuracy. In comparison, ChatGPT-3.5 has only ~20% accuracy in identifying HPO IDs for phenotype terms. When single-character typos were introduced in the phenotype terms, the accuracy of NAME and NAME+SYN is 10.2% and 36.1%, respectively, but increases to 61.8% (NAME+SYN) with additional typo-specific fine-tuning. For terms sourced from HPO vocabularies as unseen synonyms, the NAME model achieved 11.2% accuracy, while the NAME+SYN model achieved 92.7% accuracy. Conclusion Our fine-tuned models demonstrate ability to normalize phenotype terms unseen in the fine-tuning corpus, including misspellings, synonyms, terms from other ontologies, and laymen's terms. Our approach provides a solution for the use of LLM to identify named medical entities from the clinical narratives, while successfully normalizing them to standard concepts in a controlled vocabulary.
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Affiliation(s)
- Andy Wang
- Peddie School, Hightstown, NJ, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Jingye Yang
- Department of Mathematics, University of Pennsylvania, Philadelphia, PA, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
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2
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Liu Z, Fu S, He X, Dai L, Liu X, Narisu, Shi C, Gu M, Wang Y, Manda, Guo L, Bao Y, Baiyinbatu, Chang C, Liu Y, Zhang W. Integrated Multi-Tissue Transcriptome Profiling Characterizes the Genetic Basis and Biomarkers Affecting Reproduction in Sheep ( Ovis aries). Genes (Basel) 2023; 14:1881. [PMID: 37895230 PMCID: PMC10606288 DOI: 10.3390/genes14101881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
The heritability of litter size in sheep is low and controlled by multiple genes, but the research on its related genes is not sufficient. Here, to explore the expression pattern of multi-tissue genes in Chinese native sheep, we selected 10 tissues of the three adult ewes with the highest estimated breeding value in the early study of the prolific Xinggao sheep population. The global gene expression analysis showed that the ovary, uterus, and hypothalamus expressed the most genes. Using the Uniform Manifold Approximation and Projection (UMAP) cluster analysis, these samples were clustered into eight clusters. The functional enrichment analysis showed that the genes expressed in the spleen, uterus, and ovary were significantly enriched in the Ataxia Telangiectasia Mutated Protein (ATM) signaling pathway, and most genes in the liver, spleen, and ovary were enriched in the immune response pathway. Moreover, we focus on the expression genes of the hypothalamic-pituitary-ovarian axis (HPO) and found that 11,016 genes were co-expressed in the three tissues, and different tissues have different functions, but the oxytocin signaling pathway was widely enriched. To further explore the differences in the expression genes (DEGs) of HPO in different sheep breeds, we downloaded the transcriptome data in the public data, and the analysis of DEGs (Xinggao sheep vs. Sunite sheep in Hypothalamus, Xinggao sheep vs. Sunite sheep in Pituitary, and Xinggao sheep vs. Suffolk sheep in Ovary) revealed the neuroactive ligand-receptor interactions. In addition, the gene subsets of the transcription factors (TFs) of DEGs were identified. The results suggest that 51 TF genes and the homeobox TF may play an important role in transcriptional variation across the HPO. Altogether, our study provided the first fundamental resource to investigate the physiological functions and regulation mechanisms in sheep. This important data contributes to improving our understanding of the reproductive biology of sheep and isolating effecting molecular markers that can be used for genetic selection in sheep.
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Affiliation(s)
- Zaixia Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
| | - Shaoyin Fu
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (S.F.); (X.H.)
| | - Xiaolong He
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (S.F.); (X.H.)
| | - Lingli Dai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
- Veterinary Research Institute, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Xuewen Liu
- Animal Husbandry and Bioengineering, College of Agronomy, Xing’an Vocational and Technical College, Ulanhot 137400, China;
| | - Narisu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
| | - Caixia Shi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
| | - Mingjuan Gu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
| | - Yu Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China;
| | - Manda
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
| | - Lili Guo
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
- School of Life Science, Inner Mongolia University, Hohhot 010021, China;
| | - Yanchun Bao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
| | - Baiyinbatu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
| | - Chencheng Chang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
| | - Yongbin Liu
- School of Life Science, Inner Mongolia University, Hohhot 010021, China;
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
- College of Life Science, Inner Mongolia Agricultural University, Hohhot 010018, China
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González-Quintana A, Garrido-Moraga R, Palencia-Pérez SI, Hernández-Martín Á, Sánchez-Munárriz J, Lezana-Rosales JM, Quesada-Espinosa JF, Martín MA, Arteche-López A. Integration of Phenotype Term Prioritization and Gene Expression Analysis Reveals a Novel Variant in the PERP Gene Associated with Autosomal Recessive Erythrokeratoderma. Genes (Basel) 2023; 14:1494. [PMID: 37510397 PMCID: PMC10379359 DOI: 10.3390/genes14071494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Hereditary palmoplantar keratodermas (PPKs) are a clinically and genetically heterogeneous group of disorders characterized by excessive epidermal thickening of palms and soles. Several genes have been associated with PPK including PERP, a gene encoding a crucial component of desmosomes that has been associated with dominant and recessive keratoderma. We report a patient with recessive erythrokeratoderma (EK) in which whole exome sequencing (WES) prioritized by human phenotype ontology (HPO) terms revealed the presence of the novel variant c.153C > A in the N-terminal region the PERP gene. This variant is predicted to have a nonsense effect, p.(Cys51Ter), resulting in a premature stop codon. We demonstrated a marked reduction in gene expression in cultured skin fibroblasts obtained from the patient. Despite the PERP gene is expressed at low levels in fibroblasts, our finding supports a loss-of-function (LoF) mechanism for the identified variant, as previously suggested in recessive EK. Our study underscores the importance of integrating HPO analysis when using WES for molecular genetic diagnosis in a clinical setting, as it facilitates continuous updates regarding gene-clinical feature associations.
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Affiliation(s)
- Adrián González-Quintana
- Servicio Bioquímica Clínica/Análisis Clínicos, Hospital 12 de Octubre, 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
- Grupo de Enfermedades Mitocondriales y Neurometabólicas, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Rocío Garrido-Moraga
- Grupo de Enfermedades Mitocondriales y Neurometabólicas, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Sara I Palencia-Pérez
- Departamento de Dermatología, Hospital Universitario 12 de Octubre y Universidad Complutense de Madrid, 28041 Madrid, Spain
| | - Ángela Hernández-Martín
- Departamento de Dermatología, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain
| | - Jon Sánchez-Munárriz
- Servicio Bioquímica Clínica/Análisis Clínicos, Hospital 12 de Octubre, 28041 Madrid, Spain
| | - José M Lezana-Rosales
- Servicio de Genética, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- UDisGen (Unidad de Dismorfología y Genética), Hospital 12 de Octubre, 28041 Madrid, Spain
| | - Juan F Quesada-Espinosa
- Servicio de Genética, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- UDisGen (Unidad de Dismorfología y Genética), Hospital 12 de Octubre, 28041 Madrid, Spain
| | - Miguel A Martín
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
- Grupo de Enfermedades Mitocondriales y Neurometabólicas, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Servicio de Genética, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- UDisGen (Unidad de Dismorfología y Genética), Hospital 12 de Octubre, 28041 Madrid, Spain
| | - Ana Arteche-López
- Servicio de Genética, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- UDisGen (Unidad de Dismorfología y Genética), Hospital 12 de Octubre, 28041 Madrid, Spain
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4
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Scott JM, Linderman JR, Deuster PA. Hydration: Tactical and Practical Strategies. J Spec Oper Med 2023; 23:88-91. [PMID: 36827684 DOI: 10.55460/qobg-htox] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/01/2023] [Indexed: 05/24/2023]
Abstract
Full-spectrum Human Performance Optimization (HPO) is essential for Special Operations Forces (SOF). Adequate hydration is essential to all aspects of performance (physical and cognitive) and recovery. Water losses occur as a result of physical activity and can increase further depending on clothing and environmental conditions. Without intentional and appropriate strategic hydration planning, Operators are at increased risk for degradation in performance and exertional heat illness. The purpose of this article is to highlight current best practices for maintaining hydration before, during, and after activity, while considering various environmental conditions. Effective leadership and planning are necessary for preparing Operators for successful military operations.
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5
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Zamariolli M, Auwerx C, Sadler MC, van der Graaf A, Lepik K, Schoeler T, Moysés-Oliveira M, Dantas AG, Melaragno MI, Kutalik Z. The impact of 22q11.2 copy-number variants on human traits in the general population. Am J Hum Genet 2023; 110:300-313. [PMID: 36706759 PMCID: PMC9943723 DOI: 10.1016/j.ajhg.2023.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/03/2023] [Indexed: 01/27/2023] Open
Abstract
While extensively studied in clinical cohorts, the phenotypic consequences of 22q11.2 copy-number variants (CNVs) in the general population remain understudied. To address this gap, we performed a phenome-wide association scan in 405,324 unrelated UK Biobank (UKBB) participants by using CNV calls from genotyping array. We mapped 236 Human Phenotype Ontology terms linked to any of the 90 genes encompassed by the region to 170 UKBB traits and assessed the association between these traits and the copy-number state of 504 genotyping array probes in the region. We found significant associations for eight continuous and nine binary traits associated under different models (duplication-only, deletion-only, U-shape, and mirror models). The causal effect of the expression level of 22q11.2 genes on associated traits was assessed through transcriptome-wide Mendelian randomization (TWMR), revealing that increased expression of ARVCF increased BMI. Similarly, increased DGCR6 expression causally reduced mean platelet volume, in line with the corresponding CNV effect. Furthermore, cross-trait multivariable Mendelian randomization (MVMR) suggested a predominant role of genuine (horizontal) pleiotropy in the CNV region. Our findings show that within the general population, 22q11.2 CNVs are associated with traits previously linked to genes in the region, and duplications and deletions act upon traits in different fashions. We also showed that gain or loss of distinct segments within 22q11.2 may impact a trait under different association models. Our results have provided new insights to help further the understanding of the complex 22q11.2 region.
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Affiliation(s)
- Malú Zamariolli
- Genetics Division, Universidade Federal de São Paulo, São Paulo, Brazil; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Chiara Auwerx
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland; Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Marie C Sadler
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
| | | | - Kaido Lepik
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Tabea Schoeler
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | | | - Anelisa G Dantas
- Genetics Division, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland.
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6
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Santen GWE, Leitch HG, Cobben J. Gene-disease relationship evidence: A clinical perspective focusing on ultra-rare diseases. Hum Mutat 2022; 43:1082-1088. [PMID: 35266245 PMCID: PMC9544306 DOI: 10.1002/humu.24367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/26/2022] [Accepted: 03/04/2022] [Indexed: 11/09/2022]
Abstract
The ACMG framework for variant interpretation is well-established and widely used. Although formal guidelines have been published on the establishment of the gene-disease relationships as well, these are not nearly as widely acknowledged or utilized, and implementation of these guidelines is lagging. In addition, for many genes so little information is available that the framework cannot be used in sufficient detail. In this manuscript, we highlight the importance of distinguishing between phenotype-first and genotype-first gene-disease relationships. We discuss the approaches currently available to establish gene-disease relationships and suggest a checklist to assist in evaluating gene-disease relationships for genes with very little available information. Several real-life examples from clinical practice are given to illustrate the importance of a thorough thought process on gene-disease relationships. We hope that these considerations and the checklist will provide help for clinicians and clinical scientists faced which variants in genes without robustly ascertained gene-disease relationships.
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Affiliation(s)
- Gijs W. E. Santen
- Department of Clinical GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Harry G. Leitch
- North West Thames Genetics ServiceNorthwick Park and St. Mark's HospitalsLondonUK
- Centre for Paediatrics and Child Health, Faculty of MedicineImperial College LondonLondonUK
- Institute of Clinical Sciences, Faculty of MedicineImperial College LondonLondonUK
- MRC London Institute of Medical SciencesLondonUK
| | - Jan Cobben
- North West Thames Genetics ServiceNorthwick Park and St. Mark's HospitalsLondonUK
- Centre for Paediatrics and Child Health, Faculty of MedicineImperial College LondonLondonUK
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Dhombres F, Morgan P, Chaudhari BP, Filges I, Sparks TN, Lapunzina P, Roscioli T, Agarwal U, Aggarwal S, Beneteau C, Cacheiro P, Carmody LC, Collardeau‐Frachon S, Dempsey EA, Dufke A, Duyzend MH, el Ghosh M, Giordano JL, Glad R, Grinfelde I, Iliescu DG, Ladewig MS, Munoz‐Torres MC, Pollazzon M, Radio FC, Rodo C, Silva RG, Smedley D, Sundaramurthi JC, Toro S, Valenzuela I, Vasilevsky NA, Wapner RJ, Zemet R, Haendel MA, Robinson PN. Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology. Am J Med Genet C Semin Med Genet 2022; 190:231-242. [PMID: 35872606 PMCID: PMC9588534 DOI: 10.1002/ajmg.c.31989] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/01/2022] [Indexed: 01/07/2023]
Abstract
Technological advances in both genome sequencing and prenatal imaging are increasing our ability to accurately recognize and diagnose Mendelian conditions prenatally. Phenotype-driven early genetic diagnosis of fetal genetic disease can help to strategize treatment options and clinical preventive measures during the perinatal period, to plan in utero therapies, and to inform parental decision-making. Fetal phenotypes of genetic diseases are often unique and at present are not well understood; more comprehensive knowledge about prenatal phenotypes and computational resources have an enormous potential to improve diagnostics and translational research. The Human Phenotype Ontology (HPO) has been widely used to support diagnostics and translational research in human genetics. To better support prenatal usage, the HPO consortium conducted a series of workshops with a group of domain experts in a variety of medical specialties, diagnostic techniques, as well as diseases and phenotypes related to prenatal medicine, including perinatal pathology, musculoskeletal anomalies, neurology, medical genetics, hydrops fetalis, craniofacial malformations, cardiology, neonatal-perinatal medicine, fetal medicine, placental pathology, prenatal imaging, and bioinformatics. We expanded the representation of prenatal phenotypes in HPO by adding 95 new phenotype terms under the Abnormality of prenatal development or birth (HP:0001197) grouping term, and revised definitions, synonyms, and disease annotations for most of the 152 terms that existed before the beginning of this effort. The expansion of prenatal phenotypes in HPO will support phenotype-driven prenatal exome and genome sequencing for precision genetic diagnostics of rare diseases to support prenatal care.
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Affiliation(s)
- Ferdinand Dhombres
- Sorbonne University, GRC26, INSERM, Limics, Armand Trousseau Hospital, Fetal Medicine Department, APHPParisFrance
| | - Patricia Morgan
- American College of Medical Genetics and Genomics, Newborn Screening Translational Research NetworkBethesdaMarylandUSA
| | - Bimal P. Chaudhari
- Institute for Genomic MedicineNationwide Children's HospitalColumbusOhioUSA
| | - Isabel Filges
- University Hospital Basel and University of Basel, Medical GeneticsBaselSwitzerland
| | - Teresa N. Sparks
- Department of Obstetrics, Gynecology, & Reproductive SciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Pablo Lapunzina
- CIBERER and Hospital Universitario La Paz, INGEMM‐Institute of Medical and Molecular GeneticsMadridSpain
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), University of New South WalesSydneyNew South WalesAustralia
| | - Umber Agarwal
- Department of Maternal and Fetal MedicineLiverpool Women's NHS Foundation TrustLiverpoolUK
| | - Shagun Aggarwal
- Department of Medical GeneticsNizam's Institute of Medical SciencesHyderabadTelanganaIndia
| | - Claire Beneteau
- Service de Génétique Médicale, UF 9321 de Fœtopathologie et Génétique, CHU de NantesNantesFrance
| | - Pilar Cacheiro
- William Harvey Research InstituteQueen Mary University of LondonLondonUK
| | - Leigh C. Carmody
- Department of Genomic MedicineThe Jackson LaboratoryFarmingtonConnecticutUSA
| | | | - Esther A. Dempsey
- St George's University of London, Molecular and Clinical Sciences Research InstituteLondonUK
| | - Andreas Dufke
- University of Tübingen, Institute of Medical Genetics and Applied GenomicsTübingenGermany
| | | | | | - Jessica L. Giordano
- Department of Obstetrics and GynecologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Ragnhild Glad
- Department of Obstetrics and GynecologyUniversity Hospital of North NorwayTromsøNorway
| | - Ieva Grinfelde
- Department of Medical Genetics and Prenatal diagnosisChildren's University HospitalRigaLatvia
| | - Dominic G. Iliescu
- Department of Obstetrics and GynecologyUniversity of Medicine and Pharmacy CraiovaCraiovaDoljRomania
| | - Markus S. Ladewig
- Department of OphthalmologyKlinikum SaarbrückenSaarbrückenSaarlandGermany
| | - Monica C. Munoz‐Torres
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Marzia Pollazzon
- Azienda USL‐IRCCS di Reggio EmiliaMedical Genetics UnitReggio EmiliaItaly
| | | | - Carlota Rodo
- Vall d'Hebron Hospital Campus, Maternal & Fetal MedicineBarcelonaSpain
| | - Raquel Gouveia Silva
- Hospital Santa Maria, Serviço de Genética, Departamento de PediatriaHospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Centro Académico de Medicina de LisboaLisboaPortugal
| | - Damian Smedley
- William Harvey Research InstituteQueen Mary University of LondonLondonUK
| | | | - Sabrina Toro
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Irene Valenzuela
- Hospital Vall d'Hebron, Clinical and Molecular Genetics AreaBarcelonaSpain
| | - Nicole A. Vasilevsky
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Ronald J. Wapner
- Department of Obstetrics and GynecologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Roni Zemet
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Melissa A Haendel
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Peter N. Robinson
- Department of Genomic MedicineThe Jackson LaboratoryFarmingtonConnecticutUSA
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Herman I, Jolly A, Du H, Dawood M, Abdel-Salam GMH, Marafi D, Mitani T, Calame DG, Coban-Akdemir Z, Fatih JM, Hegazy I, Jhangiani SN, Gibbs RA, Pehlivan D, Posey JE, Lupski JR. Quantitative dissection of multilocus pathogenic variation in an Egyptian infant with severe neurodevelopmental disorder resulting from multiple molecular diagnoses. Am J Med Genet A 2022; 188:735-750. [PMID: 34816580 PMCID: PMC8837671 DOI: 10.1002/ajmg.a.62565] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/11/2021] [Accepted: 10/18/2021] [Indexed: 12/19/2022]
Abstract
Genomic sequencing and clinical genomics have demonstrated that substantial subsets of atypical and/or severe disease presentations result from multilocus pathogenic variation (MPV) causing blended phenotypes. In an infant with a severe neurodevelopmental disorder, four distinct molecular diagnoses were found by exome sequencing (ES). The blended phenotype that includes brain malformation, dysmorphism, and hypotonia was dissected using the Human Phenotype Ontology (HPO). ES revealed variants in CAPN3 (c.259C > G:p.L87V), MUSK (c.1781C > T:p.A594V), NAV2 (c.1996G > A:p.G666R), and ZC4H2 (c.595A > C:p.N199H). CAPN3, MUSK, and ZC4H2 are established disease genes linked to limb-girdle muscular dystrophy (OMIM# 253600), congenital myasthenia (OMIM# 616325), and Wieacker-Wolff syndrome (WWS; OMIM# 314580), respectively. NAV2 is a retinoic-acid responsive novel disease gene candidate with biological roles in neurite outgrowth and cerebellar dysgenesis in mouse models. Using semantic similarity, we show that no gene identified by ES individually explains the proband phenotype, but rather the totality of the clinically observed disease is explained by the combination of disease-contributing effects of the identified genes. These data reveal that multilocus pathogenic variation can result in a blended phenotype with each gene affecting a different part of the nervous system and nervous system-muscle connection. We provide evidence from this n = 1 study that in patients with MPV and complex blended phenotypes resulting from multiple molecular diagnoses, quantitative HPO analysis can allow for dissection of phenotypic contribution of both established disease genes and novel disease gene candidates not yet proven to cause human disease.
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Affiliation(s)
- Isabella Herman
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Ghada M. H. Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait,Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Daniel G. Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Ibrahim Hegazy
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Shalini N. Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Texas Children's Hospital, Houston, Texas, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030
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9
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Osmond M, Hartley T, Johnstone B, Andjic S, Girdea M, Gillespie M, Buske O, Dumitriu S, Koltunova V, Ramani A, Boycott KM, Brudno M. PhenomeCentral: 7 years of rare disease matchmaking. Hum Mutat 2022; 43:674-681. [PMID: 35165961 DOI: 10.1002/humu.24348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 11/08/2022]
Abstract
A major challenge in validating genetic causes for patients with rare diseases (RDs) is the difficulty in identifying other RD patients with overlapping phenotypes and variants in the same candidate gene. This process, known as matchmaking, requires robust data sharing solutions in order to be effective. In 2014 we launched PhenomeCentral, a RD data repository capable of collecting computer-readable genotypic and phenotypic data for the purposes of RD matchmaking. Over the past 7 years PhenomeCentral's features have been expanded and its dataset has consistently grown. There are currently 1,615 users registered on PhenomeCentral, which have contributed over 12,000 patient cases. Most of these cases contain detailed phenotypic terms, with a significant portion also providing genomic sequence data or other forms of clinical information. Matchmaking within PhenomeCentral, and with connections to other data repositories in the Matchmaker Exchange, have collectively resulted in over 60,000 matches, which have facilitated multiple gene discoveries. The collection of deep phenotypic and genotypic data has also positioned PhenomeCentral well to support next generation of matchmaking initiatives that utilize genome sequencing data, ensuring that PhenomeCentral will remain a useful tool in solving undiagnosed RD cases in the years to come. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, ON, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, ON, Canada
| | - Brittney Johnstone
- Cancer Genetics and High Risk Program, Sunnybrook Health Sciences Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sasha Andjic
- DATA Team and Techna Institute, University Health Network, Toronto, ON, Canada
| | - Marta Girdea
- DATA Team and Techna Institute, University Health Network, Toronto, ON, Canada
| | - Meredith Gillespie
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, ON, Canada
| | | | - Sergiu Dumitriu
- DATA Team and Techna Institute, University Health Network, Toronto, ON, Canada
| | - Veronika Koltunova
- DATA Team and Techna Institute, University Health Network, Toronto, ON, Canada
| | - Arun Ramani
- Hospital for Sick Children, Toronto, ON, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, ON, Canada
| | - Michael Brudno
- DATA Team and Techna Institute, University Health Network, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, ON, Canada.,Hospital for Sick Children, Toronto, ON, Canada
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10
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Fujiwara T, Shin JM, Yamaguchi A. Advances in the development of PubCaseFinder, including the new application programming interface and matching algorithm. Hum Mutat 2022; 43:734-742. [PMID: 35143083 PMCID: PMC9305291 DOI: 10.1002/humu.24341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/17/2022] [Accepted: 02/07/2022] [Indexed: 11/11/2022]
Abstract
Over 10,000 rare genetic diseases have been identified, and millions of newborns are affected by severe rare genetic diseases each year. A variety of Human Phenotype Ontology (HPO)-based clinical decision support systems (CDSS) and patient repositories have been developed to support clinicians in diagnosing patients with suspected rare genetic diseases. In September 2017, we released PubCaseFinder (https://pubcasefinder.dbcls.jp), a web-based CDSS that provides ranked lists of genetic and rare diseases using HPO-based phenotypic similarities, where top-listed diseases represent the most likely differential diagnosis. We also developed a Matchmaker Exchange (MME) application programming interface (API) to query PubCaseFinder, which has been adopted by several patient repositories. In this paper, we describe notable updates regarding PubCaseFinder, the GeneYenta matching algorithm implemented in PubCaseFinder, and the PubCaseFinder API. The updated GeneYenta matching algorithm improves the performance of the CDSS automated differential diagnosis function. Moreover, the updated PubCaseFinder and new API empower patient repositories participating in MME and medical professionals to actively use HPO-based resources. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Toyofumi Fujiwara
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa-shi, Chiba-ken, 277-0871, Japan
| | - Jae-Moon Shin
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa-shi, Chiba-ken, 277-0871, Japan
| | - Atsuko Yamaguchi
- Graduate School of Integrative Science and Engineering, Tokyo City University, Setagaya-ku, Tokyo, 158-8557, Japan
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11
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Yuan X, Wang J, Dai B, Sun Y, Zhang K, Chen F, Peng Q, Huang Y, Zhang X, Chen J, Xu X, Chuan J, Mu W, Li H, Fang P, Gong Q, Zhang P. Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases. Brief Bioinform 2022; 23:6521702. [PMID: 35134823 PMCID: PMC8921623 DOI: 10.1093/bib/bbac019] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/10/2022] [Accepted: 01/13/2022] [Indexed: 12/31/2022] Open
Abstract
It’s challenging work to identify disease-causing genes from the next-generation sequencing (NGS) data of patients with Mendelian disorders. To improve this situation, researchers have developed many phenotype-driven gene prioritization methods using a patient’s genotype and phenotype information, or phenotype information only as input to rank the candidate’s pathogenic genes. Evaluations of these ranking methods provide practitioners with convenience for choosing an appropriate tool for their workflows, but retrospective benchmarks are underpowered to provide statistically significant results in their attempt to differentiate. In this research, the performance of ten recognized causal-gene prioritization methods was benchmarked using 305 cases from the Deciphering Developmental Disorders (DDD) project and 209 in-house cases via a relatively unbiased methodology. The evaluation results show that methods using Human Phenotype Ontology (HPO) terms and Variant Call Format (VCF) files as input achieved better overall performance than those using phenotypic data alone. Besides, LIRICAL and AMELIE, two of the best methods in our benchmark experiments, complement each other in cases with the causal genes ranked highly, suggesting a possible integrative approach to further enhance the diagnostic efficiency. Our benchmarking provides valuable reference information to the computer-assisted rapid diagnosis in Mendelian diseases and sheds some light on the potential direction of future improvement on disease-causing gene prioritization methods.
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Affiliation(s)
- Xiao Yuan
- Changsha KingMed Center for Clinical Laboratory, Changsha, China.,Guangzhou Kingmed Center for Clinical Laboratory, Guangzhou, China.,Genetalks Biotech. Co., Ltd., Changsha, China
| | - Jing Wang
- Changsha KingMed Center for Clinical Laboratory, Changsha, China
| | - Bing Dai
- Changsha KingMed Center for Clinical Laboratory, Changsha, China
| | - Yanfang Sun
- Changsha KingMed Center for Clinical Laboratory, Changsha, China
| | - Keke Zhang
- Changsha KingMed Center for Clinical Laboratory, Changsha, China
| | - Fangfang Chen
- Changsha KingMed Center for Clinical Laboratory, Changsha, China
| | - Qian Peng
- Changsha KingMed Center for Clinical Laboratory, Changsha, China
| | - Yixuan Huang
- Beijing Geneworks Technology Co., Ltd., Beijing, China
| | - Xinlei Zhang
- Reproductive & Genetics Hospital of Citic & Xiangya, Changsha, China
| | - Junru Chen
- Genetalks Biotech. Co., Ltd., Changsha, China
| | - Xilin Xu
- Guangzhou Kingmed Center for Clinical Laboratory, Guangzhou, China
| | - Jun Chuan
- Changsha KingMed Center for Clinical Laboratory, Changsha, China.,Guangzhou Kingmed Center for Clinical Laboratory, Guangzhou, China
| | - Wenbo Mu
- Guangzhou Kingmed Center for Clinical Laboratory, Guangzhou, China
| | - Huiyuan Li
- Changsha KingMed Center for Clinical Laboratory, Changsha, China.,Guangzhou Kingmed Center for Clinical Laboratory, Guangzhou, China
| | - Ping Fang
- Guangzhou Kingmed Center for Clinical Laboratory, Guangzhou, China
| | - Qiang Gong
- Changsha KingMed Center for Clinical Laboratory, Changsha, China.,Guangzhou Kingmed Center for Clinical Laboratory, Guangzhou, China
| | - Peng Zhang
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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12
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de Waal A, Kraaijveld E. Learnings from a successful transformation to a high-performance organization: a longitudinal case study. SN Bus Econ 2022; 2:177. [PMID: 36312213 DOI: 10.1007/s43546-022-00354-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 10/11/2022] [Indexed: 11/07/2022]
Abstract
An increasing number of organizations embark on a journey to transform themselves into a high-performance organization (HPO) to be able to better deal with the changes in their environment. Unfortunately, in the current literature hardly any approaches are described that can support them during this transformation. One promising approach, the (Waal and Heijtel, Meas Bus Excell 21:101–116, 2017) HPO transformation approach, has only been validated in one instance. This study outlines an additional validated approach. A simplified version of the aforementioned transformation approach (Waal et al. The high-performance finance function, handbook for the future-oriented financial professional, IGI Global, Hershey, 2022) was used at a case company which in 5 year time transformed into an HPO. Based on a questionnaire which collected and evaluated interventions undertaken by the case company, coupled with an extensive interview on the interventions with the manager of the case company, the interventions were categorized in the HPO transformation approach. The HPO transformation approach made it possible to make a structured overview of the interventions, which gave insight into how the case company went about its successful HPO transformation. Thus, the research has both a theoretical and practical contribution. Theoretically, the currently rather limited academic literature on transformation approaches regarding high-performance organizations is extended with another validated case, thus further developing this line of research. Practically, organizations get access to a validated transformation approach, thereby increasing their chance on a successful HPO transformation.
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13
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Haimel M, Pazmandi J, Heredia RJ, Dmytrus J, Bal SK, Zoghi S, van Daele P, Briggs TA, Wouters C, Bader-Meunier B, Aeschlimann FA, Caorsi R, Eleftheriou D, Hoppenreijs E, Salzer E, Bakhtiar S, Derfalvi B, Saettini F, Kusters MAA, Elfeky R, Trück J, Rivière JG, van der Burg M, Gattorno M, Seidel MG, Burns S, Warnatz K, Hauck F, Brogan P, Gilmour KC, Schuetz C, Simon A, Bock C, Hambleton S, de Vries E, Robinson PN, van Gijn M, Boztug K. Curation and expansion of Human Phenotype Ontology for defined groups of inborn errors of immunity. J Allergy Clin Immunol 2022; 149:369-378. [PMID: 33991581 PMCID: PMC9346194 DOI: 10.1016/j.jaci.2021.04.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Accurate, detailed, and standardized phenotypic descriptions are essential to support diagnostic interpretation of genetic variants and to discover new diseases. The Human Phenotype Ontology (HPO), extensively used in rare disease research, provides a rich collection of vocabulary with standardized phenotypic descriptions in a hierarchical structure. However, to date, the use of HPO has not yet been widely implemented in the field of inborn errors of immunity (IEIs), mainly due to a lack of comprehensive IEI-related terms. OBJECTIVES We sought to systematically review available terms in HPO for the depiction of IEIs, to expand HPO, yielding more comprehensive sets of terms, and to reannotate IEIs with HPO terms to provide accurate, standardized phenotypic descriptions. METHODS We initiated a collaboration involving expert clinicians, geneticists, researchers working on IEIs, and bioinformaticians. Multiple branches of the HPO tree were restructured and extended on the basis of expert review. Our ontology-guided machine learning coupled with a 2-tier expert review was applied to reannotate defined subgroups of IEIs. RESULTS We revised and expanded 4 main branches of the HPO tree. Here, we reannotated 73 diseases from 4 International Union of Immunological Societies-defined IEI disease subgroups with HPO terms. We achieved a 4.7-fold increase in the number of phenotypic terms per disease. Given the new HPO annotations, we demonstrated improved ability to computationally match selected IEI cases to their known diagnosis, and improved phenotype-driven disease classification. CONCLUSIONS Our targeted expansion and reannotation presents enhanced precision of disease annotation, will enable superior HPO-based IEI characterization, and hence benefit both IEI diagnostic and research activities.
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Affiliation(s)
- Matthias Haimel
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Julia Pazmandi
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Raúl Jiménez Heredia
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jasmin Dmytrus
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sevgi Köstel Bal
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Samaneh Zoghi
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Paul van Daele
- Department of Clinical Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tracy A Briggs
- NW Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Carine Wouters
- Department of Microbiology and Immunology, Immunobiology, KU Leuven, Leuven, Belgium; Department of Pediatrics, Division of Pediatric Rheumatology, University Hospitals Leuven, Leuven, Belgium
| | - Brigitte Bader-Meunier
- Pediatric Immuno-Hematology and Rheumatology Unit, Necker Hospital for Sick Children - AP-HP, Paris, France; Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE), Paris, France
| | - Florence A Aeschlimann
- Pediatric Immuno-Hematology and Rheumatology Unit, Necker Hospital for Sick Children - AP-HP, Paris, France; Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE), Paris, France
| | - Roberta Caorsi
- Center for Autoinflammatory Diseases and Immunodeficiency, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Despina Eleftheriou
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Esther Hoppenreijs
- Department of Paediatric Rheumatology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Elisabeth Salzer
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; St Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Shahrzad Bakhtiar
- Department for Children and Adolescents, Division for Stem Cell Transplantation, Immunology and Intensive Care Unit, Goethe University, Frankfurt, Germany
| | - Beata Derfalvi
- Department of Pediatrics, Division of Immunology, Dalhousie University/IWK Health Centre Halifax, Halifax, Nova Scotia, Canada
| | - Francesco Saettini
- Pediatric Hematology Department, Fondazione MBBM, University of Milano Bicocca, via Pergolesi 33, Monza, Italy
| | - Maaike A A Kusters
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Reem Elfeky
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Johannes Trück
- Division of Immunology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Jacques G Rivière
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain; Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Mirjam van der Burg
- Department of Immunology, University Medical Center Rotterdam, Rotterdam, The Netherlands; Laboratory for Pediatric Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marco Gattorno
- Center for Autoinflammatory Diseases and Immunodeficiency, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Markus G Seidel
- Research Unit for Pediatric Hematology and Immunology, Division of Pediatric Hemato-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University Graz, Graz, Austria
| | - Siobhan Burns
- Department of Immunology, UCL Institute of Immunity & Transplantation, Department of Immunology, Royal Free Hospital NHS Foundation Trust, London, United Kingdom
| | - Klaus Warnatz
- Division of Immunodeficiency, Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Fabian Hauck
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany; Munich Centre for Rare Diseases (M-ZSE(LMU)), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paul Brogan
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Kimberly C Gilmour
- Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Catharina Schuetz
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Anna Simon
- Radboudumc Expertise Centre for Immunodeficiency and Autoinflammation (REIA), Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Christoph Bock
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Institute of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Sophie Hambleton
- Immunity and Inflammation Theme, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Esther de Vries
- Tranzo, Tilburg University, Tilburg, The Netherlands; Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | | | - Marielle van Gijn
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands.
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria; St Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.
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Abstract
Clinical characterization of a patient phenotype has been the quintessential approach for elucidating a differential diagnosis and a hypothesis to explore a potential clinical diagnosis. This has resulted in a language of medicine and a semantic ontology, with both specialty- and subspecialty-specific lexicons, that can be challenging to translate and interpret. There is no 'Rosetta Stone' of clinical medicine such as the genetic code that can assist translation and interpretation of the language of genetics. Nevertheless, the information content embodied within a clinical diagnosis can guide management, therapeutic intervention, and potentially prognostic outlook of disease enabling anticipatory guidance for patients and families. Clinical genomics is now established firmly in medical practice. The granularity and informative content of a personal genome is immense. Yet, we are limited in our utility of much of that personal genome information by the lack of functional characterization of the overwhelming majority of computationally annotated genes in the haploid human reference genome sequence. Whereas DNA and the genetic code have provided a 'Rosetta Stone' to translate genetic variant information, clinical medicine, and clinical genomics provide the context to understand human biology and disease. A path forward will integrate deep phenotyping, such as available in a clinical synopsis in the Online Mendelian Inheritance in Man (OMIM) entries, with personal genome analyses.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
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15
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Berger A, Rustemeier AK, Göbel J, Kadioglu D, Britz V, Schubert K, Mohnike K, Storf H, Wagner TOF. How to design a registry for undiagnosed patients in the framework of rare disease diagnosis: suggestions on software, data set and coding system. Orphanet J Rare Dis 2021; 16:198. [PMID: 33933089 PMCID: PMC8088651 DOI: 10.1186/s13023-021-01831-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/20/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND About 30 million people in the EU and USA, respectively, suffer from a rare disease. Driven by European legislative requirements, national strategies for the improvement of care in rare diseases are being developed. To improve timely and correct diagnosis for patients with rare diseases, the development of a registry for undiagnosed patients was recommended by the German National Action Plan. In this paper we focus on the question on how such a registry for undiagnosed patients can be built and which information it should contain. RESULTS To develop a registry for undiagnosed patients, a software for data acquisition and storage, an appropriate data set and an applicable terminology/classification system for the data collected are needed. We have used the open-source software Open-Source Registry System for Rare Diseases (OSSE) to build the registry for undiagnosed patients. Our data set is based on the minimal data set for rare disease patient registries recommended by the European Rare Disease Registries Platform. We extended this Common Data Set to also include symptoms, clinical findings and other diagnoses. In order to ensure findability, comparability and statistical analysis, symptoms, clinical findings and diagnoses have to be encoded. We evaluated three medical ontologies (SNOMED CT, HPO and LOINC) for their usefulness. With exact matches of 98% of tested medical terms, a mean number of five deposited synonyms, SNOMED CT seemed to fit our needs best. HPO and LOINC provided 73% and 31% of exacts matches of clinical terms respectively. Allowing more generic codes for a defined symptom, with SNOMED CT 99%, with HPO 89% and with LOINC 39% of terms could be encoded. CONCLUSIONS With the use of the OSSE software and a data set, which, in addition to the Common Data Set, focuses on symptoms and clinical findings, a functioning and meaningful registry for undiagnosed patients can be implemented. The next step is the implementation of the registry in centres for rare diseases. With the help of medical informatics and big data analysis, case similarity analyses could be realized and aid as a decision-support tool enabling diagnosis of some undiagnosed patients.
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Affiliation(s)
- Alexandra Berger
- Frankfurt Reference Centre for Rare Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
| | - Anne-Kathrin Rustemeier
- Medical Clinic II, University Hospital Gießen and Marburg, Klinikstraße 33, 35392, Gießen, Germany
| | - Jens Göbel
- Medical Informatics Group Frankfurt, University Hospital Frankfurt, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Dennis Kadioglu
- Medical Informatics Group Frankfurt, University Hospital Frankfurt, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Vanessa Britz
- Frankfurt Reference Centre for Rare Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Katharina Schubert
- Central-German Network for rare diseases, University Hospital Magdeburg A.Ö.R, Leipziger Straße 44, 39120, Magdeburg, Germany
| | - Klaus Mohnike
- Central-German Network for rare diseases, University Hospital Magdeburg A.Ö.R, Leipziger Straße 44, 39120, Magdeburg, Germany
| | - Holger Storf
- Medical Informatics Group Frankfurt, University Hospital Frankfurt, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Thomas O F Wagner
- Frankfurt Reference Centre for Rare Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
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16
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Schön U, Holzer A, Laner A, Kleinle S, Scharf F, Benet-Pagès A, Peschel O, Holinski-Feder E, Diebold I. HPO-driven virtual gene panel: a new efficient approach in molecular autopsy of sudden unexplained death. BMC Med Genomics 2021; 14:94. [PMID: 33789662 PMCID: PMC8011092 DOI: 10.1186/s12920-021-00946-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/24/2021] [Indexed: 12/29/2022] Open
Abstract
Background Molecular autopsy represents an efficient tool to save the diagnosis in up to one-third of sudden unexplained death (SUD). A defined gene panel is usually used for the examination. Alternatively, it is possible to carry out a comprehensive genetic assessment (whole exome sequencing, WES), which also identifies rare, previously unknown variants. The disadvantage is that a dramatic number of variants must be assessed to identify the causal variant. To improve the evaluation of WES, the human phenotype ontology (HPO) annotation is used internationally for deep phenotyping in the field of rare disease. However, a HPO-based evaluation of WES in SUD has not been described before. Methods We performed WES in tissue samples from 16 people after SUD. Instead of a fixed gene panel, we defined a set of HPO terms and thus created a flexible “virtual gene panel”, with the advantage, that recently identified genes are automatically associated by HPO terms in the HPO database. Results We obtained a mean value of 68,947 variants per sample. Stringent filtering ended up in a mean value of 276 variants per sample. Using the HPO-driven virtual gene panel we developed an algorithm that prioritized 1.4% of the variants. Variant interpretation resulted in eleven potentially causative variants in 16 individuals. Conclusion Our data introduce an effective diagnostic procedure in molecular autopsy of SUD with a non-specific clinical phenotype.
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Affiliation(s)
- Ulrike Schön
- MGZ - Medical Genetics Center Munich, Munich, Germany
| | - Anna Holzer
- Institute of Legal Medicine, Ludwig-Maximilians-University, Munich, Germany
| | - Andreas Laner
- MGZ - Medical Genetics Center Munich, Munich, Germany
| | | | | | | | - Oliver Peschel
- Institute of Legal Medicine, Ludwig-Maximilians-University, Munich, Germany
| | | | - Isabel Diebold
- MGZ - Medical Genetics Center Munich, Munich, Germany. .,Department of Pediatrics, Technical University of Munich School of Medicine, Munich, Germany.
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17
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Dingemans AJM, Stremmelaar DE, Vissers LELM, Jansen S, Nabais Sá MJ, van Remortele A, Jonis N, Truijen K, van de Ven S, Ewals J, Verbruggen M, Koolen DA, Brunner HG, Eichler EE, Gecz J, de Vries BBA. Human disease genes website series: An international, open and dynamic library for up-to-date clinical information. Am J Med Genet A 2021; 185:1039-1046. [PMID: 33439542 PMCID: PMC7986414 DOI: 10.1002/ajmg.a.62057] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 12/11/2022]
Abstract
Since the introduction of next‐generation sequencing, an increasing number of disorders have been discovered to have genetic etiology. To address diverse clinical questions and coordinate research activities that arise with the identification of these rare disorders, we developed the Human Disease Genes website series (HDG website series): an international digital library that records detailed information on the clinical phenotype of novel genetic variants in the human genome (https://humandiseasegenes.info/). Each gene website is moderated by a dedicated team of clinicians and researchers, focused on specific genes, and provides up‐to‐date—including unpublished—clinical information. The HDG website series is expanding rapidly with 424 genes currently adopted by 325 moderators from across the globe. On average, a gene website has detailed phenotypic information of 14.4 patients. There are multiple examples of added value, one being the ARID1B gene website, which was recently utilized in research to collect clinical information of 81 new patients. Additionally, several gene websites have more data available than currently published in the literature. In conclusion, the HDG website series provides an easily accessible, open and up‐to‐date clinical data resource for patients with pathogenic variants of individual genes. This is a valuable resource not only for clinicians dealing with rare genetic disorders such as developmental delay and autism, but other professionals working in diagnostics and basic research. Since the HDG website series is a dynamic platform, its data also include the phenotype of yet unpublished patients curated by professionals providing higher quality clinical detail to improve management of these rare disorders.
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Affiliation(s)
- Alexander J M Dingemans
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Diante E Stremmelaar
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Sandra Jansen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Maria J Nabais Sá
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Angela van Remortele
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Noraly Jonis
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Kim Truijen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Sam van de Ven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Jeroen Ewals
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Michel Verbruggen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Han G Brunner
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Jozef Gecz
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
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18
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Haijes HA, Jaeken J, van Hasselt PM. Hypothesis: determining phenotypic specificity facilitates understanding of pathophysiology in rare genetic disorders. J Inherit Metab Dis 2020; 43:701-711. [PMID: 31804708 PMCID: PMC7383723 DOI: 10.1002/jimd.12201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/28/2019] [Accepted: 12/03/2019] [Indexed: 12/17/2022]
Abstract
In the rapidly growing group of rare genetic disorders, data scarcity demands an intelligible use of available data, in order to improve understanding of underlying pathophysiology. We hypothesize, based on the principle that clinical similarities may be indicative of shared pathophysiology, that determining phenotypic specificity could provide unsuspected insights in pathophysiology of rare genetic disorders. We explored our hypothesis by studying subunit deficiencies of the conserved oligomeric Golgi (COG) complex, a subgroup of congenital disorders of glycosylation (CDG). In this systematic data assessment, all 45 reported patients with COG-CDG were included. The vocabulary of the Human Phenotype Ontology was used to annotate all phenotypic features and to assess occurrence in other genetic disorders. Gene occurrence ratios were calculated by dividing the frequency in the patient cohort over the number of associated genes, according to the Human Phenotype Ontology. Prioritisation based on phenotypic specificity was highly informative and captured phenotypic features commonly associated with glycosylation disorders. Moreover, it captured features not seen in any other glycosylation disorder, among which episodic fever, likely reflecting underappreciated other cellular functions of the COG complex. Interestingly, the COG complex was recently implicated in the autophagy pathway, as are more than half of the genes underlying disorders that present with episodic fever. This suggests that whereas many phenotypic features in these patients are caused by disrupted glycosylation, episodic fever might be caused by disrupted autophagy. Thus, we here demonstrate support for our hypothesis that determining phenotypic specificity could facilitate understanding of pathophysiology in rare genetic disorders.
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Affiliation(s)
- Hanneke A. Haijes
- Department of Biomedical Genetics, Section Metabolic DiagnosticsWilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht UniversityUtrechtThe Netherlands
- Department of Pediatrics, Subdivision Metabolic DiseasesWilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht UniversityUtrechtThe Netherlands
| | - Jaak Jaeken
- Department of PediatricsCentre for Metabolic Diseases, University Hospital GasthuisbergLeuvenBelgium
| | - Peter M. van Hasselt
- Department of Pediatrics, Subdivision Metabolic DiseasesWilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht UniversityUtrechtThe Netherlands
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19
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Köhler S, Øien NC, Buske OJ, Groza T, Jacobsen JOB, McNamara C, Vasilevsky N, Carmody LC, Gourdine JP, Gargano M, McMurry JA, Danis D, Mungall CJ, Smedley D, Haendel M, Robinson PN. Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics. ACTA ACUST UNITED AC 2020; 103:e92. [PMID: 31479590 DOI: 10.1002/cphg.92] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The Human Phenotype Ontology (HPO) is a standardized set of phenotypic terms that are organized in a hierarchical fashion. It is a widely used resource for capturing human disease phenotypes for computational analysis to support differential diagnostics. The HPO is frequently used to create a set of terms that accurately describe the observed clinical abnormalities of an individual being evaluated for suspected rare genetic disease. This profile is compared with computational disease profiles in the HPO database with the aim of identifying genetic diseases with comparable phenotypic profiles. The computational analysis can be coupled with the analysis of whole-exome or whole-genome sequencing data through applications such as Exomiser. This article explains how to choose an optimal set of HPO terms for these cases and enter them with software, such as PhenoTips and PatientArchive, and demonstrates how to use Phenomizer and Exomiser to generate a computational differential diagnosis. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Sebastian Köhler
- Charité Centrum für Therapieforschung, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Einstein Center Digital Future, Berlin, Germany.,Monarch Initiative (monarchinitiative.org)
| | | | | | | | - Julius O B Jacobsen
- Monarch Initiative (monarchinitiative.org).,Queen Mary University of London, Charterhouse Square, London, United Kingdom
| | | | - Nicole Vasilevsky
- Monarch Initiative (monarchinitiative.org).,Oregon Health & Science University, Portland, Oregon
| | - Leigh C Carmody
- Monarch Initiative (monarchinitiative.org).,The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - J P Gourdine
- Monarch Initiative (monarchinitiative.org).,Oregon Health & Science University, Portland, Oregon
| | - Michael Gargano
- Monarch Initiative (monarchinitiative.org).,The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Julie A McMurry
- Monarch Initiative (monarchinitiative.org).,Oregon State University, Corvallis, Oregon
| | - Daniel Danis
- Monarch Initiative (monarchinitiative.org).,The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Christopher J Mungall
- Monarch Initiative (monarchinitiative.org).,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Damian Smedley
- Monarch Initiative (monarchinitiative.org).,Queen Mary University of London, Charterhouse Square, London, United Kingdom
| | - Melissa Haendel
- Monarch Initiative (monarchinitiative.org).,Oregon Health & Science University, Portland, Oregon.,Oregon State University, Corvallis, Oregon
| | - Peter N Robinson
- Monarch Initiative (monarchinitiative.org).,The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Institute for Systems Genomics, University of Connecticut, Farmington, Connecticut
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20
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Jezela-Stanek A, Ciara E, Jurkiewicz D, Kucharczyk M, Jędrzejowska M, Chrzanowska KH, Krajewska-Walasek M, Żemojtel T. The phenotype-driven computational analysis yields clinical diagnosis for patients with atypical manifestations of known intellectual disability syndromes. Mol Genet Genomic Med 2020; 8:e1263. [PMID: 32337850 PMCID: PMC7507388 DOI: 10.1002/mgg3.1263] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/24/2020] [Accepted: 03/01/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Due to extensive clinical and genetic heterogeneity of intellectual disability (ID) syndromes, the process of diagnosis is very challenging even for expert clinicians. Despite recent advancements in molecular diagnostics methodologies, a significant fraction of ID patients remains without a clinical diagnosis. METHODS, RESULTS, AND CONCLUSIONS Here, in a prospective study on a cohort of 21 families (trios) with a child presenting with ID of unknown etiology, we executed phenotype-driven bioinformatic analysis method, PhenIX, utilizing targeted next-generation sequencing (NGS) data and Human Phenotype Ontology (HPO)-encoded phenotype data. This approach resulted in clinical diagnosis for eight individuals presenting with atypical manifestations of Rubinstein-Taybi syndrome 2 (MIM 613684), Spastic Paraplegia 50 (MIM 612936), Wiedemann-Steiner syndrome (MIM 605130), Cornelia de Lange syndrome 2 (MIM 300590), Cerebral creatine deficiency syndrome 1 (MIM 300352), Glass Syndrome (MIM 612313), Mental retardation, autosomal dominant 31 (MIM 616158), and Bosch-Boonstra-Schaaf optic atrophy syndrome (MIM 615722).
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Affiliation(s)
- Aleksandra Jezela-Stanek
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, Warsaw, Poland.,Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Elżbieta Ciara
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Dorota Jurkiewicz
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Marzena Kucharczyk
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Maria Jędrzejowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland.,Mossakowski Medical Research Centre, Neuromuscular Unit, Polish Academy of Sciences, Warsaw, Poland
| | - Krystyna H Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | | | - Tomasz Żemojtel
- Genomics Platform, Berlin Institute of Health, Berlin, Germany.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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21
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Abstract
Dysmorphology is the practice of defining the morphologic phenotype of syndromic disorders. Genomic sequencing has advanced our understanding of human variation and molecular dysmorphology has evolved in response to the science of relating embryologic developmental implications of abnormal gene signaling pathways to the resultant phenotypic presentation. Machine learning has enabled the application of deep convoluted neural networks to recognize the comparative likeness of these phenotypes relative to the causal genotype or disrupted gene pathway.
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Affiliation(s)
- Donald Basel
- Department of Pediatrics, Division of Genetics, Medical College of Wisconsin, 9000 West Wisconsin Avenue, MS #716, Milwaukee, WI 53226, USA.
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22
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Ma L, Zhao ZH, Peng L, Yang XJ, Fu PB, Liu Y, Huang Y. Application of gas cyclone-liquid jet absorption separator for purification of tail gas containing ammonia. Environ Technol 2019; 40:3392-3402. [PMID: 29733755 DOI: 10.1080/09593330.2018.1474266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 04/20/2018] [Indexed: 06/08/2023]
Abstract
In this experiment, with stainless steel gas cyclone-liquid jet absorption separator as carrier, NH3 as experimental gas, and water and H3PO4 solution as absorbents, corresponding NH3 absorption rate change is obtained through the adjustment of experimental parameters, such as NH3 inlet concentration, inlet velocity of mixed gas, injection flow rate of absorbent, temperature of absorbent, and H3PO4 absorbent concentration. The NH3 absorption rate decreases with the increase in NH3 inlet concentration and inlet gas velocity. The NH3 absorption rate will increase first and then tends to remain unchanged after reaching a certain degree with the increase in liquid injection flow rate and absorbent concentration. The NH3 absorption rate will increase first and then decrease with the increase in the absorbent temperature. The maximum NH3 removal efficiencies of water and H3PO4 were 96% and 99%, respectively.
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Affiliation(s)
- Liang Ma
- School of Mechanical and Power Engineering, East China University of Science and Technology , Shanghai , People's Republic of China
| | - Zhi-Huang Zhao
- School of Mechanical and Power Engineering, East China University of Science and Technology , Shanghai , People's Republic of China
| | - Lv Peng
- School of Mechanical and Power Engineering, East China University of Science and Technology , Shanghai , People's Republic of China
| | - Xue-Jing Yang
- School of Mechanical and Power Engineering, East China University of Science and Technology , Shanghai , People's Republic of China
| | - Peng-Bo Fu
- School of Mechanical and Power Engineering, East China University of Science and Technology , Shanghai , People's Republic of China
| | - Yi Liu
- School of Mechanical and Power Engineering, East China University of Science and Technology , Shanghai , People's Republic of China
| | - Yuan Huang
- School of Mechanical and Power Engineering, East China University of Science and Technology , Shanghai , People's Republic of China
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23
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Abstract
BACKGROUND Biomedical literature concerns a wide range of concepts, requiring controlled vocabularies to maintain a consistent terminology across different research groups. However, as new concepts are introduced, biomedical literature is prone to ambiguity, specifically in fields that are advancing more rapidly, for example, drug design and development. Entity linking is a text mining task that aims at linking entities mentioned in the literature to concepts in a knowledge base. For example, entity linking can help finding all documents that mention the same concept and improve relation extraction methods. Existing approaches focus on the local similarity of each entity and the global coherence of all entities in a document, but do not take into account the semantics of the domain. RESULTS We propose a method, PPR-SSM, to link entities found in documents to concepts from domain-specific ontologies. Our method is based on Personalized PageRank (PPR), using the relations of the ontology to generate a graph of candidate concepts for the mentioned entities. We demonstrate how the knowledge encoded in a domain-specific ontology can be used to calculate the coherence of a set of candidate concepts, improving the accuracy of entity linking. Furthermore, we explore weighting the edges between candidate concepts using semantic similarity measures (SSM). We show how PPR-SSM can be used to effectively link named entities to biomedical ontologies, namely chemical compounds, phenotypes, and gene-product localization and processes. CONCLUSIONS We demonstrated that PPR-SSM outperforms state-of-the-art entity linking methods in four distinct gold standards, by taking advantage of the semantic information contained in ontologies. Moreover, PPR-SSM is a graph-based method that does not require training data. Our method improved the entity linking accuracy of chemical compounds by 0.1385 when compared to a method that does not use SSMs.
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Affiliation(s)
- Andre Lamurias
- LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, Lisboa, 749-016, Portugal.
| | - Pedro Ruas
- LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, Lisboa, 749-016, Portugal
| | - Francisco M Couto
- LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, Lisboa, 749-016, Portugal
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24
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Goldsammler M, Merhi Z, Buyuk E. Role of hormonal and inflammatory alterations in obesity-related reproductive dysfunction at the level of the hypothalamic-pituitary-ovarian axis. Reprod Biol Endocrinol 2018; 16:45. [PMID: 29743077 PMCID: PMC5941782 DOI: 10.1186/s12958-018-0366-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 05/03/2018] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Besides being a risk factor for multiple metabolic disorders, obesity could affect female reproduction. While increased adiposity is associated with hormonal changes that could disrupt the function of the hypothalamus and the pituitary, compelling data suggest that obesity-related hormonal and inflammatory changes could directly impact ovarian function. OBJECTIVE To review the available data related to the mechanisms by which obesity, and its associated hormonal and inflammatory changes, could affect the female reproductive function with a focus on the hypothalamic-pituitary-ovarian (HPO) axis. METHODS PubMed database search for publications in English language until October 2017 pertaining to obesity and female reproductive function was performed. RESULTS The obesity-related changes in hormone levels, in particular leptin, adiponectin, ghrelin, neuropeptide Y and agouti-related protein, are associated with reproductive dysfunction at both the hypothalamic-pituitary and the ovarian levels. The pro-inflammatory molecules advanced glycation end products (AGEs) and monocyte chemotactic protein-1 (MCP-1) are emerging as relatively new players in the pathophysiology of obesity-related ovarian dysfunction. CONCLUSION There is an intricate crosstalk between the adipose tissue and the inflammatory system with the HPO axis function. Understanding the mechanisms behind this crosstalk could lead to potential therapies for the common obesity-related reproductive dysfunction.
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Affiliation(s)
- Michelle Goldsammler
- Montefiore’s Institute for Reproductive Medicine and Health, Department of Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Montefiore Medical Center, Hartsdale, NY USA
| | - Zaher Merhi
- 0000 0004 1936 8753grid.137628.9Department of Obstetrics and Gynecology, Division of Reproductive Biology, NYU School of Medicine, New York, NY USA
- 0000000121791997grid.251993.5Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY USA
| | - Erkan Buyuk
- Montefiore’s Institute for Reproductive Medicine and Health, Department of Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Montefiore Medical Center, Hartsdale, NY USA
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25
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Saklatvala JR, Dand N, Simpson MA. Text-mined phenotype annotation and vector-based similarity to improve identification of similar phenotypes and causative genes in monogenic disease patients. Hum Mutat 2018; 39:643-652. [PMID: 29460986 DOI: 10.1002/humu.23413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/25/2018] [Accepted: 02/16/2018] [Indexed: 11/07/2022]
Abstract
The genetic diagnosis of rare monogenic diseases using exome/genome sequencing requires the true causal variant(s) to be identified from tens of thousands of observed variants. Typically a virtual gene panel approach is taken whereby only variants in genes known to cause phenotypes resembling the patient under investigation are considered. With the number of known monogenic gene-disease pairs exceeding 5,000, manual curation of personalized virtual panels using exhaustive knowledge of the genetic basis of the human monogenic phenotypic spectrum is challenging. We present improved probabilistic methods for estimating phenotypic similarity based on Human Phenotype Ontology annotation. A limitation of existing methods for evaluating a disease's similarity to a reference set is that reference diseases are typically represented as a series of binary (present/absent) observations of phenotypic terms. We evaluate a quantified disease reference set, using term frequency in phenotypic text descriptions to approximate term relevance. We demonstrate an improved ability to identify related diseases through the use of a quantified reference set, and that vector space similarity measures perform better than established information content-based measures. These improvements enable the generation of bespoke virtual gene panels, facilitating more accurate and efficient interpretation of genomic variant profiles from individuals with rare Mendelian disorders. These methods are available online at https://atlas.genetics.kcl.ac.uk/~jake/cgi-bin/patient_sim.py.
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Affiliation(s)
- Jake R Saklatvala
- Department of Medical & Molecular Genetics, King's College London, London, United Kingdom
| | - Nick Dand
- Department of Medical & Molecular Genetics, King's College London, London, United Kingdom
| | - Michael A Simpson
- Department of Medical & Molecular Genetics, King's College London, London, United Kingdom
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26
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Feiglin A, Allen BK, Kohane IS, Kong SW. Comprehensive Analysis of Tissue-wide Gene Expression and Phenotype Data Reveals Tissues Affected in Rare Genetic Disorders. Cell Syst 2017; 5:140-148.e2. [PMID: 28822752 DOI: 10.1016/j.cels.2017.06.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 03/21/2017] [Accepted: 06/29/2017] [Indexed: 01/23/2023]
Abstract
Linking putatively pathogenic variants to the tissues they affect is necessary for determining the correct diagnostic workup and therapeutic regime in undiagnosed patients. Here, we explored how gene expression across healthy tissues can be used to infer this link. We integrated 6,665 tissue-wide transcriptomes with genetic disorder knowledge bases covering 3,397 diseases. Receiver-operating characteristics (ROC) analysis using expression levels in each tissue and across tissues indicated significant but modest associations between elevated expression and phenotype for most tissues (maximum area under ROC curve = 0.69). At extreme elevation, associations were marked. Upregulation of disease genes in affected tissues was pronounced for genes associated with autosomal dominant over recessive disorders. Pathways enriched for genes expressed and associated with phenotypes highlighted tissue functionality, including lipid metabolism in spleen and DNA repair in adipose tissue. These results suggest features useful for evaluating the likelihood of particular tissue manifestations in genetic disorders. The web address of an interactive platform integrating these data is provided.
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Affiliation(s)
- Ariel Feiglin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Bryce K Allen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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27
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Zepeda-Mendoza CJ, Ibn-Salem J, Kammin T, Harris DJ, Rita D, Gripp KW, MacKenzie JJ, Gropman A, Graham B, Shaheen R, Alkuraya FS, Brasington CK, Spence EJ, Masser-Frye D, Bird LM, Spiegel E, Sparkes RL, Ordulu Z, Talkowski ME, Andrade-Navarro MA, Robinson PN, Morton CC. Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements. Am J Hum Genet 2017; 101:206-217. [PMID: 28735859 PMCID: PMC5544382 DOI: 10.1016/j.ajhg.2017.06.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/19/2017] [Indexed: 01/08/2023] Open
Abstract
Interpretation of variants of uncertain significance, especially chromosomal rearrangements in non-coding regions of the human genome, remains one of the biggest challenges in modern molecular diagnosis. To improve our understanding and interpretation of such variants, we used high-resolution three-dimensional chromosomal structural data and transcriptional regulatory information to predict position effects and their association with pathogenic phenotypes in 17 subjects with apparently balanced chromosomal abnormalities. We found that the rearrangements predict disruption of long-range chromatin interactions between several enhancers and genes whose annotated clinical features are strongly associated with the subjects' phenotypes. We confirm gene-expression changes for a couple of candidate genes to exemplify the utility of our analysis of position effect. These results highlight the important interplay between chromosomal structure and disease and demonstrate the need to utilize chromatin conformational data for the prediction of position effects in the clinical interpretation of non-coding chromosomal rearrangements.
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Affiliation(s)
- Cinthya J Zepeda-Mendoza
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | - Tammy Kammin
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - David J Harris
- Harvard Medical School, Boston, MA 02115, USA; Boston Children's Hospital, Boston, MA 02115, USA
| | - Debra Rita
- Cytogenetics Lab, ACL laboratories, Rosemont, IL 60018, USA
| | - Karen W Gripp
- Nemours Alfred I. DuPont Hospital for Children, Wilmington, DE 19803, USA
| | | | - Andrea Gropman
- Children's National Medical Center, Washington, DC 20010, USA
| | - Brett Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 12713, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 12713, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Campbell K Brasington
- Clinical Genetics Division, Department of Pediatrics, Levine Children's Hospital at Carolinas Medical Center, Charlotte, NC 28203, USA
| | - Edward J Spence
- Clinical Genetics Division, Department of Pediatrics, Levine Children's Hospital at Carolinas Medical Center, Charlotte, NC 28203, USA
| | - Diane Masser-Frye
- Genetics and Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA 92123, USA
| | - Lynne M Bird
- Genetics and Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA 92123, USA; University of California, San Diego, La Jolla, CA 92093, USA
| | - Erica Spiegel
- Maternal Fetal Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Rebecca L Sparkes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Zehra Ordulu
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael E Talkowski
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Departments of Neurology and Psychiatry and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Peter N Robinson
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Cynthia C Morton
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Johannes Gutenberg University, Mainz 55122, Germany; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Evolution and Genomic Science, School of Biological Sciences, Manchester Academic Health Science Centre, Manchester M13 9NT, UK.
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28
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Trujillano D, Oprea GE, Schmitz Y, Bertoli-Avella AM, Abou Jamra R, Rolfs A. A comprehensive global genotype-phenotype database for rare diseases. Mol Genet Genomic Med 2016; 5:66-75. [PMID: 28116331 PMCID: PMC5241210 DOI: 10.1002/mgg3.262] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/03/2016] [Accepted: 11/01/2016] [Indexed: 12/20/2022] Open
Abstract
Background The ability to discover genetic variants in a patient runs far ahead of the ability to interpret them. Databases with accurate descriptions of the causal relationship between the variants and the phenotype are valuable since these are critical tools in clinical genetic diagnostics. Here, we introduce a comprehensive and global genotype–phenotype database focusing on rare diseases. Methods This database (CentoMD®) is a browser‐based tool that enables access to a comprehensive, independently curated system utilizing stringent high‐quality criteria and a quickly growing repository of genetic and human phenotype ontology (HPO)‐based clinical information. Its main goals are to aid the evaluation of genetic variants, to enhance the validity of the genetic analytical workflow, to increase the quality of genetic diagnoses, and to improve evaluation of treatment options for patients with hereditary diseases. The database software correlates clinical information from consented patients and probands of different geographical backgrounds with a large dataset of genetic variants and, when available, biomarker information. An automated follow‐up tool is incorporated that informs all users whenever a variant classification has changed. These unique features fully embedded in a CLIA/CAP‐accredited quality management system allow appropriate data quality and enhanced patient safety. Results More than 100,000 genetically screened individuals are documented in the database, resulting in more than 470 million variant detections. Approximately, 57% of the clinically relevant and uncertain variants in the database are novel. Notably, 3% of the genetic variants identified and previously reported in the literature as being associated with a particular rare disease were reclassified, based on internal evidence, as clinically irrelevant. Conclusions The database offers a comprehensive summary of the clinical validity and causality of detected gene variants with their associated phenotypes, and is a valuable tool for identifying new disease genes through the correlation of novel genetic variants with specific, well‐defined phenotypes.
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Affiliation(s)
| | | | | | | | - Rami Abou Jamra
- Centogene AGRostockGermany; Institute of Human GeneticsUniversity of Leipzig Hospitals and ClinicsLeipzigGermany
| | - Arndt Rolfs
- Centogene AGRostockGermany; Albrecht-Kossel-Institute for NeuroregenerationMedical University RostockRostockGermany
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29
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Buske OJ, Schiettecatte F, Hutton B, Dumitriu S, Misyura A, Huang L, Hartley T, Girdea M, Sobreira N, Mungall C, Brudno M. The Matchmaker Exchange API: automating patient matching through the exchange of structured phenotypic and genotypic profiles. Hum Mutat 2016; 36:922-7. [PMID: 26255989 DOI: 10.1002/humu.22850] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/24/2015] [Indexed: 01/28/2023]
Abstract
Despite the increasing prevalence of clinical sequencing, the difficulty of identifying additional affected families is a key obstacle to solving many rare diseases. There may only be a handful of similar patients worldwide, and their data may be stored in diverse clinical and research databases. Computational methods are necessary to enable finding similar patients across the growing number of patient repositories and registries. We present the Matchmaker Exchange Application Programming Interface (MME API), a protocol and data format for exchanging phenotype and genotype profiles to enable matchmaking among patient databases, facilitate the identification of additional cohorts, and increase the rate with which rare diseases can be researched and diagnosed. We designed the API to be straightforward and flexible in order to simplify its adoption on a large number of data types and workflows. We also provide a public test data set, curated from the literature, to facilitate implementation of the API and development of new matching algorithms. The initial version of the API has been successfully implemented by three members of the Matchmaker Exchange and was immediately able to reproduce previously identified matches and generate several new leads currently being validated. The API is available at https://github.com/ga4gh/mme-apis.
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Affiliation(s)
- Orion J Buske
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | | | | | - Sergiu Dumitriu
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Andriy Misyura
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Lijia Huang
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Marta Girdea
- Department of Computer Science, University of Toronto, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chris Mungall
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Michael Brudno
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
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30
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Xie YY, Lu Z, Kong XL, Zhou T, Bansal S, Hider R. Systematic comparison of the mono-, dimethyl- and trimethyl 3-hydroxy-4(1H)-pyridones - Attempted optimization of the orally active iron chelator, deferiprone. Eur J Med Chem 2016; 115:132-40. [PMID: 27014847 DOI: 10.1016/j.ejmech.2016.03.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/03/2016] [Accepted: 03/04/2016] [Indexed: 01/19/2023]
Abstract
A range of close analogues of deferiprone have been synthesised. The group includes mono-, di- and tri-methyl-3-hydroxy-4(1H)-pyridones. These compounds were found to possess similar pFe(3+) values to that of deferiprone, with the exception of the 2.5-dimethylated derivatives. Surprisingly the NH-containing hydroxy-4(1H)-pyridones were found to be marginally more lipophilic than the corresponding N-Me containing analogues. This same group are also metabolised less efficiently by Phase 1 hydroxylating enzymes than the corresponding N-Me analogues. As result of this study, three compounds have been identified for further investigation centred on neutropenia and agranulocytosis.
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Affiliation(s)
- Yuan-Yuan Xie
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Zidong Lu
- Institute of Pharmaceutical Science, King's College London, UK
| | - Xiao-Le Kong
- Institute of Pharmaceutical Science, King's College London, UK
| | - Tao Zhou
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Sukhi Bansal
- Institute of Pharmaceutical Science, King's College London, UK
| | - Robert Hider
- Institute of Pharmaceutical Science, King's College London, UK.
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31
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Buske OJ, Girdea M, Dumitriu S, Gallinger B, Hartley T, Trang H, Misyura A, Friedman T, Beaulieu C, Bone WP, Links AE, Washington NL, Haendel MA, Robinson PN, Boerkoel CF, Adams D, Gahl WA, Boycott KM, Brudno M. PhenomeCentral: a portal for phenotypic and genotypic matchmaking of patients with rare genetic diseases. Hum Mutat 2015; 36:931-40. [PMID: 26251998 DOI: 10.1002/humu.22851] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/28/2015] [Indexed: 01/18/2023]
Abstract
The discovery of disease-causing mutations typically requires confirmation of the variant or gene in multiple unrelated individuals, and a large number of rare genetic diseases remain unsolved due to difficulty identifying second families. To enable the secure sharing of case records by clinicians and rare disease scientists, we have developed the PhenomeCentral portal (https://phenomecentral.org). Each record includes a phenotypic description and relevant genetic information (exome or candidate genes). PhenomeCentral identifies similar patients in the database based on semantic similarity between clinical features, automatically prioritized genes from whole-exome data, and candidate genes entered by the users, enabling both hypothesis-free and hypothesis-driven matchmaking. Users can then contact other submitters to follow up on promising matches. PhenomeCentral incorporates data for over 1,000 patients with rare genetic diseases, contributed by the FORGE and Care4Rare Canada projects, the US NIH Undiagnosed Diseases Program, the EU Neuromics and ANDDIrare projects, as well as numerous independent clinicians and scientists. Though the majority of these records have associated exome data, most lack a molecular diagnosis. PhenomeCentral has already been used to identify causative mutations for several patients, and its ability to find matching patients and diagnose these diseases will grow with each additional patient that is entered.
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Affiliation(s)
- Orion J Buske
- Department of Computer Science, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Marta Girdea
- Department of Computer Science, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Sergiu Dumitriu
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Bailey Gallinger
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Heather Trang
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andriy Misyura
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Tal Friedman
- Department of Computer Science, University of Toronto, Toronto, Canada
| | - Chandree Beaulieu
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - William P Bone
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Amanda E Links
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Nicole L Washington
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Melissa A Haendel
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon
| | - Peter N Robinson
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Cornelius F Boerkoel
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - David Adams
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - William A Gahl
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
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32
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Lin F, Zhou C, Chen H, Wu H, Xin Z, Liu J, Gao Y, Yuan D, Wang T, Wei R, Chen D, Yang S, Wang Y, Pu Y, Li Z. Molecular characterization, tissue distribution and feeding related changes of NUCB2A/nesfatin-1 in Ya-fish (Schizothorax prenanti). Gene 2013; 536:238-46. [PMID: 24365590 DOI: 10.1016/j.gene.2013.12.031] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 12/02/2013] [Accepted: 12/12/2013] [Indexed: 12/24/2022]
Abstract
The protein nucleobindin-2 (NUCB2) was identified over a decade ago and recently raised great interest as its derived peptide nesfatin-1 was shown to reduce food intake and body weight in rodents. However, the involvement of NUCB2 in feeding behavior has not well been studied in fish. In the present study, we characterized the structure, distribution, and meal responsive of NUCB2A/nesfatin-1 in Ya-fish (Schizothorax prenanti) for the first time. The full length cDNA of Ya-fish was 2140base pair (bp), which encoded a polypeptide of 487 amino acid residues including a 23 amino acid signal peptide. A high conservation in NUCB2 sequences was found in vertebrates, however the proposed propeptide cleavage site (Arg-Arg) conserved among other species is not present in Ya-fish NUCB2A sequence. Tissue distribution analysis revealed that Ya-fish NUCB2A mRNA was ubiquitously expressed in all test tissues, and abundant expression was detected in several regions including the hypothalamus, hepatopancreas, ovary and intestines. NUCB2A mRNA expression respond to feeding status change may vary and be tissue specific. NUCB2A mRNA levels significantly increased (P<0.05) in the hypothalamus and intestines after feeding and substantially decreased (P<0.01) during a week food deprivation in the hypothalamus. Meanwhile, NUCB2A mRNA in the hepatopancreas was significantly elevated (P<0.001) during food deprivation, and a similar increase was also found after short-time fasting. This points toward a potential hepatopancreas specific local role for NUCB2A in the regulation of metabolism during food deprivation. Collectively, these results provide the molecular and functional evidence to support potential anorectic and metabolic roles for NUCB2A in Ya-fish.
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Affiliation(s)
- Fangjun Lin
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, 46# Xinkang Road, Ya'an, China
| | - Chaowei Zhou
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, 46# Xinkang Road, Ya'an, China
| | - Hu Chen
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, 46# Xinkang Road, Ya'an, China
| | - Hongwei Wu
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, 46# Xinkang Road, Ya'an, China
| | - Zhiming Xin
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, 46# Xinkang Road, Ya'an, China
| | - Ju Liu
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, 46# Xinkang Road, Ya'an, China
| | - Yundi Gao
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, 46# Xinkang Road, Ya'an, China
| | - Dengyue Yuan
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, 46# Xinkang Road, Ya'an, China
| | - Tao Wang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, 46# Xinkang Road, Ya'an, China
| | - Rongbin Wei
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, 46# Xinkang Road, Ya'an, China
| | - Defang Chen
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, 46# Xinkang Road, Ya'an, China
| | - Shiyong Yang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, 46# Xinkang Road, Ya'an, China
| | - Yan Wang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, 46# Xinkang Road, Ya'an, China
| | - Yundan Pu
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, 46# Xinkang Road, Ya'an, China
| | - Zhiqiong Li
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, 46# Xinkang Road, Ya'an, China.
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